Annotation of imach/src/imach.c, revision 1.319
1.319 ! brouard 1: /* $Id: imach.c,v 1.318 2022/05/24 08:10:59 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.319 ! brouard 4: Revision 1.318 2022/05/24 08:10:59 brouard
! 5: * imach.c (Module): Some attempts to find a bug of wrong estimates
! 6: of confidencce intervals with product in the equation modelC
! 7:
1.318 brouard 8: Revision 1.317 2022/05/15 15:06:23 brouard
9: * imach.c (Module): Some minor improvements
10:
1.317 brouard 11: Revision 1.316 2022/05/11 15:11:31 brouard
12: Summary: r27
13:
1.316 brouard 14: Revision 1.315 2022/05/11 15:06:32 brouard
15: *** empty log message ***
16:
1.315 brouard 17: Revision 1.314 2022/04/13 17:43:09 brouard
18: * imach.c (Module): Adding link to text data files
19:
1.314 brouard 20: Revision 1.313 2022/04/11 15:57:42 brouard
21: * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
22:
1.313 brouard 23: Revision 1.312 2022/04/05 21:24:39 brouard
24: *** empty log message ***
25:
1.312 brouard 26: Revision 1.311 2022/04/05 21:03:51 brouard
27: Summary: Fixed quantitative covariates
28:
29: Fixed covariates (dummy or quantitative)
30: with missing values have never been allowed but are ERRORS and
31: program quits. Standard deviations of fixed covariates were
32: wrongly computed. Mean and standard deviations of time varying
33: covariates are still not computed.
34:
1.311 brouard 35: Revision 1.310 2022/03/17 08:45:53 brouard
36: Summary: 99r25
37:
38: Improving detection of errors: result lines should be compatible with
39: the model.
40:
1.310 brouard 41: Revision 1.309 2021/05/20 12:39:14 brouard
42: Summary: Version 0.99r24
43:
1.309 brouard 44: Revision 1.308 2021/03/31 13:11:57 brouard
45: Summary: Version 0.99r23
46:
47:
48: * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
49:
1.308 brouard 50: Revision 1.307 2021/03/08 18:11:32 brouard
51: Summary: 0.99r22 fixed bug on result:
52:
1.307 brouard 53: Revision 1.306 2021/02/20 15:44:02 brouard
54: Summary: Version 0.99r21
55:
56: * imach.c (Module): Fix bug on quitting after result lines!
57: (Module): Version 0.99r21
58:
1.306 brouard 59: Revision 1.305 2021/02/20 15:28:30 brouard
60: * imach.c (Module): Fix bug on quitting after result lines!
61:
1.305 brouard 62: Revision 1.304 2021/02/12 11:34:20 brouard
63: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
64:
1.304 brouard 65: Revision 1.303 2021/02/11 19:50:15 brouard
66: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
67:
1.303 brouard 68: Revision 1.302 2020/02/22 21:00:05 brouard
69: * (Module): imach.c Update mle=-3 (for computing Life expectancy
70: and life table from the data without any state)
71:
1.302 brouard 72: Revision 1.301 2019/06/04 13:51:20 brouard
73: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
74:
1.301 brouard 75: Revision 1.300 2019/05/22 19:09:45 brouard
76: Summary: version 0.99r19 of May 2019
77:
1.300 brouard 78: Revision 1.299 2019/05/22 18:37:08 brouard
79: Summary: Cleaned 0.99r19
80:
1.299 brouard 81: Revision 1.298 2019/05/22 18:19:56 brouard
82: *** empty log message ***
83:
1.298 brouard 84: Revision 1.297 2019/05/22 17:56:10 brouard
85: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
86:
1.297 brouard 87: Revision 1.296 2019/05/20 13:03:18 brouard
88: Summary: Projection syntax simplified
89:
90:
91: We can now start projections, forward or backward, from the mean date
92: of inteviews up to or down to a number of years of projection:
93: prevforecast=1 yearsfproj=15.3 mobil_average=0
94: or
95: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
96: or
97: prevbackcast=1 yearsbproj=12.3 mobil_average=1
98: or
99: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
100:
1.296 brouard 101: Revision 1.295 2019/05/18 09:52:50 brouard
102: Summary: doxygen tex bug
103:
1.295 brouard 104: Revision 1.294 2019/05/16 14:54:33 brouard
105: Summary: There was some wrong lines added
106:
1.294 brouard 107: Revision 1.293 2019/05/09 15:17:34 brouard
108: *** empty log message ***
109:
1.293 brouard 110: Revision 1.292 2019/05/09 14:17:20 brouard
111: Summary: Some updates
112:
1.292 brouard 113: Revision 1.291 2019/05/09 13:44:18 brouard
114: Summary: Before ncovmax
115:
1.291 brouard 116: Revision 1.290 2019/05/09 13:39:37 brouard
117: Summary: 0.99r18 unlimited number of individuals
118:
119: The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
120:
1.290 brouard 121: Revision 1.289 2018/12/13 09:16:26 brouard
122: Summary: Bug for young ages (<-30) will be in r17
123:
1.289 brouard 124: Revision 1.288 2018/05/02 20:58:27 brouard
125: Summary: Some bugs fixed
126:
1.288 brouard 127: Revision 1.287 2018/05/01 17:57:25 brouard
128: Summary: Bug fixed by providing frequencies only for non missing covariates
129:
1.287 brouard 130: Revision 1.286 2018/04/27 14:27:04 brouard
131: Summary: some minor bugs
132:
1.286 brouard 133: Revision 1.285 2018/04/21 21:02:16 brouard
134: Summary: Some bugs fixed, valgrind tested
135:
1.285 brouard 136: Revision 1.284 2018/04/20 05:22:13 brouard
137: Summary: Computing mean and stdeviation of fixed quantitative variables
138:
1.284 brouard 139: Revision 1.283 2018/04/19 14:49:16 brouard
140: Summary: Some minor bugs fixed
141:
1.283 brouard 142: Revision 1.282 2018/02/27 22:50:02 brouard
143: *** empty log message ***
144:
1.282 brouard 145: Revision 1.281 2018/02/27 19:25:23 brouard
146: Summary: Adding second argument for quitting
147:
1.281 brouard 148: Revision 1.280 2018/02/21 07:58:13 brouard
149: Summary: 0.99r15
150:
151: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
152:
1.280 brouard 153: Revision 1.279 2017/07/20 13:35:01 brouard
154: Summary: temporary working
155:
1.279 brouard 156: Revision 1.278 2017/07/19 14:09:02 brouard
157: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
158:
1.278 brouard 159: Revision 1.277 2017/07/17 08:53:49 brouard
160: Summary: BOM files can be read now
161:
1.277 brouard 162: Revision 1.276 2017/06/30 15:48:31 brouard
163: Summary: Graphs improvements
164:
1.276 brouard 165: Revision 1.275 2017/06/30 13:39:33 brouard
166: Summary: Saito's color
167:
1.275 brouard 168: Revision 1.274 2017/06/29 09:47:08 brouard
169: Summary: Version 0.99r14
170:
1.274 brouard 171: Revision 1.273 2017/06/27 11:06:02 brouard
172: Summary: More documentation on projections
173:
1.273 brouard 174: Revision 1.272 2017/06/27 10:22:40 brouard
175: Summary: Color of backprojection changed from 6 to 5(yellow)
176:
1.272 brouard 177: Revision 1.271 2017/06/27 10:17:50 brouard
178: Summary: Some bug with rint
179:
1.271 brouard 180: Revision 1.270 2017/05/24 05:45:29 brouard
181: *** empty log message ***
182:
1.270 brouard 183: Revision 1.269 2017/05/23 08:39:25 brouard
184: Summary: Code into subroutine, cleanings
185:
1.269 brouard 186: Revision 1.268 2017/05/18 20:09:32 brouard
187: Summary: backprojection and confidence intervals of backprevalence
188:
1.268 brouard 189: Revision 1.267 2017/05/13 10:25:05 brouard
190: Summary: temporary save for backprojection
191:
1.267 brouard 192: Revision 1.266 2017/05/13 07:26:12 brouard
193: Summary: Version 0.99r13 (improvements and bugs fixed)
194:
1.266 brouard 195: Revision 1.265 2017/04/26 16:22:11 brouard
196: Summary: imach 0.99r13 Some bugs fixed
197:
1.265 brouard 198: Revision 1.264 2017/04/26 06:01:29 brouard
199: Summary: Labels in graphs
200:
1.264 brouard 201: Revision 1.263 2017/04/24 15:23:15 brouard
202: Summary: to save
203:
1.263 brouard 204: Revision 1.262 2017/04/18 16:48:12 brouard
205: *** empty log message ***
206:
1.262 brouard 207: Revision 1.261 2017/04/05 10:14:09 brouard
208: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
209:
1.261 brouard 210: Revision 1.260 2017/04/04 17:46:59 brouard
211: Summary: Gnuplot indexations fixed (humm)
212:
1.260 brouard 213: Revision 1.259 2017/04/04 13:01:16 brouard
214: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
215:
1.259 brouard 216: Revision 1.258 2017/04/03 10:17:47 brouard
217: Summary: Version 0.99r12
218:
219: Some cleanings, conformed with updated documentation.
220:
1.258 brouard 221: Revision 1.257 2017/03/29 16:53:30 brouard
222: Summary: Temp
223:
1.257 brouard 224: Revision 1.256 2017/03/27 05:50:23 brouard
225: Summary: Temporary
226:
1.256 brouard 227: Revision 1.255 2017/03/08 16:02:28 brouard
228: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
229:
1.255 brouard 230: Revision 1.254 2017/03/08 07:13:00 brouard
231: Summary: Fixing data parameter line
232:
1.254 brouard 233: Revision 1.253 2016/12/15 11:59:41 brouard
234: Summary: 0.99 in progress
235:
1.253 brouard 236: Revision 1.252 2016/09/15 21:15:37 brouard
237: *** empty log message ***
238:
1.252 brouard 239: Revision 1.251 2016/09/15 15:01:13 brouard
240: Summary: not working
241:
1.251 brouard 242: Revision 1.250 2016/09/08 16:07:27 brouard
243: Summary: continue
244:
1.250 brouard 245: Revision 1.249 2016/09/07 17:14:18 brouard
246: Summary: Starting values from frequencies
247:
1.249 brouard 248: Revision 1.248 2016/09/07 14:10:18 brouard
249: *** empty log message ***
250:
1.248 brouard 251: Revision 1.247 2016/09/02 11:11:21 brouard
252: *** empty log message ***
253:
1.247 brouard 254: Revision 1.246 2016/09/02 08:49:22 brouard
255: *** empty log message ***
256:
1.246 brouard 257: Revision 1.245 2016/09/02 07:25:01 brouard
258: *** empty log message ***
259:
1.245 brouard 260: Revision 1.244 2016/09/02 07:17:34 brouard
261: *** empty log message ***
262:
1.244 brouard 263: Revision 1.243 2016/09/02 06:45:35 brouard
264: *** empty log message ***
265:
1.243 brouard 266: Revision 1.242 2016/08/30 15:01:20 brouard
267: Summary: Fixing a lots
268:
1.242 brouard 269: Revision 1.241 2016/08/29 17:17:25 brouard
270: Summary: gnuplot problem in Back projection to fix
271:
1.241 brouard 272: Revision 1.240 2016/08/29 07:53:18 brouard
273: Summary: Better
274:
1.240 brouard 275: Revision 1.239 2016/08/26 15:51:03 brouard
276: Summary: Improvement in Powell output in order to copy and paste
277:
278: Author:
279:
1.239 brouard 280: Revision 1.238 2016/08/26 14:23:35 brouard
281: Summary: Starting tests of 0.99
282:
1.238 brouard 283: Revision 1.237 2016/08/26 09:20:19 brouard
284: Summary: to valgrind
285:
1.237 brouard 286: Revision 1.236 2016/08/25 10:50:18 brouard
287: *** empty log message ***
288:
1.236 brouard 289: Revision 1.235 2016/08/25 06:59:23 brouard
290: *** empty log message ***
291:
1.235 brouard 292: Revision 1.234 2016/08/23 16:51:20 brouard
293: *** empty log message ***
294:
1.234 brouard 295: Revision 1.233 2016/08/23 07:40:50 brouard
296: Summary: not working
297:
1.233 brouard 298: Revision 1.232 2016/08/22 14:20:21 brouard
299: Summary: not working
300:
1.232 brouard 301: Revision 1.231 2016/08/22 07:17:15 brouard
302: Summary: not working
303:
1.231 brouard 304: Revision 1.230 2016/08/22 06:55:53 brouard
305: Summary: Not working
306:
1.230 brouard 307: Revision 1.229 2016/07/23 09:45:53 brouard
308: Summary: Completing for func too
309:
1.229 brouard 310: Revision 1.228 2016/07/22 17:45:30 brouard
311: Summary: Fixing some arrays, still debugging
312:
1.227 brouard 313: Revision 1.226 2016/07/12 18:42:34 brouard
314: Summary: temp
315:
1.226 brouard 316: Revision 1.225 2016/07/12 08:40:03 brouard
317: Summary: saving but not running
318:
1.225 brouard 319: Revision 1.224 2016/07/01 13:16:01 brouard
320: Summary: Fixes
321:
1.224 brouard 322: Revision 1.223 2016/02/19 09:23:35 brouard
323: Summary: temporary
324:
1.223 brouard 325: Revision 1.222 2016/02/17 08:14:50 brouard
326: Summary: Probably last 0.98 stable version 0.98r6
327:
1.222 brouard 328: Revision 1.221 2016/02/15 23:35:36 brouard
329: Summary: minor bug
330:
1.220 brouard 331: Revision 1.219 2016/02/15 00:48:12 brouard
332: *** empty log message ***
333:
1.219 brouard 334: Revision 1.218 2016/02/12 11:29:23 brouard
335: Summary: 0.99 Back projections
336:
1.218 brouard 337: Revision 1.217 2015/12/23 17:18:31 brouard
338: Summary: Experimental backcast
339:
1.217 brouard 340: Revision 1.216 2015/12/18 17:32:11 brouard
341: Summary: 0.98r4 Warning and status=-2
342:
343: Version 0.98r4 is now:
344: - displaying an error when status is -1, date of interview unknown and date of death known;
345: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
346: Older changes concerning s=-2, dating from 2005 have been supersed.
347:
1.216 brouard 348: Revision 1.215 2015/12/16 08:52:24 brouard
349: Summary: 0.98r4 working
350:
1.215 brouard 351: Revision 1.214 2015/12/16 06:57:54 brouard
352: Summary: temporary not working
353:
1.214 brouard 354: Revision 1.213 2015/12/11 18:22:17 brouard
355: Summary: 0.98r4
356:
1.213 brouard 357: Revision 1.212 2015/11/21 12:47:24 brouard
358: Summary: minor typo
359:
1.212 brouard 360: Revision 1.211 2015/11/21 12:41:11 brouard
361: Summary: 0.98r3 with some graph of projected cross-sectional
362:
363: Author: Nicolas Brouard
364:
1.211 brouard 365: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 366: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 367: Summary: Adding ftolpl parameter
368: Author: N Brouard
369:
370: We had difficulties to get smoothed confidence intervals. It was due
371: to the period prevalence which wasn't computed accurately. The inner
372: parameter ftolpl is now an outer parameter of the .imach parameter
373: file after estepm. If ftolpl is small 1.e-4 and estepm too,
374: computation are long.
375:
1.209 brouard 376: Revision 1.208 2015/11/17 14:31:57 brouard
377: Summary: temporary
378:
1.208 brouard 379: Revision 1.207 2015/10/27 17:36:57 brouard
380: *** empty log message ***
381:
1.207 brouard 382: Revision 1.206 2015/10/24 07:14:11 brouard
383: *** empty log message ***
384:
1.206 brouard 385: Revision 1.205 2015/10/23 15:50:53 brouard
386: Summary: 0.98r3 some clarification for graphs on likelihood contributions
387:
1.205 brouard 388: Revision 1.204 2015/10/01 16:20:26 brouard
389: Summary: Some new graphs of contribution to likelihood
390:
1.204 brouard 391: Revision 1.203 2015/09/30 17:45:14 brouard
392: Summary: looking at better estimation of the hessian
393:
394: Also a better criteria for convergence to the period prevalence And
395: therefore adding the number of years needed to converge. (The
396: prevalence in any alive state shold sum to one
397:
1.203 brouard 398: Revision 1.202 2015/09/22 19:45:16 brouard
399: Summary: Adding some overall graph on contribution to likelihood. Might change
400:
1.202 brouard 401: Revision 1.201 2015/09/15 17:34:58 brouard
402: Summary: 0.98r0
403:
404: - Some new graphs like suvival functions
405: - Some bugs fixed like model=1+age+V2.
406:
1.201 brouard 407: Revision 1.200 2015/09/09 16:53:55 brouard
408: Summary: Big bug thanks to Flavia
409:
410: Even model=1+age+V2. did not work anymore
411:
1.200 brouard 412: Revision 1.199 2015/09/07 14:09:23 brouard
413: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
414:
1.199 brouard 415: Revision 1.198 2015/09/03 07:14:39 brouard
416: Summary: 0.98q5 Flavia
417:
1.198 brouard 418: Revision 1.197 2015/09/01 18:24:39 brouard
419: *** empty log message ***
420:
1.197 brouard 421: Revision 1.196 2015/08/18 23:17:52 brouard
422: Summary: 0.98q5
423:
1.196 brouard 424: Revision 1.195 2015/08/18 16:28:39 brouard
425: Summary: Adding a hack for testing purpose
426:
427: After reading the title, ftol and model lines, if the comment line has
428: a q, starting with #q, the answer at the end of the run is quit. It
429: permits to run test files in batch with ctest. The former workaround was
430: $ echo q | imach foo.imach
431:
1.195 brouard 432: Revision 1.194 2015/08/18 13:32:00 brouard
433: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
434:
1.194 brouard 435: Revision 1.193 2015/08/04 07:17:42 brouard
436: Summary: 0.98q4
437:
1.193 brouard 438: Revision 1.192 2015/07/16 16:49:02 brouard
439: Summary: Fixing some outputs
440:
1.192 brouard 441: Revision 1.191 2015/07/14 10:00:33 brouard
442: Summary: Some fixes
443:
1.191 brouard 444: Revision 1.190 2015/05/05 08:51:13 brouard
445: Summary: Adding digits in output parameters (7 digits instead of 6)
446:
447: Fix 1+age+.
448:
1.190 brouard 449: Revision 1.189 2015/04/30 14:45:16 brouard
450: Summary: 0.98q2
451:
1.189 brouard 452: Revision 1.188 2015/04/30 08:27:53 brouard
453: *** empty log message ***
454:
1.188 brouard 455: Revision 1.187 2015/04/29 09:11:15 brouard
456: *** empty log message ***
457:
1.187 brouard 458: Revision 1.186 2015/04/23 12:01:52 brouard
459: Summary: V1*age is working now, version 0.98q1
460:
461: Some codes had been disabled in order to simplify and Vn*age was
462: working in the optimization phase, ie, giving correct MLE parameters,
463: but, as usual, outputs were not correct and program core dumped.
464:
1.186 brouard 465: Revision 1.185 2015/03/11 13:26:42 brouard
466: Summary: Inclusion of compile and links command line for Intel Compiler
467:
1.185 brouard 468: Revision 1.184 2015/03/11 11:52:39 brouard
469: Summary: Back from Windows 8. Intel Compiler
470:
1.184 brouard 471: Revision 1.183 2015/03/10 20:34:32 brouard
472: Summary: 0.98q0, trying with directest, mnbrak fixed
473:
474: We use directest instead of original Powell test; probably no
475: incidence on the results, but better justifications;
476: We fixed Numerical Recipes mnbrak routine which was wrong and gave
477: wrong results.
478:
1.183 brouard 479: Revision 1.182 2015/02/12 08:19:57 brouard
480: Summary: Trying to keep directest which seems simpler and more general
481: Author: Nicolas Brouard
482:
1.182 brouard 483: Revision 1.181 2015/02/11 23:22:24 brouard
484: Summary: Comments on Powell added
485:
486: Author:
487:
1.181 brouard 488: Revision 1.180 2015/02/11 17:33:45 brouard
489: Summary: Finishing move from main to function (hpijx and prevalence_limit)
490:
1.180 brouard 491: Revision 1.179 2015/01/04 09:57:06 brouard
492: Summary: back to OS/X
493:
1.179 brouard 494: Revision 1.178 2015/01/04 09:35:48 brouard
495: *** empty log message ***
496:
1.178 brouard 497: Revision 1.177 2015/01/03 18:40:56 brouard
498: Summary: Still testing ilc32 on OSX
499:
1.177 brouard 500: Revision 1.176 2015/01/03 16:45:04 brouard
501: *** empty log message ***
502:
1.176 brouard 503: Revision 1.175 2015/01/03 16:33:42 brouard
504: *** empty log message ***
505:
1.175 brouard 506: Revision 1.174 2015/01/03 16:15:49 brouard
507: Summary: Still in cross-compilation
508:
1.174 brouard 509: Revision 1.173 2015/01/03 12:06:26 brouard
510: Summary: trying to detect cross-compilation
511:
1.173 brouard 512: Revision 1.172 2014/12/27 12:07:47 brouard
513: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
514:
1.172 brouard 515: Revision 1.171 2014/12/23 13:26:59 brouard
516: Summary: Back from Visual C
517:
518: Still problem with utsname.h on Windows
519:
1.171 brouard 520: Revision 1.170 2014/12/23 11:17:12 brouard
521: Summary: Cleaning some \%% back to %%
522:
523: The escape was mandatory for a specific compiler (which one?), but too many warnings.
524:
1.170 brouard 525: Revision 1.169 2014/12/22 23:08:31 brouard
526: Summary: 0.98p
527:
528: Outputs some informations on compiler used, OS etc. Testing on different platforms.
529:
1.169 brouard 530: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 531: Summary: update
1.169 brouard 532:
1.168 brouard 533: Revision 1.167 2014/12/22 13:50:56 brouard
534: Summary: Testing uname and compiler version and if compiled 32 or 64
535:
536: Testing on Linux 64
537:
1.167 brouard 538: Revision 1.166 2014/12/22 11:40:47 brouard
539: *** empty log message ***
540:
1.166 brouard 541: Revision 1.165 2014/12/16 11:20:36 brouard
542: Summary: After compiling on Visual C
543:
544: * imach.c (Module): Merging 1.61 to 1.162
545:
1.165 brouard 546: Revision 1.164 2014/12/16 10:52:11 brouard
547: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
548:
549: * imach.c (Module): Merging 1.61 to 1.162
550:
1.164 brouard 551: Revision 1.163 2014/12/16 10:30:11 brouard
552: * imach.c (Module): Merging 1.61 to 1.162
553:
1.163 brouard 554: Revision 1.162 2014/09/25 11:43:39 brouard
555: Summary: temporary backup 0.99!
556:
1.162 brouard 557: Revision 1.1 2014/09/16 11:06:58 brouard
558: Summary: With some code (wrong) for nlopt
559:
560: Author:
561:
562: Revision 1.161 2014/09/15 20:41:41 brouard
563: Summary: Problem with macro SQR on Intel compiler
564:
1.161 brouard 565: Revision 1.160 2014/09/02 09:24:05 brouard
566: *** empty log message ***
567:
1.160 brouard 568: Revision 1.159 2014/09/01 10:34:10 brouard
569: Summary: WIN32
570: Author: Brouard
571:
1.159 brouard 572: Revision 1.158 2014/08/27 17:11:51 brouard
573: *** empty log message ***
574:
1.158 brouard 575: Revision 1.157 2014/08/27 16:26:55 brouard
576: Summary: Preparing windows Visual studio version
577: Author: Brouard
578:
579: In order to compile on Visual studio, time.h is now correct and time_t
580: and tm struct should be used. difftime should be used but sometimes I
581: just make the differences in raw time format (time(&now).
582: Trying to suppress #ifdef LINUX
583: Add xdg-open for __linux in order to open default browser.
584:
1.157 brouard 585: Revision 1.156 2014/08/25 20:10:10 brouard
586: *** empty log message ***
587:
1.156 brouard 588: Revision 1.155 2014/08/25 18:32:34 brouard
589: Summary: New compile, minor changes
590: Author: Brouard
591:
1.155 brouard 592: Revision 1.154 2014/06/20 17:32:08 brouard
593: Summary: Outputs now all graphs of convergence to period prevalence
594:
1.154 brouard 595: Revision 1.153 2014/06/20 16:45:46 brouard
596: Summary: If 3 live state, convergence to period prevalence on same graph
597: Author: Brouard
598:
1.153 brouard 599: Revision 1.152 2014/06/18 17:54:09 brouard
600: Summary: open browser, use gnuplot on same dir than imach if not found in the path
601:
1.152 brouard 602: Revision 1.151 2014/06/18 16:43:30 brouard
603: *** empty log message ***
604:
1.151 brouard 605: Revision 1.150 2014/06/18 16:42:35 brouard
606: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
607: Author: brouard
608:
1.150 brouard 609: Revision 1.149 2014/06/18 15:51:14 brouard
610: Summary: Some fixes in parameter files errors
611: Author: Nicolas Brouard
612:
1.149 brouard 613: Revision 1.148 2014/06/17 17:38:48 brouard
614: Summary: Nothing new
615: Author: Brouard
616:
617: Just a new packaging for OS/X version 0.98nS
618:
1.148 brouard 619: Revision 1.147 2014/06/16 10:33:11 brouard
620: *** empty log message ***
621:
1.147 brouard 622: Revision 1.146 2014/06/16 10:20:28 brouard
623: Summary: Merge
624: Author: Brouard
625:
626: Merge, before building revised version.
627:
1.146 brouard 628: Revision 1.145 2014/06/10 21:23:15 brouard
629: Summary: Debugging with valgrind
630: Author: Nicolas Brouard
631:
632: Lot of changes in order to output the results with some covariates
633: After the Edimburgh REVES conference 2014, it seems mandatory to
634: improve the code.
635: No more memory valgrind error but a lot has to be done in order to
636: continue the work of splitting the code into subroutines.
637: Also, decodemodel has been improved. Tricode is still not
638: optimal. nbcode should be improved. Documentation has been added in
639: the source code.
640:
1.144 brouard 641: Revision 1.143 2014/01/26 09:45:38 brouard
642: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
643:
644: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
645: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
646:
1.143 brouard 647: Revision 1.142 2014/01/26 03:57:36 brouard
648: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
649:
650: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
651:
1.142 brouard 652: Revision 1.141 2014/01/26 02:42:01 brouard
653: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
654:
1.141 brouard 655: Revision 1.140 2011/09/02 10:37:54 brouard
656: Summary: times.h is ok with mingw32 now.
657:
1.140 brouard 658: Revision 1.139 2010/06/14 07:50:17 brouard
659: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
660: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
661:
1.139 brouard 662: Revision 1.138 2010/04/30 18:19:40 brouard
663: *** empty log message ***
664:
1.138 brouard 665: Revision 1.137 2010/04/29 18:11:38 brouard
666: (Module): Checking covariates for more complex models
667: than V1+V2. A lot of change to be done. Unstable.
668:
1.137 brouard 669: Revision 1.136 2010/04/26 20:30:53 brouard
670: (Module): merging some libgsl code. Fixing computation
671: of likelione (using inter/intrapolation if mle = 0) in order to
672: get same likelihood as if mle=1.
673: Some cleaning of code and comments added.
674:
1.136 brouard 675: Revision 1.135 2009/10/29 15:33:14 brouard
676: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
677:
1.135 brouard 678: Revision 1.134 2009/10/29 13:18:53 brouard
679: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
680:
1.134 brouard 681: Revision 1.133 2009/07/06 10:21:25 brouard
682: just nforces
683:
1.133 brouard 684: Revision 1.132 2009/07/06 08:22:05 brouard
685: Many tings
686:
1.132 brouard 687: Revision 1.131 2009/06/20 16:22:47 brouard
688: Some dimensions resccaled
689:
1.131 brouard 690: Revision 1.130 2009/05/26 06:44:34 brouard
691: (Module): Max Covariate is now set to 20 instead of 8. A
692: lot of cleaning with variables initialized to 0. Trying to make
693: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
694:
1.130 brouard 695: Revision 1.129 2007/08/31 13:49:27 lievre
696: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
697:
1.129 lievre 698: Revision 1.128 2006/06/30 13:02:05 brouard
699: (Module): Clarifications on computing e.j
700:
1.128 brouard 701: Revision 1.127 2006/04/28 18:11:50 brouard
702: (Module): Yes the sum of survivors was wrong since
703: imach-114 because nhstepm was no more computed in the age
704: loop. Now we define nhstepma in the age loop.
705: (Module): In order to speed up (in case of numerous covariates) we
706: compute health expectancies (without variances) in a first step
707: and then all the health expectancies with variances or standard
708: deviation (needs data from the Hessian matrices) which slows the
709: computation.
710: In the future we should be able to stop the program is only health
711: expectancies and graph are needed without standard deviations.
712:
1.127 brouard 713: Revision 1.126 2006/04/28 17:23:28 brouard
714: (Module): Yes the sum of survivors was wrong since
715: imach-114 because nhstepm was no more computed in the age
716: loop. Now we define nhstepma in the age loop.
717: Version 0.98h
718:
1.126 brouard 719: Revision 1.125 2006/04/04 15:20:31 lievre
720: Errors in calculation of health expectancies. Age was not initialized.
721: Forecasting file added.
722:
723: Revision 1.124 2006/03/22 17:13:53 lievre
724: Parameters are printed with %lf instead of %f (more numbers after the comma).
725: The log-likelihood is printed in the log file
726:
727: Revision 1.123 2006/03/20 10:52:43 brouard
728: * imach.c (Module): <title> changed, corresponds to .htm file
729: name. <head> headers where missing.
730:
731: * imach.c (Module): Weights can have a decimal point as for
732: English (a comma might work with a correct LC_NUMERIC environment,
733: otherwise the weight is truncated).
734: Modification of warning when the covariates values are not 0 or
735: 1.
736: Version 0.98g
737:
738: Revision 1.122 2006/03/20 09:45:41 brouard
739: (Module): Weights can have a decimal point as for
740: English (a comma might work with a correct LC_NUMERIC environment,
741: otherwise the weight is truncated).
742: Modification of warning when the covariates values are not 0 or
743: 1.
744: Version 0.98g
745:
746: Revision 1.121 2006/03/16 17:45:01 lievre
747: * imach.c (Module): Comments concerning covariates added
748:
749: * imach.c (Module): refinements in the computation of lli if
750: status=-2 in order to have more reliable computation if stepm is
751: not 1 month. Version 0.98f
752:
753: Revision 1.120 2006/03/16 15:10:38 lievre
754: (Module): refinements in the computation of lli if
755: status=-2 in order to have more reliable computation if stepm is
756: not 1 month. Version 0.98f
757:
758: Revision 1.119 2006/03/15 17:42:26 brouard
759: (Module): Bug if status = -2, the loglikelihood was
760: computed as likelihood omitting the logarithm. Version O.98e
761:
762: Revision 1.118 2006/03/14 18:20:07 brouard
763: (Module): varevsij Comments added explaining the second
764: table of variances if popbased=1 .
765: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
766: (Module): Function pstamp added
767: (Module): Version 0.98d
768:
769: Revision 1.117 2006/03/14 17:16:22 brouard
770: (Module): varevsij Comments added explaining the second
771: table of variances if popbased=1 .
772: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
773: (Module): Function pstamp added
774: (Module): Version 0.98d
775:
776: Revision 1.116 2006/03/06 10:29:27 brouard
777: (Module): Variance-covariance wrong links and
778: varian-covariance of ej. is needed (Saito).
779:
780: Revision 1.115 2006/02/27 12:17:45 brouard
781: (Module): One freematrix added in mlikeli! 0.98c
782:
783: Revision 1.114 2006/02/26 12:57:58 brouard
784: (Module): Some improvements in processing parameter
785: filename with strsep.
786:
787: Revision 1.113 2006/02/24 14:20:24 brouard
788: (Module): Memory leaks checks with valgrind and:
789: datafile was not closed, some imatrix were not freed and on matrix
790: allocation too.
791:
792: Revision 1.112 2006/01/30 09:55:26 brouard
793: (Module): Back to gnuplot.exe instead of wgnuplot.exe
794:
795: Revision 1.111 2006/01/25 20:38:18 brouard
796: (Module): Lots of cleaning and bugs added (Gompertz)
797: (Module): Comments can be added in data file. Missing date values
798: can be a simple dot '.'.
799:
800: Revision 1.110 2006/01/25 00:51:50 brouard
801: (Module): Lots of cleaning and bugs added (Gompertz)
802:
803: Revision 1.109 2006/01/24 19:37:15 brouard
804: (Module): Comments (lines starting with a #) are allowed in data.
805:
806: Revision 1.108 2006/01/19 18:05:42 lievre
807: Gnuplot problem appeared...
808: To be fixed
809:
810: Revision 1.107 2006/01/19 16:20:37 brouard
811: Test existence of gnuplot in imach path
812:
813: Revision 1.106 2006/01/19 13:24:36 brouard
814: Some cleaning and links added in html output
815:
816: Revision 1.105 2006/01/05 20:23:19 lievre
817: *** empty log message ***
818:
819: Revision 1.104 2005/09/30 16:11:43 lievre
820: (Module): sump fixed, loop imx fixed, and simplifications.
821: (Module): If the status is missing at the last wave but we know
822: that the person is alive, then we can code his/her status as -2
823: (instead of missing=-1 in earlier versions) and his/her
824: contributions to the likelihood is 1 - Prob of dying from last
825: health status (= 1-p13= p11+p12 in the easiest case of somebody in
826: the healthy state at last known wave). Version is 0.98
827:
828: Revision 1.103 2005/09/30 15:54:49 lievre
829: (Module): sump fixed, loop imx fixed, and simplifications.
830:
831: Revision 1.102 2004/09/15 17:31:30 brouard
832: Add the possibility to read data file including tab characters.
833:
834: Revision 1.101 2004/09/15 10:38:38 brouard
835: Fix on curr_time
836:
837: Revision 1.100 2004/07/12 18:29:06 brouard
838: Add version for Mac OS X. Just define UNIX in Makefile
839:
840: Revision 1.99 2004/06/05 08:57:40 brouard
841: *** empty log message ***
842:
843: Revision 1.98 2004/05/16 15:05:56 brouard
844: New version 0.97 . First attempt to estimate force of mortality
845: directly from the data i.e. without the need of knowing the health
846: state at each age, but using a Gompertz model: log u =a + b*age .
847: This is the basic analysis of mortality and should be done before any
848: other analysis, in order to test if the mortality estimated from the
849: cross-longitudinal survey is different from the mortality estimated
850: from other sources like vital statistic data.
851:
852: The same imach parameter file can be used but the option for mle should be -3.
853:
1.133 brouard 854: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 855: former routines in order to include the new code within the former code.
856:
857: The output is very simple: only an estimate of the intercept and of
858: the slope with 95% confident intervals.
859:
860: Current limitations:
861: A) Even if you enter covariates, i.e. with the
862: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
863: B) There is no computation of Life Expectancy nor Life Table.
864:
865: Revision 1.97 2004/02/20 13:25:42 lievre
866: Version 0.96d. Population forecasting command line is (temporarily)
867: suppressed.
868:
869: Revision 1.96 2003/07/15 15:38:55 brouard
870: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
871: rewritten within the same printf. Workaround: many printfs.
872:
873: Revision 1.95 2003/07/08 07:54:34 brouard
874: * imach.c (Repository):
875: (Repository): Using imachwizard code to output a more meaningful covariance
876: matrix (cov(a12,c31) instead of numbers.
877:
878: Revision 1.94 2003/06/27 13:00:02 brouard
879: Just cleaning
880:
881: Revision 1.93 2003/06/25 16:33:55 brouard
882: (Module): On windows (cygwin) function asctime_r doesn't
883: exist so I changed back to asctime which exists.
884: (Module): Version 0.96b
885:
886: Revision 1.92 2003/06/25 16:30:45 brouard
887: (Module): On windows (cygwin) function asctime_r doesn't
888: exist so I changed back to asctime which exists.
889:
890: Revision 1.91 2003/06/25 15:30:29 brouard
891: * imach.c (Repository): Duplicated warning errors corrected.
892: (Repository): Elapsed time after each iteration is now output. It
893: helps to forecast when convergence will be reached. Elapsed time
894: is stamped in powell. We created a new html file for the graphs
895: concerning matrix of covariance. It has extension -cov.htm.
896:
897: Revision 1.90 2003/06/24 12:34:15 brouard
898: (Module): Some bugs corrected for windows. Also, when
899: mle=-1 a template is output in file "or"mypar.txt with the design
900: of the covariance matrix to be input.
901:
902: Revision 1.89 2003/06/24 12:30:52 brouard
903: (Module): Some bugs corrected for windows. Also, when
904: mle=-1 a template is output in file "or"mypar.txt with the design
905: of the covariance matrix to be input.
906:
907: Revision 1.88 2003/06/23 17:54:56 brouard
908: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
909:
910: Revision 1.87 2003/06/18 12:26:01 brouard
911: Version 0.96
912:
913: Revision 1.86 2003/06/17 20:04:08 brouard
914: (Module): Change position of html and gnuplot routines and added
915: routine fileappend.
916:
917: Revision 1.85 2003/06/17 13:12:43 brouard
918: * imach.c (Repository): Check when date of death was earlier that
919: current date of interview. It may happen when the death was just
920: prior to the death. In this case, dh was negative and likelihood
921: was wrong (infinity). We still send an "Error" but patch by
922: assuming that the date of death was just one stepm after the
923: interview.
924: (Repository): Because some people have very long ID (first column)
925: we changed int to long in num[] and we added a new lvector for
926: memory allocation. But we also truncated to 8 characters (left
927: truncation)
928: (Repository): No more line truncation errors.
929:
930: Revision 1.84 2003/06/13 21:44:43 brouard
931: * imach.c (Repository): Replace "freqsummary" at a correct
932: place. It differs from routine "prevalence" which may be called
933: many times. Probs is memory consuming and must be used with
934: parcimony.
935: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
936:
937: Revision 1.83 2003/06/10 13:39:11 lievre
938: *** empty log message ***
939:
940: Revision 1.82 2003/06/05 15:57:20 brouard
941: Add log in imach.c and fullversion number is now printed.
942:
943: */
944: /*
945: Interpolated Markov Chain
946:
947: Short summary of the programme:
948:
1.227 brouard 949: This program computes Healthy Life Expectancies or State-specific
950: (if states aren't health statuses) Expectancies from
951: cross-longitudinal data. Cross-longitudinal data consist in:
952:
953: -1- a first survey ("cross") where individuals from different ages
954: are interviewed on their health status or degree of disability (in
955: the case of a health survey which is our main interest)
956:
957: -2- at least a second wave of interviews ("longitudinal") which
958: measure each change (if any) in individual health status. Health
959: expectancies are computed from the time spent in each health state
960: according to a model. More health states you consider, more time is
961: necessary to reach the Maximum Likelihood of the parameters involved
962: in the model. The simplest model is the multinomial logistic model
963: where pij is the probability to be observed in state j at the second
964: wave conditional to be observed in state i at the first
965: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
966: etc , where 'age' is age and 'sex' is a covariate. If you want to
967: have a more complex model than "constant and age", you should modify
968: the program where the markup *Covariates have to be included here
969: again* invites you to do it. More covariates you add, slower the
1.126 brouard 970: convergence.
971:
972: The advantage of this computer programme, compared to a simple
973: multinomial logistic model, is clear when the delay between waves is not
974: identical for each individual. Also, if a individual missed an
975: intermediate interview, the information is lost, but taken into
976: account using an interpolation or extrapolation.
977:
978: hPijx is the probability to be observed in state i at age x+h
979: conditional to the observed state i at age x. The delay 'h' can be
980: split into an exact number (nh*stepm) of unobserved intermediate
981: states. This elementary transition (by month, quarter,
982: semester or year) is modelled as a multinomial logistic. The hPx
983: matrix is simply the matrix product of nh*stepm elementary matrices
984: and the contribution of each individual to the likelihood is simply
985: hPijx.
986:
987: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 988: of the life expectancies. It also computes the period (stable) prevalence.
989:
990: Back prevalence and projections:
1.227 brouard 991:
992: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
993: double agemaxpar, double ftolpl, int *ncvyearp, double
994: dateprev1,double dateprev2, int firstpass, int lastpass, int
995: mobilavproj)
996:
997: Computes the back prevalence limit for any combination of
998: covariate values k at any age between ageminpar and agemaxpar and
999: returns it in **bprlim. In the loops,
1000:
1001: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
1002: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
1003:
1004: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 1005: Computes for any combination of covariates k and any age between bage and fage
1006: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1007: oldm=oldms;savm=savms;
1.227 brouard 1008:
1.267 brouard 1009: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 1010: Computes the transition matrix starting at age 'age' over
1011: 'nhstepm*hstepm*stepm' months (i.e. until
1012: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 1013: nhstepm*hstepm matrices.
1014:
1015: Returns p3mat[i][j][h] after calling
1016: p3mat[i][j][h]=matprod2(newm,
1017: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
1018: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1019: oldm);
1.226 brouard 1020:
1021: Important routines
1022:
1023: - func (or funcone), computes logit (pij) distinguishing
1024: o fixed variables (single or product dummies or quantitative);
1025: o varying variables by:
1026: (1) wave (single, product dummies, quantitative),
1027: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
1028: % fixed dummy (treated) or quantitative (not done because time-consuming);
1029: % varying dummy (not done) or quantitative (not done);
1030: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
1031: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
1032: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
1033: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
1034: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 1035:
1.226 brouard 1036:
1037:
1.133 brouard 1038: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
1039: Institut national d'études démographiques, Paris.
1.126 brouard 1040: This software have been partly granted by Euro-REVES, a concerted action
1041: from the European Union.
1042: It is copyrighted identically to a GNU software product, ie programme and
1043: software can be distributed freely for non commercial use. Latest version
1044: can be accessed at http://euroreves.ined.fr/imach .
1045:
1046: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
1047: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
1048:
1049: **********************************************************************/
1050: /*
1051: main
1052: read parameterfile
1053: read datafile
1054: concatwav
1055: freqsummary
1056: if (mle >= 1)
1057: mlikeli
1058: print results files
1059: if mle==1
1060: computes hessian
1061: read end of parameter file: agemin, agemax, bage, fage, estepm
1062: begin-prev-date,...
1063: open gnuplot file
1064: open html file
1.145 brouard 1065: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1066: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1067: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1068: freexexit2 possible for memory heap.
1069:
1070: h Pij x | pij_nom ficrestpij
1071: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1072: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1073: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1074:
1075: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1076: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1077: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1078: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1079: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1080:
1.126 brouard 1081: forecasting if prevfcast==1 prevforecast call prevalence()
1082: health expectancies
1083: Variance-covariance of DFLE
1084: prevalence()
1085: movingaverage()
1086: varevsij()
1087: if popbased==1 varevsij(,popbased)
1088: total life expectancies
1089: Variance of period (stable) prevalence
1090: end
1091: */
1092:
1.187 brouard 1093: /* #define DEBUG */
1094: /* #define DEBUGBRENT */
1.203 brouard 1095: /* #define DEBUGLINMIN */
1096: /* #define DEBUGHESS */
1097: #define DEBUGHESSIJ
1.224 brouard 1098: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1099: #define POWELL /* Instead of NLOPT */
1.224 brouard 1100: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1101: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1102: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.319 ! brouard 1103: /* #define FLATSUP *//* Suppresses directions where likelihood is flat */
1.126 brouard 1104:
1105: #include <math.h>
1106: #include <stdio.h>
1107: #include <stdlib.h>
1108: #include <string.h>
1.226 brouard 1109: #include <ctype.h>
1.159 brouard 1110:
1111: #ifdef _WIN32
1112: #include <io.h>
1.172 brouard 1113: #include <windows.h>
1114: #include <tchar.h>
1.159 brouard 1115: #else
1.126 brouard 1116: #include <unistd.h>
1.159 brouard 1117: #endif
1.126 brouard 1118:
1119: #include <limits.h>
1120: #include <sys/types.h>
1.171 brouard 1121:
1122: #if defined(__GNUC__)
1123: #include <sys/utsname.h> /* Doesn't work on Windows */
1124: #endif
1125:
1.126 brouard 1126: #include <sys/stat.h>
1127: #include <errno.h>
1.159 brouard 1128: /* extern int errno; */
1.126 brouard 1129:
1.157 brouard 1130: /* #ifdef LINUX */
1131: /* #include <time.h> */
1132: /* #include "timeval.h" */
1133: /* #else */
1134: /* #include <sys/time.h> */
1135: /* #endif */
1136:
1.126 brouard 1137: #include <time.h>
1138:
1.136 brouard 1139: #ifdef GSL
1140: #include <gsl/gsl_errno.h>
1141: #include <gsl/gsl_multimin.h>
1142: #endif
1143:
1.167 brouard 1144:
1.162 brouard 1145: #ifdef NLOPT
1146: #include <nlopt.h>
1147: typedef struct {
1148: double (* function)(double [] );
1149: } myfunc_data ;
1150: #endif
1151:
1.126 brouard 1152: /* #include <libintl.h> */
1153: /* #define _(String) gettext (String) */
1154:
1.251 brouard 1155: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1156:
1157: #define GNUPLOTPROGRAM "gnuplot"
1158: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1159: #define FILENAMELENGTH 132
1160:
1161: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1162: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1163:
1.144 brouard 1164: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1165: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1166:
1167: #define NINTERVMAX 8
1.144 brouard 1168: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1169: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.318 brouard 1170: #define NCOVMAX 30 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1171: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1172: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1173: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1174: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1175: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1176: /* #define AGESUP 130 */
1.288 brouard 1177: /* #define AGESUP 150 */
1178: #define AGESUP 200
1.268 brouard 1179: #define AGEINF 0
1.218 brouard 1180: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1181: #define AGEBASE 40
1.194 brouard 1182: #define AGEOVERFLOW 1.e20
1.164 brouard 1183: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1184: #ifdef _WIN32
1185: #define DIRSEPARATOR '\\'
1186: #define CHARSEPARATOR "\\"
1187: #define ODIRSEPARATOR '/'
1188: #else
1.126 brouard 1189: #define DIRSEPARATOR '/'
1190: #define CHARSEPARATOR "/"
1191: #define ODIRSEPARATOR '\\'
1192: #endif
1193:
1.319 ! brouard 1194: /* $Id: imach.c,v 1.318 2022/05/24 08:10:59 brouard Exp $ */
1.126 brouard 1195: /* $State: Exp $ */
1.196 brouard 1196: #include "version.h"
1197: char version[]=__IMACH_VERSION__;
1.316 brouard 1198: char copyright[]="May 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
1.319 ! brouard 1199: char fullversion[]="$Revision: 1.318 $ $Date: 2022/05/24 08:10:59 $";
1.126 brouard 1200: char strstart[80];
1201: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1202: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1203: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1204: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1205: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1206: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1207: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1208: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1209: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1210: int cptcovprodnoage=0; /**< Number of covariate products without age */
1211: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1212: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1213: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1214: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1215: int nsd=0; /**< Total number of single dummy variables (output) */
1216: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1217: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1218: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1219: int ntveff=0; /**< ntveff number of effective time varying variables */
1220: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1221: int cptcov=0; /* Working variable */
1.290 brouard 1222: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1223: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1224: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1225: int nlstate=2; /* Number of live states */
1226: int ndeath=1; /* Number of dead states */
1.130 brouard 1227: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1228: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1229: int popbased=0;
1230:
1231: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1232: int maxwav=0; /* Maxim number of waves */
1233: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1234: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1235: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1236: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1237: int mle=1, weightopt=0;
1.126 brouard 1238: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1239: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1240: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1241: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1242: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1243: int selected(int kvar); /* Is covariate kvar selected for printing results */
1244:
1.130 brouard 1245: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1246: double **matprod2(); /* test */
1.126 brouard 1247: double **oldm, **newm, **savm; /* Working pointers to matrices */
1248: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1249: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1250:
1.136 brouard 1251: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1252: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1253: FILE *ficlog, *ficrespow;
1.130 brouard 1254: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1255: double fretone; /* Only one call to likelihood */
1.130 brouard 1256: long ipmx=0; /* Number of contributions */
1.126 brouard 1257: double sw; /* Sum of weights */
1258: char filerespow[FILENAMELENGTH];
1259: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1260: FILE *ficresilk;
1261: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1262: FILE *ficresprobmorprev;
1263: FILE *fichtm, *fichtmcov; /* Html File */
1264: FILE *ficreseij;
1265: char filerese[FILENAMELENGTH];
1266: FILE *ficresstdeij;
1267: char fileresstde[FILENAMELENGTH];
1268: FILE *ficrescveij;
1269: char filerescve[FILENAMELENGTH];
1270: FILE *ficresvij;
1271: char fileresv[FILENAMELENGTH];
1.269 brouard 1272:
1.126 brouard 1273: char title[MAXLINE];
1.234 brouard 1274: char model[MAXLINE]; /**< The model line */
1.217 brouard 1275: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1276: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1277: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1278: char command[FILENAMELENGTH];
1279: int outcmd=0;
1280:
1.217 brouard 1281: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1282: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1283: char filelog[FILENAMELENGTH]; /* Log file */
1284: char filerest[FILENAMELENGTH];
1285: char fileregp[FILENAMELENGTH];
1286: char popfile[FILENAMELENGTH];
1287:
1288: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1289:
1.157 brouard 1290: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1291: /* struct timezone tzp; */
1292: /* extern int gettimeofday(); */
1293: struct tm tml, *gmtime(), *localtime();
1294:
1295: extern time_t time();
1296:
1297: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1298: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1299: struct tm tm;
1300:
1.126 brouard 1301: char strcurr[80], strfor[80];
1302:
1303: char *endptr;
1304: long lval;
1305: double dval;
1306:
1307: #define NR_END 1
1308: #define FREE_ARG char*
1309: #define FTOL 1.0e-10
1310:
1311: #define NRANSI
1.240 brouard 1312: #define ITMAX 200
1313: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1314:
1315: #define TOL 2.0e-4
1316:
1317: #define CGOLD 0.3819660
1318: #define ZEPS 1.0e-10
1319: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1320:
1321: #define GOLD 1.618034
1322: #define GLIMIT 100.0
1323: #define TINY 1.0e-20
1324:
1325: static double maxarg1,maxarg2;
1326: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1327: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1328:
1329: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1330: #define rint(a) floor(a+0.5)
1.166 brouard 1331: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1332: #define mytinydouble 1.0e-16
1.166 brouard 1333: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1334: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1335: /* static double dsqrarg; */
1336: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1337: static double sqrarg;
1338: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1339: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1340: int agegomp= AGEGOMP;
1341:
1342: int imx;
1343: int stepm=1;
1344: /* Stepm, step in month: minimum step interpolation*/
1345:
1346: int estepm;
1347: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1348:
1349: int m,nb;
1350: long *num;
1.197 brouard 1351: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1352: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1353: covariate for which somebody answered excluding
1354: undefined. Usually 2: 0 and 1. */
1355: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1356: covariate for which somebody answered including
1357: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1358: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1359: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1360: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1361: double *ageexmed,*agecens;
1362: double dateintmean=0;
1.296 brouard 1363: double anprojd, mprojd, jprojd; /* For eventual projections */
1364: double anprojf, mprojf, jprojf;
1.126 brouard 1365:
1.296 brouard 1366: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1367: double anbackf, mbackf, jbackf;
1368: double jintmean,mintmean,aintmean;
1.126 brouard 1369: double *weight;
1370: int **s; /* Status */
1.141 brouard 1371: double *agedc;
1.145 brouard 1372: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1373: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1374: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1375: double **coqvar; /* Fixed quantitative covariate nqv */
1376: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1377: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1378: double idx;
1379: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.319 ! brouard 1380: /* Some documentation */
! 1381: /* Design original data
! 1382: * V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
! 1383: * < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv
! 1384: * ntv=3 nqtv=1
! 1385: * cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11
! 1386: * For time varying covariate, quanti or dummies
! 1387: * cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
! 1388: * cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
! 1389: * cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
! 1390: * cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
! 1391: * covar[k,i], value of kth fixed covariate dummy or quanti :
! 1392: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
! 1393: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
! 1394: * k= 1 2 3 4 5 6 7 8 9 10 11
! 1395: */
! 1396: /* According to the model, more columns can be added to covar by the product of covariates */
1.318 brouard 1397: /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
1398: # States 1=Coresidence, 2 Living alone, 3 Institution
1399: # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
1400: */
1.319 ! brouard 1401: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 1402: /* k 1 2 3 4 5 6 7 8 9 */
! 1403: /*Typevar[k]= 0 0 0 2 1 0 2 1 0 *//*0 for simple covariate (dummy, quantitative,*/
! 1404: /* fixed or varying), 1 for age product, 2 for*/
! 1405: /* product */
! 1406: /*Dummy[k]= 1 0 0 1 3 1 1 2 0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
! 1407: /*(single or product without age), 2 dummy*/
! 1408: /* with age product, 3 quant with age product*/
! 1409: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
! 1410: /* nsd 1 2 3 */ /* Counting single dummies covar fixed or tv */
! 1411: /*TvarsD[nsd] 4 3 1 */ /* ID of single dummy cova fixed or timevary*/
! 1412: /*TvarsDind[k] 2 3 9 */ /* position K of single dummy cova */
! 1413: /* nsq 1 2 */ /* Counting single quantit tv */
! 1414: /* TvarsQ[k] 5 2 */ /* Number of single quantitative cova */
! 1415: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
! 1416: /* Tprod[i]=k 1 2 */ /* Position in model of the ith prod without age */
! 1417: /* cptcovage 1 2 */ /* Counting cov*age in the model equation */
! 1418: /* Tage[cptcovage]=k 5 8 */ /* Position in the model of ith cov*age */
! 1419: /* Tvard[1][1]@4={4,3,1,2} V4*V3 V1*V2 */ /* Position in model of the ith prod without age */
! 1420: /* TvarF TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1*V2, V1 */
! 1421: /* TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */
1.234 brouard 1422: /* Type */
1423: /* V 1 2 3 4 5 */
1424: /* F F V V V */
1425: /* D Q D D Q */
1426: /* */
1427: int *TvarsD;
1428: int *TvarsDind;
1429: int *TvarsQ;
1430: int *TvarsQind;
1431:
1.318 brouard 1432: #define MAXRESULTLINESPONE 10+1
1.235 brouard 1433: int nresult=0;
1.258 brouard 1434: int parameterline=0; /* # of the parameter (type) line */
1.318 brouard 1435: int TKresult[MAXRESULTLINESPONE];
1436: int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
1437: int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
1438: int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
1439: double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
1440: double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
1441: int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */
1442:
1443: /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
1444: # States 1=Coresidence, 2 Living alone, 3 Institution
1445: # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
1446: */
1.234 brouard 1447: /* int *TDvar; /\**< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
1.232 brouard 1448: int *TvarF; /**< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1449: int *TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1450: int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1451: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1452: int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1453: int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 1454: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1455: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1456: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1457: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1458: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1459: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1460: int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1461: int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1462:
1.230 brouard 1463: int *Tvarsel; /**< Selected covariates for output */
1464: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1465: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1466: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1467: int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
1.238 brouard 1468: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1469: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1470: int *Tage;
1.227 brouard 1471: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1472: int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.230 brouard 1473: int *TmodelInvind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1474: int *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.145 brouard 1475: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1476: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1477: int **Tvard;
1478: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1479: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1480: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1481: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1482: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1483: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1484: double *lsurv, *lpop, *tpop;
1485:
1.231 brouard 1486: #define FD 1; /* Fixed dummy covariate */
1487: #define FQ 2; /* Fixed quantitative covariate */
1488: #define FP 3; /* Fixed product covariate */
1489: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1490: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1491: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1492: #define VD 10; /* Varying dummy covariate */
1493: #define VQ 11; /* Varying quantitative covariate */
1494: #define VP 12; /* Varying product covariate */
1495: #define VPDD 13; /* Varying product dummy*dummy covariate */
1496: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1497: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1498: #define APFD 16; /* Age product * fixed dummy covariate */
1499: #define APFQ 17; /* Age product * fixed quantitative covariate */
1500: #define APVD 18; /* Age product * varying dummy covariate */
1501: #define APVQ 19; /* Age product * varying quantitative covariate */
1502:
1503: #define FTYPE 1; /* Fixed covariate */
1504: #define VTYPE 2; /* Varying covariate (loop in wave) */
1505: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1506:
1507: struct kmodel{
1508: int maintype; /* main type */
1509: int subtype; /* subtype */
1510: };
1511: struct kmodel modell[NCOVMAX];
1512:
1.143 brouard 1513: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1514: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1515:
1516: /**************** split *************************/
1517: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1518: {
1519: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1520: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1521: */
1522: char *ss; /* pointer */
1.186 brouard 1523: int l1=0, l2=0; /* length counters */
1.126 brouard 1524:
1525: l1 = strlen(path ); /* length of path */
1526: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1527: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1528: if ( ss == NULL ) { /* no directory, so determine current directory */
1529: strcpy( name, path ); /* we got the fullname name because no directory */
1530: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1531: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1532: /* get current working directory */
1533: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1534: #ifdef WIN32
1535: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1536: #else
1537: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1538: #endif
1.126 brouard 1539: return( GLOCK_ERROR_GETCWD );
1540: }
1541: /* got dirc from getcwd*/
1542: printf(" DIRC = %s \n",dirc);
1.205 brouard 1543: } else { /* strip directory from path */
1.126 brouard 1544: ss++; /* after this, the filename */
1545: l2 = strlen( ss ); /* length of filename */
1546: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1547: strcpy( name, ss ); /* save file name */
1548: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1549: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1550: printf(" DIRC2 = %s \n",dirc);
1551: }
1552: /* We add a separator at the end of dirc if not exists */
1553: l1 = strlen( dirc ); /* length of directory */
1554: if( dirc[l1-1] != DIRSEPARATOR ){
1555: dirc[l1] = DIRSEPARATOR;
1556: dirc[l1+1] = 0;
1557: printf(" DIRC3 = %s \n",dirc);
1558: }
1559: ss = strrchr( name, '.' ); /* find last / */
1560: if (ss >0){
1561: ss++;
1562: strcpy(ext,ss); /* save extension */
1563: l1= strlen( name);
1564: l2= strlen(ss)+1;
1565: strncpy( finame, name, l1-l2);
1566: finame[l1-l2]= 0;
1567: }
1568:
1569: return( 0 ); /* we're done */
1570: }
1571:
1572:
1573: /******************************************/
1574:
1575: void replace_back_to_slash(char *s, char*t)
1576: {
1577: int i;
1578: int lg=0;
1579: i=0;
1580: lg=strlen(t);
1581: for(i=0; i<= lg; i++) {
1582: (s[i] = t[i]);
1583: if (t[i]== '\\') s[i]='/';
1584: }
1585: }
1586:
1.132 brouard 1587: char *trimbb(char *out, char *in)
1.137 brouard 1588: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1589: char *s;
1590: s=out;
1591: while (*in != '\0'){
1.137 brouard 1592: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1593: in++;
1594: }
1595: *out++ = *in++;
1596: }
1597: *out='\0';
1598: return s;
1599: }
1600:
1.187 brouard 1601: /* char *substrchaine(char *out, char *in, char *chain) */
1602: /* { */
1603: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1604: /* char *s, *t; */
1605: /* t=in;s=out; */
1606: /* while ((*in != *chain) && (*in != '\0')){ */
1607: /* *out++ = *in++; */
1608: /* } */
1609:
1610: /* /\* *in matches *chain *\/ */
1611: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1612: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1613: /* } */
1614: /* in--; chain--; */
1615: /* while ( (*in != '\0')){ */
1616: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1617: /* *out++ = *in++; */
1618: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1619: /* } */
1620: /* *out='\0'; */
1621: /* out=s; */
1622: /* return out; */
1623: /* } */
1624: char *substrchaine(char *out, char *in, char *chain)
1625: {
1626: /* Substract chain 'chain' from 'in', return and output 'out' */
1627: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1628:
1629: char *strloc;
1630:
1631: strcpy (out, in);
1632: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1633: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1634: if(strloc != NULL){
1635: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1636: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1637: /* strcpy (strloc, strloc +strlen(chain));*/
1638: }
1639: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1640: return out;
1641: }
1642:
1643:
1.145 brouard 1644: char *cutl(char *blocc, char *alocc, char *in, char occ)
1645: {
1.187 brouard 1646: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1647: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.310 brouard 1648: gives alocc="abcdef" and blocc="ghi2j".
1.145 brouard 1649: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1650: */
1.160 brouard 1651: char *s, *t;
1.145 brouard 1652: t=in;s=in;
1653: while ((*in != occ) && (*in != '\0')){
1654: *alocc++ = *in++;
1655: }
1656: if( *in == occ){
1657: *(alocc)='\0';
1658: s=++in;
1659: }
1660:
1661: if (s == t) {/* occ not found */
1662: *(alocc-(in-s))='\0';
1663: in=s;
1664: }
1665: while ( *in != '\0'){
1666: *blocc++ = *in++;
1667: }
1668:
1669: *blocc='\0';
1670: return t;
1671: }
1.137 brouard 1672: char *cutv(char *blocc, char *alocc, char *in, char occ)
1673: {
1.187 brouard 1674: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1675: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1676: gives blocc="abcdef2ghi" and alocc="j".
1677: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1678: */
1679: char *s, *t;
1680: t=in;s=in;
1681: while (*in != '\0'){
1682: while( *in == occ){
1683: *blocc++ = *in++;
1684: s=in;
1685: }
1686: *blocc++ = *in++;
1687: }
1688: if (s == t) /* occ not found */
1689: *(blocc-(in-s))='\0';
1690: else
1691: *(blocc-(in-s)-1)='\0';
1692: in=s;
1693: while ( *in != '\0'){
1694: *alocc++ = *in++;
1695: }
1696:
1697: *alocc='\0';
1698: return s;
1699: }
1700:
1.126 brouard 1701: int nbocc(char *s, char occ)
1702: {
1703: int i,j=0;
1704: int lg=20;
1705: i=0;
1706: lg=strlen(s);
1707: for(i=0; i<= lg; i++) {
1.234 brouard 1708: if (s[i] == occ ) j++;
1.126 brouard 1709: }
1710: return j;
1711: }
1712:
1.137 brouard 1713: /* void cutv(char *u,char *v, char*t, char occ) */
1714: /* { */
1715: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1716: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1717: /* gives u="abcdef2ghi" and v="j" *\/ */
1718: /* int i,lg,j,p=0; */
1719: /* i=0; */
1720: /* lg=strlen(t); */
1721: /* for(j=0; j<=lg-1; j++) { */
1722: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1723: /* } */
1.126 brouard 1724:
1.137 brouard 1725: /* for(j=0; j<p; j++) { */
1726: /* (u[j] = t[j]); */
1727: /* } */
1728: /* u[p]='\0'; */
1.126 brouard 1729:
1.137 brouard 1730: /* for(j=0; j<= lg; j++) { */
1731: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1732: /* } */
1733: /* } */
1.126 brouard 1734:
1.160 brouard 1735: #ifdef _WIN32
1736: char * strsep(char **pp, const char *delim)
1737: {
1738: char *p, *q;
1739:
1740: if ((p = *pp) == NULL)
1741: return 0;
1742: if ((q = strpbrk (p, delim)) != NULL)
1743: {
1744: *pp = q + 1;
1745: *q = '\0';
1746: }
1747: else
1748: *pp = 0;
1749: return p;
1750: }
1751: #endif
1752:
1.126 brouard 1753: /********************** nrerror ********************/
1754:
1755: void nrerror(char error_text[])
1756: {
1757: fprintf(stderr,"ERREUR ...\n");
1758: fprintf(stderr,"%s\n",error_text);
1759: exit(EXIT_FAILURE);
1760: }
1761: /*********************** vector *******************/
1762: double *vector(int nl, int nh)
1763: {
1764: double *v;
1765: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1766: if (!v) nrerror("allocation failure in vector");
1767: return v-nl+NR_END;
1768: }
1769:
1770: /************************ free vector ******************/
1771: void free_vector(double*v, int nl, int nh)
1772: {
1773: free((FREE_ARG)(v+nl-NR_END));
1774: }
1775:
1776: /************************ivector *******************************/
1777: int *ivector(long nl,long nh)
1778: {
1779: int *v;
1780: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1781: if (!v) nrerror("allocation failure in ivector");
1782: return v-nl+NR_END;
1783: }
1784:
1785: /******************free ivector **************************/
1786: void free_ivector(int *v, long nl, long nh)
1787: {
1788: free((FREE_ARG)(v+nl-NR_END));
1789: }
1790:
1791: /************************lvector *******************************/
1792: long *lvector(long nl,long nh)
1793: {
1794: long *v;
1795: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1796: if (!v) nrerror("allocation failure in ivector");
1797: return v-nl+NR_END;
1798: }
1799:
1800: /******************free lvector **************************/
1801: void free_lvector(long *v, long nl, long nh)
1802: {
1803: free((FREE_ARG)(v+nl-NR_END));
1804: }
1805:
1806: /******************* imatrix *******************************/
1807: int **imatrix(long nrl, long nrh, long ncl, long nch)
1808: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1809: {
1810: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1811: int **m;
1812:
1813: /* allocate pointers to rows */
1814: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1815: if (!m) nrerror("allocation failure 1 in matrix()");
1816: m += NR_END;
1817: m -= nrl;
1818:
1819:
1820: /* allocate rows and set pointers to them */
1821: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1822: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1823: m[nrl] += NR_END;
1824: m[nrl] -= ncl;
1825:
1826: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1827:
1828: /* return pointer to array of pointers to rows */
1829: return m;
1830: }
1831:
1832: /****************** free_imatrix *************************/
1833: void free_imatrix(m,nrl,nrh,ncl,nch)
1834: int **m;
1835: long nch,ncl,nrh,nrl;
1836: /* free an int matrix allocated by imatrix() */
1837: {
1838: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1839: free((FREE_ARG) (m+nrl-NR_END));
1840: }
1841:
1842: /******************* matrix *******************************/
1843: double **matrix(long nrl, long nrh, long ncl, long nch)
1844: {
1845: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1846: double **m;
1847:
1848: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1849: if (!m) nrerror("allocation failure 1 in matrix()");
1850: m += NR_END;
1851: m -= nrl;
1852:
1853: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1854: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1855: m[nrl] += NR_END;
1856: m[nrl] -= ncl;
1857:
1858: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1859: return m;
1.145 brouard 1860: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1861: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1862: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1863: */
1864: }
1865:
1866: /*************************free matrix ************************/
1867: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1868: {
1869: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1870: free((FREE_ARG)(m+nrl-NR_END));
1871: }
1872:
1873: /******************* ma3x *******************************/
1874: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1875: {
1876: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1877: double ***m;
1878:
1879: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1880: if (!m) nrerror("allocation failure 1 in matrix()");
1881: m += NR_END;
1882: m -= nrl;
1883:
1884: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1885: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1886: m[nrl] += NR_END;
1887: m[nrl] -= ncl;
1888:
1889: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1890:
1891: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1892: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1893: m[nrl][ncl] += NR_END;
1894: m[nrl][ncl] -= nll;
1895: for (j=ncl+1; j<=nch; j++)
1896: m[nrl][j]=m[nrl][j-1]+nlay;
1897:
1898: for (i=nrl+1; i<=nrh; i++) {
1899: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1900: for (j=ncl+1; j<=nch; j++)
1901: m[i][j]=m[i][j-1]+nlay;
1902: }
1903: return m;
1904: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1905: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1906: */
1907: }
1908:
1909: /*************************free ma3x ************************/
1910: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1911: {
1912: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1913: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1914: free((FREE_ARG)(m+nrl-NR_END));
1915: }
1916:
1917: /*************** function subdirf ***********/
1918: char *subdirf(char fileres[])
1919: {
1920: /* Caution optionfilefiname is hidden */
1921: strcpy(tmpout,optionfilefiname);
1922: strcat(tmpout,"/"); /* Add to the right */
1923: strcat(tmpout,fileres);
1924: return tmpout;
1925: }
1926:
1927: /*************** function subdirf2 ***********/
1928: char *subdirf2(char fileres[], char *preop)
1929: {
1.314 brouard 1930: /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
1931: Errors in subdirf, 2, 3 while printing tmpout is
1.315 brouard 1932: rewritten within the same printf. Workaround: many printfs */
1.126 brouard 1933: /* Caution optionfilefiname is hidden */
1934: strcpy(tmpout,optionfilefiname);
1935: strcat(tmpout,"/");
1936: strcat(tmpout,preop);
1937: strcat(tmpout,fileres);
1938: return tmpout;
1939: }
1940:
1941: /*************** function subdirf3 ***********/
1942: char *subdirf3(char fileres[], char *preop, char *preop2)
1943: {
1944:
1945: /* Caution optionfilefiname is hidden */
1946: strcpy(tmpout,optionfilefiname);
1947: strcat(tmpout,"/");
1948: strcat(tmpout,preop);
1949: strcat(tmpout,preop2);
1950: strcat(tmpout,fileres);
1951: return tmpout;
1952: }
1.213 brouard 1953:
1954: /*************** function subdirfext ***********/
1955: char *subdirfext(char fileres[], char *preop, char *postop)
1956: {
1957:
1958: strcpy(tmpout,preop);
1959: strcat(tmpout,fileres);
1960: strcat(tmpout,postop);
1961: return tmpout;
1962: }
1.126 brouard 1963:
1.213 brouard 1964: /*************** function subdirfext3 ***********/
1965: char *subdirfext3(char fileres[], char *preop, char *postop)
1966: {
1967:
1968: /* Caution optionfilefiname is hidden */
1969: strcpy(tmpout,optionfilefiname);
1970: strcat(tmpout,"/");
1971: strcat(tmpout,preop);
1972: strcat(tmpout,fileres);
1973: strcat(tmpout,postop);
1974: return tmpout;
1975: }
1976:
1.162 brouard 1977: char *asc_diff_time(long time_sec, char ascdiff[])
1978: {
1979: long sec_left, days, hours, minutes;
1980: days = (time_sec) / (60*60*24);
1981: sec_left = (time_sec) % (60*60*24);
1982: hours = (sec_left) / (60*60) ;
1983: sec_left = (sec_left) %(60*60);
1984: minutes = (sec_left) /60;
1985: sec_left = (sec_left) % (60);
1986: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1987: return ascdiff;
1988: }
1989:
1.126 brouard 1990: /***************** f1dim *************************/
1991: extern int ncom;
1992: extern double *pcom,*xicom;
1993: extern double (*nrfunc)(double []);
1994:
1995: double f1dim(double x)
1996: {
1997: int j;
1998: double f;
1999: double *xt;
2000:
2001: xt=vector(1,ncom);
2002: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
2003: f=(*nrfunc)(xt);
2004: free_vector(xt,1,ncom);
2005: return f;
2006: }
2007:
2008: /*****************brent *************************/
2009: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 2010: {
2011: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
2012: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
2013: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
2014: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
2015: * returned function value.
2016: */
1.126 brouard 2017: int iter;
2018: double a,b,d,etemp;
1.159 brouard 2019: double fu=0,fv,fw,fx;
1.164 brouard 2020: double ftemp=0.;
1.126 brouard 2021: double p,q,r,tol1,tol2,u,v,w,x,xm;
2022: double e=0.0;
2023:
2024: a=(ax < cx ? ax : cx);
2025: b=(ax > cx ? ax : cx);
2026: x=w=v=bx;
2027: fw=fv=fx=(*f)(x);
2028: for (iter=1;iter<=ITMAX;iter++) {
2029: xm=0.5*(a+b);
2030: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
2031: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
2032: printf(".");fflush(stdout);
2033: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 2034: #ifdef DEBUGBRENT
1.126 brouard 2035: printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
2036: fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
2037: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
2038: #endif
2039: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
2040: *xmin=x;
2041: return fx;
2042: }
2043: ftemp=fu;
2044: if (fabs(e) > tol1) {
2045: r=(x-w)*(fx-fv);
2046: q=(x-v)*(fx-fw);
2047: p=(x-v)*q-(x-w)*r;
2048: q=2.0*(q-r);
2049: if (q > 0.0) p = -p;
2050: q=fabs(q);
2051: etemp=e;
2052: e=d;
2053: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 2054: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 2055: else {
1.224 brouard 2056: d=p/q;
2057: u=x+d;
2058: if (u-a < tol2 || b-u < tol2)
2059: d=SIGN(tol1,xm-x);
1.126 brouard 2060: }
2061: } else {
2062: d=CGOLD*(e=(x >= xm ? a-x : b-x));
2063: }
2064: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
2065: fu=(*f)(u);
2066: if (fu <= fx) {
2067: if (u >= x) a=x; else b=x;
2068: SHFT(v,w,x,u)
1.183 brouard 2069: SHFT(fv,fw,fx,fu)
2070: } else {
2071: if (u < x) a=u; else b=u;
2072: if (fu <= fw || w == x) {
1.224 brouard 2073: v=w;
2074: w=u;
2075: fv=fw;
2076: fw=fu;
1.183 brouard 2077: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 2078: v=u;
2079: fv=fu;
1.183 brouard 2080: }
2081: }
1.126 brouard 2082: }
2083: nrerror("Too many iterations in brent");
2084: *xmin=x;
2085: return fx;
2086: }
2087:
2088: /****************** mnbrak ***********************/
2089:
2090: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2091: double (*func)(double))
1.183 brouard 2092: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2093: the downhill direction (defined by the function as evaluated at the initial points) and returns
2094: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2095: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2096: */
1.126 brouard 2097: double ulim,u,r,q, dum;
2098: double fu;
1.187 brouard 2099:
2100: double scale=10.;
2101: int iterscale=0;
2102:
2103: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2104: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2105:
2106:
2107: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2108: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2109: /* *bx = *ax - (*ax - *bx)/scale; */
2110: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2111: /* } */
2112:
1.126 brouard 2113: if (*fb > *fa) {
2114: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2115: SHFT(dum,*fb,*fa,dum)
2116: }
1.126 brouard 2117: *cx=(*bx)+GOLD*(*bx-*ax);
2118: *fc=(*func)(*cx);
1.183 brouard 2119: #ifdef DEBUG
1.224 brouard 2120: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2121: fprintf(ficlog,"mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1.183 brouard 2122: #endif
1.224 brouard 2123: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc. If fc=inf it exits and if flat fb=fc it exits too.*/
1.126 brouard 2124: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2125: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2126: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2127: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2128: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2129: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2130: fu=(*func)(u);
1.163 brouard 2131: #ifdef DEBUG
2132: /* f(x)=A(x-u)**2+f(u) */
2133: double A, fparabu;
2134: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2135: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2136: printf("\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
2137: fprintf(ficlog,"\nmnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f, q=%lf < %lf=r)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu,q,r);
1.183 brouard 2138: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2139: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2140: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2141: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2142: #endif
1.184 brouard 2143: #ifdef MNBRAKORIGINAL
1.183 brouard 2144: #else
1.191 brouard 2145: /* if (fu > *fc) { */
2146: /* #ifdef DEBUG */
2147: /* printf("mnbrak4 fu > fc \n"); */
2148: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2149: /* #endif */
2150: /* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */
2151: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2152: /* dum=u; /\* Shifting c and u *\/ */
2153: /* u = *cx; */
2154: /* *cx = dum; */
2155: /* dum = fu; */
2156: /* fu = *fc; */
2157: /* *fc =dum; */
2158: /* } else { /\* end *\/ */
2159: /* #ifdef DEBUG */
2160: /* printf("mnbrak3 fu < fc \n"); */
2161: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2162: /* #endif */
2163: /* dum=u; /\* Shifting c and u *\/ */
2164: /* u = *cx; */
2165: /* *cx = dum; */
2166: /* dum = fu; */
2167: /* fu = *fc; */
2168: /* *fc =dum; */
2169: /* } */
1.224 brouard 2170: #ifdef DEBUGMNBRAK
2171: double A, fparabu;
2172: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2173: fparabu= *fa - A*(*ax-u)*(*ax-u);
2174: printf("\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
2175: fprintf(ficlog,"\nmnbrak35 ax=%lf fa=%lf bx=%lf fb=%lf, u=%lf fp=%lf fu=%lf < or >= fc=%lf cx=%lf, q=%lf < %lf=r \n",*ax, *fa, *bx,*fb,u,fparabu,fu,*fc,*cx,q,r);
1.183 brouard 2176: #endif
1.191 brouard 2177: dum=u; /* Shifting c and u */
2178: u = *cx;
2179: *cx = dum;
2180: dum = fu;
2181: fu = *fc;
2182: *fc =dum;
1.183 brouard 2183: #endif
1.162 brouard 2184: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2185: #ifdef DEBUG
1.224 brouard 2186: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2187: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2188: #endif
1.126 brouard 2189: fu=(*func)(u);
2190: if (fu < *fc) {
1.183 brouard 2191: #ifdef DEBUG
1.224 brouard 2192: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2193: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2194: #endif
2195: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2196: SHFT(*fb,*fc,fu,(*func)(u))
2197: #ifdef DEBUG
2198: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2199: #endif
2200: }
1.162 brouard 2201: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2202: #ifdef DEBUG
1.224 brouard 2203: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2204: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2205: #endif
1.126 brouard 2206: u=ulim;
2207: fu=(*func)(u);
1.183 brouard 2208: } else { /* u could be left to b (if r > q parabola has a maximum) */
2209: #ifdef DEBUG
1.224 brouard 2210: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2211: fprintf(ficlog,"\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1.183 brouard 2212: #endif
1.126 brouard 2213: u=(*cx)+GOLD*(*cx-*bx);
2214: fu=(*func)(u);
1.224 brouard 2215: #ifdef DEBUG
2216: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2217: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2218: #endif
1.183 brouard 2219: } /* end tests */
1.126 brouard 2220: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2221: SHFT(*fa,*fb,*fc,fu)
2222: #ifdef DEBUG
1.224 brouard 2223: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2224: fprintf(ficlog, "\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1.183 brouard 2225: #endif
2226: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 2227: }
2228:
2229: /*************** linmin ************************/
1.162 brouard 2230: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2231: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2232: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2233: the value of func at the returned location p . This is actually all accomplished by calling the
2234: routines mnbrak and brent .*/
1.126 brouard 2235: int ncom;
2236: double *pcom,*xicom;
2237: double (*nrfunc)(double []);
2238:
1.224 brouard 2239: #ifdef LINMINORIGINAL
1.126 brouard 2240: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2241: #else
2242: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2243: #endif
1.126 brouard 2244: {
2245: double brent(double ax, double bx, double cx,
2246: double (*f)(double), double tol, double *xmin);
2247: double f1dim(double x);
2248: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2249: double *fc, double (*func)(double));
2250: int j;
2251: double xx,xmin,bx,ax;
2252: double fx,fb,fa;
1.187 brouard 2253:
1.203 brouard 2254: #ifdef LINMINORIGINAL
2255: #else
2256: double scale=10., axs, xxs; /* Scale added for infinity */
2257: #endif
2258:
1.126 brouard 2259: ncom=n;
2260: pcom=vector(1,n);
2261: xicom=vector(1,n);
2262: nrfunc=func;
2263: for (j=1;j<=n;j++) {
2264: pcom[j]=p[j];
1.202 brouard 2265: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2266: }
1.187 brouard 2267:
1.203 brouard 2268: #ifdef LINMINORIGINAL
2269: xx=1.;
2270: #else
2271: axs=0.0;
2272: xxs=1.;
2273: do{
2274: xx= xxs;
2275: #endif
1.187 brouard 2276: ax=0.;
2277: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2278: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2279: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
2280: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2281: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2282: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2283: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1.203 brouard 2284: #ifdef LINMINORIGINAL
2285: #else
2286: if (fx != fx){
1.224 brouard 2287: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2288: printf("|");
2289: fprintf(ficlog,"|");
1.203 brouard 2290: #ifdef DEBUGLINMIN
1.224 brouard 2291: printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx);
1.203 brouard 2292: #endif
2293: }
1.224 brouard 2294: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2295: #endif
2296:
1.191 brouard 2297: #ifdef DEBUGLINMIN
2298: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.202 brouard 2299: fprintf(ficlog,"\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1.191 brouard 2300: #endif
1.224 brouard 2301: #ifdef LINMINORIGINAL
2302: #else
1.317 brouard 2303: if(fb == fx){ /* Flat function in the direction */
2304: xmin=xx;
1.224 brouard 2305: *flat=1;
1.317 brouard 2306: }else{
1.224 brouard 2307: *flat=0;
2308: #endif
2309: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2310: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2311: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2312: /* fmin = f(p[j] + xmin * xi[j]) */
2313: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2314: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2315: #ifdef DEBUG
1.224 brouard 2316: printf("retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
2317: fprintf(ficlog,"retour brent from bracket (a=%lf fa=%lf, xx=%lf fx=%lf, b=%lf fb=%lf): fret=%lf xmin=%lf\n",ax,fa,xx,fx,bx,fb,*fret,xmin);
2318: #endif
2319: #ifdef LINMINORIGINAL
2320: #else
2321: }
1.126 brouard 2322: #endif
1.191 brouard 2323: #ifdef DEBUGLINMIN
2324: printf("linmin end ");
1.202 brouard 2325: fprintf(ficlog,"linmin end ");
1.191 brouard 2326: #endif
1.126 brouard 2327: for (j=1;j<=n;j++) {
1.203 brouard 2328: #ifdef LINMINORIGINAL
2329: xi[j] *= xmin;
2330: #else
2331: #ifdef DEBUGLINMIN
2332: if(xxs <1.0)
2333: printf(" before xi[%d]=%12.8f", j,xi[j]);
2334: #endif
2335: xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
2336: #ifdef DEBUGLINMIN
2337: if(xxs <1.0)
2338: printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs );
2339: #endif
2340: #endif
1.187 brouard 2341: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2342: }
1.191 brouard 2343: #ifdef DEBUGLINMIN
1.203 brouard 2344: printf("\n");
1.191 brouard 2345: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2346: fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.191 brouard 2347: for (j=1;j<=n;j++) {
1.202 brouard 2348: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2349: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2350: if(j % ncovmodel == 0){
1.191 brouard 2351: printf("\n");
1.202 brouard 2352: fprintf(ficlog,"\n");
2353: }
1.191 brouard 2354: }
1.203 brouard 2355: #else
1.191 brouard 2356: #endif
1.126 brouard 2357: free_vector(xicom,1,n);
2358: free_vector(pcom,1,n);
2359: }
2360:
2361:
2362: /*************** powell ************************/
1.162 brouard 2363: /*
1.317 brouard 2364: Minimization of a function func of n variables. Input consists in an initial starting point
2365: p[1..n] ; an initial matrix xi[1..n][1..n] whose columns contain the initial set of di-
2366: rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
2367: such that failure to decrease by more than this amount in one iteration signals doneness. On
1.162 brouard 2368: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2369: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2370: */
1.224 brouard 2371: #ifdef LINMINORIGINAL
2372: #else
2373: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2374: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2375: #endif
1.126 brouard 2376: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2377: double (*func)(double []))
2378: {
1.224 brouard 2379: #ifdef LINMINORIGINAL
2380: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2381: double (*func)(double []));
1.224 brouard 2382: #else
1.241 brouard 2383: void linmin(double p[], double xi[], int n, double *fret,
2384: double (*func)(double []),int *flat);
1.224 brouard 2385: #endif
1.239 brouard 2386: int i,ibig,j,jk,k;
1.126 brouard 2387: double del,t,*pt,*ptt,*xit;
1.181 brouard 2388: double directest;
1.126 brouard 2389: double fp,fptt;
2390: double *xits;
2391: int niterf, itmp;
2392:
2393: pt=vector(1,n);
2394: ptt=vector(1,n);
2395: xit=vector(1,n);
2396: xits=vector(1,n);
2397: *fret=(*func)(p);
2398: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2399: rcurr_time = time(NULL);
1.126 brouard 2400: for (*iter=1;;++(*iter)) {
1.187 brouard 2401: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2402: ibig=0;
2403: del=0.0;
1.157 brouard 2404: rlast_time=rcurr_time;
2405: /* (void) gettimeofday(&curr_time,&tzp); */
2406: rcurr_time = time(NULL);
2407: curr_time = *localtime(&rcurr_time);
2408: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2409: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2410: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2411: for (i=1;i<=n;i++) {
1.126 brouard 2412: fprintf(ficrespow," %.12lf", p[i]);
2413: }
1.239 brouard 2414: fprintf(ficrespow,"\n");fflush(ficrespow);
2415: printf("\n#model= 1 + age ");
2416: fprintf(ficlog,"\n#model= 1 + age ");
2417: if(nagesqr==1){
1.241 brouard 2418: printf(" + age*age ");
2419: fprintf(ficlog," + age*age ");
1.239 brouard 2420: }
2421: for(j=1;j <=ncovmodel-2;j++){
2422: if(Typevar[j]==0) {
2423: printf(" + V%d ",Tvar[j]);
2424: fprintf(ficlog," + V%d ",Tvar[j]);
2425: }else if(Typevar[j]==1) {
2426: printf(" + V%d*age ",Tvar[j]);
2427: fprintf(ficlog," + V%d*age ",Tvar[j]);
2428: }else if(Typevar[j]==2) {
2429: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2430: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2431: }
2432: }
1.126 brouard 2433: printf("\n");
1.239 brouard 2434: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2435: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2436: fprintf(ficlog,"\n");
1.239 brouard 2437: for(i=1,jk=1; i <=nlstate; i++){
2438: for(k=1; k <=(nlstate+ndeath); k++){
2439: if (k != i) {
2440: printf("%d%d ",i,k);
2441: fprintf(ficlog,"%d%d ",i,k);
2442: for(j=1; j <=ncovmodel; j++){
2443: printf("%12.7f ",p[jk]);
2444: fprintf(ficlog,"%12.7f ",p[jk]);
2445: jk++;
2446: }
2447: printf("\n");
2448: fprintf(ficlog,"\n");
2449: }
2450: }
2451: }
1.241 brouard 2452: if(*iter <=3 && *iter >1){
1.157 brouard 2453: tml = *localtime(&rcurr_time);
2454: strcpy(strcurr,asctime(&tml));
2455: rforecast_time=rcurr_time;
1.126 brouard 2456: itmp = strlen(strcurr);
2457: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2458: strcurr[itmp-1]='\0';
1.162 brouard 2459: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2460: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2461: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2462: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2463: forecast_time = *localtime(&rforecast_time);
2464: strcpy(strfor,asctime(&forecast_time));
2465: itmp = strlen(strfor);
2466: if(strfor[itmp-1]=='\n')
2467: strfor[itmp-1]='\0';
2468: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
2469: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126 brouard 2470: }
2471: }
1.187 brouard 2472: for (i=1;i<=n;i++) { /* For each direction i */
2473: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2474: fptt=(*fret);
2475: #ifdef DEBUG
1.203 brouard 2476: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2477: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2478: #endif
1.203 brouard 2479: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2480: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2481: #ifdef LINMINORIGINAL
1.188 brouard 2482: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2483: #else
2484: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2485: flatdir[i]=flat; /* Function is vanishing in that direction i */
2486: #endif
2487: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2488: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2489: /* because that direction will be replaced unless the gain del is small */
2490: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2491: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2492: /* with the new direction. */
2493: del=fabs(fptt-(*fret));
2494: ibig=i;
1.126 brouard 2495: }
2496: #ifdef DEBUG
2497: printf("%d %.12e",i,(*fret));
2498: fprintf(ficlog,"%d %.12e",i,(*fret));
2499: for (j=1;j<=n;j++) {
1.224 brouard 2500: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2501: printf(" x(%d)=%.12e",j,xit[j]);
2502: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2503: }
2504: for(j=1;j<=n;j++) {
1.225 brouard 2505: printf(" p(%d)=%.12e",j,p[j]);
2506: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2507: }
2508: printf("\n");
2509: fprintf(ficlog,"\n");
2510: #endif
1.187 brouard 2511: } /* end loop on each direction i */
2512: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2513: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2514: /* New value of last point Pn is not computed, P(n-1) */
1.319 ! brouard 2515: for(j=1;j<=n;j++) {
! 2516: if(flatdir[j] >0){
! 2517: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
! 2518: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
1.302 brouard 2519: }
1.319 ! brouard 2520: /* printf("\n"); */
! 2521: /* fprintf(ficlog,"\n"); */
! 2522: }
1.243 brouard 2523: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2524: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2525: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2526: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2527: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2528: /* decreased of more than 3.84 */
2529: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2530: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2531: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2532:
1.188 brouard 2533: /* Starting the program with initial values given by a former maximization will simply change */
2534: /* the scales of the directions and the directions, because the are reset to canonical directions */
2535: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2536: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2537: #ifdef DEBUG
2538: int k[2],l;
2539: k[0]=1;
2540: k[1]=-1;
2541: printf("Max: %.12e",(*func)(p));
2542: fprintf(ficlog,"Max: %.12e",(*func)(p));
2543: for (j=1;j<=n;j++) {
2544: printf(" %.12e",p[j]);
2545: fprintf(ficlog," %.12e",p[j]);
2546: }
2547: printf("\n");
2548: fprintf(ficlog,"\n");
2549: for(l=0;l<=1;l++) {
2550: for (j=1;j<=n;j++) {
2551: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2552: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2553: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2554: }
2555: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2556: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2557: }
2558: #endif
2559:
2560: free_vector(xit,1,n);
2561: free_vector(xits,1,n);
2562: free_vector(ptt,1,n);
2563: free_vector(pt,1,n);
2564: return;
1.192 brouard 2565: } /* enough precision */
1.240 brouard 2566: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2567: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2568: ptt[j]=2.0*p[j]-pt[j];
2569: xit[j]=p[j]-pt[j];
2570: pt[j]=p[j];
2571: }
1.181 brouard 2572: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2573: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2574: if (*iter <=4) {
1.225 brouard 2575: #else
2576: #endif
1.224 brouard 2577: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2578: #else
1.161 brouard 2579: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2580: #endif
1.162 brouard 2581: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2582: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2583: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2584: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2585: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2586: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2587: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2588: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2589: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2590: /* Even if f3 <f1, directest can be negative and t >0 */
2591: /* mu² and del² are equal when f3=f1 */
2592: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2593: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2594: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2595: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2596: #ifdef NRCORIGINAL
2597: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2598: #else
2599: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161 brouard 2600: t= t- del*SQR(fp-fptt);
1.183 brouard 2601: #endif
1.202 brouard 2602: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2603: #ifdef DEBUG
1.181 brouard 2604: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
2605: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1.161 brouard 2606: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2607: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2608: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2609: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2610: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
2611: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
2612: #endif
1.183 brouard 2613: #ifdef POWELLORIGINAL
2614: if (t < 0.0) { /* Then we use it for new direction */
2615: #else
1.182 brouard 2616: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2617: printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.192 brouard 2618: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.224 brouard 2619: fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 2620: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2621: }
1.181 brouard 2622: if (directest < 0.0) { /* Then we use it for new direction */
2623: #endif
1.191 brouard 2624: #ifdef DEBUGLINMIN
1.234 brouard 2625: printf("Before linmin in direction P%d-P0\n",n);
2626: for (j=1;j<=n;j++) {
2627: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2628: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2629: if(j % ncovmodel == 0){
2630: printf("\n");
2631: fprintf(ficlog,"\n");
2632: }
2633: }
1.224 brouard 2634: #endif
2635: #ifdef LINMINORIGINAL
1.234 brouard 2636: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2637: #else
1.234 brouard 2638: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2639: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2640: #endif
1.234 brouard 2641:
1.191 brouard 2642: #ifdef DEBUGLINMIN
1.234 brouard 2643: for (j=1;j<=n;j++) {
2644: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2645: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2646: if(j % ncovmodel == 0){
2647: printf("\n");
2648: fprintf(ficlog,"\n");
2649: }
2650: }
1.224 brouard 2651: #endif
1.234 brouard 2652: for (j=1;j<=n;j++) {
2653: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2654: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2655: }
1.224 brouard 2656: #ifdef LINMINORIGINAL
2657: #else
1.234 brouard 2658: for (j=1, flatd=0;j<=n;j++) {
2659: if(flatdir[j]>0)
2660: flatd++;
2661: }
2662: if(flatd >0){
1.255 brouard 2663: printf("%d flat directions: ",flatd);
2664: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2665: for (j=1;j<=n;j++) {
2666: if(flatdir[j]>0){
2667: printf("%d ",j);
2668: fprintf(ficlog,"%d ",j);
2669: }
2670: }
2671: printf("\n");
2672: fprintf(ficlog,"\n");
1.319 ! brouard 2673: #ifdef FLATSUP
! 2674: free_vector(xit,1,n);
! 2675: free_vector(xits,1,n);
! 2676: free_vector(ptt,1,n);
! 2677: free_vector(pt,1,n);
! 2678: return;
! 2679: #endif
1.234 brouard 2680: }
1.191 brouard 2681: #endif
1.234 brouard 2682: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2683: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2684:
1.126 brouard 2685: #ifdef DEBUG
1.234 brouard 2686: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2687: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2688: for(j=1;j<=n;j++){
2689: printf(" %lf",xit[j]);
2690: fprintf(ficlog," %lf",xit[j]);
2691: }
2692: printf("\n");
2693: fprintf(ficlog,"\n");
1.126 brouard 2694: #endif
1.192 brouard 2695: } /* end of t or directest negative */
1.224 brouard 2696: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2697: #else
1.234 brouard 2698: } /* end if (fptt < fp) */
1.192 brouard 2699: #endif
1.225 brouard 2700: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2701: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2702: #else
1.224 brouard 2703: #endif
1.234 brouard 2704: } /* loop iteration */
1.126 brouard 2705: }
1.234 brouard 2706:
1.126 brouard 2707: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2708:
1.235 brouard 2709: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
1.234 brouard 2710: {
1.279 brouard 2711: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2712: * (and selected quantitative values in nres)
2713: * by left multiplying the unit
2714: * matrix by transitions matrix until convergence is reached with precision ftolpl
2715: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2716: * Wx is row vector: population in state 1, population in state 2, population dead
2717: * or prevalence in state 1, prevalence in state 2, 0
2718: * newm is the matrix after multiplications, its rows are identical at a factor.
2719: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2720: * Output is prlim.
2721: * Initial matrix pimij
2722: */
1.206 brouard 2723: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2724: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2725: /* 0, 0 , 1} */
2726: /*
2727: * and after some iteration: */
2728: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2729: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2730: /* 0, 0 , 1} */
2731: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2732: /* {0.51571254859325999, 0.4842874514067399, */
2733: /* 0.51326036147820708, 0.48673963852179264} */
2734: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2735:
1.126 brouard 2736: int i, ii,j,k;
1.209 brouard 2737: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2738: /* double **matprod2(); */ /* test */
1.218 brouard 2739: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2740: double **newm;
1.209 brouard 2741: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2742: int ncvloop=0;
1.288 brouard 2743: int first=0;
1.169 brouard 2744:
1.209 brouard 2745: min=vector(1,nlstate);
2746: max=vector(1,nlstate);
2747: meandiff=vector(1,nlstate);
2748:
1.218 brouard 2749: /* Starting with matrix unity */
1.126 brouard 2750: for (ii=1;ii<=nlstate+ndeath;ii++)
2751: for (j=1;j<=nlstate+ndeath;j++){
2752: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2753: }
1.169 brouard 2754:
2755: cov[1]=1.;
2756:
2757: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2758: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2759: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2760: ncvloop++;
1.126 brouard 2761: newm=savm;
2762: /* Covariates have to be included here again */
1.138 brouard 2763: cov[2]=agefin;
1.319 ! brouard 2764: if(nagesqr==1){
! 2765: cov[3]= agefin*agefin;
! 2766: }
1.234 brouard 2767: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2768: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2769: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.319 ! brouard 2770: /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */
1.235 brouard 2771: /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
1.234 brouard 2772: }
2773: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2774: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.319 ! brouard 2775: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
! 2776: /* cov[++k1]=Tqresult[nres][k]; */
1.235 brouard 2777: /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
1.138 brouard 2778: }
1.237 brouard 2779: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.319 ! brouard 2780: if(Dummy[Tage[k]]==2){ /* dummy with age */
1.234 brouard 2781: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319 ! brouard 2782: /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
! 2783: } else if(Dummy[Tage[k]]==3){ /* quantitative with age */
! 2784: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
! 2785: /* cov[++k1]=Tqresult[nres][k]; */
1.234 brouard 2786: }
1.235 brouard 2787: /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
1.234 brouard 2788: }
1.237 brouard 2789: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2790: /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
1.237 brouard 2791: if(Dummy[Tvard[k][1]==0]){
2792: if(Dummy[Tvard[k][2]==0]){
2793: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.319 ! brouard 2794: /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.237 brouard 2795: }else{
2796: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
1.319 ! brouard 2797: /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
1.237 brouard 2798: }
2799: }else{
2800: if(Dummy[Tvard[k][2]==0]){
2801: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
1.319 ! brouard 2802: /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
1.237 brouard 2803: }else{
2804: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
1.319 ! brouard 2805: /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
1.237 brouard 2806: }
2807: }
1.234 brouard 2808: }
1.138 brouard 2809: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2810: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2811: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2812: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2813: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.319 ! brouard 2814: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2815: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2816:
1.126 brouard 2817: savm=oldm;
2818: oldm=newm;
1.209 brouard 2819:
2820: for(j=1; j<=nlstate; j++){
2821: max[j]=0.;
2822: min[j]=1.;
2823: }
2824: for(i=1;i<=nlstate;i++){
2825: sumnew=0;
2826: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2827: for(j=1; j<=nlstate; j++){
2828: prlim[i][j]= newm[i][j]/(1-sumnew);
2829: max[j]=FMAX(max[j],prlim[i][j]);
2830: min[j]=FMIN(min[j],prlim[i][j]);
2831: }
2832: }
2833:
1.126 brouard 2834: maxmax=0.;
1.209 brouard 2835: for(j=1; j<=nlstate; j++){
2836: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2837: maxmax=FMAX(maxmax,meandiff[j]);
2838: /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169 brouard 2839: } /* j loop */
1.203 brouard 2840: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2841: /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2842: if(maxmax < ftolpl){
1.209 brouard 2843: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2844: free_vector(min,1,nlstate);
2845: free_vector(max,1,nlstate);
2846: free_vector(meandiff,1,nlstate);
1.126 brouard 2847: return prlim;
2848: }
1.288 brouard 2849: } /* agefin loop */
1.208 brouard 2850: /* After some age loop it doesn't converge */
1.288 brouard 2851: if(!first){
2852: first=1;
2853: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
1.317 brouard 2854: fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
2855: }else if (first >=1 && first <10){
2856: fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
2857: first++;
2858: }else if (first ==10){
2859: fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
2860: printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
2861: fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
2862: first++;
1.288 brouard 2863: }
2864:
1.209 brouard 2865: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
2866: free_vector(min,1,nlstate);
2867: free_vector(max,1,nlstate);
2868: free_vector(meandiff,1,nlstate);
1.208 brouard 2869:
1.169 brouard 2870: return prlim; /* should not reach here */
1.126 brouard 2871: }
2872:
1.217 brouard 2873:
2874: /**** Back Prevalence limit (stable or period prevalence) ****************/
2875:
1.218 brouard 2876: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
2877: /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
1.242 brouard 2878: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2879: {
1.264 brouard 2880: /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
1.217 brouard 2881: matrix by transitions matrix until convergence is reached with precision ftolpl */
2882: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2883: /* Wx is row vector: population in state 1, population in state 2, population dead */
2884: /* or prevalence in state 1, prevalence in state 2, 0 */
2885: /* newm is the matrix after multiplications, its rows are identical at a factor */
2886: /* Initial matrix pimij */
2887: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2888: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2889: /* 0, 0 , 1} */
2890: /*
2891: * and after some iteration: */
2892: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2893: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2894: /* 0, 0 , 1} */
2895: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2896: /* {0.51571254859325999, 0.4842874514067399, */
2897: /* 0.51326036147820708, 0.48673963852179264} */
2898: /* If we start from prlim again, prlim tends to a constant matrix */
2899:
2900: int i, ii,j,k;
1.247 brouard 2901: int first=0;
1.217 brouard 2902: double *min, *max, *meandiff, maxmax,sumnew=0.;
2903: /* double **matprod2(); */ /* test */
2904: double **out, cov[NCOVMAX+1], **bmij();
2905: double **newm;
1.218 brouard 2906: double **dnewm, **doldm, **dsavm; /* for use */
2907: double **oldm, **savm; /* for use */
2908:
1.217 brouard 2909: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2910: int ncvloop=0;
2911:
2912: min=vector(1,nlstate);
2913: max=vector(1,nlstate);
2914: meandiff=vector(1,nlstate);
2915:
1.266 brouard 2916: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2917: oldm=oldms; savm=savms;
2918:
2919: /* Starting with matrix unity */
2920: for (ii=1;ii<=nlstate+ndeath;ii++)
2921: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2922: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2923: }
2924:
2925: cov[1]=1.;
2926:
2927: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2928: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2929: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2930: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2931: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2932: ncvloop++;
1.218 brouard 2933: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2934: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2935: /* Covariates have to be included here again */
2936: cov[2]=agefin;
1.319 ! brouard 2937: if(nagesqr==1){
1.217 brouard 2938: cov[3]= agefin*agefin;;
1.319 ! brouard 2939: }
1.242 brouard 2940: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2941: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2942: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2943: /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
1.242 brouard 2944: }
2945: /* for (k=1; k<=cptcovn;k++) { */
2946: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2947: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2948: /* /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
2949: /* } */
2950: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2951: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2952: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2953: /* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
2954: }
2955: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2956: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2957: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2958: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2959: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.319 ! brouard 2960: /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/
! 2961: if(Dummy[Tage[k]]== 2){ /* dummy with age */
1.242 brouard 2962: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319 ! brouard 2963: } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
! 2964: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.242 brouard 2965: }
2966: /* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
2967: }
2968: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2969: /* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
2970: if(Dummy[Tvard[k][1]==0]){
2971: if(Dummy[Tvard[k][2]==0]){
2972: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2973: }else{
2974: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2975: }
2976: }else{
2977: if(Dummy[Tvard[k][2]==0]){
2978: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2979: }else{
2980: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2981: }
2982: }
1.217 brouard 2983: }
2984:
2985: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2986: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2987: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2988: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2989: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2990: /* ij should be linked to the correct index of cov */
2991: /* age and covariate values ij are in 'cov', but we need to pass
2992: * ij for the observed prevalence at age and status and covariate
2993: * number: prevacurrent[(int)agefin][ii][ij]
2994: */
2995: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2996: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
2997: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.268 brouard 2998: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2999: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
3000: /* for(i=1; i<=nlstate+ndeath; i++) { */
3001: /* printf("%d newm= ",i); */
3002: /* for(j=1;j<=nlstate+ndeath;j++) { */
3003: /* printf("%f ",newm[i][j]); */
3004: /* } */
3005: /* printf("oldm * "); */
3006: /* for(j=1;j<=nlstate+ndeath;j++) { */
3007: /* printf("%f ",oldm[i][j]); */
3008: /* } */
1.268 brouard 3009: /* printf(" bmmij "); */
1.266 brouard 3010: /* for(j=1;j<=nlstate+ndeath;j++) { */
3011: /* printf("%f ",pmmij[i][j]); */
3012: /* } */
3013: /* printf("\n"); */
3014: /* } */
3015: /* } */
1.217 brouard 3016: savm=oldm;
3017: oldm=newm;
1.266 brouard 3018:
1.217 brouard 3019: for(j=1; j<=nlstate; j++){
3020: max[j]=0.;
3021: min[j]=1.;
3022: }
3023: for(j=1; j<=nlstate; j++){
3024: for(i=1;i<=nlstate;i++){
1.234 brouard 3025: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
3026: bprlim[i][j]= newm[i][j];
3027: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
3028: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 3029: }
3030: }
1.218 brouard 3031:
1.217 brouard 3032: maxmax=0.;
3033: for(i=1; i<=nlstate; i++){
1.318 brouard 3034: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column, could be nan! */
1.217 brouard 3035: maxmax=FMAX(maxmax,meandiff[i]);
3036: /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
1.268 brouard 3037: } /* i loop */
1.217 brouard 3038: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 3039: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 3040: if(maxmax < ftolpl){
1.220 brouard 3041: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 3042: free_vector(min,1,nlstate);
3043: free_vector(max,1,nlstate);
3044: free_vector(meandiff,1,nlstate);
3045: return bprlim;
3046: }
1.288 brouard 3047: } /* agefin loop */
1.217 brouard 3048: /* After some age loop it doesn't converge */
1.288 brouard 3049: if(!first){
1.247 brouard 3050: first=1;
3051: printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
3052: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
3053: }
3054: fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.217 brouard 3055: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
3056: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
3057: free_vector(min,1,nlstate);
3058: free_vector(max,1,nlstate);
3059: free_vector(meandiff,1,nlstate);
3060:
3061: return bprlim; /* should not reach here */
3062: }
3063:
1.126 brouard 3064: /*************** transition probabilities ***************/
3065:
3066: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
3067: {
1.138 brouard 3068: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 3069: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 3070: model to the ncovmodel covariates (including constant and age).
3071: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3072: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3073: ncth covariate in the global vector x is given by the formula:
3074: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3075: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3076: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3077: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 3078: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 3079: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 3080: Sum on j ps[i][j] should equal to 1.
1.138 brouard 3081: */
3082: double s1, lnpijopii;
1.126 brouard 3083: /*double t34;*/
1.164 brouard 3084: int i,j, nc, ii, jj;
1.126 brouard 3085:
1.223 brouard 3086: for(i=1; i<= nlstate; i++){
3087: for(j=1; j<i;j++){
3088: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3089: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3090: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3091: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3092: }
3093: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3094: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3095: }
3096: for(j=i+1; j<=nlstate+ndeath;j++){
3097: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3098: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3099: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3100: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3101: }
3102: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3103: }
3104: }
1.218 brouard 3105:
1.223 brouard 3106: for(i=1; i<= nlstate; i++){
3107: s1=0;
3108: for(j=1; j<i; j++){
3109: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3110: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3111: }
3112: for(j=i+1; j<=nlstate+ndeath; j++){
3113: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3114: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3115: }
3116: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3117: ps[i][i]=1./(s1+1.);
3118: /* Computing other pijs */
3119: for(j=1; j<i; j++)
3120: ps[i][j]= exp(ps[i][j])*ps[i][i];
3121: for(j=i+1; j<=nlstate+ndeath; j++)
3122: ps[i][j]= exp(ps[i][j])*ps[i][i];
3123: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3124: } /* end i */
1.218 brouard 3125:
1.223 brouard 3126: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3127: for(jj=1; jj<= nlstate+ndeath; jj++){
3128: ps[ii][jj]=0;
3129: ps[ii][ii]=1;
3130: }
3131: }
1.294 brouard 3132:
3133:
1.223 brouard 3134: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3135: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3136: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3137: /* } */
3138: /* printf("\n "); */
3139: /* } */
3140: /* printf("\n ");printf("%lf ",cov[2]);*/
3141: /*
3142: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3143: goto end;*/
1.266 brouard 3144: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3145: }
3146:
1.218 brouard 3147: /*************** backward transition probabilities ***************/
3148:
3149: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ageminpar, double agemaxpar, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3150: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3151: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3152: {
1.302 brouard 3153: /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
1.266 brouard 3154: * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
1.222 brouard 3155: */
1.218 brouard 3156: int i, ii, j,k;
1.222 brouard 3157:
3158: double **out, **pmij();
3159: double sumnew=0.;
1.218 brouard 3160: double agefin;
1.292 brouard 3161: double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
1.222 brouard 3162: double **dnewm, **dsavm, **doldm;
3163: double **bbmij;
3164:
1.218 brouard 3165: doldm=ddoldms; /* global pointers */
1.222 brouard 3166: dnewm=ddnewms;
3167: dsavm=ddsavms;
1.318 brouard 3168:
3169: /* Debug */
3170: /* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
1.222 brouard 3171: agefin=cov[2];
1.268 brouard 3172: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3173: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3174: the observed prevalence (with this covariate ij) at beginning of transition */
3175: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3176:
3177: /* P_x */
1.266 brouard 3178: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3179: /* outputs pmmij which is a stochastic matrix in row */
3180:
3181: /* Diag(w_x) */
1.292 brouard 3182: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3183: sumnew=0.;
1.269 brouard 3184: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3185: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3186: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3187: sumnew+=prevacurrent[(int)agefin][ii][ij];
3188: }
3189: if(sumnew >0.01){ /* At least some value in the prevalence */
3190: for (ii=1;ii<=nlstate+ndeath;ii++){
3191: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3192: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3193: }
3194: }else{
3195: for (ii=1;ii<=nlstate+ndeath;ii++){
3196: for (j=1;j<=nlstate+ndeath;j++)
3197: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3198: }
3199: /* if(sumnew <0.9){ */
3200: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3201: /* } */
3202: }
3203: k3=0.0; /* We put the last diagonal to 0 */
3204: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3205: doldm[ii][ii]= k3;
3206: }
3207: /* End doldm, At the end doldm is diag[(w_i)] */
3208:
1.292 brouard 3209: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3210: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3211:
1.292 brouard 3212: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3213: /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
1.222 brouard 3214: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3215: sumnew=0.;
1.222 brouard 3216: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3217: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3218: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3219: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3220: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3221: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3222: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3223: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3224: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3225: /* }else */
1.268 brouard 3226: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3227: } /*End ii */
3228: } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
3229:
1.292 brouard 3230: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3231: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3232: /* end bmij */
1.266 brouard 3233: return ps; /*pointer is unchanged */
1.218 brouard 3234: }
1.217 brouard 3235: /*************** transition probabilities ***************/
3236:
1.218 brouard 3237: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3238: {
3239: /* According to parameters values stored in x and the covariate's values stored in cov,
3240: computes the probability to be observed in state j being in state i by appying the
3241: model to the ncovmodel covariates (including constant and age).
3242: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3243: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3244: ncth covariate in the global vector x is given by the formula:
3245: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3246: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3247: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3248: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3249: Outputs ps[i][j] the probability to be observed in j being in j according to
3250: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3251: */
3252: double s1, lnpijopii;
3253: /*double t34;*/
3254: int i,j, nc, ii, jj;
3255:
1.234 brouard 3256: for(i=1; i<= nlstate; i++){
3257: for(j=1; j<i;j++){
3258: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3259: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3260: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3261: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3262: }
3263: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3264: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3265: }
3266: for(j=i+1; j<=nlstate+ndeath;j++){
3267: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3268: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3269: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3270: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3271: }
3272: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3273: }
3274: }
3275:
3276: for(i=1; i<= nlstate; i++){
3277: s1=0;
3278: for(j=1; j<i; j++){
3279: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3280: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3281: }
3282: for(j=i+1; j<=nlstate+ndeath; j++){
3283: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3284: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3285: }
3286: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3287: ps[i][i]=1./(s1+1.);
3288: /* Computing other pijs */
3289: for(j=1; j<i; j++)
3290: ps[i][j]= exp(ps[i][j])*ps[i][i];
3291: for(j=i+1; j<=nlstate+ndeath; j++)
3292: ps[i][j]= exp(ps[i][j])*ps[i][i];
3293: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3294: } /* end i */
3295:
3296: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3297: for(jj=1; jj<= nlstate+ndeath; jj++){
3298: ps[ii][jj]=0;
3299: ps[ii][ii]=1;
3300: }
3301: }
1.296 brouard 3302: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3303: for(jj=1; jj<= nlstate+ndeath; jj++){
3304: s1=0.;
3305: for(ii=1; ii<= nlstate+ndeath; ii++){
3306: s1+=ps[ii][jj];
3307: }
3308: for(ii=1; ii<= nlstate; ii++){
3309: ps[ii][jj]=ps[ii][jj]/s1;
3310: }
3311: }
3312: /* Transposition */
3313: for(jj=1; jj<= nlstate+ndeath; jj++){
3314: for(ii=jj; ii<= nlstate+ndeath; ii++){
3315: s1=ps[ii][jj];
3316: ps[ii][jj]=ps[jj][ii];
3317: ps[jj][ii]=s1;
3318: }
3319: }
3320: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3321: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3322: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3323: /* } */
3324: /* printf("\n "); */
3325: /* } */
3326: /* printf("\n ");printf("%lf ",cov[2]);*/
3327: /*
3328: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3329: goto end;*/
3330: return ps;
1.217 brouard 3331: }
3332:
3333:
1.126 brouard 3334: /**************** Product of 2 matrices ******************/
3335:
1.145 brouard 3336: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3337: {
3338: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3339: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3340: /* in, b, out are matrice of pointers which should have been initialized
3341: before: only the contents of out is modified. The function returns
3342: a pointer to pointers identical to out */
1.145 brouard 3343: int i, j, k;
1.126 brouard 3344: for(i=nrl; i<= nrh; i++)
1.145 brouard 3345: for(k=ncolol; k<=ncoloh; k++){
3346: out[i][k]=0.;
3347: for(j=ncl; j<=nch; j++)
3348: out[i][k] +=in[i][j]*b[j][k];
3349: }
1.126 brouard 3350: return out;
3351: }
3352:
3353:
3354: /************* Higher Matrix Product ***************/
3355:
1.235 brouard 3356: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
1.126 brouard 3357: {
1.218 brouard 3358: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3359: 'nhstepm*hstepm*stepm' months (i.e. until
3360: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3361: nhstepm*hstepm matrices.
3362: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3363: (typically every 2 years instead of every month which is too big
3364: for the memory).
3365: Model is determined by parameters x and covariates have to be
3366: included manually here.
3367:
3368: */
3369:
3370: int i, j, d, h, k;
1.131 brouard 3371: double **out, cov[NCOVMAX+1];
1.126 brouard 3372: double **newm;
1.187 brouard 3373: double agexact;
1.214 brouard 3374: double agebegin, ageend;
1.126 brouard 3375:
3376: /* Hstepm could be zero and should return the unit matrix */
3377: for (i=1;i<=nlstate+ndeath;i++)
3378: for (j=1;j<=nlstate+ndeath;j++){
3379: oldm[i][j]=(i==j ? 1.0 : 0.0);
3380: po[i][j][0]=(i==j ? 1.0 : 0.0);
3381: }
3382: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3383: for(h=1; h <=nhstepm; h++){
3384: for(d=1; d <=hstepm; d++){
3385: newm=savm;
3386: /* Covariates have to be included here again */
3387: cov[1]=1.;
1.214 brouard 3388: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3389: cov[2]=agexact;
1.319 ! brouard 3390: if(nagesqr==1){
1.227 brouard 3391: cov[3]= agexact*agexact;
1.319 ! brouard 3392: }
1.235 brouard 3393: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
1.319 ! brouard 3394: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
! 3395: /* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 */
! 3396: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 3397: /* k 1 2 3 4 5 6 7 8 9 */
! 3398: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
! 3399: /* nsd 1 2 3 */ /* Counting single dummies covar fixed or tv */
! 3400: /*TvarsD[nsd] 4 3 1 */ /* ID of single dummy cova fixed or timevary*/
! 3401: /*TvarsDind[k] 2 3 9 */ /* position K of single dummy cova */
1.235 brouard 3402: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3403: /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
3404: }
3405: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3406: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.319 ! brouard 3407: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
1.235 brouard 3408: /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
3409: }
1.319 ! brouard 3410: for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1*age +V4 +age*V3 */
! 3411: /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/
! 3412: /* */
! 3413: if(Dummy[Tage[k]]== 2){ /* dummy with age */
! 3414: /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ */
1.235 brouard 3415: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319 ! brouard 3416: } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
! 3417: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.235 brouard 3418: }
3419: /* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
3420: }
1.319 ! brouard 3421: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 3422: /* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
1.319 ! brouard 3423: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
! 3424: if(Dummy[Tvard[k][1]==0]){
! 3425: if(Dummy[Tvard[k][2]==0]){
! 3426: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
! 3427: }else{
! 3428: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
! 3429: }
! 3430: }else{
! 3431: if(Dummy[Tvard[k][2]==0]){
! 3432: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
! 3433: }else{
! 3434: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
! 3435: }
! 3436: }
1.235 brouard 3437: }
3438: /* for (k=1; k<=cptcovn;k++) */
3439: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3440: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3441: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3442: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3443: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3444:
3445:
1.126 brouard 3446: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3447: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.319 ! brouard 3448: /* right multiplication of oldm by the current matrix */
1.126 brouard 3449: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3450: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3451: /* if((int)age == 70){ */
3452: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3453: /* for(i=1; i<=nlstate+ndeath; i++) { */
3454: /* printf("%d pmmij ",i); */
3455: /* for(j=1;j<=nlstate+ndeath;j++) { */
3456: /* printf("%f ",pmmij[i][j]); */
3457: /* } */
3458: /* printf(" oldm "); */
3459: /* for(j=1;j<=nlstate+ndeath;j++) { */
3460: /* printf("%f ",oldm[i][j]); */
3461: /* } */
3462: /* printf("\n"); */
3463: /* } */
3464: /* } */
1.126 brouard 3465: savm=oldm;
3466: oldm=newm;
3467: }
3468: for(i=1; i<=nlstate+ndeath; i++)
3469: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3470: po[i][j][h]=newm[i][j];
3471: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3472: }
1.128 brouard 3473: /*printf("h=%d ",h);*/
1.126 brouard 3474: } /* end h */
1.267 brouard 3475: /* printf("\n H=%d \n",h); */
1.126 brouard 3476: return po;
3477: }
3478:
1.217 brouard 3479: /************* Higher Back Matrix Product ***************/
1.218 brouard 3480: /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
1.267 brouard 3481: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
1.217 brouard 3482: {
1.266 brouard 3483: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3484: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3485: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3486: nhstepm*hstepm matrices.
3487: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3488: (typically every 2 years instead of every month which is too big
1.217 brouard 3489: for the memory).
1.218 brouard 3490: Model is determined by parameters x and covariates have to be
1.266 brouard 3491: included manually here. Then we use a call to bmij(x and cov)
3492: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3493: */
1.217 brouard 3494:
3495: int i, j, d, h, k;
1.266 brouard 3496: double **out, cov[NCOVMAX+1], **bmij();
3497: double **newm, ***newmm;
1.217 brouard 3498: double agexact;
3499: double agebegin, ageend;
1.222 brouard 3500: double **oldm, **savm;
1.217 brouard 3501:
1.266 brouard 3502: newmm=po; /* To be saved */
3503: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3504: /* Hstepm could be zero and should return the unit matrix */
3505: for (i=1;i<=nlstate+ndeath;i++)
3506: for (j=1;j<=nlstate+ndeath;j++){
3507: oldm[i][j]=(i==j ? 1.0 : 0.0);
3508: po[i][j][0]=(i==j ? 1.0 : 0.0);
3509: }
3510: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3511: for(h=1; h <=nhstepm; h++){
3512: for(d=1; d <=hstepm; d++){
3513: newm=savm;
3514: /* Covariates have to be included here again */
3515: cov[1]=1.;
1.271 brouard 3516: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3517: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
1.318 brouard 3518: /* Debug */
3519: /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
1.217 brouard 3520: cov[2]=agexact;
3521: if(nagesqr==1)
1.222 brouard 3522: cov[3]= agexact*agexact;
1.266 brouard 3523: for (k=1; k<=cptcovn;k++){
3524: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3525: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3526: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3527: /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
3528: }
1.267 brouard 3529: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3530: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3531: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3532: /* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
3533: }
1.319 ! brouard 3534: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */
! 3535: /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */
! 3536: if(Dummy[Tage[k]]== 2){ /* dummy with age */
1.267 brouard 3537: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.319 ! brouard 3538: } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
1.267 brouard 3539: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3540: }
3541: /* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
3542: }
3543: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3544: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3545: }
1.217 brouard 3546: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3547: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3548:
1.218 brouard 3549: /* Careful transposed matrix */
1.266 brouard 3550: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3551: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3552: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3553: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3554: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3555: /* if((int)age == 70){ */
3556: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3557: /* for(i=1; i<=nlstate+ndeath; i++) { */
3558: /* printf("%d pmmij ",i); */
3559: /* for(j=1;j<=nlstate+ndeath;j++) { */
3560: /* printf("%f ",pmmij[i][j]); */
3561: /* } */
3562: /* printf(" oldm "); */
3563: /* for(j=1;j<=nlstate+ndeath;j++) { */
3564: /* printf("%f ",oldm[i][j]); */
3565: /* } */
3566: /* printf("\n"); */
3567: /* } */
3568: /* } */
3569: savm=oldm;
3570: oldm=newm;
3571: }
3572: for(i=1; i<=nlstate+ndeath; i++)
3573: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3574: po[i][j][h]=newm[i][j];
1.268 brouard 3575: /* if(h==nhstepm) */
3576: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3577: }
1.268 brouard 3578: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3579: } /* end h */
1.268 brouard 3580: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3581: return po;
3582: }
3583:
3584:
1.162 brouard 3585: #ifdef NLOPT
3586: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3587: double fret;
3588: double *xt;
3589: int j;
3590: myfunc_data *d2 = (myfunc_data *) pd;
3591: /* xt = (p1-1); */
3592: xt=vector(1,n);
3593: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3594:
3595: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3596: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3597: printf("Function = %.12lf ",fret);
3598: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3599: printf("\n");
3600: free_vector(xt,1,n);
3601: return fret;
3602: }
3603: #endif
1.126 brouard 3604:
3605: /*************** log-likelihood *************/
3606: double func( double *x)
3607: {
1.226 brouard 3608: int i, ii, j, k, mi, d, kk;
3609: int ioffset=0;
3610: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3611: double **out;
3612: double lli; /* Individual log likelihood */
3613: int s1, s2;
1.228 brouard 3614: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
1.226 brouard 3615: double bbh, survp;
3616: long ipmx;
3617: double agexact;
3618: /*extern weight */
3619: /* We are differentiating ll according to initial status */
3620: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3621: /*for(i=1;i<imx;i++)
3622: printf(" %d\n",s[4][i]);
3623: */
1.162 brouard 3624:
1.226 brouard 3625: ++countcallfunc;
1.162 brouard 3626:
1.226 brouard 3627: cov[1]=1.;
1.126 brouard 3628:
1.226 brouard 3629: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3630: ioffset=0;
1.226 brouard 3631: if(mle==1){
3632: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3633: /* Computes the values of the ncovmodel covariates of the model
3634: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3635: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3636: to be observed in j being in i according to the model.
3637: */
1.243 brouard 3638: ioffset=2+nagesqr ;
1.233 brouard 3639: /* Fixed */
1.319 ! brouard 3640: for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
! 3641: /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
! 3642: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 3643: /* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1*V2, V1 */
! 3644: /* TvarFind; /**< TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod) */
! 3645: cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
! 3646: /* V1*V2 (7) TvarFind[2]=7, TvarFind[3]=9 */
1.234 brouard 3647: }
1.226 brouard 3648: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.319 ! brouard 3649: is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6
1.226 brouard 3650: has been calculated etc */
3651: /* For an individual i, wav[i] gives the number of effective waves */
3652: /* We compute the contribution to Likelihood of each effective transition
3653: mw[mi][i] is real wave of the mi th effectve wave */
3654: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3655: s2=s[mw[mi+1][i]][i];
3656: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3657: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3658: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3659: */
3660: for(mi=1; mi<= wav[i]-1; mi++){
1.319 ! brouard 3661: for(k=1; k <= ncovv ; k++){ /* Varying covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3) Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
! 3662: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
1.242 brouard 3663: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3664: }
3665: for (ii=1;ii<=nlstate+ndeath;ii++)
3666: for (j=1;j<=nlstate+ndeath;j++){
3667: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3668: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3669: }
3670: for(d=0; d<dh[mi][i]; d++){
3671: newm=savm;
3672: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3673: cov[2]=agexact;
3674: if(nagesqr==1)
3675: cov[3]= agexact*agexact; /* Should be changed here */
3676: for (kk=1; kk<=cptcovage;kk++) {
1.318 brouard 3677: if(!FixedV[Tvar[Tage[kk]]])
3678: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3679: else
3680: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3681: }
3682: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3683: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3684: savm=oldm;
3685: oldm=newm;
3686: } /* end mult */
3687:
3688: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3689: /* But now since version 0.9 we anticipate for bias at large stepm.
3690: * If stepm is larger than one month (smallest stepm) and if the exact delay
3691: * (in months) between two waves is not a multiple of stepm, we rounded to
3692: * the nearest (and in case of equal distance, to the lowest) interval but now
3693: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3694: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3695: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3696: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3697: * -stepm/2 to stepm/2 .
3698: * For stepm=1 the results are the same as for previous versions of Imach.
3699: * For stepm > 1 the results are less biased than in previous versions.
3700: */
1.234 brouard 3701: s1=s[mw[mi][i]][i];
3702: s2=s[mw[mi+1][i]][i];
3703: bbh=(double)bh[mi][i]/(double)stepm;
3704: /* bias bh is positive if real duration
3705: * is higher than the multiple of stepm and negative otherwise.
3706: */
3707: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3708: if( s2 > nlstate){
3709: /* i.e. if s2 is a death state and if the date of death is known
3710: then the contribution to the likelihood is the probability to
3711: die between last step unit time and current step unit time,
3712: which is also equal to probability to die before dh
3713: minus probability to die before dh-stepm .
3714: In version up to 0.92 likelihood was computed
3715: as if date of death was unknown. Death was treated as any other
3716: health state: the date of the interview describes the actual state
3717: and not the date of a change in health state. The former idea was
3718: to consider that at each interview the state was recorded
3719: (healthy, disable or death) and IMaCh was corrected; but when we
3720: introduced the exact date of death then we should have modified
3721: the contribution of an exact death to the likelihood. This new
3722: contribution is smaller and very dependent of the step unit
3723: stepm. It is no more the probability to die between last interview
3724: and month of death but the probability to survive from last
3725: interview up to one month before death multiplied by the
3726: probability to die within a month. Thanks to Chris
3727: Jackson for correcting this bug. Former versions increased
3728: mortality artificially. The bad side is that we add another loop
3729: which slows down the processing. The difference can be up to 10%
3730: lower mortality.
3731: */
3732: /* If, at the beginning of the maximization mostly, the
3733: cumulative probability or probability to be dead is
3734: constant (ie = 1) over time d, the difference is equal to
3735: 0. out[s1][3] = savm[s1][3]: probability, being at state
3736: s1 at precedent wave, to be dead a month before current
3737: wave is equal to probability, being at state s1 at
3738: precedent wave, to be dead at mont of the current
3739: wave. Then the observed probability (that this person died)
3740: is null according to current estimated parameter. In fact,
3741: it should be very low but not zero otherwise the log go to
3742: infinity.
3743: */
1.183 brouard 3744: /* #ifdef INFINITYORIGINAL */
3745: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3746: /* #else */
3747: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3748: /* lli=log(mytinydouble); */
3749: /* else */
3750: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3751: /* #endif */
1.226 brouard 3752: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3753:
1.226 brouard 3754: } else if ( s2==-1 ) { /* alive */
3755: for (j=1,survp=0. ; j<=nlstate; j++)
3756: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3757: /*survp += out[s1][j]; */
3758: lli= log(survp);
3759: }
3760: else if (s2==-4) {
3761: for (j=3,survp=0. ; j<=nlstate; j++)
3762: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3763: lli= log(survp);
3764: }
3765: else if (s2==-5) {
3766: for (j=1,survp=0. ; j<=2; j++)
3767: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3768: lli= log(survp);
3769: }
3770: else{
3771: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3772: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
3773: }
3774: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3775: /*if(lli ==000.0)*/
3776: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
3777: ipmx +=1;
3778: sw += weight[i];
3779: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3780: /* if (lli < log(mytinydouble)){ */
3781: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
3782: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
3783: /* } */
3784: } /* end of wave */
3785: } /* end of individual */
3786: } else if(mle==2){
3787: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.319 ! brouard 3788: ioffset=2+nagesqr ;
! 3789: for (k=1; k<=ncovf;k++)
! 3790: cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
1.226 brouard 3791: for(mi=1; mi<= wav[i]-1; mi++){
1.319 ! brouard 3792: for(k=1; k <= ncovv ; k++){
! 3793: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
! 3794: }
1.226 brouard 3795: for (ii=1;ii<=nlstate+ndeath;ii++)
3796: for (j=1;j<=nlstate+ndeath;j++){
3797: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3798: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3799: }
3800: for(d=0; d<=dh[mi][i]; d++){
3801: newm=savm;
3802: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3803: cov[2]=agexact;
3804: if(nagesqr==1)
3805: cov[3]= agexact*agexact;
3806: for (kk=1; kk<=cptcovage;kk++) {
3807: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3808: }
3809: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3810: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3811: savm=oldm;
3812: oldm=newm;
3813: } /* end mult */
3814:
3815: s1=s[mw[mi][i]][i];
3816: s2=s[mw[mi+1][i]][i];
3817: bbh=(double)bh[mi][i]/(double)stepm;
3818: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
3819: ipmx +=1;
3820: sw += weight[i];
3821: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3822: } /* end of wave */
3823: } /* end of individual */
3824: } else if(mle==3){ /* exponential inter-extrapolation */
3825: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3826: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3827: for(mi=1; mi<= wav[i]-1; mi++){
3828: for (ii=1;ii<=nlstate+ndeath;ii++)
3829: for (j=1;j<=nlstate+ndeath;j++){
3830: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3831: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3832: }
3833: for(d=0; d<dh[mi][i]; d++){
3834: newm=savm;
3835: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3836: cov[2]=agexact;
3837: if(nagesqr==1)
3838: cov[3]= agexact*agexact;
3839: for (kk=1; kk<=cptcovage;kk++) {
3840: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3841: }
3842: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3843: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3844: savm=oldm;
3845: oldm=newm;
3846: } /* end mult */
3847:
3848: s1=s[mw[mi][i]][i];
3849: s2=s[mw[mi+1][i]][i];
3850: bbh=(double)bh[mi][i]/(double)stepm;
3851: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
3852: ipmx +=1;
3853: sw += weight[i];
3854: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3855: } /* end of wave */
3856: } /* end of individual */
3857: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3858: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3859: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3860: for(mi=1; mi<= wav[i]-1; mi++){
3861: for (ii=1;ii<=nlstate+ndeath;ii++)
3862: for (j=1;j<=nlstate+ndeath;j++){
3863: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3864: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3865: }
3866: for(d=0; d<dh[mi][i]; d++){
3867: newm=savm;
3868: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3869: cov[2]=agexact;
3870: if(nagesqr==1)
3871: cov[3]= agexact*agexact;
3872: for (kk=1; kk<=cptcovage;kk++) {
3873: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3874: }
1.126 brouard 3875:
1.226 brouard 3876: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3877: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3878: savm=oldm;
3879: oldm=newm;
3880: } /* end mult */
3881:
3882: s1=s[mw[mi][i]][i];
3883: s2=s[mw[mi+1][i]][i];
3884: if( s2 > nlstate){
3885: lli=log(out[s1][s2] - savm[s1][s2]);
3886: } else if ( s2==-1 ) { /* alive */
3887: for (j=1,survp=0. ; j<=nlstate; j++)
3888: survp += out[s1][j];
3889: lli= log(survp);
3890: }else{
3891: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3892: }
3893: ipmx +=1;
3894: sw += weight[i];
3895: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3896: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.226 brouard 3897: } /* end of wave */
3898: } /* end of individual */
3899: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3900: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3901: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3902: for(mi=1; mi<= wav[i]-1; mi++){
3903: for (ii=1;ii<=nlstate+ndeath;ii++)
3904: for (j=1;j<=nlstate+ndeath;j++){
3905: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3906: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3907: }
3908: for(d=0; d<dh[mi][i]; d++){
3909: newm=savm;
3910: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3911: cov[2]=agexact;
3912: if(nagesqr==1)
3913: cov[3]= agexact*agexact;
3914: for (kk=1; kk<=cptcovage;kk++) {
3915: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3916: }
1.126 brouard 3917:
1.226 brouard 3918: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3919: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3920: savm=oldm;
3921: oldm=newm;
3922: } /* end mult */
3923:
3924: s1=s[mw[mi][i]][i];
3925: s2=s[mw[mi+1][i]][i];
3926: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3927: ipmx +=1;
3928: sw += weight[i];
3929: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3930: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
3931: } /* end of wave */
3932: } /* end of individual */
3933: } /* End of if */
3934: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3935: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3936: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3937: return -l;
1.126 brouard 3938: }
3939:
3940: /*************** log-likelihood *************/
3941: double funcone( double *x)
3942: {
1.228 brouard 3943: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3944: int i, ii, j, k, mi, d, kk;
1.228 brouard 3945: int ioffset=0;
1.131 brouard 3946: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3947: double **out;
3948: double lli; /* Individual log likelihood */
3949: double llt;
3950: int s1, s2;
1.228 brouard 3951: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3952:
1.126 brouard 3953: double bbh, survp;
1.187 brouard 3954: double agexact;
1.214 brouard 3955: double agebegin, ageend;
1.126 brouard 3956: /*extern weight */
3957: /* We are differentiating ll according to initial status */
3958: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3959: /*for(i=1;i<imx;i++)
3960: printf(" %d\n",s[4][i]);
3961: */
3962: cov[1]=1.;
3963:
3964: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3965: ioffset=0;
3966: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3967: /* ioffset=2+nagesqr+cptcovage; */
3968: ioffset=2+nagesqr;
1.232 brouard 3969: /* Fixed */
1.224 brouard 3970: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3971: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
1.311 brouard 3972: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
1.232 brouard 3973: cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
3974: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3975: /* cov[2+6]=covar[Tvar[6]][i]; */
3976: /* cov[2+6]=covar[2][i]; V2 */
3977: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3978: /* cov[2+7]=covar[Tvar[7]][i]; */
3979: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3980: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3981: /* cov[2+9]=covar[Tvar[9]][i]; */
3982: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3983: }
1.232 brouard 3984: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3985: /* cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
3986: /* } */
1.231 brouard 3987: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3988: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3989: /* } */
1.225 brouard 3990:
1.233 brouard 3991:
3992: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3993: /* Wave varying (but not age varying) */
3994: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3995: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3996: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3997: }
1.232 brouard 3998: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3999: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
4000: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
4001: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
4002: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
4003: /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
1.232 brouard 4004: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 4005: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
4006: /* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
4007: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 4008: /* } */
1.126 brouard 4009: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 4010: for (j=1;j<=nlstate+ndeath;j++){
4011: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
4012: savm[ii][j]=(ii==j ? 1.0 : 0.0);
4013: }
1.214 brouard 4014:
4015: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
4016: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
4017: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 4018: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 4019: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4020: and mw[mi+1][i]. dh depends on stepm.*/
4021: newm=savm;
1.247 brouard 4022: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 4023: cov[2]=agexact;
4024: if(nagesqr==1)
4025: cov[3]= agexact*agexact;
4026: for (kk=1; kk<=cptcovage;kk++) {
4027: if(!FixedV[Tvar[Tage[kk]]])
4028: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
4029: else
4030: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
4031: }
4032: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
4033: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
4034: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
4035: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
4036: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
4037: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
4038: savm=oldm;
4039: oldm=newm;
1.126 brouard 4040: } /* end mult */
4041:
4042: s1=s[mw[mi][i]][i];
4043: s2=s[mw[mi+1][i]][i];
1.217 brouard 4044: /* if(s2==-1){ */
1.268 brouard 4045: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 4046: /* /\* exit(1); *\/ */
4047: /* } */
1.126 brouard 4048: bbh=(double)bh[mi][i]/(double)stepm;
4049: /* bias is positive if real duration
4050: * is higher than the multiple of stepm and negative otherwise.
4051: */
4052: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 4053: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 4054: } else if ( s2==-1 ) { /* alive */
1.242 brouard 4055: for (j=1,survp=0. ; j<=nlstate; j++)
4056: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
4057: lli= log(survp);
1.126 brouard 4058: }else if (mle==1){
1.242 brouard 4059: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 4060: } else if(mle==2){
1.242 brouard 4061: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1.126 brouard 4062: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 4063: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1.126 brouard 4064: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 4065: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 4066: } else{ /* mle=0 back to 1 */
1.242 brouard 4067: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
4068: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 4069: } /* End of if */
4070: ipmx +=1;
4071: sw += weight[i];
4072: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 4073: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126 brouard 4074: if(globpr){
1.246 brouard 4075: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 4076: %11.6f %11.6f %11.6f ", \
1.242 brouard 4077: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.268 brouard 4078: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 4079: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
4080: llt +=ll[k]*gipmx/gsw;
4081: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
4082: }
4083: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 4084: }
1.232 brouard 4085: } /* end of wave */
4086: } /* end of individual */
4087: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
4088: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
4089: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
4090: if(globpr==0){ /* First time we count the contributions and weights */
4091: gipmx=ipmx;
4092: gsw=sw;
4093: }
4094: return -l;
1.126 brouard 4095: }
4096:
4097:
4098: /*************** function likelione ***********/
1.292 brouard 4099: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 4100: {
4101: /* This routine should help understanding what is done with
4102: the selection of individuals/waves and
4103: to check the exact contribution to the likelihood.
4104: Plotting could be done.
4105: */
4106: int k;
4107:
4108: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 4109: strcpy(fileresilk,"ILK_");
1.202 brouard 4110: strcat(fileresilk,fileresu);
1.126 brouard 4111: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
4112: printf("Problem with resultfile: %s\n", fileresilk);
4113: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
4114: }
1.214 brouard 4115: fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
4116: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 4117: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
4118: for(k=1; k<=nlstate; k++)
4119: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
4120: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
4121: }
4122:
1.292 brouard 4123: *fretone=(*func)(p);
1.126 brouard 4124: if(*globpri !=0){
4125: fclose(ficresilk);
1.205 brouard 4126: if (mle ==0)
4127: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
4128: else if(mle >=1)
4129: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
4130: fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.274 brouard 4131: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 4132:
4133: for (k=1; k<= nlstate ; k++) {
1.211 brouard 4134: fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208 brouard 4135: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
4136: }
1.207 brouard 4137: fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
1.204 brouard 4138: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4139: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 4140: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4141: fflush(fichtm);
1.205 brouard 4142: }
1.126 brouard 4143: return;
4144: }
4145:
4146:
4147: /*********** Maximum Likelihood Estimation ***************/
4148:
4149: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4150: {
1.319 ! brouard 4151: int i,j,k, jk, jkk=0, iter=0;
1.126 brouard 4152: double **xi;
4153: double fret;
4154: double fretone; /* Only one call to likelihood */
4155: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4156:
4157: #ifdef NLOPT
4158: int creturn;
4159: nlopt_opt opt;
4160: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4161: double *lb;
4162: double minf; /* the minimum objective value, upon return */
4163: double * p1; /* Shifted parameters from 0 instead of 1 */
4164: myfunc_data dinst, *d = &dinst;
4165: #endif
4166:
4167:
1.126 brouard 4168: xi=matrix(1,npar,1,npar);
4169: for (i=1;i<=npar;i++)
4170: for (j=1;j<=npar;j++)
4171: xi[i][j]=(i==j ? 1.0 : 0.0);
4172: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4173: strcpy(filerespow,"POW_");
1.126 brouard 4174: strcat(filerespow,fileres);
4175: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4176: printf("Problem with resultfile: %s\n", filerespow);
4177: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4178: }
4179: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4180: for (i=1;i<=nlstate;i++)
4181: for(j=1;j<=nlstate+ndeath;j++)
4182: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4183: fprintf(ficrespow,"\n");
1.162 brouard 4184: #ifdef POWELL
1.319 ! brouard 4185: #ifdef LINMINORIGINAL
! 4186: #else /* LINMINORIGINAL */
! 4187:
! 4188: flatdir=ivector(1,npar);
! 4189: for (j=1;j<=npar;j++) flatdir[j]=0;
! 4190: #endif /*LINMINORIGINAL */
! 4191:
! 4192: #ifdef FLATSUP
! 4193: powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
! 4194: /* reorganizing p by suppressing flat directions */
! 4195: for(i=1, jk=1; i <=nlstate; i++){
! 4196: for(k=1; k <=(nlstate+ndeath); k++){
! 4197: if (k != i) {
! 4198: printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
! 4199: if(flatdir[jk]==1){
! 4200: printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
! 4201: }
! 4202: for(j=1; j <=ncovmodel; j++){
! 4203: printf("%12.7f ",p[jk]);
! 4204: jk++;
! 4205: }
! 4206: printf("\n");
! 4207: }
! 4208: }
! 4209: }
! 4210: /* skipping */
! 4211: /* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
! 4212: for(i=1, jk=1, jkk=1;i <=nlstate; i++){
! 4213: for(k=1; k <=(nlstate+ndeath); k++){
! 4214: if (k != i) {
! 4215: printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
! 4216: if(flatdir[jk]==1){
! 4217: printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
! 4218: for(j=1; j <=ncovmodel; jk++,j++){
! 4219: printf(" p[%d]=%12.7f",jk, p[jk]);
! 4220: /*q[jjk]=p[jk];*/
! 4221: }
! 4222: }else{
! 4223: printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
! 4224: for(j=1; j <=ncovmodel; jk++,jkk++,j++){
! 4225: printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
! 4226: /*q[jjk]=p[jk];*/
! 4227: }
! 4228: }
! 4229: printf("\n");
! 4230: }
! 4231: fflush(stdout);
! 4232: }
! 4233: }
! 4234: powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
! 4235: #else /* FLATSUP */
1.126 brouard 4236: powell(p,xi,npar,ftol,&iter,&fret,func);
1.319 ! brouard 4237: #endif /* FLATSUP */
! 4238:
! 4239: #ifdef LINMINORIGINAL
! 4240: #else
! 4241: free_ivector(flatdir,1,npar);
! 4242: #endif /* LINMINORIGINAL*/
! 4243: #endif /* POWELL */
1.126 brouard 4244:
1.162 brouard 4245: #ifdef NLOPT
4246: #ifdef NEWUOA
4247: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4248: #else
4249: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4250: #endif
4251: lb=vector(0,npar-1);
4252: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4253: nlopt_set_lower_bounds(opt, lb);
4254: nlopt_set_initial_step1(opt, 0.1);
4255:
4256: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4257: d->function = func;
4258: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4259: nlopt_set_min_objective(opt, myfunc, d);
4260: nlopt_set_xtol_rel(opt, ftol);
4261: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4262: printf("nlopt failed! %d\n",creturn);
4263: }
4264: else {
4265: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4266: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4267: iter=1; /* not equal */
4268: }
4269: nlopt_destroy(opt);
4270: #endif
1.319 ! brouard 4271: #ifdef FLATSUP
! 4272: /* npared = npar -flatd/ncovmodel; */
! 4273: /* xired= matrix(1,npared,1,npared); */
! 4274: /* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
! 4275: /* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
! 4276: /* free_matrix(xire,1,npared,1,npared); */
! 4277: #else /* FLATSUP */
! 4278: #endif /* FLATSUP */
1.126 brouard 4279: free_matrix(xi,1,npar,1,npar);
4280: fclose(ficrespow);
1.203 brouard 4281: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4282: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4283: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4284:
4285: }
4286:
4287: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4288: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4289: {
4290: double **a,**y,*x,pd;
1.203 brouard 4291: /* double **hess; */
1.164 brouard 4292: int i, j;
1.126 brouard 4293: int *indx;
4294:
4295: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4296: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4297: void lubksb(double **a, int npar, int *indx, double b[]) ;
4298: void ludcmp(double **a, int npar, int *indx, double *d) ;
4299: double gompertz(double p[]);
1.203 brouard 4300: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4301:
4302: printf("\nCalculation of the hessian matrix. Wait...\n");
4303: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4304: for (i=1;i<=npar;i++){
1.203 brouard 4305: printf("%d-",i);fflush(stdout);
4306: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4307:
4308: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4309:
4310: /* printf(" %f ",p[i]);
4311: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4312: }
4313:
4314: for (i=1;i<=npar;i++) {
4315: for (j=1;j<=npar;j++) {
4316: if (j>i) {
1.203 brouard 4317: printf(".%d-%d",i,j);fflush(stdout);
4318: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4319: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4320:
4321: hess[j][i]=hess[i][j];
4322: /*printf(" %lf ",hess[i][j]);*/
4323: }
4324: }
4325: }
4326: printf("\n");
4327: fprintf(ficlog,"\n");
4328:
4329: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4330: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4331:
4332: a=matrix(1,npar,1,npar);
4333: y=matrix(1,npar,1,npar);
4334: x=vector(1,npar);
4335: indx=ivector(1,npar);
4336: for (i=1;i<=npar;i++)
4337: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4338: ludcmp(a,npar,indx,&pd);
4339:
4340: for (j=1;j<=npar;j++) {
4341: for (i=1;i<=npar;i++) x[i]=0;
4342: x[j]=1;
4343: lubksb(a,npar,indx,x);
4344: for (i=1;i<=npar;i++){
4345: matcov[i][j]=x[i];
4346: }
4347: }
4348:
4349: printf("\n#Hessian matrix#\n");
4350: fprintf(ficlog,"\n#Hessian matrix#\n");
4351: for (i=1;i<=npar;i++) {
4352: for (j=1;j<=npar;j++) {
1.203 brouard 4353: printf("%.6e ",hess[i][j]);
4354: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4355: }
4356: printf("\n");
4357: fprintf(ficlog,"\n");
4358: }
4359:
1.203 brouard 4360: /* printf("\n#Covariance matrix#\n"); */
4361: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4362: /* for (i=1;i<=npar;i++) { */
4363: /* for (j=1;j<=npar;j++) { */
4364: /* printf("%.6e ",matcov[i][j]); */
4365: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4366: /* } */
4367: /* printf("\n"); */
4368: /* fprintf(ficlog,"\n"); */
4369: /* } */
4370:
1.126 brouard 4371: /* Recompute Inverse */
1.203 brouard 4372: /* for (i=1;i<=npar;i++) */
4373: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4374: /* ludcmp(a,npar,indx,&pd); */
4375:
4376: /* printf("\n#Hessian matrix recomputed#\n"); */
4377:
4378: /* for (j=1;j<=npar;j++) { */
4379: /* for (i=1;i<=npar;i++) x[i]=0; */
4380: /* x[j]=1; */
4381: /* lubksb(a,npar,indx,x); */
4382: /* for (i=1;i<=npar;i++){ */
4383: /* y[i][j]=x[i]; */
4384: /* printf("%.3e ",y[i][j]); */
4385: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4386: /* } */
4387: /* printf("\n"); */
4388: /* fprintf(ficlog,"\n"); */
4389: /* } */
4390:
4391: /* Verifying the inverse matrix */
4392: #ifdef DEBUGHESS
4393: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4394:
1.203 brouard 4395: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4396: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4397:
4398: for (j=1;j<=npar;j++) {
4399: for (i=1;i<=npar;i++){
1.203 brouard 4400: printf("%.2f ",y[i][j]);
4401: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4402: }
4403: printf("\n");
4404: fprintf(ficlog,"\n");
4405: }
1.203 brouard 4406: #endif
1.126 brouard 4407:
4408: free_matrix(a,1,npar,1,npar);
4409: free_matrix(y,1,npar,1,npar);
4410: free_vector(x,1,npar);
4411: free_ivector(indx,1,npar);
1.203 brouard 4412: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4413:
4414:
4415: }
4416:
4417: /*************** hessian matrix ****************/
4418: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4419: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4420: int i;
4421: int l=1, lmax=20;
1.203 brouard 4422: double k1,k2, res, fx;
1.132 brouard 4423: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4424: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4425: int k=0,kmax=10;
4426: double l1;
4427:
4428: fx=func(x);
4429: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4430: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4431: l1=pow(10,l);
4432: delts=delt;
4433: for(k=1 ; k <kmax; k=k+1){
4434: delt = delta*(l1*k);
4435: p2[theta]=x[theta] +delt;
1.145 brouard 4436: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4437: p2[theta]=x[theta]-delt;
4438: k2=func(p2)-fx;
4439: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4440: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4441:
1.203 brouard 4442: #ifdef DEBUGHESSII
1.126 brouard 4443: printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
4444: fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
4445: #endif
4446: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4447: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4448: k=kmax;
4449: }
4450: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4451: k=kmax; l=lmax*10;
1.126 brouard 4452: }
4453: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4454: delts=delt;
4455: }
1.203 brouard 4456: } /* End loop k */
1.126 brouard 4457: }
4458: delti[theta]=delts;
4459: return res;
4460:
4461: }
4462:
1.203 brouard 4463: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4464: {
4465: int i;
1.164 brouard 4466: int l=1, lmax=20;
1.126 brouard 4467: double k1,k2,k3,k4,res,fx;
1.132 brouard 4468: double p2[MAXPARM+1];
1.203 brouard 4469: int k, kmax=1;
4470: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4471:
4472: int firstime=0;
1.203 brouard 4473:
1.126 brouard 4474: fx=func(x);
1.203 brouard 4475: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4476: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4477: p2[thetai]=x[thetai]+delti[thetai]*k;
4478: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4479: k1=func(p2)-fx;
4480:
1.203 brouard 4481: p2[thetai]=x[thetai]+delti[thetai]*k;
4482: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4483: k2=func(p2)-fx;
4484:
1.203 brouard 4485: p2[thetai]=x[thetai]-delti[thetai]*k;
4486: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4487: k3=func(p2)-fx;
4488:
1.203 brouard 4489: p2[thetai]=x[thetai]-delti[thetai]*k;
4490: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4491: k4=func(p2)-fx;
1.203 brouard 4492: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4493: if(k1*k2*k3*k4 <0.){
1.208 brouard 4494: firstime=1;
1.203 brouard 4495: kmax=kmax+10;
1.208 brouard 4496: }
4497: if(kmax >=10 || firstime ==1){
1.246 brouard 4498: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
4499: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203 brouard 4500: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
4501: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
4502: }
4503: #ifdef DEBUGHESSIJ
4504: v1=hess[thetai][thetai];
4505: v2=hess[thetaj][thetaj];
4506: cv12=res;
4507: /* Computing eigen value of Hessian matrix */
4508: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4509: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4510: if ((lc2 <0) || (lc1 <0) ){
4511: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4512: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4513: printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
4514: fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
4515: }
1.126 brouard 4516: #endif
4517: }
4518: return res;
4519: }
4520:
1.203 brouard 4521: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4522: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4523: /* { */
4524: /* int i; */
4525: /* int l=1, lmax=20; */
4526: /* double k1,k2,k3,k4,res,fx; */
4527: /* double p2[MAXPARM+1]; */
4528: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4529: /* int k=0,kmax=10; */
4530: /* double l1; */
4531:
4532: /* fx=func(x); */
4533: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4534: /* l1=pow(10,l); */
4535: /* delts=delt; */
4536: /* for(k=1 ; k <kmax; k=k+1){ */
4537: /* delt = delti*(l1*k); */
4538: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4539: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4540: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4541: /* k1=func(p2)-fx; */
4542:
4543: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4544: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4545: /* k2=func(p2)-fx; */
4546:
4547: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4548: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4549: /* k3=func(p2)-fx; */
4550:
4551: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4552: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4553: /* k4=func(p2)-fx; */
4554: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4555: /* #ifdef DEBUGHESSIJ */
4556: /* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
4557: /* fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
4558: /* #endif */
4559: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4560: /* k=kmax; */
4561: /* } */
4562: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4563: /* k=kmax; l=lmax*10; */
4564: /* } */
4565: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4566: /* delts=delt; */
4567: /* } */
4568: /* } /\* End loop k *\/ */
4569: /* } */
4570: /* delti[theta]=delts; */
4571: /* return res; */
4572: /* } */
4573:
4574:
1.126 brouard 4575: /************** Inverse of matrix **************/
4576: void ludcmp(double **a, int n, int *indx, double *d)
4577: {
4578: int i,imax,j,k;
4579: double big,dum,sum,temp;
4580: double *vv;
4581:
4582: vv=vector(1,n);
4583: *d=1.0;
4584: for (i=1;i<=n;i++) {
4585: big=0.0;
4586: for (j=1;j<=n;j++)
4587: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4588: if (big == 0.0){
4589: printf(" Singular Hessian matrix at row %d:\n",i);
4590: for (j=1;j<=n;j++) {
4591: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4592: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4593: }
4594: fflush(ficlog);
4595: fclose(ficlog);
4596: nrerror("Singular matrix in routine ludcmp");
4597: }
1.126 brouard 4598: vv[i]=1.0/big;
4599: }
4600: for (j=1;j<=n;j++) {
4601: for (i=1;i<j;i++) {
4602: sum=a[i][j];
4603: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4604: a[i][j]=sum;
4605: }
4606: big=0.0;
4607: for (i=j;i<=n;i++) {
4608: sum=a[i][j];
4609: for (k=1;k<j;k++)
4610: sum -= a[i][k]*a[k][j];
4611: a[i][j]=sum;
4612: if ( (dum=vv[i]*fabs(sum)) >= big) {
4613: big=dum;
4614: imax=i;
4615: }
4616: }
4617: if (j != imax) {
4618: for (k=1;k<=n;k++) {
4619: dum=a[imax][k];
4620: a[imax][k]=a[j][k];
4621: a[j][k]=dum;
4622: }
4623: *d = -(*d);
4624: vv[imax]=vv[j];
4625: }
4626: indx[j]=imax;
4627: if (a[j][j] == 0.0) a[j][j]=TINY;
4628: if (j != n) {
4629: dum=1.0/(a[j][j]);
4630: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4631: }
4632: }
4633: free_vector(vv,1,n); /* Doesn't work */
4634: ;
4635: }
4636:
4637: void lubksb(double **a, int n, int *indx, double b[])
4638: {
4639: int i,ii=0,ip,j;
4640: double sum;
4641:
4642: for (i=1;i<=n;i++) {
4643: ip=indx[i];
4644: sum=b[ip];
4645: b[ip]=b[i];
4646: if (ii)
4647: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4648: else if (sum) ii=i;
4649: b[i]=sum;
4650: }
4651: for (i=n;i>=1;i--) {
4652: sum=b[i];
4653: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4654: b[i]=sum/a[i][i];
4655: }
4656: }
4657:
4658: void pstamp(FILE *fichier)
4659: {
1.196 brouard 4660: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4661: }
4662:
1.297 brouard 4663: void date2dmy(double date,double *day, double *month, double *year){
4664: double yp=0., yp1=0., yp2=0.;
4665:
4666: yp1=modf(date,&yp);/* extracts integral of date in yp and
4667: fractional in yp1 */
4668: *year=yp;
4669: yp2=modf((yp1*12),&yp);
4670: *month=yp;
4671: yp1=modf((yp2*30.5),&yp);
4672: *day=yp;
4673: if(*day==0) *day=1;
4674: if(*month==0) *month=1;
4675: }
4676:
1.253 brouard 4677:
4678:
1.126 brouard 4679: /************ Frequencies ********************/
1.251 brouard 4680: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4681: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4682: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4683: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4684:
1.265 brouard 4685: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4686: int iind=0, iage=0;
4687: int mi; /* Effective wave */
4688: int first;
4689: double ***freq; /* Frequencies */
1.268 brouard 4690: double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
4691: int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
1.284 brouard 4692: double *meanq, *stdq, *idq;
1.226 brouard 4693: double **meanqt;
4694: double *pp, **prop, *posprop, *pospropt;
4695: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4696: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4697: double agebegin, ageend;
4698:
4699: pp=vector(1,nlstate);
1.251 brouard 4700: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4701: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4702: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4703: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4704: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4705: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4706: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4707: meanqt=matrix(1,lastpass,1,nqtveff);
4708: strcpy(fileresp,"P_");
4709: strcat(fileresp,fileresu);
4710: /*strcat(fileresphtm,fileresu);*/
4711: if((ficresp=fopen(fileresp,"w"))==NULL) {
4712: printf("Problem with prevalence resultfile: %s\n", fileresp);
4713: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4714: exit(0);
4715: }
1.240 brouard 4716:
1.226 brouard 4717: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4718: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4719: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4720: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4721: fflush(ficlog);
4722: exit(70);
4723: }
4724: else{
4725: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4726: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4727: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4728: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4729: }
1.319 ! brouard 4730: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);
1.240 brouard 4731:
1.226 brouard 4732: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4733: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4734: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4735: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4736: fflush(ficlog);
4737: exit(70);
1.240 brouard 4738: } else{
1.226 brouard 4739: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.319 ! brouard 4740: ,<hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4741: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4742: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4743: }
1.319 ! brouard 4744: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);
1.240 brouard 4745:
1.253 brouard 4746: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4747: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4748: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4749: j1=0;
1.126 brouard 4750:
1.227 brouard 4751: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4752: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4753: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4754:
4755:
1.226 brouard 4756: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4757: reference=low_education V1=0,V2=0
4758: med_educ V1=1 V2=0,
4759: high_educ V1=0 V2=1
4760: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4761: */
1.249 brouard 4762: dateintsum=0;
4763: k2cpt=0;
4764:
1.253 brouard 4765: if(cptcoveff == 0 )
1.265 brouard 4766: nl=1; /* Constant and age model only */
1.253 brouard 4767: else
4768: nl=2;
1.265 brouard 4769:
4770: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4771: /* Loop on nj=1 or 2 if dummy covariates j!=0
4772: * Loop on j1(1 to 2**cptcoveff) covariate combination
4773: * freq[s1][s2][iage] =0.
4774: * Loop on iind
4775: * ++freq[s1][s2][iage] weighted
4776: * end iind
4777: * if covariate and j!0
4778: * headers Variable on one line
4779: * endif cov j!=0
4780: * header of frequency table by age
4781: * Loop on age
4782: * pp[s1]+=freq[s1][s2][iage] weighted
4783: * pos+=freq[s1][s2][iage] weighted
4784: * Loop on s1 initial state
4785: * fprintf(ficresp
4786: * end s1
4787: * end age
4788: * if j!=0 computes starting values
4789: * end compute starting values
4790: * end j1
4791: * end nl
4792: */
1.253 brouard 4793: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4794: if(nj==1)
4795: j=0; /* First pass for the constant */
1.265 brouard 4796: else{
1.253 brouard 4797: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4798: }
1.251 brouard 4799: first=1;
1.265 brouard 4800: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
1.251 brouard 4801: posproptt=0.;
4802: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4803: scanf("%d", i);*/
4804: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4805: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4806: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4807: freq[i][s2][m]=0;
1.251 brouard 4808:
4809: for (i=1; i<=nlstate; i++) {
1.240 brouard 4810: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4811: prop[i][m]=0;
4812: posprop[i]=0;
4813: pospropt[i]=0;
4814: }
1.283 brouard 4815: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4816: idq[z1]=0.;
4817: meanq[z1]=0.;
4818: stdq[z1]=0.;
1.283 brouard 4819: }
4820: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4821: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4822: /* meanqt[m][z1]=0.; */
4823: /* } */
4824: /* } */
1.251 brouard 4825: /* dateintsum=0; */
4826: /* k2cpt=0; */
4827:
1.265 brouard 4828: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4829: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4830: bool=1;
4831: if(j !=0){
4832: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4833: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4834: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4835: /* if(Tvaraff[z1] ==-20){ */
4836: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4837: /* }else if(Tvaraff[z1] ==-10){ */
4838: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4839: /* }else */
4840: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4841: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4842: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4843: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
4844: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4845: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4846: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4847: } /* Onlyf fixed */
4848: } /* end z1 */
4849: } /* cptcovn > 0 */
4850: } /* end any */
4851: }/* end j==0 */
1.265 brouard 4852: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4853: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4854: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4855: m=mw[mi][iind];
4856: if(j!=0){
4857: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4858: for (z1=1; z1<=cptcoveff; z1++) {
4859: if( Fixed[Tmodelind[z1]]==1){
4860: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4861: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4862: value is -1, we don't select. It differs from the
4863: constant and age model which counts them. */
4864: bool=0; /* not selected */
4865: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4866: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4867: bool=0;
4868: }
4869: }
4870: }
4871: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4872: } /* end j==0 */
4873: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4874: if(bool==1){ /*Selected */
1.251 brouard 4875: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4876: and mw[mi+1][iind]. dh depends on stepm. */
4877: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4878: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4879: if(m >=firstpass && m <=lastpass){
4880: k2=anint[m][iind]+(mint[m][iind]/12.);
4881: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4882: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4883: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4884: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4885: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4886: if (m<lastpass) {
4887: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4888: /* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
4889: if(s[m][iind]==-1)
4890: printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
4891: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
1.311 brouard 4892: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
4893: if(!isnan(covar[ncovcol+z1][iind])){
4894: idq[z1]=idq[z1]+weight[iind];
4895: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4896: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
4897: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4898: }
1.284 brouard 4899: }
1.251 brouard 4900: /* if((int)agev[m][iind] == 55) */
4901: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4902: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4903: freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.234 brouard 4904: }
1.251 brouard 4905: } /* end if between passes */
4906: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4907: dateintsum=dateintsum+k2; /* on all covariates ?*/
4908: k2cpt++;
4909: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4910: }
1.251 brouard 4911: }else{
4912: bool=1;
4913: }/* end bool 2 */
4914: } /* end m */
1.284 brouard 4915: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4916: /* idq[z1]=idq[z1]+weight[iind]; */
4917: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4918: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4919: /* } */
1.251 brouard 4920: } /* end bool */
4921: } /* end iind = 1 to imx */
1.319 ! brouard 4922: /* prop[s][age] is fed for any initial and valid live state as well as
1.251 brouard 4923: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4924:
4925:
4926: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4927: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4928: pstamp(ficresp);
1.251 brouard 4929: if (cptcoveff>0 && j!=0){
1.265 brouard 4930: pstamp(ficresp);
1.251 brouard 4931: printf( "\n#********** Variable ");
4932: fprintf(ficresp, "\n#********** Variable ");
4933: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4934: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4935: fprintf(ficlog, "\n#********** Variable ");
4936: for (z1=1; z1<=cptcoveff; z1++){
4937: if(!FixedV[Tvaraff[z1]]){
4938: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4939: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4940: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4941: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4942: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4943: }else{
1.251 brouard 4944: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4945: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4946: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4947: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4948: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4949: }
4950: }
4951: printf( "**********\n#");
4952: fprintf(ficresp, "**********\n#");
4953: fprintf(ficresphtm, "**********</h3>\n");
4954: fprintf(ficresphtmfr, "**********</h3>\n");
4955: fprintf(ficlog, "**********\n");
4956: }
1.284 brouard 4957: /*
4958: Printing means of quantitative variables if any
4959: */
4960: for (z1=1; z1<= nqfveff; z1++) {
1.311 brouard 4961: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.312 brouard 4962: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
1.284 brouard 4963: if(weightopt==1){
4964: printf(" Weighted mean and standard deviation of");
4965: fprintf(ficlog," Weighted mean and standard deviation of");
4966: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4967: }
1.311 brouard 4968: /* mu = \frac{w x}{\sum w}
4969: var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
4970: */
4971: printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
4972: fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
4973: fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
1.284 brouard 4974: }
4975: /* for (z1=1; z1<= nqtveff; z1++) { */
4976: /* for(m=1;m<=lastpass;m++){ */
4977: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4978: /* } */
4979: /* } */
1.283 brouard 4980:
1.251 brouard 4981: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4982: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4983: fprintf(ficresp, " Age");
4984: if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.251 brouard 4985: for(i=1; i<=nlstate;i++) {
1.265 brouard 4986: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4987: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4988: }
1.265 brouard 4989: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4990: fprintf(ficresphtm, "\n");
4991:
4992: /* Header of frequency table by age */
4993: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4994: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4995: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4996: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4997: if(s2!=0 && m!=0)
4998: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4999: }
1.226 brouard 5000: }
1.251 brouard 5001: fprintf(ficresphtmfr, "\n");
5002:
5003: /* For each age */
5004: for(iage=iagemin; iage <= iagemax+3; iage++){
5005: fprintf(ficresphtm,"<tr>");
5006: if(iage==iagemax+1){
5007: fprintf(ficlog,"1");
5008: fprintf(ficresphtmfr,"<tr><th>0</th> ");
5009: }else if(iage==iagemax+2){
5010: fprintf(ficlog,"0");
5011: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
5012: }else if(iage==iagemax+3){
5013: fprintf(ficlog,"Total");
5014: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
5015: }else{
1.240 brouard 5016: if(first==1){
1.251 brouard 5017: first=0;
5018: printf("See log file for details...\n");
5019: }
5020: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
5021: fprintf(ficlog,"Age %d", iage);
5022: }
1.265 brouard 5023: for(s1=1; s1 <=nlstate ; s1++){
5024: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
5025: pp[s1] += freq[s1][m][iage];
1.251 brouard 5026: }
1.265 brouard 5027: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 5028: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 5029: pos += freq[s1][m][iage];
5030: if(pp[s1]>=1.e-10){
1.251 brouard 5031: if(first==1){
1.265 brouard 5032: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 5033: }
1.265 brouard 5034: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 5035: }else{
5036: if(first==1)
1.265 brouard 5037: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
5038: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 5039: }
5040: }
5041:
1.265 brouard 5042: for(s1=1; s1 <=nlstate ; s1++){
5043: /* posprop[s1]=0; */
5044: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
5045: pp[s1] += freq[s1][m][iage];
5046: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
5047:
5048: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
5049: pos += pp[s1]; /* pos is the total number of transitions until this age */
5050: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
5051: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
5052: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
5053: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
5054: }
5055:
5056: /* Writing ficresp */
5057: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
5058: if( iage <= iagemax){
5059: fprintf(ficresp," %d",iage);
5060: }
5061: }else if( nj==2){
5062: if( iage <= iagemax){
5063: fprintf(ficresp," %d",iage);
5064: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5065: }
1.240 brouard 5066: }
1.265 brouard 5067: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 5068: if(pos>=1.e-5){
1.251 brouard 5069: if(first==1)
1.265 brouard 5070: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
5071: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 5072: }else{
5073: if(first==1)
1.265 brouard 5074: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
5075: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 5076: }
5077: if( iage <= iagemax){
5078: if(pos>=1.e-5){
1.265 brouard 5079: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
5080: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
5081: }else if( nj==2){
5082: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
5083: }
5084: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
5085: /*probs[iage][s1][j1]= pp[s1]/pos;*/
5086: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
5087: } else{
5088: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
5089: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 5090: }
1.240 brouard 5091: }
1.265 brouard 5092: pospropt[s1] +=posprop[s1];
5093: } /* end loop s1 */
1.251 brouard 5094: /* pospropt=0.; */
1.265 brouard 5095: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 5096: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 5097: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 5098: if(first==1){
1.265 brouard 5099: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 5100: }
1.265 brouard 5101: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
5102: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 5103: }
1.265 brouard 5104: if(s1!=0 && m!=0)
5105: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 5106: }
1.265 brouard 5107: } /* end loop s1 */
1.251 brouard 5108: posproptt=0.;
1.265 brouard 5109: for(s1=1; s1 <=nlstate; s1++){
5110: posproptt += pospropt[s1];
1.251 brouard 5111: }
5112: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 5113: fprintf(ficresphtm,"</tr>\n");
5114: if((cptcoveff==0 && nj==1)|| nj==2 ) {
5115: if(iage <= iagemax)
5116: fprintf(ficresp,"\n");
1.240 brouard 5117: }
1.251 brouard 5118: if(first==1)
5119: printf("Others in log...\n");
5120: fprintf(ficlog,"\n");
5121: } /* end loop age iage */
1.265 brouard 5122:
1.251 brouard 5123: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 5124: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 5125: if(posproptt < 1.e-5){
1.265 brouard 5126: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 5127: }else{
1.265 brouard 5128: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 5129: }
1.226 brouard 5130: }
1.251 brouard 5131: fprintf(ficresphtm,"</tr>\n");
5132: fprintf(ficresphtm,"</table>\n");
5133: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 5134: if(posproptt < 1.e-5){
1.251 brouard 5135: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
5136: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 5137: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
5138: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 5139: invalidvarcomb[j1]=1;
1.226 brouard 5140: }else{
1.251 brouard 5141: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
5142: invalidvarcomb[j1]=0;
1.226 brouard 5143: }
1.251 brouard 5144: fprintf(ficresphtmfr,"</table>\n");
5145: fprintf(ficlog,"\n");
5146: if(j!=0){
5147: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 5148: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 5149: for(k=1; k <=(nlstate+ndeath); k++){
5150: if (k != i) {
1.265 brouard 5151: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 5152: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 5153: if(j1==1){ /* All dummy covariates to zero */
5154: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
5155: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 5156: printf("%d%d ",i,k);
5157: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 5158: printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
5159: fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
5160: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 5161: }
1.253 brouard 5162: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
5163: for(iage=iagemin; iage <= iagemax+3; iage++){
5164: x[iage]= (double)iage;
5165: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 5166: /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
1.253 brouard 5167: }
1.268 brouard 5168: /* Some are not finite, but linreg will ignore these ages */
5169: no=0;
1.253 brouard 5170: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 5171: pstart[s1]=b;
5172: pstart[s1-1]=a;
1.252 brouard 5173: }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
5174: printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
5175: printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
1.265 brouard 5176: pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
1.252 brouard 5177: printf("%d%d ",i,k);
5178: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 5179: printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
1.251 brouard 5180: }else{ /* Other cases, like quantitative fixed or varying covariates */
5181: ;
5182: }
5183: /* printf("%12.7f )", param[i][jj][k]); */
5184: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5185: s1++;
1.251 brouard 5186: } /* end jj */
5187: } /* end k!= i */
5188: } /* end k */
1.265 brouard 5189: } /* end i, s1 */
1.251 brouard 5190: } /* end j !=0 */
5191: } /* end selected combination of covariate j1 */
5192: if(j==0){ /* We can estimate starting values from the occurences in each case */
5193: printf("#Freqsummary: Starting values for the constants:\n");
5194: fprintf(ficlog,"\n");
1.265 brouard 5195: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 5196: for(k=1; k <=(nlstate+ndeath); k++){
5197: if (k != i) {
5198: printf("%d%d ",i,k);
5199: fprintf(ficlog,"%d%d ",i,k);
5200: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 5201: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 5202: if(jj==1){ /* Age has to be done */
1.265 brouard 5203: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
5204: printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
5205: fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
1.251 brouard 5206: }
5207: /* printf("%12.7f )", param[i][jj][k]); */
5208: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5209: s1++;
1.250 brouard 5210: }
1.251 brouard 5211: printf("\n");
5212: fprintf(ficlog,"\n");
1.250 brouard 5213: }
5214: }
1.284 brouard 5215: } /* end of state i */
1.251 brouard 5216: printf("#Freqsummary\n");
5217: fprintf(ficlog,"\n");
1.265 brouard 5218: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5219: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5220: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5221: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5222: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5223: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5224: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5225: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5226: /* } */
5227: }
1.265 brouard 5228: } /* end loop s1 */
1.251 brouard 5229:
5230: printf("\n");
5231: fprintf(ficlog,"\n");
5232: } /* end j=0 */
1.249 brouard 5233: } /* end j */
1.252 brouard 5234:
1.253 brouard 5235: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5236: for(i=1, jk=1; i <=nlstate; i++){
5237: for(j=1; j <=nlstate+ndeath; j++){
5238: if(j!=i){
5239: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5240: printf("%1d%1d",i,j);
5241: fprintf(ficparo,"%1d%1d",i,j);
5242: for(k=1; k<=ncovmodel;k++){
5243: /* printf(" %lf",param[i][j][k]); */
5244: /* fprintf(ficparo," %lf",param[i][j][k]); */
5245: p[jk]=pstart[jk];
5246: printf(" %f ",pstart[jk]);
5247: fprintf(ficparo," %f ",pstart[jk]);
5248: jk++;
5249: }
5250: printf("\n");
5251: fprintf(ficparo,"\n");
5252: }
5253: }
5254: }
5255: } /* end mle=-2 */
1.226 brouard 5256: dateintmean=dateintsum/k2cpt;
1.296 brouard 5257: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5258:
1.226 brouard 5259: fclose(ficresp);
5260: fclose(ficresphtm);
5261: fclose(ficresphtmfr);
1.283 brouard 5262: free_vector(idq,1,nqfveff);
1.226 brouard 5263: free_vector(meanq,1,nqfveff);
1.284 brouard 5264: free_vector(stdq,1,nqfveff);
1.226 brouard 5265: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5266: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5267: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5268: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5269: free_vector(pospropt,1,nlstate);
5270: free_vector(posprop,1,nlstate);
1.251 brouard 5271: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5272: free_vector(pp,1,nlstate);
5273: /* End of freqsummary */
5274: }
1.126 brouard 5275:
1.268 brouard 5276: /* Simple linear regression */
5277: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5278:
5279: /* y=a+bx regression */
5280: double sumx = 0.0; /* sum of x */
5281: double sumx2 = 0.0; /* sum of x**2 */
5282: double sumxy = 0.0; /* sum of x * y */
5283: double sumy = 0.0; /* sum of y */
5284: double sumy2 = 0.0; /* sum of y**2 */
5285: double sume2 = 0.0; /* sum of square or residuals */
5286: double yhat;
5287:
5288: double denom=0;
5289: int i;
5290: int ne=*no;
5291:
5292: for ( i=ifi, ne=0;i<=ila;i++) {
5293: if(!isfinite(x[i]) || !isfinite(y[i])){
5294: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5295: continue;
5296: }
5297: ne=ne+1;
5298: sumx += x[i];
5299: sumx2 += x[i]*x[i];
5300: sumxy += x[i] * y[i];
5301: sumy += y[i];
5302: sumy2 += y[i]*y[i];
5303: denom = (ne * sumx2 - sumx*sumx);
5304: /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
5305: }
5306:
5307: denom = (ne * sumx2 - sumx*sumx);
5308: if (denom == 0) {
5309: // vertical, slope m is infinity
5310: *b = INFINITY;
5311: *a = 0;
5312: if (r) *r = 0;
5313: return 1;
5314: }
5315:
5316: *b = (ne * sumxy - sumx * sumy) / denom;
5317: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5318: if (r!=NULL) {
5319: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5320: sqrt((sumx2 - sumx*sumx/ne) *
5321: (sumy2 - sumy*sumy/ne));
5322: }
5323: *no=ne;
5324: for ( i=ifi, ne=0;i<=ila;i++) {
5325: if(!isfinite(x[i]) || !isfinite(y[i])){
5326: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5327: continue;
5328: }
5329: ne=ne+1;
5330: yhat = y[i] - *a -*b* x[i];
5331: sume2 += yhat * yhat ;
5332:
5333: denom = (ne * sumx2 - sumx*sumx);
5334: /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
5335: }
5336: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5337: *sa= *sb * sqrt(sumx2/ne);
5338:
5339: return 0;
5340: }
5341:
1.126 brouard 5342: /************ Prevalence ********************/
1.227 brouard 5343: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
5344: {
5345: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5346: in each health status at the date of interview (if between dateprev1 and dateprev2).
5347: We still use firstpass and lastpass as another selection.
5348: */
1.126 brouard 5349:
1.227 brouard 5350: int i, m, jk, j1, bool, z1,j, iv;
5351: int mi; /* Effective wave */
5352: int iage;
5353: double agebegin, ageend;
5354:
5355: double **prop;
5356: double posprop;
5357: double y2; /* in fractional years */
5358: int iagemin, iagemax;
5359: int first; /** to stop verbosity which is redirected to log file */
5360:
5361: iagemin= (int) agemin;
5362: iagemax= (int) agemax;
5363: /*pp=vector(1,nlstate);*/
1.251 brouard 5364: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5365: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5366: j1=0;
1.222 brouard 5367:
1.227 brouard 5368: /*j=cptcoveff;*/
5369: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5370:
1.288 brouard 5371: first=0;
1.227 brouard 5372: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5373: for (i=1; i<=nlstate; i++)
1.251 brouard 5374: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5375: prop[i][iage]=0.0;
5376: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5377: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5378: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5379:
5380: for (i=1; i<=imx; i++) { /* Each individual */
5381: bool=1;
5382: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5383: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5384: m=mw[mi][i];
5385: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5386: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5387: for (z1=1; z1<=cptcoveff; z1++){
5388: if( Fixed[Tmodelind[z1]]==1){
5389: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5390: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5391: bool=0;
5392: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5393: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5394: bool=0;
5395: }
5396: }
5397: if(bool==1){ /* Otherwise we skip that wave/person */
5398: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5399: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5400: if(m >=firstpass && m <=lastpass){
5401: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5402: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5403: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5404: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5405: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5406: printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
5407: exit(1);
5408: }
5409: if (s[m][i]>0 && s[m][i]<=nlstate) {
5410: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
5411: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5412: prop[s[m][i]][iagemax+3] += weight[i];
5413: } /* end valid statuses */
5414: } /* end selection of dates */
5415: } /* end selection of waves */
5416: } /* end bool */
5417: } /* end wave */
5418: } /* end individual */
5419: for(i=iagemin; i <= iagemax+3; i++){
5420: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5421: posprop += prop[jk][i];
5422: }
5423:
5424: for(jk=1; jk <=nlstate ; jk++){
5425: if( i <= iagemax){
5426: if(posprop>=1.e-5){
5427: probs[i][jk][j1]= prop[jk][i]/posprop;
5428: } else{
1.288 brouard 5429: if(!first){
5430: first=1;
1.266 brouard 5431: printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
5432: }else{
1.288 brouard 5433: fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
1.227 brouard 5434: }
5435: }
5436: }
5437: }/* end jk */
5438: }/* end i */
1.222 brouard 5439: /*} *//* end i1 */
1.227 brouard 5440: } /* end j1 */
1.222 brouard 5441:
1.227 brouard 5442: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5443: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5444: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5445: } /* End of prevalence */
1.126 brouard 5446:
5447: /************* Waves Concatenation ***************/
5448:
5449: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
5450: {
1.298 brouard 5451: /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
1.126 brouard 5452: Death is a valid wave (if date is known).
5453: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5454: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5455: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5456: */
1.126 brouard 5457:
1.224 brouard 5458: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5459: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5460: double sum=0., jmean=0.;*/
1.224 brouard 5461: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5462: int j, k=0,jk, ju, jl;
5463: double sum=0.;
5464: first=0;
1.214 brouard 5465: firstwo=0;
1.217 brouard 5466: firsthree=0;
1.218 brouard 5467: firstfour=0;
1.164 brouard 5468: jmin=100000;
1.126 brouard 5469: jmax=-1;
5470: jmean=0.;
1.224 brouard 5471:
5472: /* Treating live states */
1.214 brouard 5473: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5474: mi=0; /* First valid wave */
1.227 brouard 5475: mli=0; /* Last valid wave */
1.309 brouard 5476: m=firstpass; /* Loop on waves */
5477: while(s[m][i] <= nlstate){ /* a live state or unknown state */
1.227 brouard 5478: if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
5479: mli=m-1;/* mw[++mi][i]=m-1; */
5480: }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
1.309 brouard 5481: mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition */
1.227 brouard 5482: mli=m;
1.224 brouard 5483: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5484: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5485: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5486: }
1.309 brouard 5487: else{ /* m = lastpass, eventual special issue with warning */
1.224 brouard 5488: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5489: break;
1.224 brouard 5490: #else
1.317 brouard 5491: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
1.227 brouard 5492: if(firsthree == 0){
1.302 brouard 5493: printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
1.227 brouard 5494: firsthree=1;
1.317 brouard 5495: }else if(firsthree >=1 && firsthree < 10){
5496: fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
5497: firsthree++;
5498: }else if(firsthree == 10){
5499: printf("Information, too many Information flags: no more reported to log either\n");
5500: fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
5501: firsthree++;
5502: }else{
5503: firsthree++;
1.227 brouard 5504: }
1.309 brouard 5505: mw[++mi][i]=m; /* Valid transition with unknown status */
1.227 brouard 5506: mli=m;
5507: }
5508: if(s[m][i]==-2){ /* Vital status is really unknown */
5509: nbwarn++;
1.309 brouard 5510: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */
1.227 brouard 5511: printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
5512: fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
5513: }
5514: break;
5515: }
5516: break;
1.224 brouard 5517: #endif
1.227 brouard 5518: }/* End m >= lastpass */
1.126 brouard 5519: }/* end while */
1.224 brouard 5520:
1.227 brouard 5521: /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
1.216 brouard 5522: /* After last pass */
1.224 brouard 5523: /* Treating death states */
1.214 brouard 5524: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5525: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5526: /* } */
1.126 brouard 5527: mi++; /* Death is another wave */
5528: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5529: /* Only death is a correct wave */
1.126 brouard 5530: mw[mi][i]=m;
1.257 brouard 5531: } /* else not in a death state */
1.224 brouard 5532: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5533: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5534: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.309 brouard 5535: if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
1.227 brouard 5536: nbwarn++;
5537: if(firstfiv==0){
1.309 brouard 5538: printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227 brouard 5539: firstfiv=1;
5540: }else{
1.309 brouard 5541: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227 brouard 5542: }
1.309 brouard 5543: s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
5544: }else{ /* Month of Death occured afer last wave month, potential bias */
1.227 brouard 5545: nberr++;
5546: if(firstwo==0){
1.309 brouard 5547: printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227 brouard 5548: firstwo=1;
5549: }
1.309 brouard 5550: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227 brouard 5551: }
1.257 brouard 5552: }else{ /* if date of interview is unknown */
1.227 brouard 5553: /* death is known but not confirmed by death status at any wave */
5554: if(firstfour==0){
1.309 brouard 5555: printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.227 brouard 5556: firstfour=1;
5557: }
1.309 brouard 5558: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
1.214 brouard 5559: }
1.224 brouard 5560: } /* end if date of death is known */
5561: #endif
1.309 brouard 5562: wav[i]=mi; /* mi should be the last effective wave (or mli), */
5563: /* wav[i]=mw[mi][i]; */
1.126 brouard 5564: if(mi==0){
5565: nbwarn++;
5566: if(first==0){
1.227 brouard 5567: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5568: first=1;
1.126 brouard 5569: }
5570: if(first==1){
1.227 brouard 5571: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5572: }
5573: } /* end mi==0 */
5574: } /* End individuals */
1.214 brouard 5575: /* wav and mw are no more changed */
1.223 brouard 5576:
1.317 brouard 5577: printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
5578: fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);
5579:
5580:
1.126 brouard 5581: for(i=1; i<=imx; i++){
5582: for(mi=1; mi<wav[i];mi++){
5583: if (stepm <=0)
1.227 brouard 5584: dh[mi][i]=1;
1.126 brouard 5585: else{
1.260 brouard 5586: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5587: if (agedc[i] < 2*AGESUP) {
5588: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5589: if(j==0) j=1; /* Survives at least one month after exam */
5590: else if(j<0){
5591: nberr++;
5592: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
5593: j=1; /* Temporary Dangerous patch */
5594: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
5595: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
5596: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
5597: }
5598: k=k+1;
5599: if (j >= jmax){
5600: jmax=j;
5601: ijmax=i;
5602: }
5603: if (j <= jmin){
5604: jmin=j;
5605: ijmin=i;
5606: }
5607: sum=sum+j;
5608: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5609: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5610: }
5611: }
5612: else{
5613: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5614: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
1.223 brouard 5615:
1.227 brouard 5616: k=k+1;
5617: if (j >= jmax) {
5618: jmax=j;
5619: ijmax=i;
5620: }
5621: else if (j <= jmin){
5622: jmin=j;
5623: ijmin=i;
5624: }
5625: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5626: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
5627: if(j<0){
5628: nberr++;
5629: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
5630: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
5631: }
5632: sum=sum+j;
5633: }
5634: jk= j/stepm;
5635: jl= j -jk*stepm;
5636: ju= j -(jk+1)*stepm;
5637: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5638: if(jl==0){
5639: dh[mi][i]=jk;
5640: bh[mi][i]=0;
5641: }else{ /* We want a negative bias in order to only have interpolation ie
5642: * to avoid the price of an extra matrix product in likelihood */
5643: dh[mi][i]=jk+1;
5644: bh[mi][i]=ju;
5645: }
5646: }else{
5647: if(jl <= -ju){
5648: dh[mi][i]=jk;
5649: bh[mi][i]=jl; /* bias is positive if real duration
5650: * is higher than the multiple of stepm and negative otherwise.
5651: */
5652: }
5653: else{
5654: dh[mi][i]=jk+1;
5655: bh[mi][i]=ju;
5656: }
5657: if(dh[mi][i]==0){
5658: dh[mi][i]=1; /* At least one step */
5659: bh[mi][i]=ju; /* At least one step */
5660: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
5661: }
5662: } /* end if mle */
1.126 brouard 5663: }
5664: } /* end wave */
5665: }
5666: jmean=sum/k;
5667: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141 brouard 5668: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.227 brouard 5669: }
1.126 brouard 5670:
5671: /*********** Tricode ****************************/
1.220 brouard 5672: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5673: {
5674: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5675: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5676: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5677: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5678: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5679: */
1.130 brouard 5680:
1.242 brouard 5681: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5682: int modmaxcovj=0; /* Modality max of covariates j */
5683: int cptcode=0; /* Modality max of covariates j */
5684: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5685:
5686:
1.242 brouard 5687: /* cptcoveff=0; */
5688: /* *cptcov=0; */
1.126 brouard 5689:
1.242 brouard 5690: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5691: for (k=1; k <= maxncov; k++)
5692: for(j=1; j<=2; j++)
5693: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5694:
1.242 brouard 5695: /* Loop on covariates without age and products and no quantitative variable */
5696: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5697: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5698: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5699: switch(Fixed[k]) {
5700: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.311 brouard 5701: modmaxcovj=0;
5702: modmincovj=0;
1.242 brouard 5703: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
5704: ij=(int)(covar[Tvar[k]][i]);
5705: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5706: * If product of Vn*Vm, still boolean *:
5707: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5708: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5709: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5710: modality of the nth covariate of individual i. */
5711: if (ij > modmaxcovj)
5712: modmaxcovj=ij;
5713: else if (ij < modmincovj)
5714: modmincovj=ij;
1.287 brouard 5715: if (ij <0 || ij >1 ){
1.311 brouard 5716: printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
5717: fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
5718: fflush(ficlog);
5719: exit(1);
1.287 brouard 5720: }
5721: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5722: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5723: exit(1);
5724: }else
5725: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5726: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5727: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5728: /* getting the maximum value of the modality of the covariate
5729: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5730: female ies 1, then modmaxcovj=1.
5731: */
5732: } /* end for loop on individuals i */
5733: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5734: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5735: cptcode=modmaxcovj;
5736: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5737: /*for (i=0; i<=cptcode; i++) {*/
5738: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5739: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5740: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5741: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5742: if( j != -1){
5743: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5744: covariate for which somebody answered excluding
5745: undefined. Usually 2: 0 and 1. */
5746: }
5747: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5748: covariate for which somebody answered including
5749: undefined. Usually 3: -1, 0 and 1. */
5750: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5751: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5752: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5753:
1.242 brouard 5754: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5755: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5756: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5757: /* modmincovj=3; modmaxcovj = 7; */
5758: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5759: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5760: /* defining two dummy variables: variables V1_1 and V1_2.*/
5761: /* nbcode[Tvar[j]][ij]=k; */
5762: /* nbcode[Tvar[j]][1]=0; */
5763: /* nbcode[Tvar[j]][2]=1; */
5764: /* nbcode[Tvar[j]][3]=2; */
5765: /* To be continued (not working yet). */
5766: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5767:
5768: /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
5769: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5770: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5771: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5772: /*, could be restored in the future */
5773: for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
1.242 brouard 5774: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5775: break;
5776: }
5777: ij++;
1.287 brouard 5778: nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
1.242 brouard 5779: cptcode = ij; /* New max modality for covar j */
5780: } /* end of loop on modality i=-1 to 1 or more */
5781: break;
5782: case 1: /* Testing on varying covariate, could be simple and
5783: * should look at waves or product of fixed *
5784: * varying. No time to test -1, assuming 0 and 1 only */
5785: ij=0;
5786: for(i=0; i<=1;i++){
5787: nbcode[Tvar[k]][++ij]=i;
5788: }
5789: break;
5790: default:
5791: break;
5792: } /* end switch */
5793: } /* end dummy test */
1.311 brouard 5794: if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5795: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
5796: if(isnan(covar[Tvar[k]][i])){
5797: printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
5798: fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
5799: fflush(ficlog);
5800: exit(1);
5801: }
5802: }
5803: }
1.287 brouard 5804: } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
1.242 brouard 5805:
5806: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5807: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5808: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5809: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5810: ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */
5811: Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
5812: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5813: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5814:
5815: ij=0;
5816: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5817: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5818: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5819: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5820: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5821: /* If product not in single variable we don't print results */
5822: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5823: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5824: Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
5825: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5826: TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
5827: if(Fixed[k]!=0)
5828: anyvaryingduminmodel=1;
5829: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5830: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5831: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5832: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5833: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5834: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5835: }
5836: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5837: /* ij--; */
5838: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5839: *cptcov=ij; /*Number of total real effective covariates: effective
5840: * because they can be excluded from the model and real
5841: * if in the model but excluded because missing values, but how to get k from ij?*/
5842: for(j=ij+1; j<= cptcovt; j++){
5843: Tvaraff[j]=0;
5844: Tmodelind[j]=0;
5845: }
5846: for(j=ntveff+1; j<= cptcovt; j++){
5847: TmodelInvind[j]=0;
5848: }
5849: /* To be sorted */
5850: ;
5851: }
1.126 brouard 5852:
1.145 brouard 5853:
1.126 brouard 5854: /*********** Health Expectancies ****************/
5855:
1.235 brouard 5856: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
1.126 brouard 5857:
5858: {
5859: /* Health expectancies, no variances */
1.164 brouard 5860: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5861: int nhstepma, nstepma; /* Decreasing with age */
5862: double age, agelim, hf;
5863: double ***p3mat;
5864: double eip;
5865:
1.238 brouard 5866: /* pstamp(ficreseij); */
1.126 brouard 5867: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5868: fprintf(ficreseij,"# Age");
5869: for(i=1; i<=nlstate;i++){
5870: for(j=1; j<=nlstate;j++){
5871: fprintf(ficreseij," e%1d%1d ",i,j);
5872: }
5873: fprintf(ficreseij," e%1d. ",i);
5874: }
5875: fprintf(ficreseij,"\n");
5876:
5877:
5878: if(estepm < stepm){
5879: printf ("Problem %d lower than %d\n",estepm, stepm);
5880: }
5881: else hstepm=estepm;
5882: /* We compute the life expectancy from trapezoids spaced every estepm months
5883: * This is mainly to measure the difference between two models: for example
5884: * if stepm=24 months pijx are given only every 2 years and by summing them
5885: * we are calculating an estimate of the Life Expectancy assuming a linear
5886: * progression in between and thus overestimating or underestimating according
5887: * to the curvature of the survival function. If, for the same date, we
5888: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5889: * to compare the new estimate of Life expectancy with the same linear
5890: * hypothesis. A more precise result, taking into account a more precise
5891: * curvature will be obtained if estepm is as small as stepm. */
5892:
5893: /* For example we decided to compute the life expectancy with the smallest unit */
5894: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5895: nhstepm is the number of hstepm from age to agelim
5896: nstepm is the number of stepm from age to agelin.
1.270 brouard 5897: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5898: and note for a fixed period like estepm months */
5899: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5900: survival function given by stepm (the optimization length). Unfortunately it
5901: means that if the survival funtion is printed only each two years of age and if
5902: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5903: results. So we changed our mind and took the option of the best precision.
5904: */
5905: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5906:
5907: agelim=AGESUP;
5908: /* If stepm=6 months */
5909: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5910: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5911:
5912: /* nhstepm age range expressed in number of stepm */
5913: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5914: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5915: /* if (stepm >= YEARM) hstepm=1;*/
5916: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5917: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5918:
5919: for (age=bage; age<=fage; age ++){
5920: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5921: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5922: /* if (stepm >= YEARM) hstepm=1;*/
5923: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5924:
5925: /* If stepm=6 months */
5926: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5927: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5928:
1.235 brouard 5929: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5930:
5931: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5932:
5933: printf("%d|",(int)age);fflush(stdout);
5934: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5935:
5936: /* Computing expectancies */
5937: for(i=1; i<=nlstate;i++)
5938: for(j=1; j<=nlstate;j++)
5939: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5940: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5941:
5942: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
5943:
5944: }
5945:
5946: fprintf(ficreseij,"%3.0f",age );
5947: for(i=1; i<=nlstate;i++){
5948: eip=0;
5949: for(j=1; j<=nlstate;j++){
5950: eip +=eij[i][j][(int)age];
5951: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5952: }
5953: fprintf(ficreseij,"%9.4f", eip );
5954: }
5955: fprintf(ficreseij,"\n");
5956:
5957: }
5958: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5959: printf("\n");
5960: fprintf(ficlog,"\n");
5961:
5962: }
5963:
1.235 brouard 5964: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
1.126 brouard 5965:
5966: {
5967: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5968: to initial status i, ei. .
1.126 brouard 5969: */
5970: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5971: int nhstepma, nstepma; /* Decreasing with age */
5972: double age, agelim, hf;
5973: double ***p3matp, ***p3matm, ***varhe;
5974: double **dnewm,**doldm;
5975: double *xp, *xm;
5976: double **gp, **gm;
5977: double ***gradg, ***trgradg;
5978: int theta;
5979:
5980: double eip, vip;
5981:
5982: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5983: xp=vector(1,npar);
5984: xm=vector(1,npar);
5985: dnewm=matrix(1,nlstate*nlstate,1,npar);
5986: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5987:
5988: pstamp(ficresstdeij);
5989: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5990: fprintf(ficresstdeij,"# Age");
5991: for(i=1; i<=nlstate;i++){
5992: for(j=1; j<=nlstate;j++)
5993: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5994: fprintf(ficresstdeij," e%1d. ",i);
5995: }
5996: fprintf(ficresstdeij,"\n");
5997:
5998: pstamp(ficrescveij);
5999: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
6000: fprintf(ficrescveij,"# Age");
6001: for(i=1; i<=nlstate;i++)
6002: for(j=1; j<=nlstate;j++){
6003: cptj= (j-1)*nlstate+i;
6004: for(i2=1; i2<=nlstate;i2++)
6005: for(j2=1; j2<=nlstate;j2++){
6006: cptj2= (j2-1)*nlstate+i2;
6007: if(cptj2 <= cptj)
6008: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
6009: }
6010: }
6011: fprintf(ficrescveij,"\n");
6012:
6013: if(estepm < stepm){
6014: printf ("Problem %d lower than %d\n",estepm, stepm);
6015: }
6016: else hstepm=estepm;
6017: /* We compute the life expectancy from trapezoids spaced every estepm months
6018: * This is mainly to measure the difference between two models: for example
6019: * if stepm=24 months pijx are given only every 2 years and by summing them
6020: * we are calculating an estimate of the Life Expectancy assuming a linear
6021: * progression in between and thus overestimating or underestimating according
6022: * to the curvature of the survival function. If, for the same date, we
6023: * estimate the model with stepm=1 month, we can keep estepm to 24 months
6024: * to compare the new estimate of Life expectancy with the same linear
6025: * hypothesis. A more precise result, taking into account a more precise
6026: * curvature will be obtained if estepm is as small as stepm. */
6027:
6028: /* For example we decided to compute the life expectancy with the smallest unit */
6029: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6030: nhstepm is the number of hstepm from age to agelim
6031: nstepm is the number of stepm from age to agelin.
6032: Look at hpijx to understand the reason of that which relies in memory size
6033: and note for a fixed period like estepm months */
6034: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
6035: survival function given by stepm (the optimization length). Unfortunately it
6036: means that if the survival funtion is printed only each two years of age and if
6037: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6038: results. So we changed our mind and took the option of the best precision.
6039: */
6040: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6041:
6042: /* If stepm=6 months */
6043: /* nhstepm age range expressed in number of stepm */
6044: agelim=AGESUP;
6045: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
6046: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
6047: /* if (stepm >= YEARM) hstepm=1;*/
6048: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6049:
6050: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6051: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6052: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
6053: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
6054: gp=matrix(0,nhstepm,1,nlstate*nlstate);
6055: gm=matrix(0,nhstepm,1,nlstate*nlstate);
6056:
6057: for (age=bage; age<=fage; age ++){
6058: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
6059: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
6060: /* if (stepm >= YEARM) hstepm=1;*/
6061: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 6062:
1.126 brouard 6063: /* If stepm=6 months */
6064: /* Computed by stepm unit matrices, product of hstepma matrices, stored
6065: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
6066:
6067: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 6068:
1.126 brouard 6069: /* Computing Variances of health expectancies */
6070: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
6071: decrease memory allocation */
6072: for(theta=1; theta <=npar; theta++){
6073: for(i=1; i<=npar; i++){
1.222 brouard 6074: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6075: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 6076: }
1.235 brouard 6077: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
6078: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 6079:
1.126 brouard 6080: for(j=1; j<= nlstate; j++){
1.222 brouard 6081: for(i=1; i<=nlstate; i++){
6082: for(h=0; h<=nhstepm-1; h++){
6083: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
6084: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
6085: }
6086: }
1.126 brouard 6087: }
1.218 brouard 6088:
1.126 brouard 6089: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 6090: for(h=0; h<=nhstepm-1; h++){
6091: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
6092: }
1.126 brouard 6093: }/* End theta */
6094:
6095:
6096: for(h=0; h<=nhstepm-1; h++)
6097: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 6098: for(theta=1; theta <=npar; theta++)
6099: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 6100:
1.218 brouard 6101:
1.222 brouard 6102: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 6103: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 6104: varhe[ij][ji][(int)age] =0.;
1.218 brouard 6105:
1.222 brouard 6106: printf("%d|",(int)age);fflush(stdout);
6107: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
6108: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 6109: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 6110: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
6111: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
6112: for(ij=1;ij<=nlstate*nlstate;ij++)
6113: for(ji=1;ji<=nlstate*nlstate;ji++)
6114: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 6115: }
6116: }
1.319 ! brouard 6117: if((int)age ==50){
! 6118: printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]);
! 6119: }
1.126 brouard 6120: /* Computing expectancies */
1.235 brouard 6121: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 6122: for(i=1; i<=nlstate;i++)
6123: for(j=1; j<=nlstate;j++)
1.222 brouard 6124: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
6125: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 6126:
1.222 brouard 6127: /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
1.218 brouard 6128:
1.222 brouard 6129: }
1.269 brouard 6130:
6131: /* Standard deviation of expectancies ij */
1.126 brouard 6132: fprintf(ficresstdeij,"%3.0f",age );
6133: for(i=1; i<=nlstate;i++){
6134: eip=0.;
6135: vip=0.;
6136: for(j=1; j<=nlstate;j++){
1.222 brouard 6137: eip += eij[i][j][(int)age];
6138: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
6139: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
6140: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
1.126 brouard 6141: }
6142: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
6143: }
6144: fprintf(ficresstdeij,"\n");
1.218 brouard 6145:
1.269 brouard 6146: /* Variance of expectancies ij */
1.126 brouard 6147: fprintf(ficrescveij,"%3.0f",age );
6148: for(i=1; i<=nlstate;i++)
6149: for(j=1; j<=nlstate;j++){
1.222 brouard 6150: cptj= (j-1)*nlstate+i;
6151: for(i2=1; i2<=nlstate;i2++)
6152: for(j2=1; j2<=nlstate;j2++){
6153: cptj2= (j2-1)*nlstate+i2;
6154: if(cptj2 <= cptj)
6155: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
6156: }
1.126 brouard 6157: }
6158: fprintf(ficrescveij,"\n");
1.218 brouard 6159:
1.126 brouard 6160: }
6161: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
6162: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
6163: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
6164: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
6165: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6166: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6167: printf("\n");
6168: fprintf(ficlog,"\n");
1.218 brouard 6169:
1.126 brouard 6170: free_vector(xm,1,npar);
6171: free_vector(xp,1,npar);
6172: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
6173: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
6174: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
6175: }
1.218 brouard 6176:
1.126 brouard 6177: /************ Variance ******************/
1.235 brouard 6178: void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
1.218 brouard 6179: {
1.279 brouard 6180: /** Variance of health expectancies
6181: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
6182: * double **newm;
6183: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
6184: */
1.218 brouard 6185:
6186: /* int movingaverage(); */
6187: double **dnewm,**doldm;
6188: double **dnewmp,**doldmp;
6189: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 6190: int first=0;
1.218 brouard 6191: int k;
6192: double *xp;
1.279 brouard 6193: double **gp, **gm; /**< for var eij */
6194: double ***gradg, ***trgradg; /**< for var eij */
6195: double **gradgp, **trgradgp; /**< for var p point j */
6196: double *gpp, *gmp; /**< for var p point j */
6197: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 6198: double ***p3mat;
6199: double age,agelim, hf;
6200: /* double ***mobaverage; */
6201: int theta;
6202: char digit[4];
6203: char digitp[25];
6204:
6205: char fileresprobmorprev[FILENAMELENGTH];
6206:
6207: if(popbased==1){
6208: if(mobilav!=0)
6209: strcpy(digitp,"-POPULBASED-MOBILAV_");
6210: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
6211: }
6212: else
6213: strcpy(digitp,"-STABLBASED_");
1.126 brouard 6214:
1.218 brouard 6215: /* if (mobilav!=0) { */
6216: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6217: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
6218: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6219: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6220: /* } */
6221: /* } */
6222:
6223: strcpy(fileresprobmorprev,"PRMORPREV-");
6224: sprintf(digit,"%-d",ij);
6225: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
6226: strcat(fileresprobmorprev,digit); /* Tvar to be done */
6227: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
6228: strcat(fileresprobmorprev,fileresu);
6229: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
6230: printf("Problem with resultfile: %s\n", fileresprobmorprev);
6231: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
6232: }
6233: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6234: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6235: pstamp(ficresprobmorprev);
6236: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
1.238 brouard 6237: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
6238: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
6239: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
6240: }
6241: for(j=1;j<=cptcoveff;j++)
6242: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
6243: fprintf(ficresprobmorprev,"\n");
6244:
1.218 brouard 6245: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6246: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6247: fprintf(ficresprobmorprev," p.%-d SE",j);
6248: for(i=1; i<=nlstate;i++)
6249: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6250: }
6251: fprintf(ficresprobmorprev,"\n");
6252:
6253: fprintf(ficgp,"\n# Routine varevsij");
6254: fprintf(ficgp,"\nunset title \n");
6255: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6256: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
6257: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6258:
1.218 brouard 6259: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6260: pstamp(ficresvij);
6261: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6262: if(popbased==1)
6263: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
6264: else
6265: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6266: fprintf(ficresvij,"# Age");
6267: for(i=1; i<=nlstate;i++)
6268: for(j=1; j<=nlstate;j++)
6269: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6270: fprintf(ficresvij,"\n");
6271:
6272: xp=vector(1,npar);
6273: dnewm=matrix(1,nlstate,1,npar);
6274: doldm=matrix(1,nlstate,1,nlstate);
6275: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6276: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6277:
6278: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6279: gpp=vector(nlstate+1,nlstate+ndeath);
6280: gmp=vector(nlstate+1,nlstate+ndeath);
6281: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6282:
1.218 brouard 6283: if(estepm < stepm){
6284: printf ("Problem %d lower than %d\n",estepm, stepm);
6285: }
6286: else hstepm=estepm;
6287: /* For example we decided to compute the life expectancy with the smallest unit */
6288: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6289: nhstepm is the number of hstepm from age to agelim
6290: nstepm is the number of stepm from age to agelim.
6291: Look at function hpijx to understand why because of memory size limitations,
6292: we decided (b) to get a life expectancy respecting the most precise curvature of the
6293: survival function given by stepm (the optimization length). Unfortunately it
6294: means that if the survival funtion is printed every two years of age and if
6295: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6296: results. So we changed our mind and took the option of the best precision.
6297: */
6298: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6299: agelim = AGESUP;
6300: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6301: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6302: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6303: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6304: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6305: gp=matrix(0,nhstepm,1,nlstate);
6306: gm=matrix(0,nhstepm,1,nlstate);
6307:
6308:
6309: for(theta=1; theta <=npar; theta++){
6310: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6311: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6312: }
1.279 brouard 6313: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6314: * returns into prlim .
1.288 brouard 6315: */
1.242 brouard 6316: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6317:
6318: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6319: if (popbased==1) {
6320: if(mobilav ==0){
6321: for(i=1; i<=nlstate;i++)
6322: prlim[i][i]=probs[(int)age][i][ij];
6323: }else{ /* mobilav */
6324: for(i=1; i<=nlstate;i++)
6325: prlim[i][i]=mobaverage[(int)age][i][ij];
6326: }
6327: }
1.295 brouard 6328: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6329: */
6330: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
1.292 brouard 6331: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
1.279 brouard 6332: * at horizon h in state j including mortality.
6333: */
1.218 brouard 6334: for(j=1; j<= nlstate; j++){
6335: for(h=0; h<=nhstepm; h++){
6336: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6337: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6338: }
6339: }
1.279 brouard 6340: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6341: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6342: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6343: */
6344: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6345: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6346: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6347: }
6348:
6349: /* Again with minus shift */
1.218 brouard 6350:
6351: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6352: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6353:
1.242 brouard 6354: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6355:
6356: if (popbased==1) {
6357: if(mobilav ==0){
6358: for(i=1; i<=nlstate;i++)
6359: prlim[i][i]=probs[(int)age][i][ij];
6360: }else{ /* mobilav */
6361: for(i=1; i<=nlstate;i++)
6362: prlim[i][i]=mobaverage[(int)age][i][ij];
6363: }
6364: }
6365:
1.235 brouard 6366: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6367:
6368: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6369: for(h=0; h<=nhstepm; h++){
6370: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6371: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6372: }
6373: }
6374: /* This for computing probability of death (h=1 means
6375: computed over hstepm matrices product = hstepm*stepm months)
6376: as a weighted average of prlim.
6377: */
6378: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6379: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6380: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6381: }
1.279 brouard 6382: /* end shifting computations */
6383:
6384: /**< Computing gradient matrix at horizon h
6385: */
1.218 brouard 6386: for(j=1; j<= nlstate; j++) /* vareij */
6387: for(h=0; h<=nhstepm; h++){
6388: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6389: }
1.279 brouard 6390: /**< Gradient of overall mortality p.3 (or p.j)
6391: */
6392: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6393: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6394: }
6395:
6396: } /* End theta */
1.279 brouard 6397:
6398: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6399: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6400:
6401: for(h=0; h<=nhstepm; h++) /* veij */
6402: for(j=1; j<=nlstate;j++)
6403: for(theta=1; theta <=npar; theta++)
6404: trgradg[h][j][theta]=gradg[h][theta][j];
6405:
6406: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6407: for(theta=1; theta <=npar; theta++)
6408: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6409: /**< as well as its transposed matrix
6410: */
1.218 brouard 6411:
6412: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6413: for(i=1;i<=nlstate;i++)
6414: for(j=1;j<=nlstate;j++)
6415: vareij[i][j][(int)age] =0.;
1.279 brouard 6416:
6417: /* Computing trgradg by matcov by gradg at age and summing over h
6418: * and k (nhstepm) formula 15 of article
6419: * Lievre-Brouard-Heathcote
6420: */
6421:
1.218 brouard 6422: for(h=0;h<=nhstepm;h++){
6423: for(k=0;k<=nhstepm;k++){
6424: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6425: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6426: for(i=1;i<=nlstate;i++)
6427: for(j=1;j<=nlstate;j++)
6428: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6429: }
6430: }
6431:
1.279 brouard 6432: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6433: * p.j overall mortality formula 49 but computed directly because
6434: * we compute the grad (wix pijx) instead of grad (pijx),even if
6435: * wix is independent of theta.
6436: */
1.218 brouard 6437: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6438: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6439: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6440: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6441: varppt[j][i]=doldmp[j][i];
6442: /* end ppptj */
6443: /* x centered again */
6444:
1.242 brouard 6445: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6446:
6447: if (popbased==1) {
6448: if(mobilav ==0){
6449: for(i=1; i<=nlstate;i++)
6450: prlim[i][i]=probs[(int)age][i][ij];
6451: }else{ /* mobilav */
6452: for(i=1; i<=nlstate;i++)
6453: prlim[i][i]=mobaverage[(int)age][i][ij];
6454: }
6455: }
6456:
6457: /* This for computing probability of death (h=1 means
6458: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6459: as a weighted average of prlim.
6460: */
1.235 brouard 6461: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6462: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6463: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6464: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6465: }
6466: /* end probability of death */
6467:
6468: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6469: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6470: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6471: for(i=1; i<=nlstate;i++){
6472: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6473: }
6474: }
6475: fprintf(ficresprobmorprev,"\n");
6476:
6477: fprintf(ficresvij,"%.0f ",age );
6478: for(i=1; i<=nlstate;i++)
6479: for(j=1; j<=nlstate;j++){
6480: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6481: }
6482: fprintf(ficresvij,"\n");
6483: free_matrix(gp,0,nhstepm,1,nlstate);
6484: free_matrix(gm,0,nhstepm,1,nlstate);
6485: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6486: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6487: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6488: } /* End age */
6489: free_vector(gpp,nlstate+1,nlstate+ndeath);
6490: free_vector(gmp,nlstate+1,nlstate+ndeath);
6491: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6492: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6493: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6494: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6495: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6496: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6497: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6498: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6499: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6500: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6501: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6502: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6503: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6504: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6505: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6506: /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.svg\"> <br>\n", stepm,YEARM,digitp,digit);
1.126 brouard 6507: */
1.218 brouard 6508: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6509: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6510:
1.218 brouard 6511: free_vector(xp,1,npar);
6512: free_matrix(doldm,1,nlstate,1,nlstate);
6513: free_matrix(dnewm,1,nlstate,1,npar);
6514: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6515: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6516: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6517: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6518: fclose(ficresprobmorprev);
6519: fflush(ficgp);
6520: fflush(fichtm);
6521: } /* end varevsij */
1.126 brouard 6522:
6523: /************ Variance of prevlim ******************/
1.269 brouard 6524: void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
1.126 brouard 6525: {
1.205 brouard 6526: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6527: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6528:
1.268 brouard 6529: double **dnewmpar,**doldm;
1.126 brouard 6530: int i, j, nhstepm, hstepm;
6531: double *xp;
6532: double *gp, *gm;
6533: double **gradg, **trgradg;
1.208 brouard 6534: double **mgm, **mgp;
1.126 brouard 6535: double age,agelim;
6536: int theta;
6537:
6538: pstamp(ficresvpl);
1.288 brouard 6539: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6540: fprintf(ficresvpl,"# Age ");
6541: if(nresult >=1)
6542: fprintf(ficresvpl," Result# ");
1.126 brouard 6543: for(i=1; i<=nlstate;i++)
6544: fprintf(ficresvpl," %1d-%1d",i,i);
6545: fprintf(ficresvpl,"\n");
6546:
6547: xp=vector(1,npar);
1.268 brouard 6548: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6549: doldm=matrix(1,nlstate,1,nlstate);
6550:
6551: hstepm=1*YEARM; /* Every year of age */
6552: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6553: agelim = AGESUP;
6554: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6555: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6556: if (stepm >= YEARM) hstepm=1;
6557: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6558: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6559: mgp=matrix(1,npar,1,nlstate);
6560: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6561: gp=vector(1,nlstate);
6562: gm=vector(1,nlstate);
6563:
6564: for(theta=1; theta <=npar; theta++){
6565: for(i=1; i<=npar; i++){ /* Computes gradient */
6566: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6567: }
1.288 brouard 6568: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6569: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6570: /* else */
6571: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6572: for(i=1;i<=nlstate;i++){
1.126 brouard 6573: gp[i] = prlim[i][i];
1.208 brouard 6574: mgp[theta][i] = prlim[i][i];
6575: }
1.126 brouard 6576: for(i=1; i<=npar; i++) /* Computes gradient */
6577: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6578: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6579: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6580: /* else */
6581: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6582: for(i=1;i<=nlstate;i++){
1.126 brouard 6583: gm[i] = prlim[i][i];
1.208 brouard 6584: mgm[theta][i] = prlim[i][i];
6585: }
1.126 brouard 6586: for(i=1;i<=nlstate;i++)
6587: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6588: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6589: } /* End theta */
6590:
6591: trgradg =matrix(1,nlstate,1,npar);
6592:
6593: for(j=1; j<=nlstate;j++)
6594: for(theta=1; theta <=npar; theta++)
6595: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6596: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6597: /* printf("\nmgm mgp %d ",(int)age); */
6598: /* for(j=1; j<=nlstate;j++){ */
6599: /* printf(" %d ",j); */
6600: /* for(theta=1; theta <=npar; theta++) */
6601: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6602: /* printf("\n "); */
6603: /* } */
6604: /* } */
6605: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6606: /* printf("\n gradg %d ",(int)age); */
6607: /* for(j=1; j<=nlstate;j++){ */
6608: /* printf("%d ",j); */
6609: /* for(theta=1; theta <=npar; theta++) */
6610: /* printf("%d %lf ",theta,gradg[theta][j]); */
6611: /* printf("\n "); */
6612: /* } */
6613: /* } */
1.126 brouard 6614:
6615: for(i=1;i<=nlstate;i++)
6616: varpl[i][(int)age] =0.;
1.209 brouard 6617: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6618: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6619: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6620: }else{
1.268 brouard 6621: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6622: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6623: }
1.126 brouard 6624: for(i=1;i<=nlstate;i++)
6625: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6626:
6627: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6628: if(nresult >=1)
6629: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6630: for(i=1; i<=nlstate;i++){
1.126 brouard 6631: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6632: /* for(j=1;j<=nlstate;j++) */
6633: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6634: }
1.126 brouard 6635: fprintf(ficresvpl,"\n");
6636: free_vector(gp,1,nlstate);
6637: free_vector(gm,1,nlstate);
1.208 brouard 6638: free_matrix(mgm,1,npar,1,nlstate);
6639: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6640: free_matrix(gradg,1,npar,1,nlstate);
6641: free_matrix(trgradg,1,nlstate,1,npar);
6642: } /* End age */
6643:
6644: free_vector(xp,1,npar);
6645: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6646: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6647:
6648: }
6649:
6650:
6651: /************ Variance of backprevalence limit ******************/
1.269 brouard 6652: void varbrevlim(char fileresvbl[], FILE *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
1.268 brouard 6653: {
6654: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6655: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6656:
6657: double **dnewmpar,**doldm;
6658: int i, j, nhstepm, hstepm;
6659: double *xp;
6660: double *gp, *gm;
6661: double **gradg, **trgradg;
6662: double **mgm, **mgp;
6663: double age,agelim;
6664: int theta;
6665:
6666: pstamp(ficresvbl);
6667: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6668: fprintf(ficresvbl,"# Age ");
6669: if(nresult >=1)
6670: fprintf(ficresvbl," Result# ");
6671: for(i=1; i<=nlstate;i++)
6672: fprintf(ficresvbl," %1d-%1d",i,i);
6673: fprintf(ficresvbl,"\n");
6674:
6675: xp=vector(1,npar);
6676: dnewmpar=matrix(1,nlstate,1,npar);
6677: doldm=matrix(1,nlstate,1,nlstate);
6678:
6679: hstepm=1*YEARM; /* Every year of age */
6680: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6681: agelim = AGEINF;
6682: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6683: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6684: if (stepm >= YEARM) hstepm=1;
6685: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6686: gradg=matrix(1,npar,1,nlstate);
6687: mgp=matrix(1,npar,1,nlstate);
6688: mgm=matrix(1,npar,1,nlstate);
6689: gp=vector(1,nlstate);
6690: gm=vector(1,nlstate);
6691:
6692: for(theta=1; theta <=npar; theta++){
6693: for(i=1; i<=npar; i++){ /* Computes gradient */
6694: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6695: }
6696: if(mobilavproj > 0 )
6697: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6698: else
6699: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6700: for(i=1;i<=nlstate;i++){
6701: gp[i] = bprlim[i][i];
6702: mgp[theta][i] = bprlim[i][i];
6703: }
6704: for(i=1; i<=npar; i++) /* Computes gradient */
6705: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6706: if(mobilavproj > 0 )
6707: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6708: else
6709: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6710: for(i=1;i<=nlstate;i++){
6711: gm[i] = bprlim[i][i];
6712: mgm[theta][i] = bprlim[i][i];
6713: }
6714: for(i=1;i<=nlstate;i++)
6715: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6716: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6717: } /* End theta */
6718:
6719: trgradg =matrix(1,nlstate,1,npar);
6720:
6721: for(j=1; j<=nlstate;j++)
6722: for(theta=1; theta <=npar; theta++)
6723: trgradg[j][theta]=gradg[theta][j];
6724: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6725: /* printf("\nmgm mgp %d ",(int)age); */
6726: /* for(j=1; j<=nlstate;j++){ */
6727: /* printf(" %d ",j); */
6728: /* for(theta=1; theta <=npar; theta++) */
6729: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6730: /* printf("\n "); */
6731: /* } */
6732: /* } */
6733: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6734: /* printf("\n gradg %d ",(int)age); */
6735: /* for(j=1; j<=nlstate;j++){ */
6736: /* printf("%d ",j); */
6737: /* for(theta=1; theta <=npar; theta++) */
6738: /* printf("%d %lf ",theta,gradg[theta][j]); */
6739: /* printf("\n "); */
6740: /* } */
6741: /* } */
6742:
6743: for(i=1;i<=nlstate;i++)
6744: varbpl[i][(int)age] =0.;
6745: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6746: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6747: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6748: }else{
6749: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6750: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6751: }
6752: for(i=1;i<=nlstate;i++)
6753: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6754:
6755: fprintf(ficresvbl,"%.0f ",age );
6756: if(nresult >=1)
6757: fprintf(ficresvbl,"%d ",nres );
6758: for(i=1; i<=nlstate;i++)
6759: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6760: fprintf(ficresvbl,"\n");
6761: free_vector(gp,1,nlstate);
6762: free_vector(gm,1,nlstate);
6763: free_matrix(mgm,1,npar,1,nlstate);
6764: free_matrix(mgp,1,npar,1,nlstate);
6765: free_matrix(gradg,1,npar,1,nlstate);
6766: free_matrix(trgradg,1,nlstate,1,npar);
6767: } /* End age */
6768:
6769: free_vector(xp,1,npar);
6770: free_matrix(doldm,1,nlstate,1,npar);
6771: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6772:
6773: }
6774:
6775: /************ Variance of one-step probabilities ******************/
6776: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
1.222 brouard 6777: {
6778: int i, j=0, k1, l1, tj;
6779: int k2, l2, j1, z1;
6780: int k=0, l;
6781: int first=1, first1, first2;
6782: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6783: double **dnewm,**doldm;
6784: double *xp;
6785: double *gp, *gm;
6786: double **gradg, **trgradg;
6787: double **mu;
6788: double age, cov[NCOVMAX+1];
6789: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6790: int theta;
6791: char fileresprob[FILENAMELENGTH];
6792: char fileresprobcov[FILENAMELENGTH];
6793: char fileresprobcor[FILENAMELENGTH];
6794: double ***varpij;
6795:
6796: strcpy(fileresprob,"PROB_");
6797: strcat(fileresprob,fileres);
6798: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6799: printf("Problem with resultfile: %s\n", fileresprob);
6800: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6801: }
6802: strcpy(fileresprobcov,"PROBCOV_");
6803: strcat(fileresprobcov,fileresu);
6804: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6805: printf("Problem with resultfile: %s\n", fileresprobcov);
6806: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6807: }
6808: strcpy(fileresprobcor,"PROBCOR_");
6809: strcat(fileresprobcor,fileresu);
6810: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6811: printf("Problem with resultfile: %s\n", fileresprobcor);
6812: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6813: }
6814: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6815: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6816: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6817: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6818: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6819: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6820: pstamp(ficresprob);
6821: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6822: fprintf(ficresprob,"# Age");
6823: pstamp(ficresprobcov);
6824: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6825: fprintf(ficresprobcov,"# Age");
6826: pstamp(ficresprobcor);
6827: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6828: fprintf(ficresprobcor,"# Age");
1.126 brouard 6829:
6830:
1.222 brouard 6831: for(i=1; i<=nlstate;i++)
6832: for(j=1; j<=(nlstate+ndeath);j++){
6833: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6834: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6835: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6836: }
6837: /* fprintf(ficresprob,"\n");
6838: fprintf(ficresprobcov,"\n");
6839: fprintf(ficresprobcor,"\n");
6840: */
6841: xp=vector(1,npar);
6842: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6843: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6844: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6845: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6846: first=1;
6847: fprintf(ficgp,"\n# Routine varprob");
6848: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6849: fprintf(fichtm,"\n");
6850:
1.288 brouard 6851: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
1.222 brouard 6852: fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
6853: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6854: and drawn. It helps understanding how is the covariance between two incidences.\
6855: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6856: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
1.126 brouard 6857: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6858: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6859: standard deviations wide on each axis. <br>\
6860: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6861: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6862: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6863:
1.222 brouard 6864: cov[1]=1;
6865: /* tj=cptcoveff; */
1.225 brouard 6866: tj = (int) pow(2,cptcoveff);
1.222 brouard 6867: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6868: j1=0;
1.224 brouard 6869: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6870: if (cptcovn>0) {
6871: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6872: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6873: fprintf(ficresprob, "**********\n#\n");
6874: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6875: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6876: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6877:
1.222 brouard 6878: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6879: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6880: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6881:
6882:
1.222 brouard 6883: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.319 ! brouard 6884: /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */
! 6885: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6886: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6887:
1.222 brouard 6888: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6889: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6890: fprintf(ficresprobcor, "**********\n#");
6891: if(invalidvarcomb[j1]){
6892: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6893: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6894: continue;
6895: }
6896: }
6897: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6898: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6899: gp=vector(1,(nlstate)*(nlstate+ndeath));
6900: gm=vector(1,(nlstate)*(nlstate+ndeath));
6901: for (age=bage; age<=fage; age ++){
6902: cov[2]=age;
6903: if(nagesqr==1)
6904: cov[3]= age*age;
6905: for (k=1; k<=cptcovn;k++) {
6906: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6907: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6908: * 1 1 1 1 1
6909: * 2 2 1 1 1
6910: * 3 1 2 1 1
6911: */
6912: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6913: }
1.319 ! brouard 6914: /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
! 6915: /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
! 6916: /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
! 6917: for (k=1; k<=cptcovage;k++)
! 6918: cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.222 brouard 6919: for (k=1; k<=cptcovprod;k++)
6920: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6921:
6922:
1.222 brouard 6923: for(theta=1; theta <=npar; theta++){
6924: for(i=1; i<=npar; i++)
6925: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6926:
1.222 brouard 6927: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6928:
1.222 brouard 6929: k=0;
6930: for(i=1; i<= (nlstate); i++){
6931: for(j=1; j<=(nlstate+ndeath);j++){
6932: k=k+1;
6933: gp[k]=pmmij[i][j];
6934: }
6935: }
1.220 brouard 6936:
1.222 brouard 6937: for(i=1; i<=npar; i++)
6938: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6939:
1.222 brouard 6940: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6941: k=0;
6942: for(i=1; i<=(nlstate); i++){
6943: for(j=1; j<=(nlstate+ndeath);j++){
6944: k=k+1;
6945: gm[k]=pmmij[i][j];
6946: }
6947: }
1.220 brouard 6948:
1.222 brouard 6949: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6950: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6951: }
1.126 brouard 6952:
1.222 brouard 6953: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6954: for(theta=1; theta <=npar; theta++)
6955: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6956:
1.222 brouard 6957: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6958: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6959:
1.222 brouard 6960: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6961:
1.222 brouard 6962: k=0;
6963: for(i=1; i<=(nlstate); i++){
6964: for(j=1; j<=(nlstate+ndeath);j++){
6965: k=k+1;
6966: mu[k][(int) age]=pmmij[i][j];
6967: }
6968: }
6969: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6970: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6971: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6972:
1.222 brouard 6973: /*printf("\n%d ",(int)age);
6974: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6975: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6976: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6977: }*/
1.220 brouard 6978:
1.222 brouard 6979: fprintf(ficresprob,"\n%d ",(int)age);
6980: fprintf(ficresprobcov,"\n%d ",(int)age);
6981: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6982:
1.222 brouard 6983: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6984: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6985: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6986: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6987: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6988: }
6989: i=0;
6990: for (k=1; k<=(nlstate);k++){
6991: for (l=1; l<=(nlstate+ndeath);l++){
6992: i++;
6993: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6994: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6995: for (j=1; j<=i;j++){
6996: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6997: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6998: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6999: }
7000: }
7001: }/* end of loop for state */
7002: } /* end of loop for age */
7003: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
7004: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
7005: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
7006: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
7007:
7008: /* Confidence intervalle of pij */
7009: /*
7010: fprintf(ficgp,"\nunset parametric;unset label");
7011: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
7012: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
7013: fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
7014: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
7015: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
7016: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
7017: */
7018:
7019: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
7020: first1=1;first2=2;
7021: for (k2=1; k2<=(nlstate);k2++){
7022: for (l2=1; l2<=(nlstate+ndeath);l2++){
7023: if(l2==k2) continue;
7024: j=(k2-1)*(nlstate+ndeath)+l2;
7025: for (k1=1; k1<=(nlstate);k1++){
7026: for (l1=1; l1<=(nlstate+ndeath);l1++){
7027: if(l1==k1) continue;
7028: i=(k1-1)*(nlstate+ndeath)+l1;
7029: if(i<=j) continue;
7030: for (age=bage; age<=fage; age ++){
7031: if ((int)age %5==0){
7032: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
7033: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
7034: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
7035: mu1=mu[i][(int) age]/stepm*YEARM ;
7036: mu2=mu[j][(int) age]/stepm*YEARM;
7037: c12=cv12/sqrt(v1*v2);
7038: /* Computing eigen value of matrix of covariance */
7039: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
7040: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
7041: if ((lc2 <0) || (lc1 <0) ){
7042: if(first2==1){
7043: first1=0;
7044: printf("Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
7045: }
7046: fprintf(ficlog,"Strange: j1=%d One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
7047: /* lc1=fabs(lc1); */ /* If we want to have them positive */
7048: /* lc2=fabs(lc2); */
7049: }
1.220 brouard 7050:
1.222 brouard 7051: /* Eigen vectors */
1.280 brouard 7052: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
7053: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
7054: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
7055: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
7056: }else
7057: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 7058: /*v21=sqrt(1.-v11*v11); *//* error */
7059: v21=(lc1-v1)/cv12*v11;
7060: v12=-v21;
7061: v22=v11;
7062: tnalp=v21/v11;
7063: if(first1==1){
7064: first1=0;
7065: printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
7066: }
7067: fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
7068: /*printf(fignu*/
7069: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
7070: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
7071: if(first==1){
7072: first=0;
7073: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
7074: fprintf(ficgp,"\nset parametric;unset label");
7075: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
7076: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 7077: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 7078: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 7079: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 7080: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
7081: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
7082: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
7083: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
7084: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
7085: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
7086: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
7087: fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
1.280 brouard 7088: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
7089: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 7090: }else{
7091: first=0;
7092: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
7093: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
7094: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
7095: fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
1.266 brouard 7096: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
7097: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 7098: }/* if first */
7099: } /* age mod 5 */
7100: } /* end loop age */
7101: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
7102: first=1;
7103: } /*l12 */
7104: } /* k12 */
7105: } /*l1 */
7106: }/* k1 */
7107: } /* loop on combination of covariates j1 */
7108: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
7109: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
7110: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
7111: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
7112: free_vector(xp,1,npar);
7113: fclose(ficresprob);
7114: fclose(ficresprobcov);
7115: fclose(ficresprobcor);
7116: fflush(ficgp);
7117: fflush(fichtmcov);
7118: }
1.126 brouard 7119:
7120:
7121: /******************* Printing html file ***********/
1.201 brouard 7122: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7123: int lastpass, int stepm, int weightopt, char model[],\
7124: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 7125: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
7126: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
7127: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 7128: int jj1, k1, i1, cpt, k4, nres;
1.319 ! brouard 7129: /* In fact some results are already printed in fichtm which is open */
1.126 brouard 7130: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
7131: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
7132: </ul>");
1.319 ! brouard 7133: /* fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
! 7134: /* </ul>", model); */
1.214 brouard 7135: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
7136: fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
7137: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
7138: fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213 brouard 7139: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
7140: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 7141: fprintf(fichtm,"\
7142: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 7143: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 7144: fprintf(fichtm,"\
1.217 brouard 7145: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
7146: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
7147: fprintf(fichtm,"\
1.288 brouard 7148: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 7149: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 7150: fprintf(fichtm,"\
1.288 brouard 7151: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 7152: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
7153: fprintf(fichtm,"\
1.211 brouard 7154: - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 7155: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 7156: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 7157: if(prevfcast==1){
7158: fprintf(fichtm,"\
7159: - Prevalence projections by age and states: \
1.201 brouard 7160: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 7161: }
1.126 brouard 7162:
7163:
1.225 brouard 7164: m=pow(2,cptcoveff);
1.222 brouard 7165: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7166:
1.317 brouard 7167: fprintf(fichtm," \n<ul><li><b>Graphs (first order)</b></li><p>");
1.264 brouard 7168:
7169: jj1=0;
7170:
7171: fprintf(fichtm," \n<ul>");
7172: for(nres=1; nres <= nresult; nres++) /* For each resultline */
7173: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
7174: if(m != 1 && TKresult[nres]!= k1)
7175: continue;
7176: jj1++;
7177: if (cptcovn > 0) {
7178: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
7179: for (cpt=1; cpt<=cptcoveff;cpt++){
7180: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7181: }
7182: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7183: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7184: }
7185: fprintf(fichtm,"\">");
7186:
7187: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
7188: fprintf(fichtm,"************ Results for covariates");
7189: for (cpt=1; cpt<=cptcoveff;cpt++){
7190: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7191: }
7192: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7193: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7194: }
7195: if(invalidvarcomb[k1]){
7196: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
7197: continue;
7198: }
7199: fprintf(fichtm,"</a></li>");
7200: } /* cptcovn >0 */
7201: }
1.317 brouard 7202: fprintf(fichtm," \n</ul>");
1.264 brouard 7203:
1.222 brouard 7204: jj1=0;
1.237 brouard 7205:
7206: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 7207: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 7208: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7209: continue;
1.220 brouard 7210:
1.222 brouard 7211: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7212: jj1++;
7213: if (cptcovn > 0) {
1.264 brouard 7214: fprintf(fichtm,"\n<p><a name=\"rescov");
7215: for (cpt=1; cpt<=cptcoveff;cpt++){
7216: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7217: }
7218: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7219: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7220: }
7221: fprintf(fichtm,"\"</a>");
7222:
1.222 brouard 7223: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7224: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 7225: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7226: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
7227: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7228: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 7229: }
1.237 brouard 7230: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7231: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7232: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
7233: }
7234:
1.230 brouard 7235: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 7236: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
7237: if(invalidvarcomb[k1]){
7238: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
7239: printf("\nCombination (%d) ignored because no cases \n",k1);
7240: continue;
7241: }
7242: }
7243: /* aij, bij */
1.259 brouard 7244: fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
1.241 brouard 7245: <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
1.222 brouard 7246: /* Pij */
1.241 brouard 7247: fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
7248: <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
1.222 brouard 7249: /* Quasi-incidences */
7250: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.220 brouard 7251: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7252: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
1.241 brouard 7253: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
7254: <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
1.222 brouard 7255: /* Survival functions (period) in state j */
7256: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7257: fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241 brouard 7258: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.222 brouard 7259: }
7260: /* State specific survival functions (period) */
7261: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7262: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7263: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7264: <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.222 brouard 7265: }
1.288 brouard 7266: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7267: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7268: fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7269: <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.222 brouard 7270: }
1.296 brouard 7271: if(prevbcast==1){
1.288 brouard 7272: /* Backward prevalence in each health state */
1.222 brouard 7273: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7274: fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241 brouard 7275: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.222 brouard 7276: }
1.217 brouard 7277: }
1.222 brouard 7278: if(prevfcast==1){
1.288 brouard 7279: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7280: for(cpt=1; cpt<=nlstate;cpt++){
1.314 brouard 7281: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
7282: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
7283: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
7284: subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 7285: }
7286: }
1.296 brouard 7287: if(prevbcast==1){
1.268 brouard 7288: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7289: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7290: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7291: from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
7292: account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
1.314 brouard 7293: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7294: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
7295: fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
1.268 brouard 7296: }
7297: }
1.220 brouard 7298:
1.222 brouard 7299: for(cpt=1; cpt<=nlstate;cpt++) {
1.314 brouard 7300: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
7301: fprintf(fichtm," (data from text file <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
7302: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
1.222 brouard 7303: }
7304: /* } /\* end i1 *\/ */
7305: }/* End k1 */
7306: fprintf(fichtm,"</ul>");
1.126 brouard 7307:
1.222 brouard 7308: fprintf(fichtm,"\
1.126 brouard 7309: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7310: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7311: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
1.197 brouard 7312: But because parameters are usually highly correlated (a higher incidence of disability \
7313: and a higher incidence of recovery can give very close observed transition) it might \
7314: be very useful to look not only at linear confidence intervals estimated from the \
7315: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7316: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7317: covariance matrix of the one-step probabilities. \
7318: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7319:
1.222 brouard 7320: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7321: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7322: fprintf(fichtm,"\
1.126 brouard 7323: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7324: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7325:
1.222 brouard 7326: fprintf(fichtm,"\
1.126 brouard 7327: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7328: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7329: fprintf(fichtm,"\
1.126 brouard 7330: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
7331: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7332: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7333: fprintf(fichtm,"\
1.126 brouard 7334: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
7335: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7336: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7337: fprintf(fichtm,"\
1.288 brouard 7338: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.222 brouard 7339: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7340: fprintf(fichtm,"\
1.128 brouard 7341: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7342: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7343: fprintf(fichtm,"\
1.288 brouard 7344: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7345: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7346:
7347: /* if(popforecast==1) fprintf(fichtm,"\n */
7348: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7349: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7350: /* <br>",fileres,fileres,fileres,fileres); */
7351: /* else */
7352: /* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
1.222 brouard 7353: fflush(fichtm);
1.126 brouard 7354:
1.225 brouard 7355: m=pow(2,cptcoveff);
1.222 brouard 7356: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7357:
1.317 brouard 7358: fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");
7359:
7360: jj1=0;
7361:
7362: fprintf(fichtm," \n<ul>");
7363: for(nres=1; nres <= nresult; nres++) /* For each resultline */
7364: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
7365: if(m != 1 && TKresult[nres]!= k1)
7366: continue;
7367: jj1++;
7368: if (cptcovn > 0) {
7369: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
7370: for (cpt=1; cpt<=cptcoveff;cpt++){
7371: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7372: }
7373: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7374: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7375: }
7376: fprintf(fichtm,"\">");
7377:
7378: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
7379: fprintf(fichtm,"************ Results for covariates");
7380: for (cpt=1; cpt<=cptcoveff;cpt++){
7381: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7382: }
7383: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7384: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7385: }
7386: if(invalidvarcomb[k1]){
7387: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
7388: continue;
7389: }
7390: fprintf(fichtm,"</a></li>");
7391: } /* cptcovn >0 */
7392: }
7393: fprintf(fichtm," \n</ul>");
7394:
1.222 brouard 7395: jj1=0;
1.237 brouard 7396:
1.241 brouard 7397: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7398: for(k1=1; k1<=m;k1++){
1.253 brouard 7399: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7400: continue;
1.222 brouard 7401: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7402: jj1++;
1.126 brouard 7403: if (cptcovn > 0) {
1.317 brouard 7404: fprintf(fichtm,"\n<p><a name=\"rescovsecond");
7405: for (cpt=1; cpt<=cptcoveff;cpt++){
7406: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7407: }
7408: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7409: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7410: }
7411: fprintf(fichtm,"\"</a>");
7412:
1.126 brouard 7413: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.317 brouard 7414: for (cpt=1; cpt<=cptcoveff;cpt++){ /**< cptcoveff number of variables */
1.237 brouard 7415: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
1.317 brouard 7416: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
1.237 brouard 7417: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
1.317 brouard 7418: }
1.237 brouard 7419: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7420: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7421: }
7422:
1.126 brouard 7423: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7424:
1.222 brouard 7425: if(invalidvarcomb[k1]){
7426: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7427: continue;
7428: }
1.126 brouard 7429: }
7430: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7431: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.314 brouard 7432: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7433: fprintf(fichtm," (data from text file <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
7434: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
1.126 brouard 7435: }
7436: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.314 brouard 7437: health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
1.128 brouard 7438: true period expectancies (those weighted with period prevalences are also\
7439: drawn in addition to the population based expectancies computed using\
1.314 brouard 7440: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
7441: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
7442: fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7443: /* } /\* end i1 *\/ */
7444: }/* End k1 */
1.241 brouard 7445: }/* End nres */
1.222 brouard 7446: fprintf(fichtm,"</ul>");
7447: fflush(fichtm);
1.126 brouard 7448: }
7449:
7450: /******************* Gnuplot file **************/
1.296 brouard 7451: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
1.126 brouard 7452:
7453: char dirfileres[132],optfileres[132];
1.264 brouard 7454: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7455: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
1.211 brouard 7456: int lv=0, vlv=0, kl=0;
1.130 brouard 7457: int ng=0;
1.201 brouard 7458: int vpopbased;
1.223 brouard 7459: int ioffset; /* variable offset for columns */
1.270 brouard 7460: int iyearc=1; /* variable column for year of projection */
7461: int iagec=1; /* variable column for age of projection */
1.235 brouard 7462: int nres=0; /* Index of resultline */
1.266 brouard 7463: int istart=1; /* For starting graphs in projections */
1.219 brouard 7464:
1.126 brouard 7465: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7466: /* printf("Problem with file %s",optionfilegnuplot); */
7467: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7468: /* } */
7469:
7470: /*#ifdef windows */
7471: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7472: /*#endif */
1.225 brouard 7473: m=pow(2,cptcoveff);
1.126 brouard 7474:
1.274 brouard 7475: /* diagram of the model */
7476: fprintf(ficgp,"\n#Diagram of the model \n");
7477: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7478: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7479: fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
7480:
7481: fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
7482: fprintf(ficgp,"\n#show arrow\nunset label\n");
7483: fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
7484: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7485: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7486: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7487: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7488:
1.202 brouard 7489: /* Contribution to likelihood */
7490: /* Plot the probability implied in the likelihood */
1.223 brouard 7491: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7492: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7493: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7494: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7495: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7496: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7497: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7498: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7499: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7500: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
7501: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7502: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
7503: for (i=1; i<= nlstate ; i ++) {
7504: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7505: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7506: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
7507: for (j=2; j<= nlstate+ndeath ; j ++) {
7508: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
7509: }
7510: fprintf(ficgp,";\nset out; unset ylabel;\n");
7511: }
7512: /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
7513: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7514: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7515: fprintf(ficgp,"\nset out;unset log\n");
7516: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7517:
1.126 brouard 7518: strcpy(dirfileres,optionfilefiname);
7519: strcpy(optfileres,"vpl");
1.223 brouard 7520: /* 1eme*/
1.238 brouard 7521: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7522: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7523: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7524: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7525: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7526: continue;
7527: /* We are interested in selected combination by the resultline */
1.246 brouard 7528: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7529: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7530: strcpy(gplotlabel,"(");
1.238 brouard 7531: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7532: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7533: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7534: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7535: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7536: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7537: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7538: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7539: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7540: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7541: }
7542: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7543: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7544: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7545: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7546: }
7547: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7548: /* printf("\n#\n"); */
1.238 brouard 7549: fprintf(ficgp,"\n#\n");
7550: if(invalidvarcomb[k1]){
1.260 brouard 7551: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7552: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7553: continue;
7554: }
1.235 brouard 7555:
1.241 brouard 7556: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7557: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7558: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7559: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7560: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
7561: /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
7562: /* k1-1 error should be nres-1*/
1.238 brouard 7563: for (i=1; i<= nlstate ; i ++) {
7564: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7565: else fprintf(ficgp," %%*lf (%%*lf)");
7566: }
1.288 brouard 7567: fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7568: for (i=1; i<= nlstate ; i ++) {
7569: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7570: else fprintf(ficgp," %%*lf (%%*lf)");
7571: }
1.260 brouard 7572: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7573: for (i=1; i<= nlstate ; i ++) {
7574: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7575: else fprintf(ficgp," %%*lf (%%*lf)");
7576: }
1.265 brouard 7577: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7578:
7579: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7580: if(cptcoveff ==0){
1.271 brouard 7581: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7582: }else{
7583: kl=0;
7584: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7585: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7586: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7587: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7588: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7589: vlv= nbcode[Tvaraff[k]][lv];
7590: kl++;
7591: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
7592: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7593: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7594: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7595: if(k==cptcoveff){
7596: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7597: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7598: }else{
7599: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7600: kl++;
7601: }
7602: } /* end covariate */
7603: } /* end if no covariate */
7604:
1.296 brouard 7605: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7606: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7607: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7608: if(cptcoveff ==0){
1.245 brouard 7609: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7610: }else{
7611: kl=0;
7612: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7613: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7614: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7615: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7616: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7617: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7618: kl++;
1.238 brouard 7619: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
7620: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7621: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7622: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7623: if(k==cptcoveff){
1.245 brouard 7624: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7625: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7626: }else{
7627: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7628: kl++;
7629: }
7630: } /* end covariate */
7631: } /* end if no covariate */
1.296 brouard 7632: if(prevbcast == 1){
1.268 brouard 7633: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7634: /* k1-1 error should be nres-1*/
7635: for (i=1; i<= nlstate ; i ++) {
7636: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7637: else fprintf(ficgp," %%*lf (%%*lf)");
7638: }
1.271 brouard 7639: fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
1.268 brouard 7640: for (i=1; i<= nlstate ; i ++) {
7641: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7642: else fprintf(ficgp," %%*lf (%%*lf)");
7643: }
1.276 brouard 7644: fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
1.268 brouard 7645: for (i=1; i<= nlstate ; i ++) {
7646: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7647: else fprintf(ficgp," %%*lf (%%*lf)");
7648: }
1.274 brouard 7649: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7650: } /* end if backprojcast */
1.296 brouard 7651: } /* end if prevbcast */
1.276 brouard 7652: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7653: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7654: } /* nres */
1.201 brouard 7655: } /* k1 */
7656: } /* cpt */
1.235 brouard 7657:
7658:
1.126 brouard 7659: /*2 eme*/
1.238 brouard 7660: for (k1=1; k1<= m ; k1 ++){
7661: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7662: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7663: continue;
7664: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7665: strcpy(gplotlabel,"(");
1.238 brouard 7666: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7667: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7668: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7669: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7670: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7671: vlv= nbcode[Tvaraff[k]][lv];
7672: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7673: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7674: }
1.237 brouard 7675: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7676: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7677: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7678: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7679: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7680: }
1.264 brouard 7681: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7682: fprintf(ficgp,"\n#\n");
1.223 brouard 7683: if(invalidvarcomb[k1]){
7684: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7685: continue;
7686: }
1.219 brouard 7687:
1.241 brouard 7688: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7689: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7690: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7691: if(vpopbased==0){
1.238 brouard 7692: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7693: }else
1.238 brouard 7694: fprintf(ficgp,"\nreplot ");
7695: for (i=1; i<= nlstate+1 ; i ++) {
7696: k=2*i;
1.261 brouard 7697: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
1.238 brouard 7698: for (j=1; j<= nlstate+1 ; j ++) {
7699: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7700: else fprintf(ficgp," %%*lf (%%*lf)");
7701: }
7702: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7703: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7704: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
1.238 brouard 7705: for (j=1; j<= nlstate+1 ; j ++) {
7706: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7707: else fprintf(ficgp," %%*lf (%%*lf)");
7708: }
7709: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7710: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
1.238 brouard 7711: for (j=1; j<= nlstate+1 ; j ++) {
7712: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7713: else fprintf(ficgp," %%*lf (%%*lf)");
7714: }
7715: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7716: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7717: } /* state */
7718: } /* vpopbased */
1.264 brouard 7719: fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
1.238 brouard 7720: } /* end nres */
7721: } /* k1 end 2 eme*/
7722:
7723:
7724: /*3eme*/
7725: for (k1=1; k1<= m ; k1 ++){
7726: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7727: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7728: continue;
7729:
7730: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7731: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7732: strcpy(gplotlabel,"(");
1.238 brouard 7733: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7734: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7735: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7736: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7737: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7738: vlv= nbcode[Tvaraff[k]][lv];
7739: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7740: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7741: }
7742: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7743: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7744: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7745: }
1.264 brouard 7746: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7747: fprintf(ficgp,"\n#\n");
7748: if(invalidvarcomb[k1]){
7749: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7750: continue;
7751: }
7752:
7753: /* k=2+nlstate*(2*cpt-2); */
7754: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7755: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7756: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7757: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7758: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
1.238 brouard 7759: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7760: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7761: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7762: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7763: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7764: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7765:
1.238 brouard 7766: */
7767: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7768: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
1.238 brouard 7769: /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
1.219 brouard 7770:
1.238 brouard 7771: }
1.261 brouard 7772: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
1.238 brouard 7773: }
1.264 brouard 7774: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7775: } /* end nres */
7776: } /* end kl 3eme */
1.126 brouard 7777:
1.223 brouard 7778: /* 4eme */
1.201 brouard 7779: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7780: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7781: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7782: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7783: continue;
1.238 brouard 7784: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7785: strcpy(gplotlabel,"(");
1.238 brouard 7786: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7787: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7788: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7789: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7790: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7791: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7792: vlv= nbcode[Tvaraff[k]][lv];
7793: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7794: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7795: }
7796: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7797: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7798: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7799: }
1.264 brouard 7800: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7801: fprintf(ficgp,"\n#\n");
7802: if(invalidvarcomb[k1]){
7803: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7804: continue;
1.223 brouard 7805: }
1.238 brouard 7806:
1.241 brouard 7807: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7808: fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.238 brouard 7809: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7810: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7811: k=3;
7812: for (i=1; i<= nlstate ; i ++){
7813: if(i==1){
7814: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7815: }else{
7816: fprintf(ficgp,", '' ");
7817: }
7818: l=(nlstate+ndeath)*(i-1)+1;
7819: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7820: for (j=2; j<= nlstate+ndeath ; j ++)
7821: fprintf(ficgp,"+$%d",k+l+j-1);
7822: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7823: } /* nlstate */
1.264 brouard 7824: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7825: } /* end cpt state*/
7826: } /* end nres */
7827: } /* end covariate k1 */
7828:
1.220 brouard 7829: /* 5eme */
1.201 brouard 7830: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7831: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7832: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7833: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7834: continue;
1.238 brouard 7835: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7836: strcpy(gplotlabel,"(");
1.238 brouard 7837: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
7838: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7839: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7840: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7841: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7842: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7843: vlv= nbcode[Tvaraff[k]][lv];
7844: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7845: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7846: }
7847: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7848: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7849: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7850: }
1.264 brouard 7851: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7852: fprintf(ficgp,"\n#\n");
7853: if(invalidvarcomb[k1]){
7854: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7855: continue;
7856: }
1.227 brouard 7857:
1.241 brouard 7858: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7859: fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.238 brouard 7860: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7861: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7862: k=3;
7863: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7864: if(j==1)
7865: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7866: else
7867: fprintf(ficgp,", '' ");
7868: l=(nlstate+ndeath)*(cpt-1) +j;
7869: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7870: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7871: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7872: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7873: } /* nlstate */
7874: fprintf(ficgp,", '' ");
7875: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7876: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7877: l=(nlstate+ndeath)*(cpt-1) +j;
7878: if(j < nlstate)
7879: fprintf(ficgp,"$%d +",k+l);
7880: else
7881: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7882: }
1.264 brouard 7883: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7884: } /* end cpt state*/
7885: } /* end covariate */
7886: } /* end nres */
1.227 brouard 7887:
1.220 brouard 7888: /* 6eme */
1.202 brouard 7889: /* CV preval stable (period) for each covariate */
1.237 brouard 7890: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7891: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7892: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7893: continue;
1.255 brouard 7894: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7895: strcpy(gplotlabel,"(");
1.288 brouard 7896: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7897: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7898: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7899: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7900: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7901: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7902: vlv= nbcode[Tvaraff[k]][lv];
7903: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7904: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7905: }
1.237 brouard 7906: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7907: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7908: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7909: }
1.264 brouard 7910: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7911: fprintf(ficgp,"\n#\n");
1.223 brouard 7912: if(invalidvarcomb[k1]){
1.227 brouard 7913: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7914: continue;
1.223 brouard 7915: }
1.227 brouard 7916:
1.241 brouard 7917: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7918: fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.126 brouard 7919: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7920: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7921: k=3; /* Offset */
1.255 brouard 7922: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7923: if(i==1)
7924: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7925: else
7926: fprintf(ficgp,", '' ");
1.255 brouard 7927: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7928: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7929: for (j=2; j<= nlstate ; j ++)
7930: fprintf(ficgp,"+$%d",k+l+j-1);
7931: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7932: } /* nlstate */
1.264 brouard 7933: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7934: } /* end cpt state*/
7935: } /* end covariate */
1.227 brouard 7936:
7937:
1.220 brouard 7938: /* 7eme */
1.296 brouard 7939: if(prevbcast == 1){
1.288 brouard 7940: /* CV backward prevalence for each covariate */
1.237 brouard 7941: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7942: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7943: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7944: continue;
1.268 brouard 7945: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7946: strcpy(gplotlabel,"(");
1.288 brouard 7947: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7948: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7949: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7950: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7951: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7952: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7953: vlv= nbcode[Tvaraff[k]][lv];
7954: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7955: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7956: }
1.237 brouard 7957: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7958: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7959: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7960: }
1.264 brouard 7961: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7962: fprintf(ficgp,"\n#\n");
7963: if(invalidvarcomb[k1]){
7964: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7965: continue;
7966: }
7967:
1.241 brouard 7968: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7969: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.227 brouard 7970: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7971: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7972: k=3; /* Offset */
1.268 brouard 7973: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7974: if(i==1)
7975: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7976: else
7977: fprintf(ficgp,", '' ");
7978: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7979: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7980: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7981: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
1.255 brouard 7982: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7983: /* for (j=2; j<= nlstate ; j ++) */
7984: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7985: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7986: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7987: } /* nlstate */
1.264 brouard 7988: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7989: } /* end cpt state*/
7990: } /* end covariate */
1.296 brouard 7991: } /* End if prevbcast */
1.218 brouard 7992:
1.223 brouard 7993: /* 8eme */
1.218 brouard 7994: if(prevfcast==1){
1.288 brouard 7995: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7996:
1.237 brouard 7997: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7998: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7999: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 8000: continue;
1.211 brouard 8001: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 8002: strcpy(gplotlabel,"(");
1.288 brouard 8003: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 8004: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
8005: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
8006: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8007: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8008: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8009: vlv= nbcode[Tvaraff[k]][lv];
8010: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 8011: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 8012: }
1.237 brouard 8013: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8014: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 8015: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 8016: }
1.264 brouard 8017: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 8018: fprintf(ficgp,"\n#\n");
8019: if(invalidvarcomb[k1]){
8020: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
8021: continue;
8022: }
8023:
8024: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 8025: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 8026: fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
1.227 brouard 8027: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 8028: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 8029:
8030: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
8031: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
8032: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
8033: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 8034: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8035: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
8036: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8037: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 8038: if(i==istart){
1.227 brouard 8039: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
8040: }else{
8041: fprintf(ficgp,",\\\n '' ");
8042: }
8043: if(cptcoveff ==0){ /* No covariate */
8044: ioffset=2; /* Age is in 2 */
8045: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
8046: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
8047: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
8048: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
8049: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 8050: if(i==nlstate+1){
1.270 brouard 8051: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 8052: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
8053: fprintf(ficgp,",\\\n '' ");
8054: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 8055: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 8056: offyear, \
1.268 brouard 8057: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 8058: }else
1.227 brouard 8059: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
8060: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
8061: }else{ /* more than 2 covariates */
1.270 brouard 8062: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
8063: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8064: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
8065: iyearc=ioffset-1;
8066: iagec=ioffset;
1.227 brouard 8067: fprintf(ficgp," u %d:(",ioffset);
8068: kl=0;
8069: strcpy(gplotcondition,"(");
8070: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
8071: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
8072: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8073: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8074: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8075: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
8076: kl++;
8077: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
8078: kl++;
8079: if(k <cptcoveff && cptcoveff>1)
8080: sprintf(gplotcondition+strlen(gplotcondition)," && ");
8081: }
8082: strcpy(gplotcondition+strlen(gplotcondition),")");
8083: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
8084: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
8085: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
8086: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
8087: if(i==nlstate+1){
1.270 brouard 8088: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
8089: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 8090: fprintf(ficgp,",\\\n '' ");
1.270 brouard 8091: fprintf(ficgp," u %d:(",iagec);
8092: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
8093: iyearc, iagec, offyear, \
8094: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 8095: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
1.227 brouard 8096: }else{
8097: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
8098: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
8099: }
8100: } /* end if covariate */
8101: } /* nlstate */
1.264 brouard 8102: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 8103: } /* end cpt state*/
8104: } /* end covariate */
8105: } /* End if prevfcast */
1.227 brouard 8106:
1.296 brouard 8107: if(prevbcast==1){
1.268 brouard 8108: /* Back projection from cross-sectional to stable (mixed) for each covariate */
8109:
8110: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
8111: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
8112: if(m != 1 && TKresult[nres]!= k1)
8113: continue;
8114: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
8115: strcpy(gplotlabel,"(");
8116: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
8117: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
8118: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
8119: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8120: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8121: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8122: vlv= nbcode[Tvaraff[k]][lv];
8123: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
8124: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
8125: }
8126: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8127: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8128: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8129: }
8130: strcpy(gplotlabel+strlen(gplotlabel),")");
8131: fprintf(ficgp,"\n#\n");
8132: if(invalidvarcomb[k1]){
8133: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
8134: continue;
8135: }
8136:
8137: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
8138: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
8139: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
8140: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
8141: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
8142:
8143: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
8144: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
8145: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
8146: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
8147: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8148: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
8149: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8150: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
8151: if(i==istart){
8152: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
8153: }else{
8154: fprintf(ficgp,",\\\n '' ");
8155: }
8156: if(cptcoveff ==0){ /* No covariate */
8157: ioffset=2; /* Age is in 2 */
8158: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
8159: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
8160: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
8161: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
8162: fprintf(ficgp," u %d:(", ioffset);
8163: if(i==nlstate+1){
1.270 brouard 8164: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 8165: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
8166: fprintf(ficgp,",\\\n '' ");
8167: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 8168: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 8169: offbyear, \
8170: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
8171: }else
8172: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
8173: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
8174: }else{ /* more than 2 covariates */
1.270 brouard 8175: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
8176: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
8177: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
8178: iyearc=ioffset-1;
8179: iagec=ioffset;
1.268 brouard 8180: fprintf(ficgp," u %d:(",ioffset);
8181: kl=0;
8182: strcpy(gplotcondition,"(");
8183: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
8184: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
8185: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8186: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8187: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8188: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
8189: kl++;
8190: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
8191: kl++;
8192: if(k <cptcoveff && cptcoveff>1)
8193: sprintf(gplotcondition+strlen(gplotcondition)," && ");
8194: }
8195: strcpy(gplotcondition+strlen(gplotcondition),")");
8196: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
8197: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
8198: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
8199: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
8200: if(i==nlstate+1){
1.270 brouard 8201: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
8202: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 8203: fprintf(ficgp,",\\\n '' ");
1.270 brouard 8204: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 8205: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 8206: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
8207: iyearc,iagec,offbyear, \
8208: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 8209: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
8210: }else{
8211: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
8212: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
8213: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
8214: }
8215: } /* end if covariate */
8216: } /* nlstate */
8217: fprintf(ficgp,"\nset out; unset label;\n");
8218: } /* end cpt state*/
8219: } /* end covariate */
1.296 brouard 8220: } /* End if prevbcast */
1.268 brouard 8221:
1.227 brouard 8222:
1.238 brouard 8223: /* 9eme writing MLE parameters */
8224: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 8225: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 8226: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 8227: for(k=1; k <=(nlstate+ndeath); k++){
8228: if (k != i) {
1.227 brouard 8229: fprintf(ficgp,"# current state %d\n",k);
8230: for(j=1; j <=ncovmodel; j++){
8231: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
8232: jk++;
8233: }
8234: fprintf(ficgp,"\n");
1.126 brouard 8235: }
8236: }
1.223 brouard 8237: }
1.187 brouard 8238: fprintf(ficgp,"##############\n#\n");
1.227 brouard 8239:
1.145 brouard 8240: /*goto avoid;*/
1.238 brouard 8241: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
8242: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 8243: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
8244: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
8245: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
8246: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
8247: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8248: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
8249: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8250: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
8251: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
8252: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8253: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
8254: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
8255: fprintf(ficgp,"#\n");
1.223 brouard 8256: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 8257: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 8258: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 8259: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 8260: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
8261: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 8262: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 8263: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 8264: continue;
1.264 brouard 8265: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
8266: strcpy(gplotlabel,"(");
1.276 brouard 8267: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 8268: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
8269: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
8270: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8271: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8272: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8273: vlv= nbcode[Tvaraff[k]][lv];
8274: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
8275: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
8276: }
1.237 brouard 8277: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8278: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 8279: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 8280: }
1.264 brouard 8281: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 8282: fprintf(ficgp,"\n#\n");
1.264 brouard 8283: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 8284: fprintf(ficgp,"\nset key outside ");
8285: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
8286: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 8287: fprintf(ficgp,"\nset ter svg size 640, 480 ");
8288: if (ng==1){
8289: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
8290: fprintf(ficgp,"\nunset log y");
8291: }else if (ng==2){
8292: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
8293: fprintf(ficgp,"\nset log y");
8294: }else if (ng==3){
8295: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
8296: fprintf(ficgp,"\nset log y");
8297: }else
8298: fprintf(ficgp,"\nunset title ");
8299: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
8300: i=1;
8301: for(k2=1; k2<=nlstate; k2++) {
8302: k3=i;
8303: for(k=1; k<=(nlstate+ndeath); k++) {
8304: if (k != k2){
8305: switch( ng) {
8306: case 1:
8307: if(nagesqr==0)
8308: fprintf(ficgp," p%d+p%d*x",i,i+1);
8309: else /* nagesqr =1 */
8310: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8311: break;
8312: case 2: /* ng=2 */
8313: if(nagesqr==0)
8314: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8315: else /* nagesqr =1 */
8316: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8317: break;
8318: case 3:
8319: if(nagesqr==0)
8320: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8321: else /* nagesqr =1 */
8322: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8323: break;
8324: }
8325: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8326: ijp=1; /* product no age */
8327: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8328: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8329: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8330: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8331: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8332: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8333: if(DummyV[j]==0){
8334: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8335: }else{ /* quantitative */
8336: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8337: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8338: }
8339: ij++;
1.237 brouard 8340: }
1.268 brouard 8341: }
8342: }else if(cptcovprod >0){
8343: if(j==Tprod[ijp]) { /* */
8344: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8345: if(ijp <=cptcovprod) { /* Product */
8346: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8347: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8348: /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
8349: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8350: }else{ /* Vn is dummy and Vm is quanti */
8351: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8352: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8353: }
8354: }else{ /* Vn*Vm Vn is quanti */
8355: if(DummyV[Tvard[ijp][2]]==0){
8356: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8357: }else{ /* Both quanti */
8358: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8359: }
1.237 brouard 8360: }
1.268 brouard 8361: ijp++;
1.237 brouard 8362: }
1.268 brouard 8363: } /* end Tprod */
1.237 brouard 8364: } else{ /* simple covariate */
1.264 brouard 8365: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8366: if(Dummy[j]==0){
8367: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8368: }else{ /* quantitative */
8369: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8370: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8371: }
1.237 brouard 8372: } /* end simple */
8373: } /* end j */
1.223 brouard 8374: }else{
8375: i=i-ncovmodel;
8376: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8377: fprintf(ficgp," (1.");
8378: }
1.227 brouard 8379:
1.223 brouard 8380: if(ng != 1){
8381: fprintf(ficgp,")/(1");
1.227 brouard 8382:
1.264 brouard 8383: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8384: if(nagesqr==0)
1.264 brouard 8385: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8386: else /* nagesqr =1 */
1.264 brouard 8387: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
1.217 brouard 8388:
1.223 brouard 8389: ij=1;
8390: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8391: if(cptcovage >0){
8392: if((j-2)==Tage[ij]) { /* Bug valgrind */
8393: if(ij <=cptcovage) { /* Bug valgrind */
8394: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8395: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8396: ij++;
8397: }
8398: }
8399: }else
8400: fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
1.223 brouard 8401: }
8402: fprintf(ficgp,")");
8403: }
8404: fprintf(ficgp,")");
8405: if(ng ==2)
1.276 brouard 8406: fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223 brouard 8407: else /* ng= 3 */
1.276 brouard 8408: fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223 brouard 8409: }else{ /* end ng <> 1 */
8410: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8411: fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
1.223 brouard 8412: }
8413: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8414: fprintf(ficgp,",");
8415: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8416: fprintf(ficgp,",");
8417: i=i+ncovmodel;
8418: } /* end k */
8419: } /* end k2 */
1.276 brouard 8420: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8421: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8422: } /* end k1 */
1.223 brouard 8423: } /* end ng */
8424: /* avoid: */
8425: fflush(ficgp);
1.126 brouard 8426: } /* end gnuplot */
8427:
8428:
8429: /*************** Moving average **************/
1.219 brouard 8430: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8431: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8432:
1.222 brouard 8433: int i, cpt, cptcod;
8434: int modcovmax =1;
8435: int mobilavrange, mob;
8436: int iage=0;
1.288 brouard 8437: int firstA1=0, firstA2=0;
1.222 brouard 8438:
1.266 brouard 8439: double sum=0., sumr=0.;
1.222 brouard 8440: double age;
1.266 brouard 8441: double *sumnewp, *sumnewm, *sumnewmr;
8442: double *agemingood, *agemaxgood;
8443: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8444:
8445:
1.278 brouard 8446: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8447: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8448:
8449: sumnewp = vector(1,ncovcombmax);
8450: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8451: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8452: agemingood = vector(1,ncovcombmax);
1.266 brouard 8453: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8454: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8455: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8456:
8457: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8458: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8459: sumnewp[cptcod]=0.;
1.266 brouard 8460: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8461: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8462: }
8463: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8464:
1.266 brouard 8465: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8466: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8467: else mobilavrange=mobilav;
8468: for (age=bage; age<=fage; age++)
8469: for (i=1; i<=nlstate;i++)
8470: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8471: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8472: /* We keep the original values on the extreme ages bage, fage and for
8473: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8474: we use a 5 terms etc. until the borders are no more concerned.
8475: */
8476: for (mob=3;mob <=mobilavrange;mob=mob+2){
8477: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8478: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8479: sumnewm[cptcod]=0.;
8480: for (i=1; i<=nlstate;i++){
1.222 brouard 8481: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8482: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8483: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8484: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8485: }
8486: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8487: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8488: } /* end i */
8489: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8490: } /* end cptcod */
1.222 brouard 8491: }/* end age */
8492: }/* end mob */
1.266 brouard 8493: }else{
8494: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8495: return -1;
1.266 brouard 8496: }
8497:
8498: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8499: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8500: if(invalidvarcomb[cptcod]){
8501: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8502: continue;
8503: }
1.219 brouard 8504:
1.266 brouard 8505: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8506: sumnewm[cptcod]=0.;
8507: sumnewmr[cptcod]=0.;
8508: for (i=1; i<=nlstate;i++){
8509: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8510: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8511: }
8512: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8513: agemingoodr[cptcod]=age;
8514: }
8515: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8516: agemingood[cptcod]=age;
8517: }
8518: } /* age */
8519: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8520: sumnewm[cptcod]=0.;
1.266 brouard 8521: sumnewmr[cptcod]=0.;
1.222 brouard 8522: for (i=1; i<=nlstate;i++){
8523: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8524: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8525: }
8526: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8527: agemaxgoodr[cptcod]=age;
1.222 brouard 8528: }
8529: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8530: agemaxgood[cptcod]=age;
8531: }
8532: } /* age */
8533: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8534: /* but they will change */
1.288 brouard 8535: firstA1=0;firstA2=0;
1.266 brouard 8536: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8537: sumnewm[cptcod]=0.;
8538: sumnewmr[cptcod]=0.;
8539: for (i=1; i<=nlstate;i++){
8540: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8541: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8542: }
8543: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8544: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8545: agemaxgoodr[cptcod]=age; /* age min */
8546: for (i=1; i<=nlstate;i++)
8547: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8548: }else{ /* bad we change the value with the values of good ages */
8549: for (i=1; i<=nlstate;i++){
8550: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8551: } /* i */
8552: } /* end bad */
8553: }else{
8554: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8555: agemaxgood[cptcod]=age;
8556: }else{ /* bad we change the value with the values of good ages */
8557: for (i=1; i<=nlstate;i++){
8558: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8559: } /* i */
8560: } /* end bad */
8561: }/* end else */
8562: sum=0.;sumr=0.;
8563: for (i=1; i<=nlstate;i++){
8564: sum+=mobaverage[(int)age][i][cptcod];
8565: sumr+=probs[(int)age][i][cptcod];
8566: }
8567: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8568: if(!firstA1){
8569: firstA1=1;
8570: printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
8571: }
8572: fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
1.266 brouard 8573: } /* end bad */
8574: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8575: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8576: if(!firstA2){
8577: firstA2=1;
8578: printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
8579: }
8580: fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
1.222 brouard 8581: } /* end bad */
8582: }/* age */
1.266 brouard 8583:
8584: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8585: sumnewm[cptcod]=0.;
1.266 brouard 8586: sumnewmr[cptcod]=0.;
1.222 brouard 8587: for (i=1; i<=nlstate;i++){
8588: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8589: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8590: }
8591: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8592: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8593: agemingoodr[cptcod]=age;
8594: for (i=1; i<=nlstate;i++)
8595: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8596: }else{ /* bad we change the value with the values of good ages */
8597: for (i=1; i<=nlstate;i++){
8598: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8599: } /* i */
8600: } /* end bad */
8601: }else{
8602: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8603: agemingood[cptcod]=age;
8604: }else{ /* bad */
8605: for (i=1; i<=nlstate;i++){
8606: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8607: } /* i */
8608: } /* end bad */
8609: }/* end else */
8610: sum=0.;sumr=0.;
8611: for (i=1; i<=nlstate;i++){
8612: sum+=mobaverage[(int)age][i][cptcod];
8613: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8614: }
1.266 brouard 8615: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8616: printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
1.266 brouard 8617: } /* end bad */
8618: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8619: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8620: printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
1.222 brouard 8621: } /* end bad */
8622: }/* age */
1.266 brouard 8623:
1.222 brouard 8624:
8625: for (age=bage; age<=fage; age++){
1.235 brouard 8626: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8627: sumnewp[cptcod]=0.;
8628: sumnewm[cptcod]=0.;
8629: for (i=1; i<=nlstate;i++){
8630: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8631: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8632: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8633: }
8634: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8635: }
8636: /* printf("\n"); */
8637: /* } */
1.266 brouard 8638:
1.222 brouard 8639: /* brutal averaging */
1.266 brouard 8640: /* for (i=1; i<=nlstate;i++){ */
8641: /* for (age=1; age<=bage; age++){ */
8642: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8643: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8644: /* } */
8645: /* for (age=fage; age<=AGESUP; age++){ */
8646: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8647: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8648: /* } */
8649: /* } /\* end i status *\/ */
8650: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8651: /* for (age=1; age<=AGESUP; age++){ */
8652: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8653: /* mobaverage[(int)age][i][cptcod]=0.; */
8654: /* } */
8655: /* } */
1.222 brouard 8656: }/* end cptcod */
1.266 brouard 8657: free_vector(agemaxgoodr,1, ncovcombmax);
8658: free_vector(agemaxgood,1, ncovcombmax);
8659: free_vector(agemingood,1, ncovcombmax);
8660: free_vector(agemingoodr,1, ncovcombmax);
8661: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8662: free_vector(sumnewm,1, ncovcombmax);
8663: free_vector(sumnewp,1, ncovcombmax);
8664: return 0;
8665: }/* End movingaverage */
1.218 brouard 8666:
1.126 brouard 8667:
1.296 brouard 8668:
1.126 brouard 8669: /************** Forecasting ******************/
1.296 brouard 8670: /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
8671: void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
8672: /* dateintemean, mean date of interviews
8673: dateprojd, year, month, day of starting projection
8674: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8675: agemin, agemax range of age
8676: dateprev1 dateprev2 range of dates during which prevalence is computed
8677: */
1.296 brouard 8678: /* double anprojd, mprojd, jprojd; */
8679: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8680: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8681: double agec; /* generic age */
1.296 brouard 8682: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8683: double *popeffectif,*popcount;
8684: double ***p3mat;
1.218 brouard 8685: /* double ***mobaverage; */
1.126 brouard 8686: char fileresf[FILENAMELENGTH];
8687:
8688: agelim=AGESUP;
1.211 brouard 8689: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8690: in each health status at the date of interview (if between dateprev1 and dateprev2).
8691: We still use firstpass and lastpass as another selection.
8692: */
1.214 brouard 8693: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8694: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8695:
1.201 brouard 8696: strcpy(fileresf,"F_");
8697: strcat(fileresf,fileresu);
1.126 brouard 8698: if((ficresf=fopen(fileresf,"w"))==NULL) {
8699: printf("Problem with forecast resultfile: %s\n", fileresf);
8700: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8701: }
1.235 brouard 8702: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8703: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8704:
1.225 brouard 8705: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8706:
8707:
8708: stepsize=(int) (stepm+YEARM-1)/YEARM;
8709: if (stepm<=12) stepsize=1;
8710: if(estepm < stepm){
8711: printf ("Problem %d lower than %d\n",estepm, stepm);
8712: }
1.270 brouard 8713: else{
8714: hstepm=estepm;
8715: }
8716: if(estepm > stepm){ /* Yes every two year */
8717: stepsize=2;
8718: }
1.296 brouard 8719: hstepm=hstepm/stepm;
1.126 brouard 8720:
1.296 brouard 8721:
8722: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8723: /* fractional in yp1 *\/ */
8724: /* aintmean=yp; */
8725: /* yp2=modf((yp1*12),&yp); */
8726: /* mintmean=yp; */
8727: /* yp1=modf((yp2*30.5),&yp); */
8728: /* jintmean=yp; */
8729: /* if(jintmean==0) jintmean=1; */
8730: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8731:
1.296 brouard 8732:
8733: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8734: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8735: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8736: i1=pow(2,cptcoveff);
1.126 brouard 8737: if (cptcovn < 1){i1=1;}
8738:
1.296 brouard 8739: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8740:
8741: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8742:
1.126 brouard 8743: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8744: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8745: for(k=1; k<=i1;k++){
1.253 brouard 8746: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8747: continue;
1.227 brouard 8748: if(invalidvarcomb[k]){
8749: printf("\nCombination (%d) projection ignored because no cases \n",k);
8750: continue;
8751: }
8752: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8753: for(j=1;j<=cptcoveff;j++) {
8754: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8755: }
1.235 brouard 8756: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8757: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8758: }
1.227 brouard 8759: fprintf(ficresf," yearproj age");
8760: for(j=1; j<=nlstate+ndeath;j++){
8761: for(i=1; i<=nlstate;i++)
8762: fprintf(ficresf," p%d%d",i,j);
8763: fprintf(ficresf," wp.%d",j);
8764: }
1.296 brouard 8765: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8766: fprintf(ficresf,"\n");
1.296 brouard 8767: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8768: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8769: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8770: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8771: nhstepm = nhstepm/hstepm;
8772: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8773: oldm=oldms;savm=savms;
1.268 brouard 8774: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8775: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8776: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8777: for (h=0; h<=nhstepm; h++){
8778: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8779: break;
8780: }
8781: }
8782: fprintf(ficresf,"\n");
8783: for(j=1;j<=cptcoveff;j++)
8784: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8785: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8786:
8787: for(j=1; j<=nlstate+ndeath;j++) {
8788: ppij=0.;
8789: for(i=1; i<=nlstate;i++) {
1.278 brouard 8790: if (mobilav>=1)
8791: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8792: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8793: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8794: }
1.268 brouard 8795: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8796: } /* end i */
8797: fprintf(ficresf," %.3f", ppij);
8798: }/* end j */
1.227 brouard 8799: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8800: } /* end agec */
1.266 brouard 8801: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8802: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8803: } /* end yearp */
8804: } /* end k */
1.219 brouard 8805:
1.126 brouard 8806: fclose(ficresf);
1.215 brouard 8807: printf("End of Computing forecasting \n");
8808: fprintf(ficlog,"End of Computing forecasting\n");
8809:
1.126 brouard 8810: }
8811:
1.269 brouard 8812: /************** Back Forecasting ******************/
1.296 brouard 8813: /* void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */
8814: void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
8815: /* back1, year, month, day of starting backprojection
1.267 brouard 8816: agemin, agemax range of age
8817: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8818: anback2 year of end of backprojection (same day and month as back1).
8819: prevacurrent and prev are prevalences.
1.267 brouard 8820: */
8821: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8822: double agec; /* generic age */
1.302 brouard 8823: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8824: double *popeffectif,*popcount;
8825: double ***p3mat;
8826: /* double ***mobaverage; */
8827: char fileresfb[FILENAMELENGTH];
8828:
1.268 brouard 8829: agelim=AGEINF;
1.267 brouard 8830: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8831: in each health status at the date of interview (if between dateprev1 and dateprev2).
8832: We still use firstpass and lastpass as another selection.
8833: */
8834: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8835: /* firstpass, lastpass, stepm, weightopt, model); */
8836:
8837: /*Do we need to compute prevalence again?*/
8838:
8839: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8840:
8841: strcpy(fileresfb,"FB_");
8842: strcat(fileresfb,fileresu);
8843: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8844: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8845: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8846: }
8847: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8848: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8849:
8850: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8851:
8852:
8853: stepsize=(int) (stepm+YEARM-1)/YEARM;
8854: if (stepm<=12) stepsize=1;
8855: if(estepm < stepm){
8856: printf ("Problem %d lower than %d\n",estepm, stepm);
8857: }
1.270 brouard 8858: else{
8859: hstepm=estepm;
8860: }
8861: if(estepm >= stepm){ /* Yes every two year */
8862: stepsize=2;
8863: }
1.267 brouard 8864:
8865: hstepm=hstepm/stepm;
1.296 brouard 8866: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8867: /* fractional in yp1 *\/ */
8868: /* aintmean=yp; */
8869: /* yp2=modf((yp1*12),&yp); */
8870: /* mintmean=yp; */
8871: /* yp1=modf((yp2*30.5),&yp); */
8872: /* jintmean=yp; */
8873: /* if(jintmean==0) jintmean=1; */
8874: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8875:
8876: i1=pow(2,cptcoveff);
8877: if (cptcovn < 1){i1=1;}
8878:
1.296 brouard 8879: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8880: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8881:
8882: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8883:
8884: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8885: for(k=1; k<=i1;k++){
8886: if(i1 != 1 && TKresult[nres]!= k)
8887: continue;
8888: if(invalidvarcomb[k]){
8889: printf("\nCombination (%d) projection ignored because no cases \n",k);
8890: continue;
8891: }
1.268 brouard 8892: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8893: for(j=1;j<=cptcoveff;j++) {
8894: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8895: }
8896: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8897: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8898: }
8899: fprintf(ficresfb," yearbproj age");
8900: for(j=1; j<=nlstate+ndeath;j++){
8901: for(i=1; i<=nlstate;i++)
1.268 brouard 8902: fprintf(ficresfb," b%d%d",i,j);
8903: fprintf(ficresfb," b.%d",j);
1.267 brouard 8904: }
1.296 brouard 8905: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8906: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8907: fprintf(ficresfb,"\n");
1.296 brouard 8908: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8909: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8910: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8911: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8912: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8913: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8914: nhstepm = nhstepm/hstepm;
8915: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8916: oldm=oldms;savm=savms;
1.268 brouard 8917: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8918: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8919: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8920: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8921: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8922: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8923: for (h=0; h<=nhstepm; h++){
1.268 brouard 8924: if (h*hstepm/YEARM*stepm ==-yearp) {
8925: break;
8926: }
8927: }
8928: fprintf(ficresfb,"\n");
8929: for(j=1;j<=cptcoveff;j++)
8930: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8931: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8932: for(i=1; i<=nlstate+ndeath;i++) {
8933: ppij=0.;ppi=0.;
8934: for(j=1; j<=nlstate;j++) {
8935: /* if (mobilav==1) */
1.269 brouard 8936: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8937: ppi=ppi+prevacurrent[(int)agec][j][k];
8938: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8939: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8940: /* else { */
8941: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8942: /* } */
1.268 brouard 8943: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8944: } /* end j */
8945: if(ppi <0.99){
8946: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8947: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8948: }
8949: fprintf(ficresfb," %.3f", ppij);
8950: }/* end j */
1.267 brouard 8951: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8952: } /* end agec */
8953: } /* end yearp */
8954: } /* end k */
1.217 brouard 8955:
1.267 brouard 8956: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8957:
1.267 brouard 8958: fclose(ficresfb);
8959: printf("End of Computing Back forecasting \n");
8960: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8961:
1.267 brouard 8962: }
1.217 brouard 8963:
1.269 brouard 8964: /* Variance of prevalence limit: varprlim */
8965: void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
1.288 brouard 8966: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8967:
8968: char fileresvpl[FILENAMELENGTH];
8969: FILE *ficresvpl;
8970: double **oldm, **savm;
8971: double **varpl; /* Variances of prevalence limits by age */
8972: int i1, k, nres, j ;
8973:
8974: strcpy(fileresvpl,"VPL_");
8975: strcat(fileresvpl,fileresu);
8976: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8977: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8978: exit(0);
8979: }
1.288 brouard 8980: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8981: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8982:
8983: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8984: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8985:
8986: i1=pow(2,cptcoveff);
8987: if (cptcovn < 1){i1=1;}
8988:
8989: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8990: for(k=1; k<=i1;k++){
8991: if(i1 != 1 && TKresult[nres]!= k)
8992: continue;
8993: fprintf(ficresvpl,"\n#****** ");
8994: printf("\n#****** ");
8995: fprintf(ficlog,"\n#****** ");
8996: for(j=1;j<=cptcoveff;j++) {
8997: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8998: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8999: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9000: }
9001: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9002: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9003: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9004: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9005: }
9006: fprintf(ficresvpl,"******\n");
9007: printf("******\n");
9008: fprintf(ficlog,"******\n");
9009:
9010: varpl=matrix(1,nlstate,(int) bage, (int) fage);
9011: oldm=oldms;savm=savms;
9012: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
9013: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
9014: /*}*/
9015: }
9016:
9017: fclose(ficresvpl);
1.288 brouard 9018: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
9019: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 9020:
9021: }
9022: /* Variance of back prevalence: varbprlim */
9023: void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
9024: /*------- Variance of back (stable) prevalence------*/
9025:
9026: char fileresvbl[FILENAMELENGTH];
9027: FILE *ficresvbl;
9028:
9029: double **oldm, **savm;
9030: double **varbpl; /* Variances of back prevalence limits by age */
9031: int i1, k, nres, j ;
9032:
9033: strcpy(fileresvbl,"VBL_");
9034: strcat(fileresvbl,fileresu);
9035: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
9036: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
9037: exit(0);
9038: }
9039: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
9040: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
9041:
9042:
9043: i1=pow(2,cptcoveff);
9044: if (cptcovn < 1){i1=1;}
9045:
9046: for(nres=1; nres <= nresult; nres++) /* For each resultline */
9047: for(k=1; k<=i1;k++){
9048: if(i1 != 1 && TKresult[nres]!= k)
9049: continue;
9050: fprintf(ficresvbl,"\n#****** ");
9051: printf("\n#****** ");
9052: fprintf(ficlog,"\n#****** ");
9053: for(j=1;j<=cptcoveff;j++) {
9054: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9055: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9056: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9057: }
9058: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9059: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9060: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9061: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9062: }
9063: fprintf(ficresvbl,"******\n");
9064: printf("******\n");
9065: fprintf(ficlog,"******\n");
9066:
9067: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
9068: oldm=oldms;savm=savms;
9069:
9070: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
9071: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
9072: /*}*/
9073: }
9074:
9075: fclose(ficresvbl);
9076: printf("done variance-covariance of back prevalence\n");fflush(stdout);
9077: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
9078:
9079: } /* End of varbprlim */
9080:
1.126 brouard 9081: /************** Forecasting *****not tested NB*************/
1.227 brouard 9082: /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
1.126 brouard 9083:
1.227 brouard 9084: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
9085: /* int *popage; */
9086: /* double calagedatem, agelim, kk1, kk2; */
9087: /* double *popeffectif,*popcount; */
9088: /* double ***p3mat,***tabpop,***tabpopprev; */
9089: /* /\* double ***mobaverage; *\/ */
9090: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 9091:
1.227 brouard 9092: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9093: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9094: /* agelim=AGESUP; */
9095: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 9096:
1.227 brouard 9097: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 9098:
9099:
1.227 brouard 9100: /* strcpy(filerespop,"POP_"); */
9101: /* strcat(filerespop,fileresu); */
9102: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
9103: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
9104: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
9105: /* } */
9106: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
9107: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 9108:
1.227 brouard 9109: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 9110:
1.227 brouard 9111: /* /\* if (mobilav!=0) { *\/ */
9112: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
9113: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
9114: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
9115: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
9116: /* /\* } *\/ */
9117: /* /\* } *\/ */
1.126 brouard 9118:
1.227 brouard 9119: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
9120: /* if (stepm<=12) stepsize=1; */
1.126 brouard 9121:
1.227 brouard 9122: /* agelim=AGESUP; */
1.126 brouard 9123:
1.227 brouard 9124: /* hstepm=1; */
9125: /* hstepm=hstepm/stepm; */
1.218 brouard 9126:
1.227 brouard 9127: /* if (popforecast==1) { */
9128: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
9129: /* printf("Problem with population file : %s\n",popfile);exit(0); */
9130: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
9131: /* } */
9132: /* popage=ivector(0,AGESUP); */
9133: /* popeffectif=vector(0,AGESUP); */
9134: /* popcount=vector(0,AGESUP); */
1.126 brouard 9135:
1.227 brouard 9136: /* i=1; */
9137: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 9138:
1.227 brouard 9139: /* imx=i; */
9140: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
9141: /* } */
1.218 brouard 9142:
1.227 brouard 9143: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
9144: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
9145: /* k=k+1; */
9146: /* fprintf(ficrespop,"\n#******"); */
9147: /* for(j=1;j<=cptcoveff;j++) { */
9148: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
9149: /* } */
9150: /* fprintf(ficrespop,"******\n"); */
9151: /* fprintf(ficrespop,"# Age"); */
9152: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
9153: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 9154:
1.227 brouard 9155: /* for (cpt=0; cpt<=0;cpt++) { */
9156: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 9157:
1.227 brouard 9158: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
9159: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
9160: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 9161:
1.227 brouard 9162: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
9163: /* oldm=oldms;savm=savms; */
9164: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 9165:
1.227 brouard 9166: /* for (h=0; h<=nhstepm; h++){ */
9167: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
9168: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
9169: /* } */
9170: /* for(j=1; j<=nlstate+ndeath;j++) { */
9171: /* kk1=0.;kk2=0; */
9172: /* for(i=1; i<=nlstate;i++) { */
9173: /* if (mobilav==1) */
9174: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
9175: /* else { */
9176: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
9177: /* } */
9178: /* } */
9179: /* if (h==(int)(calagedatem+12*cpt)){ */
9180: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
9181: /* /\*fprintf(ficrespop," %.3f", kk1); */
9182: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
9183: /* } */
9184: /* } */
9185: /* for(i=1; i<=nlstate;i++){ */
9186: /* kk1=0.; */
9187: /* for(j=1; j<=nlstate;j++){ */
9188: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
9189: /* } */
9190: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
9191: /* } */
1.218 brouard 9192:
1.227 brouard 9193: /* if (h==(int)(calagedatem+12*cpt)) */
9194: /* for(j=1; j<=nlstate;j++) */
9195: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
9196: /* } */
9197: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
9198: /* } */
9199: /* } */
1.218 brouard 9200:
1.227 brouard 9201: /* /\******\/ */
1.218 brouard 9202:
1.227 brouard 9203: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
9204: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
9205: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
9206: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
9207: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 9208:
1.227 brouard 9209: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
9210: /* oldm=oldms;savm=savms; */
9211: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
9212: /* for (h=0; h<=nhstepm; h++){ */
9213: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
9214: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
9215: /* } */
9216: /* for(j=1; j<=nlstate+ndeath;j++) { */
9217: /* kk1=0.;kk2=0; */
9218: /* for(i=1; i<=nlstate;i++) { */
9219: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
9220: /* } */
9221: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
9222: /* } */
9223: /* } */
9224: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
9225: /* } */
9226: /* } */
9227: /* } */
9228: /* } */
1.218 brouard 9229:
1.227 brouard 9230: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 9231:
1.227 brouard 9232: /* if (popforecast==1) { */
9233: /* free_ivector(popage,0,AGESUP); */
9234: /* free_vector(popeffectif,0,AGESUP); */
9235: /* free_vector(popcount,0,AGESUP); */
9236: /* } */
9237: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9238: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9239: /* fclose(ficrespop); */
9240: /* } /\* End of popforecast *\/ */
1.218 brouard 9241:
1.126 brouard 9242: int fileappend(FILE *fichier, char *optionfich)
9243: {
9244: if((fichier=fopen(optionfich,"a"))==NULL) {
9245: printf("Problem with file: %s\n", optionfich);
9246: fprintf(ficlog,"Problem with file: %s\n", optionfich);
9247: return (0);
9248: }
9249: fflush(fichier);
9250: return (1);
9251: }
9252:
9253:
9254: /**************** function prwizard **********************/
9255: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
9256: {
9257:
9258: /* Wizard to print covariance matrix template */
9259:
1.164 brouard 9260: char ca[32], cb[32];
9261: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 9262: int numlinepar;
9263:
9264: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9265: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9266: for(i=1; i <=nlstate; i++){
9267: jj=0;
9268: for(j=1; j <=nlstate+ndeath; j++){
9269: if(j==i) continue;
9270: jj++;
9271: /*ca[0]= k+'a'-1;ca[1]='\0';*/
9272: printf("%1d%1d",i,j);
9273: fprintf(ficparo,"%1d%1d",i,j);
9274: for(k=1; k<=ncovmodel;k++){
9275: /* printf(" %lf",param[i][j][k]); */
9276: /* fprintf(ficparo," %lf",param[i][j][k]); */
9277: printf(" 0.");
9278: fprintf(ficparo," 0.");
9279: }
9280: printf("\n");
9281: fprintf(ficparo,"\n");
9282: }
9283: }
9284: printf("# Scales (for hessian or gradient estimation)\n");
9285: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
9286: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
9287: for(i=1; i <=nlstate; i++){
9288: jj=0;
9289: for(j=1; j <=nlstate+ndeath; j++){
9290: if(j==i) continue;
9291: jj++;
9292: fprintf(ficparo,"%1d%1d",i,j);
9293: printf("%1d%1d",i,j);
9294: fflush(stdout);
9295: for(k=1; k<=ncovmodel;k++){
9296: /* printf(" %le",delti3[i][j][k]); */
9297: /* fprintf(ficparo," %le",delti3[i][j][k]); */
9298: printf(" 0.");
9299: fprintf(ficparo," 0.");
9300: }
9301: numlinepar++;
9302: printf("\n");
9303: fprintf(ficparo,"\n");
9304: }
9305: }
9306: printf("# Covariance matrix\n");
9307: /* # 121 Var(a12)\n\ */
9308: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9309: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9310: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9311: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9312: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9313: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9314: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9315: fflush(stdout);
9316: fprintf(ficparo,"# Covariance matrix\n");
9317: /* # 121 Var(a12)\n\ */
9318: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9319: /* # ...\n\ */
9320: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9321:
9322: for(itimes=1;itimes<=2;itimes++){
9323: jj=0;
9324: for(i=1; i <=nlstate; i++){
9325: for(j=1; j <=nlstate+ndeath; j++){
9326: if(j==i) continue;
9327: for(k=1; k<=ncovmodel;k++){
9328: jj++;
9329: ca[0]= k+'a'-1;ca[1]='\0';
9330: if(itimes==1){
9331: printf("#%1d%1d%d",i,j,k);
9332: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9333: }else{
9334: printf("%1d%1d%d",i,j,k);
9335: fprintf(ficparo,"%1d%1d%d",i,j,k);
9336: /* printf(" %.5le",matcov[i][j]); */
9337: }
9338: ll=0;
9339: for(li=1;li <=nlstate; li++){
9340: for(lj=1;lj <=nlstate+ndeath; lj++){
9341: if(lj==li) continue;
9342: for(lk=1;lk<=ncovmodel;lk++){
9343: ll++;
9344: if(ll<=jj){
9345: cb[0]= lk +'a'-1;cb[1]='\0';
9346: if(ll<jj){
9347: if(itimes==1){
9348: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9349: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9350: }else{
9351: printf(" 0.");
9352: fprintf(ficparo," 0.");
9353: }
9354: }else{
9355: if(itimes==1){
9356: printf(" Var(%s%1d%1d)",ca,i,j);
9357: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9358: }else{
9359: printf(" 0.");
9360: fprintf(ficparo," 0.");
9361: }
9362: }
9363: }
9364: } /* end lk */
9365: } /* end lj */
9366: } /* end li */
9367: printf("\n");
9368: fprintf(ficparo,"\n");
9369: numlinepar++;
9370: } /* end k*/
9371: } /*end j */
9372: } /* end i */
9373: } /* end itimes */
9374:
9375: } /* end of prwizard */
9376: /******************* Gompertz Likelihood ******************************/
9377: double gompertz(double x[])
9378: {
1.302 brouard 9379: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9380: int i,n=0; /* n is the size of the sample */
9381:
1.220 brouard 9382: for (i=1;i<=imx ; i++) {
1.126 brouard 9383: sump=sump+weight[i];
9384: /* sump=sump+1;*/
9385: num=num+1;
9386: }
1.302 brouard 9387: L=0.0;
9388: /* agegomp=AGEGOMP; */
1.126 brouard 9389: /* for (i=0; i<=imx; i++)
9390: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
9391:
1.302 brouard 9392: for (i=1;i<=imx ; i++) {
9393: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9394: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9395: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9396: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9397: * +
9398: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9399: */
9400: if (wav[i] > 1 || agedc[i] < AGESUP) {
9401: if (cens[i] == 1){
9402: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9403: } else if (cens[i] == 0){
1.126 brouard 9404: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9405: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9406: } else
9407: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9408: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9409: L=L+A*weight[i];
1.126 brouard 9410: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
1.302 brouard 9411: }
9412: }
1.126 brouard 9413:
1.302 brouard 9414: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9415:
9416: return -2*L*num/sump;
9417: }
9418:
1.136 brouard 9419: #ifdef GSL
9420: /******************* Gompertz_f Likelihood ******************************/
9421: double gompertz_f(const gsl_vector *v, void *params)
9422: {
1.302 brouard 9423: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9424: double *x= (double *) v->data;
9425: int i,n=0; /* n is the size of the sample */
9426:
9427: for (i=0;i<=imx-1 ; i++) {
9428: sump=sump+weight[i];
9429: /* sump=sump+1;*/
9430: num=num+1;
9431: }
9432:
9433:
9434: /* for (i=0; i<=imx; i++)
9435: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
9436: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9437: for (i=1;i<=imx ; i++)
9438: {
9439: if (cens[i] == 1 && wav[i]>1)
9440: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9441:
9442: if (cens[i] == 0 && wav[i]>1)
9443: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9444: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9445:
9446: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9447: if (wav[i] > 1 ) { /* ??? */
9448: LL=LL+A*weight[i];
9449: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
9450: }
9451: }
9452:
9453: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9454: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9455:
9456: return -2*LL*num/sump;
9457: }
9458: #endif
9459:
1.126 brouard 9460: /******************* Printing html file ***********/
1.201 brouard 9461: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9462: int lastpass, int stepm, int weightopt, char model[],\
9463: int imx, double p[],double **matcov,double agemortsup){
9464: int i,k;
9465:
9466: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9467: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9468: for (i=1;i<=2;i++)
9469: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.199 brouard 9470: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9471: fprintf(fichtm,"</ul>");
9472:
9473: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9474:
9475: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
9476:
9477: for (k=agegomp;k<(agemortsup-2);k++)
9478: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
9479:
9480:
9481: fflush(fichtm);
9482: }
9483:
9484: /******************* Gnuplot file **************/
1.201 brouard 9485: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9486:
9487: char dirfileres[132],optfileres[132];
1.164 brouard 9488:
1.126 brouard 9489: int ng;
9490:
9491:
9492: /*#ifdef windows */
9493: fprintf(ficgp,"cd \"%s\" \n",pathc);
9494: /*#endif */
9495:
9496:
9497: strcpy(dirfileres,optionfilefiname);
9498: strcpy(optfileres,"vpl");
1.199 brouard 9499: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9500: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9501: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9502: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9503: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9504:
9505: }
9506:
1.136 brouard 9507: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9508: {
1.126 brouard 9509:
1.136 brouard 9510: /*-------- data file ----------*/
9511: FILE *fic;
9512: char dummy[]=" ";
1.240 brouard 9513: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9514: int lstra;
1.136 brouard 9515: int linei, month, year,iout;
1.302 brouard 9516: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9517: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9518: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9519: char *stratrunc;
1.223 brouard 9520:
1.240 brouard 9521: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9522: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9523:
1.240 brouard 9524: for(v=1; v <=ncovcol;v++){
9525: DummyV[v]=0;
9526: FixedV[v]=0;
9527: }
9528: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9529: DummyV[v]=1;
9530: FixedV[v]=0;
9531: }
9532: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9533: DummyV[v]=0;
9534: FixedV[v]=1;
9535: }
9536: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9537: DummyV[v]=1;
9538: FixedV[v]=1;
9539: }
9540: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9541: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9542: fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9543: }
1.126 brouard 9544:
1.136 brouard 9545: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9546: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9547: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9548: }
1.126 brouard 9549:
1.302 brouard 9550: /* Is it a BOM UTF-8 Windows file? */
9551: /* First data line */
9552: linei=0;
9553: while(fgets(line, MAXLINE, fic)) {
9554: noffset=0;
9555: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9556: {
9557: noffset=noffset+3;
9558: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9559: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9560: fflush(ficlog); return 1;
9561: }
9562: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9563: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9564: {
9565: noffset=noffset+2;
1.304 brouard 9566: printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
9567: fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302 brouard 9568: fflush(ficlog); return 1;
9569: }
9570: else if( line[0] == 0 && line[1] == 0)
9571: {
9572: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9573: noffset=noffset+4;
1.304 brouard 9574: printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
9575: fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302 brouard 9576: fflush(ficlog); return 1;
9577: }
9578: } else{
9579: ;/*printf(" Not a BOM file\n");*/
9580: }
9581: /* If line starts with a # it is a comment */
9582: if (line[noffset] == '#') {
9583: linei=linei+1;
9584: break;
9585: }else{
9586: break;
9587: }
9588: }
9589: fclose(fic);
9590: if((fic=fopen(datafile,"r"))==NULL) {
9591: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9592: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9593: }
9594: /* Not a Bom file */
9595:
1.136 brouard 9596: i=1;
9597: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9598: linei=linei+1;
9599: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9600: if(line[j] == '\t')
9601: line[j] = ' ';
9602: }
9603: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9604: ;
9605: };
9606: line[j+1]=0; /* Trims blanks at end of line */
9607: if(line[0]=='#'){
9608: fprintf(ficlog,"Comment line\n%s\n",line);
9609: printf("Comment line\n%s\n",line);
9610: continue;
9611: }
9612: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9613: strcpy(line, linetmp);
1.223 brouard 9614:
9615: /* Loops on waves */
9616: for (j=maxwav;j>=1;j--){
9617: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9618: cutv(stra, strb, line, ' ');
9619: if(strb[0]=='.') { /* Missing value */
9620: lval=-1;
9621: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9622: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9623: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9624: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
9625: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
9626: return 1;
9627: }
9628: }else{
9629: errno=0;
9630: /* what_kind_of_number(strb); */
9631: dval=strtod(strb,&endptr);
9632: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9633: /* if(strb != endptr && *endptr == '\0') */
9634: /* dval=dlval; */
9635: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9636: if( strb[0]=='\0' || (*endptr != '\0')){
9637: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
9638: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
9639: return 1;
9640: }
9641: cotqvar[j][iv][i]=dval;
9642: cotvar[j][ntv+iv][i]=dval;
9643: }
9644: strcpy(line,stra);
1.223 brouard 9645: }/* end loop ntqv */
1.225 brouard 9646:
1.223 brouard 9647: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9648: cutv(stra, strb, line, ' ');
9649: if(strb[0]=='.') { /* Missing value */
9650: lval=-1;
9651: }else{
9652: errno=0;
9653: lval=strtol(strb,&endptr,10);
9654: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9655: if( strb[0]=='\0' || (*endptr != '\0')){
9656: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
9657: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
9658: return 1;
9659: }
9660: }
9661: if(lval <-1 || lval >1){
9662: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.319 ! brouard 9663: Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
1.223 brouard 9664: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9665: For example, for multinomial values like 1, 2 and 3,\n \
9666: build V1=0 V2=0 for the reference value (1),\n \
9667: V1=1 V2=0 for (2) \n \
1.223 brouard 9668: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9669: output of IMaCh is often meaningless.\n \
1.319 ! brouard 9670: Exiting.\n",lval,linei, i,line,iv,j);
1.238 brouard 9671: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.319 ! brouard 9672: Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
1.223 brouard 9673: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9674: For example, for multinomial values like 1, 2 and 3,\n \
9675: build V1=0 V2=0 for the reference value (1),\n \
9676: V1=1 V2=0 for (2) \n \
1.223 brouard 9677: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9678: output of IMaCh is often meaningless.\n \
1.319 ! brouard 9679: Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
1.238 brouard 9680: return 1;
9681: }
9682: cotvar[j][iv][i]=(double)(lval);
9683: strcpy(line,stra);
1.223 brouard 9684: }/* end loop ntv */
1.225 brouard 9685:
1.223 brouard 9686: /* Statuses at wave */
1.137 brouard 9687: cutv(stra, strb, line, ' ');
1.223 brouard 9688: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9689: lval=-1;
1.136 brouard 9690: }else{
1.238 brouard 9691: errno=0;
9692: lval=strtol(strb,&endptr,10);
9693: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9694: if( strb[0]=='\0' || (*endptr != '\0')){
9695: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
9696: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
9697: return 1;
9698: }
1.136 brouard 9699: }
1.225 brouard 9700:
1.136 brouard 9701: s[j][i]=lval;
1.225 brouard 9702:
1.223 brouard 9703: /* Date of Interview */
1.136 brouard 9704: strcpy(line,stra);
9705: cutv(stra, strb,line,' ');
1.169 brouard 9706: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9707: }
1.169 brouard 9708: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9709: month=99;
9710: year=9999;
1.136 brouard 9711: }else{
1.225 brouard 9712: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
9713: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
9714: return 1;
1.136 brouard 9715: }
9716: anint[j][i]= (double) year;
1.302 brouard 9717: mint[j][i]= (double)month;
9718: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9719: /* printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
9720: /* fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
9721: /* } */
1.136 brouard 9722: strcpy(line,stra);
1.223 brouard 9723: } /* End loop on waves */
1.225 brouard 9724:
1.223 brouard 9725: /* Date of death */
1.136 brouard 9726: cutv(stra, strb,line,' ');
1.169 brouard 9727: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9728: }
1.169 brouard 9729: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9730: month=99;
9731: year=9999;
9732: }else{
1.141 brouard 9733: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
1.225 brouard 9734: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
9735: return 1;
1.136 brouard 9736: }
9737: andc[i]=(double) year;
9738: moisdc[i]=(double) month;
9739: strcpy(line,stra);
9740:
1.223 brouard 9741: /* Date of birth */
1.136 brouard 9742: cutv(stra, strb,line,' ');
1.169 brouard 9743: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9744: }
1.169 brouard 9745: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9746: month=99;
9747: year=9999;
9748: }else{
1.141 brouard 9749: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
9750: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 9751: return 1;
1.136 brouard 9752: }
9753: if (year==9999) {
1.141 brouard 9754: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
9755: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.225 brouard 9756: return 1;
9757:
1.136 brouard 9758: }
9759: annais[i]=(double)(year);
1.302 brouard 9760: moisnais[i]=(double)(month);
9761: for (j=1;j<=maxwav;j++){
9762: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9763: printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
9764: fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
9765: }
9766: }
9767:
1.136 brouard 9768: strcpy(line,stra);
1.225 brouard 9769:
1.223 brouard 9770: /* Sample weight */
1.136 brouard 9771: cutv(stra, strb,line,' ');
9772: errno=0;
9773: dval=strtod(strb,&endptr);
9774: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9775: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9776: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 9777: fflush(ficlog);
9778: return 1;
9779: }
9780: weight[i]=dval;
9781: strcpy(line,stra);
1.225 brouard 9782:
1.223 brouard 9783: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9784: cutv(stra, strb, line, ' ');
9785: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9786: lval=-1;
1.311 brouard 9787: coqvar[iv][i]=NAN;
9788: covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
1.223 brouard 9789: }else{
1.225 brouard 9790: errno=0;
9791: /* what_kind_of_number(strb); */
9792: dval=strtod(strb,&endptr);
9793: /* if(strb != endptr && *endptr == '\0') */
9794: /* dval=dlval; */
9795: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9796: if( strb[0]=='\0' || (*endptr != '\0')){
9797: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);
9798: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value (out of %d) constant for all waves. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqv, maxwav);fflush(ficlog);
9799: return 1;
9800: }
9801: coqvar[iv][i]=dval;
1.226 brouard 9802: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9803: }
9804: strcpy(line,stra);
9805: }/* end loop nqv */
1.136 brouard 9806:
1.223 brouard 9807: /* Covariate values */
1.136 brouard 9808: for (j=ncovcol;j>=1;j--){
9809: cutv(stra, strb,line,' ');
1.223 brouard 9810: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9811: lval=-1;
1.136 brouard 9812: }else{
1.225 brouard 9813: errno=0;
9814: lval=strtol(strb,&endptr,10);
9815: if( strb[0]=='\0' || (*endptr != '\0')){
9816: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
9817: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
9818: return 1;
9819: }
1.136 brouard 9820: }
9821: if(lval <-1 || lval >1){
1.225 brouard 9822: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9823: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9824: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9825: For example, for multinomial values like 1, 2 and 3,\n \
9826: build V1=0 V2=0 for the reference value (1),\n \
9827: V1=1 V2=0 for (2) \n \
1.136 brouard 9828: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9829: output of IMaCh is often meaningless.\n \
1.136 brouard 9830: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9831: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9832: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9833: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9834: For example, for multinomial values like 1, 2 and 3,\n \
9835: build V1=0 V2=0 for the reference value (1),\n \
9836: V1=1 V2=0 for (2) \n \
1.136 brouard 9837: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9838: output of IMaCh is often meaningless.\n \
1.136 brouard 9839: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9840: return 1;
1.136 brouard 9841: }
9842: covar[j][i]=(double)(lval);
9843: strcpy(line,stra);
9844: }
9845: lstra=strlen(stra);
1.225 brouard 9846:
1.136 brouard 9847: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9848: stratrunc = &(stra[lstra-9]);
9849: num[i]=atol(stratrunc);
9850: }
9851: else
9852: num[i]=atol(stra);
9853: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9854: printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
9855:
9856: i=i+1;
9857: } /* End loop reading data */
1.225 brouard 9858:
1.136 brouard 9859: *imax=i-1; /* Number of individuals */
9860: fclose(fic);
1.225 brouard 9861:
1.136 brouard 9862: return (0);
1.164 brouard 9863: /* endread: */
1.225 brouard 9864: printf("Exiting readdata: ");
9865: fclose(fic);
9866: return (1);
1.223 brouard 9867: }
1.126 brouard 9868:
1.234 brouard 9869: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9870: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9871: while (*p2 == ' ')
1.234 brouard 9872: p2++;
9873: /* while ((*p1++ = *p2++) !=0) */
9874: /* ; */
9875: /* do */
9876: /* while (*p2 == ' ') */
9877: /* p2++; */
9878: /* while (*p1++ == *p2++); */
9879: *stri=p2;
1.145 brouard 9880: }
9881:
1.235 brouard 9882: int decoderesult ( char resultline[], int nres)
1.230 brouard 9883: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9884: {
1.235 brouard 9885: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9886: char resultsav[MAXLINE];
1.234 brouard 9887: int resultmodel[MAXLINE];
9888: int modelresult[MAXLINE];
1.230 brouard 9889: char stra[80], strb[80], strc[80], strd[80],stre[80];
9890:
1.234 brouard 9891: removefirstspace(&resultline);
1.230 brouard 9892:
9893: if (strstr(resultline,"v") !=0){
9894: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9895: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9896: return 1;
9897: }
9898: trimbb(resultsav, resultline);
9899: if (strlen(resultsav) >1){
9900: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9901: }
1.253 brouard 9902: if(j == 0){ /* Resultline but no = */
9903: TKresult[nres]=0; /* Combination for the nresult and the model */
9904: return (0);
9905: }
1.234 brouard 9906: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
1.318 brouard 9907: printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
1.310 brouard 9908: fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
1.234 brouard 9909: }
9910: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9911: if(nbocc(resultsav,'=') >1){
1.318 brouard 9912: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//* resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
9913: cutl(strc,strd,strb,'='); /* strb:"V4=1" strc="1" strd="V4" */
1.234 brouard 9914: }else
9915: cutl(strc,strd,resultsav,'=');
1.318 brouard 9916: Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
1.234 brouard 9917:
1.230 brouard 9918: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
1.318 brouard 9919: Tvarsel[k]=atoi(strc); /* 4 */ /* Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
1.230 brouard 9920: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9921: /* cptcovsel++; */
9922: if (nbocc(stra,'=') >0)
9923: strcpy(resultsav,stra); /* and analyzes it */
9924: }
1.235 brouard 9925: /* Checking for missing or useless values in comparison of current model needs */
1.318 brouard 9926: for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9927: if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.234 brouard 9928: match=0;
1.318 brouard 9929: for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9930: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9931: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.318 brouard 9932: match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
1.234 brouard 9933: break;
9934: }
9935: }
9936: if(match == 0){
1.310 brouard 9937: printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
9938: fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
9939: return 1;
1.234 brouard 9940: }
9941: }
9942: }
1.235 brouard 9943: /* Checking for missing or useless values in comparison of current model needs */
1.318 brouard 9944: for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9945: match=0;
1.318 brouard 9946: for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.235 brouard 9947: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9948: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.318 brouard 9949: resultmodel[k1]=k2; /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9950: ++match;
9951: }
9952: }
9953: }
9954: if(match == 0){
9955: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
1.310 brouard 9956: fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9957: return 1;
1.234 brouard 9958: }else if(match > 1){
9959: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
1.310 brouard 9960: fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9961: return 1;
1.234 brouard 9962: }
9963: }
1.235 brouard 9964:
1.234 brouard 9965: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9966: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9967: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9968: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9969: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9970: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9971: /* 1 0 0 0 */
9972: /* 2 1 0 0 */
9973: /* 3 0 1 0 */
9974: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9975: /* 5 0 0 1 */
9976: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9977: /* 7 0 1 1 */
9978: /* 8 1 1 1 */
1.237 brouard 9979: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9980: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9981: /* V5*age V5 known which value for nres? */
9982: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.318 brouard 9983: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */
1.235 brouard 9984: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9985: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9986: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9987: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9988: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9989: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9990: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9991: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9992: k4++;;
9993: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
1.318 brouard 9994: k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */
9995: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9996: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9997: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9998: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9999: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
10000: k4q++;;
10001: }
10002: }
1.234 brouard 10003:
1.235 brouard 10004: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 10005: return (0);
10006: }
1.235 brouard 10007:
1.230 brouard 10008: int decodemodel( char model[], int lastobs)
10009: /**< This routine decodes the model and returns:
1.224 brouard 10010: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
10011: * - nagesqr = 1 if age*age in the model, otherwise 0.
10012: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
10013: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
10014: * - cptcovage number of covariates with age*products =2
10015: * - cptcovs number of simple covariates
10016: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
10017: * which is a new column after the 9 (ncovcol) variables.
1.319 ! brouard 10018: * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
1.224 brouard 10019: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
10020: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
10021: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
10022: */
1.319 ! brouard 10023: /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
1.136 brouard 10024: {
1.238 brouard 10025: int i, j, k, ks, v;
1.227 brouard 10026: int j1, k1, k2, k3, k4;
1.136 brouard 10027: char modelsav[80];
1.145 brouard 10028: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 10029: char *strpt;
1.136 brouard 10030:
1.145 brouard 10031: /*removespace(model);*/
1.136 brouard 10032: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 10033: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 10034: if (strstr(model,"AGE") !=0){
1.192 brouard 10035: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
10036: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 10037: return 1;
10038: }
1.141 brouard 10039: if (strstr(model,"v") !=0){
10040: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
10041: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
10042: return 1;
10043: }
1.187 brouard 10044: strcpy(modelsav,model);
10045: if ((strpt=strstr(model,"age*age")) !=0){
10046: printf(" strpt=%s, model=%s\n",strpt, model);
10047: if(strpt != model){
1.234 brouard 10048: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 10049: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 10050: corresponding column of parameters.\n",model);
1.234 brouard 10051: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 10052: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 10053: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 10054: return 1;
1.225 brouard 10055: }
1.187 brouard 10056: nagesqr=1;
10057: if (strstr(model,"+age*age") !=0)
1.234 brouard 10058: substrchaine(modelsav, model, "+age*age");
1.187 brouard 10059: else if (strstr(model,"age*age+") !=0)
1.234 brouard 10060: substrchaine(modelsav, model, "age*age+");
1.187 brouard 10061: else
1.234 brouard 10062: substrchaine(modelsav, model, "age*age");
1.187 brouard 10063: }else
10064: nagesqr=0;
10065: if (strlen(modelsav) >1){
10066: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
10067: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 10068: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 10069: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 10070: * cst, age and age*age
10071: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
10072: /* including age products which are counted in cptcovage.
10073: * but the covariates which are products must be treated
10074: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 10075: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
10076: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 10077:
10078:
1.187 brouard 10079: /* Design
10080: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
10081: * < ncovcol=8 >
10082: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
10083: * k= 1 2 3 4 5 6 7 8
10084: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
10085: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 10086: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
10087: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 10088: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
10089: * Tage[++cptcovage]=k
10090: * if products, new covar are created after ncovcol with k1
10091: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
10092: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
10093: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
10094: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
10095: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
10096: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
10097: * < ncovcol=8 >
10098: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
10099: * k= 1 2 3 4 5 6 7 8 9 10 11 12
10100: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
1.319 ! brouard 10101: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
1.187 brouard 10102: * p Tprod[1]@2={ 6, 5}
10103: *p Tvard[1][1]@4= {7, 8, 5, 6}
10104: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
10105: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1.319 ! brouard 10106: *How to reorganize? Tvars(orted)
1.187 brouard 10107: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
10108: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
10109: * {2, 1, 4, 8, 5, 6, 3, 7}
10110: * Struct []
10111: */
1.225 brouard 10112:
1.187 brouard 10113: /* This loop fills the array Tvar from the string 'model'.*/
10114: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
10115: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
10116: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
10117: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
10118: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
10119: /* k=1 Tvar[1]=2 (from V2) */
10120: /* k=5 Tvar[5] */
10121: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 10122: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 10123: /* } */
1.198 brouard 10124: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 10125: /*
10126: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 10127: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
10128: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
10129: }
1.187 brouard 10130: cptcovage=0;
1.319 ! brouard 10131: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
! 10132: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
! 10133: modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */ /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
! 10134: if (nbocc(modelsav,'+')==0)
! 10135: strcpy(strb,modelsav); /* and analyzes it */
1.234 brouard 10136: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
10137: /*scanf("%d",i);*/
1.319 ! brouard 10138: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */
! 10139: cutl(strc,strd,strb,'*'); /**< k=1 strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
1.234 brouard 10140: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
10141: /* covar is not filled and then is empty */
10142: cptcovprod--;
10143: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
1.319 ! brouard 10144: Tvar[k]=atoi(stre); /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
1.234 brouard 10145: Typevar[k]=1; /* 1 for age product */
1.319 ! brouard 10146: cptcovage++; /* Counts the number of covariates which include age as a product */
! 10147: Tage[cptcovage]=k; /* V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
1.234 brouard 10148: /*printf("stre=%s ", stre);*/
10149: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
10150: cptcovprod--;
10151: cutl(stre,strb,strc,'V');
10152: Tvar[k]=atoi(stre);
10153: Typevar[k]=1; /* 1 for age product */
10154: cptcovage++;
10155: Tage[cptcovage]=k;
10156: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
10157: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
10158: cptcovn++;
10159: cptcovprodnoage++;k1++;
10160: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
10161: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
10162: because this model-covariate is a construction we invent a new column
10163: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
1.319 ! brouard 10164: If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2
! 10165: thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
! 10166: Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */
1.234 brouard 10167: Typevar[k]=2; /* 2 for double fixed dummy covariates */
10168: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
10169: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.319 ! brouard 10170: Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
1.234 brouard 10171: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
10172: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
10173: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
10174: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
10175: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 10176: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 10177: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
10178: for (i=1; i<=lastobs;i++){
10179: /* Computes the new covariate which is a product of
10180: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
10181: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
10182: }
10183: } /* End age is not in the model */
10184: } /* End if model includes a product */
1.319 ! brouard 10185: else { /* not a product */
1.234 brouard 10186: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
10187: /* scanf("%d",i);*/
10188: cutl(strd,strc,strb,'V');
10189: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
10190: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
10191: Tvar[k]=atoi(strd);
10192: Typevar[k]=0; /* 0 for simple covariates */
10193: }
10194: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 10195: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 10196: scanf("%d",i);*/
1.187 brouard 10197: } /* end of loop + on total covariates */
10198: } /* end if strlen(modelsave == 0) age*age might exist */
10199: } /* end if strlen(model == 0) */
1.136 brouard 10200:
10201: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
10202: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 10203:
1.136 brouard 10204: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 10205: printf("cptcovprod=%d ", cptcovprod);
10206: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
10207: scanf("%d ",i);*/
10208:
10209:
1.230 brouard 10210: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
10211: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 10212: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
10213: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
10214: k = 1 2 3 4 5 6 7 8 9
10215: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
1.319 ! brouard 10216: Typevar[k]= 0 0 0 2 1 0 2 1 0
1.227 brouard 10217: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
10218: Dummy[k] 1 0 0 0 3 1 1 2 3
10219: Tmodelind[combination of covar]=k;
1.225 brouard 10220: */
10221: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 10222: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 10223: /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=Vn*Vm for product */
1.226 brouard 10224: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.318 brouard 10225: printf("Model=1+age+%s\n\
1.227 brouard 10226: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
10227: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
10228: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
1.318 brouard 10229: fprintf(ficlog,"Model=1+age+%s\n\
1.227 brouard 10230: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
10231: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
10232: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
1.285 brouard 10233: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 10234: for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
10235: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 10236: Fixed[k]= 0;
10237: Dummy[k]= 0;
1.225 brouard 10238: ncoveff++;
1.232 brouard 10239: ncovf++;
1.234 brouard 10240: nsd++;
10241: modell[k].maintype= FTYPE;
10242: TvarsD[nsd]=Tvar[k];
10243: TvarsDind[nsd]=k;
10244: TvarF[ncovf]=Tvar[k];
10245: TvarFind[ncovf]=k;
10246: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
10247: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
10248: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
10249: Fixed[k]= 0;
10250: Dummy[k]= 0;
10251: ncoveff++;
10252: ncovf++;
10253: modell[k].maintype= FTYPE;
10254: TvarF[ncovf]=Tvar[k];
10255: TvarFind[ncovf]=k;
1.230 brouard 10256: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 10257: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 10258: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
1.227 brouard 10259: Fixed[k]= 0;
10260: Dummy[k]= 1;
1.230 brouard 10261: nqfveff++;
1.234 brouard 10262: modell[k].maintype= FTYPE;
10263: modell[k].subtype= FQ;
10264: nsq++;
10265: TvarsQ[nsq]=Tvar[k];
10266: TvarsQind[nsq]=k;
1.232 brouard 10267: ncovf++;
1.234 brouard 10268: TvarF[ncovf]=Tvar[k];
10269: TvarFind[ncovf]=k;
1.231 brouard 10270: TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.230 brouard 10271: TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1.242 brouard 10272: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 10273: Fixed[k]= 1;
10274: Dummy[k]= 0;
1.225 brouard 10275: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 10276: modell[k].maintype= VTYPE;
10277: modell[k].subtype= VD;
10278: nsd++;
10279: TvarsD[nsd]=Tvar[k];
10280: TvarsDind[nsd]=k;
10281: ncovv++; /* Only simple time varying variables */
10282: TvarV[ncovv]=Tvar[k];
1.242 brouard 10283: TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
1.231 brouard 10284: TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
10285: TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
1.228 brouard 10286: printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
10287: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 10288: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 10289: Fixed[k]= 1;
10290: Dummy[k]= 1;
10291: nqtveff++;
10292: modell[k].maintype= VTYPE;
10293: modell[k].subtype= VQ;
10294: ncovv++; /* Only simple time varying variables */
10295: nsq++;
1.319 ! brouard 10296: TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
1.234 brouard 10297: TvarsQind[nsq]=k;
10298: TvarV[ncovv]=Tvar[k];
1.242 brouard 10299: TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
1.231 brouard 10300: TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
10301: TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
1.234 brouard 10302: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
10303: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
10304: printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
1.228 brouard 10305: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 10306: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 10307: ncova++;
10308: TvarA[ncova]=Tvar[k];
10309: TvarAind[ncova]=k;
1.231 brouard 10310: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10311: Fixed[k]= 2;
10312: Dummy[k]= 2;
10313: modell[k].maintype= ATYPE;
10314: modell[k].subtype= APFD;
10315: /* ncoveff++; */
1.227 brouard 10316: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10317: Fixed[k]= 2;
10318: Dummy[k]= 3;
10319: modell[k].maintype= ATYPE;
10320: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10321: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10322: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10323: Fixed[k]= 3;
10324: Dummy[k]= 2;
10325: modell[k].maintype= ATYPE;
10326: modell[k].subtype= APVD; /* Product age * varying dummy */
10327: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10328: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10329: Fixed[k]= 3;
10330: Dummy[k]= 3;
10331: modell[k].maintype= ATYPE;
10332: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10333: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10334: }
10335: }else if (Typevar[k] == 2) { /* product without age */
10336: k1=Tposprod[k];
10337: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10338: if(Tvard[k1][2] <=ncovcol){
10339: Fixed[k]= 1;
10340: Dummy[k]= 0;
10341: modell[k].maintype= FTYPE;
10342: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10343: ncovf++; /* Fixed variables without age */
10344: TvarF[ncovf]=Tvar[k];
10345: TvarFind[ncovf]=k;
10346: }else if(Tvard[k1][2] <=ncovcol+nqv){
10347: Fixed[k]= 0; /* or 2 ?*/
10348: Dummy[k]= 1;
10349: modell[k].maintype= FTYPE;
10350: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10351: ncovf++; /* Varying variables without age */
10352: TvarF[ncovf]=Tvar[k];
10353: TvarFind[ncovf]=k;
10354: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10355: Fixed[k]= 1;
10356: Dummy[k]= 0;
10357: modell[k].maintype= VTYPE;
10358: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10359: ncovv++; /* Varying variables without age */
10360: TvarV[ncovv]=Tvar[k];
10361: TvarVind[ncovv]=k;
10362: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10363: Fixed[k]= 1;
10364: Dummy[k]= 1;
10365: modell[k].maintype= VTYPE;
10366: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10367: ncovv++; /* Varying variables without age */
10368: TvarV[ncovv]=Tvar[k];
10369: TvarVind[ncovv]=k;
10370: }
1.227 brouard 10371: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10372: if(Tvard[k1][2] <=ncovcol){
10373: Fixed[k]= 0; /* or 2 ?*/
10374: Dummy[k]= 1;
10375: modell[k].maintype= FTYPE;
10376: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10377: ncovf++; /* Fixed variables without age */
10378: TvarF[ncovf]=Tvar[k];
10379: TvarFind[ncovf]=k;
10380: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10381: Fixed[k]= 1;
10382: Dummy[k]= 1;
10383: modell[k].maintype= VTYPE;
10384: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10385: ncovv++; /* Varying variables without age */
10386: TvarV[ncovv]=Tvar[k];
10387: TvarVind[ncovv]=k;
10388: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10389: Fixed[k]= 1;
10390: Dummy[k]= 1;
10391: modell[k].maintype= VTYPE;
10392: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10393: ncovv++; /* Varying variables without age */
10394: TvarV[ncovv]=Tvar[k];
10395: TvarVind[ncovv]=k;
10396: ncovv++; /* Varying variables without age */
10397: TvarV[ncovv]=Tvar[k];
10398: TvarVind[ncovv]=k;
10399: }
1.227 brouard 10400: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10401: if(Tvard[k1][2] <=ncovcol){
10402: Fixed[k]= 1;
10403: Dummy[k]= 1;
10404: modell[k].maintype= VTYPE;
10405: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10406: ncovv++; /* Varying variables without age */
10407: TvarV[ncovv]=Tvar[k];
10408: TvarVind[ncovv]=k;
10409: }else if(Tvard[k1][2] <=ncovcol+nqv){
10410: Fixed[k]= 1;
10411: Dummy[k]= 1;
10412: modell[k].maintype= VTYPE;
10413: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10414: ncovv++; /* Varying variables without age */
10415: TvarV[ncovv]=Tvar[k];
10416: TvarVind[ncovv]=k;
10417: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10418: Fixed[k]= 1;
10419: Dummy[k]= 0;
10420: modell[k].maintype= VTYPE;
10421: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10422: ncovv++; /* Varying variables without age */
10423: TvarV[ncovv]=Tvar[k];
10424: TvarVind[ncovv]=k;
10425: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10426: Fixed[k]= 1;
10427: Dummy[k]= 1;
10428: modell[k].maintype= VTYPE;
10429: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10430: ncovv++; /* Varying variables without age */
10431: TvarV[ncovv]=Tvar[k];
10432: TvarVind[ncovv]=k;
10433: }
1.227 brouard 10434: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10435: if(Tvard[k1][2] <=ncovcol){
10436: Fixed[k]= 1;
10437: Dummy[k]= 1;
10438: modell[k].maintype= VTYPE;
10439: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10440: ncovv++; /* Varying variables without age */
10441: TvarV[ncovv]=Tvar[k];
10442: TvarVind[ncovv]=k;
10443: }else if(Tvard[k1][2] <=ncovcol+nqv){
10444: Fixed[k]= 1;
10445: Dummy[k]= 1;
10446: modell[k].maintype= VTYPE;
10447: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10448: ncovv++; /* Varying variables without age */
10449: TvarV[ncovv]=Tvar[k];
10450: TvarVind[ncovv]=k;
10451: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10452: Fixed[k]= 1;
10453: Dummy[k]= 1;
10454: modell[k].maintype= VTYPE;
10455: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10456: ncovv++; /* Varying variables without age */
10457: TvarV[ncovv]=Tvar[k];
10458: TvarVind[ncovv]=k;
10459: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10460: Fixed[k]= 1;
10461: Dummy[k]= 1;
10462: modell[k].maintype= VTYPE;
10463: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10464: ncovv++; /* Varying variables without age */
10465: TvarV[ncovv]=Tvar[k];
10466: TvarVind[ncovv]=k;
10467: }
1.227 brouard 10468: }else{
1.240 brouard 10469: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10470: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10471: } /*end k1*/
1.225 brouard 10472: }else{
1.226 brouard 10473: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10474: fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
1.225 brouard 10475: }
1.227 brouard 10476: printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
1.231 brouard 10477: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10478: fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
10479: }
10480: /* Searching for doublons in the model */
10481: for(k1=1; k1<= cptcovt;k1++){
10482: for(k2=1; k2 <k1;k2++){
1.285 brouard 10483: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10484: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10485: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10486: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10487: printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
10488: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
1.234 brouard 10489: return(1);
10490: }
10491: }else if (Typevar[k1] ==2){
10492: k3=Tposprod[k1];
10493: k4=Tposprod[k2];
10494: if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
10495: printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
10496: fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
10497: return(1);
10498: }
10499: }
1.227 brouard 10500: }
10501: }
1.225 brouard 10502: }
10503: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10504: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10505: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10506: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10507: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10508: /*endread:*/
1.225 brouard 10509: printf("Exiting decodemodel: ");
10510: return (1);
1.136 brouard 10511: }
10512:
1.169 brouard 10513: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10514: {/* Check ages at death */
1.136 brouard 10515: int i, m;
1.218 brouard 10516: int firstone=0;
10517:
1.136 brouard 10518: for (i=1; i<=imx; i++) {
10519: for(m=2; (m<= maxwav); m++) {
10520: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10521: anint[m][i]=9999;
1.216 brouard 10522: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10523: s[m][i]=-1;
1.136 brouard 10524: }
10525: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10526: *nberr = *nberr + 1;
1.218 brouard 10527: if(firstone == 0){
10528: firstone=1;
1.260 brouard 10529: printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
1.218 brouard 10530: }
1.262 brouard 10531: fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
1.260 brouard 10532: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10533: }
10534: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10535: (*nberr)++;
1.259 brouard 10536: printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
1.262 brouard 10537: fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
1.259 brouard 10538: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10539: }
10540: }
10541: }
10542:
10543: for (i=1; i<=imx; i++) {
10544: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10545: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10546: if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136 brouard 10547: if (s[m][i] >= nlstate+1) {
1.169 brouard 10548: if(agedc[i]>0){
10549: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10550: agev[m][i]=agedc[i];
1.214 brouard 10551: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10552: }else {
1.136 brouard 10553: if ((int)andc[i]!=9999){
10554: nbwarn++;
10555: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10556: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10557: agev[m][i]=-1;
10558: }
10559: }
1.169 brouard 10560: } /* agedc > 0 */
1.214 brouard 10561: } /* end if */
1.136 brouard 10562: else if(s[m][i] !=9){ /* Standard case, age in fractional
10563: years but with the precision of a month */
10564: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10565: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10566: agev[m][i]=1;
10567: else if(agev[m][i] < *agemin){
10568: *agemin=agev[m][i];
10569: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10570: }
10571: else if(agev[m][i] >*agemax){
10572: *agemax=agev[m][i];
1.156 brouard 10573: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10574: }
10575: /*agev[m][i]=anint[m][i]-annais[i];*/
10576: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10577: } /* en if 9*/
1.136 brouard 10578: else { /* =9 */
1.214 brouard 10579: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10580: agev[m][i]=1;
10581: s[m][i]=-1;
10582: }
10583: }
1.214 brouard 10584: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10585: agev[m][i]=1;
1.214 brouard 10586: else{
10587: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10588: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10589: agev[m][i]=0;
10590: }
10591: } /* End for lastpass */
10592: }
1.136 brouard 10593:
10594: for (i=1; i<=imx; i++) {
10595: for(m=firstpass; (m<=lastpass); m++){
10596: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10597: (*nberr)++;
1.136 brouard 10598: printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
10599: fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
10600: return 1;
10601: }
10602: }
10603: }
10604:
10605: /*for (i=1; i<=imx; i++){
10606: for (m=firstpass; (m<lastpass); m++){
10607: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10608: }
10609:
10610: }*/
10611:
10612:
1.139 brouard 10613: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10614: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10615:
10616: return (0);
1.164 brouard 10617: /* endread:*/
1.136 brouard 10618: printf("Exiting calandcheckages: ");
10619: return (1);
10620: }
10621:
1.172 brouard 10622: #if defined(_MSC_VER)
10623: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10624: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10625: //#include "stdafx.h"
10626: //#include <stdio.h>
10627: //#include <tchar.h>
10628: //#include <windows.h>
10629: //#include <iostream>
10630: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10631:
10632: LPFN_ISWOW64PROCESS fnIsWow64Process;
10633:
10634: BOOL IsWow64()
10635: {
10636: BOOL bIsWow64 = FALSE;
10637:
10638: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10639: // (HANDLE, PBOOL);
10640:
10641: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10642:
10643: HMODULE module = GetModuleHandle(_T("kernel32"));
10644: const char funcName[] = "IsWow64Process";
10645: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10646: GetProcAddress(module, funcName);
10647:
10648: if (NULL != fnIsWow64Process)
10649: {
10650: if (!fnIsWow64Process(GetCurrentProcess(),
10651: &bIsWow64))
10652: //throw std::exception("Unknown error");
10653: printf("Unknown error\n");
10654: }
10655: return bIsWow64 != FALSE;
10656: }
10657: #endif
1.177 brouard 10658:
1.191 brouard 10659: void syscompilerinfo(int logged)
1.292 brouard 10660: {
10661: #include <stdint.h>
10662:
10663: /* #include "syscompilerinfo.h"*/
1.185 brouard 10664: /* command line Intel compiler 32bit windows, XP compatible:*/
10665: /* /GS /W3 /Gy
10666: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10667: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10668: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10669: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10670: */
10671: /* 64 bits */
1.185 brouard 10672: /*
10673: /GS /W3 /Gy
10674: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10675: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10676: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10677: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10678: /* Optimization are useless and O3 is slower than O2 */
10679: /*
10680: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10681: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10682: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10683: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10684: */
1.186 brouard 10685: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10686: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10687: /PDB:"visual studio
10688: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10689: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10690: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10691: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10692: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10693: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10694: uiAccess='false'"
10695: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10696: /NOLOGO /TLBID:1
10697: */
1.292 brouard 10698:
10699:
1.177 brouard 10700: #if defined __INTEL_COMPILER
1.178 brouard 10701: #if defined(__GNUC__)
10702: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10703: #endif
1.177 brouard 10704: #elif defined(__GNUC__)
1.179 brouard 10705: #ifndef __APPLE__
1.174 brouard 10706: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10707: #endif
1.177 brouard 10708: struct utsname sysInfo;
1.178 brouard 10709: int cross = CROSS;
10710: if (cross){
10711: printf("Cross-");
1.191 brouard 10712: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10713: }
1.174 brouard 10714: #endif
10715:
1.191 brouard 10716: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10717: #if defined(__clang__)
1.191 brouard 10718: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10719: #endif
10720: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10721: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10722: #endif
10723: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10724: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10725: #endif
10726: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10727: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10728: #endif
10729: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10730: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10731: #endif
10732: #if defined(_MSC_VER)
1.191 brouard 10733: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10734: #endif
10735: #if defined(__PGI)
1.191 brouard 10736: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10737: #endif
10738: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10739: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10740: #endif
1.191 brouard 10741: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10742:
1.167 brouard 10743: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10744: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10745: // Windows (x64 and x86)
1.191 brouard 10746: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10747: #elif __unix__ // all unices, not all compilers
10748: // Unix
1.191 brouard 10749: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10750: #elif __linux__
10751: // linux
1.191 brouard 10752: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10753: #elif __APPLE__
1.174 brouard 10754: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10755: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10756: #endif
10757:
10758: /* __MINGW32__ */
10759: /* __CYGWIN__ */
10760: /* __MINGW64__ */
10761: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10762: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10763: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10764: /* _WIN64 // Defined for applications for Win64. */
10765: /* _M_X64 // Defined for compilations that target x64 processors. */
10766: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10767:
1.167 brouard 10768: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10769: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10770: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10771: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10772: #else
1.191 brouard 10773: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10774: #endif
10775:
1.169 brouard 10776: #if defined(__GNUC__)
10777: # if defined(__GNUC_PATCHLEVEL__)
10778: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10779: + __GNUC_MINOR__ * 100 \
10780: + __GNUC_PATCHLEVEL__)
10781: # else
10782: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10783: + __GNUC_MINOR__ * 100)
10784: # endif
1.174 brouard 10785: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10786: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10787:
10788: if (uname(&sysInfo) != -1) {
10789: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10790: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176 brouard 10791: }
10792: else
10793: perror("uname() error");
1.179 brouard 10794: //#ifndef __INTEL_COMPILER
10795: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10796: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10797: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10798: #endif
1.169 brouard 10799: #endif
1.172 brouard 10800:
1.286 brouard 10801: // void main ()
1.172 brouard 10802: // {
1.169 brouard 10803: #if defined(_MSC_VER)
1.174 brouard 10804: if (IsWow64()){
1.191 brouard 10805: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10806: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10807: }
10808: else{
1.191 brouard 10809: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10810: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10811: }
1.172 brouard 10812: // printf("\nPress Enter to continue...");
10813: // getchar();
10814: // }
10815:
1.169 brouard 10816: #endif
10817:
1.167 brouard 10818:
1.219 brouard 10819: }
1.136 brouard 10820:
1.219 brouard 10821: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10822: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10823: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10824: /* double ftolpl = 1.e-10; */
1.180 brouard 10825: double age, agebase, agelim;
1.203 brouard 10826: double tot;
1.180 brouard 10827:
1.202 brouard 10828: strcpy(filerespl,"PL_");
10829: strcat(filerespl,fileresu);
10830: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10831: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10832: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10833: }
1.288 brouard 10834: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10835: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10836: pstamp(ficrespl);
1.288 brouard 10837: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10838: fprintf(ficrespl,"#Age ");
10839: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10840: fprintf(ficrespl,"\n");
1.180 brouard 10841:
1.219 brouard 10842: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10843:
1.219 brouard 10844: agebase=ageminpar;
10845: agelim=agemaxpar;
1.180 brouard 10846:
1.227 brouard 10847: /* i1=pow(2,ncoveff); */
1.234 brouard 10848: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10849: if (cptcovn < 1){i1=1;}
1.180 brouard 10850:
1.238 brouard 10851: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10852: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10853: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10854: continue;
1.235 brouard 10855:
1.238 brouard 10856: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10857: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10858: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10859: /* k=k+1; */
10860: /* to clean */
10861: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10862: fprintf(ficrespl,"#******");
10863: printf("#******");
10864: fprintf(ficlog,"#******");
10865: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10866: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10867: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10868: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10869: }
10870: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10871: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10872: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10873: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10874: }
10875: fprintf(ficrespl,"******\n");
10876: printf("******\n");
10877: fprintf(ficlog,"******\n");
10878: if(invalidvarcomb[k]){
10879: printf("\nCombination (%d) ignored because no case \n",k);
10880: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10881: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10882: continue;
10883: }
1.219 brouard 10884:
1.238 brouard 10885: fprintf(ficrespl,"#Age ");
10886: for(j=1;j<=cptcoveff;j++) {
10887: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10888: }
10889: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10890: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10891:
1.238 brouard 10892: for (age=agebase; age<=agelim; age++){
10893: /* for (age=agebase; age<=agebase; age++){ */
10894: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10895: fprintf(ficrespl,"%.0f ",age );
10896: for(j=1;j<=cptcoveff;j++)
10897: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10898: tot=0.;
10899: for(i=1; i<=nlstate;i++){
10900: tot += prlim[i][i];
10901: fprintf(ficrespl," %.5f", prlim[i][i]);
10902: }
10903: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10904: } /* Age */
10905: /* was end of cptcod */
10906: } /* cptcov */
10907: } /* nres */
1.219 brouard 10908: return 0;
1.180 brouard 10909: }
10910:
1.218 brouard 10911: int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
1.288 brouard 10912: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10913:
10914: /* Computes the back prevalence limit for any combination of covariate values
10915: * at any age between ageminpar and agemaxpar
10916: */
1.235 brouard 10917: int i, j, k, i1, nres=0 ;
1.217 brouard 10918: /* double ftolpl = 1.e-10; */
10919: double age, agebase, agelim;
10920: double tot;
1.218 brouard 10921: /* double ***mobaverage; */
10922: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10923:
10924: strcpy(fileresplb,"PLB_");
10925: strcat(fileresplb,fileresu);
10926: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10927: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10928: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10929: }
1.288 brouard 10930: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10931: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10932: pstamp(ficresplb);
1.288 brouard 10933: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10934: fprintf(ficresplb,"#Age ");
10935: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10936: fprintf(ficresplb,"\n");
10937:
1.218 brouard 10938:
10939: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10940:
10941: agebase=ageminpar;
10942: agelim=agemaxpar;
10943:
10944:
1.227 brouard 10945: i1=pow(2,cptcoveff);
1.218 brouard 10946: if (cptcovn < 1){i1=1;}
1.227 brouard 10947:
1.238 brouard 10948: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10949: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10950: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10951: continue;
10952: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10953: fprintf(ficresplb,"#******");
10954: printf("#******");
10955: fprintf(ficlog,"#******");
10956: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10957: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10958: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10959: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10960: }
10961: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10962: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10963: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10964: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10965: }
10966: fprintf(ficresplb,"******\n");
10967: printf("******\n");
10968: fprintf(ficlog,"******\n");
10969: if(invalidvarcomb[k]){
10970: printf("\nCombination (%d) ignored because no cases \n",k);
10971: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10972: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10973: continue;
10974: }
1.218 brouard 10975:
1.238 brouard 10976: fprintf(ficresplb,"#Age ");
10977: for(j=1;j<=cptcoveff;j++) {
10978: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10979: }
10980: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10981: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10982:
10983:
1.238 brouard 10984: for (age=agebase; age<=agelim; age++){
10985: /* for (age=agebase; age<=agebase; age++){ */
10986: if(mobilavproj > 0){
10987: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10988: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10989: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10990: }else if (mobilavproj == 0){
10991: printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
10992: fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
10993: exit(1);
10994: }else{
10995: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10996: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10997: /* printf("TOTOT\n"); */
10998: /* exit(1); */
1.238 brouard 10999: }
11000: fprintf(ficresplb,"%.0f ",age );
11001: for(j=1;j<=cptcoveff;j++)
11002: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11003: tot=0.;
11004: for(i=1; i<=nlstate;i++){
11005: tot += bprlim[i][i];
11006: fprintf(ficresplb," %.5f", bprlim[i][i]);
11007: }
11008: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
11009: } /* Age */
11010: /* was end of cptcod */
1.255 brouard 11011: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 11012: } /* end of any combination */
11013: } /* end of nres */
1.218 brouard 11014: /* hBijx(p, bage, fage); */
11015: /* fclose(ficrespijb); */
11016:
11017: return 0;
1.217 brouard 11018: }
1.218 brouard 11019:
1.180 brouard 11020: int hPijx(double *p, int bage, int fage){
11021: /*------------- h Pij x at various ages ------------*/
11022:
11023: int stepsize;
11024: int agelim;
11025: int hstepm;
11026: int nhstepm;
1.235 brouard 11027: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 11028:
11029: double agedeb;
11030: double ***p3mat;
11031:
1.201 brouard 11032: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 11033: if((ficrespij=fopen(filerespij,"w"))==NULL) {
11034: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
11035: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
11036: }
11037: printf("Computing pij: result on file '%s' \n", filerespij);
11038: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
11039:
11040: stepsize=(int) (stepm+YEARM-1)/YEARM;
11041: /*if (stepm<=24) stepsize=2;*/
11042:
11043: agelim=AGESUP;
11044: hstepm=stepsize*YEARM; /* Every year of age */
11045: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 11046:
1.180 brouard 11047: /* hstepm=1; aff par mois*/
11048: pstamp(ficrespij);
11049: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 11050: i1= pow(2,cptcoveff);
1.218 brouard 11051: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
11052: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
11053: /* k=k+1; */
1.235 brouard 11054: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11055: for(k=1; k<=i1;k++){
1.253 brouard 11056: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 11057: continue;
1.183 brouard 11058: fprintf(ficrespij,"\n#****** ");
1.227 brouard 11059: for(j=1;j<=cptcoveff;j++)
1.198 brouard 11060: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 11061: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
11062: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
11063: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
11064: }
1.183 brouard 11065: fprintf(ficrespij,"******\n");
11066:
11067: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
11068: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
11069: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
11070:
11071: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 11072:
1.183 brouard 11073: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
11074: oldm=oldms;savm=savms;
1.235 brouard 11075: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 11076: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
11077: for(i=1; i<=nlstate;i++)
11078: for(j=1; j<=nlstate+ndeath;j++)
11079: fprintf(ficrespij," %1d-%1d",i,j);
11080: fprintf(ficrespij,"\n");
11081: for (h=0; h<=nhstepm; h++){
11082: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
11083: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 11084: for(i=1; i<=nlstate;i++)
11085: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 11086: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 11087: fprintf(ficrespij,"\n");
11088: }
1.183 brouard 11089: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
11090: fprintf(ficrespij,"\n");
11091: }
1.180 brouard 11092: /*}*/
11093: }
1.218 brouard 11094: return 0;
1.180 brouard 11095: }
1.218 brouard 11096:
11097: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 11098: /*------------- h Bij x at various ages ------------*/
11099:
11100: int stepsize;
1.218 brouard 11101: /* int agelim; */
11102: int ageminl;
1.217 brouard 11103: int hstepm;
11104: int nhstepm;
1.238 brouard 11105: int h, i, i1, j, k, nres;
1.218 brouard 11106:
1.217 brouard 11107: double agedeb;
11108: double ***p3mat;
1.218 brouard 11109:
11110: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
11111: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
11112: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
11113: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
11114: }
11115: printf("Computing pij back: result on file '%s' \n", filerespijb);
11116: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
11117:
11118: stepsize=(int) (stepm+YEARM-1)/YEARM;
11119: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 11120:
1.218 brouard 11121: /* agelim=AGESUP; */
1.289 brouard 11122: ageminl=AGEINF; /* was 30 */
1.218 brouard 11123: hstepm=stepsize*YEARM; /* Every year of age */
11124: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
11125:
11126: /* hstepm=1; aff par mois*/
11127: pstamp(ficrespijb);
1.255 brouard 11128: fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
1.227 brouard 11129: i1= pow(2,cptcoveff);
1.218 brouard 11130: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
11131: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
11132: /* k=k+1; */
1.238 brouard 11133: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
11134: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 11135: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 11136: continue;
11137: fprintf(ficrespijb,"\n#****** ");
11138: for(j=1;j<=cptcoveff;j++)
11139: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11140: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11141: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11142: }
11143: fprintf(ficrespijb,"******\n");
1.264 brouard 11144: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 11145: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
11146: continue;
11147: }
11148:
11149: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
11150: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
11151: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 11152: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
11153: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 11154:
11155: /* nhstepm=nhstepm*YEARM; aff par mois*/
11156:
1.266 brouard 11157: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
11158: /* and memory limitations if stepm is small */
11159:
1.238 brouard 11160: /* oldm=oldms;savm=savms; */
11161: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 11162: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 11163: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 11164: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 11165: for(i=1; i<=nlstate;i++)
11166: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 11167: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 11168: fprintf(ficrespijb,"\n");
1.238 brouard 11169: for (h=0; h<=nhstepm; h++){
11170: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
11171: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
11172: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
11173: for(i=1; i<=nlstate;i++)
11174: for(j=1; j<=nlstate+ndeath;j++)
11175: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
11176: fprintf(ficrespijb,"\n");
11177: }
11178: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
11179: fprintf(ficrespijb,"\n");
11180: } /* end age deb */
11181: } /* end combination */
11182: } /* end nres */
1.218 brouard 11183: return 0;
11184: } /* hBijx */
1.217 brouard 11185:
1.180 brouard 11186:
1.136 brouard 11187: /***********************************************/
11188: /**************** Main Program *****************/
11189: /***********************************************/
11190:
11191: int main(int argc, char *argv[])
11192: {
11193: #ifdef GSL
11194: const gsl_multimin_fminimizer_type *T;
11195: size_t iteri = 0, it;
11196: int rval = GSL_CONTINUE;
11197: int status = GSL_SUCCESS;
11198: double ssval;
11199: #endif
11200: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 11201: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
11202: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 11203: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 11204: int jj, ll, li, lj, lk;
1.136 brouard 11205: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 11206: int num_filled;
1.136 brouard 11207: int itimes;
11208: int NDIM=2;
11209: int vpopbased=0;
1.235 brouard 11210: int nres=0;
1.258 brouard 11211: int endishere=0;
1.277 brouard 11212: int noffset=0;
1.274 brouard 11213: int ncurrv=0; /* Temporary variable */
11214:
1.164 brouard 11215: char ca[32], cb[32];
1.136 brouard 11216: /* FILE *fichtm; *//* Html File */
11217: /* FILE *ficgp;*/ /*Gnuplot File */
11218: struct stat info;
1.191 brouard 11219: double agedeb=0.;
1.194 brouard 11220:
11221: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 11222: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 11223:
1.165 brouard 11224: double fret;
1.191 brouard 11225: double dum=0.; /* Dummy variable */
1.136 brouard 11226: double ***p3mat;
1.218 brouard 11227: /* double ***mobaverage; */
1.319 ! brouard 11228: double wald;
1.164 brouard 11229:
11230: char line[MAXLINE];
1.197 brouard 11231: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
11232:
1.234 brouard 11233: char modeltemp[MAXLINE];
1.230 brouard 11234: char resultline[MAXLINE];
11235:
1.136 brouard 11236: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 11237: char *tok, *val; /* pathtot */
1.290 brouard 11238: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 11239: int c, h , cpt, c2;
1.191 brouard 11240: int jl=0;
11241: int i1, j1, jk, stepsize=0;
1.194 brouard 11242: int count=0;
11243:
1.164 brouard 11244: int *tab;
1.136 brouard 11245: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 11246: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
11247: /* double anprojf, mprojf, jprojf; */
11248: /* double jintmean,mintmean,aintmean; */
11249: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
11250: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
11251: double yrfproj= 10.0; /* Number of years of forward projections */
11252: double yrbproj= 10.0; /* Number of years of backward projections */
11253: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 11254: int mobilav=0,popforecast=0;
1.191 brouard 11255: int hstepm=0, nhstepm=0;
1.136 brouard 11256: int agemortsup;
11257: float sumlpop=0.;
11258: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
11259: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
11260:
1.191 brouard 11261: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 11262: double ftolpl=FTOL;
11263: double **prlim;
1.217 brouard 11264: double **bprlim;
1.317 brouard 11265: double ***param; /* Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
11266: state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
1.251 brouard 11267: double ***paramstart; /* Matrix of starting parameter values */
11268: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 11269: double **matcov; /* Matrix of covariance */
1.203 brouard 11270: double **hess; /* Hessian matrix */
1.136 brouard 11271: double ***delti3; /* Scale */
11272: double *delti; /* Scale */
11273: double ***eij, ***vareij;
11274: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 11275:
1.136 brouard 11276: double *epj, vepp;
1.164 brouard 11277:
1.273 brouard 11278: double dateprev1, dateprev2;
1.296 brouard 11279: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
11280: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
11281:
1.217 brouard 11282:
1.136 brouard 11283: double **ximort;
1.145 brouard 11284: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 11285: int *dcwave;
11286:
1.164 brouard 11287: char z[1]="c";
1.136 brouard 11288:
11289: /*char *strt;*/
11290: char strtend[80];
1.126 brouard 11291:
1.164 brouard 11292:
1.126 brouard 11293: /* setlocale (LC_ALL, ""); */
11294: /* bindtextdomain (PACKAGE, LOCALEDIR); */
11295: /* textdomain (PACKAGE); */
11296: /* setlocale (LC_CTYPE, ""); */
11297: /* setlocale (LC_MESSAGES, ""); */
11298:
11299: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 11300: rstart_time = time(NULL);
11301: /* (void) gettimeofday(&start_time,&tzp);*/
11302: start_time = *localtime(&rstart_time);
1.126 brouard 11303: curr_time=start_time;
1.157 brouard 11304: /*tml = *localtime(&start_time.tm_sec);*/
11305: /* strcpy(strstart,asctime(&tml)); */
11306: strcpy(strstart,asctime(&start_time));
1.126 brouard 11307:
11308: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 11309: /* tp.tm_sec = tp.tm_sec +86400; */
11310: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 11311: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11312: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11313: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11314: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11315: /* strt=asctime(&tmg); */
11316: /* printf("Time(after) =%s",strstart); */
11317: /* (void) time (&time_value);
11318: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11319: * tm = *localtime(&time_value);
11320: * strstart=asctime(&tm);
11321: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11322: */
11323:
11324: nberr=0; /* Number of errors and warnings */
11325: nbwarn=0;
1.184 brouard 11326: #ifdef WIN32
11327: _getcwd(pathcd, size);
11328: #else
1.126 brouard 11329: getcwd(pathcd, size);
1.184 brouard 11330: #endif
1.191 brouard 11331: syscompilerinfo(0);
1.196 brouard 11332: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11333: if(argc <=1){
11334: printf("\nEnter the parameter file name: ");
1.205 brouard 11335: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11336: printf("ERROR Empty parameter file name\n");
11337: goto end;
11338: }
1.126 brouard 11339: i=strlen(pathr);
11340: if(pathr[i-1]=='\n')
11341: pathr[i-1]='\0';
1.156 brouard 11342: i=strlen(pathr);
1.205 brouard 11343: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11344: pathr[i-1]='\0';
1.205 brouard 11345: }
11346: i=strlen(pathr);
11347: if( i==0 ){
11348: printf("ERROR Empty parameter file name\n");
11349: goto end;
11350: }
11351: for (tok = pathr; tok != NULL; ){
1.126 brouard 11352: printf("Pathr |%s|\n",pathr);
11353: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11354: printf("val= |%s| pathr=%s\n",val,pathr);
11355: strcpy (pathtot, val);
11356: if(pathr[0] == '\0') break; /* Dirty */
11357: }
11358: }
1.281 brouard 11359: else if (argc<=2){
11360: strcpy(pathtot,argv[1]);
11361: }
1.126 brouard 11362: else{
11363: strcpy(pathtot,argv[1]);
1.281 brouard 11364: strcpy(z,argv[2]);
11365: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11366: }
11367: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11368: /*cygwin_split_path(pathtot,path,optionfile);
11369: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11370: /* cutv(path,optionfile,pathtot,'\\');*/
11371:
11372: /* Split argv[0], imach program to get pathimach */
11373: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11374: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11375: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11376: /* strcpy(pathimach,argv[0]); */
11377: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11378: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11379: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11380: #ifdef WIN32
11381: _chdir(path); /* Can be a relative path */
11382: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11383: #else
1.126 brouard 11384: chdir(path); /* Can be a relative path */
1.184 brouard 11385: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11386: #endif
11387: printf("Current directory %s!\n",pathcd);
1.126 brouard 11388: strcpy(command,"mkdir ");
11389: strcat(command,optionfilefiname);
11390: if((outcmd=system(command)) != 0){
1.169 brouard 11391: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11392: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11393: /* fclose(ficlog); */
11394: /* exit(1); */
11395: }
11396: /* if((imk=mkdir(optionfilefiname))<0){ */
11397: /* perror("mkdir"); */
11398: /* } */
11399:
11400: /*-------- arguments in the command line --------*/
11401:
1.186 brouard 11402: /* Main Log file */
1.126 brouard 11403: strcat(filelog, optionfilefiname);
11404: strcat(filelog,".log"); /* */
11405: if((ficlog=fopen(filelog,"w"))==NULL) {
11406: printf("Problem with logfile %s\n",filelog);
11407: goto end;
11408: }
11409: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11410: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11411: fprintf(ficlog,"\nEnter the parameter file name: \n");
11412: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11413: path=%s \n\
11414: optionfile=%s\n\
11415: optionfilext=%s\n\
1.156 brouard 11416: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11417:
1.197 brouard 11418: syscompilerinfo(1);
1.167 brouard 11419:
1.126 brouard 11420: printf("Local time (at start):%s",strstart);
11421: fprintf(ficlog,"Local time (at start): %s",strstart);
11422: fflush(ficlog);
11423: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11424: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11425:
11426: /* */
11427: strcpy(fileres,"r");
11428: strcat(fileres, optionfilefiname);
1.201 brouard 11429: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11430: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11431: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11432:
1.186 brouard 11433: /* Main ---------arguments file --------*/
1.126 brouard 11434:
11435: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11436: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11437: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11438: fflush(ficlog);
1.149 brouard 11439: /* goto end; */
11440: exit(70);
1.126 brouard 11441: }
11442:
11443: strcpy(filereso,"o");
1.201 brouard 11444: strcat(filereso,fileresu);
1.126 brouard 11445: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11446: printf("Problem with Output resultfile: %s\n", filereso);
11447: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11448: fflush(ficlog);
11449: goto end;
11450: }
1.278 brouard 11451: /*-------- Rewriting parameter file ----------*/
11452: strcpy(rfileres,"r"); /* "Rparameterfile */
11453: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11454: strcat(rfileres,"."); /* */
11455: strcat(rfileres,optionfilext); /* Other files have txt extension */
11456: if((ficres =fopen(rfileres,"w"))==NULL) {
11457: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11458: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11459: fflush(ficlog);
11460: goto end;
11461: }
11462: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11463:
1.278 brouard 11464:
1.126 brouard 11465: /* Reads comments: lines beginning with '#' */
11466: numlinepar=0;
1.277 brouard 11467: /* Is it a BOM UTF-8 Windows file? */
11468: /* First parameter line */
1.197 brouard 11469: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11470: noffset=0;
11471: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11472: {
11473: noffset=noffset+3;
11474: printf("# File is an UTF8 Bom.\n"); // 0xBF
11475: }
1.302 brouard 11476: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11477: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11478: {
11479: noffset=noffset+2;
11480: printf("# File is an UTF16BE BOM file\n");
11481: }
11482: else if( line[0] == 0 && line[1] == 0)
11483: {
11484: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11485: noffset=noffset+4;
11486: printf("# File is an UTF16BE BOM file\n");
11487: }
11488: } else{
11489: ;/*printf(" Not a BOM file\n");*/
11490: }
11491:
1.197 brouard 11492: /* If line starts with a # it is a comment */
1.277 brouard 11493: if (line[noffset] == '#') {
1.197 brouard 11494: numlinepar++;
11495: fputs(line,stdout);
11496: fputs(line,ficparo);
1.278 brouard 11497: fputs(line,ficres);
1.197 brouard 11498: fputs(line,ficlog);
11499: continue;
11500: }else
11501: break;
11502: }
11503: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11504: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11505: if (num_filled != 5) {
11506: printf("Should be 5 parameters\n");
1.283 brouard 11507: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11508: }
1.126 brouard 11509: numlinepar++;
1.197 brouard 11510: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11511: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11512: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11513: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11514: }
11515: /* Second parameter line */
11516: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11517: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11518: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11519: if (line[0] == '#') {
11520: numlinepar++;
1.283 brouard 11521: printf("%s",line);
11522: fprintf(ficres,"%s",line);
11523: fprintf(ficparo,"%s",line);
11524: fprintf(ficlog,"%s",line);
1.197 brouard 11525: continue;
11526: }else
11527: break;
11528: }
1.223 brouard 11529: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
11530: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11531: if (num_filled != 11) {
11532: printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
1.209 brouard 11533: printf("but line=%s\n",line);
1.283 brouard 11534: fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
11535: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11536: }
1.286 brouard 11537: if( lastpass > maxwav){
11538: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11539: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11540: fflush(ficlog);
11541: goto end;
11542: }
11543: printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.283 brouard 11544: fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.286 brouard 11545: fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
1.283 brouard 11546: fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
1.126 brouard 11547: }
1.203 brouard 11548: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11549: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11550: /* Third parameter line */
11551: while(fgets(line, MAXLINE, ficpar)) {
11552: /* If line starts with a # it is a comment */
11553: if (line[0] == '#') {
11554: numlinepar++;
1.283 brouard 11555: printf("%s",line);
11556: fprintf(ficres,"%s",line);
11557: fprintf(ficparo,"%s",line);
11558: fprintf(ficlog,"%s",line);
1.197 brouard 11559: continue;
11560: }else
11561: break;
11562: }
1.201 brouard 11563: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11564: if (num_filled != 1){
1.302 brouard 11565: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11566: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11567: model[0]='\0';
11568: goto end;
11569: }
11570: else{
11571: if (model[0]=='+'){
11572: for(i=1; i<=strlen(model);i++)
11573: modeltemp[i-1]=model[i];
1.201 brouard 11574: strcpy(model,modeltemp);
1.197 brouard 11575: }
11576: }
1.199 brouard 11577: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11578: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11579: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11580: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11581: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11582: }
11583: /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
11584: /* numlinepar=numlinepar+3; /\* In general *\/ */
11585: /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
1.283 brouard 11586: /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
11587: /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
1.126 brouard 11588: fflush(ficlog);
1.190 brouard 11589: /* if(model[0]=='#'|| model[0]== '\0'){ */
11590: if(model[0]=='#'){
1.279 brouard 11591: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11592: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11593: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11594: if(mle != -1){
1.279 brouard 11595: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
1.187 brouard 11596: exit(1);
11597: }
11598: }
1.126 brouard 11599: while((c=getc(ficpar))=='#' && c!= EOF){
11600: ungetc(c,ficpar);
11601: fgets(line, MAXLINE, ficpar);
11602: numlinepar++;
1.195 brouard 11603: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11604: z[0]=line[1];
11605: }
11606: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11607: fputs(line, stdout);
11608: //puts(line);
1.126 brouard 11609: fputs(line,ficparo);
11610: fputs(line,ficlog);
11611: }
11612: ungetc(c,ficpar);
11613:
11614:
1.290 brouard 11615: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11616: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11617: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11618: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11619: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11620: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11621: v1+v2*age+v2*v3 makes cptcovn = 3
11622: */
11623: if (strlen(model)>1)
1.187 brouard 11624: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7,age*age makes 3*/
1.145 brouard 11625: else
1.187 brouard 11626: ncovmodel=2; /* Constant and age */
1.133 brouard 11627: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11628: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11629: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11630: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
11631: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
11632: fflush(stdout);
11633: fclose (ficlog);
11634: goto end;
11635: }
1.126 brouard 11636: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11637: delti=delti3[1][1];
11638: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11639: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11640: /* We could also provide initial parameters values giving by simple logistic regression
11641: * only one way, that is without matrix product. We will have nlstate maximizations */
11642: /* for(i=1;i<nlstate;i++){ */
11643: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11644: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11645: /* } */
1.126 brouard 11646: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11647: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11648: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11649: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11650: fclose (ficparo);
11651: fclose (ficlog);
11652: goto end;
11653: exit(0);
1.220 brouard 11654: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11655: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11656: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11657: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11658: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11659: matcov=matrix(1,npar,1,npar);
1.203 brouard 11660: hess=matrix(1,npar,1,npar);
1.220 brouard 11661: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11662: /* Read guessed parameters */
1.126 brouard 11663: /* Reads comments: lines beginning with '#' */
11664: while((c=getc(ficpar))=='#' && c!= EOF){
11665: ungetc(c,ficpar);
11666: fgets(line, MAXLINE, ficpar);
11667: numlinepar++;
1.141 brouard 11668: fputs(line,stdout);
1.126 brouard 11669: fputs(line,ficparo);
11670: fputs(line,ficlog);
11671: }
11672: ungetc(c,ficpar);
11673:
11674: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11675: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11676: for(i=1; i <=nlstate; i++){
1.234 brouard 11677: j=0;
1.126 brouard 11678: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11679: if(jj==i) continue;
11680: j++;
1.292 brouard 11681: while((c=getc(ficpar))=='#' && c!= EOF){
11682: ungetc(c,ficpar);
11683: fgets(line, MAXLINE, ficpar);
11684: numlinepar++;
11685: fputs(line,stdout);
11686: fputs(line,ficparo);
11687: fputs(line,ficlog);
11688: }
11689: ungetc(c,ficpar);
1.234 brouard 11690: fscanf(ficpar,"%1d%1d",&i1,&j1);
11691: if ((i1 != i) || (j1 != jj)){
11692: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11693: It might be a problem of design; if ncovcol and the model are correct\n \
11694: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11695: exit(1);
11696: }
11697: fprintf(ficparo,"%1d%1d",i1,j1);
11698: if(mle==1)
11699: printf("%1d%1d",i,jj);
11700: fprintf(ficlog,"%1d%1d",i,jj);
11701: for(k=1; k<=ncovmodel;k++){
11702: fscanf(ficpar," %lf",¶m[i][j][k]);
11703: if(mle==1){
11704: printf(" %lf",param[i][j][k]);
11705: fprintf(ficlog," %lf",param[i][j][k]);
11706: }
11707: else
11708: fprintf(ficlog," %lf",param[i][j][k]);
11709: fprintf(ficparo," %lf",param[i][j][k]);
11710: }
11711: fscanf(ficpar,"\n");
11712: numlinepar++;
11713: if(mle==1)
11714: printf("\n");
11715: fprintf(ficlog,"\n");
11716: fprintf(ficparo,"\n");
1.126 brouard 11717: }
11718: }
11719: fflush(ficlog);
1.234 brouard 11720:
1.251 brouard 11721: /* Reads parameters values */
1.126 brouard 11722: p=param[1][1];
1.251 brouard 11723: pstart=paramstart[1][1];
1.126 brouard 11724:
11725: /* Reads comments: lines beginning with '#' */
11726: while((c=getc(ficpar))=='#' && c!= EOF){
11727: ungetc(c,ficpar);
11728: fgets(line, MAXLINE, ficpar);
11729: numlinepar++;
1.141 brouard 11730: fputs(line,stdout);
1.126 brouard 11731: fputs(line,ficparo);
11732: fputs(line,ficlog);
11733: }
11734: ungetc(c,ficpar);
11735:
11736: for(i=1; i <=nlstate; i++){
11737: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11738: fscanf(ficpar,"%1d%1d",&i1,&j1);
11739: if ( (i1-i) * (j1-j) != 0){
11740: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11741: exit(1);
11742: }
11743: printf("%1d%1d",i,j);
11744: fprintf(ficparo,"%1d%1d",i1,j1);
11745: fprintf(ficlog,"%1d%1d",i1,j1);
11746: for(k=1; k<=ncovmodel;k++){
11747: fscanf(ficpar,"%le",&delti3[i][j][k]);
11748: printf(" %le",delti3[i][j][k]);
11749: fprintf(ficparo," %le",delti3[i][j][k]);
11750: fprintf(ficlog," %le",delti3[i][j][k]);
11751: }
11752: fscanf(ficpar,"\n");
11753: numlinepar++;
11754: printf("\n");
11755: fprintf(ficparo,"\n");
11756: fprintf(ficlog,"\n");
1.126 brouard 11757: }
11758: }
11759: fflush(ficlog);
1.234 brouard 11760:
1.145 brouard 11761: /* Reads covariance matrix */
1.126 brouard 11762: delti=delti3[1][1];
1.220 brouard 11763:
11764:
1.126 brouard 11765: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
1.220 brouard 11766:
1.126 brouard 11767: /* Reads comments: lines beginning with '#' */
11768: while((c=getc(ficpar))=='#' && c!= EOF){
11769: ungetc(c,ficpar);
11770: fgets(line, MAXLINE, ficpar);
11771: numlinepar++;
1.141 brouard 11772: fputs(line,stdout);
1.126 brouard 11773: fputs(line,ficparo);
11774: fputs(line,ficlog);
11775: }
11776: ungetc(c,ficpar);
1.220 brouard 11777:
1.126 brouard 11778: matcov=matrix(1,npar,1,npar);
1.203 brouard 11779: hess=matrix(1,npar,1,npar);
1.131 brouard 11780: for(i=1; i <=npar; i++)
11781: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11782:
1.194 brouard 11783: /* Scans npar lines */
1.126 brouard 11784: for(i=1; i <=npar; i++){
1.226 brouard 11785: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11786: if(count != 3){
1.226 brouard 11787: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11788: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11789: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11790: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11791: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11792: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11793: exit(1);
1.220 brouard 11794: }else{
1.226 brouard 11795: if(mle==1)
11796: printf("%1d%1d%d",i1,j1,jk);
11797: }
11798: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11799: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11800: for(j=1; j <=i; j++){
1.226 brouard 11801: fscanf(ficpar," %le",&matcov[i][j]);
11802: if(mle==1){
11803: printf(" %.5le",matcov[i][j]);
11804: }
11805: fprintf(ficlog," %.5le",matcov[i][j]);
11806: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11807: }
11808: fscanf(ficpar,"\n");
11809: numlinepar++;
11810: if(mle==1)
1.220 brouard 11811: printf("\n");
1.126 brouard 11812: fprintf(ficlog,"\n");
11813: fprintf(ficparo,"\n");
11814: }
1.194 brouard 11815: /* End of read covariance matrix npar lines */
1.126 brouard 11816: for(i=1; i <=npar; i++)
11817: for(j=i+1;j<=npar;j++)
1.226 brouard 11818: matcov[i][j]=matcov[j][i];
1.126 brouard 11819:
11820: if(mle==1)
11821: printf("\n");
11822: fprintf(ficlog,"\n");
11823:
11824: fflush(ficlog);
11825:
11826: } /* End of mle != -3 */
1.218 brouard 11827:
1.186 brouard 11828: /* Main data
11829: */
1.290 brouard 11830: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11831: /* num=lvector(1,n); */
11832: /* moisnais=vector(1,n); */
11833: /* annais=vector(1,n); */
11834: /* moisdc=vector(1,n); */
11835: /* andc=vector(1,n); */
11836: /* weight=vector(1,n); */
11837: /* agedc=vector(1,n); */
11838: /* cod=ivector(1,n); */
11839: /* for(i=1;i<=n;i++){ */
11840: num=lvector(firstobs,lastobs);
11841: moisnais=vector(firstobs,lastobs);
11842: annais=vector(firstobs,lastobs);
11843: moisdc=vector(firstobs,lastobs);
11844: andc=vector(firstobs,lastobs);
11845: weight=vector(firstobs,lastobs);
11846: agedc=vector(firstobs,lastobs);
11847: cod=ivector(firstobs,lastobs);
11848: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11849: num[i]=0;
11850: moisnais[i]=0;
11851: annais[i]=0;
11852: moisdc[i]=0;
11853: andc[i]=0;
11854: agedc[i]=0;
11855: cod[i]=0;
11856: weight[i]=1.0; /* Equal weights, 1 by default */
11857: }
1.290 brouard 11858: mint=matrix(1,maxwav,firstobs,lastobs);
11859: anint=matrix(1,maxwav,firstobs,lastobs);
11860: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11861: tab=ivector(1,NCOVMAX);
1.144 brouard 11862: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11863: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 11864:
1.136 brouard 11865: /* Reads data from file datafile */
11866: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11867: goto end;
11868:
11869: /* Calculation of the number of parameters from char model */
1.234 brouard 11870: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11871: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11872: k=3 V4 Tvar[k=3]= 4 (from V4)
11873: k=2 V1 Tvar[k=2]= 1 (from V1)
11874: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11875: */
11876:
11877: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11878: TvarsDind=ivector(1,NCOVMAX); /* */
11879: TvarsD=ivector(1,NCOVMAX); /* */
11880: TvarsQind=ivector(1,NCOVMAX); /* */
11881: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11882: TvarF=ivector(1,NCOVMAX); /* */
11883: TvarFind=ivector(1,NCOVMAX); /* */
11884: TvarV=ivector(1,NCOVMAX); /* */
11885: TvarVind=ivector(1,NCOVMAX); /* */
11886: TvarA=ivector(1,NCOVMAX); /* */
11887: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11888: TvarFD=ivector(1,NCOVMAX); /* */
11889: TvarFDind=ivector(1,NCOVMAX); /* */
11890: TvarFQ=ivector(1,NCOVMAX); /* */
11891: TvarFQind=ivector(1,NCOVMAX); /* */
11892: TvarVD=ivector(1,NCOVMAX); /* */
11893: TvarVDind=ivector(1,NCOVMAX); /* */
11894: TvarVQ=ivector(1,NCOVMAX); /* */
11895: TvarVQind=ivector(1,NCOVMAX); /* */
11896:
1.230 brouard 11897: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11898: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11899: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11900: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11901: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11902: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11903: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11904: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11905: */
11906: /* For model-covariate k tells which data-covariate to use but
11907: because this model-covariate is a construction we invent a new column
11908: ncovcol + k1
11909: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11910: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11911: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11912: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11913: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11914: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11915: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11916: */
1.145 brouard 11917: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11918: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 11919: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11920: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11921: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11922: 4 covariates (3 plus signs)
11923: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11924: */
1.230 brouard 11925: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11926: * individual dummy, fixed or varying:
11927: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11928: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11929: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11930: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11931: * Tmodelind[1]@9={9,0,3,2,}*/
11932: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11933: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11934: * individual quantitative, fixed or varying:
11935: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11936: * 3, 1, 0, 0, 0, 0, 0, 0},
11937: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11938: /* Main decodemodel */
11939:
1.187 brouard 11940:
1.223 brouard 11941: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11942: goto end;
11943:
1.137 brouard 11944: if((double)(lastobs-imx)/(double)imx > 1.10){
11945: nbwarn++;
11946: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
11947: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
11948: }
1.136 brouard 11949: /* if(mle==1){*/
1.137 brouard 11950: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11951: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11952: }
11953:
11954: /*-calculation of age at interview from date of interview and age at death -*/
11955: agev=matrix(1,maxwav,1,imx);
11956:
11957: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11958: goto end;
11959:
1.126 brouard 11960:
1.136 brouard 11961: agegomp=(int)agemin;
1.290 brouard 11962: free_vector(moisnais,firstobs,lastobs);
11963: free_vector(annais,firstobs,lastobs);
1.126 brouard 11964: /* free_matrix(mint,1,maxwav,1,n);
11965: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11966: /* free_vector(moisdc,1,n); */
11967: /* free_vector(andc,1,n); */
1.145 brouard 11968: /* */
11969:
1.126 brouard 11970: wav=ivector(1,imx);
1.214 brouard 11971: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11972: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11973: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11974: dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
11975: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11976: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11977:
11978: /* Concatenates waves */
1.214 brouard 11979: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11980: Death is a valid wave (if date is known).
11981: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11982: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11983: and mw[mi+1][i]. dh depends on stepm.
11984: */
11985:
1.126 brouard 11986: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11987: /* Concatenates waves */
1.145 brouard 11988:
1.290 brouard 11989: free_vector(moisdc,firstobs,lastobs);
11990: free_vector(andc,firstobs,lastobs);
1.215 brouard 11991:
1.126 brouard 11992: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11993: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11994: ncodemax[1]=1;
1.145 brouard 11995: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11996: cptcoveff=0;
1.220 brouard 11997: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11998: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11999: }
12000:
12001: ncovcombmax=pow(2,cptcoveff);
12002: invalidvarcomb=ivector(1, ncovcombmax);
12003: for(i=1;i<ncovcombmax;i++)
12004: invalidvarcomb[i]=0;
12005:
1.211 brouard 12006: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 12007: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 12008: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 12009:
1.200 brouard 12010: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 12011: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 12012: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 12013: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
12014: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
12015: * (currently 0 or 1) in the data.
12016: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
12017: * corresponding modality (h,j).
12018: */
12019:
1.145 brouard 12020: h=0;
12021: /*if (cptcovn > 0) */
1.126 brouard 12022: m=pow(2,cptcoveff);
12023:
1.144 brouard 12024: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 12025: * For k=4 covariates, h goes from 1 to m=2**k
12026: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
12027: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 12028: * h\k 1 2 3 4
1.143 brouard 12029: *______________________________
12030: * 1 i=1 1 i=1 1 i=1 1 i=1 1
12031: * 2 2 1 1 1
12032: * 3 i=2 1 2 1 1
12033: * 4 2 2 1 1
12034: * 5 i=3 1 i=2 1 2 1
12035: * 6 2 1 2 1
12036: * 7 i=4 1 2 2 1
12037: * 8 2 2 2 1
1.197 brouard 12038: * 9 i=5 1 i=3 1 i=2 1 2
12039: * 10 2 1 1 2
12040: * 11 i=6 1 2 1 2
12041: * 12 2 2 1 2
12042: * 13 i=7 1 i=4 1 2 2
12043: * 14 2 1 2 2
12044: * 15 i=8 1 2 2 2
12045: * 16 2 2 2 2
1.143 brouard 12046: */
1.212 brouard 12047: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 12048: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
12049: * and the value of each covariate?
12050: * V1=1, V2=1, V3=2, V4=1 ?
12051: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
12052: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
12053: * In order to get the real value in the data, we use nbcode
12054: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
12055: * We are keeping this crazy system in order to be able (in the future?)
12056: * to have more than 2 values (0 or 1) for a covariate.
12057: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
12058: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
12059: * bbbbbbbb
12060: * 76543210
12061: * h-1 00000101 (6-1=5)
1.219 brouard 12062: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 12063: * &
12064: * 1 00000001 (1)
1.219 brouard 12065: * 00000000 = 1 & ((h-1) >> (k-1))
12066: * +1= 00000001 =1
1.211 brouard 12067: *
12068: * h=14, k=3 => h'=h-1=13, k'=k-1=2
12069: * h' 1101 =2^3+2^2+0x2^1+2^0
12070: * >>k' 11
12071: * & 00000001
12072: * = 00000001
12073: * +1 = 00000010=2 = codtabm(14,3)
12074: * Reverse h=6 and m=16?
12075: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
12076: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
12077: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
12078: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
12079: * V3=decodtabm(14,3,2**4)=2
12080: * h'=13 1101 =2^3+2^2+0x2^1+2^0
12081: *(h-1) >> (j-1) 0011 =13 >> 2
12082: * &1 000000001
12083: * = 000000001
12084: * +1= 000000010 =2
12085: * 2211
12086: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
12087: * V3=2
1.220 brouard 12088: * codtabm and decodtabm are identical
1.211 brouard 12089: */
12090:
1.145 brouard 12091:
12092: free_ivector(Ndum,-1,NCOVMAX);
12093:
12094:
1.126 brouard 12095:
1.186 brouard 12096: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 12097: strcpy(optionfilegnuplot,optionfilefiname);
12098: if(mle==-3)
1.201 brouard 12099: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 12100: strcat(optionfilegnuplot,".gp");
12101:
12102: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
12103: printf("Problem with file %s",optionfilegnuplot);
12104: }
12105: else{
1.204 brouard 12106: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 12107: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 12108: //fprintf(ficgp,"set missing 'NaNq'\n");
12109: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 12110: }
12111: /* fclose(ficgp);*/
1.186 brouard 12112:
12113:
12114: /* Initialisation of --------- index.htm --------*/
1.126 brouard 12115:
12116: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
12117: if(mle==-3)
1.201 brouard 12118: strcat(optionfilehtm,"-MORT_");
1.126 brouard 12119: strcat(optionfilehtm,".htm");
12120: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 12121: printf("Problem with %s \n",optionfilehtm);
12122: exit(0);
1.126 brouard 12123: }
12124:
12125: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
12126: strcat(optionfilehtmcov,"-cov.htm");
12127: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
12128: printf("Problem with %s \n",optionfilehtmcov), exit(0);
12129: }
12130: else{
12131: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
12132: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 12133: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 12134: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
12135: }
12136:
1.213 brouard 12137: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本å¦è¡“振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
1.204 brouard 12138: <hr size=\"2\" color=\"#EC5E5E\"> \n\
12139: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 12140: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 12141: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 12142: \n\
12143: <hr size=\"2\" color=\"#EC5E5E\">\
12144: <ul><li><h4>Parameter files</h4>\n\
12145: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
12146: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
12147: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
12148: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
12149: - Date and time at start: %s</ul>\n",\
12150: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
12151: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
12152: fileres,fileres,\
12153: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
12154: fflush(fichtm);
12155:
12156: strcpy(pathr,path);
12157: strcat(pathr,optionfilefiname);
1.184 brouard 12158: #ifdef WIN32
12159: _chdir(optionfilefiname); /* Move to directory named optionfile */
12160: #else
1.126 brouard 12161: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 12162: #endif
12163:
1.126 brouard 12164:
1.220 brouard 12165: /* Calculates basic frequencies. Computes observed prevalence at single age
12166: and for any valid combination of covariates
1.126 brouard 12167: and prints on file fileres'p'. */
1.251 brouard 12168: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 12169: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 12170:
12171: fprintf(fichtm,"\n");
1.286 brouard 12172: fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
1.274 brouard 12173: ftol, stepm);
12174: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
12175: ncurrv=1;
12176: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
12177: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
12178: ncurrv=i;
12179: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 12180: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 12181: ncurrv=i;
12182: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 12183: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 12184: ncurrv=i;
12185: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
12186: fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
12187: nlstate, ndeath, maxwav, mle, weightopt);
12188:
12189: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
12190: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
12191:
12192:
1.317 brouard 12193: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
1.126 brouard 12194: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
12195: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 12196: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 12197: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 12198: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
12199: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
12200: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
12201: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 12202:
1.126 brouard 12203: /* For Powell, parameters are in a vector p[] starting at p[1]
12204: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
12205: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
12206:
12207: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 12208: /* For mortality only */
1.126 brouard 12209: if (mle==-3){
1.136 brouard 12210: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 12211: for(i=1;i<=NDIM;i++)
12212: for(j=1;j<=NDIM;j++)
12213: ximort[i][j]=0.;
1.186 brouard 12214: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 12215: cens=ivector(firstobs,lastobs);
12216: ageexmed=vector(firstobs,lastobs);
12217: agecens=vector(firstobs,lastobs);
12218: dcwave=ivector(firstobs,lastobs);
1.223 brouard 12219:
1.126 brouard 12220: for (i=1; i<=imx; i++){
12221: dcwave[i]=-1;
12222: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 12223: if (s[m][i]>nlstate) {
12224: dcwave[i]=m;
12225: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
12226: break;
12227: }
1.126 brouard 12228: }
1.226 brouard 12229:
1.126 brouard 12230: for (i=1; i<=imx; i++) {
12231: if (wav[i]>0){
1.226 brouard 12232: ageexmed[i]=agev[mw[1][i]][i];
12233: j=wav[i];
12234: agecens[i]=1.;
12235:
12236: if (ageexmed[i]> 1 && wav[i] > 0){
12237: agecens[i]=agev[mw[j][i]][i];
12238: cens[i]= 1;
12239: }else if (ageexmed[i]< 1)
12240: cens[i]= -1;
12241: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
12242: cens[i]=0 ;
1.126 brouard 12243: }
12244: else cens[i]=-1;
12245: }
12246:
12247: for (i=1;i<=NDIM;i++) {
12248: for (j=1;j<=NDIM;j++)
1.226 brouard 12249: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 12250: }
12251:
1.302 brouard 12252: p[1]=0.0268; p[NDIM]=0.083;
12253: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 12254:
12255:
1.136 brouard 12256: #ifdef GSL
12257: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 12258: #else
1.126 brouard 12259: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 12260: #endif
1.201 brouard 12261: strcpy(filerespow,"POW-MORT_");
12262: strcat(filerespow,fileresu);
1.126 brouard 12263: if((ficrespow=fopen(filerespow,"w"))==NULL) {
12264: printf("Problem with resultfile: %s\n", filerespow);
12265: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
12266: }
1.136 brouard 12267: #ifdef GSL
12268: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 12269: #else
1.126 brouard 12270: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 12271: #endif
1.126 brouard 12272: /* for (i=1;i<=nlstate;i++)
12273: for(j=1;j<=nlstate+ndeath;j++)
12274: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
12275: */
12276: fprintf(ficrespow,"\n");
1.136 brouard 12277: #ifdef GSL
12278: /* gsl starts here */
12279: T = gsl_multimin_fminimizer_nmsimplex;
12280: gsl_multimin_fminimizer *sfm = NULL;
12281: gsl_vector *ss, *x;
12282: gsl_multimin_function minex_func;
12283:
12284: /* Initial vertex size vector */
12285: ss = gsl_vector_alloc (NDIM);
12286:
12287: if (ss == NULL){
12288: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
12289: }
12290: /* Set all step sizes to 1 */
12291: gsl_vector_set_all (ss, 0.001);
12292:
12293: /* Starting point */
1.126 brouard 12294:
1.136 brouard 12295: x = gsl_vector_alloc (NDIM);
12296:
12297: if (x == NULL){
12298: gsl_vector_free(ss);
12299: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
12300: }
12301:
12302: /* Initialize method and iterate */
12303: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 12304: /* gsl_vector_set(x, 0, 0.0268); */
12305: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 12306: gsl_vector_set(x, 0, p[1]);
12307: gsl_vector_set(x, 1, p[2]);
12308:
12309: minex_func.f = &gompertz_f;
12310: minex_func.n = NDIM;
12311: minex_func.params = (void *)&p; /* ??? */
12312:
12313: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12314: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12315:
12316: printf("Iterations beginning .....\n\n");
12317: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12318:
12319: iteri=0;
12320: while (rval == GSL_CONTINUE){
12321: iteri++;
12322: status = gsl_multimin_fminimizer_iterate(sfm);
12323:
12324: if (status) printf("error: %s\n", gsl_strerror (status));
12325: fflush(0);
12326:
12327: if (status)
12328: break;
12329:
12330: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12331: ssval = gsl_multimin_fminimizer_size (sfm);
12332:
12333: if (rval == GSL_SUCCESS)
12334: printf ("converged to a local maximum at\n");
12335:
12336: printf("%5d ", iteri);
12337: for (it = 0; it < NDIM; it++){
12338: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12339: }
12340: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12341: }
12342:
12343: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12344:
12345: gsl_vector_free(x); /* initial values */
12346: gsl_vector_free(ss); /* inital step size */
12347: for (it=0; it<NDIM; it++){
12348: p[it+1]=gsl_vector_get(sfm->x,it);
12349: fprintf(ficrespow," %.12lf", p[it]);
12350: }
12351: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12352: #endif
12353: #ifdef POWELL
12354: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12355: #endif
1.126 brouard 12356: fclose(ficrespow);
12357:
1.203 brouard 12358: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12359:
12360: for(i=1; i <=NDIM; i++)
12361: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12362: matcov[i][j]=matcov[j][i];
1.126 brouard 12363:
12364: printf("\nCovariance matrix\n ");
1.203 brouard 12365: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12366: for(i=1; i <=NDIM; i++) {
12367: for(j=1;j<=NDIM;j++){
1.220 brouard 12368: printf("%f ",matcov[i][j]);
12369: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12370: }
1.203 brouard 12371: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12372: }
12373:
12374: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12375: for (i=1;i<=NDIM;i++) {
1.126 brouard 12376: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12377: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12378: }
1.302 brouard 12379: lsurv=vector(agegomp,AGESUP);
12380: lpop=vector(agegomp,AGESUP);
12381: tpop=vector(agegomp,AGESUP);
1.126 brouard 12382: lsurv[agegomp]=100000;
12383:
12384: for (k=agegomp;k<=AGESUP;k++) {
12385: agemortsup=k;
12386: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12387: }
12388:
12389: for (k=agegomp;k<agemortsup;k++)
12390: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12391:
12392: for (k=agegomp;k<agemortsup;k++){
12393: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12394: sumlpop=sumlpop+lpop[k];
12395: }
12396:
12397: tpop[agegomp]=sumlpop;
12398: for (k=agegomp;k<(agemortsup-3);k++){
12399: /* tpop[k+1]=2;*/
12400: tpop[k+1]=tpop[k]-lpop[k];
12401: }
12402:
12403:
12404: printf("\nAge lx qx dx Lx Tx e(x)\n");
12405: for (k=agegomp;k<(agemortsup-2);k++)
12406: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
12407:
12408:
12409: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12410: ageminpar=50;
12411: agemaxpar=100;
1.194 brouard 12412: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12413: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12414: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12415: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12416: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12417: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12418: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12419: }else{
12420: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12421: fprintf(ficlog,"Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
1.201 brouard 12422: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12423: }
1.201 brouard 12424: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12425: stepm, weightopt,\
12426: model,imx,p,matcov,agemortsup);
12427:
1.302 brouard 12428: free_vector(lsurv,agegomp,AGESUP);
12429: free_vector(lpop,agegomp,AGESUP);
12430: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12431: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12432: free_ivector(dcwave,firstobs,lastobs);
12433: free_vector(agecens,firstobs,lastobs);
12434: free_vector(ageexmed,firstobs,lastobs);
12435: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12436: #ifdef GSL
1.136 brouard 12437: #endif
1.186 brouard 12438: } /* Endof if mle==-3 mortality only */
1.205 brouard 12439: /* Standard */
12440: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12441: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12442: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12443: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12444: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12445: for (k=1; k<=npar;k++)
12446: printf(" %d %8.5f",k,p[k]);
12447: printf("\n");
1.205 brouard 12448: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12449: /* mlikeli uses func not funcone */
1.247 brouard 12450: /* for(i=1;i<nlstate;i++){ */
12451: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12452: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12453: /* } */
1.205 brouard 12454: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12455: }
12456: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12457: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12458: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12459: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12460: }
12461: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12462: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12463: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12464: for (k=1; k<=npar;k++)
12465: printf(" %d %8.5f",k,p[k]);
12466: printf("\n");
12467:
12468: /*--------- results files --------------*/
1.283 brouard 12469: /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
1.126 brouard 12470:
12471:
12472: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.319 ! brouard 12473: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); /* Printing model equation */
1.126 brouard 12474: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
1.319 ! brouard 12475:
! 12476: printf("#model= 1 + age ");
! 12477: fprintf(ficres,"#model= 1 + age ");
! 12478: fprintf(ficlog,"#model= 1 + age ");
! 12479: fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
! 12480: </ul>", model);
! 12481:
! 12482: fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
! 12483: fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
! 12484: if(nagesqr==1){
! 12485: printf(" + age*age ");
! 12486: fprintf(ficres," + age*age ");
! 12487: fprintf(ficlog," + age*age ");
! 12488: fprintf(fichtm, "<th>+ age*age</th>");
! 12489: }
! 12490: for(j=1;j <=ncovmodel-2;j++){
! 12491: if(Typevar[j]==0) {
! 12492: printf(" + V%d ",Tvar[j]);
! 12493: fprintf(ficres," + V%d ",Tvar[j]);
! 12494: fprintf(ficlog," + V%d ",Tvar[j]);
! 12495: fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
! 12496: }else if(Typevar[j]==1) {
! 12497: printf(" + V%d*age ",Tvar[j]);
! 12498: fprintf(ficres," + V%d*age ",Tvar[j]);
! 12499: fprintf(ficlog," + V%d*age ",Tvar[j]);
! 12500: fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
! 12501: }else if(Typevar[j]==2) {
! 12502: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
! 12503: fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
! 12504: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
! 12505: fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
! 12506: }
! 12507: }
! 12508: printf("\n");
! 12509: fprintf(ficres,"\n");
! 12510: fprintf(ficlog,"\n");
! 12511: fprintf(fichtm, "</tr>");
! 12512: fprintf(fichtm, "\n");
! 12513:
! 12514:
1.126 brouard 12515: for(i=1,jk=1; i <=nlstate; i++){
12516: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12517: if (k != i) {
1.319 ! brouard 12518: fprintf(fichtm, "<tr>");
1.225 brouard 12519: printf("%d%d ",i,k);
12520: fprintf(ficlog,"%d%d ",i,k);
12521: fprintf(ficres,"%1d%1d ",i,k);
1.319 ! brouard 12522: fprintf(fichtm, "<td>%1d%1d</td>",i,k);
1.225 brouard 12523: for(j=1; j <=ncovmodel; j++){
12524: printf("%12.7f ",p[jk]);
12525: fprintf(ficlog,"%12.7f ",p[jk]);
12526: fprintf(ficres,"%12.7f ",p[jk]);
1.319 ! brouard 12527: fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
1.225 brouard 12528: jk++;
12529: }
12530: printf("\n");
12531: fprintf(ficlog,"\n");
12532: fprintf(ficres,"\n");
1.319 ! brouard 12533: fprintf(fichtm, "</tr>\n");
1.225 brouard 12534: }
1.126 brouard 12535: }
12536: }
1.319 ! brouard 12537: /* fprintf(fichtm,"</tr>\n"); */
! 12538: fprintf(fichtm,"</table>\n");
! 12539: fprintf(fichtm, "\n");
! 12540:
1.203 brouard 12541: if(mle != 0){
12542: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12543: ftolhess=ftol; /* Usually correct */
1.203 brouard 12544: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12545: printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
12546: fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
1.319 ! brouard 12547: fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
! 12548: fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
! 12549: if(nagesqr==1){
! 12550: printf(" + age*age ");
! 12551: fprintf(ficres," + age*age ");
! 12552: fprintf(ficlog," + age*age ");
! 12553: fprintf(fichtm, "<th>+ age*age</th>");
! 12554: }
! 12555: for(j=1;j <=ncovmodel-2;j++){
! 12556: if(Typevar[j]==0) {
! 12557: printf(" + V%d ",Tvar[j]);
! 12558: fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
! 12559: }else if(Typevar[j]==1) {
! 12560: printf(" + V%d*age ",Tvar[j]);
! 12561: fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
! 12562: }else if(Typevar[j]==2) {
! 12563: fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
! 12564: }
! 12565: }
! 12566: fprintf(fichtm, "</tr>\n");
! 12567:
1.203 brouard 12568: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12569: for(k=1; k <=(nlstate+ndeath); k++){
12570: if (k != i) {
1.319 ! brouard 12571: fprintf(fichtm, "<tr valign=top>");
1.225 brouard 12572: printf("%d%d ",i,k);
12573: fprintf(ficlog,"%d%d ",i,k);
1.319 ! brouard 12574: fprintf(fichtm, "<td>%1d%1d</td>",i,k);
1.225 brouard 12575: for(j=1; j <=ncovmodel; j++){
1.319 ! brouard 12576: wald=p[jk]/sqrt(matcov[jk][jk]);
! 12577: printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
! 12578: fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
! 12579: if(fabs(wald) > 1.96){
! 12580: fprintf(fichtm, "<td><b>%12.7f</b> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
! 12581: fprintf(fichtm,"<b>W=%8.3f</b></br>",wald);
! 12582: }else{
! 12583: fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
! 12584: fprintf(fichtm,"W=%8.3f</br>",wald);
! 12585: }
! 12586: fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
1.225 brouard 12587: jk++;
12588: }
12589: printf("\n");
12590: fprintf(ficlog,"\n");
1.319 ! brouard 12591: fprintf(fichtm, "</tr>\n");
1.225 brouard 12592: }
12593: }
1.193 brouard 12594: }
1.203 brouard 12595: } /* end of hesscov and Wald tests */
1.319 ! brouard 12596: fprintf(fichtm,"</table>\n");
1.225 brouard 12597:
1.203 brouard 12598: /* */
1.126 brouard 12599: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12600: printf("# Scales (for hessian or gradient estimation)\n");
12601: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12602: for(i=1,jk=1; i <=nlstate; i++){
12603: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12604: if (j!=i) {
12605: fprintf(ficres,"%1d%1d",i,j);
12606: printf("%1d%1d",i,j);
12607: fprintf(ficlog,"%1d%1d",i,j);
12608: for(k=1; k<=ncovmodel;k++){
12609: printf(" %.5e",delti[jk]);
12610: fprintf(ficlog," %.5e",delti[jk]);
12611: fprintf(ficres," %.5e",delti[jk]);
12612: jk++;
12613: }
12614: printf("\n");
12615: fprintf(ficlog,"\n");
12616: fprintf(ficres,"\n");
12617: }
1.126 brouard 12618: }
12619: }
12620:
12621: fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
1.203 brouard 12622: if(mle >= 1) /* To big for the screen */
1.126 brouard 12623: printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
12624: fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
12625: /* # 121 Var(a12)\n\ */
12626: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12627: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12628: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12629: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12630: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12631: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12632: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12633:
12634:
12635: /* Just to have a covariance matrix which will be more understandable
12636: even is we still don't want to manage dictionary of variables
12637: */
12638: for(itimes=1;itimes<=2;itimes++){
12639: jj=0;
12640: for(i=1; i <=nlstate; i++){
1.225 brouard 12641: for(j=1; j <=nlstate+ndeath; j++){
12642: if(j==i) continue;
12643: for(k=1; k<=ncovmodel;k++){
12644: jj++;
12645: ca[0]= k+'a'-1;ca[1]='\0';
12646: if(itimes==1){
12647: if(mle>=1)
12648: printf("#%1d%1d%d",i,j,k);
12649: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12650: fprintf(ficres,"#%1d%1d%d",i,j,k);
12651: }else{
12652: if(mle>=1)
12653: printf("%1d%1d%d",i,j,k);
12654: fprintf(ficlog,"%1d%1d%d",i,j,k);
12655: fprintf(ficres,"%1d%1d%d",i,j,k);
12656: }
12657: ll=0;
12658: for(li=1;li <=nlstate; li++){
12659: for(lj=1;lj <=nlstate+ndeath; lj++){
12660: if(lj==li) continue;
12661: for(lk=1;lk<=ncovmodel;lk++){
12662: ll++;
12663: if(ll<=jj){
12664: cb[0]= lk +'a'-1;cb[1]='\0';
12665: if(ll<jj){
12666: if(itimes==1){
12667: if(mle>=1)
12668: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12669: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12670: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12671: }else{
12672: if(mle>=1)
12673: printf(" %.5e",matcov[jj][ll]);
12674: fprintf(ficlog," %.5e",matcov[jj][ll]);
12675: fprintf(ficres," %.5e",matcov[jj][ll]);
12676: }
12677: }else{
12678: if(itimes==1){
12679: if(mle>=1)
12680: printf(" Var(%s%1d%1d)",ca,i,j);
12681: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12682: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12683: }else{
12684: if(mle>=1)
12685: printf(" %.7e",matcov[jj][ll]);
12686: fprintf(ficlog," %.7e",matcov[jj][ll]);
12687: fprintf(ficres," %.7e",matcov[jj][ll]);
12688: }
12689: }
12690: }
12691: } /* end lk */
12692: } /* end lj */
12693: } /* end li */
12694: if(mle>=1)
12695: printf("\n");
12696: fprintf(ficlog,"\n");
12697: fprintf(ficres,"\n");
12698: numlinepar++;
12699: } /* end k*/
12700: } /*end j */
1.126 brouard 12701: } /* end i */
12702: } /* end itimes */
12703:
12704: fflush(ficlog);
12705: fflush(ficres);
1.225 brouard 12706: while(fgets(line, MAXLINE, ficpar)) {
12707: /* If line starts with a # it is a comment */
12708: if (line[0] == '#') {
12709: numlinepar++;
12710: fputs(line,stdout);
12711: fputs(line,ficparo);
12712: fputs(line,ficlog);
1.299 brouard 12713: fputs(line,ficres);
1.225 brouard 12714: continue;
12715: }else
12716: break;
12717: }
12718:
1.209 brouard 12719: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12720: /* ungetc(c,ficpar); */
12721: /* fgets(line, MAXLINE, ficpar); */
12722: /* fputs(line,stdout); */
12723: /* fputs(line,ficparo); */
12724: /* } */
12725: /* ungetc(c,ficpar); */
1.126 brouard 12726:
12727: estepm=0;
1.209 brouard 12728: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
1.225 brouard 12729:
12730: if (num_filled != 6) {
12731: printf("Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
12732: fprintf(ficlog,"Error: Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n, your line=%s . Probably you are running an older format.\n",line);
12733: goto end;
12734: }
12735: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12736: }
12737: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12738: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12739:
1.209 brouard 12740: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12741: if (estepm==0 || estepm < stepm) estepm=stepm;
12742: if (fage <= 2) {
12743: bage = ageminpar;
12744: fage = agemaxpar;
12745: }
12746:
12747: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12748: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12749: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12750:
1.186 brouard 12751: /* Other stuffs, more or less useful */
1.254 brouard 12752: while(fgets(line, MAXLINE, ficpar)) {
12753: /* If line starts with a # it is a comment */
12754: if (line[0] == '#') {
12755: numlinepar++;
12756: fputs(line,stdout);
12757: fputs(line,ficparo);
12758: fputs(line,ficlog);
1.299 brouard 12759: fputs(line,ficres);
1.254 brouard 12760: continue;
12761: }else
12762: break;
12763: }
12764:
12765: if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
12766:
12767: if (num_filled != 7) {
12768: printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12769: fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12770: goto end;
12771: }
12772: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12773: fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12774: fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12775: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
1.126 brouard 12776: }
1.254 brouard 12777:
12778: while(fgets(line, MAXLINE, ficpar)) {
12779: /* If line starts with a # it is a comment */
12780: if (line[0] == '#') {
12781: numlinepar++;
12782: fputs(line,stdout);
12783: fputs(line,ficparo);
12784: fputs(line,ficlog);
1.299 brouard 12785: fputs(line,ficres);
1.254 brouard 12786: continue;
12787: }else
12788: break;
1.126 brouard 12789: }
12790:
12791:
12792: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12793: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12794:
1.254 brouard 12795: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12796: if (num_filled != 1) {
12797: printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12798: fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12799: goto end;
12800: }
12801: printf("pop_based=%d\n",popbased);
12802: fprintf(ficlog,"pop_based=%d\n",popbased);
12803: fprintf(ficparo,"pop_based=%d\n",popbased);
12804: fprintf(ficres,"pop_based=%d\n",popbased);
12805: }
12806:
1.258 brouard 12807: /* Results */
1.307 brouard 12808: endishere=0;
1.258 brouard 12809: nresult=0;
1.308 brouard 12810: parameterline=0;
1.258 brouard 12811: do{
12812: if(!fgets(line, MAXLINE, ficpar)){
12813: endishere=1;
1.308 brouard 12814: parameterline=15;
1.258 brouard 12815: }else if (line[0] == '#') {
12816: /* If line starts with a # it is a comment */
1.254 brouard 12817: numlinepar++;
12818: fputs(line,stdout);
12819: fputs(line,ficparo);
12820: fputs(line,ficlog);
1.299 brouard 12821: fputs(line,ficres);
1.254 brouard 12822: continue;
1.258 brouard 12823: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12824: parameterline=11;
1.296 brouard 12825: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12826: parameterline=12;
1.307 brouard 12827: else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258 brouard 12828: parameterline=13;
1.307 brouard 12829: }
1.258 brouard 12830: else{
12831: parameterline=14;
1.254 brouard 12832: }
1.308 brouard 12833: switch (parameterline){ /* =0 only if only comments */
1.258 brouard 12834: case 11:
1.296 brouard 12835: if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
12836: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.258 brouard 12837: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
12838: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
12839: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
12840: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12841: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12842: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12843: prvforecast = 1;
12844: }
12845: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.313 brouard 12846: printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12847: fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12848: fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12849: prvforecast = 2;
12850: }
12851: else {
12852: printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12853: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12854: goto end;
1.258 brouard 12855: }
1.254 brouard 12856: break;
1.258 brouard 12857: case 12:
1.296 brouard 12858: if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
12859: fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12860: printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12861: fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12862: fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12863: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12864: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12865: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12866: prvbackcast = 1;
12867: }
12868: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.313 brouard 12869: printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12870: fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12871: fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12872: prvbackcast = 2;
12873: }
12874: else {
12875: printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12876: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12877: goto end;
1.258 brouard 12878: }
1.230 brouard 12879: break;
1.258 brouard 12880: case 13:
1.307 brouard 12881: num_filled=sscanf(line,"result:%[^\n]\n",resultline);
12882: nresult++; /* Sum of resultlines */
12883: printf("Result %d: result:%s\n",nresult, resultline);
1.318 brouard 12884: if(nresult > MAXRESULTLINESPONE-1){
12885: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
12886: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
1.307 brouard 12887: goto end;
12888: }
1.310 brouard 12889: if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.314 brouard 12890: fprintf(ficparo,"result: %s\n",resultline);
12891: fprintf(ficres,"result: %s\n",resultline);
12892: fprintf(ficlog,"result: %s\n",resultline);
1.310 brouard 12893: } else
12894: goto end;
1.307 brouard 12895: break;
12896: case 14:
12897: printf("Error: Unknown command '%s'\n",line);
12898: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
1.314 brouard 12899: if(line[0] == ' ' || line[0] == '\n'){
12900: printf("It should not be an empty line '%s'\n",line);
12901: fprintf(ficlog,"It should not be an empty line '%s'\n",line);
12902: }
1.307 brouard 12903: if(ncovmodel >=2 && nresult==0 ){
12904: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
12905: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12906: }
1.307 brouard 12907: /* goto end; */
12908: break;
1.308 brouard 12909: case 15:
12910: printf("End of resultlines.\n");
12911: fprintf(ficlog,"End of resultlines.\n");
12912: break;
12913: default: /* parameterline =0 */
1.307 brouard 12914: nresult=1;
12915: decoderesult(".",nresult ); /* No covariate */
1.258 brouard 12916: } /* End switch parameterline */
12917: }while(endishere==0); /* End do */
1.126 brouard 12918:
1.230 brouard 12919: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12920: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12921:
12922: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12923: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12924: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12925: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12926: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12927: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12928: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12929: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12930: }else{
1.270 brouard 12931: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12932: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12933: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12934: if(prvforecast==1){
12935: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12936: jprojd=jproj1;
12937: mprojd=mproj1;
12938: anprojd=anproj1;
12939: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12940: jprojf=jproj2;
12941: mprojf=mproj2;
12942: anprojf=anproj2;
12943: } else if(prvforecast == 2){
12944: dateprojd=dateintmean;
12945: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12946: dateprojf=dateintmean+yrfproj;
12947: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12948: }
12949: if(prvbackcast==1){
12950: datebackd=(jback1+12*mback1+365*anback1)/365;
12951: jbackd=jback1;
12952: mbackd=mback1;
12953: anbackd=anback1;
12954: datebackf=(jback2+12*mback2+365*anback2)/365;
12955: jbackf=jback2;
12956: mbackf=mback2;
12957: anbackf=anback2;
12958: } else if(prvbackcast == 2){
12959: datebackd=dateintmean;
12960: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12961: datebackf=dateintmean-yrbproj;
12962: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12963: }
12964:
12965: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12966: }
12967: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12968: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12969: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12970:
1.225 brouard 12971: /*------------ free_vector -------------*/
12972: /* chdir(path); */
1.220 brouard 12973:
1.215 brouard 12974: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12975: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12976: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12977: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12978: free_lvector(num,firstobs,lastobs);
12979: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12980: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12981: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12982: fclose(ficparo);
12983: fclose(ficres);
1.220 brouard 12984:
12985:
1.186 brouard 12986: /* Other results (useful)*/
1.220 brouard 12987:
12988:
1.126 brouard 12989: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12990: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12991: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12992: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12993: fclose(ficrespl);
12994:
12995: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12996: /*#include "hpijx.h"*/
12997: hPijx(p, bage, fage);
1.145 brouard 12998: fclose(ficrespij);
1.227 brouard 12999:
1.220 brouard 13000: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 13001: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 13002: k=1;
1.126 brouard 13003: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 13004:
1.269 brouard 13005: /* Prevalence for each covariate combination in probs[age][status][cov] */
13006: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
13007: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 13008: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 13009: for(k=1;k<=ncovcombmax;k++)
13010: probs[i][j][k]=0.;
1.269 brouard 13011: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
13012: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 13013: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 13014: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
13015: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 13016: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 13017: for(k=1;k<=ncovcombmax;k++)
13018: mobaverages[i][j][k]=0.;
1.219 brouard 13019: mobaverage=mobaverages;
13020: if (mobilav!=0) {
1.235 brouard 13021: printf("Movingaveraging observed prevalence\n");
1.258 brouard 13022: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 13023: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
13024: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
13025: printf(" Error in movingaverage mobilav=%d\n",mobilav);
13026: }
1.269 brouard 13027: } else if (mobilavproj !=0) {
1.235 brouard 13028: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 13029: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 13030: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
13031: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
13032: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
13033: }
1.269 brouard 13034: }else{
13035: printf("Internal error moving average\n");
13036: fflush(stdout);
13037: exit(1);
1.219 brouard 13038: }
13039: }/* end if moving average */
1.227 brouard 13040:
1.126 brouard 13041: /*---------- Forecasting ------------------*/
1.296 brouard 13042: if(prevfcast==1){
13043: /* /\* if(stepm ==1){*\/ */
13044: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
13045: /*This done previously after freqsummary.*/
13046: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
13047: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
13048:
13049: /* } else if (prvforecast==2){ */
13050: /* /\* if(stepm ==1){*\/ */
13051: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
13052: /* } */
13053: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
13054: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 13055: }
1.269 brouard 13056:
1.296 brouard 13057: /* Prevbcasting */
13058: if(prevbcast==1){
1.219 brouard 13059: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
13060: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
13061: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
13062:
13063: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
13064:
13065: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 13066:
1.219 brouard 13067: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
13068: fclose(ficresplb);
13069:
1.222 brouard 13070: hBijx(p, bage, fage, mobaverage);
13071: fclose(ficrespijb);
1.219 brouard 13072:
1.296 brouard 13073: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
13074: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
13075: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
13076: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
13077: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
13078: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
13079:
13080:
1.269 brouard 13081: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 13082:
13083:
1.269 brouard 13084: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 13085: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
13086: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
13087: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 13088: } /* end Prevbcasting */
1.268 brouard 13089:
1.186 brouard 13090:
13091: /* ------ Other prevalence ratios------------ */
1.126 brouard 13092:
1.215 brouard 13093: free_ivector(wav,1,imx);
13094: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
13095: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
13096: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 13097:
13098:
1.127 brouard 13099: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 13100:
1.201 brouard 13101: strcpy(filerese,"E_");
13102: strcat(filerese,fileresu);
1.126 brouard 13103: if((ficreseij=fopen(filerese,"w"))==NULL) {
13104: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
13105: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
13106: }
1.208 brouard 13107: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
13108: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 13109:
13110: pstamp(ficreseij);
1.219 brouard 13111:
1.235 brouard 13112: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
13113: if (cptcovn < 1){i1=1;}
13114:
13115: for(nres=1; nres <= nresult; nres++) /* For each resultline */
13116: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 13117: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 13118: continue;
1.219 brouard 13119: fprintf(ficreseij,"\n#****** ");
1.235 brouard 13120: printf("\n#****** ");
1.225 brouard 13121: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 13122: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 13123: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
13124: }
13125: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
13126: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13127: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 13128: }
13129: fprintf(ficreseij,"******\n");
1.235 brouard 13130: printf("******\n");
1.219 brouard 13131:
13132: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
13133: oldm=oldms;savm=savms;
1.235 brouard 13134: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 13135:
1.219 brouard 13136: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 13137: }
13138: fclose(ficreseij);
1.208 brouard 13139: printf("done evsij\n");fflush(stdout);
13140: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 13141:
1.218 brouard 13142:
1.227 brouard 13143: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 13144:
1.201 brouard 13145: strcpy(filerest,"T_");
13146: strcat(filerest,fileresu);
1.127 brouard 13147: if((ficrest=fopen(filerest,"w"))==NULL) {
13148: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
13149: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
13150: }
1.208 brouard 13151: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
13152: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 13153: strcpy(fileresstde,"STDE_");
13154: strcat(fileresstde,fileresu);
1.126 brouard 13155: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 13156: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
13157: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 13158: }
1.227 brouard 13159: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
13160: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 13161:
1.201 brouard 13162: strcpy(filerescve,"CVE_");
13163: strcat(filerescve,fileresu);
1.126 brouard 13164: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 13165: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
13166: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 13167: }
1.227 brouard 13168: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
13169: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 13170:
1.201 brouard 13171: strcpy(fileresv,"V_");
13172: strcat(fileresv,fileresu);
1.126 brouard 13173: if((ficresvij=fopen(fileresv,"w"))==NULL) {
13174: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
13175: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
13176: }
1.227 brouard 13177: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
13178: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 13179:
1.235 brouard 13180: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
13181: if (cptcovn < 1){i1=1;}
13182:
13183: for(nres=1; nres <= nresult; nres++) /* For each resultline */
13184: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 13185: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 13186: continue;
1.242 brouard 13187: printf("\n#****** Result for:");
13188: fprintf(ficrest,"\n#****** Result for:");
13189: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 13190: for(j=1;j<=cptcoveff;j++){
13191: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
13192: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
13193: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
13194: }
1.235 brouard 13195: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
13196: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13197: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13198: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13199: }
1.208 brouard 13200: fprintf(ficrest,"******\n");
1.227 brouard 13201: fprintf(ficlog,"******\n");
13202: printf("******\n");
1.208 brouard 13203:
13204: fprintf(ficresstdeij,"\n#****** ");
13205: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 13206: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 13207: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
13208: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 13209: }
1.235 brouard 13210: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
13211: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13212: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13213: }
1.208 brouard 13214: fprintf(ficresstdeij,"******\n");
13215: fprintf(ficrescveij,"******\n");
13216:
13217: fprintf(ficresvij,"\n#****** ");
1.238 brouard 13218: /* pstamp(ficresvij); */
1.225 brouard 13219: for(j=1;j<=cptcoveff;j++)
1.227 brouard 13220: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 13221: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
13222: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
13223: }
1.208 brouard 13224: fprintf(ficresvij,"******\n");
13225:
13226: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
13227: oldm=oldms;savm=savms;
1.235 brouard 13228: printf(" cvevsij ");
13229: fprintf(ficlog, " cvevsij ");
13230: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 13231: printf(" end cvevsij \n ");
13232: fprintf(ficlog, " end cvevsij \n ");
13233:
13234: /*
13235: */
13236: /* goto endfree; */
13237:
13238: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
13239: pstamp(ficrest);
13240:
1.269 brouard 13241: epj=vector(1,nlstate+1);
1.208 brouard 13242: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 13243: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
13244: cptcod= 0; /* To be deleted */
13245: printf("varevsij vpopbased=%d \n",vpopbased);
13246: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 13247: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
1.227 brouard 13248: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
13249: if(vpopbased==1)
13250: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
13251: else
1.288 brouard 13252: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 13253: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
13254: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
13255: fprintf(ficrest,"\n");
13256: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 13257: printf("Computing age specific forward period (stable) prevalences in each health state \n");
13258: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 13259: for(age=bage; age <=fage ;age++){
1.235 brouard 13260: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 13261: if (vpopbased==1) {
13262: if(mobilav ==0){
13263: for(i=1; i<=nlstate;i++)
13264: prlim[i][i]=probs[(int)age][i][k];
13265: }else{ /* mobilav */
13266: for(i=1; i<=nlstate;i++)
13267: prlim[i][i]=mobaverage[(int)age][i][k];
13268: }
13269: }
1.219 brouard 13270:
1.227 brouard 13271: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
13272: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
13273: /* printf(" age %4.0f ",age); */
13274: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
13275: for(i=1, epj[j]=0.;i <=nlstate;i++) {
13276: epj[j] += prlim[i][i]*eij[i][j][(int)age];
13277: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
13278: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
13279: }
13280: epj[nlstate+1] +=epj[j];
13281: }
13282: /* printf(" age %4.0f \n",age); */
1.219 brouard 13283:
1.227 brouard 13284: for(i=1, vepp=0.;i <=nlstate;i++)
13285: for(j=1;j <=nlstate;j++)
13286: vepp += vareij[i][j][(int)age];
13287: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
13288: for(j=1;j <=nlstate;j++){
13289: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
13290: }
13291: fprintf(ficrest,"\n");
13292: }
1.208 brouard 13293: } /* End vpopbased */
1.269 brouard 13294: free_vector(epj,1,nlstate+1);
1.208 brouard 13295: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
13296: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 13297: printf("done selection\n");fflush(stdout);
13298: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 13299:
1.235 brouard 13300: } /* End k selection */
1.227 brouard 13301:
13302: printf("done State-specific expectancies\n");fflush(stdout);
13303: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
13304:
1.288 brouard 13305: /* variance-covariance of forward period prevalence*/
1.269 brouard 13306: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 13307:
1.227 brouard 13308:
1.290 brouard 13309: free_vector(weight,firstobs,lastobs);
1.227 brouard 13310: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 13311: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
13312: free_matrix(anint,1,maxwav,firstobs,lastobs);
13313: free_matrix(mint,1,maxwav,firstobs,lastobs);
13314: free_ivector(cod,firstobs,lastobs);
1.227 brouard 13315: free_ivector(tab,1,NCOVMAX);
13316: fclose(ficresstdeij);
13317: fclose(ficrescveij);
13318: fclose(ficresvij);
13319: fclose(ficrest);
13320: fclose(ficpar);
13321:
13322:
1.126 brouard 13323: /*---------- End : free ----------------*/
1.219 brouard 13324: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 13325: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
13326: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 13327: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
13328: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 13329: } /* mle==-3 arrives here for freeing */
1.227 brouard 13330: /* endfree:*/
13331: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
13332: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
13333: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 13334: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
13335: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
13336: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
13337: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 13338: free_matrix(matcov,1,npar,1,npar);
13339: free_matrix(hess,1,npar,1,npar);
13340: /*free_vector(delti,1,npar);*/
13341: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
13342: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 13343: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 13344: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
13345:
13346: free_ivector(ncodemax,1,NCOVMAX);
13347: free_ivector(ncodemaxwundef,1,NCOVMAX);
13348: free_ivector(Dummy,-1,NCOVMAX);
13349: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 13350: free_ivector(DummyV,1,NCOVMAX);
13351: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 13352: free_ivector(Typevar,-1,NCOVMAX);
13353: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 13354: free_ivector(TvarsQ,1,NCOVMAX);
13355: free_ivector(TvarsQind,1,NCOVMAX);
13356: free_ivector(TvarsD,1,NCOVMAX);
13357: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 13358: free_ivector(TvarFD,1,NCOVMAX);
13359: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 13360: free_ivector(TvarF,1,NCOVMAX);
13361: free_ivector(TvarFind,1,NCOVMAX);
13362: free_ivector(TvarV,1,NCOVMAX);
13363: free_ivector(TvarVind,1,NCOVMAX);
13364: free_ivector(TvarA,1,NCOVMAX);
13365: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 13366: free_ivector(TvarFQ,1,NCOVMAX);
13367: free_ivector(TvarFQind,1,NCOVMAX);
13368: free_ivector(TvarVD,1,NCOVMAX);
13369: free_ivector(TvarVDind,1,NCOVMAX);
13370: free_ivector(TvarVQ,1,NCOVMAX);
13371: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 13372: free_ivector(Tvarsel,1,NCOVMAX);
13373: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 13374: free_ivector(Tposprod,1,NCOVMAX);
13375: free_ivector(Tprod,1,NCOVMAX);
13376: free_ivector(Tvaraff,1,NCOVMAX);
13377: free_ivector(invalidvarcomb,1,ncovcombmax);
13378: free_ivector(Tage,1,NCOVMAX);
13379: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 13380: free_ivector(TmodelInvind,1,NCOVMAX);
13381: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 13382:
13383: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
13384: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 13385: fflush(fichtm);
13386: fflush(ficgp);
13387:
1.227 brouard 13388:
1.126 brouard 13389: if((nberr >0) || (nbwarn>0)){
1.216 brouard 13390: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
13391: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
1.126 brouard 13392: }else{
13393: printf("End of Imach\n");
13394: fprintf(ficlog,"End of Imach\n");
13395: }
13396: printf("See log file on %s\n",filelog);
13397: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 13398: /*(void) gettimeofday(&end_time,&tzp);*/
13399: rend_time = time(NULL);
13400: end_time = *localtime(&rend_time);
13401: /* tml = *localtime(&end_time.tm_sec); */
13402: strcpy(strtend,asctime(&end_time));
1.126 brouard 13403: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13404: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13405: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13406:
1.157 brouard 13407: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13408: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13409: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13410: /* printf("Total time was %d uSec.\n", total_usecs);*/
13411: /* if(fileappend(fichtm,optionfilehtm)){ */
13412: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13413: fclose(fichtm);
13414: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13415: fclose(fichtmcov);
13416: fclose(ficgp);
13417: fclose(ficlog);
13418: /*------ End -----------*/
1.227 brouard 13419:
1.281 brouard 13420:
13421: /* Executes gnuplot */
1.227 brouard 13422:
13423: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13424: #ifdef WIN32
1.227 brouard 13425: if (_chdir(pathcd) != 0)
13426: printf("Can't move to directory %s!\n",path);
13427: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13428: #else
1.227 brouard 13429: if(chdir(pathcd) != 0)
13430: printf("Can't move to directory %s!\n", path);
13431: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13432: #endif
1.126 brouard 13433: printf("Current directory %s!\n",pathcd);
13434: /*strcat(plotcmd,CHARSEPARATOR);*/
13435: sprintf(plotcmd,"gnuplot");
1.157 brouard 13436: #ifdef _WIN32
1.126 brouard 13437: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13438: #endif
13439: if(!stat(plotcmd,&info)){
1.158 brouard 13440: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13441: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13442: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13443: }else
13444: strcpy(pplotcmd,plotcmd);
1.157 brouard 13445: #ifdef __unix
1.126 brouard 13446: strcpy(plotcmd,GNUPLOTPROGRAM);
13447: if(!stat(plotcmd,&info)){
1.158 brouard 13448: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13449: }else
13450: strcpy(pplotcmd,plotcmd);
13451: #endif
13452: }else
13453: strcpy(pplotcmd,plotcmd);
13454:
13455: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13456: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13457: strcpy(pplotcmd,plotcmd);
1.227 brouard 13458:
1.126 brouard 13459: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13460: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13461: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13462: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13463: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13464: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13465: strcpy(plotcmd,pplotcmd);
13466: }
1.126 brouard 13467: }
1.158 brouard 13468: printf(" Successful, please wait...");
1.126 brouard 13469: while (z[0] != 'q') {
13470: /* chdir(path); */
1.154 brouard 13471: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13472: scanf("%s",z);
13473: /* if (z[0] == 'c') system("./imach"); */
13474: if (z[0] == 'e') {
1.158 brouard 13475: #ifdef __APPLE__
1.152 brouard 13476: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13477: #elif __linux
13478: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13479: #else
1.152 brouard 13480: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13481: #endif
13482: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13483: system(pplotcmd);
1.126 brouard 13484: }
13485: else if (z[0] == 'g') system(plotcmd);
13486: else if (z[0] == 'q') exit(0);
13487: }
1.227 brouard 13488: end:
1.126 brouard 13489: while (z[0] != 'q') {
1.195 brouard 13490: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13491: scanf("%s",z);
13492: }
1.283 brouard 13493: printf("End\n");
1.282 brouard 13494: exit(0);
1.126 brouard 13495: }
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