Annotation of imach/src/imach.c, revision 1.316
1.316 ! brouard 1: /* $Id: imach.c,v 1.315 2022/05/11 15:06:32 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.316 ! brouard 4: Revision 1.315 2022/05/11 15:06:32 brouard
! 5: *** empty log message ***
! 6:
1.315 brouard 7: Revision 1.314 2022/04/13 17:43:09 brouard
8: * imach.c (Module): Adding link to text data files
9:
1.314 brouard 10: Revision 1.313 2022/04/11 15:57:42 brouard
11: * imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed
12:
1.313 brouard 13: Revision 1.312 2022/04/05 21:24:39 brouard
14: *** empty log message ***
15:
1.312 brouard 16: Revision 1.311 2022/04/05 21:03:51 brouard
17: Summary: Fixed quantitative covariates
18:
19: Fixed covariates (dummy or quantitative)
20: with missing values have never been allowed but are ERRORS and
21: program quits. Standard deviations of fixed covariates were
22: wrongly computed. Mean and standard deviations of time varying
23: covariates are still not computed.
24:
1.311 brouard 25: Revision 1.310 2022/03/17 08:45:53 brouard
26: Summary: 99r25
27:
28: Improving detection of errors: result lines should be compatible with
29: the model.
30:
1.310 brouard 31: Revision 1.309 2021/05/20 12:39:14 brouard
32: Summary: Version 0.99r24
33:
1.309 brouard 34: Revision 1.308 2021/03/31 13:11:57 brouard
35: Summary: Version 0.99r23
36:
37:
38: * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
39:
1.308 brouard 40: Revision 1.307 2021/03/08 18:11:32 brouard
41: Summary: 0.99r22 fixed bug on result:
42:
1.307 brouard 43: Revision 1.306 2021/02/20 15:44:02 brouard
44: Summary: Version 0.99r21
45:
46: * imach.c (Module): Fix bug on quitting after result lines!
47: (Module): Version 0.99r21
48:
1.306 brouard 49: Revision 1.305 2021/02/20 15:28:30 brouard
50: * imach.c (Module): Fix bug on quitting after result lines!
51:
1.305 brouard 52: Revision 1.304 2021/02/12 11:34:20 brouard
53: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
54:
1.304 brouard 55: Revision 1.303 2021/02/11 19:50:15 brouard
56: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
57:
1.303 brouard 58: Revision 1.302 2020/02/22 21:00:05 brouard
59: * (Module): imach.c Update mle=-3 (for computing Life expectancy
60: and life table from the data without any state)
61:
1.302 brouard 62: Revision 1.301 2019/06/04 13:51:20 brouard
63: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
64:
1.301 brouard 65: Revision 1.300 2019/05/22 19:09:45 brouard
66: Summary: version 0.99r19 of May 2019
67:
1.300 brouard 68: Revision 1.299 2019/05/22 18:37:08 brouard
69: Summary: Cleaned 0.99r19
70:
1.299 brouard 71: Revision 1.298 2019/05/22 18:19:56 brouard
72: *** empty log message ***
73:
1.298 brouard 74: Revision 1.297 2019/05/22 17:56:10 brouard
75: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
76:
1.297 brouard 77: Revision 1.296 2019/05/20 13:03:18 brouard
78: Summary: Projection syntax simplified
79:
80:
81: We can now start projections, forward or backward, from the mean date
82: of inteviews up to or down to a number of years of projection:
83: prevforecast=1 yearsfproj=15.3 mobil_average=0
84: or
85: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
86: or
87: prevbackcast=1 yearsbproj=12.3 mobil_average=1
88: or
89: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
90:
1.296 brouard 91: Revision 1.295 2019/05/18 09:52:50 brouard
92: Summary: doxygen tex bug
93:
1.295 brouard 94: Revision 1.294 2019/05/16 14:54:33 brouard
95: Summary: There was some wrong lines added
96:
1.294 brouard 97: Revision 1.293 2019/05/09 15:17:34 brouard
98: *** empty log message ***
99:
1.293 brouard 100: Revision 1.292 2019/05/09 14:17:20 brouard
101: Summary: Some updates
102:
1.292 brouard 103: Revision 1.291 2019/05/09 13:44:18 brouard
104: Summary: Before ncovmax
105:
1.291 brouard 106: Revision 1.290 2019/05/09 13:39:37 brouard
107: Summary: 0.99r18 unlimited number of individuals
108:
109: 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.
110:
1.290 brouard 111: Revision 1.289 2018/12/13 09:16:26 brouard
112: Summary: Bug for young ages (<-30) will be in r17
113:
1.289 brouard 114: Revision 1.288 2018/05/02 20:58:27 brouard
115: Summary: Some bugs fixed
116:
1.288 brouard 117: Revision 1.287 2018/05/01 17:57:25 brouard
118: Summary: Bug fixed by providing frequencies only for non missing covariates
119:
1.287 brouard 120: Revision 1.286 2018/04/27 14:27:04 brouard
121: Summary: some minor bugs
122:
1.286 brouard 123: Revision 1.285 2018/04/21 21:02:16 brouard
124: Summary: Some bugs fixed, valgrind tested
125:
1.285 brouard 126: Revision 1.284 2018/04/20 05:22:13 brouard
127: Summary: Computing mean and stdeviation of fixed quantitative variables
128:
1.284 brouard 129: Revision 1.283 2018/04/19 14:49:16 brouard
130: Summary: Some minor bugs fixed
131:
1.283 brouard 132: Revision 1.282 2018/02/27 22:50:02 brouard
133: *** empty log message ***
134:
1.282 brouard 135: Revision 1.281 2018/02/27 19:25:23 brouard
136: Summary: Adding second argument for quitting
137:
1.281 brouard 138: Revision 1.280 2018/02/21 07:58:13 brouard
139: Summary: 0.99r15
140:
141: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
142:
1.280 brouard 143: Revision 1.279 2017/07/20 13:35:01 brouard
144: Summary: temporary working
145:
1.279 brouard 146: Revision 1.278 2017/07/19 14:09:02 brouard
147: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
148:
1.278 brouard 149: Revision 1.277 2017/07/17 08:53:49 brouard
150: Summary: BOM files can be read now
151:
1.277 brouard 152: Revision 1.276 2017/06/30 15:48:31 brouard
153: Summary: Graphs improvements
154:
1.276 brouard 155: Revision 1.275 2017/06/30 13:39:33 brouard
156: Summary: Saito's color
157:
1.275 brouard 158: Revision 1.274 2017/06/29 09:47:08 brouard
159: Summary: Version 0.99r14
160:
1.274 brouard 161: Revision 1.273 2017/06/27 11:06:02 brouard
162: Summary: More documentation on projections
163:
1.273 brouard 164: Revision 1.272 2017/06/27 10:22:40 brouard
165: Summary: Color of backprojection changed from 6 to 5(yellow)
166:
1.272 brouard 167: Revision 1.271 2017/06/27 10:17:50 brouard
168: Summary: Some bug with rint
169:
1.271 brouard 170: Revision 1.270 2017/05/24 05:45:29 brouard
171: *** empty log message ***
172:
1.270 brouard 173: Revision 1.269 2017/05/23 08:39:25 brouard
174: Summary: Code into subroutine, cleanings
175:
1.269 brouard 176: Revision 1.268 2017/05/18 20:09:32 brouard
177: Summary: backprojection and confidence intervals of backprevalence
178:
1.268 brouard 179: Revision 1.267 2017/05/13 10:25:05 brouard
180: Summary: temporary save for backprojection
181:
1.267 brouard 182: Revision 1.266 2017/05/13 07:26:12 brouard
183: Summary: Version 0.99r13 (improvements and bugs fixed)
184:
1.266 brouard 185: Revision 1.265 2017/04/26 16:22:11 brouard
186: Summary: imach 0.99r13 Some bugs fixed
187:
1.265 brouard 188: Revision 1.264 2017/04/26 06:01:29 brouard
189: Summary: Labels in graphs
190:
1.264 brouard 191: Revision 1.263 2017/04/24 15:23:15 brouard
192: Summary: to save
193:
1.263 brouard 194: Revision 1.262 2017/04/18 16:48:12 brouard
195: *** empty log message ***
196:
1.262 brouard 197: Revision 1.261 2017/04/05 10:14:09 brouard
198: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
199:
1.261 brouard 200: Revision 1.260 2017/04/04 17:46:59 brouard
201: Summary: Gnuplot indexations fixed (humm)
202:
1.260 brouard 203: Revision 1.259 2017/04/04 13:01:16 brouard
204: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
205:
1.259 brouard 206: Revision 1.258 2017/04/03 10:17:47 brouard
207: Summary: Version 0.99r12
208:
209: Some cleanings, conformed with updated documentation.
210:
1.258 brouard 211: Revision 1.257 2017/03/29 16:53:30 brouard
212: Summary: Temp
213:
1.257 brouard 214: Revision 1.256 2017/03/27 05:50:23 brouard
215: Summary: Temporary
216:
1.256 brouard 217: Revision 1.255 2017/03/08 16:02:28 brouard
218: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
219:
1.255 brouard 220: Revision 1.254 2017/03/08 07:13:00 brouard
221: Summary: Fixing data parameter line
222:
1.254 brouard 223: Revision 1.253 2016/12/15 11:59:41 brouard
224: Summary: 0.99 in progress
225:
1.253 brouard 226: Revision 1.252 2016/09/15 21:15:37 brouard
227: *** empty log message ***
228:
1.252 brouard 229: Revision 1.251 2016/09/15 15:01:13 brouard
230: Summary: not working
231:
1.251 brouard 232: Revision 1.250 2016/09/08 16:07:27 brouard
233: Summary: continue
234:
1.250 brouard 235: Revision 1.249 2016/09/07 17:14:18 brouard
236: Summary: Starting values from frequencies
237:
1.249 brouard 238: Revision 1.248 2016/09/07 14:10:18 brouard
239: *** empty log message ***
240:
1.248 brouard 241: Revision 1.247 2016/09/02 11:11:21 brouard
242: *** empty log message ***
243:
1.247 brouard 244: Revision 1.246 2016/09/02 08:49:22 brouard
245: *** empty log message ***
246:
1.246 brouard 247: Revision 1.245 2016/09/02 07:25:01 brouard
248: *** empty log message ***
249:
1.245 brouard 250: Revision 1.244 2016/09/02 07:17:34 brouard
251: *** empty log message ***
252:
1.244 brouard 253: Revision 1.243 2016/09/02 06:45:35 brouard
254: *** empty log message ***
255:
1.243 brouard 256: Revision 1.242 2016/08/30 15:01:20 brouard
257: Summary: Fixing a lots
258:
1.242 brouard 259: Revision 1.241 2016/08/29 17:17:25 brouard
260: Summary: gnuplot problem in Back projection to fix
261:
1.241 brouard 262: Revision 1.240 2016/08/29 07:53:18 brouard
263: Summary: Better
264:
1.240 brouard 265: Revision 1.239 2016/08/26 15:51:03 brouard
266: Summary: Improvement in Powell output in order to copy and paste
267:
268: Author:
269:
1.239 brouard 270: Revision 1.238 2016/08/26 14:23:35 brouard
271: Summary: Starting tests of 0.99
272:
1.238 brouard 273: Revision 1.237 2016/08/26 09:20:19 brouard
274: Summary: to valgrind
275:
1.237 brouard 276: Revision 1.236 2016/08/25 10:50:18 brouard
277: *** empty log message ***
278:
1.236 brouard 279: Revision 1.235 2016/08/25 06:59:23 brouard
280: *** empty log message ***
281:
1.235 brouard 282: Revision 1.234 2016/08/23 16:51:20 brouard
283: *** empty log message ***
284:
1.234 brouard 285: Revision 1.233 2016/08/23 07:40:50 brouard
286: Summary: not working
287:
1.233 brouard 288: Revision 1.232 2016/08/22 14:20:21 brouard
289: Summary: not working
290:
1.232 brouard 291: Revision 1.231 2016/08/22 07:17:15 brouard
292: Summary: not working
293:
1.231 brouard 294: Revision 1.230 2016/08/22 06:55:53 brouard
295: Summary: Not working
296:
1.230 brouard 297: Revision 1.229 2016/07/23 09:45:53 brouard
298: Summary: Completing for func too
299:
1.229 brouard 300: Revision 1.228 2016/07/22 17:45:30 brouard
301: Summary: Fixing some arrays, still debugging
302:
1.227 brouard 303: Revision 1.226 2016/07/12 18:42:34 brouard
304: Summary: temp
305:
1.226 brouard 306: Revision 1.225 2016/07/12 08:40:03 brouard
307: Summary: saving but not running
308:
1.225 brouard 309: Revision 1.224 2016/07/01 13:16:01 brouard
310: Summary: Fixes
311:
1.224 brouard 312: Revision 1.223 2016/02/19 09:23:35 brouard
313: Summary: temporary
314:
1.223 brouard 315: Revision 1.222 2016/02/17 08:14:50 brouard
316: Summary: Probably last 0.98 stable version 0.98r6
317:
1.222 brouard 318: Revision 1.221 2016/02/15 23:35:36 brouard
319: Summary: minor bug
320:
1.220 brouard 321: Revision 1.219 2016/02/15 00:48:12 brouard
322: *** empty log message ***
323:
1.219 brouard 324: Revision 1.218 2016/02/12 11:29:23 brouard
325: Summary: 0.99 Back projections
326:
1.218 brouard 327: Revision 1.217 2015/12/23 17:18:31 brouard
328: Summary: Experimental backcast
329:
1.217 brouard 330: Revision 1.216 2015/12/18 17:32:11 brouard
331: Summary: 0.98r4 Warning and status=-2
332:
333: Version 0.98r4 is now:
334: - displaying an error when status is -1, date of interview unknown and date of death known;
335: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
336: Older changes concerning s=-2, dating from 2005 have been supersed.
337:
1.216 brouard 338: Revision 1.215 2015/12/16 08:52:24 brouard
339: Summary: 0.98r4 working
340:
1.215 brouard 341: Revision 1.214 2015/12/16 06:57:54 brouard
342: Summary: temporary not working
343:
1.214 brouard 344: Revision 1.213 2015/12/11 18:22:17 brouard
345: Summary: 0.98r4
346:
1.213 brouard 347: Revision 1.212 2015/11/21 12:47:24 brouard
348: Summary: minor typo
349:
1.212 brouard 350: Revision 1.211 2015/11/21 12:41:11 brouard
351: Summary: 0.98r3 with some graph of projected cross-sectional
352:
353: Author: Nicolas Brouard
354:
1.211 brouard 355: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 356: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 357: Summary: Adding ftolpl parameter
358: Author: N Brouard
359:
360: We had difficulties to get smoothed confidence intervals. It was due
361: to the period prevalence which wasn't computed accurately. The inner
362: parameter ftolpl is now an outer parameter of the .imach parameter
363: file after estepm. If ftolpl is small 1.e-4 and estepm too,
364: computation are long.
365:
1.209 brouard 366: Revision 1.208 2015/11/17 14:31:57 brouard
367: Summary: temporary
368:
1.208 brouard 369: Revision 1.207 2015/10/27 17:36:57 brouard
370: *** empty log message ***
371:
1.207 brouard 372: Revision 1.206 2015/10/24 07:14:11 brouard
373: *** empty log message ***
374:
1.206 brouard 375: Revision 1.205 2015/10/23 15:50:53 brouard
376: Summary: 0.98r3 some clarification for graphs on likelihood contributions
377:
1.205 brouard 378: Revision 1.204 2015/10/01 16:20:26 brouard
379: Summary: Some new graphs of contribution to likelihood
380:
1.204 brouard 381: Revision 1.203 2015/09/30 17:45:14 brouard
382: Summary: looking at better estimation of the hessian
383:
384: Also a better criteria for convergence to the period prevalence And
385: therefore adding the number of years needed to converge. (The
386: prevalence in any alive state shold sum to one
387:
1.203 brouard 388: Revision 1.202 2015/09/22 19:45:16 brouard
389: Summary: Adding some overall graph on contribution to likelihood. Might change
390:
1.202 brouard 391: Revision 1.201 2015/09/15 17:34:58 brouard
392: Summary: 0.98r0
393:
394: - Some new graphs like suvival functions
395: - Some bugs fixed like model=1+age+V2.
396:
1.201 brouard 397: Revision 1.200 2015/09/09 16:53:55 brouard
398: Summary: Big bug thanks to Flavia
399:
400: Even model=1+age+V2. did not work anymore
401:
1.200 brouard 402: Revision 1.199 2015/09/07 14:09:23 brouard
403: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
404:
1.199 brouard 405: Revision 1.198 2015/09/03 07:14:39 brouard
406: Summary: 0.98q5 Flavia
407:
1.198 brouard 408: Revision 1.197 2015/09/01 18:24:39 brouard
409: *** empty log message ***
410:
1.197 brouard 411: Revision 1.196 2015/08/18 23:17:52 brouard
412: Summary: 0.98q5
413:
1.196 brouard 414: Revision 1.195 2015/08/18 16:28:39 brouard
415: Summary: Adding a hack for testing purpose
416:
417: After reading the title, ftol and model lines, if the comment line has
418: a q, starting with #q, the answer at the end of the run is quit. It
419: permits to run test files in batch with ctest. The former workaround was
420: $ echo q | imach foo.imach
421:
1.195 brouard 422: Revision 1.194 2015/08/18 13:32:00 brouard
423: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
424:
1.194 brouard 425: Revision 1.193 2015/08/04 07:17:42 brouard
426: Summary: 0.98q4
427:
1.193 brouard 428: Revision 1.192 2015/07/16 16:49:02 brouard
429: Summary: Fixing some outputs
430:
1.192 brouard 431: Revision 1.191 2015/07/14 10:00:33 brouard
432: Summary: Some fixes
433:
1.191 brouard 434: Revision 1.190 2015/05/05 08:51:13 brouard
435: Summary: Adding digits in output parameters (7 digits instead of 6)
436:
437: Fix 1+age+.
438:
1.190 brouard 439: Revision 1.189 2015/04/30 14:45:16 brouard
440: Summary: 0.98q2
441:
1.189 brouard 442: Revision 1.188 2015/04/30 08:27:53 brouard
443: *** empty log message ***
444:
1.188 brouard 445: Revision 1.187 2015/04/29 09:11:15 brouard
446: *** empty log message ***
447:
1.187 brouard 448: Revision 1.186 2015/04/23 12:01:52 brouard
449: Summary: V1*age is working now, version 0.98q1
450:
451: Some codes had been disabled in order to simplify and Vn*age was
452: working in the optimization phase, ie, giving correct MLE parameters,
453: but, as usual, outputs were not correct and program core dumped.
454:
1.186 brouard 455: Revision 1.185 2015/03/11 13:26:42 brouard
456: Summary: Inclusion of compile and links command line for Intel Compiler
457:
1.185 brouard 458: Revision 1.184 2015/03/11 11:52:39 brouard
459: Summary: Back from Windows 8. Intel Compiler
460:
1.184 brouard 461: Revision 1.183 2015/03/10 20:34:32 brouard
462: Summary: 0.98q0, trying with directest, mnbrak fixed
463:
464: We use directest instead of original Powell test; probably no
465: incidence on the results, but better justifications;
466: We fixed Numerical Recipes mnbrak routine which was wrong and gave
467: wrong results.
468:
1.183 brouard 469: Revision 1.182 2015/02/12 08:19:57 brouard
470: Summary: Trying to keep directest which seems simpler and more general
471: Author: Nicolas Brouard
472:
1.182 brouard 473: Revision 1.181 2015/02/11 23:22:24 brouard
474: Summary: Comments on Powell added
475:
476: Author:
477:
1.181 brouard 478: Revision 1.180 2015/02/11 17:33:45 brouard
479: Summary: Finishing move from main to function (hpijx and prevalence_limit)
480:
1.180 brouard 481: Revision 1.179 2015/01/04 09:57:06 brouard
482: Summary: back to OS/X
483:
1.179 brouard 484: Revision 1.178 2015/01/04 09:35:48 brouard
485: *** empty log message ***
486:
1.178 brouard 487: Revision 1.177 2015/01/03 18:40:56 brouard
488: Summary: Still testing ilc32 on OSX
489:
1.177 brouard 490: Revision 1.176 2015/01/03 16:45:04 brouard
491: *** empty log message ***
492:
1.176 brouard 493: Revision 1.175 2015/01/03 16:33:42 brouard
494: *** empty log message ***
495:
1.175 brouard 496: Revision 1.174 2015/01/03 16:15:49 brouard
497: Summary: Still in cross-compilation
498:
1.174 brouard 499: Revision 1.173 2015/01/03 12:06:26 brouard
500: Summary: trying to detect cross-compilation
501:
1.173 brouard 502: Revision 1.172 2014/12/27 12:07:47 brouard
503: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
504:
1.172 brouard 505: Revision 1.171 2014/12/23 13:26:59 brouard
506: Summary: Back from Visual C
507:
508: Still problem with utsname.h on Windows
509:
1.171 brouard 510: Revision 1.170 2014/12/23 11:17:12 brouard
511: Summary: Cleaning some \%% back to %%
512:
513: The escape was mandatory for a specific compiler (which one?), but too many warnings.
514:
1.170 brouard 515: Revision 1.169 2014/12/22 23:08:31 brouard
516: Summary: 0.98p
517:
518: Outputs some informations on compiler used, OS etc. Testing on different platforms.
519:
1.169 brouard 520: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 521: Summary: update
1.169 brouard 522:
1.168 brouard 523: Revision 1.167 2014/12/22 13:50:56 brouard
524: Summary: Testing uname and compiler version and if compiled 32 or 64
525:
526: Testing on Linux 64
527:
1.167 brouard 528: Revision 1.166 2014/12/22 11:40:47 brouard
529: *** empty log message ***
530:
1.166 brouard 531: Revision 1.165 2014/12/16 11:20:36 brouard
532: Summary: After compiling on Visual C
533:
534: * imach.c (Module): Merging 1.61 to 1.162
535:
1.165 brouard 536: Revision 1.164 2014/12/16 10:52:11 brouard
537: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
538:
539: * imach.c (Module): Merging 1.61 to 1.162
540:
1.164 brouard 541: Revision 1.163 2014/12/16 10:30:11 brouard
542: * imach.c (Module): Merging 1.61 to 1.162
543:
1.163 brouard 544: Revision 1.162 2014/09/25 11:43:39 brouard
545: Summary: temporary backup 0.99!
546:
1.162 brouard 547: Revision 1.1 2014/09/16 11:06:58 brouard
548: Summary: With some code (wrong) for nlopt
549:
550: Author:
551:
552: Revision 1.161 2014/09/15 20:41:41 brouard
553: Summary: Problem with macro SQR on Intel compiler
554:
1.161 brouard 555: Revision 1.160 2014/09/02 09:24:05 brouard
556: *** empty log message ***
557:
1.160 brouard 558: Revision 1.159 2014/09/01 10:34:10 brouard
559: Summary: WIN32
560: Author: Brouard
561:
1.159 brouard 562: Revision 1.158 2014/08/27 17:11:51 brouard
563: *** empty log message ***
564:
1.158 brouard 565: Revision 1.157 2014/08/27 16:26:55 brouard
566: Summary: Preparing windows Visual studio version
567: Author: Brouard
568:
569: In order to compile on Visual studio, time.h is now correct and time_t
570: and tm struct should be used. difftime should be used but sometimes I
571: just make the differences in raw time format (time(&now).
572: Trying to suppress #ifdef LINUX
573: Add xdg-open for __linux in order to open default browser.
574:
1.157 brouard 575: Revision 1.156 2014/08/25 20:10:10 brouard
576: *** empty log message ***
577:
1.156 brouard 578: Revision 1.155 2014/08/25 18:32:34 brouard
579: Summary: New compile, minor changes
580: Author: Brouard
581:
1.155 brouard 582: Revision 1.154 2014/06/20 17:32:08 brouard
583: Summary: Outputs now all graphs of convergence to period prevalence
584:
1.154 brouard 585: Revision 1.153 2014/06/20 16:45:46 brouard
586: Summary: If 3 live state, convergence to period prevalence on same graph
587: Author: Brouard
588:
1.153 brouard 589: Revision 1.152 2014/06/18 17:54:09 brouard
590: Summary: open browser, use gnuplot on same dir than imach if not found in the path
591:
1.152 brouard 592: Revision 1.151 2014/06/18 16:43:30 brouard
593: *** empty log message ***
594:
1.151 brouard 595: Revision 1.150 2014/06/18 16:42:35 brouard
596: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
597: Author: brouard
598:
1.150 brouard 599: Revision 1.149 2014/06/18 15:51:14 brouard
600: Summary: Some fixes in parameter files errors
601: Author: Nicolas Brouard
602:
1.149 brouard 603: Revision 1.148 2014/06/17 17:38:48 brouard
604: Summary: Nothing new
605: Author: Brouard
606:
607: Just a new packaging for OS/X version 0.98nS
608:
1.148 brouard 609: Revision 1.147 2014/06/16 10:33:11 brouard
610: *** empty log message ***
611:
1.147 brouard 612: Revision 1.146 2014/06/16 10:20:28 brouard
613: Summary: Merge
614: Author: Brouard
615:
616: Merge, before building revised version.
617:
1.146 brouard 618: Revision 1.145 2014/06/10 21:23:15 brouard
619: Summary: Debugging with valgrind
620: Author: Nicolas Brouard
621:
622: Lot of changes in order to output the results with some covariates
623: After the Edimburgh REVES conference 2014, it seems mandatory to
624: improve the code.
625: No more memory valgrind error but a lot has to be done in order to
626: continue the work of splitting the code into subroutines.
627: Also, decodemodel has been improved. Tricode is still not
628: optimal. nbcode should be improved. Documentation has been added in
629: the source code.
630:
1.144 brouard 631: Revision 1.143 2014/01/26 09:45:38 brouard
632: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
633:
634: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
635: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
636:
1.143 brouard 637: Revision 1.142 2014/01/26 03:57:36 brouard
638: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
639:
640: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
641:
1.142 brouard 642: Revision 1.141 2014/01/26 02:42:01 brouard
643: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
644:
1.141 brouard 645: Revision 1.140 2011/09/02 10:37:54 brouard
646: Summary: times.h is ok with mingw32 now.
647:
1.140 brouard 648: Revision 1.139 2010/06/14 07:50:17 brouard
649: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
650: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
651:
1.139 brouard 652: Revision 1.138 2010/04/30 18:19:40 brouard
653: *** empty log message ***
654:
1.138 brouard 655: Revision 1.137 2010/04/29 18:11:38 brouard
656: (Module): Checking covariates for more complex models
657: than V1+V2. A lot of change to be done. Unstable.
658:
1.137 brouard 659: Revision 1.136 2010/04/26 20:30:53 brouard
660: (Module): merging some libgsl code. Fixing computation
661: of likelione (using inter/intrapolation if mle = 0) in order to
662: get same likelihood as if mle=1.
663: Some cleaning of code and comments added.
664:
1.136 brouard 665: Revision 1.135 2009/10/29 15:33:14 brouard
666: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
667:
1.135 brouard 668: Revision 1.134 2009/10/29 13:18:53 brouard
669: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
670:
1.134 brouard 671: Revision 1.133 2009/07/06 10:21:25 brouard
672: just nforces
673:
1.133 brouard 674: Revision 1.132 2009/07/06 08:22:05 brouard
675: Many tings
676:
1.132 brouard 677: Revision 1.131 2009/06/20 16:22:47 brouard
678: Some dimensions resccaled
679:
1.131 brouard 680: Revision 1.130 2009/05/26 06:44:34 brouard
681: (Module): Max Covariate is now set to 20 instead of 8. A
682: lot of cleaning with variables initialized to 0. Trying to make
683: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
684:
1.130 brouard 685: Revision 1.129 2007/08/31 13:49:27 lievre
686: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
687:
1.129 lievre 688: Revision 1.128 2006/06/30 13:02:05 brouard
689: (Module): Clarifications on computing e.j
690:
1.128 brouard 691: Revision 1.127 2006/04/28 18:11:50 brouard
692: (Module): Yes the sum of survivors was wrong since
693: imach-114 because nhstepm was no more computed in the age
694: loop. Now we define nhstepma in the age loop.
695: (Module): In order to speed up (in case of numerous covariates) we
696: compute health expectancies (without variances) in a first step
697: and then all the health expectancies with variances or standard
698: deviation (needs data from the Hessian matrices) which slows the
699: computation.
700: In the future we should be able to stop the program is only health
701: expectancies and graph are needed without standard deviations.
702:
1.127 brouard 703: Revision 1.126 2006/04/28 17:23:28 brouard
704: (Module): Yes the sum of survivors was wrong since
705: imach-114 because nhstepm was no more computed in the age
706: loop. Now we define nhstepma in the age loop.
707: Version 0.98h
708:
1.126 brouard 709: Revision 1.125 2006/04/04 15:20:31 lievre
710: Errors in calculation of health expectancies. Age was not initialized.
711: Forecasting file added.
712:
713: Revision 1.124 2006/03/22 17:13:53 lievre
714: Parameters are printed with %lf instead of %f (more numbers after the comma).
715: The log-likelihood is printed in the log file
716:
717: Revision 1.123 2006/03/20 10:52:43 brouard
718: * imach.c (Module): <title> changed, corresponds to .htm file
719: name. <head> headers where missing.
720:
721: * imach.c (Module): Weights can have a decimal point as for
722: English (a comma might work with a correct LC_NUMERIC environment,
723: otherwise the weight is truncated).
724: Modification of warning when the covariates values are not 0 or
725: 1.
726: Version 0.98g
727:
728: Revision 1.122 2006/03/20 09:45:41 brouard
729: (Module): Weights can have a decimal point as for
730: English (a comma might work with a correct LC_NUMERIC environment,
731: otherwise the weight is truncated).
732: Modification of warning when the covariates values are not 0 or
733: 1.
734: Version 0.98g
735:
736: Revision 1.121 2006/03/16 17:45:01 lievre
737: * imach.c (Module): Comments concerning covariates added
738:
739: * imach.c (Module): refinements in the computation of lli if
740: status=-2 in order to have more reliable computation if stepm is
741: not 1 month. Version 0.98f
742:
743: Revision 1.120 2006/03/16 15:10:38 lievre
744: (Module): refinements in the computation of lli if
745: status=-2 in order to have more reliable computation if stepm is
746: not 1 month. Version 0.98f
747:
748: Revision 1.119 2006/03/15 17:42:26 brouard
749: (Module): Bug if status = -2, the loglikelihood was
750: computed as likelihood omitting the logarithm. Version O.98e
751:
752: Revision 1.118 2006/03/14 18:20:07 brouard
753: (Module): varevsij Comments added explaining the second
754: table of variances if popbased=1 .
755: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
756: (Module): Function pstamp added
757: (Module): Version 0.98d
758:
759: Revision 1.117 2006/03/14 17:16:22 brouard
760: (Module): varevsij Comments added explaining the second
761: table of variances if popbased=1 .
762: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
763: (Module): Function pstamp added
764: (Module): Version 0.98d
765:
766: Revision 1.116 2006/03/06 10:29:27 brouard
767: (Module): Variance-covariance wrong links and
768: varian-covariance of ej. is needed (Saito).
769:
770: Revision 1.115 2006/02/27 12:17:45 brouard
771: (Module): One freematrix added in mlikeli! 0.98c
772:
773: Revision 1.114 2006/02/26 12:57:58 brouard
774: (Module): Some improvements in processing parameter
775: filename with strsep.
776:
777: Revision 1.113 2006/02/24 14:20:24 brouard
778: (Module): Memory leaks checks with valgrind and:
779: datafile was not closed, some imatrix were not freed and on matrix
780: allocation too.
781:
782: Revision 1.112 2006/01/30 09:55:26 brouard
783: (Module): Back to gnuplot.exe instead of wgnuplot.exe
784:
785: Revision 1.111 2006/01/25 20:38:18 brouard
786: (Module): Lots of cleaning and bugs added (Gompertz)
787: (Module): Comments can be added in data file. Missing date values
788: can be a simple dot '.'.
789:
790: Revision 1.110 2006/01/25 00:51:50 brouard
791: (Module): Lots of cleaning and bugs added (Gompertz)
792:
793: Revision 1.109 2006/01/24 19:37:15 brouard
794: (Module): Comments (lines starting with a #) are allowed in data.
795:
796: Revision 1.108 2006/01/19 18:05:42 lievre
797: Gnuplot problem appeared...
798: To be fixed
799:
800: Revision 1.107 2006/01/19 16:20:37 brouard
801: Test existence of gnuplot in imach path
802:
803: Revision 1.106 2006/01/19 13:24:36 brouard
804: Some cleaning and links added in html output
805:
806: Revision 1.105 2006/01/05 20:23:19 lievre
807: *** empty log message ***
808:
809: Revision 1.104 2005/09/30 16:11:43 lievre
810: (Module): sump fixed, loop imx fixed, and simplifications.
811: (Module): If the status is missing at the last wave but we know
812: that the person is alive, then we can code his/her status as -2
813: (instead of missing=-1 in earlier versions) and his/her
814: contributions to the likelihood is 1 - Prob of dying from last
815: health status (= 1-p13= p11+p12 in the easiest case of somebody in
816: the healthy state at last known wave). Version is 0.98
817:
818: Revision 1.103 2005/09/30 15:54:49 lievre
819: (Module): sump fixed, loop imx fixed, and simplifications.
820:
821: Revision 1.102 2004/09/15 17:31:30 brouard
822: Add the possibility to read data file including tab characters.
823:
824: Revision 1.101 2004/09/15 10:38:38 brouard
825: Fix on curr_time
826:
827: Revision 1.100 2004/07/12 18:29:06 brouard
828: Add version for Mac OS X. Just define UNIX in Makefile
829:
830: Revision 1.99 2004/06/05 08:57:40 brouard
831: *** empty log message ***
832:
833: Revision 1.98 2004/05/16 15:05:56 brouard
834: New version 0.97 . First attempt to estimate force of mortality
835: directly from the data i.e. without the need of knowing the health
836: state at each age, but using a Gompertz model: log u =a + b*age .
837: This is the basic analysis of mortality and should be done before any
838: other analysis, in order to test if the mortality estimated from the
839: cross-longitudinal survey is different from the mortality estimated
840: from other sources like vital statistic data.
841:
842: The same imach parameter file can be used but the option for mle should be -3.
843:
1.133 brouard 844: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 845: former routines in order to include the new code within the former code.
846:
847: The output is very simple: only an estimate of the intercept and of
848: the slope with 95% confident intervals.
849:
850: Current limitations:
851: A) Even if you enter covariates, i.e. with the
852: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
853: B) There is no computation of Life Expectancy nor Life Table.
854:
855: Revision 1.97 2004/02/20 13:25:42 lievre
856: Version 0.96d. Population forecasting command line is (temporarily)
857: suppressed.
858:
859: Revision 1.96 2003/07/15 15:38:55 brouard
860: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
861: rewritten within the same printf. Workaround: many printfs.
862:
863: Revision 1.95 2003/07/08 07:54:34 brouard
864: * imach.c (Repository):
865: (Repository): Using imachwizard code to output a more meaningful covariance
866: matrix (cov(a12,c31) instead of numbers.
867:
868: Revision 1.94 2003/06/27 13:00:02 brouard
869: Just cleaning
870:
871: Revision 1.93 2003/06/25 16:33:55 brouard
872: (Module): On windows (cygwin) function asctime_r doesn't
873: exist so I changed back to asctime which exists.
874: (Module): Version 0.96b
875:
876: Revision 1.92 2003/06/25 16:30:45 brouard
877: (Module): On windows (cygwin) function asctime_r doesn't
878: exist so I changed back to asctime which exists.
879:
880: Revision 1.91 2003/06/25 15:30:29 brouard
881: * imach.c (Repository): Duplicated warning errors corrected.
882: (Repository): Elapsed time after each iteration is now output. It
883: helps to forecast when convergence will be reached. Elapsed time
884: is stamped in powell. We created a new html file for the graphs
885: concerning matrix of covariance. It has extension -cov.htm.
886:
887: Revision 1.90 2003/06/24 12:34:15 brouard
888: (Module): Some bugs corrected for windows. Also, when
889: mle=-1 a template is output in file "or"mypar.txt with the design
890: of the covariance matrix to be input.
891:
892: Revision 1.89 2003/06/24 12:30:52 brouard
893: (Module): Some bugs corrected for windows. Also, when
894: mle=-1 a template is output in file "or"mypar.txt with the design
895: of the covariance matrix to be input.
896:
897: Revision 1.88 2003/06/23 17:54:56 brouard
898: * 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.
899:
900: Revision 1.87 2003/06/18 12:26:01 brouard
901: Version 0.96
902:
903: Revision 1.86 2003/06/17 20:04:08 brouard
904: (Module): Change position of html and gnuplot routines and added
905: routine fileappend.
906:
907: Revision 1.85 2003/06/17 13:12:43 brouard
908: * imach.c (Repository): Check when date of death was earlier that
909: current date of interview. It may happen when the death was just
910: prior to the death. In this case, dh was negative and likelihood
911: was wrong (infinity). We still send an "Error" but patch by
912: assuming that the date of death was just one stepm after the
913: interview.
914: (Repository): Because some people have very long ID (first column)
915: we changed int to long in num[] and we added a new lvector for
916: memory allocation. But we also truncated to 8 characters (left
917: truncation)
918: (Repository): No more line truncation errors.
919:
920: Revision 1.84 2003/06/13 21:44:43 brouard
921: * imach.c (Repository): Replace "freqsummary" at a correct
922: place. It differs from routine "prevalence" which may be called
923: many times. Probs is memory consuming and must be used with
924: parcimony.
925: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
926:
927: Revision 1.83 2003/06/10 13:39:11 lievre
928: *** empty log message ***
929:
930: Revision 1.82 2003/06/05 15:57:20 brouard
931: Add log in imach.c and fullversion number is now printed.
932:
933: */
934: /*
935: Interpolated Markov Chain
936:
937: Short summary of the programme:
938:
1.227 brouard 939: This program computes Healthy Life Expectancies or State-specific
940: (if states aren't health statuses) Expectancies from
941: cross-longitudinal data. Cross-longitudinal data consist in:
942:
943: -1- a first survey ("cross") where individuals from different ages
944: are interviewed on their health status or degree of disability (in
945: the case of a health survey which is our main interest)
946:
947: -2- at least a second wave of interviews ("longitudinal") which
948: measure each change (if any) in individual health status. Health
949: expectancies are computed from the time spent in each health state
950: according to a model. More health states you consider, more time is
951: necessary to reach the Maximum Likelihood of the parameters involved
952: in the model. The simplest model is the multinomial logistic model
953: where pij is the probability to be observed in state j at the second
954: wave conditional to be observed in state i at the first
955: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
956: etc , where 'age' is age and 'sex' is a covariate. If you want to
957: have a more complex model than "constant and age", you should modify
958: the program where the markup *Covariates have to be included here
959: again* invites you to do it. More covariates you add, slower the
1.126 brouard 960: convergence.
961:
962: The advantage of this computer programme, compared to a simple
963: multinomial logistic model, is clear when the delay between waves is not
964: identical for each individual. Also, if a individual missed an
965: intermediate interview, the information is lost, but taken into
966: account using an interpolation or extrapolation.
967:
968: hPijx is the probability to be observed in state i at age x+h
969: conditional to the observed state i at age x. The delay 'h' can be
970: split into an exact number (nh*stepm) of unobserved intermediate
971: states. This elementary transition (by month, quarter,
972: semester or year) is modelled as a multinomial logistic. The hPx
973: matrix is simply the matrix product of nh*stepm elementary matrices
974: and the contribution of each individual to the likelihood is simply
975: hPijx.
976:
977: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 978: of the life expectancies. It also computes the period (stable) prevalence.
979:
980: Back prevalence and projections:
1.227 brouard 981:
982: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
983: double agemaxpar, double ftolpl, int *ncvyearp, double
984: dateprev1,double dateprev2, int firstpass, int lastpass, int
985: mobilavproj)
986:
987: Computes the back prevalence limit for any combination of
988: covariate values k at any age between ageminpar and agemaxpar and
989: returns it in **bprlim. In the loops,
990:
991: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
992: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
993:
994: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 995: Computes for any combination of covariates k and any age between bage and fage
996: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
997: oldm=oldms;savm=savms;
1.227 brouard 998:
1.267 brouard 999: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 1000: Computes the transition matrix starting at age 'age' over
1001: 'nhstepm*hstepm*stepm' months (i.e. until
1002: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 1003: nhstepm*hstepm matrices.
1004:
1005: Returns p3mat[i][j][h] after calling
1006: p3mat[i][j][h]=matprod2(newm,
1007: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
1008: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1009: oldm);
1.226 brouard 1010:
1011: Important routines
1012:
1013: - func (or funcone), computes logit (pij) distinguishing
1014: o fixed variables (single or product dummies or quantitative);
1015: o varying variables by:
1016: (1) wave (single, product dummies, quantitative),
1017: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
1018: % fixed dummy (treated) or quantitative (not done because time-consuming);
1019: % varying dummy (not done) or quantitative (not done);
1020: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
1021: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
1022: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
1023: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
1024: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 1025:
1.226 brouard 1026:
1027:
1.133 brouard 1028: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
1029: Institut national d'études démographiques, Paris.
1.126 brouard 1030: This software have been partly granted by Euro-REVES, a concerted action
1031: from the European Union.
1032: It is copyrighted identically to a GNU software product, ie programme and
1033: software can be distributed freely for non commercial use. Latest version
1034: can be accessed at http://euroreves.ined.fr/imach .
1035:
1036: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
1037: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
1038:
1039: **********************************************************************/
1040: /*
1041: main
1042: read parameterfile
1043: read datafile
1044: concatwav
1045: freqsummary
1046: if (mle >= 1)
1047: mlikeli
1048: print results files
1049: if mle==1
1050: computes hessian
1051: read end of parameter file: agemin, agemax, bage, fage, estepm
1052: begin-prev-date,...
1053: open gnuplot file
1054: open html file
1.145 brouard 1055: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1056: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1057: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1058: freexexit2 possible for memory heap.
1059:
1060: h Pij x | pij_nom ficrestpij
1061: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1062: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1063: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1064:
1065: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1066: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1067: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1068: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1069: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1070:
1.126 brouard 1071: forecasting if prevfcast==1 prevforecast call prevalence()
1072: health expectancies
1073: Variance-covariance of DFLE
1074: prevalence()
1075: movingaverage()
1076: varevsij()
1077: if popbased==1 varevsij(,popbased)
1078: total life expectancies
1079: Variance of period (stable) prevalence
1080: end
1081: */
1082:
1.187 brouard 1083: /* #define DEBUG */
1084: /* #define DEBUGBRENT */
1.203 brouard 1085: /* #define DEBUGLINMIN */
1086: /* #define DEBUGHESS */
1087: #define DEBUGHESSIJ
1.224 brouard 1088: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1089: #define POWELL /* Instead of NLOPT */
1.224 brouard 1090: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1091: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1092: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1093:
1094: #include <math.h>
1095: #include <stdio.h>
1096: #include <stdlib.h>
1097: #include <string.h>
1.226 brouard 1098: #include <ctype.h>
1.159 brouard 1099:
1100: #ifdef _WIN32
1101: #include <io.h>
1.172 brouard 1102: #include <windows.h>
1103: #include <tchar.h>
1.159 brouard 1104: #else
1.126 brouard 1105: #include <unistd.h>
1.159 brouard 1106: #endif
1.126 brouard 1107:
1108: #include <limits.h>
1109: #include <sys/types.h>
1.171 brouard 1110:
1111: #if defined(__GNUC__)
1112: #include <sys/utsname.h> /* Doesn't work on Windows */
1113: #endif
1114:
1.126 brouard 1115: #include <sys/stat.h>
1116: #include <errno.h>
1.159 brouard 1117: /* extern int errno; */
1.126 brouard 1118:
1.157 brouard 1119: /* #ifdef LINUX */
1120: /* #include <time.h> */
1121: /* #include "timeval.h" */
1122: /* #else */
1123: /* #include <sys/time.h> */
1124: /* #endif */
1125:
1.126 brouard 1126: #include <time.h>
1127:
1.136 brouard 1128: #ifdef GSL
1129: #include <gsl/gsl_errno.h>
1130: #include <gsl/gsl_multimin.h>
1131: #endif
1132:
1.167 brouard 1133:
1.162 brouard 1134: #ifdef NLOPT
1135: #include <nlopt.h>
1136: typedef struct {
1137: double (* function)(double [] );
1138: } myfunc_data ;
1139: #endif
1140:
1.126 brouard 1141: /* #include <libintl.h> */
1142: /* #define _(String) gettext (String) */
1143:
1.251 brouard 1144: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1145:
1146: #define GNUPLOTPROGRAM "gnuplot"
1147: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1148: #define FILENAMELENGTH 132
1149:
1150: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1151: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1152:
1.144 brouard 1153: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1154: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1155:
1156: #define NINTERVMAX 8
1.144 brouard 1157: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1158: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1159: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1160: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1161: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1162: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1163: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1164: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1165: /* #define AGESUP 130 */
1.288 brouard 1166: /* #define AGESUP 150 */
1167: #define AGESUP 200
1.268 brouard 1168: #define AGEINF 0
1.218 brouard 1169: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1170: #define AGEBASE 40
1.194 brouard 1171: #define AGEOVERFLOW 1.e20
1.164 brouard 1172: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1173: #ifdef _WIN32
1174: #define DIRSEPARATOR '\\'
1175: #define CHARSEPARATOR "\\"
1176: #define ODIRSEPARATOR '/'
1177: #else
1.126 brouard 1178: #define DIRSEPARATOR '/'
1179: #define CHARSEPARATOR "/"
1180: #define ODIRSEPARATOR '\\'
1181: #endif
1182:
1.316 ! brouard 1183: /* $Id: imach.c,v 1.315 2022/05/11 15:06:32 brouard Exp $ */
1.126 brouard 1184: /* $State: Exp $ */
1.196 brouard 1185: #include "version.h"
1186: char version[]=__IMACH_VERSION__;
1.316 ! brouard 1187: 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";
! 1188: char fullversion[]="$Revision: 1.315 $ $Date: 2022/05/11 15:06:32 $";
1.126 brouard 1189: char strstart[80];
1190: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1191: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1192: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1193: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1194: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1195: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1196: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1197: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1198: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1199: int cptcovprodnoage=0; /**< Number of covariate products without age */
1200: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1201: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1202: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1203: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1204: int nsd=0; /**< Total number of single dummy variables (output) */
1205: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1206: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1207: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1208: int ntveff=0; /**< ntveff number of effective time varying variables */
1209: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1210: int cptcov=0; /* Working variable */
1.290 brouard 1211: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1212: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1213: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1214: int nlstate=2; /* Number of live states */
1215: int ndeath=1; /* Number of dead states */
1.130 brouard 1216: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1217: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1218: int popbased=0;
1219:
1220: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1221: int maxwav=0; /* Maxim number of waves */
1222: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1223: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1224: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1225: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1226: int mle=1, weightopt=0;
1.126 brouard 1227: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1228: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1229: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1230: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1231: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1232: int selected(int kvar); /* Is covariate kvar selected for printing results */
1233:
1.130 brouard 1234: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1235: double **matprod2(); /* test */
1.126 brouard 1236: double **oldm, **newm, **savm; /* Working pointers to matrices */
1237: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1238: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1239:
1.136 brouard 1240: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1241: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1242: FILE *ficlog, *ficrespow;
1.130 brouard 1243: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1244: double fretone; /* Only one call to likelihood */
1.130 brouard 1245: long ipmx=0; /* Number of contributions */
1.126 brouard 1246: double sw; /* Sum of weights */
1247: char filerespow[FILENAMELENGTH];
1248: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1249: FILE *ficresilk;
1250: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1251: FILE *ficresprobmorprev;
1252: FILE *fichtm, *fichtmcov; /* Html File */
1253: FILE *ficreseij;
1254: char filerese[FILENAMELENGTH];
1255: FILE *ficresstdeij;
1256: char fileresstde[FILENAMELENGTH];
1257: FILE *ficrescveij;
1258: char filerescve[FILENAMELENGTH];
1259: FILE *ficresvij;
1260: char fileresv[FILENAMELENGTH];
1.269 brouard 1261:
1.126 brouard 1262: char title[MAXLINE];
1.234 brouard 1263: char model[MAXLINE]; /**< The model line */
1.217 brouard 1264: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1265: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1266: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1267: char command[FILENAMELENGTH];
1268: int outcmd=0;
1269:
1.217 brouard 1270: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1271: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1272: char filelog[FILENAMELENGTH]; /* Log file */
1273: char filerest[FILENAMELENGTH];
1274: char fileregp[FILENAMELENGTH];
1275: char popfile[FILENAMELENGTH];
1276:
1277: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1278:
1.157 brouard 1279: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1280: /* struct timezone tzp; */
1281: /* extern int gettimeofday(); */
1282: struct tm tml, *gmtime(), *localtime();
1283:
1284: extern time_t time();
1285:
1286: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1287: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1288: struct tm tm;
1289:
1.126 brouard 1290: char strcurr[80], strfor[80];
1291:
1292: char *endptr;
1293: long lval;
1294: double dval;
1295:
1296: #define NR_END 1
1297: #define FREE_ARG char*
1298: #define FTOL 1.0e-10
1299:
1300: #define NRANSI
1.240 brouard 1301: #define ITMAX 200
1302: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1303:
1304: #define TOL 2.0e-4
1305:
1306: #define CGOLD 0.3819660
1307: #define ZEPS 1.0e-10
1308: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1309:
1310: #define GOLD 1.618034
1311: #define GLIMIT 100.0
1312: #define TINY 1.0e-20
1313:
1314: static double maxarg1,maxarg2;
1315: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1316: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1317:
1318: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1319: #define rint(a) floor(a+0.5)
1.166 brouard 1320: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1321: #define mytinydouble 1.0e-16
1.166 brouard 1322: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1323: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1324: /* static double dsqrarg; */
1325: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1326: static double sqrarg;
1327: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1328: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1329: int agegomp= AGEGOMP;
1330:
1331: int imx;
1332: int stepm=1;
1333: /* Stepm, step in month: minimum step interpolation*/
1334:
1335: int estepm;
1336: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1337:
1338: int m,nb;
1339: long *num;
1.197 brouard 1340: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1341: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1342: covariate for which somebody answered excluding
1343: undefined. Usually 2: 0 and 1. */
1344: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1345: covariate for which somebody answered including
1346: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1347: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1348: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1349: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1350: double *ageexmed,*agecens;
1351: double dateintmean=0;
1.296 brouard 1352: double anprojd, mprojd, jprojd; /* For eventual projections */
1353: double anprojf, mprojf, jprojf;
1.126 brouard 1354:
1.296 brouard 1355: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1356: double anbackf, mbackf, jbackf;
1357: double jintmean,mintmean,aintmean;
1.126 brouard 1358: double *weight;
1359: int **s; /* Status */
1.141 brouard 1360: double *agedc;
1.145 brouard 1361: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1362: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1363: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1364: double **coqvar; /* Fixed quantitative covariate nqv */
1365: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1366: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1367: double idx;
1368: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1369: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1370: /*k 1 2 3 4 5 6 7 8 9 */
1371: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1372: /* Tndvar[k] 1 2 3 4 5 */
1373: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1374: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1375: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1376: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1377: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1378: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1379: /* Tprod[i]=k 4 7 */
1380: /* Tage[i]=k 5 8 */
1381: /* */
1382: /* Type */
1383: /* V 1 2 3 4 5 */
1384: /* F F V V V */
1385: /* D Q D D Q */
1386: /* */
1387: int *TvarsD;
1388: int *TvarsDind;
1389: int *TvarsQ;
1390: int *TvarsQind;
1391:
1.235 brouard 1392: #define MAXRESULTLINES 10
1393: int nresult=0;
1.258 brouard 1394: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1395: int TKresult[MAXRESULTLINES];
1.237 brouard 1396: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1397: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1398: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1399: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1400: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1401: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1402:
1.234 brouard 1403: /* 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 1404: 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 */
1405: 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 */
1406: 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 */
1407: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1408: 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 */
1409: 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 1410: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1411: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1412: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1413: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1414: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1415: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1416: 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 */
1417: 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 */
1418:
1.230 brouard 1419: int *Tvarsel; /**< Selected covariates for output */
1420: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1421: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1422: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1423: 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 1424: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1425: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1426: int *Tage;
1.227 brouard 1427: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1428: 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 1429: 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*/
1430: 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 1431: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1432: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1433: int **Tvard;
1434: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1435: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1436: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1437: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1438: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1439: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1440: double *lsurv, *lpop, *tpop;
1441:
1.231 brouard 1442: #define FD 1; /* Fixed dummy covariate */
1443: #define FQ 2; /* Fixed quantitative covariate */
1444: #define FP 3; /* Fixed product covariate */
1445: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1446: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1447: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1448: #define VD 10; /* Varying dummy covariate */
1449: #define VQ 11; /* Varying quantitative covariate */
1450: #define VP 12; /* Varying product covariate */
1451: #define VPDD 13; /* Varying product dummy*dummy covariate */
1452: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1453: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1454: #define APFD 16; /* Age product * fixed dummy covariate */
1455: #define APFQ 17; /* Age product * fixed quantitative covariate */
1456: #define APVD 18; /* Age product * varying dummy covariate */
1457: #define APVQ 19; /* Age product * varying quantitative covariate */
1458:
1459: #define FTYPE 1; /* Fixed covariate */
1460: #define VTYPE 2; /* Varying covariate (loop in wave) */
1461: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1462:
1463: struct kmodel{
1464: int maintype; /* main type */
1465: int subtype; /* subtype */
1466: };
1467: struct kmodel modell[NCOVMAX];
1468:
1.143 brouard 1469: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1470: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1471:
1472: /**************** split *************************/
1473: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1474: {
1475: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1476: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1477: */
1478: char *ss; /* pointer */
1.186 brouard 1479: int l1=0, l2=0; /* length counters */
1.126 brouard 1480:
1481: l1 = strlen(path ); /* length of path */
1482: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1483: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1484: if ( ss == NULL ) { /* no directory, so determine current directory */
1485: strcpy( name, path ); /* we got the fullname name because no directory */
1486: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1487: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1488: /* get current working directory */
1489: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1490: #ifdef WIN32
1491: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1492: #else
1493: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1494: #endif
1.126 brouard 1495: return( GLOCK_ERROR_GETCWD );
1496: }
1497: /* got dirc from getcwd*/
1498: printf(" DIRC = %s \n",dirc);
1.205 brouard 1499: } else { /* strip directory from path */
1.126 brouard 1500: ss++; /* after this, the filename */
1501: l2 = strlen( ss ); /* length of filename */
1502: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1503: strcpy( name, ss ); /* save file name */
1504: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1505: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1506: printf(" DIRC2 = %s \n",dirc);
1507: }
1508: /* We add a separator at the end of dirc if not exists */
1509: l1 = strlen( dirc ); /* length of directory */
1510: if( dirc[l1-1] != DIRSEPARATOR ){
1511: dirc[l1] = DIRSEPARATOR;
1512: dirc[l1+1] = 0;
1513: printf(" DIRC3 = %s \n",dirc);
1514: }
1515: ss = strrchr( name, '.' ); /* find last / */
1516: if (ss >0){
1517: ss++;
1518: strcpy(ext,ss); /* save extension */
1519: l1= strlen( name);
1520: l2= strlen(ss)+1;
1521: strncpy( finame, name, l1-l2);
1522: finame[l1-l2]= 0;
1523: }
1524:
1525: return( 0 ); /* we're done */
1526: }
1527:
1528:
1529: /******************************************/
1530:
1531: void replace_back_to_slash(char *s, char*t)
1532: {
1533: int i;
1534: int lg=0;
1535: i=0;
1536: lg=strlen(t);
1537: for(i=0; i<= lg; i++) {
1538: (s[i] = t[i]);
1539: if (t[i]== '\\') s[i]='/';
1540: }
1541: }
1542:
1.132 brouard 1543: char *trimbb(char *out, char *in)
1.137 brouard 1544: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1545: char *s;
1546: s=out;
1547: while (*in != '\0'){
1.137 brouard 1548: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1549: in++;
1550: }
1551: *out++ = *in++;
1552: }
1553: *out='\0';
1554: return s;
1555: }
1556:
1.187 brouard 1557: /* char *substrchaine(char *out, char *in, char *chain) */
1558: /* { */
1559: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1560: /* char *s, *t; */
1561: /* t=in;s=out; */
1562: /* while ((*in != *chain) && (*in != '\0')){ */
1563: /* *out++ = *in++; */
1564: /* } */
1565:
1566: /* /\* *in matches *chain *\/ */
1567: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1568: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1569: /* } */
1570: /* in--; chain--; */
1571: /* while ( (*in != '\0')){ */
1572: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1573: /* *out++ = *in++; */
1574: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1575: /* } */
1576: /* *out='\0'; */
1577: /* out=s; */
1578: /* return out; */
1579: /* } */
1580: char *substrchaine(char *out, char *in, char *chain)
1581: {
1582: /* Substract chain 'chain' from 'in', return and output 'out' */
1583: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1584:
1585: char *strloc;
1586:
1587: strcpy (out, in);
1588: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1589: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1590: if(strloc != NULL){
1591: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1592: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1593: /* strcpy (strloc, strloc +strlen(chain));*/
1594: }
1595: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1596: return out;
1597: }
1598:
1599:
1.145 brouard 1600: char *cutl(char *blocc, char *alocc, char *in, char occ)
1601: {
1.187 brouard 1602: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1603: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.310 brouard 1604: gives alocc="abcdef" and blocc="ghi2j".
1.145 brouard 1605: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1606: */
1.160 brouard 1607: char *s, *t;
1.145 brouard 1608: t=in;s=in;
1609: while ((*in != occ) && (*in != '\0')){
1610: *alocc++ = *in++;
1611: }
1612: if( *in == occ){
1613: *(alocc)='\0';
1614: s=++in;
1615: }
1616:
1617: if (s == t) {/* occ not found */
1618: *(alocc-(in-s))='\0';
1619: in=s;
1620: }
1621: while ( *in != '\0'){
1622: *blocc++ = *in++;
1623: }
1624:
1625: *blocc='\0';
1626: return t;
1627: }
1.137 brouard 1628: char *cutv(char *blocc, char *alocc, char *in, char occ)
1629: {
1.187 brouard 1630: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1631: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1632: gives blocc="abcdef2ghi" and alocc="j".
1633: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1634: */
1635: char *s, *t;
1636: t=in;s=in;
1637: while (*in != '\0'){
1638: while( *in == occ){
1639: *blocc++ = *in++;
1640: s=in;
1641: }
1642: *blocc++ = *in++;
1643: }
1644: if (s == t) /* occ not found */
1645: *(blocc-(in-s))='\0';
1646: else
1647: *(blocc-(in-s)-1)='\0';
1648: in=s;
1649: while ( *in != '\0'){
1650: *alocc++ = *in++;
1651: }
1652:
1653: *alocc='\0';
1654: return s;
1655: }
1656:
1.126 brouard 1657: int nbocc(char *s, char occ)
1658: {
1659: int i,j=0;
1660: int lg=20;
1661: i=0;
1662: lg=strlen(s);
1663: for(i=0; i<= lg; i++) {
1.234 brouard 1664: if (s[i] == occ ) j++;
1.126 brouard 1665: }
1666: return j;
1667: }
1668:
1.137 brouard 1669: /* void cutv(char *u,char *v, char*t, char occ) */
1670: /* { */
1671: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1672: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1673: /* gives u="abcdef2ghi" and v="j" *\/ */
1674: /* int i,lg,j,p=0; */
1675: /* i=0; */
1676: /* lg=strlen(t); */
1677: /* for(j=0; j<=lg-1; j++) { */
1678: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1679: /* } */
1.126 brouard 1680:
1.137 brouard 1681: /* for(j=0; j<p; j++) { */
1682: /* (u[j] = t[j]); */
1683: /* } */
1684: /* u[p]='\0'; */
1.126 brouard 1685:
1.137 brouard 1686: /* for(j=0; j<= lg; j++) { */
1687: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1688: /* } */
1689: /* } */
1.126 brouard 1690:
1.160 brouard 1691: #ifdef _WIN32
1692: char * strsep(char **pp, const char *delim)
1693: {
1694: char *p, *q;
1695:
1696: if ((p = *pp) == NULL)
1697: return 0;
1698: if ((q = strpbrk (p, delim)) != NULL)
1699: {
1700: *pp = q + 1;
1701: *q = '\0';
1702: }
1703: else
1704: *pp = 0;
1705: return p;
1706: }
1707: #endif
1708:
1.126 brouard 1709: /********************** nrerror ********************/
1710:
1711: void nrerror(char error_text[])
1712: {
1713: fprintf(stderr,"ERREUR ...\n");
1714: fprintf(stderr,"%s\n",error_text);
1715: exit(EXIT_FAILURE);
1716: }
1717: /*********************** vector *******************/
1718: double *vector(int nl, int nh)
1719: {
1720: double *v;
1721: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1722: if (!v) nrerror("allocation failure in vector");
1723: return v-nl+NR_END;
1724: }
1725:
1726: /************************ free vector ******************/
1727: void free_vector(double*v, int nl, int nh)
1728: {
1729: free((FREE_ARG)(v+nl-NR_END));
1730: }
1731:
1732: /************************ivector *******************************/
1733: int *ivector(long nl,long nh)
1734: {
1735: int *v;
1736: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1737: if (!v) nrerror("allocation failure in ivector");
1738: return v-nl+NR_END;
1739: }
1740:
1741: /******************free ivector **************************/
1742: void free_ivector(int *v, long nl, long nh)
1743: {
1744: free((FREE_ARG)(v+nl-NR_END));
1745: }
1746:
1747: /************************lvector *******************************/
1748: long *lvector(long nl,long nh)
1749: {
1750: long *v;
1751: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1752: if (!v) nrerror("allocation failure in ivector");
1753: return v-nl+NR_END;
1754: }
1755:
1756: /******************free lvector **************************/
1757: void free_lvector(long *v, long nl, long nh)
1758: {
1759: free((FREE_ARG)(v+nl-NR_END));
1760: }
1761:
1762: /******************* imatrix *******************************/
1763: int **imatrix(long nrl, long nrh, long ncl, long nch)
1764: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1765: {
1766: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1767: int **m;
1768:
1769: /* allocate pointers to rows */
1770: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1771: if (!m) nrerror("allocation failure 1 in matrix()");
1772: m += NR_END;
1773: m -= nrl;
1774:
1775:
1776: /* allocate rows and set pointers to them */
1777: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1778: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1779: m[nrl] += NR_END;
1780: m[nrl] -= ncl;
1781:
1782: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1783:
1784: /* return pointer to array of pointers to rows */
1785: return m;
1786: }
1787:
1788: /****************** free_imatrix *************************/
1789: void free_imatrix(m,nrl,nrh,ncl,nch)
1790: int **m;
1791: long nch,ncl,nrh,nrl;
1792: /* free an int matrix allocated by imatrix() */
1793: {
1794: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1795: free((FREE_ARG) (m+nrl-NR_END));
1796: }
1797:
1798: /******************* matrix *******************************/
1799: double **matrix(long nrl, long nrh, long ncl, long nch)
1800: {
1801: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1802: double **m;
1803:
1804: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1805: if (!m) nrerror("allocation failure 1 in matrix()");
1806: m += NR_END;
1807: m -= nrl;
1808:
1809: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1810: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1811: m[nrl] += NR_END;
1812: m[nrl] -= ncl;
1813:
1814: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1815: return m;
1.145 brouard 1816: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1817: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1818: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1819: */
1820: }
1821:
1822: /*************************free matrix ************************/
1823: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1824: {
1825: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1826: free((FREE_ARG)(m+nrl-NR_END));
1827: }
1828:
1829: /******************* ma3x *******************************/
1830: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1831: {
1832: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1833: double ***m;
1834:
1835: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1836: if (!m) nrerror("allocation failure 1 in matrix()");
1837: m += NR_END;
1838: m -= nrl;
1839:
1840: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1841: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1842: m[nrl] += NR_END;
1843: m[nrl] -= ncl;
1844:
1845: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1846:
1847: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1848: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1849: m[nrl][ncl] += NR_END;
1850: m[nrl][ncl] -= nll;
1851: for (j=ncl+1; j<=nch; j++)
1852: m[nrl][j]=m[nrl][j-1]+nlay;
1853:
1854: for (i=nrl+1; i<=nrh; i++) {
1855: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1856: for (j=ncl+1; j<=nch; j++)
1857: m[i][j]=m[i][j-1]+nlay;
1858: }
1859: return m;
1860: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1861: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1862: */
1863: }
1864:
1865: /*************************free ma3x ************************/
1866: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1867: {
1868: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1869: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1870: free((FREE_ARG)(m+nrl-NR_END));
1871: }
1872:
1873: /*************** function subdirf ***********/
1874: char *subdirf(char fileres[])
1875: {
1876: /* Caution optionfilefiname is hidden */
1877: strcpy(tmpout,optionfilefiname);
1878: strcat(tmpout,"/"); /* Add to the right */
1879: strcat(tmpout,fileres);
1880: return tmpout;
1881: }
1882:
1883: /*************** function subdirf2 ***********/
1884: char *subdirf2(char fileres[], char *preop)
1885: {
1.314 brouard 1886: /* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
1887: Errors in subdirf, 2, 3 while printing tmpout is
1.315 brouard 1888: rewritten within the same printf. Workaround: many printfs */
1.126 brouard 1889: /* Caution optionfilefiname is hidden */
1890: strcpy(tmpout,optionfilefiname);
1891: strcat(tmpout,"/");
1892: strcat(tmpout,preop);
1893: strcat(tmpout,fileres);
1894: return tmpout;
1895: }
1896:
1897: /*************** function subdirf3 ***********/
1898: char *subdirf3(char fileres[], char *preop, char *preop2)
1899: {
1900:
1901: /* Caution optionfilefiname is hidden */
1902: strcpy(tmpout,optionfilefiname);
1903: strcat(tmpout,"/");
1904: strcat(tmpout,preop);
1905: strcat(tmpout,preop2);
1906: strcat(tmpout,fileres);
1907: return tmpout;
1908: }
1.213 brouard 1909:
1910: /*************** function subdirfext ***********/
1911: char *subdirfext(char fileres[], char *preop, char *postop)
1912: {
1913:
1914: strcpy(tmpout,preop);
1915: strcat(tmpout,fileres);
1916: strcat(tmpout,postop);
1917: return tmpout;
1918: }
1.126 brouard 1919:
1.213 brouard 1920: /*************** function subdirfext3 ***********/
1921: char *subdirfext3(char fileres[], char *preop, char *postop)
1922: {
1923:
1924: /* Caution optionfilefiname is hidden */
1925: strcpy(tmpout,optionfilefiname);
1926: strcat(tmpout,"/");
1927: strcat(tmpout,preop);
1928: strcat(tmpout,fileres);
1929: strcat(tmpout,postop);
1930: return tmpout;
1931: }
1932:
1.162 brouard 1933: char *asc_diff_time(long time_sec, char ascdiff[])
1934: {
1935: long sec_left, days, hours, minutes;
1936: days = (time_sec) / (60*60*24);
1937: sec_left = (time_sec) % (60*60*24);
1938: hours = (sec_left) / (60*60) ;
1939: sec_left = (sec_left) %(60*60);
1940: minutes = (sec_left) /60;
1941: sec_left = (sec_left) % (60);
1942: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1943: return ascdiff;
1944: }
1945:
1.126 brouard 1946: /***************** f1dim *************************/
1947: extern int ncom;
1948: extern double *pcom,*xicom;
1949: extern double (*nrfunc)(double []);
1950:
1951: double f1dim(double x)
1952: {
1953: int j;
1954: double f;
1955: double *xt;
1956:
1957: xt=vector(1,ncom);
1958: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1959: f=(*nrfunc)(xt);
1960: free_vector(xt,1,ncom);
1961: return f;
1962: }
1963:
1964: /*****************brent *************************/
1965: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1966: {
1967: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1968: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1969: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1970: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1971: * returned function value.
1972: */
1.126 brouard 1973: int iter;
1974: double a,b,d,etemp;
1.159 brouard 1975: double fu=0,fv,fw,fx;
1.164 brouard 1976: double ftemp=0.;
1.126 brouard 1977: double p,q,r,tol1,tol2,u,v,w,x,xm;
1978: double e=0.0;
1979:
1980: a=(ax < cx ? ax : cx);
1981: b=(ax > cx ? ax : cx);
1982: x=w=v=bx;
1983: fw=fv=fx=(*f)(x);
1984: for (iter=1;iter<=ITMAX;iter++) {
1985: xm=0.5*(a+b);
1986: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1987: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1988: printf(".");fflush(stdout);
1989: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1990: #ifdef DEBUGBRENT
1.126 brouard 1991: 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);
1992: 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);
1993: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1994: #endif
1995: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1996: *xmin=x;
1997: return fx;
1998: }
1999: ftemp=fu;
2000: if (fabs(e) > tol1) {
2001: r=(x-w)*(fx-fv);
2002: q=(x-v)*(fx-fw);
2003: p=(x-v)*q-(x-w)*r;
2004: q=2.0*(q-r);
2005: if (q > 0.0) p = -p;
2006: q=fabs(q);
2007: etemp=e;
2008: e=d;
2009: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 2010: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 2011: else {
1.224 brouard 2012: d=p/q;
2013: u=x+d;
2014: if (u-a < tol2 || b-u < tol2)
2015: d=SIGN(tol1,xm-x);
1.126 brouard 2016: }
2017: } else {
2018: d=CGOLD*(e=(x >= xm ? a-x : b-x));
2019: }
2020: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
2021: fu=(*f)(u);
2022: if (fu <= fx) {
2023: if (u >= x) a=x; else b=x;
2024: SHFT(v,w,x,u)
1.183 brouard 2025: SHFT(fv,fw,fx,fu)
2026: } else {
2027: if (u < x) a=u; else b=u;
2028: if (fu <= fw || w == x) {
1.224 brouard 2029: v=w;
2030: w=u;
2031: fv=fw;
2032: fw=fu;
1.183 brouard 2033: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 2034: v=u;
2035: fv=fu;
1.183 brouard 2036: }
2037: }
1.126 brouard 2038: }
2039: nrerror("Too many iterations in brent");
2040: *xmin=x;
2041: return fx;
2042: }
2043:
2044: /****************** mnbrak ***********************/
2045:
2046: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2047: double (*func)(double))
1.183 brouard 2048: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2049: the downhill direction (defined by the function as evaluated at the initial points) and returns
2050: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2051: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2052: */
1.126 brouard 2053: double ulim,u,r,q, dum;
2054: double fu;
1.187 brouard 2055:
2056: double scale=10.;
2057: int iterscale=0;
2058:
2059: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2060: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2061:
2062:
2063: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2064: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2065: /* *bx = *ax - (*ax - *bx)/scale; */
2066: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2067: /* } */
2068:
1.126 brouard 2069: if (*fb > *fa) {
2070: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2071: SHFT(dum,*fb,*fa,dum)
2072: }
1.126 brouard 2073: *cx=(*bx)+GOLD*(*bx-*ax);
2074: *fc=(*func)(*cx);
1.183 brouard 2075: #ifdef DEBUG
1.224 brouard 2076: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2077: 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 2078: #endif
1.224 brouard 2079: 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 2080: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2081: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2082: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2083: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2084: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2085: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2086: fu=(*func)(u);
1.163 brouard 2087: #ifdef DEBUG
2088: /* f(x)=A(x-u)**2+f(u) */
2089: double A, fparabu;
2090: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2091: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2092: 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);
2093: 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 2094: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2095: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2096: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2097: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2098: #endif
1.184 brouard 2099: #ifdef MNBRAKORIGINAL
1.183 brouard 2100: #else
1.191 brouard 2101: /* if (fu > *fc) { */
2102: /* #ifdef DEBUG */
2103: /* printf("mnbrak4 fu > fc \n"); */
2104: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2105: /* #endif */
2106: /* /\* 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 *\\/ *\/ */
2107: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2108: /* dum=u; /\* Shifting c and u *\/ */
2109: /* u = *cx; */
2110: /* *cx = dum; */
2111: /* dum = fu; */
2112: /* fu = *fc; */
2113: /* *fc =dum; */
2114: /* } else { /\* end *\/ */
2115: /* #ifdef DEBUG */
2116: /* printf("mnbrak3 fu < fc \n"); */
2117: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2118: /* #endif */
2119: /* dum=u; /\* Shifting c and u *\/ */
2120: /* u = *cx; */
2121: /* *cx = dum; */
2122: /* dum = fu; */
2123: /* fu = *fc; */
2124: /* *fc =dum; */
2125: /* } */
1.224 brouard 2126: #ifdef DEBUGMNBRAK
2127: double A, fparabu;
2128: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2129: fparabu= *fa - A*(*ax-u)*(*ax-u);
2130: 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);
2131: 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 2132: #endif
1.191 brouard 2133: dum=u; /* Shifting c and u */
2134: u = *cx;
2135: *cx = dum;
2136: dum = fu;
2137: fu = *fc;
2138: *fc =dum;
1.183 brouard 2139: #endif
1.162 brouard 2140: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2141: #ifdef DEBUG
1.224 brouard 2142: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2143: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2144: #endif
1.126 brouard 2145: fu=(*func)(u);
2146: if (fu < *fc) {
1.183 brouard 2147: #ifdef DEBUG
1.224 brouard 2148: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2149: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2150: #endif
2151: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2152: SHFT(*fb,*fc,fu,(*func)(u))
2153: #ifdef DEBUG
2154: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2155: #endif
2156: }
1.162 brouard 2157: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2158: #ifdef DEBUG
1.224 brouard 2159: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2160: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2161: #endif
1.126 brouard 2162: u=ulim;
2163: fu=(*func)(u);
1.183 brouard 2164: } else { /* u could be left to b (if r > q parabola has a maximum) */
2165: #ifdef DEBUG
1.224 brouard 2166: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2167: 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 2168: #endif
1.126 brouard 2169: u=(*cx)+GOLD*(*cx-*bx);
2170: fu=(*func)(u);
1.224 brouard 2171: #ifdef DEBUG
2172: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2173: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2174: #endif
1.183 brouard 2175: } /* end tests */
1.126 brouard 2176: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2177: SHFT(*fa,*fb,*fc,fu)
2178: #ifdef DEBUG
1.224 brouard 2179: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2180: 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 2181: #endif
2182: } /* 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 2183: }
2184:
2185: /*************** linmin ************************/
1.162 brouard 2186: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2187: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2188: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2189: the value of func at the returned location p . This is actually all accomplished by calling the
2190: routines mnbrak and brent .*/
1.126 brouard 2191: int ncom;
2192: double *pcom,*xicom;
2193: double (*nrfunc)(double []);
2194:
1.224 brouard 2195: #ifdef LINMINORIGINAL
1.126 brouard 2196: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2197: #else
2198: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2199: #endif
1.126 brouard 2200: {
2201: double brent(double ax, double bx, double cx,
2202: double (*f)(double), double tol, double *xmin);
2203: double f1dim(double x);
2204: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2205: double *fc, double (*func)(double));
2206: int j;
2207: double xx,xmin,bx,ax;
2208: double fx,fb,fa;
1.187 brouard 2209:
1.203 brouard 2210: #ifdef LINMINORIGINAL
2211: #else
2212: double scale=10., axs, xxs; /* Scale added for infinity */
2213: #endif
2214:
1.126 brouard 2215: ncom=n;
2216: pcom=vector(1,n);
2217: xicom=vector(1,n);
2218: nrfunc=func;
2219: for (j=1;j<=n;j++) {
2220: pcom[j]=p[j];
1.202 brouard 2221: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2222: }
1.187 brouard 2223:
1.203 brouard 2224: #ifdef LINMINORIGINAL
2225: xx=1.;
2226: #else
2227: axs=0.0;
2228: xxs=1.;
2229: do{
2230: xx= xxs;
2231: #endif
1.187 brouard 2232: ax=0.;
2233: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2234: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2235: /* 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)) */
2236: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2237: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2238: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2239: /* 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 2240: #ifdef LINMINORIGINAL
2241: #else
2242: if (fx != fx){
1.224 brouard 2243: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2244: printf("|");
2245: fprintf(ficlog,"|");
1.203 brouard 2246: #ifdef DEBUGLINMIN
1.224 brouard 2247: 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 2248: #endif
2249: }
1.224 brouard 2250: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2251: #endif
2252:
1.191 brouard 2253: #ifdef DEBUGLINMIN
2254: 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 2255: 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 2256: #endif
1.224 brouard 2257: #ifdef LINMINORIGINAL
2258: #else
2259: if(fb == fx){ /* Flat function in the direction */
2260: xmin=xx;
2261: *flat=1;
2262: }else{
2263: *flat=0;
2264: #endif
2265: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2266: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2267: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2268: /* fmin = f(p[j] + xmin * xi[j]) */
2269: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2270: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2271: #ifdef DEBUG
1.224 brouard 2272: 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);
2273: 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);
2274: #endif
2275: #ifdef LINMINORIGINAL
2276: #else
2277: }
1.126 brouard 2278: #endif
1.191 brouard 2279: #ifdef DEBUGLINMIN
2280: printf("linmin end ");
1.202 brouard 2281: fprintf(ficlog,"linmin end ");
1.191 brouard 2282: #endif
1.126 brouard 2283: for (j=1;j<=n;j++) {
1.203 brouard 2284: #ifdef LINMINORIGINAL
2285: xi[j] *= xmin;
2286: #else
2287: #ifdef DEBUGLINMIN
2288: if(xxs <1.0)
2289: printf(" before xi[%d]=%12.8f", j,xi[j]);
2290: #endif
2291: 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) */
2292: #ifdef DEBUGLINMIN
2293: if(xxs <1.0)
2294: 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 );
2295: #endif
2296: #endif
1.187 brouard 2297: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2298: }
1.191 brouard 2299: #ifdef DEBUGLINMIN
1.203 brouard 2300: printf("\n");
1.191 brouard 2301: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2302: 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 2303: for (j=1;j<=n;j++) {
1.202 brouard 2304: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2305: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2306: if(j % ncovmodel == 0){
1.191 brouard 2307: printf("\n");
1.202 brouard 2308: fprintf(ficlog,"\n");
2309: }
1.191 brouard 2310: }
1.203 brouard 2311: #else
1.191 brouard 2312: #endif
1.126 brouard 2313: free_vector(xicom,1,n);
2314: free_vector(pcom,1,n);
2315: }
2316:
2317:
2318: /*************** powell ************************/
1.162 brouard 2319: /*
2320: Minimization of a function func of n variables. Input consists of an initial starting point
2321: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2322: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2323: such that failure to decrease by more than this amount on one iteration signals doneness. On
2324: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2325: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2326: */
1.224 brouard 2327: #ifdef LINMINORIGINAL
2328: #else
2329: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2330: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2331: #endif
1.126 brouard 2332: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2333: double (*func)(double []))
2334: {
1.224 brouard 2335: #ifdef LINMINORIGINAL
2336: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2337: double (*func)(double []));
1.224 brouard 2338: #else
1.241 brouard 2339: void linmin(double p[], double xi[], int n, double *fret,
2340: double (*func)(double []),int *flat);
1.224 brouard 2341: #endif
1.239 brouard 2342: int i,ibig,j,jk,k;
1.126 brouard 2343: double del,t,*pt,*ptt,*xit;
1.181 brouard 2344: double directest;
1.126 brouard 2345: double fp,fptt;
2346: double *xits;
2347: int niterf, itmp;
1.224 brouard 2348: #ifdef LINMINORIGINAL
2349: #else
2350:
2351: flatdir=ivector(1,n);
2352: for (j=1;j<=n;j++) flatdir[j]=0;
2353: #endif
1.126 brouard 2354:
2355: pt=vector(1,n);
2356: ptt=vector(1,n);
2357: xit=vector(1,n);
2358: xits=vector(1,n);
2359: *fret=(*func)(p);
2360: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2361: rcurr_time = time(NULL);
1.126 brouard 2362: for (*iter=1;;++(*iter)) {
1.187 brouard 2363: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2364: ibig=0;
2365: del=0.0;
1.157 brouard 2366: rlast_time=rcurr_time;
2367: /* (void) gettimeofday(&curr_time,&tzp); */
2368: rcurr_time = time(NULL);
2369: curr_time = *localtime(&rcurr_time);
2370: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2371: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2372: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2373: for (i=1;i<=n;i++) {
1.126 brouard 2374: fprintf(ficrespow," %.12lf", p[i]);
2375: }
1.239 brouard 2376: fprintf(ficrespow,"\n");fflush(ficrespow);
2377: printf("\n#model= 1 + age ");
2378: fprintf(ficlog,"\n#model= 1 + age ");
2379: if(nagesqr==1){
1.241 brouard 2380: printf(" + age*age ");
2381: fprintf(ficlog," + age*age ");
1.239 brouard 2382: }
2383: for(j=1;j <=ncovmodel-2;j++){
2384: if(Typevar[j]==0) {
2385: printf(" + V%d ",Tvar[j]);
2386: fprintf(ficlog," + V%d ",Tvar[j]);
2387: }else if(Typevar[j]==1) {
2388: printf(" + V%d*age ",Tvar[j]);
2389: fprintf(ficlog," + V%d*age ",Tvar[j]);
2390: }else if(Typevar[j]==2) {
2391: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2392: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2393: }
2394: }
1.126 brouard 2395: printf("\n");
1.239 brouard 2396: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2397: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2398: fprintf(ficlog,"\n");
1.239 brouard 2399: for(i=1,jk=1; i <=nlstate; i++){
2400: for(k=1; k <=(nlstate+ndeath); k++){
2401: if (k != i) {
2402: printf("%d%d ",i,k);
2403: fprintf(ficlog,"%d%d ",i,k);
2404: for(j=1; j <=ncovmodel; j++){
2405: printf("%12.7f ",p[jk]);
2406: fprintf(ficlog,"%12.7f ",p[jk]);
2407: jk++;
2408: }
2409: printf("\n");
2410: fprintf(ficlog,"\n");
2411: }
2412: }
2413: }
1.241 brouard 2414: if(*iter <=3 && *iter >1){
1.157 brouard 2415: tml = *localtime(&rcurr_time);
2416: strcpy(strcurr,asctime(&tml));
2417: rforecast_time=rcurr_time;
1.126 brouard 2418: itmp = strlen(strcurr);
2419: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2420: strcurr[itmp-1]='\0';
1.162 brouard 2421: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2422: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2423: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2424: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2425: forecast_time = *localtime(&rforecast_time);
2426: strcpy(strfor,asctime(&forecast_time));
2427: itmp = strlen(strfor);
2428: if(strfor[itmp-1]=='\n')
2429: strfor[itmp-1]='\0';
2430: 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);
2431: 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 2432: }
2433: }
1.187 brouard 2434: for (i=1;i<=n;i++) { /* For each direction i */
2435: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2436: fptt=(*fret);
2437: #ifdef DEBUG
1.203 brouard 2438: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2439: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2440: #endif
1.203 brouard 2441: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2442: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2443: #ifdef LINMINORIGINAL
1.188 brouard 2444: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2445: #else
2446: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2447: flatdir[i]=flat; /* Function is vanishing in that direction i */
2448: #endif
2449: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2450: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2451: /* because that direction will be replaced unless the gain del is small */
2452: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2453: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2454: /* with the new direction. */
2455: del=fabs(fptt-(*fret));
2456: ibig=i;
1.126 brouard 2457: }
2458: #ifdef DEBUG
2459: printf("%d %.12e",i,(*fret));
2460: fprintf(ficlog,"%d %.12e",i,(*fret));
2461: for (j=1;j<=n;j++) {
1.224 brouard 2462: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2463: printf(" x(%d)=%.12e",j,xit[j]);
2464: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2465: }
2466: for(j=1;j<=n;j++) {
1.225 brouard 2467: printf(" p(%d)=%.12e",j,p[j]);
2468: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2469: }
2470: printf("\n");
2471: fprintf(ficlog,"\n");
2472: #endif
1.187 brouard 2473: } /* end loop on each direction i */
2474: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2475: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2476: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2477: for(j=1;j<=n;j++) {
1.302 brouard 2478: if(flatdir[j] >0){
2479: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2480: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2481: }
2482: /* printf("\n"); */
2483: /* fprintf(ficlog,"\n"); */
2484: }
1.243 brouard 2485: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2486: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2487: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2488: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2489: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2490: /* decreased of more than 3.84 */
2491: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2492: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2493: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2494:
1.188 brouard 2495: /* Starting the program with initial values given by a former maximization will simply change */
2496: /* the scales of the directions and the directions, because the are reset to canonical directions */
2497: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2498: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2499: #ifdef DEBUG
2500: int k[2],l;
2501: k[0]=1;
2502: k[1]=-1;
2503: printf("Max: %.12e",(*func)(p));
2504: fprintf(ficlog,"Max: %.12e",(*func)(p));
2505: for (j=1;j<=n;j++) {
2506: printf(" %.12e",p[j]);
2507: fprintf(ficlog," %.12e",p[j]);
2508: }
2509: printf("\n");
2510: fprintf(ficlog,"\n");
2511: for(l=0;l<=1;l++) {
2512: for (j=1;j<=n;j++) {
2513: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2514: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2515: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2516: }
2517: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2518: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2519: }
2520: #endif
2521:
1.224 brouard 2522: #ifdef LINMINORIGINAL
2523: #else
2524: free_ivector(flatdir,1,n);
2525: #endif
1.126 brouard 2526: free_vector(xit,1,n);
2527: free_vector(xits,1,n);
2528: free_vector(ptt,1,n);
2529: free_vector(pt,1,n);
2530: return;
1.192 brouard 2531: } /* enough precision */
1.240 brouard 2532: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2533: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2534: ptt[j]=2.0*p[j]-pt[j];
2535: xit[j]=p[j]-pt[j];
2536: pt[j]=p[j];
2537: }
1.181 brouard 2538: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2539: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2540: if (*iter <=4) {
1.225 brouard 2541: #else
2542: #endif
1.224 brouard 2543: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2544: #else
1.161 brouard 2545: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2546: #endif
1.162 brouard 2547: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2548: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2549: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2550: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2551: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2552: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2553: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2554: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2555: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2556: /* Even if f3 <f1, directest can be negative and t >0 */
2557: /* mu² and del² are equal when f3=f1 */
2558: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2559: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2560: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2561: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2562: #ifdef NRCORIGINAL
2563: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2564: #else
2565: 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 2566: t= t- del*SQR(fp-fptt);
1.183 brouard 2567: #endif
1.202 brouard 2568: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2569: #ifdef DEBUG
1.181 brouard 2570: 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);
2571: 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 2572: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2573: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2574: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2575: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2576: 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);
2577: 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);
2578: #endif
1.183 brouard 2579: #ifdef POWELLORIGINAL
2580: if (t < 0.0) { /* Then we use it for new direction */
2581: #else
1.182 brouard 2582: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2583: 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 2584: 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 2585: 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 2586: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2587: }
1.181 brouard 2588: if (directest < 0.0) { /* Then we use it for new direction */
2589: #endif
1.191 brouard 2590: #ifdef DEBUGLINMIN
1.234 brouard 2591: printf("Before linmin in direction P%d-P0\n",n);
2592: for (j=1;j<=n;j++) {
2593: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2594: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2595: if(j % ncovmodel == 0){
2596: printf("\n");
2597: fprintf(ficlog,"\n");
2598: }
2599: }
1.224 brouard 2600: #endif
2601: #ifdef LINMINORIGINAL
1.234 brouard 2602: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2603: #else
1.234 brouard 2604: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2605: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2606: #endif
1.234 brouard 2607:
1.191 brouard 2608: #ifdef DEBUGLINMIN
1.234 brouard 2609: for (j=1;j<=n;j++) {
2610: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2611: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2612: if(j % ncovmodel == 0){
2613: printf("\n");
2614: fprintf(ficlog,"\n");
2615: }
2616: }
1.224 brouard 2617: #endif
1.234 brouard 2618: for (j=1;j<=n;j++) {
2619: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2620: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2621: }
1.224 brouard 2622: #ifdef LINMINORIGINAL
2623: #else
1.234 brouard 2624: for (j=1, flatd=0;j<=n;j++) {
2625: if(flatdir[j]>0)
2626: flatd++;
2627: }
2628: if(flatd >0){
1.255 brouard 2629: printf("%d flat directions: ",flatd);
2630: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2631: for (j=1;j<=n;j++) {
2632: if(flatdir[j]>0){
2633: printf("%d ",j);
2634: fprintf(ficlog,"%d ",j);
2635: }
2636: }
2637: printf("\n");
2638: fprintf(ficlog,"\n");
2639: }
1.191 brouard 2640: #endif
1.234 brouard 2641: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2642: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2643:
1.126 brouard 2644: #ifdef DEBUG
1.234 brouard 2645: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2646: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2647: for(j=1;j<=n;j++){
2648: printf(" %lf",xit[j]);
2649: fprintf(ficlog," %lf",xit[j]);
2650: }
2651: printf("\n");
2652: fprintf(ficlog,"\n");
1.126 brouard 2653: #endif
1.192 brouard 2654: } /* end of t or directest negative */
1.224 brouard 2655: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2656: #else
1.234 brouard 2657: } /* end if (fptt < fp) */
1.192 brouard 2658: #endif
1.225 brouard 2659: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2660: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2661: #else
1.224 brouard 2662: #endif
1.234 brouard 2663: } /* loop iteration */
1.126 brouard 2664: }
1.234 brouard 2665:
1.126 brouard 2666: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2667:
1.235 brouard 2668: 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 2669: {
1.279 brouard 2670: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2671: * (and selected quantitative values in nres)
2672: * by left multiplying the unit
2673: * matrix by transitions matrix until convergence is reached with precision ftolpl
2674: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2675: * Wx is row vector: population in state 1, population in state 2, population dead
2676: * or prevalence in state 1, prevalence in state 2, 0
2677: * newm is the matrix after multiplications, its rows are identical at a factor.
2678: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2679: * Output is prlim.
2680: * Initial matrix pimij
2681: */
1.206 brouard 2682: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2683: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2684: /* 0, 0 , 1} */
2685: /*
2686: * and after some iteration: */
2687: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2688: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2689: /* 0, 0 , 1} */
2690: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2691: /* {0.51571254859325999, 0.4842874514067399, */
2692: /* 0.51326036147820708, 0.48673963852179264} */
2693: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2694:
1.126 brouard 2695: int i, ii,j,k;
1.209 brouard 2696: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2697: /* double **matprod2(); */ /* test */
1.218 brouard 2698: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2699: double **newm;
1.209 brouard 2700: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2701: int ncvloop=0;
1.288 brouard 2702: int first=0;
1.169 brouard 2703:
1.209 brouard 2704: min=vector(1,nlstate);
2705: max=vector(1,nlstate);
2706: meandiff=vector(1,nlstate);
2707:
1.218 brouard 2708: /* Starting with matrix unity */
1.126 brouard 2709: for (ii=1;ii<=nlstate+ndeath;ii++)
2710: for (j=1;j<=nlstate+ndeath;j++){
2711: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2712: }
1.169 brouard 2713:
2714: cov[1]=1.;
2715:
2716: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2717: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2718: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2719: ncvloop++;
1.126 brouard 2720: newm=savm;
2721: /* Covariates have to be included here again */
1.138 brouard 2722: cov[2]=agefin;
1.187 brouard 2723: if(nagesqr==1)
2724: cov[3]= agefin*agefin;;
1.234 brouard 2725: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2726: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2727: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2728: /* 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 2729: }
2730: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2731: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2732: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2733: /* 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 2734: }
1.237 brouard 2735: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2736: if(Dummy[Tvar[Tage[k]]]){
2737: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2738: } else{
1.235 brouard 2739: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2740: }
1.235 brouard 2741: /* 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 2742: }
1.237 brouard 2743: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2744: /* 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 2745: if(Dummy[Tvard[k][1]==0]){
2746: if(Dummy[Tvard[k][2]==0]){
2747: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2748: }else{
2749: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2750: }
2751: }else{
2752: if(Dummy[Tvard[k][2]==0]){
2753: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2754: }else{
2755: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2756: }
2757: }
1.234 brouard 2758: }
1.138 brouard 2759: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2760: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2761: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2762: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2763: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2764: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2765: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2766:
1.126 brouard 2767: savm=oldm;
2768: oldm=newm;
1.209 brouard 2769:
2770: for(j=1; j<=nlstate; j++){
2771: max[j]=0.;
2772: min[j]=1.;
2773: }
2774: for(i=1;i<=nlstate;i++){
2775: sumnew=0;
2776: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2777: for(j=1; j<=nlstate; j++){
2778: prlim[i][j]= newm[i][j]/(1-sumnew);
2779: max[j]=FMAX(max[j],prlim[i][j]);
2780: min[j]=FMIN(min[j],prlim[i][j]);
2781: }
2782: }
2783:
1.126 brouard 2784: maxmax=0.;
1.209 brouard 2785: for(j=1; j<=nlstate; j++){
2786: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2787: maxmax=FMAX(maxmax,meandiff[j]);
2788: /* 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 2789: } /* j loop */
1.203 brouard 2790: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2791: /* 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 2792: if(maxmax < ftolpl){
1.209 brouard 2793: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2794: free_vector(min,1,nlstate);
2795: free_vector(max,1,nlstate);
2796: free_vector(meandiff,1,nlstate);
1.126 brouard 2797: return prlim;
2798: }
1.288 brouard 2799: } /* agefin loop */
1.208 brouard 2800: /* After some age loop it doesn't converge */
1.288 brouard 2801: if(!first){
2802: first=1;
2803: 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);
2804: }
2805: 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);
2806:
1.209 brouard 2807: /* 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); */
2808: free_vector(min,1,nlstate);
2809: free_vector(max,1,nlstate);
2810: free_vector(meandiff,1,nlstate);
1.208 brouard 2811:
1.169 brouard 2812: return prlim; /* should not reach here */
1.126 brouard 2813: }
2814:
1.217 brouard 2815:
2816: /**** Back Prevalence limit (stable or period prevalence) ****************/
2817:
1.218 brouard 2818: /* 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) */
2819: /* 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 2820: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2821: {
1.264 brouard 2822: /* 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 2823: matrix by transitions matrix until convergence is reached with precision ftolpl */
2824: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2825: /* Wx is row vector: population in state 1, population in state 2, population dead */
2826: /* or prevalence in state 1, prevalence in state 2, 0 */
2827: /* newm is the matrix after multiplications, its rows are identical at a factor */
2828: /* Initial matrix pimij */
2829: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2830: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2831: /* 0, 0 , 1} */
2832: /*
2833: * and after some iteration: */
2834: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2835: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2836: /* 0, 0 , 1} */
2837: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2838: /* {0.51571254859325999, 0.4842874514067399, */
2839: /* 0.51326036147820708, 0.48673963852179264} */
2840: /* If we start from prlim again, prlim tends to a constant matrix */
2841:
2842: int i, ii,j,k;
1.247 brouard 2843: int first=0;
1.217 brouard 2844: double *min, *max, *meandiff, maxmax,sumnew=0.;
2845: /* double **matprod2(); */ /* test */
2846: double **out, cov[NCOVMAX+1], **bmij();
2847: double **newm;
1.218 brouard 2848: double **dnewm, **doldm, **dsavm; /* for use */
2849: double **oldm, **savm; /* for use */
2850:
1.217 brouard 2851: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2852: int ncvloop=0;
2853:
2854: min=vector(1,nlstate);
2855: max=vector(1,nlstate);
2856: meandiff=vector(1,nlstate);
2857:
1.266 brouard 2858: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2859: oldm=oldms; savm=savms;
2860:
2861: /* Starting with matrix unity */
2862: for (ii=1;ii<=nlstate+ndeath;ii++)
2863: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2864: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2865: }
2866:
2867: cov[1]=1.;
2868:
2869: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2870: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2871: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2872: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2873: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2874: ncvloop++;
1.218 brouard 2875: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2876: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2877: /* Covariates have to be included here again */
2878: cov[2]=agefin;
2879: if(nagesqr==1)
2880: cov[3]= agefin*agefin;;
1.242 brouard 2881: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2882: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2883: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2884: /* 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 2885: }
2886: /* for (k=1; k<=cptcovn;k++) { */
2887: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2888: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2889: /* /\* 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])]); *\/ */
2890: /* } */
2891: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2892: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2893: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2894: /* 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]); */
2895: }
2896: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2897: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2898: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2899: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2900: for (k=1; k<=cptcovage;k++){ /* For product with age */
2901: if(Dummy[Tvar[Tage[k]]]){
2902: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2903: } else{
2904: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2905: }
2906: /* 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]); */
2907: }
2908: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2909: /* 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]); */
2910: if(Dummy[Tvard[k][1]==0]){
2911: if(Dummy[Tvard[k][2]==0]){
2912: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2913: }else{
2914: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2915: }
2916: }else{
2917: if(Dummy[Tvard[k][2]==0]){
2918: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2919: }else{
2920: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2921: }
2922: }
1.217 brouard 2923: }
2924:
2925: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2926: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2927: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2928: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2929: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2930: /* ij should be linked to the correct index of cov */
2931: /* age and covariate values ij are in 'cov', but we need to pass
2932: * ij for the observed prevalence at age and status and covariate
2933: * number: prevacurrent[(int)agefin][ii][ij]
2934: */
2935: /* 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 *\/ */
2936: /* 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 *\/ */
2937: 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 2938: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2939: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2940: /* for(i=1; i<=nlstate+ndeath; i++) { */
2941: /* printf("%d newm= ",i); */
2942: /* for(j=1;j<=nlstate+ndeath;j++) { */
2943: /* printf("%f ",newm[i][j]); */
2944: /* } */
2945: /* printf("oldm * "); */
2946: /* for(j=1;j<=nlstate+ndeath;j++) { */
2947: /* printf("%f ",oldm[i][j]); */
2948: /* } */
1.268 brouard 2949: /* printf(" bmmij "); */
1.266 brouard 2950: /* for(j=1;j<=nlstate+ndeath;j++) { */
2951: /* printf("%f ",pmmij[i][j]); */
2952: /* } */
2953: /* printf("\n"); */
2954: /* } */
2955: /* } */
1.217 brouard 2956: savm=oldm;
2957: oldm=newm;
1.266 brouard 2958:
1.217 brouard 2959: for(j=1; j<=nlstate; j++){
2960: max[j]=0.;
2961: min[j]=1.;
2962: }
2963: for(j=1; j<=nlstate; j++){
2964: for(i=1;i<=nlstate;i++){
1.234 brouard 2965: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2966: bprlim[i][j]= newm[i][j];
2967: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2968: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2969: }
2970: }
1.218 brouard 2971:
1.217 brouard 2972: maxmax=0.;
2973: for(i=1; i<=nlstate; i++){
2974: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2975: maxmax=FMAX(maxmax,meandiff[i]);
2976: /* 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 2977: } /* i loop */
1.217 brouard 2978: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2979: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2980: if(maxmax < ftolpl){
1.220 brouard 2981: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2982: free_vector(min,1,nlstate);
2983: free_vector(max,1,nlstate);
2984: free_vector(meandiff,1,nlstate);
2985: return bprlim;
2986: }
1.288 brouard 2987: } /* agefin loop */
1.217 brouard 2988: /* After some age loop it doesn't converge */
1.288 brouard 2989: if(!first){
1.247 brouard 2990: first=1;
2991: 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\
2992: 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);
2993: }
2994: 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 2995: 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);
2996: /* 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); */
2997: free_vector(min,1,nlstate);
2998: free_vector(max,1,nlstate);
2999: free_vector(meandiff,1,nlstate);
3000:
3001: return bprlim; /* should not reach here */
3002: }
3003:
1.126 brouard 3004: /*************** transition probabilities ***************/
3005:
3006: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
3007: {
1.138 brouard 3008: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 3009: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 3010: model to the ncovmodel covariates (including constant and age).
3011: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3012: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3013: ncth covariate in the global vector x is given by the formula:
3014: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3015: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3016: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3017: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 3018: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 3019: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 3020: Sum on j ps[i][j] should equal to 1.
1.138 brouard 3021: */
3022: double s1, lnpijopii;
1.126 brouard 3023: /*double t34;*/
1.164 brouard 3024: int i,j, nc, ii, jj;
1.126 brouard 3025:
1.223 brouard 3026: for(i=1; i<= nlstate; i++){
3027: for(j=1; j<i;j++){
3028: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3029: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3030: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3031: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3032: }
3033: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3034: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3035: }
3036: for(j=i+1; j<=nlstate+ndeath;j++){
3037: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3038: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3039: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3040: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3041: }
3042: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3043: }
3044: }
1.218 brouard 3045:
1.223 brouard 3046: for(i=1; i<= nlstate; i++){
3047: s1=0;
3048: for(j=1; j<i; j++){
3049: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3050: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3051: }
3052: for(j=i+1; j<=nlstate+ndeath; j++){
3053: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3054: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3055: }
3056: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3057: ps[i][i]=1./(s1+1.);
3058: /* Computing other pijs */
3059: for(j=1; j<i; j++)
3060: ps[i][j]= exp(ps[i][j])*ps[i][i];
3061: for(j=i+1; j<=nlstate+ndeath; j++)
3062: ps[i][j]= exp(ps[i][j])*ps[i][i];
3063: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3064: } /* end i */
1.218 brouard 3065:
1.223 brouard 3066: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3067: for(jj=1; jj<= nlstate+ndeath; jj++){
3068: ps[ii][jj]=0;
3069: ps[ii][ii]=1;
3070: }
3071: }
1.294 brouard 3072:
3073:
1.223 brouard 3074: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3075: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3076: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3077: /* } */
3078: /* printf("\n "); */
3079: /* } */
3080: /* printf("\n ");printf("%lf ",cov[2]);*/
3081: /*
3082: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3083: goto end;*/
1.266 brouard 3084: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3085: }
3086:
1.218 brouard 3087: /*************** backward transition probabilities ***************/
3088:
3089: /* 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 ) */
3090: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3091: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3092: {
1.302 brouard 3093: /* 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 3094: * 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 3095: */
1.218 brouard 3096: int i, ii, j,k;
1.222 brouard 3097:
3098: double **out, **pmij();
3099: double sumnew=0.;
1.218 brouard 3100: double agefin;
1.292 brouard 3101: 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 3102: double **dnewm, **dsavm, **doldm;
3103: double **bbmij;
3104:
1.218 brouard 3105: doldm=ddoldms; /* global pointers */
1.222 brouard 3106: dnewm=ddnewms;
3107: dsavm=ddsavms;
3108:
3109: agefin=cov[2];
1.268 brouard 3110: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3111: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3112: the observed prevalence (with this covariate ij) at beginning of transition */
3113: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3114:
3115: /* P_x */
1.266 brouard 3116: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3117: /* outputs pmmij which is a stochastic matrix in row */
3118:
3119: /* Diag(w_x) */
1.292 brouard 3120: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3121: sumnew=0.;
1.269 brouard 3122: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3123: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3124: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3125: sumnew+=prevacurrent[(int)agefin][ii][ij];
3126: }
3127: if(sumnew >0.01){ /* At least some value in the prevalence */
3128: for (ii=1;ii<=nlstate+ndeath;ii++){
3129: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3130: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3131: }
3132: }else{
3133: for (ii=1;ii<=nlstate+ndeath;ii++){
3134: for (j=1;j<=nlstate+ndeath;j++)
3135: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3136: }
3137: /* if(sumnew <0.9){ */
3138: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3139: /* } */
3140: }
3141: k3=0.0; /* We put the last diagonal to 0 */
3142: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3143: doldm[ii][ii]= k3;
3144: }
3145: /* End doldm, At the end doldm is diag[(w_i)] */
3146:
1.292 brouard 3147: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3148: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3149:
1.292 brouard 3150: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3151: /* 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 3152: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3153: sumnew=0.;
1.222 brouard 3154: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3155: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3156: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3157: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3158: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3159: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3160: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3161: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3162: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3163: /* }else */
1.268 brouard 3164: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3165: } /*End ii */
3166: } /* 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 */
3167:
1.292 brouard 3168: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3169: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3170: /* end bmij */
1.266 brouard 3171: return ps; /*pointer is unchanged */
1.218 brouard 3172: }
1.217 brouard 3173: /*************** transition probabilities ***************/
3174:
1.218 brouard 3175: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3176: {
3177: /* According to parameters values stored in x and the covariate's values stored in cov,
3178: computes the probability to be observed in state j being in state i by appying the
3179: model to the ncovmodel covariates (including constant and age).
3180: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3181: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3182: ncth covariate in the global vector x is given by the formula:
3183: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3184: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3185: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3186: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3187: Outputs ps[i][j] the probability to be observed in j being in j according to
3188: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3189: */
3190: double s1, lnpijopii;
3191: /*double t34;*/
3192: int i,j, nc, ii, jj;
3193:
1.234 brouard 3194: for(i=1; i<= nlstate; i++){
3195: for(j=1; j<i;j++){
3196: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3197: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3198: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3199: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3200: }
3201: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3202: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3203: }
3204: for(j=i+1; j<=nlstate+ndeath;j++){
3205: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3206: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3207: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3208: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3209: }
3210: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3211: }
3212: }
3213:
3214: for(i=1; i<= nlstate; i++){
3215: s1=0;
3216: for(j=1; j<i; j++){
3217: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3218: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3219: }
3220: for(j=i+1; j<=nlstate+ndeath; j++){
3221: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3222: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3223: }
3224: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3225: ps[i][i]=1./(s1+1.);
3226: /* Computing other pijs */
3227: for(j=1; j<i; j++)
3228: ps[i][j]= exp(ps[i][j])*ps[i][i];
3229: for(j=i+1; j<=nlstate+ndeath; j++)
3230: ps[i][j]= exp(ps[i][j])*ps[i][i];
3231: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3232: } /* end i */
3233:
3234: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3235: for(jj=1; jj<= nlstate+ndeath; jj++){
3236: ps[ii][jj]=0;
3237: ps[ii][ii]=1;
3238: }
3239: }
1.296 brouard 3240: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3241: for(jj=1; jj<= nlstate+ndeath; jj++){
3242: s1=0.;
3243: for(ii=1; ii<= nlstate+ndeath; ii++){
3244: s1+=ps[ii][jj];
3245: }
3246: for(ii=1; ii<= nlstate; ii++){
3247: ps[ii][jj]=ps[ii][jj]/s1;
3248: }
3249: }
3250: /* Transposition */
3251: for(jj=1; jj<= nlstate+ndeath; jj++){
3252: for(ii=jj; ii<= nlstate+ndeath; ii++){
3253: s1=ps[ii][jj];
3254: ps[ii][jj]=ps[jj][ii];
3255: ps[jj][ii]=s1;
3256: }
3257: }
3258: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3259: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3260: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3261: /* } */
3262: /* printf("\n "); */
3263: /* } */
3264: /* printf("\n ");printf("%lf ",cov[2]);*/
3265: /*
3266: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3267: goto end;*/
3268: return ps;
1.217 brouard 3269: }
3270:
3271:
1.126 brouard 3272: /**************** Product of 2 matrices ******************/
3273:
1.145 brouard 3274: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3275: {
3276: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3277: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3278: /* in, b, out are matrice of pointers which should have been initialized
3279: before: only the contents of out is modified. The function returns
3280: a pointer to pointers identical to out */
1.145 brouard 3281: int i, j, k;
1.126 brouard 3282: for(i=nrl; i<= nrh; i++)
1.145 brouard 3283: for(k=ncolol; k<=ncoloh; k++){
3284: out[i][k]=0.;
3285: for(j=ncl; j<=nch; j++)
3286: out[i][k] +=in[i][j]*b[j][k];
3287: }
1.126 brouard 3288: return out;
3289: }
3290:
3291:
3292: /************* Higher Matrix Product ***************/
3293:
1.235 brouard 3294: 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 3295: {
1.218 brouard 3296: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3297: 'nhstepm*hstepm*stepm' months (i.e. until
3298: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3299: nhstepm*hstepm matrices.
3300: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3301: (typically every 2 years instead of every month which is too big
3302: for the memory).
3303: Model is determined by parameters x and covariates have to be
3304: included manually here.
3305:
3306: */
3307:
3308: int i, j, d, h, k;
1.131 brouard 3309: double **out, cov[NCOVMAX+1];
1.126 brouard 3310: double **newm;
1.187 brouard 3311: double agexact;
1.214 brouard 3312: double agebegin, ageend;
1.126 brouard 3313:
3314: /* Hstepm could be zero and should return the unit matrix */
3315: for (i=1;i<=nlstate+ndeath;i++)
3316: for (j=1;j<=nlstate+ndeath;j++){
3317: oldm[i][j]=(i==j ? 1.0 : 0.0);
3318: po[i][j][0]=(i==j ? 1.0 : 0.0);
3319: }
3320: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3321: for(h=1; h <=nhstepm; h++){
3322: for(d=1; d <=hstepm; d++){
3323: newm=savm;
3324: /* Covariates have to be included here again */
3325: cov[1]=1.;
1.214 brouard 3326: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3327: cov[2]=agexact;
3328: if(nagesqr==1)
1.227 brouard 3329: cov[3]= agexact*agexact;
1.235 brouard 3330: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3331: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3332: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3333: /* 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)); */
3334: }
3335: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3336: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3337: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3338: /* 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]); */
3339: }
3340: for (k=1; k<=cptcovage;k++){
3341: if(Dummy[Tvar[Tage[k]]]){
3342: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3343: } else{
3344: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3345: }
3346: /* 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]); */
3347: }
3348: for (k=1; k<=cptcovprod;k++){ /* */
3349: /* 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]); */
3350: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3351: }
3352: /* for (k=1; k<=cptcovn;k++) */
3353: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3354: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3355: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3356: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3357: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3358:
3359:
1.126 brouard 3360: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3361: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3362: /* right multiplication of oldm by the current matrix */
1.126 brouard 3363: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3364: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3365: /* if((int)age == 70){ */
3366: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3367: /* for(i=1; i<=nlstate+ndeath; i++) { */
3368: /* printf("%d pmmij ",i); */
3369: /* for(j=1;j<=nlstate+ndeath;j++) { */
3370: /* printf("%f ",pmmij[i][j]); */
3371: /* } */
3372: /* printf(" oldm "); */
3373: /* for(j=1;j<=nlstate+ndeath;j++) { */
3374: /* printf("%f ",oldm[i][j]); */
3375: /* } */
3376: /* printf("\n"); */
3377: /* } */
3378: /* } */
1.126 brouard 3379: savm=oldm;
3380: oldm=newm;
3381: }
3382: for(i=1; i<=nlstate+ndeath; i++)
3383: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3384: po[i][j][h]=newm[i][j];
3385: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3386: }
1.128 brouard 3387: /*printf("h=%d ",h);*/
1.126 brouard 3388: } /* end h */
1.267 brouard 3389: /* printf("\n H=%d \n",h); */
1.126 brouard 3390: return po;
3391: }
3392:
1.217 brouard 3393: /************* Higher Back Matrix Product ***************/
1.218 brouard 3394: /* 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 3395: 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 3396: {
1.266 brouard 3397: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3398: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3399: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3400: nhstepm*hstepm matrices.
3401: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3402: (typically every 2 years instead of every month which is too big
1.217 brouard 3403: for the memory).
1.218 brouard 3404: Model is determined by parameters x and covariates have to be
1.266 brouard 3405: included manually here. Then we use a call to bmij(x and cov)
3406: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3407: */
1.217 brouard 3408:
3409: int i, j, d, h, k;
1.266 brouard 3410: double **out, cov[NCOVMAX+1], **bmij();
3411: double **newm, ***newmm;
1.217 brouard 3412: double agexact;
3413: double agebegin, ageend;
1.222 brouard 3414: double **oldm, **savm;
1.217 brouard 3415:
1.266 brouard 3416: newmm=po; /* To be saved */
3417: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3418: /* Hstepm could be zero and should return the unit matrix */
3419: for (i=1;i<=nlstate+ndeath;i++)
3420: for (j=1;j<=nlstate+ndeath;j++){
3421: oldm[i][j]=(i==j ? 1.0 : 0.0);
3422: po[i][j][0]=(i==j ? 1.0 : 0.0);
3423: }
3424: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3425: for(h=1; h <=nhstepm; h++){
3426: for(d=1; d <=hstepm; d++){
3427: newm=savm;
3428: /* Covariates have to be included here again */
3429: cov[1]=1.;
1.271 brouard 3430: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3431: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3432: cov[2]=agexact;
3433: if(nagesqr==1)
1.222 brouard 3434: cov[3]= agexact*agexact;
1.266 brouard 3435: for (k=1; k<=cptcovn;k++){
3436: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3437: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3438: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3439: /* 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)); */
3440: }
1.267 brouard 3441: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3442: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3443: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3444: /* 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]); */
3445: }
3446: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3447: if(Dummy[Tvar[Tage[k]]]){
3448: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3449: } else{
3450: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3451: }
3452: /* 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]); */
3453: }
3454: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3455: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3456: }
1.217 brouard 3457: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3458: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3459:
1.218 brouard 3460: /* Careful transposed matrix */
1.266 brouard 3461: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3462: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3463: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3464: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3465: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3466: /* if((int)age == 70){ */
3467: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3468: /* for(i=1; i<=nlstate+ndeath; i++) { */
3469: /* printf("%d pmmij ",i); */
3470: /* for(j=1;j<=nlstate+ndeath;j++) { */
3471: /* printf("%f ",pmmij[i][j]); */
3472: /* } */
3473: /* printf(" oldm "); */
3474: /* for(j=1;j<=nlstate+ndeath;j++) { */
3475: /* printf("%f ",oldm[i][j]); */
3476: /* } */
3477: /* printf("\n"); */
3478: /* } */
3479: /* } */
3480: savm=oldm;
3481: oldm=newm;
3482: }
3483: for(i=1; i<=nlstate+ndeath; i++)
3484: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3485: po[i][j][h]=newm[i][j];
1.268 brouard 3486: /* if(h==nhstepm) */
3487: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3488: }
1.268 brouard 3489: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3490: } /* end h */
1.268 brouard 3491: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3492: return po;
3493: }
3494:
3495:
1.162 brouard 3496: #ifdef NLOPT
3497: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3498: double fret;
3499: double *xt;
3500: int j;
3501: myfunc_data *d2 = (myfunc_data *) pd;
3502: /* xt = (p1-1); */
3503: xt=vector(1,n);
3504: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3505:
3506: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3507: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3508: printf("Function = %.12lf ",fret);
3509: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3510: printf("\n");
3511: free_vector(xt,1,n);
3512: return fret;
3513: }
3514: #endif
1.126 brouard 3515:
3516: /*************** log-likelihood *************/
3517: double func( double *x)
3518: {
1.226 brouard 3519: int i, ii, j, k, mi, d, kk;
3520: int ioffset=0;
3521: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3522: double **out;
3523: double lli; /* Individual log likelihood */
3524: int s1, s2;
1.228 brouard 3525: 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 3526: double bbh, survp;
3527: long ipmx;
3528: double agexact;
3529: /*extern weight */
3530: /* We are differentiating ll according to initial status */
3531: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3532: /*for(i=1;i<imx;i++)
3533: printf(" %d\n",s[4][i]);
3534: */
1.162 brouard 3535:
1.226 brouard 3536: ++countcallfunc;
1.162 brouard 3537:
1.226 brouard 3538: cov[1]=1.;
1.126 brouard 3539:
1.226 brouard 3540: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3541: ioffset=0;
1.226 brouard 3542: if(mle==1){
3543: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3544: /* Computes the values of the ncovmodel covariates of the model
3545: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3546: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3547: to be observed in j being in i according to the model.
3548: */
1.243 brouard 3549: ioffset=2+nagesqr ;
1.233 brouard 3550: /* Fixed */
1.234 brouard 3551: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3552: 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)*/
3553: }
1.226 brouard 3554: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3555: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3556: has been calculated etc */
3557: /* For an individual i, wav[i] gives the number of effective waves */
3558: /* We compute the contribution to Likelihood of each effective transition
3559: mw[mi][i] is real wave of the mi th effectve wave */
3560: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3561: s2=s[mw[mi+1][i]][i];
3562: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3563: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3564: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3565: */
3566: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3567: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3568: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3569: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3570: }
3571: for (ii=1;ii<=nlstate+ndeath;ii++)
3572: for (j=1;j<=nlstate+ndeath;j++){
3573: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3574: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3575: }
3576: for(d=0; d<dh[mi][i]; d++){
3577: newm=savm;
3578: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3579: cov[2]=agexact;
3580: if(nagesqr==1)
3581: cov[3]= agexact*agexact; /* Should be changed here */
3582: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3583: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3584: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3585: else
3586: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3587: }
3588: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3589: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3590: savm=oldm;
3591: oldm=newm;
3592: } /* end mult */
3593:
3594: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3595: /* But now since version 0.9 we anticipate for bias at large stepm.
3596: * If stepm is larger than one month (smallest stepm) and if the exact delay
3597: * (in months) between two waves is not a multiple of stepm, we rounded to
3598: * the nearest (and in case of equal distance, to the lowest) interval but now
3599: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3600: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3601: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3602: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3603: * -stepm/2 to stepm/2 .
3604: * For stepm=1 the results are the same as for previous versions of Imach.
3605: * For stepm > 1 the results are less biased than in previous versions.
3606: */
1.234 brouard 3607: s1=s[mw[mi][i]][i];
3608: s2=s[mw[mi+1][i]][i];
3609: bbh=(double)bh[mi][i]/(double)stepm;
3610: /* bias bh is positive if real duration
3611: * is higher than the multiple of stepm and negative otherwise.
3612: */
3613: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3614: if( s2 > nlstate){
3615: /* i.e. if s2 is a death state and if the date of death is known
3616: then the contribution to the likelihood is the probability to
3617: die between last step unit time and current step unit time,
3618: which is also equal to probability to die before dh
3619: minus probability to die before dh-stepm .
3620: In version up to 0.92 likelihood was computed
3621: as if date of death was unknown. Death was treated as any other
3622: health state: the date of the interview describes the actual state
3623: and not the date of a change in health state. The former idea was
3624: to consider that at each interview the state was recorded
3625: (healthy, disable or death) and IMaCh was corrected; but when we
3626: introduced the exact date of death then we should have modified
3627: the contribution of an exact death to the likelihood. This new
3628: contribution is smaller and very dependent of the step unit
3629: stepm. It is no more the probability to die between last interview
3630: and month of death but the probability to survive from last
3631: interview up to one month before death multiplied by the
3632: probability to die within a month. Thanks to Chris
3633: Jackson for correcting this bug. Former versions increased
3634: mortality artificially. The bad side is that we add another loop
3635: which slows down the processing. The difference can be up to 10%
3636: lower mortality.
3637: */
3638: /* If, at the beginning of the maximization mostly, the
3639: cumulative probability or probability to be dead is
3640: constant (ie = 1) over time d, the difference is equal to
3641: 0. out[s1][3] = savm[s1][3]: probability, being at state
3642: s1 at precedent wave, to be dead a month before current
3643: wave is equal to probability, being at state s1 at
3644: precedent wave, to be dead at mont of the current
3645: wave. Then the observed probability (that this person died)
3646: is null according to current estimated parameter. In fact,
3647: it should be very low but not zero otherwise the log go to
3648: infinity.
3649: */
1.183 brouard 3650: /* #ifdef INFINITYORIGINAL */
3651: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3652: /* #else */
3653: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3654: /* lli=log(mytinydouble); */
3655: /* else */
3656: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3657: /* #endif */
1.226 brouard 3658: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3659:
1.226 brouard 3660: } else if ( s2==-1 ) { /* alive */
3661: for (j=1,survp=0. ; j<=nlstate; j++)
3662: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3663: /*survp += out[s1][j]; */
3664: lli= log(survp);
3665: }
3666: else if (s2==-4) {
3667: for (j=3,survp=0. ; j<=nlstate; j++)
3668: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3669: lli= log(survp);
3670: }
3671: else if (s2==-5) {
3672: for (j=1,survp=0. ; j<=2; j++)
3673: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3674: lli= log(survp);
3675: }
3676: else{
3677: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3678: /* 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 */
3679: }
3680: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3681: /*if(lli ==000.0)*/
3682: /*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); */
3683: ipmx +=1;
3684: sw += weight[i];
3685: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3686: /* if (lli < log(mytinydouble)){ */
3687: /* 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); */
3688: /* 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]); */
3689: /* } */
3690: } /* end of wave */
3691: } /* end of individual */
3692: } else if(mle==2){
3693: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3694: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3695: for(mi=1; mi<= wav[i]-1; mi++){
3696: for (ii=1;ii<=nlstate+ndeath;ii++)
3697: for (j=1;j<=nlstate+ndeath;j++){
3698: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3699: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3700: }
3701: for(d=0; d<=dh[mi][i]; d++){
3702: newm=savm;
3703: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3704: cov[2]=agexact;
3705: if(nagesqr==1)
3706: cov[3]= agexact*agexact;
3707: for (kk=1; kk<=cptcovage;kk++) {
3708: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3709: }
3710: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3711: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3712: savm=oldm;
3713: oldm=newm;
3714: } /* end mult */
3715:
3716: s1=s[mw[mi][i]][i];
3717: s2=s[mw[mi+1][i]][i];
3718: bbh=(double)bh[mi][i]/(double)stepm;
3719: 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 */
3720: ipmx +=1;
3721: sw += weight[i];
3722: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3723: } /* end of wave */
3724: } /* end of individual */
3725: } else if(mle==3){ /* exponential inter-extrapolation */
3726: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3727: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3728: for(mi=1; mi<= wav[i]-1; mi++){
3729: for (ii=1;ii<=nlstate+ndeath;ii++)
3730: for (j=1;j<=nlstate+ndeath;j++){
3731: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3732: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3733: }
3734: for(d=0; d<dh[mi][i]; d++){
3735: newm=savm;
3736: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3737: cov[2]=agexact;
3738: if(nagesqr==1)
3739: cov[3]= agexact*agexact;
3740: for (kk=1; kk<=cptcovage;kk++) {
3741: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3742: }
3743: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3744: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3745: savm=oldm;
3746: oldm=newm;
3747: } /* end mult */
3748:
3749: s1=s[mw[mi][i]][i];
3750: s2=s[mw[mi+1][i]][i];
3751: bbh=(double)bh[mi][i]/(double)stepm;
3752: 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 */
3753: ipmx +=1;
3754: sw += weight[i];
3755: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3756: } /* end of wave */
3757: } /* end of individual */
3758: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3759: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3760: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3761: for(mi=1; mi<= wav[i]-1; mi++){
3762: for (ii=1;ii<=nlstate+ndeath;ii++)
3763: for (j=1;j<=nlstate+ndeath;j++){
3764: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3765: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3766: }
3767: for(d=0; d<dh[mi][i]; d++){
3768: newm=savm;
3769: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3770: cov[2]=agexact;
3771: if(nagesqr==1)
3772: cov[3]= agexact*agexact;
3773: for (kk=1; kk<=cptcovage;kk++) {
3774: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3775: }
1.126 brouard 3776:
1.226 brouard 3777: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3778: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3779: savm=oldm;
3780: oldm=newm;
3781: } /* end mult */
3782:
3783: s1=s[mw[mi][i]][i];
3784: s2=s[mw[mi+1][i]][i];
3785: if( s2 > nlstate){
3786: lli=log(out[s1][s2] - savm[s1][s2]);
3787: } else if ( s2==-1 ) { /* alive */
3788: for (j=1,survp=0. ; j<=nlstate; j++)
3789: survp += out[s1][j];
3790: lli= log(survp);
3791: }else{
3792: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3793: }
3794: ipmx +=1;
3795: sw += weight[i];
3796: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3797: /* 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 3798: } /* end of wave */
3799: } /* end of individual */
3800: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3801: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3802: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3803: for(mi=1; mi<= wav[i]-1; mi++){
3804: for (ii=1;ii<=nlstate+ndeath;ii++)
3805: for (j=1;j<=nlstate+ndeath;j++){
3806: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3807: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3808: }
3809: for(d=0; d<dh[mi][i]; d++){
3810: newm=savm;
3811: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3812: cov[2]=agexact;
3813: if(nagesqr==1)
3814: cov[3]= agexact*agexact;
3815: for (kk=1; kk<=cptcovage;kk++) {
3816: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3817: }
1.126 brouard 3818:
1.226 brouard 3819: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3820: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3821: savm=oldm;
3822: oldm=newm;
3823: } /* end mult */
3824:
3825: s1=s[mw[mi][i]][i];
3826: s2=s[mw[mi+1][i]][i];
3827: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3828: ipmx +=1;
3829: sw += weight[i];
3830: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3831: /*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]);*/
3832: } /* end of wave */
3833: } /* end of individual */
3834: } /* End of if */
3835: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3836: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3837: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3838: return -l;
1.126 brouard 3839: }
3840:
3841: /*************** log-likelihood *************/
3842: double funcone( double *x)
3843: {
1.228 brouard 3844: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3845: int i, ii, j, k, mi, d, kk;
1.228 brouard 3846: int ioffset=0;
1.131 brouard 3847: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3848: double **out;
3849: double lli; /* Individual log likelihood */
3850: double llt;
3851: int s1, s2;
1.228 brouard 3852: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3853:
1.126 brouard 3854: double bbh, survp;
1.187 brouard 3855: double agexact;
1.214 brouard 3856: double agebegin, ageend;
1.126 brouard 3857: /*extern weight */
3858: /* We are differentiating ll according to initial status */
3859: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3860: /*for(i=1;i<imx;i++)
3861: printf(" %d\n",s[4][i]);
3862: */
3863: cov[1]=1.;
3864:
3865: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3866: ioffset=0;
3867: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3868: /* ioffset=2+nagesqr+cptcovage; */
3869: ioffset=2+nagesqr;
1.232 brouard 3870: /* Fixed */
1.224 brouard 3871: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3872: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
1.311 brouard 3873: 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 3874: 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)*/
3875: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3876: /* cov[2+6]=covar[Tvar[6]][i]; */
3877: /* cov[2+6]=covar[2][i]; V2 */
3878: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3879: /* cov[2+7]=covar[Tvar[7]][i]; */
3880: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3881: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3882: /* cov[2+9]=covar[Tvar[9]][i]; */
3883: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3884: }
1.232 brouard 3885: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3886: /* 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?)*\/ */
3887: /* } */
1.231 brouard 3888: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3889: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3890: /* } */
1.225 brouard 3891:
1.233 brouard 3892:
3893: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3894: /* Wave varying (but not age varying) */
3895: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3896: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3897: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3898: }
1.232 brouard 3899: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3900: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3901: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3902: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3903: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3904: /* 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 3905: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3906: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3907: /* /\* 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]); *\/ */
3908: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3909: /* } */
1.126 brouard 3910: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3911: for (j=1;j<=nlstate+ndeath;j++){
3912: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3913: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3914: }
1.214 brouard 3915:
3916: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3917: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3918: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3919: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3920: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3921: and mw[mi+1][i]. dh depends on stepm.*/
3922: newm=savm;
1.247 brouard 3923: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3924: cov[2]=agexact;
3925: if(nagesqr==1)
3926: cov[3]= agexact*agexact;
3927: for (kk=1; kk<=cptcovage;kk++) {
3928: if(!FixedV[Tvar[Tage[kk]]])
3929: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3930: else
3931: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3932: }
3933: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3934: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3935: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3936: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3937: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3938: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3939: savm=oldm;
3940: oldm=newm;
1.126 brouard 3941: } /* end mult */
3942:
3943: s1=s[mw[mi][i]][i];
3944: s2=s[mw[mi+1][i]][i];
1.217 brouard 3945: /* if(s2==-1){ */
1.268 brouard 3946: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3947: /* /\* exit(1); *\/ */
3948: /* } */
1.126 brouard 3949: bbh=(double)bh[mi][i]/(double)stepm;
3950: /* bias is positive if real duration
3951: * is higher than the multiple of stepm and negative otherwise.
3952: */
3953: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3954: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3955: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3956: for (j=1,survp=0. ; j<=nlstate; j++)
3957: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3958: lli= log(survp);
1.126 brouard 3959: }else if (mle==1){
1.242 brouard 3960: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3961: } else if(mle==2){
1.242 brouard 3962: 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 3963: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3964: 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 3965: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3966: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3967: } else{ /* mle=0 back to 1 */
1.242 brouard 3968: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3969: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3970: } /* End of if */
3971: ipmx +=1;
3972: sw += weight[i];
3973: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3974: /*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 3975: if(globpr){
1.246 brouard 3976: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3977: %11.6f %11.6f %11.6f ", \
1.242 brouard 3978: 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 3979: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3980: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3981: llt +=ll[k]*gipmx/gsw;
3982: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3983: }
3984: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3985: }
1.232 brouard 3986: } /* end of wave */
3987: } /* end of individual */
3988: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3989: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3990: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3991: if(globpr==0){ /* First time we count the contributions and weights */
3992: gipmx=ipmx;
3993: gsw=sw;
3994: }
3995: return -l;
1.126 brouard 3996: }
3997:
3998:
3999: /*************** function likelione ***********/
1.292 brouard 4000: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 4001: {
4002: /* This routine should help understanding what is done with
4003: the selection of individuals/waves and
4004: to check the exact contribution to the likelihood.
4005: Plotting could be done.
4006: */
4007: int k;
4008:
4009: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 4010: strcpy(fileresilk,"ILK_");
1.202 brouard 4011: strcat(fileresilk,fileresu);
1.126 brouard 4012: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
4013: printf("Problem with resultfile: %s\n", fileresilk);
4014: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
4015: }
1.214 brouard 4016: 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");
4017: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 4018: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
4019: for(k=1; k<=nlstate; k++)
4020: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
4021: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
4022: }
4023:
1.292 brouard 4024: *fretone=(*func)(p);
1.126 brouard 4025: if(*globpri !=0){
4026: fclose(ficresilk);
1.205 brouard 4027: if (mle ==0)
4028: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
4029: else if(mle >=1)
4030: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
4031: 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 4032: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 4033:
4034: for (k=1; k<= nlstate ; k++) {
1.211 brouard 4035: 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 4036: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
4037: }
1.207 brouard 4038: 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 4039: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4040: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 4041: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4042: fflush(fichtm);
1.205 brouard 4043: }
1.126 brouard 4044: return;
4045: }
4046:
4047:
4048: /*********** Maximum Likelihood Estimation ***************/
4049:
4050: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4051: {
1.165 brouard 4052: int i,j, iter=0;
1.126 brouard 4053: double **xi;
4054: double fret;
4055: double fretone; /* Only one call to likelihood */
4056: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4057:
4058: #ifdef NLOPT
4059: int creturn;
4060: nlopt_opt opt;
4061: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4062: double *lb;
4063: double minf; /* the minimum objective value, upon return */
4064: double * p1; /* Shifted parameters from 0 instead of 1 */
4065: myfunc_data dinst, *d = &dinst;
4066: #endif
4067:
4068:
1.126 brouard 4069: xi=matrix(1,npar,1,npar);
4070: for (i=1;i<=npar;i++)
4071: for (j=1;j<=npar;j++)
4072: xi[i][j]=(i==j ? 1.0 : 0.0);
4073: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4074: strcpy(filerespow,"POW_");
1.126 brouard 4075: strcat(filerespow,fileres);
4076: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4077: printf("Problem with resultfile: %s\n", filerespow);
4078: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4079: }
4080: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4081: for (i=1;i<=nlstate;i++)
4082: for(j=1;j<=nlstate+ndeath;j++)
4083: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4084: fprintf(ficrespow,"\n");
1.162 brouard 4085: #ifdef POWELL
1.126 brouard 4086: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4087: #endif
1.126 brouard 4088:
1.162 brouard 4089: #ifdef NLOPT
4090: #ifdef NEWUOA
4091: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4092: #else
4093: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4094: #endif
4095: lb=vector(0,npar-1);
4096: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4097: nlopt_set_lower_bounds(opt, lb);
4098: nlopt_set_initial_step1(opt, 0.1);
4099:
4100: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4101: d->function = func;
4102: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4103: nlopt_set_min_objective(opt, myfunc, d);
4104: nlopt_set_xtol_rel(opt, ftol);
4105: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4106: printf("nlopt failed! %d\n",creturn);
4107: }
4108: else {
4109: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4110: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4111: iter=1; /* not equal */
4112: }
4113: nlopt_destroy(opt);
4114: #endif
1.126 brouard 4115: free_matrix(xi,1,npar,1,npar);
4116: fclose(ficrespow);
1.203 brouard 4117: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4118: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4119: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4120:
4121: }
4122:
4123: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4124: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4125: {
4126: double **a,**y,*x,pd;
1.203 brouard 4127: /* double **hess; */
1.164 brouard 4128: int i, j;
1.126 brouard 4129: int *indx;
4130:
4131: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4132: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4133: void lubksb(double **a, int npar, int *indx, double b[]) ;
4134: void ludcmp(double **a, int npar, int *indx, double *d) ;
4135: double gompertz(double p[]);
1.203 brouard 4136: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4137:
4138: printf("\nCalculation of the hessian matrix. Wait...\n");
4139: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4140: for (i=1;i<=npar;i++){
1.203 brouard 4141: printf("%d-",i);fflush(stdout);
4142: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4143:
4144: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4145:
4146: /* printf(" %f ",p[i]);
4147: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4148: }
4149:
4150: for (i=1;i<=npar;i++) {
4151: for (j=1;j<=npar;j++) {
4152: if (j>i) {
1.203 brouard 4153: printf(".%d-%d",i,j);fflush(stdout);
4154: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4155: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4156:
4157: hess[j][i]=hess[i][j];
4158: /*printf(" %lf ",hess[i][j]);*/
4159: }
4160: }
4161: }
4162: printf("\n");
4163: fprintf(ficlog,"\n");
4164:
4165: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4166: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4167:
4168: a=matrix(1,npar,1,npar);
4169: y=matrix(1,npar,1,npar);
4170: x=vector(1,npar);
4171: indx=ivector(1,npar);
4172: for (i=1;i<=npar;i++)
4173: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4174: ludcmp(a,npar,indx,&pd);
4175:
4176: for (j=1;j<=npar;j++) {
4177: for (i=1;i<=npar;i++) x[i]=0;
4178: x[j]=1;
4179: lubksb(a,npar,indx,x);
4180: for (i=1;i<=npar;i++){
4181: matcov[i][j]=x[i];
4182: }
4183: }
4184:
4185: printf("\n#Hessian matrix#\n");
4186: fprintf(ficlog,"\n#Hessian matrix#\n");
4187: for (i=1;i<=npar;i++) {
4188: for (j=1;j<=npar;j++) {
1.203 brouard 4189: printf("%.6e ",hess[i][j]);
4190: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4191: }
4192: printf("\n");
4193: fprintf(ficlog,"\n");
4194: }
4195:
1.203 brouard 4196: /* printf("\n#Covariance matrix#\n"); */
4197: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4198: /* for (i=1;i<=npar;i++) { */
4199: /* for (j=1;j<=npar;j++) { */
4200: /* printf("%.6e ",matcov[i][j]); */
4201: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4202: /* } */
4203: /* printf("\n"); */
4204: /* fprintf(ficlog,"\n"); */
4205: /* } */
4206:
1.126 brouard 4207: /* Recompute Inverse */
1.203 brouard 4208: /* for (i=1;i<=npar;i++) */
4209: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4210: /* ludcmp(a,npar,indx,&pd); */
4211:
4212: /* printf("\n#Hessian matrix recomputed#\n"); */
4213:
4214: /* for (j=1;j<=npar;j++) { */
4215: /* for (i=1;i<=npar;i++) x[i]=0; */
4216: /* x[j]=1; */
4217: /* lubksb(a,npar,indx,x); */
4218: /* for (i=1;i<=npar;i++){ */
4219: /* y[i][j]=x[i]; */
4220: /* printf("%.3e ",y[i][j]); */
4221: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4222: /* } */
4223: /* printf("\n"); */
4224: /* fprintf(ficlog,"\n"); */
4225: /* } */
4226:
4227: /* Verifying the inverse matrix */
4228: #ifdef DEBUGHESS
4229: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4230:
1.203 brouard 4231: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4232: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4233:
4234: for (j=1;j<=npar;j++) {
4235: for (i=1;i<=npar;i++){
1.203 brouard 4236: printf("%.2f ",y[i][j]);
4237: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4238: }
4239: printf("\n");
4240: fprintf(ficlog,"\n");
4241: }
1.203 brouard 4242: #endif
1.126 brouard 4243:
4244: free_matrix(a,1,npar,1,npar);
4245: free_matrix(y,1,npar,1,npar);
4246: free_vector(x,1,npar);
4247: free_ivector(indx,1,npar);
1.203 brouard 4248: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4249:
4250:
4251: }
4252:
4253: /*************** hessian matrix ****************/
4254: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4255: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4256: int i;
4257: int l=1, lmax=20;
1.203 brouard 4258: double k1,k2, res, fx;
1.132 brouard 4259: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4260: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4261: int k=0,kmax=10;
4262: double l1;
4263:
4264: fx=func(x);
4265: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4266: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4267: l1=pow(10,l);
4268: delts=delt;
4269: for(k=1 ; k <kmax; k=k+1){
4270: delt = delta*(l1*k);
4271: p2[theta]=x[theta] +delt;
1.145 brouard 4272: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4273: p2[theta]=x[theta]-delt;
4274: k2=func(p2)-fx;
4275: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4276: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4277:
1.203 brouard 4278: #ifdef DEBUGHESSII
1.126 brouard 4279: 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);
4280: 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);
4281: #endif
4282: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4283: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4284: k=kmax;
4285: }
4286: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4287: k=kmax; l=lmax*10;
1.126 brouard 4288: }
4289: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4290: delts=delt;
4291: }
1.203 brouard 4292: } /* End loop k */
1.126 brouard 4293: }
4294: delti[theta]=delts;
4295: return res;
4296:
4297: }
4298:
1.203 brouard 4299: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4300: {
4301: int i;
1.164 brouard 4302: int l=1, lmax=20;
1.126 brouard 4303: double k1,k2,k3,k4,res,fx;
1.132 brouard 4304: double p2[MAXPARM+1];
1.203 brouard 4305: int k, kmax=1;
4306: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4307:
4308: int firstime=0;
1.203 brouard 4309:
1.126 brouard 4310: fx=func(x);
1.203 brouard 4311: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4312: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4313: p2[thetai]=x[thetai]+delti[thetai]*k;
4314: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4315: k1=func(p2)-fx;
4316:
1.203 brouard 4317: p2[thetai]=x[thetai]+delti[thetai]*k;
4318: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4319: k2=func(p2)-fx;
4320:
1.203 brouard 4321: p2[thetai]=x[thetai]-delti[thetai]*k;
4322: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4323: k3=func(p2)-fx;
4324:
1.203 brouard 4325: p2[thetai]=x[thetai]-delti[thetai]*k;
4326: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4327: k4=func(p2)-fx;
1.203 brouard 4328: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4329: if(k1*k2*k3*k4 <0.){
1.208 brouard 4330: firstime=1;
1.203 brouard 4331: kmax=kmax+10;
1.208 brouard 4332: }
4333: if(kmax >=10 || firstime ==1){
1.246 brouard 4334: 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);
4335: 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 4336: 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);
4337: 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);
4338: }
4339: #ifdef DEBUGHESSIJ
4340: v1=hess[thetai][thetai];
4341: v2=hess[thetaj][thetaj];
4342: cv12=res;
4343: /* Computing eigen value of Hessian matrix */
4344: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4345: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4346: if ((lc2 <0) || (lc1 <0) ){
4347: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4348: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4349: 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);
4350: 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);
4351: }
1.126 brouard 4352: #endif
4353: }
4354: return res;
4355: }
4356:
1.203 brouard 4357: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4358: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4359: /* { */
4360: /* int i; */
4361: /* int l=1, lmax=20; */
4362: /* double k1,k2,k3,k4,res,fx; */
4363: /* double p2[MAXPARM+1]; */
4364: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4365: /* int k=0,kmax=10; */
4366: /* double l1; */
4367:
4368: /* fx=func(x); */
4369: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4370: /* l1=pow(10,l); */
4371: /* delts=delt; */
4372: /* for(k=1 ; k <kmax; k=k+1){ */
4373: /* delt = delti*(l1*k); */
4374: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4375: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4376: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4377: /* k1=func(p2)-fx; */
4378:
4379: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4380: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4381: /* k2=func(p2)-fx; */
4382:
4383: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4384: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4385: /* k3=func(p2)-fx; */
4386:
4387: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4388: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4389: /* k4=func(p2)-fx; */
4390: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4391: /* #ifdef DEBUGHESSIJ */
4392: /* 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); */
4393: /* 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); */
4394: /* #endif */
4395: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4396: /* k=kmax; */
4397: /* } */
4398: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4399: /* k=kmax; l=lmax*10; */
4400: /* } */
4401: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4402: /* delts=delt; */
4403: /* } */
4404: /* } /\* End loop k *\/ */
4405: /* } */
4406: /* delti[theta]=delts; */
4407: /* return res; */
4408: /* } */
4409:
4410:
1.126 brouard 4411: /************** Inverse of matrix **************/
4412: void ludcmp(double **a, int n, int *indx, double *d)
4413: {
4414: int i,imax,j,k;
4415: double big,dum,sum,temp;
4416: double *vv;
4417:
4418: vv=vector(1,n);
4419: *d=1.0;
4420: for (i=1;i<=n;i++) {
4421: big=0.0;
4422: for (j=1;j<=n;j++)
4423: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4424: if (big == 0.0){
4425: printf(" Singular Hessian matrix at row %d:\n",i);
4426: for (j=1;j<=n;j++) {
4427: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4428: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4429: }
4430: fflush(ficlog);
4431: fclose(ficlog);
4432: nrerror("Singular matrix in routine ludcmp");
4433: }
1.126 brouard 4434: vv[i]=1.0/big;
4435: }
4436: for (j=1;j<=n;j++) {
4437: for (i=1;i<j;i++) {
4438: sum=a[i][j];
4439: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4440: a[i][j]=sum;
4441: }
4442: big=0.0;
4443: for (i=j;i<=n;i++) {
4444: sum=a[i][j];
4445: for (k=1;k<j;k++)
4446: sum -= a[i][k]*a[k][j];
4447: a[i][j]=sum;
4448: if ( (dum=vv[i]*fabs(sum)) >= big) {
4449: big=dum;
4450: imax=i;
4451: }
4452: }
4453: if (j != imax) {
4454: for (k=1;k<=n;k++) {
4455: dum=a[imax][k];
4456: a[imax][k]=a[j][k];
4457: a[j][k]=dum;
4458: }
4459: *d = -(*d);
4460: vv[imax]=vv[j];
4461: }
4462: indx[j]=imax;
4463: if (a[j][j] == 0.0) a[j][j]=TINY;
4464: if (j != n) {
4465: dum=1.0/(a[j][j]);
4466: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4467: }
4468: }
4469: free_vector(vv,1,n); /* Doesn't work */
4470: ;
4471: }
4472:
4473: void lubksb(double **a, int n, int *indx, double b[])
4474: {
4475: int i,ii=0,ip,j;
4476: double sum;
4477:
4478: for (i=1;i<=n;i++) {
4479: ip=indx[i];
4480: sum=b[ip];
4481: b[ip]=b[i];
4482: if (ii)
4483: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4484: else if (sum) ii=i;
4485: b[i]=sum;
4486: }
4487: for (i=n;i>=1;i--) {
4488: sum=b[i];
4489: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4490: b[i]=sum/a[i][i];
4491: }
4492: }
4493:
4494: void pstamp(FILE *fichier)
4495: {
1.196 brouard 4496: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4497: }
4498:
1.297 brouard 4499: void date2dmy(double date,double *day, double *month, double *year){
4500: double yp=0., yp1=0., yp2=0.;
4501:
4502: yp1=modf(date,&yp);/* extracts integral of date in yp and
4503: fractional in yp1 */
4504: *year=yp;
4505: yp2=modf((yp1*12),&yp);
4506: *month=yp;
4507: yp1=modf((yp2*30.5),&yp);
4508: *day=yp;
4509: if(*day==0) *day=1;
4510: if(*month==0) *month=1;
4511: }
4512:
1.253 brouard 4513:
4514:
1.126 brouard 4515: /************ Frequencies ********************/
1.251 brouard 4516: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4517: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4518: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4519: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4520:
1.265 brouard 4521: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4522: int iind=0, iage=0;
4523: int mi; /* Effective wave */
4524: int first;
4525: double ***freq; /* Frequencies */
1.268 brouard 4526: 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 */
4527: 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 4528: double *meanq, *stdq, *idq;
1.226 brouard 4529: double **meanqt;
4530: double *pp, **prop, *posprop, *pospropt;
4531: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4532: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4533: double agebegin, ageend;
4534:
4535: pp=vector(1,nlstate);
1.251 brouard 4536: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4537: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4538: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4539: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4540: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4541: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4542: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4543: meanqt=matrix(1,lastpass,1,nqtveff);
4544: strcpy(fileresp,"P_");
4545: strcat(fileresp,fileresu);
4546: /*strcat(fileresphtm,fileresu);*/
4547: if((ficresp=fopen(fileresp,"w"))==NULL) {
4548: printf("Problem with prevalence resultfile: %s\n", fileresp);
4549: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4550: exit(0);
4551: }
1.240 brouard 4552:
1.226 brouard 4553: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4554: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4555: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4556: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4557: fflush(ficlog);
4558: exit(70);
4559: }
4560: else{
4561: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4562: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4563: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4564: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4565: }
1.237 brouard 4566: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
1.240 brouard 4567:
1.226 brouard 4568: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4569: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4570: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4571: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4572: fflush(ficlog);
4573: exit(70);
1.240 brouard 4574: } else{
1.226 brouard 4575: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4576: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4577: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4578: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4579: }
1.240 brouard 4580: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>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);
4581:
1.253 brouard 4582: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4583: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4584: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4585: j1=0;
1.126 brouard 4586:
1.227 brouard 4587: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4588: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4589: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4590:
4591:
1.226 brouard 4592: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4593: reference=low_education V1=0,V2=0
4594: med_educ V1=1 V2=0,
4595: high_educ V1=0 V2=1
4596: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4597: */
1.249 brouard 4598: dateintsum=0;
4599: k2cpt=0;
4600:
1.253 brouard 4601: if(cptcoveff == 0 )
1.265 brouard 4602: nl=1; /* Constant and age model only */
1.253 brouard 4603: else
4604: nl=2;
1.265 brouard 4605:
4606: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4607: /* Loop on nj=1 or 2 if dummy covariates j!=0
4608: * Loop on j1(1 to 2**cptcoveff) covariate combination
4609: * freq[s1][s2][iage] =0.
4610: * Loop on iind
4611: * ++freq[s1][s2][iage] weighted
4612: * end iind
4613: * if covariate and j!0
4614: * headers Variable on one line
4615: * endif cov j!=0
4616: * header of frequency table by age
4617: * Loop on age
4618: * pp[s1]+=freq[s1][s2][iage] weighted
4619: * pos+=freq[s1][s2][iage] weighted
4620: * Loop on s1 initial state
4621: * fprintf(ficresp
4622: * end s1
4623: * end age
4624: * if j!=0 computes starting values
4625: * end compute starting values
4626: * end j1
4627: * end nl
4628: */
1.253 brouard 4629: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4630: if(nj==1)
4631: j=0; /* First pass for the constant */
1.265 brouard 4632: else{
1.253 brouard 4633: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4634: }
1.251 brouard 4635: first=1;
1.265 brouard 4636: 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 4637: posproptt=0.;
4638: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4639: scanf("%d", i);*/
4640: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4641: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4642: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4643: freq[i][s2][m]=0;
1.251 brouard 4644:
4645: for (i=1; i<=nlstate; i++) {
1.240 brouard 4646: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4647: prop[i][m]=0;
4648: posprop[i]=0;
4649: pospropt[i]=0;
4650: }
1.283 brouard 4651: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4652: idq[z1]=0.;
4653: meanq[z1]=0.;
4654: stdq[z1]=0.;
1.283 brouard 4655: }
4656: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4657: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4658: /* meanqt[m][z1]=0.; */
4659: /* } */
4660: /* } */
1.251 brouard 4661: /* dateintsum=0; */
4662: /* k2cpt=0; */
4663:
1.265 brouard 4664: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4665: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4666: bool=1;
4667: if(j !=0){
4668: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4669: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4670: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4671: /* if(Tvaraff[z1] ==-20){ */
4672: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4673: /* }else if(Tvaraff[z1] ==-10){ */
4674: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4675: /* }else */
4676: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4677: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4678: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4679: /* 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",
4680: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4681: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4682: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4683: } /* Onlyf fixed */
4684: } /* end z1 */
4685: } /* cptcovn > 0 */
4686: } /* end any */
4687: }/* end j==0 */
1.265 brouard 4688: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4689: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4690: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4691: m=mw[mi][iind];
4692: if(j!=0){
4693: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4694: for (z1=1; z1<=cptcoveff; z1++) {
4695: if( Fixed[Tmodelind[z1]]==1){
4696: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4697: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4698: value is -1, we don't select. It differs from the
4699: constant and age model which counts them. */
4700: bool=0; /* not selected */
4701: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4702: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4703: bool=0;
4704: }
4705: }
4706: }
4707: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4708: } /* end j==0 */
4709: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4710: if(bool==1){ /*Selected */
1.251 brouard 4711: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4712: and mw[mi+1][iind]. dh depends on stepm. */
4713: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4714: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4715: if(m >=firstpass && m <=lastpass){
4716: k2=anint[m][iind]+(mint[m][iind]/12.);
4717: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4718: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4719: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4720: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4721: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4722: if (m<lastpass) {
4723: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4724: /* 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]); */
4725: if(s[m][iind]==-1)
4726: 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.));
4727: 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 4728: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
4729: if(!isnan(covar[ncovcol+z1][iind])){
4730: idq[z1]=idq[z1]+weight[iind];
4731: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4732: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
4733: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4734: }
1.284 brouard 4735: }
1.251 brouard 4736: /* if((int)agev[m][iind] == 55) */
4737: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4738: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4739: 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 4740: }
1.251 brouard 4741: } /* end if between passes */
4742: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4743: dateintsum=dateintsum+k2; /* on all covariates ?*/
4744: k2cpt++;
4745: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4746: }
1.251 brouard 4747: }else{
4748: bool=1;
4749: }/* end bool 2 */
4750: } /* end m */
1.284 brouard 4751: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4752: /* idq[z1]=idq[z1]+weight[iind]; */
4753: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4754: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4755: /* } */
1.251 brouard 4756: } /* end bool */
4757: } /* end iind = 1 to imx */
4758: /* prop[s][age] is feeded for any initial and valid live state as well as
4759: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4760:
4761:
4762: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4763: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4764: pstamp(ficresp);
1.251 brouard 4765: if (cptcoveff>0 && j!=0){
1.265 brouard 4766: pstamp(ficresp);
1.251 brouard 4767: printf( "\n#********** Variable ");
4768: fprintf(ficresp, "\n#********** Variable ");
4769: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4770: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4771: fprintf(ficlog, "\n#********** Variable ");
4772: for (z1=1; z1<=cptcoveff; z1++){
4773: if(!FixedV[Tvaraff[z1]]){
4774: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4775: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4776: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4777: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4778: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4779: }else{
1.251 brouard 4780: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4781: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4782: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4783: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4784: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4785: }
4786: }
4787: printf( "**********\n#");
4788: fprintf(ficresp, "**********\n#");
4789: fprintf(ficresphtm, "**********</h3>\n");
4790: fprintf(ficresphtmfr, "**********</h3>\n");
4791: fprintf(ficlog, "**********\n");
4792: }
1.284 brouard 4793: /*
4794: Printing means of quantitative variables if any
4795: */
4796: for (z1=1; z1<= nqfveff; z1++) {
1.311 brouard 4797: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.312 brouard 4798: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
1.284 brouard 4799: if(weightopt==1){
4800: printf(" Weighted mean and standard deviation of");
4801: fprintf(ficlog," Weighted mean and standard deviation of");
4802: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4803: }
1.311 brouard 4804: /* mu = \frac{w x}{\sum w}
4805: var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
4806: */
4807: 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]));
4808: 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]));
4809: 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 4810: }
4811: /* for (z1=1; z1<= nqtveff; z1++) { */
4812: /* for(m=1;m<=lastpass;m++){ */
4813: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4814: /* } */
4815: /* } */
1.283 brouard 4816:
1.251 brouard 4817: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4818: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4819: fprintf(ficresp, " Age");
4820: 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 4821: for(i=1; i<=nlstate;i++) {
1.265 brouard 4822: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4823: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4824: }
1.265 brouard 4825: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4826: fprintf(ficresphtm, "\n");
4827:
4828: /* Header of frequency table by age */
4829: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4830: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4831: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4832: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4833: if(s2!=0 && m!=0)
4834: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4835: }
1.226 brouard 4836: }
1.251 brouard 4837: fprintf(ficresphtmfr, "\n");
4838:
4839: /* For each age */
4840: for(iage=iagemin; iage <= iagemax+3; iage++){
4841: fprintf(ficresphtm,"<tr>");
4842: if(iage==iagemax+1){
4843: fprintf(ficlog,"1");
4844: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4845: }else if(iage==iagemax+2){
4846: fprintf(ficlog,"0");
4847: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4848: }else if(iage==iagemax+3){
4849: fprintf(ficlog,"Total");
4850: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4851: }else{
1.240 brouard 4852: if(first==1){
1.251 brouard 4853: first=0;
4854: printf("See log file for details...\n");
4855: }
4856: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4857: fprintf(ficlog,"Age %d", iage);
4858: }
1.265 brouard 4859: for(s1=1; s1 <=nlstate ; s1++){
4860: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4861: pp[s1] += freq[s1][m][iage];
1.251 brouard 4862: }
1.265 brouard 4863: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4864: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4865: pos += freq[s1][m][iage];
4866: if(pp[s1]>=1.e-10){
1.251 brouard 4867: if(first==1){
1.265 brouard 4868: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4869: }
1.265 brouard 4870: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4871: }else{
4872: if(first==1)
1.265 brouard 4873: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4874: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4875: }
4876: }
4877:
1.265 brouard 4878: for(s1=1; s1 <=nlstate ; s1++){
4879: /* posprop[s1]=0; */
4880: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4881: pp[s1] += freq[s1][m][iage];
4882: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4883:
4884: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4885: pos += pp[s1]; /* pos is the total number of transitions until this age */
4886: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4887: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4888: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4889: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4890: }
4891:
4892: /* Writing ficresp */
4893: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4894: if( iage <= iagemax){
4895: fprintf(ficresp," %d",iage);
4896: }
4897: }else if( nj==2){
4898: if( iage <= iagemax){
4899: fprintf(ficresp," %d",iage);
4900: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4901: }
1.240 brouard 4902: }
1.265 brouard 4903: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4904: if(pos>=1.e-5){
1.251 brouard 4905: if(first==1)
1.265 brouard 4906: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4907: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4908: }else{
4909: if(first==1)
1.265 brouard 4910: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4911: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4912: }
4913: if( iage <= iagemax){
4914: if(pos>=1.e-5){
1.265 brouard 4915: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4916: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4917: }else if( nj==2){
4918: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4919: }
4920: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4921: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4922: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4923: } else{
4924: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4925: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4926: }
1.240 brouard 4927: }
1.265 brouard 4928: pospropt[s1] +=posprop[s1];
4929: } /* end loop s1 */
1.251 brouard 4930: /* pospropt=0.; */
1.265 brouard 4931: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4932: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4933: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4934: if(first==1){
1.265 brouard 4935: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4936: }
1.265 brouard 4937: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4938: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4939: }
1.265 brouard 4940: if(s1!=0 && m!=0)
4941: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4942: }
1.265 brouard 4943: } /* end loop s1 */
1.251 brouard 4944: posproptt=0.;
1.265 brouard 4945: for(s1=1; s1 <=nlstate; s1++){
4946: posproptt += pospropt[s1];
1.251 brouard 4947: }
4948: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4949: fprintf(ficresphtm,"</tr>\n");
4950: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4951: if(iage <= iagemax)
4952: fprintf(ficresp,"\n");
1.240 brouard 4953: }
1.251 brouard 4954: if(first==1)
4955: printf("Others in log...\n");
4956: fprintf(ficlog,"\n");
4957: } /* end loop age iage */
1.265 brouard 4958:
1.251 brouard 4959: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4960: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4961: if(posproptt < 1.e-5){
1.265 brouard 4962: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4963: }else{
1.265 brouard 4964: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4965: }
1.226 brouard 4966: }
1.251 brouard 4967: fprintf(ficresphtm,"</tr>\n");
4968: fprintf(ficresphtm,"</table>\n");
4969: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4970: if(posproptt < 1.e-5){
1.251 brouard 4971: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4972: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4973: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4974: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4975: invalidvarcomb[j1]=1;
1.226 brouard 4976: }else{
1.251 brouard 4977: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4978: invalidvarcomb[j1]=0;
1.226 brouard 4979: }
1.251 brouard 4980: fprintf(ficresphtmfr,"</table>\n");
4981: fprintf(ficlog,"\n");
4982: if(j!=0){
4983: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4984: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4985: for(k=1; k <=(nlstate+ndeath); k++){
4986: if (k != i) {
1.265 brouard 4987: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4988: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4989: if(j1==1){ /* All dummy covariates to zero */
4990: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4991: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4992: printf("%d%d ",i,k);
4993: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4994: 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]));
4995: 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]));
4996: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4997: }
1.253 brouard 4998: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4999: for(iage=iagemin; iage <= iagemax+3; iage++){
5000: x[iage]= (double)iage;
5001: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 5002: /* 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 5003: }
1.268 brouard 5004: /* Some are not finite, but linreg will ignore these ages */
5005: no=0;
1.253 brouard 5006: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 5007: pstart[s1]=b;
5008: pstart[s1-1]=a;
1.252 brouard 5009: }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 */
5010: 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]);
5011: 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 5012: 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 5013: printf("%d%d ",i,k);
5014: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 5015: 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 5016: }else{ /* Other cases, like quantitative fixed or varying covariates */
5017: ;
5018: }
5019: /* printf("%12.7f )", param[i][jj][k]); */
5020: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5021: s1++;
1.251 brouard 5022: } /* end jj */
5023: } /* end k!= i */
5024: } /* end k */
1.265 brouard 5025: } /* end i, s1 */
1.251 brouard 5026: } /* end j !=0 */
5027: } /* end selected combination of covariate j1 */
5028: if(j==0){ /* We can estimate starting values from the occurences in each case */
5029: printf("#Freqsummary: Starting values for the constants:\n");
5030: fprintf(ficlog,"\n");
1.265 brouard 5031: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 5032: for(k=1; k <=(nlstate+ndeath); k++){
5033: if (k != i) {
5034: printf("%d%d ",i,k);
5035: fprintf(ficlog,"%d%d ",i,k);
5036: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 5037: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 5038: if(jj==1){ /* Age has to be done */
1.265 brouard 5039: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
5040: 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]));
5041: 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 5042: }
5043: /* printf("%12.7f )", param[i][jj][k]); */
5044: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5045: s1++;
1.250 brouard 5046: }
1.251 brouard 5047: printf("\n");
5048: fprintf(ficlog,"\n");
1.250 brouard 5049: }
5050: }
1.284 brouard 5051: } /* end of state i */
1.251 brouard 5052: printf("#Freqsummary\n");
5053: fprintf(ficlog,"\n");
1.265 brouard 5054: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5055: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5056: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5057: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5058: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5059: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5060: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5061: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5062: /* } */
5063: }
1.265 brouard 5064: } /* end loop s1 */
1.251 brouard 5065:
5066: printf("\n");
5067: fprintf(ficlog,"\n");
5068: } /* end j=0 */
1.249 brouard 5069: } /* end j */
1.252 brouard 5070:
1.253 brouard 5071: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5072: for(i=1, jk=1; i <=nlstate; i++){
5073: for(j=1; j <=nlstate+ndeath; j++){
5074: if(j!=i){
5075: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5076: printf("%1d%1d",i,j);
5077: fprintf(ficparo,"%1d%1d",i,j);
5078: for(k=1; k<=ncovmodel;k++){
5079: /* printf(" %lf",param[i][j][k]); */
5080: /* fprintf(ficparo," %lf",param[i][j][k]); */
5081: p[jk]=pstart[jk];
5082: printf(" %f ",pstart[jk]);
5083: fprintf(ficparo," %f ",pstart[jk]);
5084: jk++;
5085: }
5086: printf("\n");
5087: fprintf(ficparo,"\n");
5088: }
5089: }
5090: }
5091: } /* end mle=-2 */
1.226 brouard 5092: dateintmean=dateintsum/k2cpt;
1.296 brouard 5093: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5094:
1.226 brouard 5095: fclose(ficresp);
5096: fclose(ficresphtm);
5097: fclose(ficresphtmfr);
1.283 brouard 5098: free_vector(idq,1,nqfveff);
1.226 brouard 5099: free_vector(meanq,1,nqfveff);
1.284 brouard 5100: free_vector(stdq,1,nqfveff);
1.226 brouard 5101: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5102: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5103: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5104: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5105: free_vector(pospropt,1,nlstate);
5106: free_vector(posprop,1,nlstate);
1.251 brouard 5107: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5108: free_vector(pp,1,nlstate);
5109: /* End of freqsummary */
5110: }
1.126 brouard 5111:
1.268 brouard 5112: /* Simple linear regression */
5113: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5114:
5115: /* y=a+bx regression */
5116: double sumx = 0.0; /* sum of x */
5117: double sumx2 = 0.0; /* sum of x**2 */
5118: double sumxy = 0.0; /* sum of x * y */
5119: double sumy = 0.0; /* sum of y */
5120: double sumy2 = 0.0; /* sum of y**2 */
5121: double sume2 = 0.0; /* sum of square or residuals */
5122: double yhat;
5123:
5124: double denom=0;
5125: int i;
5126: int ne=*no;
5127:
5128: for ( i=ifi, ne=0;i<=ila;i++) {
5129: if(!isfinite(x[i]) || !isfinite(y[i])){
5130: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5131: continue;
5132: }
5133: ne=ne+1;
5134: sumx += x[i];
5135: sumx2 += x[i]*x[i];
5136: sumxy += x[i] * y[i];
5137: sumy += y[i];
5138: sumy2 += y[i]*y[i];
5139: denom = (ne * sumx2 - sumx*sumx);
5140: /* 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); */
5141: }
5142:
5143: denom = (ne * sumx2 - sumx*sumx);
5144: if (denom == 0) {
5145: // vertical, slope m is infinity
5146: *b = INFINITY;
5147: *a = 0;
5148: if (r) *r = 0;
5149: return 1;
5150: }
5151:
5152: *b = (ne * sumxy - sumx * sumy) / denom;
5153: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5154: if (r!=NULL) {
5155: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5156: sqrt((sumx2 - sumx*sumx/ne) *
5157: (sumy2 - sumy*sumy/ne));
5158: }
5159: *no=ne;
5160: for ( i=ifi, ne=0;i<=ila;i++) {
5161: if(!isfinite(x[i]) || !isfinite(y[i])){
5162: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5163: continue;
5164: }
5165: ne=ne+1;
5166: yhat = y[i] - *a -*b* x[i];
5167: sume2 += yhat * yhat ;
5168:
5169: denom = (ne * sumx2 - sumx*sumx);
5170: /* 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); */
5171: }
5172: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5173: *sa= *sb * sqrt(sumx2/ne);
5174:
5175: return 0;
5176: }
5177:
1.126 brouard 5178: /************ Prevalence ********************/
1.227 brouard 5179: 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)
5180: {
5181: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5182: in each health status at the date of interview (if between dateprev1 and dateprev2).
5183: We still use firstpass and lastpass as another selection.
5184: */
1.126 brouard 5185:
1.227 brouard 5186: int i, m, jk, j1, bool, z1,j, iv;
5187: int mi; /* Effective wave */
5188: int iage;
5189: double agebegin, ageend;
5190:
5191: double **prop;
5192: double posprop;
5193: double y2; /* in fractional years */
5194: int iagemin, iagemax;
5195: int first; /** to stop verbosity which is redirected to log file */
5196:
5197: iagemin= (int) agemin;
5198: iagemax= (int) agemax;
5199: /*pp=vector(1,nlstate);*/
1.251 brouard 5200: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5201: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5202: j1=0;
1.222 brouard 5203:
1.227 brouard 5204: /*j=cptcoveff;*/
5205: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5206:
1.288 brouard 5207: first=0;
1.227 brouard 5208: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5209: for (i=1; i<=nlstate; i++)
1.251 brouard 5210: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5211: prop[i][iage]=0.0;
5212: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5213: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5214: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5215:
5216: for (i=1; i<=imx; i++) { /* Each individual */
5217: bool=1;
5218: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5219: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5220: m=mw[mi][i];
5221: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5222: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5223: for (z1=1; z1<=cptcoveff; z1++){
5224: if( Fixed[Tmodelind[z1]]==1){
5225: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5226: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5227: bool=0;
5228: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5229: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5230: bool=0;
5231: }
5232: }
5233: if(bool==1){ /* Otherwise we skip that wave/person */
5234: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5235: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5236: if(m >=firstpass && m <=lastpass){
5237: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5238: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5239: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5240: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5241: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5242: 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);
5243: exit(1);
5244: }
5245: if (s[m][i]>0 && s[m][i]<=nlstate) {
5246: /*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]]);*/
5247: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5248: prop[s[m][i]][iagemax+3] += weight[i];
5249: } /* end valid statuses */
5250: } /* end selection of dates */
5251: } /* end selection of waves */
5252: } /* end bool */
5253: } /* end wave */
5254: } /* end individual */
5255: for(i=iagemin; i <= iagemax+3; i++){
5256: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5257: posprop += prop[jk][i];
5258: }
5259:
5260: for(jk=1; jk <=nlstate ; jk++){
5261: if( i <= iagemax){
5262: if(posprop>=1.e-5){
5263: probs[i][jk][j1]= prop[jk][i]/posprop;
5264: } else{
1.288 brouard 5265: if(!first){
5266: first=1;
1.266 brouard 5267: 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]);
5268: }else{
1.288 brouard 5269: 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 5270: }
5271: }
5272: }
5273: }/* end jk */
5274: }/* end i */
1.222 brouard 5275: /*} *//* end i1 */
1.227 brouard 5276: } /* end j1 */
1.222 brouard 5277:
1.227 brouard 5278: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5279: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5280: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5281: } /* End of prevalence */
1.126 brouard 5282:
5283: /************* Waves Concatenation ***************/
5284:
5285: 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)
5286: {
1.298 brouard 5287: /* 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 5288: Death is a valid wave (if date is known).
5289: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5290: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5291: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5292: */
1.126 brouard 5293:
1.224 brouard 5294: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5295: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5296: double sum=0., jmean=0.;*/
1.224 brouard 5297: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5298: int j, k=0,jk, ju, jl;
5299: double sum=0.;
5300: first=0;
1.214 brouard 5301: firstwo=0;
1.217 brouard 5302: firsthree=0;
1.218 brouard 5303: firstfour=0;
1.164 brouard 5304: jmin=100000;
1.126 brouard 5305: jmax=-1;
5306: jmean=0.;
1.224 brouard 5307:
5308: /* Treating live states */
1.214 brouard 5309: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5310: mi=0; /* First valid wave */
1.227 brouard 5311: mli=0; /* Last valid wave */
1.309 brouard 5312: m=firstpass; /* Loop on waves */
5313: while(s[m][i] <= nlstate){ /* a live state or unknown state */
1.227 brouard 5314: 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 */
5315: mli=m-1;/* mw[++mi][i]=m-1; */
5316: }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 5317: 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 5318: mli=m;
1.224 brouard 5319: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5320: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5321: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5322: }
1.309 brouard 5323: else{ /* m = lastpass, eventual special issue with warning */
1.224 brouard 5324: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5325: break;
1.224 brouard 5326: #else
1.309 brouard 5327: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* case -2 (vital status unknown is warned later */
1.227 brouard 5328: if(firsthree == 0){
1.302 brouard 5329: 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 5330: firsthree=1;
5331: }
1.302 brouard 5332: 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);
1.309 brouard 5333: mw[++mi][i]=m; /* Valid transition with unknown status */
1.227 brouard 5334: mli=m;
5335: }
5336: if(s[m][i]==-2){ /* Vital status is really unknown */
5337: nbwarn++;
1.309 brouard 5338: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */
1.227 brouard 5339: 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);
5340: 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);
5341: }
5342: break;
5343: }
5344: break;
1.224 brouard 5345: #endif
1.227 brouard 5346: }/* End m >= lastpass */
1.126 brouard 5347: }/* end while */
1.224 brouard 5348:
1.227 brouard 5349: /* 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 5350: /* After last pass */
1.224 brouard 5351: /* Treating death states */
1.214 brouard 5352: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5353: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5354: /* } */
1.126 brouard 5355: mi++; /* Death is another wave */
5356: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5357: /* Only death is a correct wave */
1.126 brouard 5358: mw[mi][i]=m;
1.257 brouard 5359: } /* else not in a death state */
1.224 brouard 5360: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5361: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5362: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.309 brouard 5363: 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 5364: nbwarn++;
5365: if(firstfiv==0){
1.309 brouard 5366: 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 5367: firstfiv=1;
5368: }else{
1.309 brouard 5369: 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 5370: }
1.309 brouard 5371: s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
5372: }else{ /* Month of Death occured afer last wave month, potential bias */
1.227 brouard 5373: nberr++;
5374: if(firstwo==0){
1.309 brouard 5375: 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 5376: firstwo=1;
5377: }
1.309 brouard 5378: 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 5379: }
1.257 brouard 5380: }else{ /* if date of interview is unknown */
1.227 brouard 5381: /* death is known but not confirmed by death status at any wave */
5382: if(firstfour==0){
1.309 brouard 5383: 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 5384: firstfour=1;
5385: }
1.309 brouard 5386: 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 5387: }
1.224 brouard 5388: } /* end if date of death is known */
5389: #endif
1.309 brouard 5390: wav[i]=mi; /* mi should be the last effective wave (or mli), */
5391: /* wav[i]=mw[mi][i]; */
1.126 brouard 5392: if(mi==0){
5393: nbwarn++;
5394: if(first==0){
1.227 brouard 5395: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5396: first=1;
1.126 brouard 5397: }
5398: if(first==1){
1.227 brouard 5399: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5400: }
5401: } /* end mi==0 */
5402: } /* End individuals */
1.214 brouard 5403: /* wav and mw are no more changed */
1.223 brouard 5404:
1.214 brouard 5405:
1.126 brouard 5406: for(i=1; i<=imx; i++){
5407: for(mi=1; mi<wav[i];mi++){
5408: if (stepm <=0)
1.227 brouard 5409: dh[mi][i]=1;
1.126 brouard 5410: else{
1.260 brouard 5411: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5412: if (agedc[i] < 2*AGESUP) {
5413: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5414: if(j==0) j=1; /* Survives at least one month after exam */
5415: else if(j<0){
5416: nberr++;
5417: 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]);
5418: j=1; /* Temporary Dangerous patch */
5419: 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);
5420: 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]);
5421: 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);
5422: }
5423: k=k+1;
5424: if (j >= jmax){
5425: jmax=j;
5426: ijmax=i;
5427: }
5428: if (j <= jmin){
5429: jmin=j;
5430: ijmin=i;
5431: }
5432: sum=sum+j;
5433: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5434: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5435: }
5436: }
5437: else{
5438: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5439: /* 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 5440:
1.227 brouard 5441: k=k+1;
5442: if (j >= jmax) {
5443: jmax=j;
5444: ijmax=i;
5445: }
5446: else if (j <= jmin){
5447: jmin=j;
5448: ijmin=i;
5449: }
5450: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5451: /*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]);*/
5452: if(j<0){
5453: nberr++;
5454: 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]);
5455: 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]);
5456: }
5457: sum=sum+j;
5458: }
5459: jk= j/stepm;
5460: jl= j -jk*stepm;
5461: ju= j -(jk+1)*stepm;
5462: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5463: if(jl==0){
5464: dh[mi][i]=jk;
5465: bh[mi][i]=0;
5466: }else{ /* We want a negative bias in order to only have interpolation ie
5467: * to avoid the price of an extra matrix product in likelihood */
5468: dh[mi][i]=jk+1;
5469: bh[mi][i]=ju;
5470: }
5471: }else{
5472: if(jl <= -ju){
5473: dh[mi][i]=jk;
5474: bh[mi][i]=jl; /* bias is positive if real duration
5475: * is higher than the multiple of stepm and negative otherwise.
5476: */
5477: }
5478: else{
5479: dh[mi][i]=jk+1;
5480: bh[mi][i]=ju;
5481: }
5482: if(dh[mi][i]==0){
5483: dh[mi][i]=1; /* At least one step */
5484: bh[mi][i]=ju; /* At least one step */
5485: /* 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);*/
5486: }
5487: } /* end if mle */
1.126 brouard 5488: }
5489: } /* end wave */
5490: }
5491: jmean=sum/k;
5492: 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 5493: 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 5494: }
1.126 brouard 5495:
5496: /*********** Tricode ****************************/
1.220 brouard 5497: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5498: {
5499: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5500: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5501: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5502: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5503: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5504: */
1.130 brouard 5505:
1.242 brouard 5506: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5507: int modmaxcovj=0; /* Modality max of covariates j */
5508: int cptcode=0; /* Modality max of covariates j */
5509: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5510:
5511:
1.242 brouard 5512: /* cptcoveff=0; */
5513: /* *cptcov=0; */
1.126 brouard 5514:
1.242 brouard 5515: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5516: for (k=1; k <= maxncov; k++)
5517: for(j=1; j<=2; j++)
5518: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5519:
1.242 brouard 5520: /* Loop on covariates without age and products and no quantitative variable */
5521: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5522: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5523: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5524: switch(Fixed[k]) {
5525: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.311 brouard 5526: modmaxcovj=0;
5527: modmincovj=0;
1.242 brouard 5528: 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*/
5529: ij=(int)(covar[Tvar[k]][i]);
5530: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5531: * If product of Vn*Vm, still boolean *:
5532: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5533: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5534: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5535: modality of the nth covariate of individual i. */
5536: if (ij > modmaxcovj)
5537: modmaxcovj=ij;
5538: else if (ij < modmincovj)
5539: modmincovj=ij;
1.287 brouard 5540: if (ij <0 || ij >1 ){
1.311 brouard 5541: printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
5542: fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
5543: fflush(ficlog);
5544: exit(1);
1.287 brouard 5545: }
5546: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5547: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5548: exit(1);
5549: }else
5550: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5551: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5552: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5553: /* getting the maximum value of the modality of the covariate
5554: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5555: female ies 1, then modmaxcovj=1.
5556: */
5557: } /* end for loop on individuals i */
5558: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5559: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5560: cptcode=modmaxcovj;
5561: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5562: /*for (i=0; i<=cptcode; i++) {*/
5563: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5564: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5565: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5566: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5567: if( j != -1){
5568: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5569: covariate for which somebody answered excluding
5570: undefined. Usually 2: 0 and 1. */
5571: }
5572: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5573: covariate for which somebody answered including
5574: undefined. Usually 3: -1, 0 and 1. */
5575: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5576: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5577: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5578:
1.242 brouard 5579: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5580: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5581: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5582: /* modmincovj=3; modmaxcovj = 7; */
5583: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5584: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5585: /* defining two dummy variables: variables V1_1 and V1_2.*/
5586: /* nbcode[Tvar[j]][ij]=k; */
5587: /* nbcode[Tvar[j]][1]=0; */
5588: /* nbcode[Tvar[j]][2]=1; */
5589: /* nbcode[Tvar[j]][3]=2; */
5590: /* To be continued (not working yet). */
5591: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5592:
5593: /* 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*/
5594: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5595: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5596: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5597: /*, could be restored in the future */
5598: 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 5599: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5600: break;
5601: }
5602: ij++;
1.287 brouard 5603: 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 5604: cptcode = ij; /* New max modality for covar j */
5605: } /* end of loop on modality i=-1 to 1 or more */
5606: break;
5607: case 1: /* Testing on varying covariate, could be simple and
5608: * should look at waves or product of fixed *
5609: * varying. No time to test -1, assuming 0 and 1 only */
5610: ij=0;
5611: for(i=0; i<=1;i++){
5612: nbcode[Tvar[k]][++ij]=i;
5613: }
5614: break;
5615: default:
5616: break;
5617: } /* end switch */
5618: } /* end dummy test */
1.311 brouard 5619: if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5620: 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*/
5621: if(isnan(covar[Tvar[k]][i])){
5622: printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
5623: fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
5624: fflush(ficlog);
5625: exit(1);
5626: }
5627: }
5628: }
1.287 brouard 5629: } /* 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 5630:
5631: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5632: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5633: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5634: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5635: 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 */
5636: 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 */
5637: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5638: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5639:
5640: ij=0;
5641: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5642: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5643: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5644: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5645: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5646: /* If product not in single variable we don't print results */
5647: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5648: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5649: 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*/
5650: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5651: 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 */
5652: if(Fixed[k]!=0)
5653: anyvaryingduminmodel=1;
5654: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5655: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5656: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5657: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5658: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5659: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5660: }
5661: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5662: /* ij--; */
5663: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5664: *cptcov=ij; /*Number of total real effective covariates: effective
5665: * because they can be excluded from the model and real
5666: * if in the model but excluded because missing values, but how to get k from ij?*/
5667: for(j=ij+1; j<= cptcovt; j++){
5668: Tvaraff[j]=0;
5669: Tmodelind[j]=0;
5670: }
5671: for(j=ntveff+1; j<= cptcovt; j++){
5672: TmodelInvind[j]=0;
5673: }
5674: /* To be sorted */
5675: ;
5676: }
1.126 brouard 5677:
1.145 brouard 5678:
1.126 brouard 5679: /*********** Health Expectancies ****************/
5680:
1.235 brouard 5681: 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 5682:
5683: {
5684: /* Health expectancies, no variances */
1.164 brouard 5685: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5686: int nhstepma, nstepma; /* Decreasing with age */
5687: double age, agelim, hf;
5688: double ***p3mat;
5689: double eip;
5690:
1.238 brouard 5691: /* pstamp(ficreseij); */
1.126 brouard 5692: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5693: fprintf(ficreseij,"# Age");
5694: for(i=1; i<=nlstate;i++){
5695: for(j=1; j<=nlstate;j++){
5696: fprintf(ficreseij," e%1d%1d ",i,j);
5697: }
5698: fprintf(ficreseij," e%1d. ",i);
5699: }
5700: fprintf(ficreseij,"\n");
5701:
5702:
5703: if(estepm < stepm){
5704: printf ("Problem %d lower than %d\n",estepm, stepm);
5705: }
5706: else hstepm=estepm;
5707: /* We compute the life expectancy from trapezoids spaced every estepm months
5708: * This is mainly to measure the difference between two models: for example
5709: * if stepm=24 months pijx are given only every 2 years and by summing them
5710: * we are calculating an estimate of the Life Expectancy assuming a linear
5711: * progression in between and thus overestimating or underestimating according
5712: * to the curvature of the survival function. If, for the same date, we
5713: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5714: * to compare the new estimate of Life expectancy with the same linear
5715: * hypothesis. A more precise result, taking into account a more precise
5716: * curvature will be obtained if estepm is as small as stepm. */
5717:
5718: /* For example we decided to compute the life expectancy with the smallest unit */
5719: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5720: nhstepm is the number of hstepm from age to agelim
5721: nstepm is the number of stepm from age to agelin.
1.270 brouard 5722: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5723: and note for a fixed period like estepm months */
5724: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5725: survival function given by stepm (the optimization length). Unfortunately it
5726: means that if the survival funtion is printed only each two years of age and if
5727: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5728: results. So we changed our mind and took the option of the best precision.
5729: */
5730: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5731:
5732: agelim=AGESUP;
5733: /* If stepm=6 months */
5734: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5735: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5736:
5737: /* nhstepm age range expressed in number of stepm */
5738: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5739: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5740: /* if (stepm >= YEARM) hstepm=1;*/
5741: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5742: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5743:
5744: for (age=bage; age<=fage; age ++){
5745: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5746: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5747: /* if (stepm >= YEARM) hstepm=1;*/
5748: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5749:
5750: /* If stepm=6 months */
5751: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5752: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5753:
1.235 brouard 5754: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5755:
5756: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5757:
5758: printf("%d|",(int)age);fflush(stdout);
5759: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5760:
5761: /* Computing expectancies */
5762: for(i=1; i<=nlstate;i++)
5763: for(j=1; j<=nlstate;j++)
5764: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5765: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5766:
5767: /* 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]);*/
5768:
5769: }
5770:
5771: fprintf(ficreseij,"%3.0f",age );
5772: for(i=1; i<=nlstate;i++){
5773: eip=0;
5774: for(j=1; j<=nlstate;j++){
5775: eip +=eij[i][j][(int)age];
5776: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5777: }
5778: fprintf(ficreseij,"%9.4f", eip );
5779: }
5780: fprintf(ficreseij,"\n");
5781:
5782: }
5783: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5784: printf("\n");
5785: fprintf(ficlog,"\n");
5786:
5787: }
5788:
1.235 brouard 5789: 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 5790:
5791: {
5792: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5793: to initial status i, ei. .
1.126 brouard 5794: */
5795: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5796: int nhstepma, nstepma; /* Decreasing with age */
5797: double age, agelim, hf;
5798: double ***p3matp, ***p3matm, ***varhe;
5799: double **dnewm,**doldm;
5800: double *xp, *xm;
5801: double **gp, **gm;
5802: double ***gradg, ***trgradg;
5803: int theta;
5804:
5805: double eip, vip;
5806:
5807: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5808: xp=vector(1,npar);
5809: xm=vector(1,npar);
5810: dnewm=matrix(1,nlstate*nlstate,1,npar);
5811: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5812:
5813: pstamp(ficresstdeij);
5814: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5815: fprintf(ficresstdeij,"# Age");
5816: for(i=1; i<=nlstate;i++){
5817: for(j=1; j<=nlstate;j++)
5818: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5819: fprintf(ficresstdeij," e%1d. ",i);
5820: }
5821: fprintf(ficresstdeij,"\n");
5822:
5823: pstamp(ficrescveij);
5824: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5825: fprintf(ficrescveij,"# Age");
5826: for(i=1; i<=nlstate;i++)
5827: for(j=1; j<=nlstate;j++){
5828: cptj= (j-1)*nlstate+i;
5829: for(i2=1; i2<=nlstate;i2++)
5830: for(j2=1; j2<=nlstate;j2++){
5831: cptj2= (j2-1)*nlstate+i2;
5832: if(cptj2 <= cptj)
5833: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5834: }
5835: }
5836: fprintf(ficrescveij,"\n");
5837:
5838: if(estepm < stepm){
5839: printf ("Problem %d lower than %d\n",estepm, stepm);
5840: }
5841: else hstepm=estepm;
5842: /* We compute the life expectancy from trapezoids spaced every estepm months
5843: * This is mainly to measure the difference between two models: for example
5844: * if stepm=24 months pijx are given only every 2 years and by summing them
5845: * we are calculating an estimate of the Life Expectancy assuming a linear
5846: * progression in between and thus overestimating or underestimating according
5847: * to the curvature of the survival function. If, for the same date, we
5848: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5849: * to compare the new estimate of Life expectancy with the same linear
5850: * hypothesis. A more precise result, taking into account a more precise
5851: * curvature will be obtained if estepm is as small as stepm. */
5852:
5853: /* For example we decided to compute the life expectancy with the smallest unit */
5854: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5855: nhstepm is the number of hstepm from age to agelim
5856: nstepm is the number of stepm from age to agelin.
5857: Look at hpijx to understand the reason of that which relies in memory size
5858: and note for a fixed period like estepm months */
5859: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5860: survival function given by stepm (the optimization length). Unfortunately it
5861: means that if the survival funtion is printed only each two years of age and if
5862: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5863: results. So we changed our mind and took the option of the best precision.
5864: */
5865: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5866:
5867: /* If stepm=6 months */
5868: /* nhstepm age range expressed in number of stepm */
5869: agelim=AGESUP;
5870: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5871: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5872: /* if (stepm >= YEARM) hstepm=1;*/
5873: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5874:
5875: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5876: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5877: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5878: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5879: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5880: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5881:
5882: for (age=bage; age<=fage; age ++){
5883: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5884: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5885: /* if (stepm >= YEARM) hstepm=1;*/
5886: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5887:
1.126 brouard 5888: /* If stepm=6 months */
5889: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5890: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5891:
5892: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5893:
1.126 brouard 5894: /* Computing Variances of health expectancies */
5895: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5896: decrease memory allocation */
5897: for(theta=1; theta <=npar; theta++){
5898: for(i=1; i<=npar; i++){
1.222 brouard 5899: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5900: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5901: }
1.235 brouard 5902: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5903: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5904:
1.126 brouard 5905: for(j=1; j<= nlstate; j++){
1.222 brouard 5906: for(i=1; i<=nlstate; i++){
5907: for(h=0; h<=nhstepm-1; h++){
5908: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5909: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5910: }
5911: }
1.126 brouard 5912: }
1.218 brouard 5913:
1.126 brouard 5914: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5915: for(h=0; h<=nhstepm-1; h++){
5916: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5917: }
1.126 brouard 5918: }/* End theta */
5919:
5920:
5921: for(h=0; h<=nhstepm-1; h++)
5922: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5923: for(theta=1; theta <=npar; theta++)
5924: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5925:
1.218 brouard 5926:
1.222 brouard 5927: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5928: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5929: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5930:
1.222 brouard 5931: printf("%d|",(int)age);fflush(stdout);
5932: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5933: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5934: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5935: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5936: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5937: for(ij=1;ij<=nlstate*nlstate;ij++)
5938: for(ji=1;ji<=nlstate*nlstate;ji++)
5939: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5940: }
5941: }
1.218 brouard 5942:
1.126 brouard 5943: /* Computing expectancies */
1.235 brouard 5944: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5945: for(i=1; i<=nlstate;i++)
5946: for(j=1; j<=nlstate;j++)
1.222 brouard 5947: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5948: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5949:
1.222 brouard 5950: /* 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 5951:
1.222 brouard 5952: }
1.269 brouard 5953:
5954: /* Standard deviation of expectancies ij */
1.126 brouard 5955: fprintf(ficresstdeij,"%3.0f",age );
5956: for(i=1; i<=nlstate;i++){
5957: eip=0.;
5958: vip=0.;
5959: for(j=1; j<=nlstate;j++){
1.222 brouard 5960: eip += eij[i][j][(int)age];
5961: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5962: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5963: 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 5964: }
5965: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5966: }
5967: fprintf(ficresstdeij,"\n");
1.218 brouard 5968:
1.269 brouard 5969: /* Variance of expectancies ij */
1.126 brouard 5970: fprintf(ficrescveij,"%3.0f",age );
5971: for(i=1; i<=nlstate;i++)
5972: for(j=1; j<=nlstate;j++){
1.222 brouard 5973: cptj= (j-1)*nlstate+i;
5974: for(i2=1; i2<=nlstate;i2++)
5975: for(j2=1; j2<=nlstate;j2++){
5976: cptj2= (j2-1)*nlstate+i2;
5977: if(cptj2 <= cptj)
5978: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5979: }
1.126 brouard 5980: }
5981: fprintf(ficrescveij,"\n");
1.218 brouard 5982:
1.126 brouard 5983: }
5984: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5985: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5986: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5987: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5988: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5989: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5990: printf("\n");
5991: fprintf(ficlog,"\n");
1.218 brouard 5992:
1.126 brouard 5993: free_vector(xm,1,npar);
5994: free_vector(xp,1,npar);
5995: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5996: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5997: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5998: }
1.218 brouard 5999:
1.126 brouard 6000: /************ Variance ******************/
1.235 brouard 6001: 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 6002: {
1.279 brouard 6003: /** Variance of health expectancies
6004: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
6005: * double **newm;
6006: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
6007: */
1.218 brouard 6008:
6009: /* int movingaverage(); */
6010: double **dnewm,**doldm;
6011: double **dnewmp,**doldmp;
6012: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 6013: int first=0;
1.218 brouard 6014: int k;
6015: double *xp;
1.279 brouard 6016: double **gp, **gm; /**< for var eij */
6017: double ***gradg, ***trgradg; /**< for var eij */
6018: double **gradgp, **trgradgp; /**< for var p point j */
6019: double *gpp, *gmp; /**< for var p point j */
6020: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 6021: double ***p3mat;
6022: double age,agelim, hf;
6023: /* double ***mobaverage; */
6024: int theta;
6025: char digit[4];
6026: char digitp[25];
6027:
6028: char fileresprobmorprev[FILENAMELENGTH];
6029:
6030: if(popbased==1){
6031: if(mobilav!=0)
6032: strcpy(digitp,"-POPULBASED-MOBILAV_");
6033: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
6034: }
6035: else
6036: strcpy(digitp,"-STABLBASED_");
1.126 brouard 6037:
1.218 brouard 6038: /* if (mobilav!=0) { */
6039: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6040: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
6041: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6042: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6043: /* } */
6044: /* } */
6045:
6046: strcpy(fileresprobmorprev,"PRMORPREV-");
6047: sprintf(digit,"%-d",ij);
6048: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
6049: strcat(fileresprobmorprev,digit); /* Tvar to be done */
6050: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
6051: strcat(fileresprobmorprev,fileresu);
6052: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
6053: printf("Problem with resultfile: %s\n", fileresprobmorprev);
6054: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
6055: }
6056: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6057: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6058: pstamp(ficresprobmorprev);
6059: 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 6060: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
6061: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
6062: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
6063: }
6064: for(j=1;j<=cptcoveff;j++)
6065: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
6066: fprintf(ficresprobmorprev,"\n");
6067:
1.218 brouard 6068: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6069: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6070: fprintf(ficresprobmorprev," p.%-d SE",j);
6071: for(i=1; i<=nlstate;i++)
6072: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6073: }
6074: fprintf(ficresprobmorprev,"\n");
6075:
6076: fprintf(ficgp,"\n# Routine varevsij");
6077: fprintf(ficgp,"\nunset title \n");
6078: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6079: 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");
6080: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6081:
1.218 brouard 6082: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6083: pstamp(ficresvij);
6084: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6085: if(popbased==1)
6086: 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);
6087: else
6088: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6089: fprintf(ficresvij,"# Age");
6090: for(i=1; i<=nlstate;i++)
6091: for(j=1; j<=nlstate;j++)
6092: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6093: fprintf(ficresvij,"\n");
6094:
6095: xp=vector(1,npar);
6096: dnewm=matrix(1,nlstate,1,npar);
6097: doldm=matrix(1,nlstate,1,nlstate);
6098: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6099: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6100:
6101: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6102: gpp=vector(nlstate+1,nlstate+ndeath);
6103: gmp=vector(nlstate+1,nlstate+ndeath);
6104: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6105:
1.218 brouard 6106: if(estepm < stepm){
6107: printf ("Problem %d lower than %d\n",estepm, stepm);
6108: }
6109: else hstepm=estepm;
6110: /* For example we decided to compute the life expectancy with the smallest unit */
6111: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6112: nhstepm is the number of hstepm from age to agelim
6113: nstepm is the number of stepm from age to agelim.
6114: Look at function hpijx to understand why because of memory size limitations,
6115: we decided (b) to get a life expectancy respecting the most precise curvature of the
6116: survival function given by stepm (the optimization length). Unfortunately it
6117: means that if the survival funtion is printed every two years of age and if
6118: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6119: results. So we changed our mind and took the option of the best precision.
6120: */
6121: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6122: agelim = AGESUP;
6123: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6124: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6125: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6126: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6127: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6128: gp=matrix(0,nhstepm,1,nlstate);
6129: gm=matrix(0,nhstepm,1,nlstate);
6130:
6131:
6132: for(theta=1; theta <=npar; theta++){
6133: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6134: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6135: }
1.279 brouard 6136: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6137: * returns into prlim .
1.288 brouard 6138: */
1.242 brouard 6139: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6140:
6141: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6142: if (popbased==1) {
6143: if(mobilav ==0){
6144: for(i=1; i<=nlstate;i++)
6145: prlim[i][i]=probs[(int)age][i][ij];
6146: }else{ /* mobilav */
6147: for(i=1; i<=nlstate;i++)
6148: prlim[i][i]=mobaverage[(int)age][i][ij];
6149: }
6150: }
1.295 brouard 6151: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6152: */
6153: 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 6154: /**< 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 6155: * at horizon h in state j including mortality.
6156: */
1.218 brouard 6157: for(j=1; j<= nlstate; j++){
6158: for(h=0; h<=nhstepm; h++){
6159: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6160: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6161: }
6162: }
1.279 brouard 6163: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6164: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6165: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6166: */
6167: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6168: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6169: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6170: }
6171:
6172: /* Again with minus shift */
1.218 brouard 6173:
6174: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6175: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6176:
1.242 brouard 6177: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6178:
6179: if (popbased==1) {
6180: if(mobilav ==0){
6181: for(i=1; i<=nlstate;i++)
6182: prlim[i][i]=probs[(int)age][i][ij];
6183: }else{ /* mobilav */
6184: for(i=1; i<=nlstate;i++)
6185: prlim[i][i]=mobaverage[(int)age][i][ij];
6186: }
6187: }
6188:
1.235 brouard 6189: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6190:
6191: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6192: for(h=0; h<=nhstepm; h++){
6193: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6194: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6195: }
6196: }
6197: /* This for computing probability of death (h=1 means
6198: computed over hstepm matrices product = hstepm*stepm months)
6199: as a weighted average of prlim.
6200: */
6201: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6202: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6203: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6204: }
1.279 brouard 6205: /* end shifting computations */
6206:
6207: /**< Computing gradient matrix at horizon h
6208: */
1.218 brouard 6209: for(j=1; j<= nlstate; j++) /* vareij */
6210: for(h=0; h<=nhstepm; h++){
6211: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6212: }
1.279 brouard 6213: /**< Gradient of overall mortality p.3 (or p.j)
6214: */
6215: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6216: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6217: }
6218:
6219: } /* End theta */
1.279 brouard 6220:
6221: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6222: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6223:
6224: for(h=0; h<=nhstepm; h++) /* veij */
6225: for(j=1; j<=nlstate;j++)
6226: for(theta=1; theta <=npar; theta++)
6227: trgradg[h][j][theta]=gradg[h][theta][j];
6228:
6229: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6230: for(theta=1; theta <=npar; theta++)
6231: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6232: /**< as well as its transposed matrix
6233: */
1.218 brouard 6234:
6235: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6236: for(i=1;i<=nlstate;i++)
6237: for(j=1;j<=nlstate;j++)
6238: vareij[i][j][(int)age] =0.;
1.279 brouard 6239:
6240: /* Computing trgradg by matcov by gradg at age and summing over h
6241: * and k (nhstepm) formula 15 of article
6242: * Lievre-Brouard-Heathcote
6243: */
6244:
1.218 brouard 6245: for(h=0;h<=nhstepm;h++){
6246: for(k=0;k<=nhstepm;k++){
6247: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6248: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6249: for(i=1;i<=nlstate;i++)
6250: for(j=1;j<=nlstate;j++)
6251: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6252: }
6253: }
6254:
1.279 brouard 6255: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6256: * p.j overall mortality formula 49 but computed directly because
6257: * we compute the grad (wix pijx) instead of grad (pijx),even if
6258: * wix is independent of theta.
6259: */
1.218 brouard 6260: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6261: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6262: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6263: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6264: varppt[j][i]=doldmp[j][i];
6265: /* end ppptj */
6266: /* x centered again */
6267:
1.242 brouard 6268: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6269:
6270: if (popbased==1) {
6271: if(mobilav ==0){
6272: for(i=1; i<=nlstate;i++)
6273: prlim[i][i]=probs[(int)age][i][ij];
6274: }else{ /* mobilav */
6275: for(i=1; i<=nlstate;i++)
6276: prlim[i][i]=mobaverage[(int)age][i][ij];
6277: }
6278: }
6279:
6280: /* This for computing probability of death (h=1 means
6281: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6282: as a weighted average of prlim.
6283: */
1.235 brouard 6284: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6285: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6286: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6287: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6288: }
6289: /* end probability of death */
6290:
6291: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6292: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6293: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6294: for(i=1; i<=nlstate;i++){
6295: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6296: }
6297: }
6298: fprintf(ficresprobmorprev,"\n");
6299:
6300: fprintf(ficresvij,"%.0f ",age );
6301: for(i=1; i<=nlstate;i++)
6302: for(j=1; j<=nlstate;j++){
6303: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6304: }
6305: fprintf(ficresvij,"\n");
6306: free_matrix(gp,0,nhstepm,1,nlstate);
6307: free_matrix(gm,0,nhstepm,1,nlstate);
6308: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6309: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6310: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6311: } /* End age */
6312: free_vector(gpp,nlstate+1,nlstate+ndeath);
6313: free_vector(gmp,nlstate+1,nlstate+ndeath);
6314: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6315: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6316: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6317: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6318: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6319: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6320: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6321: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6322: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6323: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6324: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6325: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6326: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6327: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6328: 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);
6329: /* 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 6330: */
1.218 brouard 6331: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6332: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6333:
1.218 brouard 6334: free_vector(xp,1,npar);
6335: free_matrix(doldm,1,nlstate,1,nlstate);
6336: free_matrix(dnewm,1,nlstate,1,npar);
6337: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6338: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6339: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6340: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6341: fclose(ficresprobmorprev);
6342: fflush(ficgp);
6343: fflush(fichtm);
6344: } /* end varevsij */
1.126 brouard 6345:
6346: /************ Variance of prevlim ******************/
1.269 brouard 6347: 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 6348: {
1.205 brouard 6349: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6350: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6351:
1.268 brouard 6352: double **dnewmpar,**doldm;
1.126 brouard 6353: int i, j, nhstepm, hstepm;
6354: double *xp;
6355: double *gp, *gm;
6356: double **gradg, **trgradg;
1.208 brouard 6357: double **mgm, **mgp;
1.126 brouard 6358: double age,agelim;
6359: int theta;
6360:
6361: pstamp(ficresvpl);
1.288 brouard 6362: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6363: fprintf(ficresvpl,"# Age ");
6364: if(nresult >=1)
6365: fprintf(ficresvpl," Result# ");
1.126 brouard 6366: for(i=1; i<=nlstate;i++)
6367: fprintf(ficresvpl," %1d-%1d",i,i);
6368: fprintf(ficresvpl,"\n");
6369:
6370: xp=vector(1,npar);
1.268 brouard 6371: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6372: doldm=matrix(1,nlstate,1,nlstate);
6373:
6374: hstepm=1*YEARM; /* Every year of age */
6375: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6376: agelim = AGESUP;
6377: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6378: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6379: if (stepm >= YEARM) hstepm=1;
6380: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6381: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6382: mgp=matrix(1,npar,1,nlstate);
6383: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6384: gp=vector(1,nlstate);
6385: gm=vector(1,nlstate);
6386:
6387: for(theta=1; theta <=npar; theta++){
6388: for(i=1; i<=npar; i++){ /* Computes gradient */
6389: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6390: }
1.288 brouard 6391: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6392: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6393: /* else */
6394: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6395: for(i=1;i<=nlstate;i++){
1.126 brouard 6396: gp[i] = prlim[i][i];
1.208 brouard 6397: mgp[theta][i] = prlim[i][i];
6398: }
1.126 brouard 6399: for(i=1; i<=npar; i++) /* Computes gradient */
6400: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6401: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6402: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6403: /* else */
6404: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6405: for(i=1;i<=nlstate;i++){
1.126 brouard 6406: gm[i] = prlim[i][i];
1.208 brouard 6407: mgm[theta][i] = prlim[i][i];
6408: }
1.126 brouard 6409: for(i=1;i<=nlstate;i++)
6410: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6411: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6412: } /* End theta */
6413:
6414: trgradg =matrix(1,nlstate,1,npar);
6415:
6416: for(j=1; j<=nlstate;j++)
6417: for(theta=1; theta <=npar; theta++)
6418: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6419: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6420: /* printf("\nmgm mgp %d ",(int)age); */
6421: /* for(j=1; j<=nlstate;j++){ */
6422: /* printf(" %d ",j); */
6423: /* for(theta=1; theta <=npar; theta++) */
6424: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6425: /* printf("\n "); */
6426: /* } */
6427: /* } */
6428: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6429: /* printf("\n gradg %d ",(int)age); */
6430: /* for(j=1; j<=nlstate;j++){ */
6431: /* printf("%d ",j); */
6432: /* for(theta=1; theta <=npar; theta++) */
6433: /* printf("%d %lf ",theta,gradg[theta][j]); */
6434: /* printf("\n "); */
6435: /* } */
6436: /* } */
1.126 brouard 6437:
6438: for(i=1;i<=nlstate;i++)
6439: varpl[i][(int)age] =0.;
1.209 brouard 6440: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6441: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6442: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6443: }else{
1.268 brouard 6444: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6445: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6446: }
1.126 brouard 6447: for(i=1;i<=nlstate;i++)
6448: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6449:
6450: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6451: if(nresult >=1)
6452: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6453: for(i=1; i<=nlstate;i++){
1.126 brouard 6454: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6455: /* for(j=1;j<=nlstate;j++) */
6456: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6457: }
1.126 brouard 6458: fprintf(ficresvpl,"\n");
6459: free_vector(gp,1,nlstate);
6460: free_vector(gm,1,nlstate);
1.208 brouard 6461: free_matrix(mgm,1,npar,1,nlstate);
6462: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6463: free_matrix(gradg,1,npar,1,nlstate);
6464: free_matrix(trgradg,1,nlstate,1,npar);
6465: } /* End age */
6466:
6467: free_vector(xp,1,npar);
6468: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6469: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6470:
6471: }
6472:
6473:
6474: /************ Variance of backprevalence limit ******************/
1.269 brouard 6475: 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 6476: {
6477: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6478: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6479:
6480: double **dnewmpar,**doldm;
6481: int i, j, nhstepm, hstepm;
6482: double *xp;
6483: double *gp, *gm;
6484: double **gradg, **trgradg;
6485: double **mgm, **mgp;
6486: double age,agelim;
6487: int theta;
6488:
6489: pstamp(ficresvbl);
6490: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6491: fprintf(ficresvbl,"# Age ");
6492: if(nresult >=1)
6493: fprintf(ficresvbl," Result# ");
6494: for(i=1; i<=nlstate;i++)
6495: fprintf(ficresvbl," %1d-%1d",i,i);
6496: fprintf(ficresvbl,"\n");
6497:
6498: xp=vector(1,npar);
6499: dnewmpar=matrix(1,nlstate,1,npar);
6500: doldm=matrix(1,nlstate,1,nlstate);
6501:
6502: hstepm=1*YEARM; /* Every year of age */
6503: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6504: agelim = AGEINF;
6505: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6506: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6507: if (stepm >= YEARM) hstepm=1;
6508: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6509: gradg=matrix(1,npar,1,nlstate);
6510: mgp=matrix(1,npar,1,nlstate);
6511: mgm=matrix(1,npar,1,nlstate);
6512: gp=vector(1,nlstate);
6513: gm=vector(1,nlstate);
6514:
6515: for(theta=1; theta <=npar; theta++){
6516: for(i=1; i<=npar; i++){ /* Computes gradient */
6517: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6518: }
6519: if(mobilavproj > 0 )
6520: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6521: else
6522: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6523: for(i=1;i<=nlstate;i++){
6524: gp[i] = bprlim[i][i];
6525: mgp[theta][i] = bprlim[i][i];
6526: }
6527: for(i=1; i<=npar; i++) /* Computes gradient */
6528: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6529: if(mobilavproj > 0 )
6530: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6531: else
6532: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6533: for(i=1;i<=nlstate;i++){
6534: gm[i] = bprlim[i][i];
6535: mgm[theta][i] = bprlim[i][i];
6536: }
6537: for(i=1;i<=nlstate;i++)
6538: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6539: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6540: } /* End theta */
6541:
6542: trgradg =matrix(1,nlstate,1,npar);
6543:
6544: for(j=1; j<=nlstate;j++)
6545: for(theta=1; theta <=npar; theta++)
6546: trgradg[j][theta]=gradg[theta][j];
6547: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6548: /* printf("\nmgm mgp %d ",(int)age); */
6549: /* for(j=1; j<=nlstate;j++){ */
6550: /* printf(" %d ",j); */
6551: /* for(theta=1; theta <=npar; theta++) */
6552: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6553: /* printf("\n "); */
6554: /* } */
6555: /* } */
6556: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6557: /* printf("\n gradg %d ",(int)age); */
6558: /* for(j=1; j<=nlstate;j++){ */
6559: /* printf("%d ",j); */
6560: /* for(theta=1; theta <=npar; theta++) */
6561: /* printf("%d %lf ",theta,gradg[theta][j]); */
6562: /* printf("\n "); */
6563: /* } */
6564: /* } */
6565:
6566: for(i=1;i<=nlstate;i++)
6567: varbpl[i][(int)age] =0.;
6568: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6569: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6570: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6571: }else{
6572: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6573: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6574: }
6575: for(i=1;i<=nlstate;i++)
6576: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6577:
6578: fprintf(ficresvbl,"%.0f ",age );
6579: if(nresult >=1)
6580: fprintf(ficresvbl,"%d ",nres );
6581: for(i=1; i<=nlstate;i++)
6582: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6583: fprintf(ficresvbl,"\n");
6584: free_vector(gp,1,nlstate);
6585: free_vector(gm,1,nlstate);
6586: free_matrix(mgm,1,npar,1,nlstate);
6587: free_matrix(mgp,1,npar,1,nlstate);
6588: free_matrix(gradg,1,npar,1,nlstate);
6589: free_matrix(trgradg,1,nlstate,1,npar);
6590: } /* End age */
6591:
6592: free_vector(xp,1,npar);
6593: free_matrix(doldm,1,nlstate,1,npar);
6594: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6595:
6596: }
6597:
6598: /************ Variance of one-step probabilities ******************/
6599: 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 6600: {
6601: int i, j=0, k1, l1, tj;
6602: int k2, l2, j1, z1;
6603: int k=0, l;
6604: int first=1, first1, first2;
6605: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6606: double **dnewm,**doldm;
6607: double *xp;
6608: double *gp, *gm;
6609: double **gradg, **trgradg;
6610: double **mu;
6611: double age, cov[NCOVMAX+1];
6612: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6613: int theta;
6614: char fileresprob[FILENAMELENGTH];
6615: char fileresprobcov[FILENAMELENGTH];
6616: char fileresprobcor[FILENAMELENGTH];
6617: double ***varpij;
6618:
6619: strcpy(fileresprob,"PROB_");
6620: strcat(fileresprob,fileres);
6621: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6622: printf("Problem with resultfile: %s\n", fileresprob);
6623: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6624: }
6625: strcpy(fileresprobcov,"PROBCOV_");
6626: strcat(fileresprobcov,fileresu);
6627: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6628: printf("Problem with resultfile: %s\n", fileresprobcov);
6629: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6630: }
6631: strcpy(fileresprobcor,"PROBCOR_");
6632: strcat(fileresprobcor,fileresu);
6633: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6634: printf("Problem with resultfile: %s\n", fileresprobcor);
6635: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6636: }
6637: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6638: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6639: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6640: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6641: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6642: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6643: pstamp(ficresprob);
6644: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6645: fprintf(ficresprob,"# Age");
6646: pstamp(ficresprobcov);
6647: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6648: fprintf(ficresprobcov,"# Age");
6649: pstamp(ficresprobcor);
6650: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6651: fprintf(ficresprobcor,"# Age");
1.126 brouard 6652:
6653:
1.222 brouard 6654: for(i=1; i<=nlstate;i++)
6655: for(j=1; j<=(nlstate+ndeath);j++){
6656: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6657: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6658: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6659: }
6660: /* fprintf(ficresprob,"\n");
6661: fprintf(ficresprobcov,"\n");
6662: fprintf(ficresprobcor,"\n");
6663: */
6664: xp=vector(1,npar);
6665: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6666: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6667: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6668: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6669: first=1;
6670: fprintf(ficgp,"\n# Routine varprob");
6671: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6672: fprintf(fichtm,"\n");
6673:
1.288 brouard 6674: 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 6675: 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);
6676: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6677: and drawn. It helps understanding how is the covariance between two incidences.\
6678: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6679: 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 6680: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6681: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6682: standard deviations wide on each axis. <br>\
6683: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6684: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6685: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6686:
1.222 brouard 6687: cov[1]=1;
6688: /* tj=cptcoveff; */
1.225 brouard 6689: tj = (int) pow(2,cptcoveff);
1.222 brouard 6690: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6691: j1=0;
1.224 brouard 6692: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6693: if (cptcovn>0) {
6694: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6695: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6696: fprintf(ficresprob, "**********\n#\n");
6697: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6698: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6699: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6700:
1.222 brouard 6701: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6702: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6703: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6704:
6705:
1.222 brouard 6706: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6707: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6708: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6709:
1.222 brouard 6710: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6711: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6712: fprintf(ficresprobcor, "**********\n#");
6713: if(invalidvarcomb[j1]){
6714: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6715: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6716: continue;
6717: }
6718: }
6719: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6720: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6721: gp=vector(1,(nlstate)*(nlstate+ndeath));
6722: gm=vector(1,(nlstate)*(nlstate+ndeath));
6723: for (age=bage; age<=fage; age ++){
6724: cov[2]=age;
6725: if(nagesqr==1)
6726: cov[3]= age*age;
6727: for (k=1; k<=cptcovn;k++) {
6728: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6729: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6730: * 1 1 1 1 1
6731: * 2 2 1 1 1
6732: * 3 1 2 1 1
6733: */
6734: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6735: }
6736: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6737: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6738: for (k=1; k<=cptcovprod;k++)
6739: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6740:
6741:
1.222 brouard 6742: for(theta=1; theta <=npar; theta++){
6743: for(i=1; i<=npar; i++)
6744: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6745:
1.222 brouard 6746: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6747:
1.222 brouard 6748: k=0;
6749: for(i=1; i<= (nlstate); i++){
6750: for(j=1; j<=(nlstate+ndeath);j++){
6751: k=k+1;
6752: gp[k]=pmmij[i][j];
6753: }
6754: }
1.220 brouard 6755:
1.222 brouard 6756: for(i=1; i<=npar; i++)
6757: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6758:
1.222 brouard 6759: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6760: k=0;
6761: for(i=1; i<=(nlstate); i++){
6762: for(j=1; j<=(nlstate+ndeath);j++){
6763: k=k+1;
6764: gm[k]=pmmij[i][j];
6765: }
6766: }
1.220 brouard 6767:
1.222 brouard 6768: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6769: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6770: }
1.126 brouard 6771:
1.222 brouard 6772: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6773: for(theta=1; theta <=npar; theta++)
6774: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6775:
1.222 brouard 6776: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6777: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6778:
1.222 brouard 6779: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6780:
1.222 brouard 6781: k=0;
6782: for(i=1; i<=(nlstate); i++){
6783: for(j=1; j<=(nlstate+ndeath);j++){
6784: k=k+1;
6785: mu[k][(int) age]=pmmij[i][j];
6786: }
6787: }
6788: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6789: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6790: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6791:
1.222 brouard 6792: /*printf("\n%d ",(int)age);
6793: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6794: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6795: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6796: }*/
1.220 brouard 6797:
1.222 brouard 6798: fprintf(ficresprob,"\n%d ",(int)age);
6799: fprintf(ficresprobcov,"\n%d ",(int)age);
6800: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6801:
1.222 brouard 6802: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6803: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6804: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6805: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6806: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6807: }
6808: i=0;
6809: for (k=1; k<=(nlstate);k++){
6810: for (l=1; l<=(nlstate+ndeath);l++){
6811: i++;
6812: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6813: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6814: for (j=1; j<=i;j++){
6815: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6816: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6817: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6818: }
6819: }
6820: }/* end of loop for state */
6821: } /* end of loop for age */
6822: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6823: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6824: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6825: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6826:
6827: /* Confidence intervalle of pij */
6828: /*
6829: fprintf(ficgp,"\nunset parametric;unset label");
6830: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6831: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6832: 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);
6833: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6834: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6835: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6836: */
6837:
6838: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6839: first1=1;first2=2;
6840: for (k2=1; k2<=(nlstate);k2++){
6841: for (l2=1; l2<=(nlstate+ndeath);l2++){
6842: if(l2==k2) continue;
6843: j=(k2-1)*(nlstate+ndeath)+l2;
6844: for (k1=1; k1<=(nlstate);k1++){
6845: for (l1=1; l1<=(nlstate+ndeath);l1++){
6846: if(l1==k1) continue;
6847: i=(k1-1)*(nlstate+ndeath)+l1;
6848: if(i<=j) continue;
6849: for (age=bage; age<=fage; age ++){
6850: if ((int)age %5==0){
6851: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6852: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6853: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6854: mu1=mu[i][(int) age]/stepm*YEARM ;
6855: mu2=mu[j][(int) age]/stepm*YEARM;
6856: c12=cv12/sqrt(v1*v2);
6857: /* Computing eigen value of matrix of covariance */
6858: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6859: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6860: if ((lc2 <0) || (lc1 <0) ){
6861: if(first2==1){
6862: first1=0;
6863: 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);
6864: }
6865: 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);
6866: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6867: /* lc2=fabs(lc2); */
6868: }
1.220 brouard 6869:
1.222 brouard 6870: /* Eigen vectors */
1.280 brouard 6871: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6872: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6873: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6874: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6875: }else
6876: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6877: /*v21=sqrt(1.-v11*v11); *//* error */
6878: v21=(lc1-v1)/cv12*v11;
6879: v12=-v21;
6880: v22=v11;
6881: tnalp=v21/v11;
6882: if(first1==1){
6883: first1=0;
6884: 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);
6885: }
6886: 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);
6887: /*printf(fignu*/
6888: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6889: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6890: if(first==1){
6891: first=0;
6892: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6893: fprintf(ficgp,"\nset parametric;unset label");
6894: 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);
6895: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6896: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6897: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6898: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6899: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6900: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6901: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6902: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6903: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6904: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6905: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6906: 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 6907: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6908: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6909: }else{
6910: first=0;
6911: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6912: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6913: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6914: 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 6915: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6916: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6917: }/* if first */
6918: } /* age mod 5 */
6919: } /* end loop age */
6920: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6921: first=1;
6922: } /*l12 */
6923: } /* k12 */
6924: } /*l1 */
6925: }/* k1 */
6926: } /* loop on combination of covariates j1 */
6927: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6928: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6929: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6930: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6931: free_vector(xp,1,npar);
6932: fclose(ficresprob);
6933: fclose(ficresprobcov);
6934: fclose(ficresprobcor);
6935: fflush(ficgp);
6936: fflush(fichtmcov);
6937: }
1.126 brouard 6938:
6939:
6940: /******************* Printing html file ***********/
1.201 brouard 6941: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6942: int lastpass, int stepm, int weightopt, char model[],\
6943: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6944: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6945: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6946: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6947: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6948:
6949: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6950: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6951: </ul>");
1.237 brouard 6952: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6953: </ul>", model);
1.214 brouard 6954: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6955: 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",
6956: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6957: 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 6958: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6959: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6960: fprintf(fichtm,"\
6961: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6962: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6963: fprintf(fichtm,"\
1.217 brouard 6964: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6965: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6966: fprintf(fichtm,"\
1.288 brouard 6967: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6968: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6969: fprintf(fichtm,"\
1.288 brouard 6970: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6971: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6972: fprintf(fichtm,"\
1.211 brouard 6973: - (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 6974: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6975: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6976: if(prevfcast==1){
6977: fprintf(fichtm,"\
6978: - Prevalence projections by age and states: \
1.201 brouard 6979: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6980: }
1.126 brouard 6981:
6982:
1.225 brouard 6983: m=pow(2,cptcoveff);
1.222 brouard 6984: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6985:
1.264 brouard 6986: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6987:
6988: jj1=0;
6989:
6990: fprintf(fichtm," \n<ul>");
6991: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6992: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6993: if(m != 1 && TKresult[nres]!= k1)
6994: continue;
6995: jj1++;
6996: if (cptcovn > 0) {
6997: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6998: for (cpt=1; cpt<=cptcoveff;cpt++){
6999: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7000: }
7001: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7002: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7003: }
7004: fprintf(fichtm,"\">");
7005:
7006: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
7007: fprintf(fichtm,"************ Results for covariates");
7008: for (cpt=1; cpt<=cptcoveff;cpt++){
7009: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7010: }
7011: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7012: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7013: }
7014: if(invalidvarcomb[k1]){
7015: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
7016: continue;
7017: }
7018: fprintf(fichtm,"</a></li>");
7019: } /* cptcovn >0 */
7020: }
7021: fprintf(fichtm," \n</ul>");
7022:
1.222 brouard 7023: jj1=0;
1.237 brouard 7024:
7025: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 7026: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 7027: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7028: continue;
1.220 brouard 7029:
1.222 brouard 7030: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7031: jj1++;
7032: if (cptcovn > 0) {
1.264 brouard 7033: fprintf(fichtm,"\n<p><a name=\"rescov");
7034: for (cpt=1; cpt<=cptcoveff;cpt++){
7035: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7036: }
7037: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7038: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
7039: }
7040: fprintf(fichtm,"\"</a>");
7041:
1.222 brouard 7042: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7043: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 7044: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
7045: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
7046: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7047: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 7048: }
1.237 brouard 7049: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7050: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7051: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
7052: }
7053:
1.230 brouard 7054: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 7055: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
7056: if(invalidvarcomb[k1]){
7057: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
7058: printf("\nCombination (%d) ignored because no cases \n",k1);
7059: continue;
7060: }
7061: }
7062: /* aij, bij */
1.259 brouard 7063: 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 7064: <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 7065: /* Pij */
1.241 brouard 7066: 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> \
7067: <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 7068: /* Quasi-incidences */
7069: 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 7070: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7071: 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 7072: 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> \
7073: <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 7074: /* Survival functions (period) in state j */
7075: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7076: 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 7077: <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 7078: }
7079: /* State specific survival functions (period) */
7080: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7081: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7082: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7083: <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 7084: }
1.288 brouard 7085: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7086: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7087: 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> \
7088: <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 7089: }
1.296 brouard 7090: if(prevbcast==1){
1.288 brouard 7091: /* Backward prevalence in each health state */
1.222 brouard 7092: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7093: 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 7094: <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 7095: }
1.217 brouard 7096: }
1.222 brouard 7097: if(prevfcast==1){
1.288 brouard 7098: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7099: for(cpt=1; cpt<=nlstate;cpt++){
1.314 brouard 7100: 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);
7101: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
7102: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
7103: subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 7104: }
7105: }
1.296 brouard 7106: if(prevbcast==1){
1.268 brouard 7107: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7108: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7109: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7110: 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 \
7111: 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 7112: 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);
7113: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
7114: fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
1.268 brouard 7115: }
7116: }
1.220 brouard 7117:
1.222 brouard 7118: for(cpt=1; cpt<=nlstate;cpt++) {
1.314 brouard 7119: 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);
7120: fprintf(fichtm," (data from text file <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
7121: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
1.222 brouard 7122: }
7123: /* } /\* end i1 *\/ */
7124: }/* End k1 */
7125: fprintf(fichtm,"</ul>");
1.126 brouard 7126:
1.222 brouard 7127: fprintf(fichtm,"\
1.126 brouard 7128: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7129: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7130: - 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 7131: But because parameters are usually highly correlated (a higher incidence of disability \
7132: and a higher incidence of recovery can give very close observed transition) it might \
7133: be very useful to look not only at linear confidence intervals estimated from the \
7134: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7135: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7136: covariance matrix of the one-step probabilities. \
7137: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7138:
1.222 brouard 7139: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7140: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7141: fprintf(fichtm,"\
1.126 brouard 7142: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7143: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7144:
1.222 brouard 7145: fprintf(fichtm,"\
1.126 brouard 7146: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7147: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7148: fprintf(fichtm,"\
1.126 brouard 7149: - 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): \
7150: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7151: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7152: fprintf(fichtm,"\
1.126 brouard 7153: - (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): \
7154: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7155: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7156: fprintf(fichtm,"\
1.288 brouard 7157: - 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 7158: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7159: fprintf(fichtm,"\
1.128 brouard 7160: - 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 7161: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7162: fprintf(fichtm,"\
1.288 brouard 7163: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7164: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7165:
7166: /* if(popforecast==1) fprintf(fichtm,"\n */
7167: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7168: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7169: /* <br>",fileres,fileres,fileres,fileres); */
7170: /* else */
7171: /* 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 7172: fflush(fichtm);
7173: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7174:
1.225 brouard 7175: m=pow(2,cptcoveff);
1.222 brouard 7176: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7177:
1.222 brouard 7178: jj1=0;
1.237 brouard 7179:
1.241 brouard 7180: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7181: for(k1=1; k1<=m;k1++){
1.253 brouard 7182: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7183: continue;
1.222 brouard 7184: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7185: jj1++;
1.126 brouard 7186: if (cptcovn > 0) {
7187: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7188: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7189: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7190: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7191: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7192: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7193: }
7194:
1.126 brouard 7195: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7196:
1.222 brouard 7197: if(invalidvarcomb[k1]){
7198: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7199: continue;
7200: }
1.126 brouard 7201: }
7202: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7203: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.314 brouard 7204: 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);
7205: fprintf(fichtm," (data from text file <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
7206: fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
1.126 brouard 7207: }
7208: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.314 brouard 7209: health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
1.128 brouard 7210: true period expectancies (those weighted with period prevalences are also\
7211: drawn in addition to the population based expectancies computed using\
1.314 brouard 7212: 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);
7213: fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
7214: fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7215: /* } /\* end i1 *\/ */
7216: }/* End k1 */
1.241 brouard 7217: }/* End nres */
1.222 brouard 7218: fprintf(fichtm,"</ul>");
7219: fflush(fichtm);
1.126 brouard 7220: }
7221:
7222: /******************* Gnuplot file **************/
1.296 brouard 7223: 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 7224:
7225: char dirfileres[132],optfileres[132];
1.264 brouard 7226: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7227: 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 7228: int lv=0, vlv=0, kl=0;
1.130 brouard 7229: int ng=0;
1.201 brouard 7230: int vpopbased;
1.223 brouard 7231: int ioffset; /* variable offset for columns */
1.270 brouard 7232: int iyearc=1; /* variable column for year of projection */
7233: int iagec=1; /* variable column for age of projection */
1.235 brouard 7234: int nres=0; /* Index of resultline */
1.266 brouard 7235: int istart=1; /* For starting graphs in projections */
1.219 brouard 7236:
1.126 brouard 7237: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7238: /* printf("Problem with file %s",optionfilegnuplot); */
7239: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7240: /* } */
7241:
7242: /*#ifdef windows */
7243: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7244: /*#endif */
1.225 brouard 7245: m=pow(2,cptcoveff);
1.126 brouard 7246:
1.274 brouard 7247: /* diagram of the model */
7248: fprintf(ficgp,"\n#Diagram of the model \n");
7249: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7250: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7251: 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);
7252:
7253: 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);
7254: fprintf(ficgp,"\n#show arrow\nunset label\n");
7255: 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);
7256: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7257: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7258: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7259: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7260:
1.202 brouard 7261: /* Contribution to likelihood */
7262: /* Plot the probability implied in the likelihood */
1.223 brouard 7263: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7264: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7265: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7266: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7267: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7268: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7269: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7270: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7271: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7272: 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));
7273: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7274: 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));
7275: for (i=1; i<= nlstate ; i ++) {
7276: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7277: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7278: 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);
7279: for (j=2; j<= nlstate+ndeath ; j ++) {
7280: 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);
7281: }
7282: fprintf(ficgp,";\nset out; unset ylabel;\n");
7283: }
7284: /* 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 */
7285: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7286: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7287: fprintf(ficgp,"\nset out;unset log\n");
7288: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7289:
1.126 brouard 7290: strcpy(dirfileres,optionfilefiname);
7291: strcpy(optfileres,"vpl");
1.223 brouard 7292: /* 1eme*/
1.238 brouard 7293: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7294: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7295: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7296: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7297: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7298: continue;
7299: /* We are interested in selected combination by the resultline */
1.246 brouard 7300: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7301: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7302: strcpy(gplotlabel,"(");
1.238 brouard 7303: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7304: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7305: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7306: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7307: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7308: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7309: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7310: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7311: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7312: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7313: }
7314: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7315: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7316: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7317: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7318: }
7319: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7320: /* printf("\n#\n"); */
1.238 brouard 7321: fprintf(ficgp,"\n#\n");
7322: if(invalidvarcomb[k1]){
1.260 brouard 7323: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7324: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7325: continue;
7326: }
1.235 brouard 7327:
1.241 brouard 7328: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7329: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7330: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7331: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7332: 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);
7333: /* 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); */
7334: /* k1-1 error should be nres-1*/
1.238 brouard 7335: for (i=1; i<= nlstate ; i ++) {
7336: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7337: else fprintf(ficgp," %%*lf (%%*lf)");
7338: }
1.288 brouard 7339: 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 7340: for (i=1; i<= nlstate ; i ++) {
7341: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7342: else fprintf(ficgp," %%*lf (%%*lf)");
7343: }
1.260 brouard 7344: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7345: for (i=1; i<= nlstate ; i ++) {
7346: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7347: else fprintf(ficgp," %%*lf (%%*lf)");
7348: }
1.265 brouard 7349: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7350:
7351: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7352: if(cptcoveff ==0){
1.271 brouard 7353: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7354: }else{
7355: kl=0;
7356: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7357: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7358: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7359: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7360: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7361: vlv= nbcode[Tvaraff[k]][lv];
7362: kl++;
7363: /* 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 *\/ */
7364: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7365: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7366: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7367: if(k==cptcoveff){
7368: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7369: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7370: }else{
7371: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7372: kl++;
7373: }
7374: } /* end covariate */
7375: } /* end if no covariate */
7376:
1.296 brouard 7377: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7378: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7379: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7380: if(cptcoveff ==0){
1.245 brouard 7381: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7382: }else{
7383: kl=0;
7384: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7385: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7386: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7387: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7388: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7389: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7390: kl++;
1.238 brouard 7391: /* 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 *\/ */
7392: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7393: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7394: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7395: if(k==cptcoveff){
1.245 brouard 7396: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7397: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7398: }else{
7399: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7400: kl++;
7401: }
7402: } /* end covariate */
7403: } /* end if no covariate */
1.296 brouard 7404: if(prevbcast == 1){
1.268 brouard 7405: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7406: /* k1-1 error should be nres-1*/
7407: for (i=1; i<= nlstate ; i ++) {
7408: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7409: else fprintf(ficgp," %%*lf (%%*lf)");
7410: }
1.271 brouard 7411: 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 7412: for (i=1; i<= nlstate ; i ++) {
7413: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7414: else fprintf(ficgp," %%*lf (%%*lf)");
7415: }
1.276 brouard 7416: 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 7417: for (i=1; i<= nlstate ; i ++) {
7418: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7419: else fprintf(ficgp," %%*lf (%%*lf)");
7420: }
1.274 brouard 7421: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7422: } /* end if backprojcast */
1.296 brouard 7423: } /* end if prevbcast */
1.276 brouard 7424: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7425: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7426: } /* nres */
1.201 brouard 7427: } /* k1 */
7428: } /* cpt */
1.235 brouard 7429:
7430:
1.126 brouard 7431: /*2 eme*/
1.238 brouard 7432: for (k1=1; k1<= m ; k1 ++){
7433: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7434: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7435: continue;
7436: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7437: strcpy(gplotlabel,"(");
1.238 brouard 7438: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7439: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7440: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7441: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7442: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7443: vlv= nbcode[Tvaraff[k]][lv];
7444: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7445: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7446: }
1.237 brouard 7447: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7448: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7449: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7450: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7451: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7452: }
1.264 brouard 7453: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7454: fprintf(ficgp,"\n#\n");
1.223 brouard 7455: if(invalidvarcomb[k1]){
7456: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7457: continue;
7458: }
1.219 brouard 7459:
1.241 brouard 7460: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7461: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7462: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7463: if(vpopbased==0){
1.238 brouard 7464: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7465: }else
1.238 brouard 7466: fprintf(ficgp,"\nreplot ");
7467: for (i=1; i<= nlstate+1 ; i ++) {
7468: k=2*i;
1.261 brouard 7469: 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 7470: for (j=1; j<= nlstate+1 ; j ++) {
7471: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7472: else fprintf(ficgp," %%*lf (%%*lf)");
7473: }
7474: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7475: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7476: 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 7477: for (j=1; j<= nlstate+1 ; j ++) {
7478: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7479: else fprintf(ficgp," %%*lf (%%*lf)");
7480: }
7481: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7482: 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 7483: for (j=1; j<= nlstate+1 ; j ++) {
7484: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7485: else fprintf(ficgp," %%*lf (%%*lf)");
7486: }
7487: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7488: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7489: } /* state */
7490: } /* vpopbased */
1.264 brouard 7491: 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 7492: } /* end nres */
7493: } /* k1 end 2 eme*/
7494:
7495:
7496: /*3eme*/
7497: for (k1=1; k1<= m ; k1 ++){
7498: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7499: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7500: continue;
7501:
7502: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7503: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7504: strcpy(gplotlabel,"(");
1.238 brouard 7505: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7506: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7507: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7508: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7509: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7510: vlv= nbcode[Tvaraff[k]][lv];
7511: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7512: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7513: }
7514: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7515: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7516: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7517: }
1.264 brouard 7518: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7519: fprintf(ficgp,"\n#\n");
7520: if(invalidvarcomb[k1]){
7521: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7522: continue;
7523: }
7524:
7525: /* k=2+nlstate*(2*cpt-2); */
7526: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7527: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7528: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7529: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7530: 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 7531: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7532: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7533: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7534: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7535: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7536: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7537:
1.238 brouard 7538: */
7539: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7540: 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 7541: /* 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 7542:
1.238 brouard 7543: }
1.261 brouard 7544: 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 7545: }
1.264 brouard 7546: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7547: } /* end nres */
7548: } /* end kl 3eme */
1.126 brouard 7549:
1.223 brouard 7550: /* 4eme */
1.201 brouard 7551: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7552: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7553: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7554: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7555: continue;
1.238 brouard 7556: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7557: strcpy(gplotlabel,"(");
1.238 brouard 7558: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7559: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7560: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7561: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7562: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7563: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7564: vlv= nbcode[Tvaraff[k]][lv];
7565: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7566: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7567: }
7568: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7569: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7570: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7571: }
1.264 brouard 7572: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7573: fprintf(ficgp,"\n#\n");
7574: if(invalidvarcomb[k1]){
7575: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7576: continue;
1.223 brouard 7577: }
1.238 brouard 7578:
1.241 brouard 7579: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7580: 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 7581: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7582: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7583: k=3;
7584: for (i=1; i<= nlstate ; i ++){
7585: if(i==1){
7586: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7587: }else{
7588: fprintf(ficgp,", '' ");
7589: }
7590: l=(nlstate+ndeath)*(i-1)+1;
7591: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7592: for (j=2; j<= nlstate+ndeath ; j ++)
7593: fprintf(ficgp,"+$%d",k+l+j-1);
7594: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7595: } /* nlstate */
1.264 brouard 7596: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7597: } /* end cpt state*/
7598: } /* end nres */
7599: } /* end covariate k1 */
7600:
1.220 brouard 7601: /* 5eme */
1.201 brouard 7602: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7603: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7604: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7605: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7606: continue;
1.238 brouard 7607: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7608: strcpy(gplotlabel,"(");
1.238 brouard 7609: 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);
7610: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7611: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7612: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7613: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7614: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7615: vlv= nbcode[Tvaraff[k]][lv];
7616: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7617: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7618: }
7619: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7620: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7621: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7622: }
1.264 brouard 7623: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7624: fprintf(ficgp,"\n#\n");
7625: if(invalidvarcomb[k1]){
7626: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7627: continue;
7628: }
1.227 brouard 7629:
1.241 brouard 7630: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7631: 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 7632: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7633: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7634: k=3;
7635: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7636: if(j==1)
7637: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7638: else
7639: fprintf(ficgp,", '' ");
7640: l=(nlstate+ndeath)*(cpt-1) +j;
7641: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7642: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7643: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7644: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7645: } /* nlstate */
7646: fprintf(ficgp,", '' ");
7647: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7648: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7649: l=(nlstate+ndeath)*(cpt-1) +j;
7650: if(j < nlstate)
7651: fprintf(ficgp,"$%d +",k+l);
7652: else
7653: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7654: }
1.264 brouard 7655: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7656: } /* end cpt state*/
7657: } /* end covariate */
7658: } /* end nres */
1.227 brouard 7659:
1.220 brouard 7660: /* 6eme */
1.202 brouard 7661: /* CV preval stable (period) for each covariate */
1.237 brouard 7662: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7663: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7664: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7665: continue;
1.255 brouard 7666: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7667: strcpy(gplotlabel,"(");
1.288 brouard 7668: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7669: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7670: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7671: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7672: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7673: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7674: vlv= nbcode[Tvaraff[k]][lv];
7675: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7676: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7677: }
1.237 brouard 7678: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7679: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7680: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7681: }
1.264 brouard 7682: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7683: fprintf(ficgp,"\n#\n");
1.223 brouard 7684: if(invalidvarcomb[k1]){
1.227 brouard 7685: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7686: continue;
1.223 brouard 7687: }
1.227 brouard 7688:
1.241 brouard 7689: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7690: 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 7691: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7692: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7693: k=3; /* Offset */
1.255 brouard 7694: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7695: if(i==1)
7696: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7697: else
7698: fprintf(ficgp,", '' ");
1.255 brouard 7699: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7700: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7701: for (j=2; j<= nlstate ; j ++)
7702: fprintf(ficgp,"+$%d",k+l+j-1);
7703: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7704: } /* nlstate */
1.264 brouard 7705: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7706: } /* end cpt state*/
7707: } /* end covariate */
1.227 brouard 7708:
7709:
1.220 brouard 7710: /* 7eme */
1.296 brouard 7711: if(prevbcast == 1){
1.288 brouard 7712: /* CV backward prevalence for each covariate */
1.237 brouard 7713: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7714: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7715: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7716: continue;
1.268 brouard 7717: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7718: strcpy(gplotlabel,"(");
1.288 brouard 7719: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7720: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7721: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7722: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7723: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7724: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7725: vlv= nbcode[Tvaraff[k]][lv];
7726: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7727: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7728: }
1.237 brouard 7729: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7730: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7731: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7732: }
1.264 brouard 7733: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7734: fprintf(ficgp,"\n#\n");
7735: if(invalidvarcomb[k1]){
7736: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7737: continue;
7738: }
7739:
1.241 brouard 7740: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7741: 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 7742: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7743: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7744: k=3; /* Offset */
1.268 brouard 7745: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7746: if(i==1)
7747: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7748: else
7749: fprintf(ficgp,", '' ");
7750: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7751: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7752: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7753: /* 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 7754: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7755: /* for (j=2; j<= nlstate ; j ++) */
7756: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7757: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7758: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7759: } /* nlstate */
1.264 brouard 7760: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7761: } /* end cpt state*/
7762: } /* end covariate */
1.296 brouard 7763: } /* End if prevbcast */
1.218 brouard 7764:
1.223 brouard 7765: /* 8eme */
1.218 brouard 7766: if(prevfcast==1){
1.288 brouard 7767: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7768:
1.237 brouard 7769: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7770: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7771: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7772: continue;
1.211 brouard 7773: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7774: strcpy(gplotlabel,"(");
1.288 brouard 7775: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7776: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7777: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7778: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7779: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7780: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7781: vlv= nbcode[Tvaraff[k]][lv];
7782: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7783: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7784: }
1.237 brouard 7785: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7786: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7787: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7788: }
1.264 brouard 7789: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7790: fprintf(ficgp,"\n#\n");
7791: if(invalidvarcomb[k1]){
7792: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7793: continue;
7794: }
7795:
7796: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7797: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7798: 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 7799: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7800: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7801:
7802: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7803: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7804: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7805: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7806: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7807: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7808: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7809: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7810: if(i==istart){
1.227 brouard 7811: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7812: }else{
7813: fprintf(ficgp,",\\\n '' ");
7814: }
7815: if(cptcoveff ==0){ /* No covariate */
7816: ioffset=2; /* Age is in 2 */
7817: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7818: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7819: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7820: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7821: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7822: if(i==nlstate+1){
1.270 brouard 7823: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7824: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7825: fprintf(ficgp,",\\\n '' ");
7826: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7827: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7828: offyear, \
1.268 brouard 7829: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7830: }else
1.227 brouard 7831: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7832: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7833: }else{ /* more than 2 covariates */
1.270 brouard 7834: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7835: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7836: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7837: iyearc=ioffset-1;
7838: iagec=ioffset;
1.227 brouard 7839: fprintf(ficgp," u %d:(",ioffset);
7840: kl=0;
7841: strcpy(gplotcondition,"(");
7842: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7843: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7844: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7845: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7846: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7847: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7848: kl++;
7849: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7850: kl++;
7851: if(k <cptcoveff && cptcoveff>1)
7852: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7853: }
7854: strcpy(gplotcondition+strlen(gplotcondition),")");
7855: /* 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 *\/ */
7856: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7857: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7858: /* '' 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*/
7859: if(i==nlstate+1){
1.270 brouard 7860: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7861: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7862: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7863: fprintf(ficgp," u %d:(",iagec);
7864: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7865: iyearc, iagec, offyear, \
7866: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7867: /* '' 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 7868: }else{
7869: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7870: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7871: }
7872: } /* end if covariate */
7873: } /* nlstate */
1.264 brouard 7874: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7875: } /* end cpt state*/
7876: } /* end covariate */
7877: } /* End if prevfcast */
1.227 brouard 7878:
1.296 brouard 7879: if(prevbcast==1){
1.268 brouard 7880: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7881:
7882: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7883: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7884: if(m != 1 && TKresult[nres]!= k1)
7885: continue;
7886: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7887: strcpy(gplotlabel,"(");
7888: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7889: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7890: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7891: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7892: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7893: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7894: vlv= nbcode[Tvaraff[k]][lv];
7895: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7896: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7897: }
7898: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7899: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7900: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7901: }
7902: strcpy(gplotlabel+strlen(gplotlabel),")");
7903: fprintf(ficgp,"\n#\n");
7904: if(invalidvarcomb[k1]){
7905: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7906: continue;
7907: }
7908:
7909: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7910: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7911: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7912: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7913: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7914:
7915: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7916: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7917: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7918: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7919: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7920: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7921: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7922: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7923: if(i==istart){
7924: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7925: }else{
7926: fprintf(ficgp,",\\\n '' ");
7927: }
7928: if(cptcoveff ==0){ /* No covariate */
7929: ioffset=2; /* Age is in 2 */
7930: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7931: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7932: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7933: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7934: fprintf(ficgp," u %d:(", ioffset);
7935: if(i==nlstate+1){
1.270 brouard 7936: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7937: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7938: fprintf(ficgp,",\\\n '' ");
7939: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7940: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7941: offbyear, \
7942: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7943: }else
7944: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7945: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7946: }else{ /* more than 2 covariates */
1.270 brouard 7947: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7948: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7949: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7950: iyearc=ioffset-1;
7951: iagec=ioffset;
1.268 brouard 7952: fprintf(ficgp," u %d:(",ioffset);
7953: kl=0;
7954: strcpy(gplotcondition,"(");
7955: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7956: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7957: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7958: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7959: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7960: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7961: kl++;
7962: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7963: kl++;
7964: if(k <cptcoveff && cptcoveff>1)
7965: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7966: }
7967: strcpy(gplotcondition+strlen(gplotcondition),")");
7968: /* 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 *\/ */
7969: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7970: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7971: /* '' 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*/
7972: if(i==nlstate+1){
1.270 brouard 7973: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7974: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7975: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7976: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7977: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7978: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7979: iyearc,iagec,offbyear, \
7980: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7981: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7982: }else{
7983: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7984: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7985: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7986: }
7987: } /* end if covariate */
7988: } /* nlstate */
7989: fprintf(ficgp,"\nset out; unset label;\n");
7990: } /* end cpt state*/
7991: } /* end covariate */
1.296 brouard 7992: } /* End if prevbcast */
1.268 brouard 7993:
1.227 brouard 7994:
1.238 brouard 7995: /* 9eme writing MLE parameters */
7996: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7997: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7998: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7999: for(k=1; k <=(nlstate+ndeath); k++){
8000: if (k != i) {
1.227 brouard 8001: fprintf(ficgp,"# current state %d\n",k);
8002: for(j=1; j <=ncovmodel; j++){
8003: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
8004: jk++;
8005: }
8006: fprintf(ficgp,"\n");
1.126 brouard 8007: }
8008: }
1.223 brouard 8009: }
1.187 brouard 8010: fprintf(ficgp,"##############\n#\n");
1.227 brouard 8011:
1.145 brouard 8012: /*goto avoid;*/
1.238 brouard 8013: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
8014: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 8015: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
8016: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
8017: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
8018: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
8019: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8020: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
8021: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8022: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
8023: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
8024: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
8025: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
8026: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
8027: fprintf(ficgp,"#\n");
1.223 brouard 8028: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 8029: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 8030: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 8031: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 8032: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
8033: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 8034: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 8035: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 8036: continue;
1.264 brouard 8037: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
8038: strcpy(gplotlabel,"(");
1.276 brouard 8039: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 8040: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
8041: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
8042: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
8043: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
8044: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
8045: vlv= nbcode[Tvaraff[k]][lv];
8046: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
8047: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
8048: }
1.237 brouard 8049: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8050: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 8051: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 8052: }
1.264 brouard 8053: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 8054: fprintf(ficgp,"\n#\n");
1.264 brouard 8055: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 8056: fprintf(ficgp,"\nset key outside ");
8057: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
8058: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 8059: fprintf(ficgp,"\nset ter svg size 640, 480 ");
8060: if (ng==1){
8061: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
8062: fprintf(ficgp,"\nunset log y");
8063: }else if (ng==2){
8064: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
8065: fprintf(ficgp,"\nset log y");
8066: }else if (ng==3){
8067: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
8068: fprintf(ficgp,"\nset log y");
8069: }else
8070: fprintf(ficgp,"\nunset title ");
8071: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
8072: i=1;
8073: for(k2=1; k2<=nlstate; k2++) {
8074: k3=i;
8075: for(k=1; k<=(nlstate+ndeath); k++) {
8076: if (k != k2){
8077: switch( ng) {
8078: case 1:
8079: if(nagesqr==0)
8080: fprintf(ficgp," p%d+p%d*x",i,i+1);
8081: else /* nagesqr =1 */
8082: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8083: break;
8084: case 2: /* ng=2 */
8085: if(nagesqr==0)
8086: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8087: else /* nagesqr =1 */
8088: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8089: break;
8090: case 3:
8091: if(nagesqr==0)
8092: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8093: else /* nagesqr =1 */
8094: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8095: break;
8096: }
8097: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8098: ijp=1; /* product no age */
8099: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8100: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8101: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8102: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8103: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8104: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8105: if(DummyV[j]==0){
8106: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8107: }else{ /* quantitative */
8108: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8109: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8110: }
8111: ij++;
1.237 brouard 8112: }
1.268 brouard 8113: }
8114: }else if(cptcovprod >0){
8115: if(j==Tprod[ijp]) { /* */
8116: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8117: if(ijp <=cptcovprod) { /* Product */
8118: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8119: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8120: /* 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)]); */
8121: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8122: }else{ /* Vn is dummy and Vm is quanti */
8123: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8124: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8125: }
8126: }else{ /* Vn*Vm Vn is quanti */
8127: if(DummyV[Tvard[ijp][2]]==0){
8128: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8129: }else{ /* Both quanti */
8130: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8131: }
1.237 brouard 8132: }
1.268 brouard 8133: ijp++;
1.237 brouard 8134: }
1.268 brouard 8135: } /* end Tprod */
1.237 brouard 8136: } else{ /* simple covariate */
1.264 brouard 8137: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8138: if(Dummy[j]==0){
8139: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8140: }else{ /* quantitative */
8141: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8142: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8143: }
1.237 brouard 8144: } /* end simple */
8145: } /* end j */
1.223 brouard 8146: }else{
8147: i=i-ncovmodel;
8148: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8149: fprintf(ficgp," (1.");
8150: }
1.227 brouard 8151:
1.223 brouard 8152: if(ng != 1){
8153: fprintf(ficgp,")/(1");
1.227 brouard 8154:
1.264 brouard 8155: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8156: if(nagesqr==0)
1.264 brouard 8157: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8158: else /* nagesqr =1 */
1.264 brouard 8159: 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 8160:
1.223 brouard 8161: ij=1;
8162: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8163: if(cptcovage >0){
8164: if((j-2)==Tage[ij]) { /* Bug valgrind */
8165: if(ij <=cptcovage) { /* Bug valgrind */
8166: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8167: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8168: ij++;
8169: }
8170: }
8171: }else
8172: 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 8173: }
8174: fprintf(ficgp,")");
8175: }
8176: fprintf(ficgp,")");
8177: if(ng ==2)
1.276 brouard 8178: 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 8179: else /* ng= 3 */
1.276 brouard 8180: 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 8181: }else{ /* end ng <> 1 */
8182: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8183: 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 8184: }
8185: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8186: fprintf(ficgp,",");
8187: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8188: fprintf(ficgp,",");
8189: i=i+ncovmodel;
8190: } /* end k */
8191: } /* end k2 */
1.276 brouard 8192: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8193: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8194: } /* end k1 */
1.223 brouard 8195: } /* end ng */
8196: /* avoid: */
8197: fflush(ficgp);
1.126 brouard 8198: } /* end gnuplot */
8199:
8200:
8201: /*************** Moving average **************/
1.219 brouard 8202: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8203: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8204:
1.222 brouard 8205: int i, cpt, cptcod;
8206: int modcovmax =1;
8207: int mobilavrange, mob;
8208: int iage=0;
1.288 brouard 8209: int firstA1=0, firstA2=0;
1.222 brouard 8210:
1.266 brouard 8211: double sum=0., sumr=0.;
1.222 brouard 8212: double age;
1.266 brouard 8213: double *sumnewp, *sumnewm, *sumnewmr;
8214: double *agemingood, *agemaxgood;
8215: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8216:
8217:
1.278 brouard 8218: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8219: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8220:
8221: sumnewp = vector(1,ncovcombmax);
8222: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8223: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8224: agemingood = vector(1,ncovcombmax);
1.266 brouard 8225: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8226: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8227: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8228:
8229: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8230: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8231: sumnewp[cptcod]=0.;
1.266 brouard 8232: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8233: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8234: }
8235: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8236:
1.266 brouard 8237: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8238: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8239: else mobilavrange=mobilav;
8240: for (age=bage; age<=fage; age++)
8241: for (i=1; i<=nlstate;i++)
8242: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8243: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8244: /* We keep the original values on the extreme ages bage, fage and for
8245: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8246: we use a 5 terms etc. until the borders are no more concerned.
8247: */
8248: for (mob=3;mob <=mobilavrange;mob=mob+2){
8249: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8250: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8251: sumnewm[cptcod]=0.;
8252: for (i=1; i<=nlstate;i++){
1.222 brouard 8253: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8254: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8255: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8256: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8257: }
8258: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8259: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8260: } /* end i */
8261: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8262: } /* end cptcod */
1.222 brouard 8263: }/* end age */
8264: }/* end mob */
1.266 brouard 8265: }else{
8266: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8267: return -1;
1.266 brouard 8268: }
8269:
8270: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8271: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8272: if(invalidvarcomb[cptcod]){
8273: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8274: continue;
8275: }
1.219 brouard 8276:
1.266 brouard 8277: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8278: sumnewm[cptcod]=0.;
8279: sumnewmr[cptcod]=0.;
8280: for (i=1; i<=nlstate;i++){
8281: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8282: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8283: }
8284: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8285: agemingoodr[cptcod]=age;
8286: }
8287: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8288: agemingood[cptcod]=age;
8289: }
8290: } /* age */
8291: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8292: sumnewm[cptcod]=0.;
1.266 brouard 8293: sumnewmr[cptcod]=0.;
1.222 brouard 8294: for (i=1; i<=nlstate;i++){
8295: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8296: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8297: }
8298: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8299: agemaxgoodr[cptcod]=age;
1.222 brouard 8300: }
8301: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8302: agemaxgood[cptcod]=age;
8303: }
8304: } /* age */
8305: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8306: /* but they will change */
1.288 brouard 8307: firstA1=0;firstA2=0;
1.266 brouard 8308: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8309: sumnewm[cptcod]=0.;
8310: sumnewmr[cptcod]=0.;
8311: for (i=1; i<=nlstate;i++){
8312: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8313: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8314: }
8315: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8316: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8317: agemaxgoodr[cptcod]=age; /* age min */
8318: for (i=1; i<=nlstate;i++)
8319: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8320: }else{ /* bad we change the value with the values of good ages */
8321: for (i=1; i<=nlstate;i++){
8322: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8323: } /* i */
8324: } /* end bad */
8325: }else{
8326: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8327: agemaxgood[cptcod]=age;
8328: }else{ /* bad we change the value with the values of good ages */
8329: for (i=1; i<=nlstate;i++){
8330: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8331: } /* i */
8332: } /* end bad */
8333: }/* end else */
8334: sum=0.;sumr=0.;
8335: for (i=1; i<=nlstate;i++){
8336: sum+=mobaverage[(int)age][i][cptcod];
8337: sumr+=probs[(int)age][i][cptcod];
8338: }
8339: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8340: if(!firstA1){
8341: firstA1=1;
8342: 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);
8343: }
8344: 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 8345: } /* end bad */
8346: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8347: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8348: if(!firstA2){
8349: firstA2=1;
8350: 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);
8351: }
8352: 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 8353: } /* end bad */
8354: }/* age */
1.266 brouard 8355:
8356: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8357: sumnewm[cptcod]=0.;
1.266 brouard 8358: sumnewmr[cptcod]=0.;
1.222 brouard 8359: for (i=1; i<=nlstate;i++){
8360: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8361: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8362: }
8363: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8364: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8365: agemingoodr[cptcod]=age;
8366: for (i=1; i<=nlstate;i++)
8367: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8368: }else{ /* bad we change the value with the values of good ages */
8369: for (i=1; i<=nlstate;i++){
8370: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8371: } /* i */
8372: } /* end bad */
8373: }else{
8374: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8375: agemingood[cptcod]=age;
8376: }else{ /* bad */
8377: for (i=1; i<=nlstate;i++){
8378: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8379: } /* i */
8380: } /* end bad */
8381: }/* end else */
8382: sum=0.;sumr=0.;
8383: for (i=1; i<=nlstate;i++){
8384: sum+=mobaverage[(int)age][i][cptcod];
8385: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8386: }
1.266 brouard 8387: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8388: 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 8389: } /* end bad */
8390: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8391: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8392: 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 8393: } /* end bad */
8394: }/* age */
1.266 brouard 8395:
1.222 brouard 8396:
8397: for (age=bage; age<=fage; age++){
1.235 brouard 8398: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8399: sumnewp[cptcod]=0.;
8400: sumnewm[cptcod]=0.;
8401: for (i=1; i<=nlstate;i++){
8402: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8403: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8404: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8405: }
8406: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8407: }
8408: /* printf("\n"); */
8409: /* } */
1.266 brouard 8410:
1.222 brouard 8411: /* brutal averaging */
1.266 brouard 8412: /* for (i=1; i<=nlstate;i++){ */
8413: /* for (age=1; age<=bage; age++){ */
8414: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8415: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8416: /* } */
8417: /* for (age=fage; age<=AGESUP; age++){ */
8418: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8419: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8420: /* } */
8421: /* } /\* end i status *\/ */
8422: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8423: /* for (age=1; age<=AGESUP; age++){ */
8424: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8425: /* mobaverage[(int)age][i][cptcod]=0.; */
8426: /* } */
8427: /* } */
1.222 brouard 8428: }/* end cptcod */
1.266 brouard 8429: free_vector(agemaxgoodr,1, ncovcombmax);
8430: free_vector(agemaxgood,1, ncovcombmax);
8431: free_vector(agemingood,1, ncovcombmax);
8432: free_vector(agemingoodr,1, ncovcombmax);
8433: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8434: free_vector(sumnewm,1, ncovcombmax);
8435: free_vector(sumnewp,1, ncovcombmax);
8436: return 0;
8437: }/* End movingaverage */
1.218 brouard 8438:
1.126 brouard 8439:
1.296 brouard 8440:
1.126 brouard 8441: /************** Forecasting ******************/
1.296 brouard 8442: /* 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)*/
8443: 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){
8444: /* dateintemean, mean date of interviews
8445: dateprojd, year, month, day of starting projection
8446: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8447: agemin, agemax range of age
8448: dateprev1 dateprev2 range of dates during which prevalence is computed
8449: */
1.296 brouard 8450: /* double anprojd, mprojd, jprojd; */
8451: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8452: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8453: double agec; /* generic age */
1.296 brouard 8454: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8455: double *popeffectif,*popcount;
8456: double ***p3mat;
1.218 brouard 8457: /* double ***mobaverage; */
1.126 brouard 8458: char fileresf[FILENAMELENGTH];
8459:
8460: agelim=AGESUP;
1.211 brouard 8461: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8462: in each health status at the date of interview (if between dateprev1 and dateprev2).
8463: We still use firstpass and lastpass as another selection.
8464: */
1.214 brouard 8465: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8466: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8467:
1.201 brouard 8468: strcpy(fileresf,"F_");
8469: strcat(fileresf,fileresu);
1.126 brouard 8470: if((ficresf=fopen(fileresf,"w"))==NULL) {
8471: printf("Problem with forecast resultfile: %s\n", fileresf);
8472: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8473: }
1.235 brouard 8474: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8475: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8476:
1.225 brouard 8477: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8478:
8479:
8480: stepsize=(int) (stepm+YEARM-1)/YEARM;
8481: if (stepm<=12) stepsize=1;
8482: if(estepm < stepm){
8483: printf ("Problem %d lower than %d\n",estepm, stepm);
8484: }
1.270 brouard 8485: else{
8486: hstepm=estepm;
8487: }
8488: if(estepm > stepm){ /* Yes every two year */
8489: stepsize=2;
8490: }
1.296 brouard 8491: hstepm=hstepm/stepm;
1.126 brouard 8492:
1.296 brouard 8493:
8494: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8495: /* fractional in yp1 *\/ */
8496: /* aintmean=yp; */
8497: /* yp2=modf((yp1*12),&yp); */
8498: /* mintmean=yp; */
8499: /* yp1=modf((yp2*30.5),&yp); */
8500: /* jintmean=yp; */
8501: /* if(jintmean==0) jintmean=1; */
8502: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8503:
1.296 brouard 8504:
8505: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8506: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8507: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8508: i1=pow(2,cptcoveff);
1.126 brouard 8509: if (cptcovn < 1){i1=1;}
8510:
1.296 brouard 8511: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8512:
8513: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8514:
1.126 brouard 8515: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8516: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8517: for(k=1; k<=i1;k++){
1.253 brouard 8518: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8519: continue;
1.227 brouard 8520: if(invalidvarcomb[k]){
8521: printf("\nCombination (%d) projection ignored because no cases \n",k);
8522: continue;
8523: }
8524: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8525: for(j=1;j<=cptcoveff;j++) {
8526: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8527: }
1.235 brouard 8528: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8529: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8530: }
1.227 brouard 8531: fprintf(ficresf," yearproj age");
8532: for(j=1; j<=nlstate+ndeath;j++){
8533: for(i=1; i<=nlstate;i++)
8534: fprintf(ficresf," p%d%d",i,j);
8535: fprintf(ficresf," wp.%d",j);
8536: }
1.296 brouard 8537: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8538: fprintf(ficresf,"\n");
1.296 brouard 8539: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8540: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8541: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8542: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8543: nhstepm = nhstepm/hstepm;
8544: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8545: oldm=oldms;savm=savms;
1.268 brouard 8546: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8547: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8548: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8549: for (h=0; h<=nhstepm; h++){
8550: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8551: break;
8552: }
8553: }
8554: fprintf(ficresf,"\n");
8555: for(j=1;j<=cptcoveff;j++)
8556: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8557: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8558:
8559: for(j=1; j<=nlstate+ndeath;j++) {
8560: ppij=0.;
8561: for(i=1; i<=nlstate;i++) {
1.278 brouard 8562: if (mobilav>=1)
8563: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8564: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8565: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8566: }
1.268 brouard 8567: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8568: } /* end i */
8569: fprintf(ficresf," %.3f", ppij);
8570: }/* end j */
1.227 brouard 8571: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8572: } /* end agec */
1.266 brouard 8573: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8574: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8575: } /* end yearp */
8576: } /* end k */
1.219 brouard 8577:
1.126 brouard 8578: fclose(ficresf);
1.215 brouard 8579: printf("End of Computing forecasting \n");
8580: fprintf(ficlog,"End of Computing forecasting\n");
8581:
1.126 brouard 8582: }
8583:
1.269 brouard 8584: /************** Back Forecasting ******************/
1.296 brouard 8585: /* 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){ */
8586: 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){
8587: /* back1, year, month, day of starting backprojection
1.267 brouard 8588: agemin, agemax range of age
8589: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8590: anback2 year of end of backprojection (same day and month as back1).
8591: prevacurrent and prev are prevalences.
1.267 brouard 8592: */
8593: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8594: double agec; /* generic age */
1.302 brouard 8595: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8596: double *popeffectif,*popcount;
8597: double ***p3mat;
8598: /* double ***mobaverage; */
8599: char fileresfb[FILENAMELENGTH];
8600:
1.268 brouard 8601: agelim=AGEINF;
1.267 brouard 8602: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8603: in each health status at the date of interview (if between dateprev1 and dateprev2).
8604: We still use firstpass and lastpass as another selection.
8605: */
8606: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8607: /* firstpass, lastpass, stepm, weightopt, model); */
8608:
8609: /*Do we need to compute prevalence again?*/
8610:
8611: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8612:
8613: strcpy(fileresfb,"FB_");
8614: strcat(fileresfb,fileresu);
8615: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8616: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8617: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8618: }
8619: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8620: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8621:
8622: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8623:
8624:
8625: stepsize=(int) (stepm+YEARM-1)/YEARM;
8626: if (stepm<=12) stepsize=1;
8627: if(estepm < stepm){
8628: printf ("Problem %d lower than %d\n",estepm, stepm);
8629: }
1.270 brouard 8630: else{
8631: hstepm=estepm;
8632: }
8633: if(estepm >= stepm){ /* Yes every two year */
8634: stepsize=2;
8635: }
1.267 brouard 8636:
8637: hstepm=hstepm/stepm;
1.296 brouard 8638: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8639: /* fractional in yp1 *\/ */
8640: /* aintmean=yp; */
8641: /* yp2=modf((yp1*12),&yp); */
8642: /* mintmean=yp; */
8643: /* yp1=modf((yp2*30.5),&yp); */
8644: /* jintmean=yp; */
8645: /* if(jintmean==0) jintmean=1; */
8646: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8647:
8648: i1=pow(2,cptcoveff);
8649: if (cptcovn < 1){i1=1;}
8650:
1.296 brouard 8651: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8652: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8653:
8654: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8655:
8656: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8657: for(k=1; k<=i1;k++){
8658: if(i1 != 1 && TKresult[nres]!= k)
8659: continue;
8660: if(invalidvarcomb[k]){
8661: printf("\nCombination (%d) projection ignored because no cases \n",k);
8662: continue;
8663: }
1.268 brouard 8664: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8665: for(j=1;j<=cptcoveff;j++) {
8666: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8667: }
8668: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8669: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8670: }
8671: fprintf(ficresfb," yearbproj age");
8672: for(j=1; j<=nlstate+ndeath;j++){
8673: for(i=1; i<=nlstate;i++)
1.268 brouard 8674: fprintf(ficresfb," b%d%d",i,j);
8675: fprintf(ficresfb," b.%d",j);
1.267 brouard 8676: }
1.296 brouard 8677: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8678: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8679: fprintf(ficresfb,"\n");
1.296 brouard 8680: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8681: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8682: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8683: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8684: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8685: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8686: nhstepm = nhstepm/hstepm;
8687: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8688: oldm=oldms;savm=savms;
1.268 brouard 8689: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8690: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8691: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8692: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8693: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8694: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8695: for (h=0; h<=nhstepm; h++){
1.268 brouard 8696: if (h*hstepm/YEARM*stepm ==-yearp) {
8697: break;
8698: }
8699: }
8700: fprintf(ficresfb,"\n");
8701: for(j=1;j<=cptcoveff;j++)
8702: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8703: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8704: for(i=1; i<=nlstate+ndeath;i++) {
8705: ppij=0.;ppi=0.;
8706: for(j=1; j<=nlstate;j++) {
8707: /* if (mobilav==1) */
1.269 brouard 8708: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8709: ppi=ppi+prevacurrent[(int)agec][j][k];
8710: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8711: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8712: /* else { */
8713: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8714: /* } */
1.268 brouard 8715: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8716: } /* end j */
8717: if(ppi <0.99){
8718: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8719: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8720: }
8721: fprintf(ficresfb," %.3f", ppij);
8722: }/* end j */
1.267 brouard 8723: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8724: } /* end agec */
8725: } /* end yearp */
8726: } /* end k */
1.217 brouard 8727:
1.267 brouard 8728: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8729:
1.267 brouard 8730: fclose(ficresfb);
8731: printf("End of Computing Back forecasting \n");
8732: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8733:
1.267 brouard 8734: }
1.217 brouard 8735:
1.269 brouard 8736: /* Variance of prevalence limit: varprlim */
8737: 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 8738: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8739:
8740: char fileresvpl[FILENAMELENGTH];
8741: FILE *ficresvpl;
8742: double **oldm, **savm;
8743: double **varpl; /* Variances of prevalence limits by age */
8744: int i1, k, nres, j ;
8745:
8746: strcpy(fileresvpl,"VPL_");
8747: strcat(fileresvpl,fileresu);
8748: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8749: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8750: exit(0);
8751: }
1.288 brouard 8752: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8753: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8754:
8755: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8756: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8757:
8758: i1=pow(2,cptcoveff);
8759: if (cptcovn < 1){i1=1;}
8760:
8761: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8762: for(k=1; k<=i1;k++){
8763: if(i1 != 1 && TKresult[nres]!= k)
8764: continue;
8765: fprintf(ficresvpl,"\n#****** ");
8766: printf("\n#****** ");
8767: fprintf(ficlog,"\n#****** ");
8768: for(j=1;j<=cptcoveff;j++) {
8769: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8770: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8771: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8772: }
8773: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8774: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8775: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8776: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8777: }
8778: fprintf(ficresvpl,"******\n");
8779: printf("******\n");
8780: fprintf(ficlog,"******\n");
8781:
8782: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8783: oldm=oldms;savm=savms;
8784: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8785: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8786: /*}*/
8787: }
8788:
8789: fclose(ficresvpl);
1.288 brouard 8790: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8791: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8792:
8793: }
8794: /* Variance of back prevalence: varbprlim */
8795: 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){
8796: /*------- Variance of back (stable) prevalence------*/
8797:
8798: char fileresvbl[FILENAMELENGTH];
8799: FILE *ficresvbl;
8800:
8801: double **oldm, **savm;
8802: double **varbpl; /* Variances of back prevalence limits by age */
8803: int i1, k, nres, j ;
8804:
8805: strcpy(fileresvbl,"VBL_");
8806: strcat(fileresvbl,fileresu);
8807: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8808: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8809: exit(0);
8810: }
8811: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8812: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8813:
8814:
8815: i1=pow(2,cptcoveff);
8816: if (cptcovn < 1){i1=1;}
8817:
8818: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8819: for(k=1; k<=i1;k++){
8820: if(i1 != 1 && TKresult[nres]!= k)
8821: continue;
8822: fprintf(ficresvbl,"\n#****** ");
8823: printf("\n#****** ");
8824: fprintf(ficlog,"\n#****** ");
8825: for(j=1;j<=cptcoveff;j++) {
8826: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8827: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8828: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8829: }
8830: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8831: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8832: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8833: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8834: }
8835: fprintf(ficresvbl,"******\n");
8836: printf("******\n");
8837: fprintf(ficlog,"******\n");
8838:
8839: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8840: oldm=oldms;savm=savms;
8841:
8842: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8843: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8844: /*}*/
8845: }
8846:
8847: fclose(ficresvbl);
8848: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8849: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8850:
8851: } /* End of varbprlim */
8852:
1.126 brouard 8853: /************** Forecasting *****not tested NB*************/
1.227 brouard 8854: /* 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 8855:
1.227 brouard 8856: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8857: /* int *popage; */
8858: /* double calagedatem, agelim, kk1, kk2; */
8859: /* double *popeffectif,*popcount; */
8860: /* double ***p3mat,***tabpop,***tabpopprev; */
8861: /* /\* double ***mobaverage; *\/ */
8862: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8863:
1.227 brouard 8864: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8865: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8866: /* agelim=AGESUP; */
8867: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8868:
1.227 brouard 8869: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8870:
8871:
1.227 brouard 8872: /* strcpy(filerespop,"POP_"); */
8873: /* strcat(filerespop,fileresu); */
8874: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8875: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8876: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8877: /* } */
8878: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8879: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8880:
1.227 brouard 8881: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8882:
1.227 brouard 8883: /* /\* if (mobilav!=0) { *\/ */
8884: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8885: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8886: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8887: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8888: /* /\* } *\/ */
8889: /* /\* } *\/ */
1.126 brouard 8890:
1.227 brouard 8891: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8892: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8893:
1.227 brouard 8894: /* agelim=AGESUP; */
1.126 brouard 8895:
1.227 brouard 8896: /* hstepm=1; */
8897: /* hstepm=hstepm/stepm; */
1.218 brouard 8898:
1.227 brouard 8899: /* if (popforecast==1) { */
8900: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8901: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8902: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8903: /* } */
8904: /* popage=ivector(0,AGESUP); */
8905: /* popeffectif=vector(0,AGESUP); */
8906: /* popcount=vector(0,AGESUP); */
1.126 brouard 8907:
1.227 brouard 8908: /* i=1; */
8909: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8910:
1.227 brouard 8911: /* imx=i; */
8912: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8913: /* } */
1.218 brouard 8914:
1.227 brouard 8915: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8916: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8917: /* k=k+1; */
8918: /* fprintf(ficrespop,"\n#******"); */
8919: /* for(j=1;j<=cptcoveff;j++) { */
8920: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8921: /* } */
8922: /* fprintf(ficrespop,"******\n"); */
8923: /* fprintf(ficrespop,"# Age"); */
8924: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8925: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8926:
1.227 brouard 8927: /* for (cpt=0; cpt<=0;cpt++) { */
8928: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8929:
1.227 brouard 8930: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8931: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8932: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8933:
1.227 brouard 8934: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8935: /* oldm=oldms;savm=savms; */
8936: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8937:
1.227 brouard 8938: /* for (h=0; h<=nhstepm; h++){ */
8939: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8940: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8941: /* } */
8942: /* for(j=1; j<=nlstate+ndeath;j++) { */
8943: /* kk1=0.;kk2=0; */
8944: /* for(i=1; i<=nlstate;i++) { */
8945: /* if (mobilav==1) */
8946: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8947: /* else { */
8948: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8949: /* } */
8950: /* } */
8951: /* if (h==(int)(calagedatem+12*cpt)){ */
8952: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8953: /* /\*fprintf(ficrespop," %.3f", kk1); */
8954: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8955: /* } */
8956: /* } */
8957: /* for(i=1; i<=nlstate;i++){ */
8958: /* kk1=0.; */
8959: /* for(j=1; j<=nlstate;j++){ */
8960: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8961: /* } */
8962: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8963: /* } */
1.218 brouard 8964:
1.227 brouard 8965: /* if (h==(int)(calagedatem+12*cpt)) */
8966: /* for(j=1; j<=nlstate;j++) */
8967: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8968: /* } */
8969: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8970: /* } */
8971: /* } */
1.218 brouard 8972:
1.227 brouard 8973: /* /\******\/ */
1.218 brouard 8974:
1.227 brouard 8975: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8976: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8977: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8978: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8979: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8980:
1.227 brouard 8981: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8982: /* oldm=oldms;savm=savms; */
8983: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8984: /* for (h=0; h<=nhstepm; h++){ */
8985: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8986: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8987: /* } */
8988: /* for(j=1; j<=nlstate+ndeath;j++) { */
8989: /* kk1=0.;kk2=0; */
8990: /* for(i=1; i<=nlstate;i++) { */
8991: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8992: /* } */
8993: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8994: /* } */
8995: /* } */
8996: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8997: /* } */
8998: /* } */
8999: /* } */
9000: /* } */
1.218 brouard 9001:
1.227 brouard 9002: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 9003:
1.227 brouard 9004: /* if (popforecast==1) { */
9005: /* free_ivector(popage,0,AGESUP); */
9006: /* free_vector(popeffectif,0,AGESUP); */
9007: /* free_vector(popcount,0,AGESUP); */
9008: /* } */
9009: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9010: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
9011: /* fclose(ficrespop); */
9012: /* } /\* End of popforecast *\/ */
1.218 brouard 9013:
1.126 brouard 9014: int fileappend(FILE *fichier, char *optionfich)
9015: {
9016: if((fichier=fopen(optionfich,"a"))==NULL) {
9017: printf("Problem with file: %s\n", optionfich);
9018: fprintf(ficlog,"Problem with file: %s\n", optionfich);
9019: return (0);
9020: }
9021: fflush(fichier);
9022: return (1);
9023: }
9024:
9025:
9026: /**************** function prwizard **********************/
9027: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
9028: {
9029:
9030: /* Wizard to print covariance matrix template */
9031:
1.164 brouard 9032: char ca[32], cb[32];
9033: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 9034: int numlinepar;
9035:
9036: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9037: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9038: for(i=1; i <=nlstate; i++){
9039: jj=0;
9040: for(j=1; j <=nlstate+ndeath; j++){
9041: if(j==i) continue;
9042: jj++;
9043: /*ca[0]= k+'a'-1;ca[1]='\0';*/
9044: printf("%1d%1d",i,j);
9045: fprintf(ficparo,"%1d%1d",i,j);
9046: for(k=1; k<=ncovmodel;k++){
9047: /* printf(" %lf",param[i][j][k]); */
9048: /* fprintf(ficparo," %lf",param[i][j][k]); */
9049: printf(" 0.");
9050: fprintf(ficparo," 0.");
9051: }
9052: printf("\n");
9053: fprintf(ficparo,"\n");
9054: }
9055: }
9056: printf("# Scales (for hessian or gradient estimation)\n");
9057: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
9058: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
9059: for(i=1; i <=nlstate; i++){
9060: jj=0;
9061: for(j=1; j <=nlstate+ndeath; j++){
9062: if(j==i) continue;
9063: jj++;
9064: fprintf(ficparo,"%1d%1d",i,j);
9065: printf("%1d%1d",i,j);
9066: fflush(stdout);
9067: for(k=1; k<=ncovmodel;k++){
9068: /* printf(" %le",delti3[i][j][k]); */
9069: /* fprintf(ficparo," %le",delti3[i][j][k]); */
9070: printf(" 0.");
9071: fprintf(ficparo," 0.");
9072: }
9073: numlinepar++;
9074: printf("\n");
9075: fprintf(ficparo,"\n");
9076: }
9077: }
9078: printf("# Covariance matrix\n");
9079: /* # 121 Var(a12)\n\ */
9080: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9081: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9082: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9083: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9084: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9085: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9086: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9087: fflush(stdout);
9088: fprintf(ficparo,"# Covariance matrix\n");
9089: /* # 121 Var(a12)\n\ */
9090: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9091: /* # ...\n\ */
9092: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9093:
9094: for(itimes=1;itimes<=2;itimes++){
9095: jj=0;
9096: for(i=1; i <=nlstate; i++){
9097: for(j=1; j <=nlstate+ndeath; j++){
9098: if(j==i) continue;
9099: for(k=1; k<=ncovmodel;k++){
9100: jj++;
9101: ca[0]= k+'a'-1;ca[1]='\0';
9102: if(itimes==1){
9103: printf("#%1d%1d%d",i,j,k);
9104: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9105: }else{
9106: printf("%1d%1d%d",i,j,k);
9107: fprintf(ficparo,"%1d%1d%d",i,j,k);
9108: /* printf(" %.5le",matcov[i][j]); */
9109: }
9110: ll=0;
9111: for(li=1;li <=nlstate; li++){
9112: for(lj=1;lj <=nlstate+ndeath; lj++){
9113: if(lj==li) continue;
9114: for(lk=1;lk<=ncovmodel;lk++){
9115: ll++;
9116: if(ll<=jj){
9117: cb[0]= lk +'a'-1;cb[1]='\0';
9118: if(ll<jj){
9119: if(itimes==1){
9120: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9121: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9122: }else{
9123: printf(" 0.");
9124: fprintf(ficparo," 0.");
9125: }
9126: }else{
9127: if(itimes==1){
9128: printf(" Var(%s%1d%1d)",ca,i,j);
9129: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9130: }else{
9131: printf(" 0.");
9132: fprintf(ficparo," 0.");
9133: }
9134: }
9135: }
9136: } /* end lk */
9137: } /* end lj */
9138: } /* end li */
9139: printf("\n");
9140: fprintf(ficparo,"\n");
9141: numlinepar++;
9142: } /* end k*/
9143: } /*end j */
9144: } /* end i */
9145: } /* end itimes */
9146:
9147: } /* end of prwizard */
9148: /******************* Gompertz Likelihood ******************************/
9149: double gompertz(double x[])
9150: {
1.302 brouard 9151: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9152: int i,n=0; /* n is the size of the sample */
9153:
1.220 brouard 9154: for (i=1;i<=imx ; i++) {
1.126 brouard 9155: sump=sump+weight[i];
9156: /* sump=sump+1;*/
9157: num=num+1;
9158: }
1.302 brouard 9159: L=0.0;
9160: /* agegomp=AGEGOMP; */
1.126 brouard 9161: /* for (i=0; i<=imx; i++)
9162: 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]);*/
9163:
1.302 brouard 9164: for (i=1;i<=imx ; i++) {
9165: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9166: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9167: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9168: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9169: * +
9170: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9171: */
9172: if (wav[i] > 1 || agedc[i] < AGESUP) {
9173: if (cens[i] == 1){
9174: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9175: } else if (cens[i] == 0){
1.126 brouard 9176: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9177: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9178: } else
9179: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9180: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9181: L=L+A*weight[i];
1.126 brouard 9182: /* 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 9183: }
9184: }
1.126 brouard 9185:
1.302 brouard 9186: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9187:
9188: return -2*L*num/sump;
9189: }
9190:
1.136 brouard 9191: #ifdef GSL
9192: /******************* Gompertz_f Likelihood ******************************/
9193: double gompertz_f(const gsl_vector *v, void *params)
9194: {
1.302 brouard 9195: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9196: double *x= (double *) v->data;
9197: int i,n=0; /* n is the size of the sample */
9198:
9199: for (i=0;i<=imx-1 ; i++) {
9200: sump=sump+weight[i];
9201: /* sump=sump+1;*/
9202: num=num+1;
9203: }
9204:
9205:
9206: /* for (i=0; i<=imx; i++)
9207: 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]);*/
9208: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9209: for (i=1;i<=imx ; i++)
9210: {
9211: if (cens[i] == 1 && wav[i]>1)
9212: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9213:
9214: if (cens[i] == 0 && wav[i]>1)
9215: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9216: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9217:
9218: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9219: if (wav[i] > 1 ) { /* ??? */
9220: LL=LL+A*weight[i];
9221: /* 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]);*/
9222: }
9223: }
9224:
9225: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9226: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9227:
9228: return -2*LL*num/sump;
9229: }
9230: #endif
9231:
1.126 brouard 9232: /******************* Printing html file ***********/
1.201 brouard 9233: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9234: int lastpass, int stepm, int weightopt, char model[],\
9235: int imx, double p[],double **matcov,double agemortsup){
9236: int i,k;
9237:
9238: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9239: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9240: for (i=1;i<=2;i++)
9241: 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 9242: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9243: fprintf(fichtm,"</ul>");
9244:
9245: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9246:
9247: 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>");
9248:
9249: for (k=agegomp;k<(agemortsup-2);k++)
9250: 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]);
9251:
9252:
9253: fflush(fichtm);
9254: }
9255:
9256: /******************* Gnuplot file **************/
1.201 brouard 9257: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9258:
9259: char dirfileres[132],optfileres[132];
1.164 brouard 9260:
1.126 brouard 9261: int ng;
9262:
9263:
9264: /*#ifdef windows */
9265: fprintf(ficgp,"cd \"%s\" \n",pathc);
9266: /*#endif */
9267:
9268:
9269: strcpy(dirfileres,optionfilefiname);
9270: strcpy(optfileres,"vpl");
1.199 brouard 9271: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9272: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9273: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9274: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9275: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9276:
9277: }
9278:
1.136 brouard 9279: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9280: {
1.126 brouard 9281:
1.136 brouard 9282: /*-------- data file ----------*/
9283: FILE *fic;
9284: char dummy[]=" ";
1.240 brouard 9285: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9286: int lstra;
1.136 brouard 9287: int linei, month, year,iout;
1.302 brouard 9288: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9289: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9290: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9291: char *stratrunc;
1.223 brouard 9292:
1.240 brouard 9293: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9294: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9295:
1.240 brouard 9296: for(v=1; v <=ncovcol;v++){
9297: DummyV[v]=0;
9298: FixedV[v]=0;
9299: }
9300: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9301: DummyV[v]=1;
9302: FixedV[v]=0;
9303: }
9304: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9305: DummyV[v]=0;
9306: FixedV[v]=1;
9307: }
9308: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9309: DummyV[v]=1;
9310: FixedV[v]=1;
9311: }
9312: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9313: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9314: 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]);
9315: }
1.126 brouard 9316:
1.136 brouard 9317: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9318: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9319: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9320: }
1.126 brouard 9321:
1.302 brouard 9322: /* Is it a BOM UTF-8 Windows file? */
9323: /* First data line */
9324: linei=0;
9325: while(fgets(line, MAXLINE, fic)) {
9326: noffset=0;
9327: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9328: {
9329: noffset=noffset+3;
9330: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9331: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9332: fflush(ficlog); return 1;
9333: }
9334: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9335: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9336: {
9337: noffset=noffset+2;
1.304 brouard 9338: 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);
9339: 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 9340: fflush(ficlog); return 1;
9341: }
9342: else if( line[0] == 0 && line[1] == 0)
9343: {
9344: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9345: noffset=noffset+4;
1.304 brouard 9346: 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);
9347: 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 9348: fflush(ficlog); return 1;
9349: }
9350: } else{
9351: ;/*printf(" Not a BOM file\n");*/
9352: }
9353: /* If line starts with a # it is a comment */
9354: if (line[noffset] == '#') {
9355: linei=linei+1;
9356: break;
9357: }else{
9358: break;
9359: }
9360: }
9361: fclose(fic);
9362: if((fic=fopen(datafile,"r"))==NULL) {
9363: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9364: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9365: }
9366: /* Not a Bom file */
9367:
1.136 brouard 9368: i=1;
9369: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9370: linei=linei+1;
9371: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9372: if(line[j] == '\t')
9373: line[j] = ' ';
9374: }
9375: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9376: ;
9377: };
9378: line[j+1]=0; /* Trims blanks at end of line */
9379: if(line[0]=='#'){
9380: fprintf(ficlog,"Comment line\n%s\n",line);
9381: printf("Comment line\n%s\n",line);
9382: continue;
9383: }
9384: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9385: strcpy(line, linetmp);
1.223 brouard 9386:
9387: /* Loops on waves */
9388: for (j=maxwav;j>=1;j--){
9389: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9390: cutv(stra, strb, line, ' ');
9391: if(strb[0]=='.') { /* Missing value */
9392: lval=-1;
9393: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9394: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9395: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9396: 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);
9397: 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);
9398: return 1;
9399: }
9400: }else{
9401: errno=0;
9402: /* what_kind_of_number(strb); */
9403: dval=strtod(strb,&endptr);
9404: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9405: /* if(strb != endptr && *endptr == '\0') */
9406: /* dval=dlval; */
9407: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9408: if( strb[0]=='\0' || (*endptr != '\0')){
9409: 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);
9410: 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);
9411: return 1;
9412: }
9413: cotqvar[j][iv][i]=dval;
9414: cotvar[j][ntv+iv][i]=dval;
9415: }
9416: strcpy(line,stra);
1.223 brouard 9417: }/* end loop ntqv */
1.225 brouard 9418:
1.223 brouard 9419: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9420: cutv(stra, strb, line, ' ');
9421: if(strb[0]=='.') { /* Missing value */
9422: lval=-1;
9423: }else{
9424: errno=0;
9425: lval=strtol(strb,&endptr,10);
9426: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9427: if( strb[0]=='\0' || (*endptr != '\0')){
9428: 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);
9429: 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);
9430: return 1;
9431: }
9432: }
9433: if(lval <-1 || lval >1){
9434: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9435: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9436: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9437: For example, for multinomial values like 1, 2 and 3,\n \
9438: build V1=0 V2=0 for the reference value (1),\n \
9439: V1=1 V2=0 for (2) \n \
1.223 brouard 9440: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9441: output of IMaCh is often meaningless.\n \
1.223 brouard 9442: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9443: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9444: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9445: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9446: For example, for multinomial values like 1, 2 and 3,\n \
9447: build V1=0 V2=0 for the reference value (1),\n \
9448: V1=1 V2=0 for (2) \n \
1.223 brouard 9449: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9450: output of IMaCh is often meaningless.\n \
1.223 brouard 9451: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9452: return 1;
9453: }
9454: cotvar[j][iv][i]=(double)(lval);
9455: strcpy(line,stra);
1.223 brouard 9456: }/* end loop ntv */
1.225 brouard 9457:
1.223 brouard 9458: /* Statuses at wave */
1.137 brouard 9459: cutv(stra, strb, line, ' ');
1.223 brouard 9460: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9461: lval=-1;
1.136 brouard 9462: }else{
1.238 brouard 9463: errno=0;
9464: lval=strtol(strb,&endptr,10);
9465: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9466: if( strb[0]=='\0' || (*endptr != '\0')){
9467: 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);
9468: 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);
9469: return 1;
9470: }
1.136 brouard 9471: }
1.225 brouard 9472:
1.136 brouard 9473: s[j][i]=lval;
1.225 brouard 9474:
1.223 brouard 9475: /* Date of Interview */
1.136 brouard 9476: strcpy(line,stra);
9477: cutv(stra, strb,line,' ');
1.169 brouard 9478: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9479: }
1.169 brouard 9480: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9481: month=99;
9482: year=9999;
1.136 brouard 9483: }else{
1.225 brouard 9484: 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);
9485: 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);
9486: return 1;
1.136 brouard 9487: }
9488: anint[j][i]= (double) year;
1.302 brouard 9489: mint[j][i]= (double)month;
9490: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9491: /* 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]); */
9492: /* 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]); */
9493: /* } */
1.136 brouard 9494: strcpy(line,stra);
1.223 brouard 9495: } /* End loop on waves */
1.225 brouard 9496:
1.223 brouard 9497: /* Date of death */
1.136 brouard 9498: cutv(stra, strb,line,' ');
1.169 brouard 9499: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9500: }
1.169 brouard 9501: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9502: month=99;
9503: year=9999;
9504: }else{
1.141 brouard 9505: 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 9506: 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);
9507: return 1;
1.136 brouard 9508: }
9509: andc[i]=(double) year;
9510: moisdc[i]=(double) month;
9511: strcpy(line,stra);
9512:
1.223 brouard 9513: /* Date of birth */
1.136 brouard 9514: cutv(stra, strb,line,' ');
1.169 brouard 9515: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9516: }
1.169 brouard 9517: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9518: month=99;
9519: year=9999;
9520: }else{
1.141 brouard 9521: 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);
9522: 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 9523: return 1;
1.136 brouard 9524: }
9525: if (year==9999) {
1.141 brouard 9526: 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);
9527: 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 9528: return 1;
9529:
1.136 brouard 9530: }
9531: annais[i]=(double)(year);
1.302 brouard 9532: moisnais[i]=(double)(month);
9533: for (j=1;j<=maxwav;j++){
9534: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9535: 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]);
9536: 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]);
9537: }
9538: }
9539:
1.136 brouard 9540: strcpy(line,stra);
1.225 brouard 9541:
1.223 brouard 9542: /* Sample weight */
1.136 brouard 9543: cutv(stra, strb,line,' ');
9544: errno=0;
9545: dval=strtod(strb,&endptr);
9546: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9547: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9548: 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 9549: fflush(ficlog);
9550: return 1;
9551: }
9552: weight[i]=dval;
9553: strcpy(line,stra);
1.225 brouard 9554:
1.223 brouard 9555: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9556: cutv(stra, strb, line, ' ');
9557: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9558: lval=-1;
1.311 brouard 9559: coqvar[iv][i]=NAN;
9560: covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
1.223 brouard 9561: }else{
1.225 brouard 9562: errno=0;
9563: /* what_kind_of_number(strb); */
9564: dval=strtod(strb,&endptr);
9565: /* if(strb != endptr && *endptr == '\0') */
9566: /* dval=dlval; */
9567: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9568: if( strb[0]=='\0' || (*endptr != '\0')){
9569: 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);
9570: 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);
9571: return 1;
9572: }
9573: coqvar[iv][i]=dval;
1.226 brouard 9574: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9575: }
9576: strcpy(line,stra);
9577: }/* end loop nqv */
1.136 brouard 9578:
1.223 brouard 9579: /* Covariate values */
1.136 brouard 9580: for (j=ncovcol;j>=1;j--){
9581: cutv(stra, strb,line,' ');
1.223 brouard 9582: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9583: lval=-1;
1.136 brouard 9584: }else{
1.225 brouard 9585: errno=0;
9586: lval=strtol(strb,&endptr,10);
9587: if( strb[0]=='\0' || (*endptr != '\0')){
9588: 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);
9589: 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);
9590: return 1;
9591: }
1.136 brouard 9592: }
9593: if(lval <-1 || lval >1){
1.225 brouard 9594: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9595: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9596: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9597: For example, for multinomial values like 1, 2 and 3,\n \
9598: build V1=0 V2=0 for the reference value (1),\n \
9599: V1=1 V2=0 for (2) \n \
1.136 brouard 9600: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9601: output of IMaCh is often meaningless.\n \
1.136 brouard 9602: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9603: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9604: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9605: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9606: For example, for multinomial values like 1, 2 and 3,\n \
9607: build V1=0 V2=0 for the reference value (1),\n \
9608: V1=1 V2=0 for (2) \n \
1.136 brouard 9609: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9610: output of IMaCh is often meaningless.\n \
1.136 brouard 9611: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9612: return 1;
1.136 brouard 9613: }
9614: covar[j][i]=(double)(lval);
9615: strcpy(line,stra);
9616: }
9617: lstra=strlen(stra);
1.225 brouard 9618:
1.136 brouard 9619: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9620: stratrunc = &(stra[lstra-9]);
9621: num[i]=atol(stratrunc);
9622: }
9623: else
9624: num[i]=atol(stra);
9625: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9626: 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;}*/
9627:
9628: i=i+1;
9629: } /* End loop reading data */
1.225 brouard 9630:
1.136 brouard 9631: *imax=i-1; /* Number of individuals */
9632: fclose(fic);
1.225 brouard 9633:
1.136 brouard 9634: return (0);
1.164 brouard 9635: /* endread: */
1.225 brouard 9636: printf("Exiting readdata: ");
9637: fclose(fic);
9638: return (1);
1.223 brouard 9639: }
1.126 brouard 9640:
1.234 brouard 9641: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9642: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9643: while (*p2 == ' ')
1.234 brouard 9644: p2++;
9645: /* while ((*p1++ = *p2++) !=0) */
9646: /* ; */
9647: /* do */
9648: /* while (*p2 == ' ') */
9649: /* p2++; */
9650: /* while (*p1++ == *p2++); */
9651: *stri=p2;
1.145 brouard 9652: }
9653:
1.235 brouard 9654: int decoderesult ( char resultline[], int nres)
1.230 brouard 9655: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9656: {
1.235 brouard 9657: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9658: char resultsav[MAXLINE];
1.234 brouard 9659: int resultmodel[MAXLINE];
9660: int modelresult[MAXLINE];
1.230 brouard 9661: char stra[80], strb[80], strc[80], strd[80],stre[80];
9662:
1.234 brouard 9663: removefirstspace(&resultline);
1.230 brouard 9664:
9665: if (strstr(resultline,"v") !=0){
9666: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9667: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9668: return 1;
9669: }
9670: trimbb(resultsav, resultline);
9671: if (strlen(resultsav) >1){
9672: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9673: }
1.253 brouard 9674: if(j == 0){ /* Resultline but no = */
9675: TKresult[nres]=0; /* Combination for the nresult and the model */
9676: return (0);
9677: }
1.234 brouard 9678: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
1.310 brouard 9679: printf("ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);
9680: 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 9681: }
9682: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9683: if(nbocc(resultsav,'=') >1){
9684: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
1.310 brouard 9685: resultsav= V4=1 V5=25.1 V3=0 stra= V5=25.1 V3=0 strb= V4=1 */
1.234 brouard 9686: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9687: }else
9688: cutl(strc,strd,resultsav,'=');
1.230 brouard 9689: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9690:
1.230 brouard 9691: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9692: Tvarsel[k]=atoi(strc);
9693: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9694: /* cptcovsel++; */
9695: if (nbocc(stra,'=') >0)
9696: strcpy(resultsav,stra); /* and analyzes it */
9697: }
1.235 brouard 9698: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9699: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9700: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9701: match=0;
1.236 brouard 9702: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9703: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9704: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9705: match=1;
9706: break;
9707: }
9708: }
9709: if(match == 0){
1.310 brouard 9710: printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
9711: fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
9712: return 1;
1.234 brouard 9713: }
9714: }
9715: }
1.235 brouard 9716: /* Checking for missing or useless values in comparison of current model needs */
9717: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9718: match=0;
1.235 brouard 9719: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9720: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9721: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9722: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9723: ++match;
9724: }
9725: }
9726: }
9727: if(match == 0){
9728: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
1.310 brouard 9729: fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9730: return 1;
1.234 brouard 9731: }else if(match > 1){
9732: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
1.310 brouard 9733: fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9734: return 1;
1.234 brouard 9735: }
9736: }
1.235 brouard 9737:
1.234 brouard 9738: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9739: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9740: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9741: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9742: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9743: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9744: /* 1 0 0 0 */
9745: /* 2 1 0 0 */
9746: /* 3 0 1 0 */
9747: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9748: /* 5 0 0 1 */
9749: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9750: /* 7 0 1 1 */
9751: /* 8 1 1 1 */
1.237 brouard 9752: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9753: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9754: /* V5*age V5 known which value for nres? */
9755: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9756: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9757: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9758: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9759: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9760: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9761: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9762: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9763: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9764: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9765: k4++;;
9766: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9767: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9768: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9769: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9770: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9771: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9772: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9773: k4q++;;
9774: }
9775: }
1.234 brouard 9776:
1.235 brouard 9777: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9778: return (0);
9779: }
1.235 brouard 9780:
1.230 brouard 9781: int decodemodel( char model[], int lastobs)
9782: /**< This routine decodes the model and returns:
1.224 brouard 9783: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9784: * - nagesqr = 1 if age*age in the model, otherwise 0.
9785: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9786: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9787: * - cptcovage number of covariates with age*products =2
9788: * - cptcovs number of simple covariates
9789: * - 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
9790: * which is a new column after the 9 (ncovcol) variables.
9791: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9792: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9793: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9794: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9795: */
1.136 brouard 9796: {
1.238 brouard 9797: int i, j, k, ks, v;
1.227 brouard 9798: int j1, k1, k2, k3, k4;
1.136 brouard 9799: char modelsav[80];
1.145 brouard 9800: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9801: char *strpt;
1.136 brouard 9802:
1.145 brouard 9803: /*removespace(model);*/
1.136 brouard 9804: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9805: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9806: if (strstr(model,"AGE") !=0){
1.192 brouard 9807: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9808: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9809: return 1;
9810: }
1.141 brouard 9811: if (strstr(model,"v") !=0){
9812: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9813: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9814: return 1;
9815: }
1.187 brouard 9816: strcpy(modelsav,model);
9817: if ((strpt=strstr(model,"age*age")) !=0){
9818: printf(" strpt=%s, model=%s\n",strpt, model);
9819: if(strpt != model){
1.234 brouard 9820: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9821: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9822: corresponding column of parameters.\n",model);
1.234 brouard 9823: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9824: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9825: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9826: return 1;
1.225 brouard 9827: }
1.187 brouard 9828: nagesqr=1;
9829: if (strstr(model,"+age*age") !=0)
1.234 brouard 9830: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9831: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9832: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9833: else
1.234 brouard 9834: substrchaine(modelsav, model, "age*age");
1.187 brouard 9835: }else
9836: nagesqr=0;
9837: if (strlen(modelsav) >1){
9838: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9839: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9840: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9841: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9842: * cst, age and age*age
9843: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9844: /* including age products which are counted in cptcovage.
9845: * but the covariates which are products must be treated
9846: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9847: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9848: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9849:
9850:
1.187 brouard 9851: /* Design
9852: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9853: * < ncovcol=8 >
9854: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9855: * k= 1 2 3 4 5 6 7 8
9856: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9857: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9858: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9859: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9860: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9861: * Tage[++cptcovage]=k
9862: * if products, new covar are created after ncovcol with k1
9863: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9864: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9865: * 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
9866: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9867: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9868: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9869: * < ncovcol=8 >
9870: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9871: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9872: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9873: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9874: * p Tprod[1]@2={ 6, 5}
9875: *p Tvard[1][1]@4= {7, 8, 5, 6}
9876: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9877: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9878: *How to reorganize?
9879: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9880: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9881: * {2, 1, 4, 8, 5, 6, 3, 7}
9882: * Struct []
9883: */
1.225 brouard 9884:
1.187 brouard 9885: /* This loop fills the array Tvar from the string 'model'.*/
9886: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9887: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9888: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9889: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9890: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9891: /* k=1 Tvar[1]=2 (from V2) */
9892: /* k=5 Tvar[5] */
9893: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9894: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9895: /* } */
1.198 brouard 9896: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9897: /*
9898: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9899: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9900: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9901: }
1.187 brouard 9902: cptcovage=0;
9903: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9904: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9905: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9906: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9907: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9908: /*scanf("%d",i);*/
9909: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9910: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9911: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9912: /* covar is not filled and then is empty */
9913: cptcovprod--;
9914: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9915: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9916: Typevar[k]=1; /* 1 for age product */
9917: cptcovage++; /* Sums the number of covariates which include age as a product */
9918: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9919: /*printf("stre=%s ", stre);*/
9920: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9921: cptcovprod--;
9922: cutl(stre,strb,strc,'V');
9923: Tvar[k]=atoi(stre);
9924: Typevar[k]=1; /* 1 for age product */
9925: cptcovage++;
9926: Tage[cptcovage]=k;
9927: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9928: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9929: cptcovn++;
9930: cptcovprodnoage++;k1++;
9931: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9932: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9933: because this model-covariate is a construction we invent a new column
9934: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9935: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9936: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9937: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9938: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9939: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9940: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9941: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9942: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9943: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9944: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9945: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9946: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9947: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9948: for (i=1; i<=lastobs;i++){
9949: /* Computes the new covariate which is a product of
9950: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9951: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9952: }
9953: } /* End age is not in the model */
9954: } /* End if model includes a product */
9955: else { /* no more sum */
9956: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9957: /* scanf("%d",i);*/
9958: cutl(strd,strc,strb,'V');
9959: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9960: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9961: Tvar[k]=atoi(strd);
9962: Typevar[k]=0; /* 0 for simple covariates */
9963: }
9964: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9965: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9966: scanf("%d",i);*/
1.187 brouard 9967: } /* end of loop + on total covariates */
9968: } /* end if strlen(modelsave == 0) age*age might exist */
9969: } /* end if strlen(model == 0) */
1.136 brouard 9970:
9971: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9972: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9973:
1.136 brouard 9974: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9975: printf("cptcovprod=%d ", cptcovprod);
9976: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9977: scanf("%d ",i);*/
9978:
9979:
1.230 brouard 9980: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9981: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9982: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9983: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9984: k = 1 2 3 4 5 6 7 8 9
9985: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9986: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9987: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9988: Dummy[k] 1 0 0 0 3 1 1 2 3
9989: Tmodelind[combination of covar]=k;
1.225 brouard 9990: */
9991: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9992: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9993: /* 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 9994: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9995: printf("Model=%s\n\
9996: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9997: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9998: 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);
9999: fprintf(ficlog,"Model=%s\n\
10000: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
10001: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
10002: 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 10003: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 10004: 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 */
10005: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 10006: Fixed[k]= 0;
10007: Dummy[k]= 0;
1.225 brouard 10008: ncoveff++;
1.232 brouard 10009: ncovf++;
1.234 brouard 10010: nsd++;
10011: modell[k].maintype= FTYPE;
10012: TvarsD[nsd]=Tvar[k];
10013: TvarsDind[nsd]=k;
10014: TvarF[ncovf]=Tvar[k];
10015: TvarFind[ncovf]=k;
10016: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
10017: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
10018: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
10019: Fixed[k]= 0;
10020: Dummy[k]= 0;
10021: ncoveff++;
10022: ncovf++;
10023: modell[k].maintype= FTYPE;
10024: TvarF[ncovf]=Tvar[k];
10025: TvarFind[ncovf]=k;
1.230 brouard 10026: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 10027: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 10028: }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 10029: Fixed[k]= 0;
10030: Dummy[k]= 1;
1.230 brouard 10031: nqfveff++;
1.234 brouard 10032: modell[k].maintype= FTYPE;
10033: modell[k].subtype= FQ;
10034: nsq++;
10035: TvarsQ[nsq]=Tvar[k];
10036: TvarsQind[nsq]=k;
1.232 brouard 10037: ncovf++;
1.234 brouard 10038: TvarF[ncovf]=Tvar[k];
10039: TvarFind[ncovf]=k;
1.231 brouard 10040: 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 10041: 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 10042: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 10043: Fixed[k]= 1;
10044: Dummy[k]= 0;
1.225 brouard 10045: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 10046: modell[k].maintype= VTYPE;
10047: modell[k].subtype= VD;
10048: nsd++;
10049: TvarsD[nsd]=Tvar[k];
10050: TvarsDind[nsd]=k;
10051: ncovv++; /* Only simple time varying variables */
10052: TvarV[ncovv]=Tvar[k];
1.242 brouard 10053: 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 10054: 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 */
10055: 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 10056: 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);
10057: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 10058: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 10059: Fixed[k]= 1;
10060: Dummy[k]= 1;
10061: nqtveff++;
10062: modell[k].maintype= VTYPE;
10063: modell[k].subtype= VQ;
10064: ncovv++; /* Only simple time varying variables */
10065: nsq++;
10066: TvarsQ[nsq]=Tvar[k];
10067: TvarsQind[nsq]=k;
10068: TvarV[ncovv]=Tvar[k];
1.242 brouard 10069: 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 10070: 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 */
10071: 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 10072: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
10073: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
10074: 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 10075: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 10076: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 10077: ncova++;
10078: TvarA[ncova]=Tvar[k];
10079: TvarAind[ncova]=k;
1.231 brouard 10080: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10081: Fixed[k]= 2;
10082: Dummy[k]= 2;
10083: modell[k].maintype= ATYPE;
10084: modell[k].subtype= APFD;
10085: /* ncoveff++; */
1.227 brouard 10086: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10087: Fixed[k]= 2;
10088: Dummy[k]= 3;
10089: modell[k].maintype= ATYPE;
10090: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10091: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10092: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10093: Fixed[k]= 3;
10094: Dummy[k]= 2;
10095: modell[k].maintype= ATYPE;
10096: modell[k].subtype= APVD; /* Product age * varying dummy */
10097: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10098: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10099: Fixed[k]= 3;
10100: Dummy[k]= 3;
10101: modell[k].maintype= ATYPE;
10102: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10103: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10104: }
10105: }else if (Typevar[k] == 2) { /* product without age */
10106: k1=Tposprod[k];
10107: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10108: if(Tvard[k1][2] <=ncovcol){
10109: Fixed[k]= 1;
10110: Dummy[k]= 0;
10111: modell[k].maintype= FTYPE;
10112: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10113: ncovf++; /* Fixed variables without age */
10114: TvarF[ncovf]=Tvar[k];
10115: TvarFind[ncovf]=k;
10116: }else if(Tvard[k1][2] <=ncovcol+nqv){
10117: Fixed[k]= 0; /* or 2 ?*/
10118: Dummy[k]= 1;
10119: modell[k].maintype= FTYPE;
10120: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10121: ncovf++; /* Varying variables without age */
10122: TvarF[ncovf]=Tvar[k];
10123: TvarFind[ncovf]=k;
10124: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10125: Fixed[k]= 1;
10126: Dummy[k]= 0;
10127: modell[k].maintype= VTYPE;
10128: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10129: ncovv++; /* Varying variables without age */
10130: TvarV[ncovv]=Tvar[k];
10131: TvarVind[ncovv]=k;
10132: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10133: Fixed[k]= 1;
10134: Dummy[k]= 1;
10135: modell[k].maintype= VTYPE;
10136: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10137: ncovv++; /* Varying variables without age */
10138: TvarV[ncovv]=Tvar[k];
10139: TvarVind[ncovv]=k;
10140: }
1.227 brouard 10141: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10142: if(Tvard[k1][2] <=ncovcol){
10143: Fixed[k]= 0; /* or 2 ?*/
10144: Dummy[k]= 1;
10145: modell[k].maintype= FTYPE;
10146: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10147: ncovf++; /* Fixed variables without age */
10148: TvarF[ncovf]=Tvar[k];
10149: TvarFind[ncovf]=k;
10150: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10151: Fixed[k]= 1;
10152: Dummy[k]= 1;
10153: modell[k].maintype= VTYPE;
10154: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10155: ncovv++; /* Varying variables without age */
10156: TvarV[ncovv]=Tvar[k];
10157: TvarVind[ncovv]=k;
10158: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10159: Fixed[k]= 1;
10160: Dummy[k]= 1;
10161: modell[k].maintype= VTYPE;
10162: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10163: ncovv++; /* Varying variables without age */
10164: TvarV[ncovv]=Tvar[k];
10165: TvarVind[ncovv]=k;
10166: ncovv++; /* Varying variables without age */
10167: TvarV[ncovv]=Tvar[k];
10168: TvarVind[ncovv]=k;
10169: }
1.227 brouard 10170: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10171: if(Tvard[k1][2] <=ncovcol){
10172: Fixed[k]= 1;
10173: Dummy[k]= 1;
10174: modell[k].maintype= VTYPE;
10175: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10176: ncovv++; /* Varying variables without age */
10177: TvarV[ncovv]=Tvar[k];
10178: TvarVind[ncovv]=k;
10179: }else if(Tvard[k1][2] <=ncovcol+nqv){
10180: Fixed[k]= 1;
10181: Dummy[k]= 1;
10182: modell[k].maintype= VTYPE;
10183: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10184: ncovv++; /* Varying variables without age */
10185: TvarV[ncovv]=Tvar[k];
10186: TvarVind[ncovv]=k;
10187: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10188: Fixed[k]= 1;
10189: Dummy[k]= 0;
10190: modell[k].maintype= VTYPE;
10191: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10192: ncovv++; /* Varying variables without age */
10193: TvarV[ncovv]=Tvar[k];
10194: TvarVind[ncovv]=k;
10195: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10196: Fixed[k]= 1;
10197: Dummy[k]= 1;
10198: modell[k].maintype= VTYPE;
10199: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10200: ncovv++; /* Varying variables without age */
10201: TvarV[ncovv]=Tvar[k];
10202: TvarVind[ncovv]=k;
10203: }
1.227 brouard 10204: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10205: if(Tvard[k1][2] <=ncovcol){
10206: Fixed[k]= 1;
10207: Dummy[k]= 1;
10208: modell[k].maintype= VTYPE;
10209: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10210: ncovv++; /* Varying variables without age */
10211: TvarV[ncovv]=Tvar[k];
10212: TvarVind[ncovv]=k;
10213: }else if(Tvard[k1][2] <=ncovcol+nqv){
10214: Fixed[k]= 1;
10215: Dummy[k]= 1;
10216: modell[k].maintype= VTYPE;
10217: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10218: ncovv++; /* Varying variables without age */
10219: TvarV[ncovv]=Tvar[k];
10220: TvarVind[ncovv]=k;
10221: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10222: Fixed[k]= 1;
10223: Dummy[k]= 1;
10224: modell[k].maintype= VTYPE;
10225: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10226: ncovv++; /* Varying variables without age */
10227: TvarV[ncovv]=Tvar[k];
10228: TvarVind[ncovv]=k;
10229: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10230: Fixed[k]= 1;
10231: Dummy[k]= 1;
10232: modell[k].maintype= VTYPE;
10233: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10234: ncovv++; /* Varying variables without age */
10235: TvarV[ncovv]=Tvar[k];
10236: TvarVind[ncovv]=k;
10237: }
1.227 brouard 10238: }else{
1.240 brouard 10239: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10240: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10241: } /*end k1*/
1.225 brouard 10242: }else{
1.226 brouard 10243: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10244: 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 10245: }
1.227 brouard 10246: 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 10247: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10248: 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]);
10249: }
10250: /* Searching for doublons in the model */
10251: for(k1=1; k1<= cptcovt;k1++){
10252: for(k2=1; k2 <k1;k2++){
1.285 brouard 10253: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10254: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10255: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10256: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10257: 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]);
10258: 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 10259: return(1);
10260: }
10261: }else if (Typevar[k1] ==2){
10262: k3=Tposprod[k1];
10263: k4=Tposprod[k2];
10264: 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])) ){
10265: 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]]);
10266: 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);
10267: return(1);
10268: }
10269: }
1.227 brouard 10270: }
10271: }
1.225 brouard 10272: }
10273: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10274: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10275: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10276: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10277: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10278: /*endread:*/
1.225 brouard 10279: printf("Exiting decodemodel: ");
10280: return (1);
1.136 brouard 10281: }
10282:
1.169 brouard 10283: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10284: {/* Check ages at death */
1.136 brouard 10285: int i, m;
1.218 brouard 10286: int firstone=0;
10287:
1.136 brouard 10288: for (i=1; i<=imx; i++) {
10289: for(m=2; (m<= maxwav); m++) {
10290: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10291: anint[m][i]=9999;
1.216 brouard 10292: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10293: s[m][i]=-1;
1.136 brouard 10294: }
10295: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10296: *nberr = *nberr + 1;
1.218 brouard 10297: if(firstone == 0){
10298: firstone=1;
1.260 brouard 10299: 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 10300: }
1.262 brouard 10301: 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 10302: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10303: }
10304: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10305: (*nberr)++;
1.259 brouard 10306: 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 10307: 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 10308: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10309: }
10310: }
10311: }
10312:
10313: for (i=1; i<=imx; i++) {
10314: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10315: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10316: 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 10317: if (s[m][i] >= nlstate+1) {
1.169 brouard 10318: if(agedc[i]>0){
10319: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10320: agev[m][i]=agedc[i];
1.214 brouard 10321: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10322: }else {
1.136 brouard 10323: if ((int)andc[i]!=9999){
10324: nbwarn++;
10325: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10326: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10327: agev[m][i]=-1;
10328: }
10329: }
1.169 brouard 10330: } /* agedc > 0 */
1.214 brouard 10331: } /* end if */
1.136 brouard 10332: else if(s[m][i] !=9){ /* Standard case, age in fractional
10333: years but with the precision of a month */
10334: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10335: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10336: agev[m][i]=1;
10337: else if(agev[m][i] < *agemin){
10338: *agemin=agev[m][i];
10339: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10340: }
10341: else if(agev[m][i] >*agemax){
10342: *agemax=agev[m][i];
1.156 brouard 10343: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10344: }
10345: /*agev[m][i]=anint[m][i]-annais[i];*/
10346: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10347: } /* en if 9*/
1.136 brouard 10348: else { /* =9 */
1.214 brouard 10349: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10350: agev[m][i]=1;
10351: s[m][i]=-1;
10352: }
10353: }
1.214 brouard 10354: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10355: agev[m][i]=1;
1.214 brouard 10356: else{
10357: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10358: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10359: agev[m][i]=0;
10360: }
10361: } /* End for lastpass */
10362: }
1.136 brouard 10363:
10364: for (i=1; i<=imx; i++) {
10365: for(m=firstpass; (m<=lastpass); m++){
10366: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10367: (*nberr)++;
1.136 brouard 10368: 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);
10369: 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);
10370: return 1;
10371: }
10372: }
10373: }
10374:
10375: /*for (i=1; i<=imx; i++){
10376: for (m=firstpass; (m<lastpass); m++){
10377: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10378: }
10379:
10380: }*/
10381:
10382:
1.139 brouard 10383: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10384: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10385:
10386: return (0);
1.164 brouard 10387: /* endread:*/
1.136 brouard 10388: printf("Exiting calandcheckages: ");
10389: return (1);
10390: }
10391:
1.172 brouard 10392: #if defined(_MSC_VER)
10393: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10394: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10395: //#include "stdafx.h"
10396: //#include <stdio.h>
10397: //#include <tchar.h>
10398: //#include <windows.h>
10399: //#include <iostream>
10400: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10401:
10402: LPFN_ISWOW64PROCESS fnIsWow64Process;
10403:
10404: BOOL IsWow64()
10405: {
10406: BOOL bIsWow64 = FALSE;
10407:
10408: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10409: // (HANDLE, PBOOL);
10410:
10411: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10412:
10413: HMODULE module = GetModuleHandle(_T("kernel32"));
10414: const char funcName[] = "IsWow64Process";
10415: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10416: GetProcAddress(module, funcName);
10417:
10418: if (NULL != fnIsWow64Process)
10419: {
10420: if (!fnIsWow64Process(GetCurrentProcess(),
10421: &bIsWow64))
10422: //throw std::exception("Unknown error");
10423: printf("Unknown error\n");
10424: }
10425: return bIsWow64 != FALSE;
10426: }
10427: #endif
1.177 brouard 10428:
1.191 brouard 10429: void syscompilerinfo(int logged)
1.292 brouard 10430: {
10431: #include <stdint.h>
10432:
10433: /* #include "syscompilerinfo.h"*/
1.185 brouard 10434: /* command line Intel compiler 32bit windows, XP compatible:*/
10435: /* /GS /W3 /Gy
10436: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10437: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10438: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10439: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10440: */
10441: /* 64 bits */
1.185 brouard 10442: /*
10443: /GS /W3 /Gy
10444: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10445: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10446: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10447: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10448: /* Optimization are useless and O3 is slower than O2 */
10449: /*
10450: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10451: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10452: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10453: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10454: */
1.186 brouard 10455: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10456: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10457: /PDB:"visual studio
10458: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10459: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10460: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10461: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10462: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10463: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10464: uiAccess='false'"
10465: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10466: /NOLOGO /TLBID:1
10467: */
1.292 brouard 10468:
10469:
1.177 brouard 10470: #if defined __INTEL_COMPILER
1.178 brouard 10471: #if defined(__GNUC__)
10472: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10473: #endif
1.177 brouard 10474: #elif defined(__GNUC__)
1.179 brouard 10475: #ifndef __APPLE__
1.174 brouard 10476: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10477: #endif
1.177 brouard 10478: struct utsname sysInfo;
1.178 brouard 10479: int cross = CROSS;
10480: if (cross){
10481: printf("Cross-");
1.191 brouard 10482: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10483: }
1.174 brouard 10484: #endif
10485:
1.191 brouard 10486: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10487: #if defined(__clang__)
1.191 brouard 10488: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10489: #endif
10490: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10491: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10492: #endif
10493: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10494: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10495: #endif
10496: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10497: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10498: #endif
10499: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10500: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10501: #endif
10502: #if defined(_MSC_VER)
1.191 brouard 10503: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10504: #endif
10505: #if defined(__PGI)
1.191 brouard 10506: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10507: #endif
10508: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10509: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10510: #endif
1.191 brouard 10511: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10512:
1.167 brouard 10513: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10514: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10515: // Windows (x64 and x86)
1.191 brouard 10516: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10517: #elif __unix__ // all unices, not all compilers
10518: // Unix
1.191 brouard 10519: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10520: #elif __linux__
10521: // linux
1.191 brouard 10522: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10523: #elif __APPLE__
1.174 brouard 10524: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10525: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10526: #endif
10527:
10528: /* __MINGW32__ */
10529: /* __CYGWIN__ */
10530: /* __MINGW64__ */
10531: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10532: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10533: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10534: /* _WIN64 // Defined for applications for Win64. */
10535: /* _M_X64 // Defined for compilations that target x64 processors. */
10536: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10537:
1.167 brouard 10538: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10539: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10540: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10541: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10542: #else
1.191 brouard 10543: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10544: #endif
10545:
1.169 brouard 10546: #if defined(__GNUC__)
10547: # if defined(__GNUC_PATCHLEVEL__)
10548: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10549: + __GNUC_MINOR__ * 100 \
10550: + __GNUC_PATCHLEVEL__)
10551: # else
10552: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10553: + __GNUC_MINOR__ * 100)
10554: # endif
1.174 brouard 10555: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10556: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10557:
10558: if (uname(&sysInfo) != -1) {
10559: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10560: 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 10561: }
10562: else
10563: perror("uname() error");
1.179 brouard 10564: //#ifndef __INTEL_COMPILER
10565: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10566: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10567: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10568: #endif
1.169 brouard 10569: #endif
1.172 brouard 10570:
1.286 brouard 10571: // void main ()
1.172 brouard 10572: // {
1.169 brouard 10573: #if defined(_MSC_VER)
1.174 brouard 10574: if (IsWow64()){
1.191 brouard 10575: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10576: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10577: }
10578: else{
1.191 brouard 10579: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10580: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10581: }
1.172 brouard 10582: // printf("\nPress Enter to continue...");
10583: // getchar();
10584: // }
10585:
1.169 brouard 10586: #endif
10587:
1.167 brouard 10588:
1.219 brouard 10589: }
1.136 brouard 10590:
1.219 brouard 10591: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10592: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10593: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10594: /* double ftolpl = 1.e-10; */
1.180 brouard 10595: double age, agebase, agelim;
1.203 brouard 10596: double tot;
1.180 brouard 10597:
1.202 brouard 10598: strcpy(filerespl,"PL_");
10599: strcat(filerespl,fileresu);
10600: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10601: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10602: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10603: }
1.288 brouard 10604: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10605: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10606: pstamp(ficrespl);
1.288 brouard 10607: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10608: fprintf(ficrespl,"#Age ");
10609: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10610: fprintf(ficrespl,"\n");
1.180 brouard 10611:
1.219 brouard 10612: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10613:
1.219 brouard 10614: agebase=ageminpar;
10615: agelim=agemaxpar;
1.180 brouard 10616:
1.227 brouard 10617: /* i1=pow(2,ncoveff); */
1.234 brouard 10618: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10619: if (cptcovn < 1){i1=1;}
1.180 brouard 10620:
1.238 brouard 10621: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10622: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10623: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10624: continue;
1.235 brouard 10625:
1.238 brouard 10626: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10627: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10628: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10629: /* k=k+1; */
10630: /* to clean */
10631: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10632: fprintf(ficrespl,"#******");
10633: printf("#******");
10634: fprintf(ficlog,"#******");
10635: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10636: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10637: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10638: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10639: }
10640: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10641: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10642: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10643: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10644: }
10645: fprintf(ficrespl,"******\n");
10646: printf("******\n");
10647: fprintf(ficlog,"******\n");
10648: if(invalidvarcomb[k]){
10649: printf("\nCombination (%d) ignored because no case \n",k);
10650: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10651: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10652: continue;
10653: }
1.219 brouard 10654:
1.238 brouard 10655: fprintf(ficrespl,"#Age ");
10656: for(j=1;j<=cptcoveff;j++) {
10657: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10658: }
10659: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10660: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10661:
1.238 brouard 10662: for (age=agebase; age<=agelim; age++){
10663: /* for (age=agebase; age<=agebase; age++){ */
10664: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10665: fprintf(ficrespl,"%.0f ",age );
10666: for(j=1;j<=cptcoveff;j++)
10667: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10668: tot=0.;
10669: for(i=1; i<=nlstate;i++){
10670: tot += prlim[i][i];
10671: fprintf(ficrespl," %.5f", prlim[i][i]);
10672: }
10673: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10674: } /* Age */
10675: /* was end of cptcod */
10676: } /* cptcov */
10677: } /* nres */
1.219 brouard 10678: return 0;
1.180 brouard 10679: }
10680:
1.218 brouard 10681: 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 10682: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10683:
10684: /* Computes the back prevalence limit for any combination of covariate values
10685: * at any age between ageminpar and agemaxpar
10686: */
1.235 brouard 10687: int i, j, k, i1, nres=0 ;
1.217 brouard 10688: /* double ftolpl = 1.e-10; */
10689: double age, agebase, agelim;
10690: double tot;
1.218 brouard 10691: /* double ***mobaverage; */
10692: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10693:
10694: strcpy(fileresplb,"PLB_");
10695: strcat(fileresplb,fileresu);
10696: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10697: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10698: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10699: }
1.288 brouard 10700: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10701: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10702: pstamp(ficresplb);
1.288 brouard 10703: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10704: fprintf(ficresplb,"#Age ");
10705: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10706: fprintf(ficresplb,"\n");
10707:
1.218 brouard 10708:
10709: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10710:
10711: agebase=ageminpar;
10712: agelim=agemaxpar;
10713:
10714:
1.227 brouard 10715: i1=pow(2,cptcoveff);
1.218 brouard 10716: if (cptcovn < 1){i1=1;}
1.227 brouard 10717:
1.238 brouard 10718: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10719: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10720: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10721: continue;
10722: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10723: fprintf(ficresplb,"#******");
10724: printf("#******");
10725: fprintf(ficlog,"#******");
10726: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10727: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10728: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10729: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10730: }
10731: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10732: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10733: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10734: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10735: }
10736: fprintf(ficresplb,"******\n");
10737: printf("******\n");
10738: fprintf(ficlog,"******\n");
10739: if(invalidvarcomb[k]){
10740: printf("\nCombination (%d) ignored because no cases \n",k);
10741: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10742: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10743: continue;
10744: }
1.218 brouard 10745:
1.238 brouard 10746: fprintf(ficresplb,"#Age ");
10747: for(j=1;j<=cptcoveff;j++) {
10748: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10749: }
10750: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10751: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10752:
10753:
1.238 brouard 10754: for (age=agebase; age<=agelim; age++){
10755: /* for (age=agebase; age<=agebase; age++){ */
10756: if(mobilavproj > 0){
10757: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10758: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10759: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10760: }else if (mobilavproj == 0){
10761: 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);
10762: 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);
10763: exit(1);
10764: }else{
10765: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10766: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10767: /* printf("TOTOT\n"); */
10768: /* exit(1); */
1.238 brouard 10769: }
10770: fprintf(ficresplb,"%.0f ",age );
10771: for(j=1;j<=cptcoveff;j++)
10772: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10773: tot=0.;
10774: for(i=1; i<=nlstate;i++){
10775: tot += bprlim[i][i];
10776: fprintf(ficresplb," %.5f", bprlim[i][i]);
10777: }
10778: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10779: } /* Age */
10780: /* was end of cptcod */
1.255 brouard 10781: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10782: } /* end of any combination */
10783: } /* end of nres */
1.218 brouard 10784: /* hBijx(p, bage, fage); */
10785: /* fclose(ficrespijb); */
10786:
10787: return 0;
1.217 brouard 10788: }
1.218 brouard 10789:
1.180 brouard 10790: int hPijx(double *p, int bage, int fage){
10791: /*------------- h Pij x at various ages ------------*/
10792:
10793: int stepsize;
10794: int agelim;
10795: int hstepm;
10796: int nhstepm;
1.235 brouard 10797: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10798:
10799: double agedeb;
10800: double ***p3mat;
10801:
1.201 brouard 10802: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10803: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10804: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10805: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10806: }
10807: printf("Computing pij: result on file '%s' \n", filerespij);
10808: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10809:
10810: stepsize=(int) (stepm+YEARM-1)/YEARM;
10811: /*if (stepm<=24) stepsize=2;*/
10812:
10813: agelim=AGESUP;
10814: hstepm=stepsize*YEARM; /* Every year of age */
10815: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10816:
1.180 brouard 10817: /* hstepm=1; aff par mois*/
10818: pstamp(ficrespij);
10819: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10820: i1= pow(2,cptcoveff);
1.218 brouard 10821: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10822: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10823: /* k=k+1; */
1.235 brouard 10824: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10825: for(k=1; k<=i1;k++){
1.253 brouard 10826: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10827: continue;
1.183 brouard 10828: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10829: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10830: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10831: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10832: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10833: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10834: }
1.183 brouard 10835: fprintf(ficrespij,"******\n");
10836:
10837: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10838: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10839: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10840:
10841: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10842:
1.183 brouard 10843: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10844: oldm=oldms;savm=savms;
1.235 brouard 10845: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10846: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10847: for(i=1; i<=nlstate;i++)
10848: for(j=1; j<=nlstate+ndeath;j++)
10849: fprintf(ficrespij," %1d-%1d",i,j);
10850: fprintf(ficrespij,"\n");
10851: for (h=0; h<=nhstepm; h++){
10852: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10853: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10854: for(i=1; i<=nlstate;i++)
10855: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10856: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10857: fprintf(ficrespij,"\n");
10858: }
1.183 brouard 10859: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10860: fprintf(ficrespij,"\n");
10861: }
1.180 brouard 10862: /*}*/
10863: }
1.218 brouard 10864: return 0;
1.180 brouard 10865: }
1.218 brouard 10866:
10867: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10868: /*------------- h Bij x at various ages ------------*/
10869:
10870: int stepsize;
1.218 brouard 10871: /* int agelim; */
10872: int ageminl;
1.217 brouard 10873: int hstepm;
10874: int nhstepm;
1.238 brouard 10875: int h, i, i1, j, k, nres;
1.218 brouard 10876:
1.217 brouard 10877: double agedeb;
10878: double ***p3mat;
1.218 brouard 10879:
10880: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10881: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10882: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10883: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10884: }
10885: printf("Computing pij back: result on file '%s' \n", filerespijb);
10886: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10887:
10888: stepsize=(int) (stepm+YEARM-1)/YEARM;
10889: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10890:
1.218 brouard 10891: /* agelim=AGESUP; */
1.289 brouard 10892: ageminl=AGEINF; /* was 30 */
1.218 brouard 10893: hstepm=stepsize*YEARM; /* Every year of age */
10894: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10895:
10896: /* hstepm=1; aff par mois*/
10897: pstamp(ficrespijb);
1.255 brouard 10898: 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 10899: i1= pow(2,cptcoveff);
1.218 brouard 10900: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10901: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10902: /* k=k+1; */
1.238 brouard 10903: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10904: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10905: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10906: continue;
10907: fprintf(ficrespijb,"\n#****** ");
10908: for(j=1;j<=cptcoveff;j++)
10909: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10910: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10911: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10912: }
10913: fprintf(ficrespijb,"******\n");
1.264 brouard 10914: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10915: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10916: continue;
10917: }
10918:
10919: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10920: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10921: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10922: 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 */
10923: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10924:
10925: /* nhstepm=nhstepm*YEARM; aff par mois*/
10926:
1.266 brouard 10927: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10928: /* and memory limitations if stepm is small */
10929:
1.238 brouard 10930: /* oldm=oldms;savm=savms; */
10931: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10932: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10933: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10934: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10935: for(i=1; i<=nlstate;i++)
10936: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10937: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10938: fprintf(ficrespijb,"\n");
1.238 brouard 10939: for (h=0; h<=nhstepm; h++){
10940: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10941: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10942: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10943: for(i=1; i<=nlstate;i++)
10944: for(j=1; j<=nlstate+ndeath;j++)
10945: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10946: fprintf(ficrespijb,"\n");
10947: }
10948: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10949: fprintf(ficrespijb,"\n");
10950: } /* end age deb */
10951: } /* end combination */
10952: } /* end nres */
1.218 brouard 10953: return 0;
10954: } /* hBijx */
1.217 brouard 10955:
1.180 brouard 10956:
1.136 brouard 10957: /***********************************************/
10958: /**************** Main Program *****************/
10959: /***********************************************/
10960:
10961: int main(int argc, char *argv[])
10962: {
10963: #ifdef GSL
10964: const gsl_multimin_fminimizer_type *T;
10965: size_t iteri = 0, it;
10966: int rval = GSL_CONTINUE;
10967: int status = GSL_SUCCESS;
10968: double ssval;
10969: #endif
10970: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10971: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10972: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10973: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10974: int jj, ll, li, lj, lk;
1.136 brouard 10975: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10976: int num_filled;
1.136 brouard 10977: int itimes;
10978: int NDIM=2;
10979: int vpopbased=0;
1.235 brouard 10980: int nres=0;
1.258 brouard 10981: int endishere=0;
1.277 brouard 10982: int noffset=0;
1.274 brouard 10983: int ncurrv=0; /* Temporary variable */
10984:
1.164 brouard 10985: char ca[32], cb[32];
1.136 brouard 10986: /* FILE *fichtm; *//* Html File */
10987: /* FILE *ficgp;*/ /*Gnuplot File */
10988: struct stat info;
1.191 brouard 10989: double agedeb=0.;
1.194 brouard 10990:
10991: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10992: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10993:
1.165 brouard 10994: double fret;
1.191 brouard 10995: double dum=0.; /* Dummy variable */
1.136 brouard 10996: double ***p3mat;
1.218 brouard 10997: /* double ***mobaverage; */
1.164 brouard 10998:
10999: char line[MAXLINE];
1.197 brouard 11000: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
11001:
1.234 brouard 11002: char modeltemp[MAXLINE];
1.230 brouard 11003: char resultline[MAXLINE];
11004:
1.136 brouard 11005: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 11006: char *tok, *val; /* pathtot */
1.290 brouard 11007: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 11008: int c, h , cpt, c2;
1.191 brouard 11009: int jl=0;
11010: int i1, j1, jk, stepsize=0;
1.194 brouard 11011: int count=0;
11012:
1.164 brouard 11013: int *tab;
1.136 brouard 11014: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 11015: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
11016: /* double anprojf, mprojf, jprojf; */
11017: /* double jintmean,mintmean,aintmean; */
11018: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
11019: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
11020: double yrfproj= 10.0; /* Number of years of forward projections */
11021: double yrbproj= 10.0; /* Number of years of backward projections */
11022: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 11023: int mobilav=0,popforecast=0;
1.191 brouard 11024: int hstepm=0, nhstepm=0;
1.136 brouard 11025: int agemortsup;
11026: float sumlpop=0.;
11027: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
11028: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
11029:
1.191 brouard 11030: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 11031: double ftolpl=FTOL;
11032: double **prlim;
1.217 brouard 11033: double **bprlim;
1.136 brouard 11034: double ***param; /* Matrix of parameters */
1.251 brouard 11035: double ***paramstart; /* Matrix of starting parameter values */
11036: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 11037: double **matcov; /* Matrix of covariance */
1.203 brouard 11038: double **hess; /* Hessian matrix */
1.136 brouard 11039: double ***delti3; /* Scale */
11040: double *delti; /* Scale */
11041: double ***eij, ***vareij;
11042: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 11043:
1.136 brouard 11044: double *epj, vepp;
1.164 brouard 11045:
1.273 brouard 11046: double dateprev1, dateprev2;
1.296 brouard 11047: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
11048: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
11049:
1.217 brouard 11050:
1.136 brouard 11051: double **ximort;
1.145 brouard 11052: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 11053: int *dcwave;
11054:
1.164 brouard 11055: char z[1]="c";
1.136 brouard 11056:
11057: /*char *strt;*/
11058: char strtend[80];
1.126 brouard 11059:
1.164 brouard 11060:
1.126 brouard 11061: /* setlocale (LC_ALL, ""); */
11062: /* bindtextdomain (PACKAGE, LOCALEDIR); */
11063: /* textdomain (PACKAGE); */
11064: /* setlocale (LC_CTYPE, ""); */
11065: /* setlocale (LC_MESSAGES, ""); */
11066:
11067: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 11068: rstart_time = time(NULL);
11069: /* (void) gettimeofday(&start_time,&tzp);*/
11070: start_time = *localtime(&rstart_time);
1.126 brouard 11071: curr_time=start_time;
1.157 brouard 11072: /*tml = *localtime(&start_time.tm_sec);*/
11073: /* strcpy(strstart,asctime(&tml)); */
11074: strcpy(strstart,asctime(&start_time));
1.126 brouard 11075:
11076: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 11077: /* tp.tm_sec = tp.tm_sec +86400; */
11078: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 11079: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11080: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11081: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11082: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11083: /* strt=asctime(&tmg); */
11084: /* printf("Time(after) =%s",strstart); */
11085: /* (void) time (&time_value);
11086: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11087: * tm = *localtime(&time_value);
11088: * strstart=asctime(&tm);
11089: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11090: */
11091:
11092: nberr=0; /* Number of errors and warnings */
11093: nbwarn=0;
1.184 brouard 11094: #ifdef WIN32
11095: _getcwd(pathcd, size);
11096: #else
1.126 brouard 11097: getcwd(pathcd, size);
1.184 brouard 11098: #endif
1.191 brouard 11099: syscompilerinfo(0);
1.196 brouard 11100: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11101: if(argc <=1){
11102: printf("\nEnter the parameter file name: ");
1.205 brouard 11103: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11104: printf("ERROR Empty parameter file name\n");
11105: goto end;
11106: }
1.126 brouard 11107: i=strlen(pathr);
11108: if(pathr[i-1]=='\n')
11109: pathr[i-1]='\0';
1.156 brouard 11110: i=strlen(pathr);
1.205 brouard 11111: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11112: pathr[i-1]='\0';
1.205 brouard 11113: }
11114: i=strlen(pathr);
11115: if( i==0 ){
11116: printf("ERROR Empty parameter file name\n");
11117: goto end;
11118: }
11119: for (tok = pathr; tok != NULL; ){
1.126 brouard 11120: printf("Pathr |%s|\n",pathr);
11121: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11122: printf("val= |%s| pathr=%s\n",val,pathr);
11123: strcpy (pathtot, val);
11124: if(pathr[0] == '\0') break; /* Dirty */
11125: }
11126: }
1.281 brouard 11127: else if (argc<=2){
11128: strcpy(pathtot,argv[1]);
11129: }
1.126 brouard 11130: else{
11131: strcpy(pathtot,argv[1]);
1.281 brouard 11132: strcpy(z,argv[2]);
11133: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11134: }
11135: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11136: /*cygwin_split_path(pathtot,path,optionfile);
11137: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11138: /* cutv(path,optionfile,pathtot,'\\');*/
11139:
11140: /* Split argv[0], imach program to get pathimach */
11141: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11142: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11143: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11144: /* strcpy(pathimach,argv[0]); */
11145: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11146: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11147: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11148: #ifdef WIN32
11149: _chdir(path); /* Can be a relative path */
11150: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11151: #else
1.126 brouard 11152: chdir(path); /* Can be a relative path */
1.184 brouard 11153: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11154: #endif
11155: printf("Current directory %s!\n",pathcd);
1.126 brouard 11156: strcpy(command,"mkdir ");
11157: strcat(command,optionfilefiname);
11158: if((outcmd=system(command)) != 0){
1.169 brouard 11159: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11160: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11161: /* fclose(ficlog); */
11162: /* exit(1); */
11163: }
11164: /* if((imk=mkdir(optionfilefiname))<0){ */
11165: /* perror("mkdir"); */
11166: /* } */
11167:
11168: /*-------- arguments in the command line --------*/
11169:
1.186 brouard 11170: /* Main Log file */
1.126 brouard 11171: strcat(filelog, optionfilefiname);
11172: strcat(filelog,".log"); /* */
11173: if((ficlog=fopen(filelog,"w"))==NULL) {
11174: printf("Problem with logfile %s\n",filelog);
11175: goto end;
11176: }
11177: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11178: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11179: fprintf(ficlog,"\nEnter the parameter file name: \n");
11180: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11181: path=%s \n\
11182: optionfile=%s\n\
11183: optionfilext=%s\n\
1.156 brouard 11184: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11185:
1.197 brouard 11186: syscompilerinfo(1);
1.167 brouard 11187:
1.126 brouard 11188: printf("Local time (at start):%s",strstart);
11189: fprintf(ficlog,"Local time (at start): %s",strstart);
11190: fflush(ficlog);
11191: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11192: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11193:
11194: /* */
11195: strcpy(fileres,"r");
11196: strcat(fileres, optionfilefiname);
1.201 brouard 11197: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11198: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11199: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11200:
1.186 brouard 11201: /* Main ---------arguments file --------*/
1.126 brouard 11202:
11203: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11204: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11205: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11206: fflush(ficlog);
1.149 brouard 11207: /* goto end; */
11208: exit(70);
1.126 brouard 11209: }
11210:
11211: strcpy(filereso,"o");
1.201 brouard 11212: strcat(filereso,fileresu);
1.126 brouard 11213: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11214: printf("Problem with Output resultfile: %s\n", filereso);
11215: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11216: fflush(ficlog);
11217: goto end;
11218: }
1.278 brouard 11219: /*-------- Rewriting parameter file ----------*/
11220: strcpy(rfileres,"r"); /* "Rparameterfile */
11221: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11222: strcat(rfileres,"."); /* */
11223: strcat(rfileres,optionfilext); /* Other files have txt extension */
11224: if((ficres =fopen(rfileres,"w"))==NULL) {
11225: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11226: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11227: fflush(ficlog);
11228: goto end;
11229: }
11230: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11231:
1.278 brouard 11232:
1.126 brouard 11233: /* Reads comments: lines beginning with '#' */
11234: numlinepar=0;
1.277 brouard 11235: /* Is it a BOM UTF-8 Windows file? */
11236: /* First parameter line */
1.197 brouard 11237: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11238: noffset=0;
11239: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11240: {
11241: noffset=noffset+3;
11242: printf("# File is an UTF8 Bom.\n"); // 0xBF
11243: }
1.302 brouard 11244: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11245: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11246: {
11247: noffset=noffset+2;
11248: printf("# File is an UTF16BE BOM file\n");
11249: }
11250: else if( line[0] == 0 && line[1] == 0)
11251: {
11252: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11253: noffset=noffset+4;
11254: printf("# File is an UTF16BE BOM file\n");
11255: }
11256: } else{
11257: ;/*printf(" Not a BOM file\n");*/
11258: }
11259:
1.197 brouard 11260: /* If line starts with a # it is a comment */
1.277 brouard 11261: if (line[noffset] == '#') {
1.197 brouard 11262: numlinepar++;
11263: fputs(line,stdout);
11264: fputs(line,ficparo);
1.278 brouard 11265: fputs(line,ficres);
1.197 brouard 11266: fputs(line,ficlog);
11267: continue;
11268: }else
11269: break;
11270: }
11271: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11272: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11273: if (num_filled != 5) {
11274: printf("Should be 5 parameters\n");
1.283 brouard 11275: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11276: }
1.126 brouard 11277: numlinepar++;
1.197 brouard 11278: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11279: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11280: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11281: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11282: }
11283: /* Second parameter line */
11284: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11285: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11286: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11287: if (line[0] == '#') {
11288: numlinepar++;
1.283 brouard 11289: printf("%s",line);
11290: fprintf(ficres,"%s",line);
11291: fprintf(ficparo,"%s",line);
11292: fprintf(ficlog,"%s",line);
1.197 brouard 11293: continue;
11294: }else
11295: break;
11296: }
1.223 brouard 11297: 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", \
11298: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11299: if (num_filled != 11) {
11300: 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 11301: printf("but line=%s\n",line);
1.283 brouard 11302: 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");
11303: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11304: }
1.286 brouard 11305: if( lastpass > maxwav){
11306: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11307: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11308: fflush(ficlog);
11309: goto end;
11310: }
11311: 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 11312: 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 11313: 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 11314: 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 11315: }
1.203 brouard 11316: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11317: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11318: /* Third parameter line */
11319: while(fgets(line, MAXLINE, ficpar)) {
11320: /* If line starts with a # it is a comment */
11321: if (line[0] == '#') {
11322: numlinepar++;
1.283 brouard 11323: printf("%s",line);
11324: fprintf(ficres,"%s",line);
11325: fprintf(ficparo,"%s",line);
11326: fprintf(ficlog,"%s",line);
1.197 brouard 11327: continue;
11328: }else
11329: break;
11330: }
1.201 brouard 11331: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11332: if (num_filled != 1){
1.302 brouard 11333: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11334: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11335: model[0]='\0';
11336: goto end;
11337: }
11338: else{
11339: if (model[0]=='+'){
11340: for(i=1; i<=strlen(model);i++)
11341: modeltemp[i-1]=model[i];
1.201 brouard 11342: strcpy(model,modeltemp);
1.197 brouard 11343: }
11344: }
1.199 brouard 11345: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11346: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11347: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11348: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11349: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11350: }
11351: /* 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); */
11352: /* numlinepar=numlinepar+3; /\* In general *\/ */
11353: /* 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 11354: /* 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); */
11355: /* 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 11356: fflush(ficlog);
1.190 brouard 11357: /* if(model[0]=='#'|| model[0]== '\0'){ */
11358: if(model[0]=='#'){
1.279 brouard 11359: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11360: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11361: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11362: if(mle != -1){
1.279 brouard 11363: 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 11364: exit(1);
11365: }
11366: }
1.126 brouard 11367: while((c=getc(ficpar))=='#' && c!= EOF){
11368: ungetc(c,ficpar);
11369: fgets(line, MAXLINE, ficpar);
11370: numlinepar++;
1.195 brouard 11371: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11372: z[0]=line[1];
11373: }
11374: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11375: fputs(line, stdout);
11376: //puts(line);
1.126 brouard 11377: fputs(line,ficparo);
11378: fputs(line,ficlog);
11379: }
11380: ungetc(c,ficpar);
11381:
11382:
1.290 brouard 11383: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11384: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11385: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11386: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11387: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11388: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11389: v1+v2*age+v2*v3 makes cptcovn = 3
11390: */
11391: if (strlen(model)>1)
1.187 brouard 11392: 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 11393: else
1.187 brouard 11394: ncovmodel=2; /* Constant and age */
1.133 brouard 11395: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11396: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11397: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11398: 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);
11399: 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);
11400: fflush(stdout);
11401: fclose (ficlog);
11402: goto end;
11403: }
1.126 brouard 11404: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11405: delti=delti3[1][1];
11406: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11407: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11408: /* We could also provide initial parameters values giving by simple logistic regression
11409: * only one way, that is without matrix product. We will have nlstate maximizations */
11410: /* for(i=1;i<nlstate;i++){ */
11411: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11412: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11413: /* } */
1.126 brouard 11414: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11415: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11416: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11417: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11418: fclose (ficparo);
11419: fclose (ficlog);
11420: goto end;
11421: exit(0);
1.220 brouard 11422: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11423: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11424: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11425: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11426: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11427: matcov=matrix(1,npar,1,npar);
1.203 brouard 11428: hess=matrix(1,npar,1,npar);
1.220 brouard 11429: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11430: /* Read guessed parameters */
1.126 brouard 11431: /* Reads comments: lines beginning with '#' */
11432: while((c=getc(ficpar))=='#' && c!= EOF){
11433: ungetc(c,ficpar);
11434: fgets(line, MAXLINE, ficpar);
11435: numlinepar++;
1.141 brouard 11436: fputs(line,stdout);
1.126 brouard 11437: fputs(line,ficparo);
11438: fputs(line,ficlog);
11439: }
11440: ungetc(c,ficpar);
11441:
11442: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11443: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11444: for(i=1; i <=nlstate; i++){
1.234 brouard 11445: j=0;
1.126 brouard 11446: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11447: if(jj==i) continue;
11448: j++;
1.292 brouard 11449: while((c=getc(ficpar))=='#' && c!= EOF){
11450: ungetc(c,ficpar);
11451: fgets(line, MAXLINE, ficpar);
11452: numlinepar++;
11453: fputs(line,stdout);
11454: fputs(line,ficparo);
11455: fputs(line,ficlog);
11456: }
11457: ungetc(c,ficpar);
1.234 brouard 11458: fscanf(ficpar,"%1d%1d",&i1,&j1);
11459: if ((i1 != i) || (j1 != jj)){
11460: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11461: It might be a problem of design; if ncovcol and the model are correct\n \
11462: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11463: exit(1);
11464: }
11465: fprintf(ficparo,"%1d%1d",i1,j1);
11466: if(mle==1)
11467: printf("%1d%1d",i,jj);
11468: fprintf(ficlog,"%1d%1d",i,jj);
11469: for(k=1; k<=ncovmodel;k++){
11470: fscanf(ficpar," %lf",¶m[i][j][k]);
11471: if(mle==1){
11472: printf(" %lf",param[i][j][k]);
11473: fprintf(ficlog," %lf",param[i][j][k]);
11474: }
11475: else
11476: fprintf(ficlog," %lf",param[i][j][k]);
11477: fprintf(ficparo," %lf",param[i][j][k]);
11478: }
11479: fscanf(ficpar,"\n");
11480: numlinepar++;
11481: if(mle==1)
11482: printf("\n");
11483: fprintf(ficlog,"\n");
11484: fprintf(ficparo,"\n");
1.126 brouard 11485: }
11486: }
11487: fflush(ficlog);
1.234 brouard 11488:
1.251 brouard 11489: /* Reads parameters values */
1.126 brouard 11490: p=param[1][1];
1.251 brouard 11491: pstart=paramstart[1][1];
1.126 brouard 11492:
11493: /* Reads comments: lines beginning with '#' */
11494: while((c=getc(ficpar))=='#' && c!= EOF){
11495: ungetc(c,ficpar);
11496: fgets(line, MAXLINE, ficpar);
11497: numlinepar++;
1.141 brouard 11498: fputs(line,stdout);
1.126 brouard 11499: fputs(line,ficparo);
11500: fputs(line,ficlog);
11501: }
11502: ungetc(c,ficpar);
11503:
11504: for(i=1; i <=nlstate; i++){
11505: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11506: fscanf(ficpar,"%1d%1d",&i1,&j1);
11507: if ( (i1-i) * (j1-j) != 0){
11508: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11509: exit(1);
11510: }
11511: printf("%1d%1d",i,j);
11512: fprintf(ficparo,"%1d%1d",i1,j1);
11513: fprintf(ficlog,"%1d%1d",i1,j1);
11514: for(k=1; k<=ncovmodel;k++){
11515: fscanf(ficpar,"%le",&delti3[i][j][k]);
11516: printf(" %le",delti3[i][j][k]);
11517: fprintf(ficparo," %le",delti3[i][j][k]);
11518: fprintf(ficlog," %le",delti3[i][j][k]);
11519: }
11520: fscanf(ficpar,"\n");
11521: numlinepar++;
11522: printf("\n");
11523: fprintf(ficparo,"\n");
11524: fprintf(ficlog,"\n");
1.126 brouard 11525: }
11526: }
11527: fflush(ficlog);
1.234 brouard 11528:
1.145 brouard 11529: /* Reads covariance matrix */
1.126 brouard 11530: delti=delti3[1][1];
1.220 brouard 11531:
11532:
1.126 brouard 11533: /* 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 11534:
1.126 brouard 11535: /* Reads comments: lines beginning with '#' */
11536: while((c=getc(ficpar))=='#' && c!= EOF){
11537: ungetc(c,ficpar);
11538: fgets(line, MAXLINE, ficpar);
11539: numlinepar++;
1.141 brouard 11540: fputs(line,stdout);
1.126 brouard 11541: fputs(line,ficparo);
11542: fputs(line,ficlog);
11543: }
11544: ungetc(c,ficpar);
1.220 brouard 11545:
1.126 brouard 11546: matcov=matrix(1,npar,1,npar);
1.203 brouard 11547: hess=matrix(1,npar,1,npar);
1.131 brouard 11548: for(i=1; i <=npar; i++)
11549: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11550:
1.194 brouard 11551: /* Scans npar lines */
1.126 brouard 11552: for(i=1; i <=npar; i++){
1.226 brouard 11553: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11554: if(count != 3){
1.226 brouard 11555: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11556: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11557: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11558: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11559: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11560: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11561: exit(1);
1.220 brouard 11562: }else{
1.226 brouard 11563: if(mle==1)
11564: printf("%1d%1d%d",i1,j1,jk);
11565: }
11566: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11567: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11568: for(j=1; j <=i; j++){
1.226 brouard 11569: fscanf(ficpar," %le",&matcov[i][j]);
11570: if(mle==1){
11571: printf(" %.5le",matcov[i][j]);
11572: }
11573: fprintf(ficlog," %.5le",matcov[i][j]);
11574: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11575: }
11576: fscanf(ficpar,"\n");
11577: numlinepar++;
11578: if(mle==1)
1.220 brouard 11579: printf("\n");
1.126 brouard 11580: fprintf(ficlog,"\n");
11581: fprintf(ficparo,"\n");
11582: }
1.194 brouard 11583: /* End of read covariance matrix npar lines */
1.126 brouard 11584: for(i=1; i <=npar; i++)
11585: for(j=i+1;j<=npar;j++)
1.226 brouard 11586: matcov[i][j]=matcov[j][i];
1.126 brouard 11587:
11588: if(mle==1)
11589: printf("\n");
11590: fprintf(ficlog,"\n");
11591:
11592: fflush(ficlog);
11593:
11594: } /* End of mle != -3 */
1.218 brouard 11595:
1.186 brouard 11596: /* Main data
11597: */
1.290 brouard 11598: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11599: /* num=lvector(1,n); */
11600: /* moisnais=vector(1,n); */
11601: /* annais=vector(1,n); */
11602: /* moisdc=vector(1,n); */
11603: /* andc=vector(1,n); */
11604: /* weight=vector(1,n); */
11605: /* agedc=vector(1,n); */
11606: /* cod=ivector(1,n); */
11607: /* for(i=1;i<=n;i++){ */
11608: num=lvector(firstobs,lastobs);
11609: moisnais=vector(firstobs,lastobs);
11610: annais=vector(firstobs,lastobs);
11611: moisdc=vector(firstobs,lastobs);
11612: andc=vector(firstobs,lastobs);
11613: weight=vector(firstobs,lastobs);
11614: agedc=vector(firstobs,lastobs);
11615: cod=ivector(firstobs,lastobs);
11616: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11617: num[i]=0;
11618: moisnais[i]=0;
11619: annais[i]=0;
11620: moisdc[i]=0;
11621: andc[i]=0;
11622: agedc[i]=0;
11623: cod[i]=0;
11624: weight[i]=1.0; /* Equal weights, 1 by default */
11625: }
1.290 brouard 11626: mint=matrix(1,maxwav,firstobs,lastobs);
11627: anint=matrix(1,maxwav,firstobs,lastobs);
11628: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11629: tab=ivector(1,NCOVMAX);
1.144 brouard 11630: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11631: 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 11632:
1.136 brouard 11633: /* Reads data from file datafile */
11634: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11635: goto end;
11636:
11637: /* Calculation of the number of parameters from char model */
1.234 brouard 11638: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11639: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11640: k=3 V4 Tvar[k=3]= 4 (from V4)
11641: k=2 V1 Tvar[k=2]= 1 (from V1)
11642: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11643: */
11644:
11645: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11646: TvarsDind=ivector(1,NCOVMAX); /* */
11647: TvarsD=ivector(1,NCOVMAX); /* */
11648: TvarsQind=ivector(1,NCOVMAX); /* */
11649: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11650: TvarF=ivector(1,NCOVMAX); /* */
11651: TvarFind=ivector(1,NCOVMAX); /* */
11652: TvarV=ivector(1,NCOVMAX); /* */
11653: TvarVind=ivector(1,NCOVMAX); /* */
11654: TvarA=ivector(1,NCOVMAX); /* */
11655: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11656: TvarFD=ivector(1,NCOVMAX); /* */
11657: TvarFDind=ivector(1,NCOVMAX); /* */
11658: TvarFQ=ivector(1,NCOVMAX); /* */
11659: TvarFQind=ivector(1,NCOVMAX); /* */
11660: TvarVD=ivector(1,NCOVMAX); /* */
11661: TvarVDind=ivector(1,NCOVMAX); /* */
11662: TvarVQ=ivector(1,NCOVMAX); /* */
11663: TvarVQind=ivector(1,NCOVMAX); /* */
11664:
1.230 brouard 11665: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11666: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11667: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11668: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11669: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11670: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11671: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11672: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11673: */
11674: /* For model-covariate k tells which data-covariate to use but
11675: because this model-covariate is a construction we invent a new column
11676: ncovcol + k1
11677: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11678: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11679: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11680: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11681: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11682: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11683: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11684: */
1.145 brouard 11685: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11686: 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 11687: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11688: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11689: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11690: 4 covariates (3 plus signs)
11691: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11692: */
1.230 brouard 11693: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11694: * individual dummy, fixed or varying:
11695: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11696: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11697: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11698: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11699: * Tmodelind[1]@9={9,0,3,2,}*/
11700: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11701: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11702: * individual quantitative, fixed or varying:
11703: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11704: * 3, 1, 0, 0, 0, 0, 0, 0},
11705: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11706: /* Main decodemodel */
11707:
1.187 brouard 11708:
1.223 brouard 11709: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11710: goto end;
11711:
1.137 brouard 11712: if((double)(lastobs-imx)/(double)imx > 1.10){
11713: nbwarn++;
11714: 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);
11715: 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);
11716: }
1.136 brouard 11717: /* if(mle==1){*/
1.137 brouard 11718: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11719: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11720: }
11721:
11722: /*-calculation of age at interview from date of interview and age at death -*/
11723: agev=matrix(1,maxwav,1,imx);
11724:
11725: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11726: goto end;
11727:
1.126 brouard 11728:
1.136 brouard 11729: agegomp=(int)agemin;
1.290 brouard 11730: free_vector(moisnais,firstobs,lastobs);
11731: free_vector(annais,firstobs,lastobs);
1.126 brouard 11732: /* free_matrix(mint,1,maxwav,1,n);
11733: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11734: /* free_vector(moisdc,1,n); */
11735: /* free_vector(andc,1,n); */
1.145 brouard 11736: /* */
11737:
1.126 brouard 11738: wav=ivector(1,imx);
1.214 brouard 11739: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11740: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11741: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11742: 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.*/
11743: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11744: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11745:
11746: /* Concatenates waves */
1.214 brouard 11747: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11748: Death is a valid wave (if date is known).
11749: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11750: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11751: and mw[mi+1][i]. dh depends on stepm.
11752: */
11753:
1.126 brouard 11754: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11755: /* Concatenates waves */
1.145 brouard 11756:
1.290 brouard 11757: free_vector(moisdc,firstobs,lastobs);
11758: free_vector(andc,firstobs,lastobs);
1.215 brouard 11759:
1.126 brouard 11760: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11761: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11762: ncodemax[1]=1;
1.145 brouard 11763: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11764: cptcoveff=0;
1.220 brouard 11765: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11766: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11767: }
11768:
11769: ncovcombmax=pow(2,cptcoveff);
11770: invalidvarcomb=ivector(1, ncovcombmax);
11771: for(i=1;i<ncovcombmax;i++)
11772: invalidvarcomb[i]=0;
11773:
1.211 brouard 11774: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11775: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11776: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11777:
1.200 brouard 11778: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11779: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11780: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11781: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11782: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11783: * (currently 0 or 1) in the data.
11784: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11785: * corresponding modality (h,j).
11786: */
11787:
1.145 brouard 11788: h=0;
11789: /*if (cptcovn > 0) */
1.126 brouard 11790: m=pow(2,cptcoveff);
11791:
1.144 brouard 11792: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11793: * For k=4 covariates, h goes from 1 to m=2**k
11794: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11795: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11796: * h\k 1 2 3 4
1.143 brouard 11797: *______________________________
11798: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11799: * 2 2 1 1 1
11800: * 3 i=2 1 2 1 1
11801: * 4 2 2 1 1
11802: * 5 i=3 1 i=2 1 2 1
11803: * 6 2 1 2 1
11804: * 7 i=4 1 2 2 1
11805: * 8 2 2 2 1
1.197 brouard 11806: * 9 i=5 1 i=3 1 i=2 1 2
11807: * 10 2 1 1 2
11808: * 11 i=6 1 2 1 2
11809: * 12 2 2 1 2
11810: * 13 i=7 1 i=4 1 2 2
11811: * 14 2 1 2 2
11812: * 15 i=8 1 2 2 2
11813: * 16 2 2 2 2
1.143 brouard 11814: */
1.212 brouard 11815: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11816: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11817: * and the value of each covariate?
11818: * V1=1, V2=1, V3=2, V4=1 ?
11819: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11820: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11821: * In order to get the real value in the data, we use nbcode
11822: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11823: * We are keeping this crazy system in order to be able (in the future?)
11824: * to have more than 2 values (0 or 1) for a covariate.
11825: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11826: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11827: * bbbbbbbb
11828: * 76543210
11829: * h-1 00000101 (6-1=5)
1.219 brouard 11830: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11831: * &
11832: * 1 00000001 (1)
1.219 brouard 11833: * 00000000 = 1 & ((h-1) >> (k-1))
11834: * +1= 00000001 =1
1.211 brouard 11835: *
11836: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11837: * h' 1101 =2^3+2^2+0x2^1+2^0
11838: * >>k' 11
11839: * & 00000001
11840: * = 00000001
11841: * +1 = 00000010=2 = codtabm(14,3)
11842: * Reverse h=6 and m=16?
11843: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11844: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11845: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11846: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11847: * V3=decodtabm(14,3,2**4)=2
11848: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11849: *(h-1) >> (j-1) 0011 =13 >> 2
11850: * &1 000000001
11851: * = 000000001
11852: * +1= 000000010 =2
11853: * 2211
11854: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11855: * V3=2
1.220 brouard 11856: * codtabm and decodtabm are identical
1.211 brouard 11857: */
11858:
1.145 brouard 11859:
11860: free_ivector(Ndum,-1,NCOVMAX);
11861:
11862:
1.126 brouard 11863:
1.186 brouard 11864: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11865: strcpy(optionfilegnuplot,optionfilefiname);
11866: if(mle==-3)
1.201 brouard 11867: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11868: strcat(optionfilegnuplot,".gp");
11869:
11870: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11871: printf("Problem with file %s",optionfilegnuplot);
11872: }
11873: else{
1.204 brouard 11874: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11875: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11876: //fprintf(ficgp,"set missing 'NaNq'\n");
11877: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11878: }
11879: /* fclose(ficgp);*/
1.186 brouard 11880:
11881:
11882: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11883:
11884: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11885: if(mle==-3)
1.201 brouard 11886: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11887: strcat(optionfilehtm,".htm");
11888: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11889: printf("Problem with %s \n",optionfilehtm);
11890: exit(0);
1.126 brouard 11891: }
11892:
11893: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11894: strcat(optionfilehtmcov,"-cov.htm");
11895: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11896: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11897: }
11898: else{
11899: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11900: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11901: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11902: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11903: }
11904:
1.213 brouard 11905: 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 11906: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11907: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11908: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11909: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11910: \n\
11911: <hr size=\"2\" color=\"#EC5E5E\">\
11912: <ul><li><h4>Parameter files</h4>\n\
11913: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11914: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11915: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11916: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11917: - Date and time at start: %s</ul>\n",\
11918: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11919: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11920: fileres,fileres,\
11921: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11922: fflush(fichtm);
11923:
11924: strcpy(pathr,path);
11925: strcat(pathr,optionfilefiname);
1.184 brouard 11926: #ifdef WIN32
11927: _chdir(optionfilefiname); /* Move to directory named optionfile */
11928: #else
1.126 brouard 11929: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11930: #endif
11931:
1.126 brouard 11932:
1.220 brouard 11933: /* Calculates basic frequencies. Computes observed prevalence at single age
11934: and for any valid combination of covariates
1.126 brouard 11935: and prints on file fileres'p'. */
1.251 brouard 11936: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11937: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11938:
11939: fprintf(fichtm,"\n");
1.286 brouard 11940: 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 11941: ftol, stepm);
11942: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11943: ncurrv=1;
11944: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11945: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11946: ncurrv=i;
11947: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11948: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11949: ncurrv=i;
11950: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11951: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11952: ncurrv=i;
11953: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11954: 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", \
11955: nlstate, ndeath, maxwav, mle, weightopt);
11956:
11957: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11958: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11959:
11960:
11961: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11962: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11963: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11964: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11965: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11966: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11967: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11968: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11969: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11970:
1.126 brouard 11971: /* For Powell, parameters are in a vector p[] starting at p[1]
11972: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11973: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11974:
11975: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11976: /* For mortality only */
1.126 brouard 11977: if (mle==-3){
1.136 brouard 11978: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11979: for(i=1;i<=NDIM;i++)
11980: for(j=1;j<=NDIM;j++)
11981: ximort[i][j]=0.;
1.186 brouard 11982: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11983: cens=ivector(firstobs,lastobs);
11984: ageexmed=vector(firstobs,lastobs);
11985: agecens=vector(firstobs,lastobs);
11986: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11987:
1.126 brouard 11988: for (i=1; i<=imx; i++){
11989: dcwave[i]=-1;
11990: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11991: if (s[m][i]>nlstate) {
11992: dcwave[i]=m;
11993: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11994: break;
11995: }
1.126 brouard 11996: }
1.226 brouard 11997:
1.126 brouard 11998: for (i=1; i<=imx; i++) {
11999: if (wav[i]>0){
1.226 brouard 12000: ageexmed[i]=agev[mw[1][i]][i];
12001: j=wav[i];
12002: agecens[i]=1.;
12003:
12004: if (ageexmed[i]> 1 && wav[i] > 0){
12005: agecens[i]=agev[mw[j][i]][i];
12006: cens[i]= 1;
12007: }else if (ageexmed[i]< 1)
12008: cens[i]= -1;
12009: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
12010: cens[i]=0 ;
1.126 brouard 12011: }
12012: else cens[i]=-1;
12013: }
12014:
12015: for (i=1;i<=NDIM;i++) {
12016: for (j=1;j<=NDIM;j++)
1.226 brouard 12017: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 12018: }
12019:
1.302 brouard 12020: p[1]=0.0268; p[NDIM]=0.083;
12021: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 12022:
12023:
1.136 brouard 12024: #ifdef GSL
12025: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 12026: #else
1.126 brouard 12027: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 12028: #endif
1.201 brouard 12029: strcpy(filerespow,"POW-MORT_");
12030: strcat(filerespow,fileresu);
1.126 brouard 12031: if((ficrespow=fopen(filerespow,"w"))==NULL) {
12032: printf("Problem with resultfile: %s\n", filerespow);
12033: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
12034: }
1.136 brouard 12035: #ifdef GSL
12036: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 12037: #else
1.126 brouard 12038: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 12039: #endif
1.126 brouard 12040: /* for (i=1;i<=nlstate;i++)
12041: for(j=1;j<=nlstate+ndeath;j++)
12042: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
12043: */
12044: fprintf(ficrespow,"\n");
1.136 brouard 12045: #ifdef GSL
12046: /* gsl starts here */
12047: T = gsl_multimin_fminimizer_nmsimplex;
12048: gsl_multimin_fminimizer *sfm = NULL;
12049: gsl_vector *ss, *x;
12050: gsl_multimin_function minex_func;
12051:
12052: /* Initial vertex size vector */
12053: ss = gsl_vector_alloc (NDIM);
12054:
12055: if (ss == NULL){
12056: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
12057: }
12058: /* Set all step sizes to 1 */
12059: gsl_vector_set_all (ss, 0.001);
12060:
12061: /* Starting point */
1.126 brouard 12062:
1.136 brouard 12063: x = gsl_vector_alloc (NDIM);
12064:
12065: if (x == NULL){
12066: gsl_vector_free(ss);
12067: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
12068: }
12069:
12070: /* Initialize method and iterate */
12071: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 12072: /* gsl_vector_set(x, 0, 0.0268); */
12073: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 12074: gsl_vector_set(x, 0, p[1]);
12075: gsl_vector_set(x, 1, p[2]);
12076:
12077: minex_func.f = &gompertz_f;
12078: minex_func.n = NDIM;
12079: minex_func.params = (void *)&p; /* ??? */
12080:
12081: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12082: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12083:
12084: printf("Iterations beginning .....\n\n");
12085: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12086:
12087: iteri=0;
12088: while (rval == GSL_CONTINUE){
12089: iteri++;
12090: status = gsl_multimin_fminimizer_iterate(sfm);
12091:
12092: if (status) printf("error: %s\n", gsl_strerror (status));
12093: fflush(0);
12094:
12095: if (status)
12096: break;
12097:
12098: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12099: ssval = gsl_multimin_fminimizer_size (sfm);
12100:
12101: if (rval == GSL_SUCCESS)
12102: printf ("converged to a local maximum at\n");
12103:
12104: printf("%5d ", iteri);
12105: for (it = 0; it < NDIM; it++){
12106: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12107: }
12108: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12109: }
12110:
12111: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12112:
12113: gsl_vector_free(x); /* initial values */
12114: gsl_vector_free(ss); /* inital step size */
12115: for (it=0; it<NDIM; it++){
12116: p[it+1]=gsl_vector_get(sfm->x,it);
12117: fprintf(ficrespow," %.12lf", p[it]);
12118: }
12119: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12120: #endif
12121: #ifdef POWELL
12122: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12123: #endif
1.126 brouard 12124: fclose(ficrespow);
12125:
1.203 brouard 12126: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12127:
12128: for(i=1; i <=NDIM; i++)
12129: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12130: matcov[i][j]=matcov[j][i];
1.126 brouard 12131:
12132: printf("\nCovariance matrix\n ");
1.203 brouard 12133: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12134: for(i=1; i <=NDIM; i++) {
12135: for(j=1;j<=NDIM;j++){
1.220 brouard 12136: printf("%f ",matcov[i][j]);
12137: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12138: }
1.203 brouard 12139: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12140: }
12141:
12142: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12143: for (i=1;i<=NDIM;i++) {
1.126 brouard 12144: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12145: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12146: }
1.302 brouard 12147: lsurv=vector(agegomp,AGESUP);
12148: lpop=vector(agegomp,AGESUP);
12149: tpop=vector(agegomp,AGESUP);
1.126 brouard 12150: lsurv[agegomp]=100000;
12151:
12152: for (k=agegomp;k<=AGESUP;k++) {
12153: agemortsup=k;
12154: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12155: }
12156:
12157: for (k=agegomp;k<agemortsup;k++)
12158: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12159:
12160: for (k=agegomp;k<agemortsup;k++){
12161: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12162: sumlpop=sumlpop+lpop[k];
12163: }
12164:
12165: tpop[agegomp]=sumlpop;
12166: for (k=agegomp;k<(agemortsup-3);k++){
12167: /* tpop[k+1]=2;*/
12168: tpop[k+1]=tpop[k]-lpop[k];
12169: }
12170:
12171:
12172: printf("\nAge lx qx dx Lx Tx e(x)\n");
12173: for (k=agegomp;k<(agemortsup-2);k++)
12174: 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]);
12175:
12176:
12177: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12178: ageminpar=50;
12179: agemaxpar=100;
1.194 brouard 12180: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12181: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12182: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12183: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12184: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12185: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12186: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12187: }else{
12188: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12189: 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 12190: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12191: }
1.201 brouard 12192: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12193: stepm, weightopt,\
12194: model,imx,p,matcov,agemortsup);
12195:
1.302 brouard 12196: free_vector(lsurv,agegomp,AGESUP);
12197: free_vector(lpop,agegomp,AGESUP);
12198: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12199: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12200: free_ivector(dcwave,firstobs,lastobs);
12201: free_vector(agecens,firstobs,lastobs);
12202: free_vector(ageexmed,firstobs,lastobs);
12203: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12204: #ifdef GSL
1.136 brouard 12205: #endif
1.186 brouard 12206: } /* Endof if mle==-3 mortality only */
1.205 brouard 12207: /* Standard */
12208: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12209: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12210: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12211: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12212: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12213: for (k=1; k<=npar;k++)
12214: printf(" %d %8.5f",k,p[k]);
12215: printf("\n");
1.205 brouard 12216: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12217: /* mlikeli uses func not funcone */
1.247 brouard 12218: /* for(i=1;i<nlstate;i++){ */
12219: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12220: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12221: /* } */
1.205 brouard 12222: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12223: }
12224: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12225: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12226: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12227: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12228: }
12229: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12230: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12231: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12232: for (k=1; k<=npar;k++)
12233: printf(" %d %8.5f",k,p[k]);
12234: printf("\n");
12235:
12236: /*--------- results files --------------*/
1.283 brouard 12237: /* 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 12238:
12239:
12240: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12241: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12242: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12243: for(i=1,jk=1; i <=nlstate; i++){
12244: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12245: if (k != i) {
12246: printf("%d%d ",i,k);
12247: fprintf(ficlog,"%d%d ",i,k);
12248: fprintf(ficres,"%1d%1d ",i,k);
12249: for(j=1; j <=ncovmodel; j++){
12250: printf("%12.7f ",p[jk]);
12251: fprintf(ficlog,"%12.7f ",p[jk]);
12252: fprintf(ficres,"%12.7f ",p[jk]);
12253: jk++;
12254: }
12255: printf("\n");
12256: fprintf(ficlog,"\n");
12257: fprintf(ficres,"\n");
12258: }
1.126 brouard 12259: }
12260: }
1.203 brouard 12261: if(mle != 0){
12262: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12263: ftolhess=ftol; /* Usually correct */
1.203 brouard 12264: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12265: 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");
12266: 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");
12267: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12268: for(k=1; k <=(nlstate+ndeath); k++){
12269: if (k != i) {
12270: printf("%d%d ",i,k);
12271: fprintf(ficlog,"%d%d ",i,k);
12272: for(j=1; j <=ncovmodel; j++){
12273: printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
12274: fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
12275: jk++;
12276: }
12277: printf("\n");
12278: fprintf(ficlog,"\n");
12279: }
12280: }
1.193 brouard 12281: }
1.203 brouard 12282: } /* end of hesscov and Wald tests */
1.225 brouard 12283:
1.203 brouard 12284: /* */
1.126 brouard 12285: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12286: printf("# Scales (for hessian or gradient estimation)\n");
12287: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12288: for(i=1,jk=1; i <=nlstate; i++){
12289: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12290: if (j!=i) {
12291: fprintf(ficres,"%1d%1d",i,j);
12292: printf("%1d%1d",i,j);
12293: fprintf(ficlog,"%1d%1d",i,j);
12294: for(k=1; k<=ncovmodel;k++){
12295: printf(" %.5e",delti[jk]);
12296: fprintf(ficlog," %.5e",delti[jk]);
12297: fprintf(ficres," %.5e",delti[jk]);
12298: jk++;
12299: }
12300: printf("\n");
12301: fprintf(ficlog,"\n");
12302: fprintf(ficres,"\n");
12303: }
1.126 brouard 12304: }
12305: }
12306:
12307: 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 12308: if(mle >= 1) /* To big for the screen */
1.126 brouard 12309: 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");
12310: 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");
12311: /* # 121 Var(a12)\n\ */
12312: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12313: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12314: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12315: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12316: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12317: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12318: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12319:
12320:
12321: /* Just to have a covariance matrix which will be more understandable
12322: even is we still don't want to manage dictionary of variables
12323: */
12324: for(itimes=1;itimes<=2;itimes++){
12325: jj=0;
12326: for(i=1; i <=nlstate; i++){
1.225 brouard 12327: for(j=1; j <=nlstate+ndeath; j++){
12328: if(j==i) continue;
12329: for(k=1; k<=ncovmodel;k++){
12330: jj++;
12331: ca[0]= k+'a'-1;ca[1]='\0';
12332: if(itimes==1){
12333: if(mle>=1)
12334: printf("#%1d%1d%d",i,j,k);
12335: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12336: fprintf(ficres,"#%1d%1d%d",i,j,k);
12337: }else{
12338: if(mle>=1)
12339: printf("%1d%1d%d",i,j,k);
12340: fprintf(ficlog,"%1d%1d%d",i,j,k);
12341: fprintf(ficres,"%1d%1d%d",i,j,k);
12342: }
12343: ll=0;
12344: for(li=1;li <=nlstate; li++){
12345: for(lj=1;lj <=nlstate+ndeath; lj++){
12346: if(lj==li) continue;
12347: for(lk=1;lk<=ncovmodel;lk++){
12348: ll++;
12349: if(ll<=jj){
12350: cb[0]= lk +'a'-1;cb[1]='\0';
12351: if(ll<jj){
12352: if(itimes==1){
12353: if(mle>=1)
12354: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12355: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12356: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12357: }else{
12358: if(mle>=1)
12359: printf(" %.5e",matcov[jj][ll]);
12360: fprintf(ficlog," %.5e",matcov[jj][ll]);
12361: fprintf(ficres," %.5e",matcov[jj][ll]);
12362: }
12363: }else{
12364: if(itimes==1){
12365: if(mle>=1)
12366: printf(" Var(%s%1d%1d)",ca,i,j);
12367: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12368: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12369: }else{
12370: if(mle>=1)
12371: printf(" %.7e",matcov[jj][ll]);
12372: fprintf(ficlog," %.7e",matcov[jj][ll]);
12373: fprintf(ficres," %.7e",matcov[jj][ll]);
12374: }
12375: }
12376: }
12377: } /* end lk */
12378: } /* end lj */
12379: } /* end li */
12380: if(mle>=1)
12381: printf("\n");
12382: fprintf(ficlog,"\n");
12383: fprintf(ficres,"\n");
12384: numlinepar++;
12385: } /* end k*/
12386: } /*end j */
1.126 brouard 12387: } /* end i */
12388: } /* end itimes */
12389:
12390: fflush(ficlog);
12391: fflush(ficres);
1.225 brouard 12392: while(fgets(line, MAXLINE, ficpar)) {
12393: /* If line starts with a # it is a comment */
12394: if (line[0] == '#') {
12395: numlinepar++;
12396: fputs(line,stdout);
12397: fputs(line,ficparo);
12398: fputs(line,ficlog);
1.299 brouard 12399: fputs(line,ficres);
1.225 brouard 12400: continue;
12401: }else
12402: break;
12403: }
12404:
1.209 brouard 12405: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12406: /* ungetc(c,ficpar); */
12407: /* fgets(line, MAXLINE, ficpar); */
12408: /* fputs(line,stdout); */
12409: /* fputs(line,ficparo); */
12410: /* } */
12411: /* ungetc(c,ficpar); */
1.126 brouard 12412:
12413: estepm=0;
1.209 brouard 12414: 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 12415:
12416: if (num_filled != 6) {
12417: 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);
12418: 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);
12419: goto end;
12420: }
12421: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12422: }
12423: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12424: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12425:
1.209 brouard 12426: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12427: if (estepm==0 || estepm < stepm) estepm=stepm;
12428: if (fage <= 2) {
12429: bage = ageminpar;
12430: fage = agemaxpar;
12431: }
12432:
12433: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12434: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12435: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12436:
1.186 brouard 12437: /* Other stuffs, more or less useful */
1.254 brouard 12438: while(fgets(line, MAXLINE, ficpar)) {
12439: /* If line starts with a # it is a comment */
12440: if (line[0] == '#') {
12441: numlinepar++;
12442: fputs(line,stdout);
12443: fputs(line,ficparo);
12444: fputs(line,ficlog);
1.299 brouard 12445: fputs(line,ficres);
1.254 brouard 12446: continue;
12447: }else
12448: break;
12449: }
12450:
12451: 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){
12452:
12453: if (num_filled != 7) {
12454: 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);
12455: 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);
12456: goto end;
12457: }
12458: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12459: 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);
12460: 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);
12461: 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 12462: }
1.254 brouard 12463:
12464: while(fgets(line, MAXLINE, ficpar)) {
12465: /* If line starts with a # it is a comment */
12466: if (line[0] == '#') {
12467: numlinepar++;
12468: fputs(line,stdout);
12469: fputs(line,ficparo);
12470: fputs(line,ficlog);
1.299 brouard 12471: fputs(line,ficres);
1.254 brouard 12472: continue;
12473: }else
12474: break;
1.126 brouard 12475: }
12476:
12477:
12478: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12479: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12480:
1.254 brouard 12481: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12482: if (num_filled != 1) {
12483: 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);
12484: 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);
12485: goto end;
12486: }
12487: printf("pop_based=%d\n",popbased);
12488: fprintf(ficlog,"pop_based=%d\n",popbased);
12489: fprintf(ficparo,"pop_based=%d\n",popbased);
12490: fprintf(ficres,"pop_based=%d\n",popbased);
12491: }
12492:
1.258 brouard 12493: /* Results */
1.307 brouard 12494: endishere=0;
1.258 brouard 12495: nresult=0;
1.308 brouard 12496: parameterline=0;
1.258 brouard 12497: do{
12498: if(!fgets(line, MAXLINE, ficpar)){
12499: endishere=1;
1.308 brouard 12500: parameterline=15;
1.258 brouard 12501: }else if (line[0] == '#') {
12502: /* If line starts with a # it is a comment */
1.254 brouard 12503: numlinepar++;
12504: fputs(line,stdout);
12505: fputs(line,ficparo);
12506: fputs(line,ficlog);
1.299 brouard 12507: fputs(line,ficres);
1.254 brouard 12508: continue;
1.258 brouard 12509: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12510: parameterline=11;
1.296 brouard 12511: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12512: parameterline=12;
1.307 brouard 12513: else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258 brouard 12514: parameterline=13;
1.307 brouard 12515: }
1.258 brouard 12516: else{
12517: parameterline=14;
1.254 brouard 12518: }
1.308 brouard 12519: switch (parameterline){ /* =0 only if only comments */
1.258 brouard 12520: case 11:
1.296 brouard 12521: 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)){
12522: 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 12523: 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);
12524: 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);
12525: 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);
12526: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12527: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12528: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12529: prvforecast = 1;
12530: }
12531: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.313 brouard 12532: printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12533: fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12534: fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12535: prvforecast = 2;
12536: }
12537: else {
12538: 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);
12539: 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);
12540: goto end;
1.258 brouard 12541: }
1.254 brouard 12542: break;
1.258 brouard 12543: case 12:
1.296 brouard 12544: 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)){
12545: 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);
12546: 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);
12547: 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);
12548: 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);
12549: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12550: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12551: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12552: prvbackcast = 1;
12553: }
12554: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.313 brouard 12555: printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12556: fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12557: fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12558: prvbackcast = 2;
12559: }
12560: else {
12561: 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);
12562: 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);
12563: goto end;
1.258 brouard 12564: }
1.230 brouard 12565: break;
1.258 brouard 12566: case 13:
1.307 brouard 12567: num_filled=sscanf(line,"result:%[^\n]\n",resultline);
12568: nresult++; /* Sum of resultlines */
12569: printf("Result %d: result:%s\n",nresult, resultline);
12570: if(nresult > MAXRESULTLINES){
12571: 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. ",MAXRESULTLINES,nresult,rfileres);
12572: 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. ",MAXRESULTLINES,nresult,rfileres);
12573: goto end;
12574: }
1.310 brouard 12575: if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.314 brouard 12576: fprintf(ficparo,"result: %s\n",resultline);
12577: fprintf(ficres,"result: %s\n",resultline);
12578: fprintf(ficlog,"result: %s\n",resultline);
1.310 brouard 12579: } else
12580: goto end;
1.307 brouard 12581: break;
12582: case 14:
12583: printf("Error: Unknown command '%s'\n",line);
12584: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
1.314 brouard 12585: if(line[0] == ' ' || line[0] == '\n'){
12586: printf("It should not be an empty line '%s'\n",line);
12587: fprintf(ficlog,"It should not be an empty line '%s'\n",line);
12588: }
1.307 brouard 12589: if(ncovmodel >=2 && nresult==0 ){
12590: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
12591: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12592: }
1.307 brouard 12593: /* goto end; */
12594: break;
1.308 brouard 12595: case 15:
12596: printf("End of resultlines.\n");
12597: fprintf(ficlog,"End of resultlines.\n");
12598: break;
12599: default: /* parameterline =0 */
1.307 brouard 12600: nresult=1;
12601: decoderesult(".",nresult ); /* No covariate */
1.258 brouard 12602: } /* End switch parameterline */
12603: }while(endishere==0); /* End do */
1.126 brouard 12604:
1.230 brouard 12605: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12606: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12607:
12608: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12609: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12610: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12611: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12612: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12613: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12614: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12615: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12616: }else{
1.270 brouard 12617: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12618: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12619: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12620: if(prvforecast==1){
12621: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12622: jprojd=jproj1;
12623: mprojd=mproj1;
12624: anprojd=anproj1;
12625: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12626: jprojf=jproj2;
12627: mprojf=mproj2;
12628: anprojf=anproj2;
12629: } else if(prvforecast == 2){
12630: dateprojd=dateintmean;
12631: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12632: dateprojf=dateintmean+yrfproj;
12633: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12634: }
12635: if(prvbackcast==1){
12636: datebackd=(jback1+12*mback1+365*anback1)/365;
12637: jbackd=jback1;
12638: mbackd=mback1;
12639: anbackd=anback1;
12640: datebackf=(jback2+12*mback2+365*anback2)/365;
12641: jbackf=jback2;
12642: mbackf=mback2;
12643: anbackf=anback2;
12644: } else if(prvbackcast == 2){
12645: datebackd=dateintmean;
12646: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12647: datebackf=dateintmean-yrbproj;
12648: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12649: }
12650:
12651: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12652: }
12653: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12654: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12655: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12656:
1.225 brouard 12657: /*------------ free_vector -------------*/
12658: /* chdir(path); */
1.220 brouard 12659:
1.215 brouard 12660: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12661: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12662: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12663: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12664: free_lvector(num,firstobs,lastobs);
12665: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12666: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12667: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12668: fclose(ficparo);
12669: fclose(ficres);
1.220 brouard 12670:
12671:
1.186 brouard 12672: /* Other results (useful)*/
1.220 brouard 12673:
12674:
1.126 brouard 12675: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12676: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12677: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12678: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12679: fclose(ficrespl);
12680:
12681: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12682: /*#include "hpijx.h"*/
12683: hPijx(p, bage, fage);
1.145 brouard 12684: fclose(ficrespij);
1.227 brouard 12685:
1.220 brouard 12686: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12687: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12688: k=1;
1.126 brouard 12689: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12690:
1.269 brouard 12691: /* Prevalence for each covariate combination in probs[age][status][cov] */
12692: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12693: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12694: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12695: for(k=1;k<=ncovcombmax;k++)
12696: probs[i][j][k]=0.;
1.269 brouard 12697: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12698: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12699: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12700: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12701: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12702: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12703: for(k=1;k<=ncovcombmax;k++)
12704: mobaverages[i][j][k]=0.;
1.219 brouard 12705: mobaverage=mobaverages;
12706: if (mobilav!=0) {
1.235 brouard 12707: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12708: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12709: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12710: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12711: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12712: }
1.269 brouard 12713: } else if (mobilavproj !=0) {
1.235 brouard 12714: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12715: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12716: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12717: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12718: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12719: }
1.269 brouard 12720: }else{
12721: printf("Internal error moving average\n");
12722: fflush(stdout);
12723: exit(1);
1.219 brouard 12724: }
12725: }/* end if moving average */
1.227 brouard 12726:
1.126 brouard 12727: /*---------- Forecasting ------------------*/
1.296 brouard 12728: if(prevfcast==1){
12729: /* /\* if(stepm ==1){*\/ */
12730: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12731: /*This done previously after freqsummary.*/
12732: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12733: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12734:
12735: /* } else if (prvforecast==2){ */
12736: /* /\* if(stepm ==1){*\/ */
12737: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12738: /* } */
12739: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12740: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12741: }
1.269 brouard 12742:
1.296 brouard 12743: /* Prevbcasting */
12744: if(prevbcast==1){
1.219 brouard 12745: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12746: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12747: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12748:
12749: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12750:
12751: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12752:
1.219 brouard 12753: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12754: fclose(ficresplb);
12755:
1.222 brouard 12756: hBijx(p, bage, fage, mobaverage);
12757: fclose(ficrespijb);
1.219 brouard 12758:
1.296 brouard 12759: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12760: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12761: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12762: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12763: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12764: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12765:
12766:
1.269 brouard 12767: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12768:
12769:
1.269 brouard 12770: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12771: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12772: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12773: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12774: } /* end Prevbcasting */
1.268 brouard 12775:
1.186 brouard 12776:
12777: /* ------ Other prevalence ratios------------ */
1.126 brouard 12778:
1.215 brouard 12779: free_ivector(wav,1,imx);
12780: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12781: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12782: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12783:
12784:
1.127 brouard 12785: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12786:
1.201 brouard 12787: strcpy(filerese,"E_");
12788: strcat(filerese,fileresu);
1.126 brouard 12789: if((ficreseij=fopen(filerese,"w"))==NULL) {
12790: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12791: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12792: }
1.208 brouard 12793: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12794: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12795:
12796: pstamp(ficreseij);
1.219 brouard 12797:
1.235 brouard 12798: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12799: if (cptcovn < 1){i1=1;}
12800:
12801: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12802: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12803: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12804: continue;
1.219 brouard 12805: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12806: printf("\n#****** ");
1.225 brouard 12807: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12808: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12809: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12810: }
12811: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12812: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12813: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12814: }
12815: fprintf(ficreseij,"******\n");
1.235 brouard 12816: printf("******\n");
1.219 brouard 12817:
12818: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12819: oldm=oldms;savm=savms;
1.235 brouard 12820: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12821:
1.219 brouard 12822: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12823: }
12824: fclose(ficreseij);
1.208 brouard 12825: printf("done evsij\n");fflush(stdout);
12826: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12827:
1.218 brouard 12828:
1.227 brouard 12829: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12830:
1.201 brouard 12831: strcpy(filerest,"T_");
12832: strcat(filerest,fileresu);
1.127 brouard 12833: if((ficrest=fopen(filerest,"w"))==NULL) {
12834: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12835: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12836: }
1.208 brouard 12837: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12838: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12839: strcpy(fileresstde,"STDE_");
12840: strcat(fileresstde,fileresu);
1.126 brouard 12841: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12842: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12843: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12844: }
1.227 brouard 12845: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12846: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12847:
1.201 brouard 12848: strcpy(filerescve,"CVE_");
12849: strcat(filerescve,fileresu);
1.126 brouard 12850: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12851: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12852: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12853: }
1.227 brouard 12854: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12855: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12856:
1.201 brouard 12857: strcpy(fileresv,"V_");
12858: strcat(fileresv,fileresu);
1.126 brouard 12859: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12860: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12861: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12862: }
1.227 brouard 12863: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12864: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12865:
1.235 brouard 12866: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12867: if (cptcovn < 1){i1=1;}
12868:
12869: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12870: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12871: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12872: continue;
1.242 brouard 12873: printf("\n#****** Result for:");
12874: fprintf(ficrest,"\n#****** Result for:");
12875: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12876: for(j=1;j<=cptcoveff;j++){
12877: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12878: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12879: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12880: }
1.235 brouard 12881: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12882: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12883: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12884: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12885: }
1.208 brouard 12886: fprintf(ficrest,"******\n");
1.227 brouard 12887: fprintf(ficlog,"******\n");
12888: printf("******\n");
1.208 brouard 12889:
12890: fprintf(ficresstdeij,"\n#****** ");
12891: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12892: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12893: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12894: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12895: }
1.235 brouard 12896: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12897: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12898: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12899: }
1.208 brouard 12900: fprintf(ficresstdeij,"******\n");
12901: fprintf(ficrescveij,"******\n");
12902:
12903: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12904: /* pstamp(ficresvij); */
1.225 brouard 12905: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12906: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12907: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12908: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12909: }
1.208 brouard 12910: fprintf(ficresvij,"******\n");
12911:
12912: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12913: oldm=oldms;savm=savms;
1.235 brouard 12914: printf(" cvevsij ");
12915: fprintf(ficlog, " cvevsij ");
12916: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12917: printf(" end cvevsij \n ");
12918: fprintf(ficlog, " end cvevsij \n ");
12919:
12920: /*
12921: */
12922: /* goto endfree; */
12923:
12924: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12925: pstamp(ficrest);
12926:
1.269 brouard 12927: epj=vector(1,nlstate+1);
1.208 brouard 12928: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12929: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12930: cptcod= 0; /* To be deleted */
12931: printf("varevsij vpopbased=%d \n",vpopbased);
12932: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12933: 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 12934: 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 ");
12935: if(vpopbased==1)
12936: 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);
12937: else
1.288 brouard 12938: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12939: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12940: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12941: fprintf(ficrest,"\n");
12942: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12943: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12944: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12945: for(age=bage; age <=fage ;age++){
1.235 brouard 12946: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12947: if (vpopbased==1) {
12948: if(mobilav ==0){
12949: for(i=1; i<=nlstate;i++)
12950: prlim[i][i]=probs[(int)age][i][k];
12951: }else{ /* mobilav */
12952: for(i=1; i<=nlstate;i++)
12953: prlim[i][i]=mobaverage[(int)age][i][k];
12954: }
12955: }
1.219 brouard 12956:
1.227 brouard 12957: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12958: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12959: /* printf(" age %4.0f ",age); */
12960: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12961: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12962: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12963: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12964: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12965: }
12966: epj[nlstate+1] +=epj[j];
12967: }
12968: /* printf(" age %4.0f \n",age); */
1.219 brouard 12969:
1.227 brouard 12970: for(i=1, vepp=0.;i <=nlstate;i++)
12971: for(j=1;j <=nlstate;j++)
12972: vepp += vareij[i][j][(int)age];
12973: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12974: for(j=1;j <=nlstate;j++){
12975: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12976: }
12977: fprintf(ficrest,"\n");
12978: }
1.208 brouard 12979: } /* End vpopbased */
1.269 brouard 12980: free_vector(epj,1,nlstate+1);
1.208 brouard 12981: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12982: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12983: printf("done selection\n");fflush(stdout);
12984: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12985:
1.235 brouard 12986: } /* End k selection */
1.227 brouard 12987:
12988: printf("done State-specific expectancies\n");fflush(stdout);
12989: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12990:
1.288 brouard 12991: /* variance-covariance of forward period prevalence*/
1.269 brouard 12992: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12993:
1.227 brouard 12994:
1.290 brouard 12995: free_vector(weight,firstobs,lastobs);
1.227 brouard 12996: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12997: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12998: free_matrix(anint,1,maxwav,firstobs,lastobs);
12999: free_matrix(mint,1,maxwav,firstobs,lastobs);
13000: free_ivector(cod,firstobs,lastobs);
1.227 brouard 13001: free_ivector(tab,1,NCOVMAX);
13002: fclose(ficresstdeij);
13003: fclose(ficrescveij);
13004: fclose(ficresvij);
13005: fclose(ficrest);
13006: fclose(ficpar);
13007:
13008:
1.126 brouard 13009: /*---------- End : free ----------------*/
1.219 brouard 13010: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 13011: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
13012: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 13013: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
13014: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 13015: } /* mle==-3 arrives here for freeing */
1.227 brouard 13016: /* endfree:*/
13017: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
13018: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
13019: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 13020: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
13021: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
13022: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
13023: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 13024: free_matrix(matcov,1,npar,1,npar);
13025: free_matrix(hess,1,npar,1,npar);
13026: /*free_vector(delti,1,npar);*/
13027: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
13028: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 13029: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 13030: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
13031:
13032: free_ivector(ncodemax,1,NCOVMAX);
13033: free_ivector(ncodemaxwundef,1,NCOVMAX);
13034: free_ivector(Dummy,-1,NCOVMAX);
13035: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 13036: free_ivector(DummyV,1,NCOVMAX);
13037: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 13038: free_ivector(Typevar,-1,NCOVMAX);
13039: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 13040: free_ivector(TvarsQ,1,NCOVMAX);
13041: free_ivector(TvarsQind,1,NCOVMAX);
13042: free_ivector(TvarsD,1,NCOVMAX);
13043: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 13044: free_ivector(TvarFD,1,NCOVMAX);
13045: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 13046: free_ivector(TvarF,1,NCOVMAX);
13047: free_ivector(TvarFind,1,NCOVMAX);
13048: free_ivector(TvarV,1,NCOVMAX);
13049: free_ivector(TvarVind,1,NCOVMAX);
13050: free_ivector(TvarA,1,NCOVMAX);
13051: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 13052: free_ivector(TvarFQ,1,NCOVMAX);
13053: free_ivector(TvarFQind,1,NCOVMAX);
13054: free_ivector(TvarVD,1,NCOVMAX);
13055: free_ivector(TvarVDind,1,NCOVMAX);
13056: free_ivector(TvarVQ,1,NCOVMAX);
13057: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 13058: free_ivector(Tvarsel,1,NCOVMAX);
13059: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 13060: free_ivector(Tposprod,1,NCOVMAX);
13061: free_ivector(Tprod,1,NCOVMAX);
13062: free_ivector(Tvaraff,1,NCOVMAX);
13063: free_ivector(invalidvarcomb,1,ncovcombmax);
13064: free_ivector(Tage,1,NCOVMAX);
13065: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 13066: free_ivector(TmodelInvind,1,NCOVMAX);
13067: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 13068:
13069: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
13070: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 13071: fflush(fichtm);
13072: fflush(ficgp);
13073:
1.227 brouard 13074:
1.126 brouard 13075: if((nberr >0) || (nbwarn>0)){
1.216 brouard 13076: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
13077: 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 13078: }else{
13079: printf("End of Imach\n");
13080: fprintf(ficlog,"End of Imach\n");
13081: }
13082: printf("See log file on %s\n",filelog);
13083: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 13084: /*(void) gettimeofday(&end_time,&tzp);*/
13085: rend_time = time(NULL);
13086: end_time = *localtime(&rend_time);
13087: /* tml = *localtime(&end_time.tm_sec); */
13088: strcpy(strtend,asctime(&end_time));
1.126 brouard 13089: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13090: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13091: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13092:
1.157 brouard 13093: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13094: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13095: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13096: /* printf("Total time was %d uSec.\n", total_usecs);*/
13097: /* if(fileappend(fichtm,optionfilehtm)){ */
13098: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13099: fclose(fichtm);
13100: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13101: fclose(fichtmcov);
13102: fclose(ficgp);
13103: fclose(ficlog);
13104: /*------ End -----------*/
1.227 brouard 13105:
1.281 brouard 13106:
13107: /* Executes gnuplot */
1.227 brouard 13108:
13109: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13110: #ifdef WIN32
1.227 brouard 13111: if (_chdir(pathcd) != 0)
13112: printf("Can't move to directory %s!\n",path);
13113: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13114: #else
1.227 brouard 13115: if(chdir(pathcd) != 0)
13116: printf("Can't move to directory %s!\n", path);
13117: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13118: #endif
1.126 brouard 13119: printf("Current directory %s!\n",pathcd);
13120: /*strcat(plotcmd,CHARSEPARATOR);*/
13121: sprintf(plotcmd,"gnuplot");
1.157 brouard 13122: #ifdef _WIN32
1.126 brouard 13123: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13124: #endif
13125: if(!stat(plotcmd,&info)){
1.158 brouard 13126: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13127: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13128: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13129: }else
13130: strcpy(pplotcmd,plotcmd);
1.157 brouard 13131: #ifdef __unix
1.126 brouard 13132: strcpy(plotcmd,GNUPLOTPROGRAM);
13133: if(!stat(plotcmd,&info)){
1.158 brouard 13134: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13135: }else
13136: strcpy(pplotcmd,plotcmd);
13137: #endif
13138: }else
13139: strcpy(pplotcmd,plotcmd);
13140:
13141: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13142: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13143: strcpy(pplotcmd,plotcmd);
1.227 brouard 13144:
1.126 brouard 13145: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13146: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13147: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13148: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13149: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13150: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13151: strcpy(plotcmd,pplotcmd);
13152: }
1.126 brouard 13153: }
1.158 brouard 13154: printf(" Successful, please wait...");
1.126 brouard 13155: while (z[0] != 'q') {
13156: /* chdir(path); */
1.154 brouard 13157: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13158: scanf("%s",z);
13159: /* if (z[0] == 'c') system("./imach"); */
13160: if (z[0] == 'e') {
1.158 brouard 13161: #ifdef __APPLE__
1.152 brouard 13162: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13163: #elif __linux
13164: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13165: #else
1.152 brouard 13166: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13167: #endif
13168: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13169: system(pplotcmd);
1.126 brouard 13170: }
13171: else if (z[0] == 'g') system(plotcmd);
13172: else if (z[0] == 'q') exit(0);
13173: }
1.227 brouard 13174: end:
1.126 brouard 13175: while (z[0] != 'q') {
1.195 brouard 13176: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13177: scanf("%s",z);
13178: }
1.283 brouard 13179: printf("End\n");
1.282 brouard 13180: exit(0);
1.126 brouard 13181: }
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