Annotation of imach/src/imach.c, revision 1.310
1.310 ! brouard 1: /* $Id: imach.c,v 1.309 2021/05/20 12:39:14 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.310 ! brouard 4: Revision 1.309 2021/05/20 12:39:14 brouard
! 5: Summary: Version 0.99r24
! 6:
1.309 brouard 7: Revision 1.308 2021/03/31 13:11:57 brouard
8: Summary: Version 0.99r23
9:
10:
11: * imach.c (Module): Still bugs in the result loop. Thank to Holly Benett
12:
1.308 brouard 13: Revision 1.307 2021/03/08 18:11:32 brouard
14: Summary: 0.99r22 fixed bug on result:
15:
1.307 brouard 16: Revision 1.306 2021/02/20 15:44:02 brouard
17: Summary: Version 0.99r21
18:
19: * imach.c (Module): Fix bug on quitting after result lines!
20: (Module): Version 0.99r21
21:
1.306 brouard 22: Revision 1.305 2021/02/20 15:28:30 brouard
23: * imach.c (Module): Fix bug on quitting after result lines!
24:
1.305 brouard 25: Revision 1.304 2021/02/12 11:34:20 brouard
26: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
27:
1.304 brouard 28: Revision 1.303 2021/02/11 19:50:15 brouard
29: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
30:
1.303 brouard 31: Revision 1.302 2020/02/22 21:00:05 brouard
32: * (Module): imach.c Update mle=-3 (for computing Life expectancy
33: and life table from the data without any state)
34:
1.302 brouard 35: Revision 1.301 2019/06/04 13:51:20 brouard
36: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
37:
1.301 brouard 38: Revision 1.300 2019/05/22 19:09:45 brouard
39: Summary: version 0.99r19 of May 2019
40:
1.300 brouard 41: Revision 1.299 2019/05/22 18:37:08 brouard
42: Summary: Cleaned 0.99r19
43:
1.299 brouard 44: Revision 1.298 2019/05/22 18:19:56 brouard
45: *** empty log message ***
46:
1.298 brouard 47: Revision 1.297 2019/05/22 17:56:10 brouard
48: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
49:
1.297 brouard 50: Revision 1.296 2019/05/20 13:03:18 brouard
51: Summary: Projection syntax simplified
52:
53:
54: We can now start projections, forward or backward, from the mean date
55: of inteviews up to or down to a number of years of projection:
56: prevforecast=1 yearsfproj=15.3 mobil_average=0
57: or
58: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
59: or
60: prevbackcast=1 yearsbproj=12.3 mobil_average=1
61: or
62: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
63:
1.296 brouard 64: Revision 1.295 2019/05/18 09:52:50 brouard
65: Summary: doxygen tex bug
66:
1.295 brouard 67: Revision 1.294 2019/05/16 14:54:33 brouard
68: Summary: There was some wrong lines added
69:
1.294 brouard 70: Revision 1.293 2019/05/09 15:17:34 brouard
71: *** empty log message ***
72:
1.293 brouard 73: Revision 1.292 2019/05/09 14:17:20 brouard
74: Summary: Some updates
75:
1.292 brouard 76: Revision 1.291 2019/05/09 13:44:18 brouard
77: Summary: Before ncovmax
78:
1.291 brouard 79: Revision 1.290 2019/05/09 13:39:37 brouard
80: Summary: 0.99r18 unlimited number of individuals
81:
82: 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.
83:
1.290 brouard 84: Revision 1.289 2018/12/13 09:16:26 brouard
85: Summary: Bug for young ages (<-30) will be in r17
86:
1.289 brouard 87: Revision 1.288 2018/05/02 20:58:27 brouard
88: Summary: Some bugs fixed
89:
1.288 brouard 90: Revision 1.287 2018/05/01 17:57:25 brouard
91: Summary: Bug fixed by providing frequencies only for non missing covariates
92:
1.287 brouard 93: Revision 1.286 2018/04/27 14:27:04 brouard
94: Summary: some minor bugs
95:
1.286 brouard 96: Revision 1.285 2018/04/21 21:02:16 brouard
97: Summary: Some bugs fixed, valgrind tested
98:
1.285 brouard 99: Revision 1.284 2018/04/20 05:22:13 brouard
100: Summary: Computing mean and stdeviation of fixed quantitative variables
101:
1.284 brouard 102: Revision 1.283 2018/04/19 14:49:16 brouard
103: Summary: Some minor bugs fixed
104:
1.283 brouard 105: Revision 1.282 2018/02/27 22:50:02 brouard
106: *** empty log message ***
107:
1.282 brouard 108: Revision 1.281 2018/02/27 19:25:23 brouard
109: Summary: Adding second argument for quitting
110:
1.281 brouard 111: Revision 1.280 2018/02/21 07:58:13 brouard
112: Summary: 0.99r15
113:
114: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
115:
1.280 brouard 116: Revision 1.279 2017/07/20 13:35:01 brouard
117: Summary: temporary working
118:
1.279 brouard 119: Revision 1.278 2017/07/19 14:09:02 brouard
120: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
121:
1.278 brouard 122: Revision 1.277 2017/07/17 08:53:49 brouard
123: Summary: BOM files can be read now
124:
1.277 brouard 125: Revision 1.276 2017/06/30 15:48:31 brouard
126: Summary: Graphs improvements
127:
1.276 brouard 128: Revision 1.275 2017/06/30 13:39:33 brouard
129: Summary: Saito's color
130:
1.275 brouard 131: Revision 1.274 2017/06/29 09:47:08 brouard
132: Summary: Version 0.99r14
133:
1.274 brouard 134: Revision 1.273 2017/06/27 11:06:02 brouard
135: Summary: More documentation on projections
136:
1.273 brouard 137: Revision 1.272 2017/06/27 10:22:40 brouard
138: Summary: Color of backprojection changed from 6 to 5(yellow)
139:
1.272 brouard 140: Revision 1.271 2017/06/27 10:17:50 brouard
141: Summary: Some bug with rint
142:
1.271 brouard 143: Revision 1.270 2017/05/24 05:45:29 brouard
144: *** empty log message ***
145:
1.270 brouard 146: Revision 1.269 2017/05/23 08:39:25 brouard
147: Summary: Code into subroutine, cleanings
148:
1.269 brouard 149: Revision 1.268 2017/05/18 20:09:32 brouard
150: Summary: backprojection and confidence intervals of backprevalence
151:
1.268 brouard 152: Revision 1.267 2017/05/13 10:25:05 brouard
153: Summary: temporary save for backprojection
154:
1.267 brouard 155: Revision 1.266 2017/05/13 07:26:12 brouard
156: Summary: Version 0.99r13 (improvements and bugs fixed)
157:
1.266 brouard 158: Revision 1.265 2017/04/26 16:22:11 brouard
159: Summary: imach 0.99r13 Some bugs fixed
160:
1.265 brouard 161: Revision 1.264 2017/04/26 06:01:29 brouard
162: Summary: Labels in graphs
163:
1.264 brouard 164: Revision 1.263 2017/04/24 15:23:15 brouard
165: Summary: to save
166:
1.263 brouard 167: Revision 1.262 2017/04/18 16:48:12 brouard
168: *** empty log message ***
169:
1.262 brouard 170: Revision 1.261 2017/04/05 10:14:09 brouard
171: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
172:
1.261 brouard 173: Revision 1.260 2017/04/04 17:46:59 brouard
174: Summary: Gnuplot indexations fixed (humm)
175:
1.260 brouard 176: Revision 1.259 2017/04/04 13:01:16 brouard
177: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
178:
1.259 brouard 179: Revision 1.258 2017/04/03 10:17:47 brouard
180: Summary: Version 0.99r12
181:
182: Some cleanings, conformed with updated documentation.
183:
1.258 brouard 184: Revision 1.257 2017/03/29 16:53:30 brouard
185: Summary: Temp
186:
1.257 brouard 187: Revision 1.256 2017/03/27 05:50:23 brouard
188: Summary: Temporary
189:
1.256 brouard 190: Revision 1.255 2017/03/08 16:02:28 brouard
191: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
192:
1.255 brouard 193: Revision 1.254 2017/03/08 07:13:00 brouard
194: Summary: Fixing data parameter line
195:
1.254 brouard 196: Revision 1.253 2016/12/15 11:59:41 brouard
197: Summary: 0.99 in progress
198:
1.253 brouard 199: Revision 1.252 2016/09/15 21:15:37 brouard
200: *** empty log message ***
201:
1.252 brouard 202: Revision 1.251 2016/09/15 15:01:13 brouard
203: Summary: not working
204:
1.251 brouard 205: Revision 1.250 2016/09/08 16:07:27 brouard
206: Summary: continue
207:
1.250 brouard 208: Revision 1.249 2016/09/07 17:14:18 brouard
209: Summary: Starting values from frequencies
210:
1.249 brouard 211: Revision 1.248 2016/09/07 14:10:18 brouard
212: *** empty log message ***
213:
1.248 brouard 214: Revision 1.247 2016/09/02 11:11:21 brouard
215: *** empty log message ***
216:
1.247 brouard 217: Revision 1.246 2016/09/02 08:49:22 brouard
218: *** empty log message ***
219:
1.246 brouard 220: Revision 1.245 2016/09/02 07:25:01 brouard
221: *** empty log message ***
222:
1.245 brouard 223: Revision 1.244 2016/09/02 07:17:34 brouard
224: *** empty log message ***
225:
1.244 brouard 226: Revision 1.243 2016/09/02 06:45:35 brouard
227: *** empty log message ***
228:
1.243 brouard 229: Revision 1.242 2016/08/30 15:01:20 brouard
230: Summary: Fixing a lots
231:
1.242 brouard 232: Revision 1.241 2016/08/29 17:17:25 brouard
233: Summary: gnuplot problem in Back projection to fix
234:
1.241 brouard 235: Revision 1.240 2016/08/29 07:53:18 brouard
236: Summary: Better
237:
1.240 brouard 238: Revision 1.239 2016/08/26 15:51:03 brouard
239: Summary: Improvement in Powell output in order to copy and paste
240:
241: Author:
242:
1.239 brouard 243: Revision 1.238 2016/08/26 14:23:35 brouard
244: Summary: Starting tests of 0.99
245:
1.238 brouard 246: Revision 1.237 2016/08/26 09:20:19 brouard
247: Summary: to valgrind
248:
1.237 brouard 249: Revision 1.236 2016/08/25 10:50:18 brouard
250: *** empty log message ***
251:
1.236 brouard 252: Revision 1.235 2016/08/25 06:59:23 brouard
253: *** empty log message ***
254:
1.235 brouard 255: Revision 1.234 2016/08/23 16:51:20 brouard
256: *** empty log message ***
257:
1.234 brouard 258: Revision 1.233 2016/08/23 07:40:50 brouard
259: Summary: not working
260:
1.233 brouard 261: Revision 1.232 2016/08/22 14:20:21 brouard
262: Summary: not working
263:
1.232 brouard 264: Revision 1.231 2016/08/22 07:17:15 brouard
265: Summary: not working
266:
1.231 brouard 267: Revision 1.230 2016/08/22 06:55:53 brouard
268: Summary: Not working
269:
1.230 brouard 270: Revision 1.229 2016/07/23 09:45:53 brouard
271: Summary: Completing for func too
272:
1.229 brouard 273: Revision 1.228 2016/07/22 17:45:30 brouard
274: Summary: Fixing some arrays, still debugging
275:
1.227 brouard 276: Revision 1.226 2016/07/12 18:42:34 brouard
277: Summary: temp
278:
1.226 brouard 279: Revision 1.225 2016/07/12 08:40:03 brouard
280: Summary: saving but not running
281:
1.225 brouard 282: Revision 1.224 2016/07/01 13:16:01 brouard
283: Summary: Fixes
284:
1.224 brouard 285: Revision 1.223 2016/02/19 09:23:35 brouard
286: Summary: temporary
287:
1.223 brouard 288: Revision 1.222 2016/02/17 08:14:50 brouard
289: Summary: Probably last 0.98 stable version 0.98r6
290:
1.222 brouard 291: Revision 1.221 2016/02/15 23:35:36 brouard
292: Summary: minor bug
293:
1.220 brouard 294: Revision 1.219 2016/02/15 00:48:12 brouard
295: *** empty log message ***
296:
1.219 brouard 297: Revision 1.218 2016/02/12 11:29:23 brouard
298: Summary: 0.99 Back projections
299:
1.218 brouard 300: Revision 1.217 2015/12/23 17:18:31 brouard
301: Summary: Experimental backcast
302:
1.217 brouard 303: Revision 1.216 2015/12/18 17:32:11 brouard
304: Summary: 0.98r4 Warning and status=-2
305:
306: Version 0.98r4 is now:
307: - displaying an error when status is -1, date of interview unknown and date of death known;
308: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
309: Older changes concerning s=-2, dating from 2005 have been supersed.
310:
1.216 brouard 311: Revision 1.215 2015/12/16 08:52:24 brouard
312: Summary: 0.98r4 working
313:
1.215 brouard 314: Revision 1.214 2015/12/16 06:57:54 brouard
315: Summary: temporary not working
316:
1.214 brouard 317: Revision 1.213 2015/12/11 18:22:17 brouard
318: Summary: 0.98r4
319:
1.213 brouard 320: Revision 1.212 2015/11/21 12:47:24 brouard
321: Summary: minor typo
322:
1.212 brouard 323: Revision 1.211 2015/11/21 12:41:11 brouard
324: Summary: 0.98r3 with some graph of projected cross-sectional
325:
326: Author: Nicolas Brouard
327:
1.211 brouard 328: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 329: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 330: Summary: Adding ftolpl parameter
331: Author: N Brouard
332:
333: We had difficulties to get smoothed confidence intervals. It was due
334: to the period prevalence which wasn't computed accurately. The inner
335: parameter ftolpl is now an outer parameter of the .imach parameter
336: file after estepm. If ftolpl is small 1.e-4 and estepm too,
337: computation are long.
338:
1.209 brouard 339: Revision 1.208 2015/11/17 14:31:57 brouard
340: Summary: temporary
341:
1.208 brouard 342: Revision 1.207 2015/10/27 17:36:57 brouard
343: *** empty log message ***
344:
1.207 brouard 345: Revision 1.206 2015/10/24 07:14:11 brouard
346: *** empty log message ***
347:
1.206 brouard 348: Revision 1.205 2015/10/23 15:50:53 brouard
349: Summary: 0.98r3 some clarification for graphs on likelihood contributions
350:
1.205 brouard 351: Revision 1.204 2015/10/01 16:20:26 brouard
352: Summary: Some new graphs of contribution to likelihood
353:
1.204 brouard 354: Revision 1.203 2015/09/30 17:45:14 brouard
355: Summary: looking at better estimation of the hessian
356:
357: Also a better criteria for convergence to the period prevalence And
358: therefore adding the number of years needed to converge. (The
359: prevalence in any alive state shold sum to one
360:
1.203 brouard 361: Revision 1.202 2015/09/22 19:45:16 brouard
362: Summary: Adding some overall graph on contribution to likelihood. Might change
363:
1.202 brouard 364: Revision 1.201 2015/09/15 17:34:58 brouard
365: Summary: 0.98r0
366:
367: - Some new graphs like suvival functions
368: - Some bugs fixed like model=1+age+V2.
369:
1.201 brouard 370: Revision 1.200 2015/09/09 16:53:55 brouard
371: Summary: Big bug thanks to Flavia
372:
373: Even model=1+age+V2. did not work anymore
374:
1.200 brouard 375: Revision 1.199 2015/09/07 14:09:23 brouard
376: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
377:
1.199 brouard 378: Revision 1.198 2015/09/03 07:14:39 brouard
379: Summary: 0.98q5 Flavia
380:
1.198 brouard 381: Revision 1.197 2015/09/01 18:24:39 brouard
382: *** empty log message ***
383:
1.197 brouard 384: Revision 1.196 2015/08/18 23:17:52 brouard
385: Summary: 0.98q5
386:
1.196 brouard 387: Revision 1.195 2015/08/18 16:28:39 brouard
388: Summary: Adding a hack for testing purpose
389:
390: After reading the title, ftol and model lines, if the comment line has
391: a q, starting with #q, the answer at the end of the run is quit. It
392: permits to run test files in batch with ctest. The former workaround was
393: $ echo q | imach foo.imach
394:
1.195 brouard 395: Revision 1.194 2015/08/18 13:32:00 brouard
396: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
397:
1.194 brouard 398: Revision 1.193 2015/08/04 07:17:42 brouard
399: Summary: 0.98q4
400:
1.193 brouard 401: Revision 1.192 2015/07/16 16:49:02 brouard
402: Summary: Fixing some outputs
403:
1.192 brouard 404: Revision 1.191 2015/07/14 10:00:33 brouard
405: Summary: Some fixes
406:
1.191 brouard 407: Revision 1.190 2015/05/05 08:51:13 brouard
408: Summary: Adding digits in output parameters (7 digits instead of 6)
409:
410: Fix 1+age+.
411:
1.190 brouard 412: Revision 1.189 2015/04/30 14:45:16 brouard
413: Summary: 0.98q2
414:
1.189 brouard 415: Revision 1.188 2015/04/30 08:27:53 brouard
416: *** empty log message ***
417:
1.188 brouard 418: Revision 1.187 2015/04/29 09:11:15 brouard
419: *** empty log message ***
420:
1.187 brouard 421: Revision 1.186 2015/04/23 12:01:52 brouard
422: Summary: V1*age is working now, version 0.98q1
423:
424: Some codes had been disabled in order to simplify and Vn*age was
425: working in the optimization phase, ie, giving correct MLE parameters,
426: but, as usual, outputs were not correct and program core dumped.
427:
1.186 brouard 428: Revision 1.185 2015/03/11 13:26:42 brouard
429: Summary: Inclusion of compile and links command line for Intel Compiler
430:
1.185 brouard 431: Revision 1.184 2015/03/11 11:52:39 brouard
432: Summary: Back from Windows 8. Intel Compiler
433:
1.184 brouard 434: Revision 1.183 2015/03/10 20:34:32 brouard
435: Summary: 0.98q0, trying with directest, mnbrak fixed
436:
437: We use directest instead of original Powell test; probably no
438: incidence on the results, but better justifications;
439: We fixed Numerical Recipes mnbrak routine which was wrong and gave
440: wrong results.
441:
1.183 brouard 442: Revision 1.182 2015/02/12 08:19:57 brouard
443: Summary: Trying to keep directest which seems simpler and more general
444: Author: Nicolas Brouard
445:
1.182 brouard 446: Revision 1.181 2015/02/11 23:22:24 brouard
447: Summary: Comments on Powell added
448:
449: Author:
450:
1.181 brouard 451: Revision 1.180 2015/02/11 17:33:45 brouard
452: Summary: Finishing move from main to function (hpijx and prevalence_limit)
453:
1.180 brouard 454: Revision 1.179 2015/01/04 09:57:06 brouard
455: Summary: back to OS/X
456:
1.179 brouard 457: Revision 1.178 2015/01/04 09:35:48 brouard
458: *** empty log message ***
459:
1.178 brouard 460: Revision 1.177 2015/01/03 18:40:56 brouard
461: Summary: Still testing ilc32 on OSX
462:
1.177 brouard 463: Revision 1.176 2015/01/03 16:45:04 brouard
464: *** empty log message ***
465:
1.176 brouard 466: Revision 1.175 2015/01/03 16:33:42 brouard
467: *** empty log message ***
468:
1.175 brouard 469: Revision 1.174 2015/01/03 16:15:49 brouard
470: Summary: Still in cross-compilation
471:
1.174 brouard 472: Revision 1.173 2015/01/03 12:06:26 brouard
473: Summary: trying to detect cross-compilation
474:
1.173 brouard 475: Revision 1.172 2014/12/27 12:07:47 brouard
476: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
477:
1.172 brouard 478: Revision 1.171 2014/12/23 13:26:59 brouard
479: Summary: Back from Visual C
480:
481: Still problem with utsname.h on Windows
482:
1.171 brouard 483: Revision 1.170 2014/12/23 11:17:12 brouard
484: Summary: Cleaning some \%% back to %%
485:
486: The escape was mandatory for a specific compiler (which one?), but too many warnings.
487:
1.170 brouard 488: Revision 1.169 2014/12/22 23:08:31 brouard
489: Summary: 0.98p
490:
491: Outputs some informations on compiler used, OS etc. Testing on different platforms.
492:
1.169 brouard 493: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 494: Summary: update
1.169 brouard 495:
1.168 brouard 496: Revision 1.167 2014/12/22 13:50:56 brouard
497: Summary: Testing uname and compiler version and if compiled 32 or 64
498:
499: Testing on Linux 64
500:
1.167 brouard 501: Revision 1.166 2014/12/22 11:40:47 brouard
502: *** empty log message ***
503:
1.166 brouard 504: Revision 1.165 2014/12/16 11:20:36 brouard
505: Summary: After compiling on Visual C
506:
507: * imach.c (Module): Merging 1.61 to 1.162
508:
1.165 brouard 509: Revision 1.164 2014/12/16 10:52:11 brouard
510: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
511:
512: * imach.c (Module): Merging 1.61 to 1.162
513:
1.164 brouard 514: Revision 1.163 2014/12/16 10:30:11 brouard
515: * imach.c (Module): Merging 1.61 to 1.162
516:
1.163 brouard 517: Revision 1.162 2014/09/25 11:43:39 brouard
518: Summary: temporary backup 0.99!
519:
1.162 brouard 520: Revision 1.1 2014/09/16 11:06:58 brouard
521: Summary: With some code (wrong) for nlopt
522:
523: Author:
524:
525: Revision 1.161 2014/09/15 20:41:41 brouard
526: Summary: Problem with macro SQR on Intel compiler
527:
1.161 brouard 528: Revision 1.160 2014/09/02 09:24:05 brouard
529: *** empty log message ***
530:
1.160 brouard 531: Revision 1.159 2014/09/01 10:34:10 brouard
532: Summary: WIN32
533: Author: Brouard
534:
1.159 brouard 535: Revision 1.158 2014/08/27 17:11:51 brouard
536: *** empty log message ***
537:
1.158 brouard 538: Revision 1.157 2014/08/27 16:26:55 brouard
539: Summary: Preparing windows Visual studio version
540: Author: Brouard
541:
542: In order to compile on Visual studio, time.h is now correct and time_t
543: and tm struct should be used. difftime should be used but sometimes I
544: just make the differences in raw time format (time(&now).
545: Trying to suppress #ifdef LINUX
546: Add xdg-open for __linux in order to open default browser.
547:
1.157 brouard 548: Revision 1.156 2014/08/25 20:10:10 brouard
549: *** empty log message ***
550:
1.156 brouard 551: Revision 1.155 2014/08/25 18:32:34 brouard
552: Summary: New compile, minor changes
553: Author: Brouard
554:
1.155 brouard 555: Revision 1.154 2014/06/20 17:32:08 brouard
556: Summary: Outputs now all graphs of convergence to period prevalence
557:
1.154 brouard 558: Revision 1.153 2014/06/20 16:45:46 brouard
559: Summary: If 3 live state, convergence to period prevalence on same graph
560: Author: Brouard
561:
1.153 brouard 562: Revision 1.152 2014/06/18 17:54:09 brouard
563: Summary: open browser, use gnuplot on same dir than imach if not found in the path
564:
1.152 brouard 565: Revision 1.151 2014/06/18 16:43:30 brouard
566: *** empty log message ***
567:
1.151 brouard 568: Revision 1.150 2014/06/18 16:42:35 brouard
569: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
570: Author: brouard
571:
1.150 brouard 572: Revision 1.149 2014/06/18 15:51:14 brouard
573: Summary: Some fixes in parameter files errors
574: Author: Nicolas Brouard
575:
1.149 brouard 576: Revision 1.148 2014/06/17 17:38:48 brouard
577: Summary: Nothing new
578: Author: Brouard
579:
580: Just a new packaging for OS/X version 0.98nS
581:
1.148 brouard 582: Revision 1.147 2014/06/16 10:33:11 brouard
583: *** empty log message ***
584:
1.147 brouard 585: Revision 1.146 2014/06/16 10:20:28 brouard
586: Summary: Merge
587: Author: Brouard
588:
589: Merge, before building revised version.
590:
1.146 brouard 591: Revision 1.145 2014/06/10 21:23:15 brouard
592: Summary: Debugging with valgrind
593: Author: Nicolas Brouard
594:
595: Lot of changes in order to output the results with some covariates
596: After the Edimburgh REVES conference 2014, it seems mandatory to
597: improve the code.
598: No more memory valgrind error but a lot has to be done in order to
599: continue the work of splitting the code into subroutines.
600: Also, decodemodel has been improved. Tricode is still not
601: optimal. nbcode should be improved. Documentation has been added in
602: the source code.
603:
1.144 brouard 604: Revision 1.143 2014/01/26 09:45:38 brouard
605: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
606:
607: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
608: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
609:
1.143 brouard 610: Revision 1.142 2014/01/26 03:57:36 brouard
611: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
612:
613: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
614:
1.142 brouard 615: Revision 1.141 2014/01/26 02:42:01 brouard
616: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
617:
1.141 brouard 618: Revision 1.140 2011/09/02 10:37:54 brouard
619: Summary: times.h is ok with mingw32 now.
620:
1.140 brouard 621: Revision 1.139 2010/06/14 07:50:17 brouard
622: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
623: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
624:
1.139 brouard 625: Revision 1.138 2010/04/30 18:19:40 brouard
626: *** empty log message ***
627:
1.138 brouard 628: Revision 1.137 2010/04/29 18:11:38 brouard
629: (Module): Checking covariates for more complex models
630: than V1+V2. A lot of change to be done. Unstable.
631:
1.137 brouard 632: Revision 1.136 2010/04/26 20:30:53 brouard
633: (Module): merging some libgsl code. Fixing computation
634: of likelione (using inter/intrapolation if mle = 0) in order to
635: get same likelihood as if mle=1.
636: Some cleaning of code and comments added.
637:
1.136 brouard 638: Revision 1.135 2009/10/29 15:33:14 brouard
639: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
640:
1.135 brouard 641: Revision 1.134 2009/10/29 13:18:53 brouard
642: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
643:
1.134 brouard 644: Revision 1.133 2009/07/06 10:21:25 brouard
645: just nforces
646:
1.133 brouard 647: Revision 1.132 2009/07/06 08:22:05 brouard
648: Many tings
649:
1.132 brouard 650: Revision 1.131 2009/06/20 16:22:47 brouard
651: Some dimensions resccaled
652:
1.131 brouard 653: Revision 1.130 2009/05/26 06:44:34 brouard
654: (Module): Max Covariate is now set to 20 instead of 8. A
655: lot of cleaning with variables initialized to 0. Trying to make
656: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
657:
1.130 brouard 658: Revision 1.129 2007/08/31 13:49:27 lievre
659: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
660:
1.129 lievre 661: Revision 1.128 2006/06/30 13:02:05 brouard
662: (Module): Clarifications on computing e.j
663:
1.128 brouard 664: Revision 1.127 2006/04/28 18:11:50 brouard
665: (Module): Yes the sum of survivors was wrong since
666: imach-114 because nhstepm was no more computed in the age
667: loop. Now we define nhstepma in the age loop.
668: (Module): In order to speed up (in case of numerous covariates) we
669: compute health expectancies (without variances) in a first step
670: and then all the health expectancies with variances or standard
671: deviation (needs data from the Hessian matrices) which slows the
672: computation.
673: In the future we should be able to stop the program is only health
674: expectancies and graph are needed without standard deviations.
675:
1.127 brouard 676: Revision 1.126 2006/04/28 17:23:28 brouard
677: (Module): Yes the sum of survivors was wrong since
678: imach-114 because nhstepm was no more computed in the age
679: loop. Now we define nhstepma in the age loop.
680: Version 0.98h
681:
1.126 brouard 682: Revision 1.125 2006/04/04 15:20:31 lievre
683: Errors in calculation of health expectancies. Age was not initialized.
684: Forecasting file added.
685:
686: Revision 1.124 2006/03/22 17:13:53 lievre
687: Parameters are printed with %lf instead of %f (more numbers after the comma).
688: The log-likelihood is printed in the log file
689:
690: Revision 1.123 2006/03/20 10:52:43 brouard
691: * imach.c (Module): <title> changed, corresponds to .htm file
692: name. <head> headers where missing.
693:
694: * imach.c (Module): Weights can have a decimal point as for
695: English (a comma might work with a correct LC_NUMERIC environment,
696: otherwise the weight is truncated).
697: Modification of warning when the covariates values are not 0 or
698: 1.
699: Version 0.98g
700:
701: Revision 1.122 2006/03/20 09:45:41 brouard
702: (Module): Weights can have a decimal point as for
703: English (a comma might work with a correct LC_NUMERIC environment,
704: otherwise the weight is truncated).
705: Modification of warning when the covariates values are not 0 or
706: 1.
707: Version 0.98g
708:
709: Revision 1.121 2006/03/16 17:45:01 lievre
710: * imach.c (Module): Comments concerning covariates added
711:
712: * imach.c (Module): refinements in the computation of lli if
713: status=-2 in order to have more reliable computation if stepm is
714: not 1 month. Version 0.98f
715:
716: Revision 1.120 2006/03/16 15:10:38 lievre
717: (Module): refinements in the computation of lli if
718: status=-2 in order to have more reliable computation if stepm is
719: not 1 month. Version 0.98f
720:
721: Revision 1.119 2006/03/15 17:42:26 brouard
722: (Module): Bug if status = -2, the loglikelihood was
723: computed as likelihood omitting the logarithm. Version O.98e
724:
725: Revision 1.118 2006/03/14 18:20:07 brouard
726: (Module): varevsij Comments added explaining the second
727: table of variances if popbased=1 .
728: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
729: (Module): Function pstamp added
730: (Module): Version 0.98d
731:
732: Revision 1.117 2006/03/14 17:16:22 brouard
733: (Module): varevsij Comments added explaining the second
734: table of variances if popbased=1 .
735: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
736: (Module): Function pstamp added
737: (Module): Version 0.98d
738:
739: Revision 1.116 2006/03/06 10:29:27 brouard
740: (Module): Variance-covariance wrong links and
741: varian-covariance of ej. is needed (Saito).
742:
743: Revision 1.115 2006/02/27 12:17:45 brouard
744: (Module): One freematrix added in mlikeli! 0.98c
745:
746: Revision 1.114 2006/02/26 12:57:58 brouard
747: (Module): Some improvements in processing parameter
748: filename with strsep.
749:
750: Revision 1.113 2006/02/24 14:20:24 brouard
751: (Module): Memory leaks checks with valgrind and:
752: datafile was not closed, some imatrix were not freed and on matrix
753: allocation too.
754:
755: Revision 1.112 2006/01/30 09:55:26 brouard
756: (Module): Back to gnuplot.exe instead of wgnuplot.exe
757:
758: Revision 1.111 2006/01/25 20:38:18 brouard
759: (Module): Lots of cleaning and bugs added (Gompertz)
760: (Module): Comments can be added in data file. Missing date values
761: can be a simple dot '.'.
762:
763: Revision 1.110 2006/01/25 00:51:50 brouard
764: (Module): Lots of cleaning and bugs added (Gompertz)
765:
766: Revision 1.109 2006/01/24 19:37:15 brouard
767: (Module): Comments (lines starting with a #) are allowed in data.
768:
769: Revision 1.108 2006/01/19 18:05:42 lievre
770: Gnuplot problem appeared...
771: To be fixed
772:
773: Revision 1.107 2006/01/19 16:20:37 brouard
774: Test existence of gnuplot in imach path
775:
776: Revision 1.106 2006/01/19 13:24:36 brouard
777: Some cleaning and links added in html output
778:
779: Revision 1.105 2006/01/05 20:23:19 lievre
780: *** empty log message ***
781:
782: Revision 1.104 2005/09/30 16:11:43 lievre
783: (Module): sump fixed, loop imx fixed, and simplifications.
784: (Module): If the status is missing at the last wave but we know
785: that the person is alive, then we can code his/her status as -2
786: (instead of missing=-1 in earlier versions) and his/her
787: contributions to the likelihood is 1 - Prob of dying from last
788: health status (= 1-p13= p11+p12 in the easiest case of somebody in
789: the healthy state at last known wave). Version is 0.98
790:
791: Revision 1.103 2005/09/30 15:54:49 lievre
792: (Module): sump fixed, loop imx fixed, and simplifications.
793:
794: Revision 1.102 2004/09/15 17:31:30 brouard
795: Add the possibility to read data file including tab characters.
796:
797: Revision 1.101 2004/09/15 10:38:38 brouard
798: Fix on curr_time
799:
800: Revision 1.100 2004/07/12 18:29:06 brouard
801: Add version for Mac OS X. Just define UNIX in Makefile
802:
803: Revision 1.99 2004/06/05 08:57:40 brouard
804: *** empty log message ***
805:
806: Revision 1.98 2004/05/16 15:05:56 brouard
807: New version 0.97 . First attempt to estimate force of mortality
808: directly from the data i.e. without the need of knowing the health
809: state at each age, but using a Gompertz model: log u =a + b*age .
810: This is the basic analysis of mortality and should be done before any
811: other analysis, in order to test if the mortality estimated from the
812: cross-longitudinal survey is different from the mortality estimated
813: from other sources like vital statistic data.
814:
815: The same imach parameter file can be used but the option for mle should be -3.
816:
1.133 brouard 817: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 818: former routines in order to include the new code within the former code.
819:
820: The output is very simple: only an estimate of the intercept and of
821: the slope with 95% confident intervals.
822:
823: Current limitations:
824: A) Even if you enter covariates, i.e. with the
825: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
826: B) There is no computation of Life Expectancy nor Life Table.
827:
828: Revision 1.97 2004/02/20 13:25:42 lievre
829: Version 0.96d. Population forecasting command line is (temporarily)
830: suppressed.
831:
832: Revision 1.96 2003/07/15 15:38:55 brouard
833: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
834: rewritten within the same printf. Workaround: many printfs.
835:
836: Revision 1.95 2003/07/08 07:54:34 brouard
837: * imach.c (Repository):
838: (Repository): Using imachwizard code to output a more meaningful covariance
839: matrix (cov(a12,c31) instead of numbers.
840:
841: Revision 1.94 2003/06/27 13:00:02 brouard
842: Just cleaning
843:
844: Revision 1.93 2003/06/25 16:33:55 brouard
845: (Module): On windows (cygwin) function asctime_r doesn't
846: exist so I changed back to asctime which exists.
847: (Module): Version 0.96b
848:
849: Revision 1.92 2003/06/25 16:30:45 brouard
850: (Module): On windows (cygwin) function asctime_r doesn't
851: exist so I changed back to asctime which exists.
852:
853: Revision 1.91 2003/06/25 15:30:29 brouard
854: * imach.c (Repository): Duplicated warning errors corrected.
855: (Repository): Elapsed time after each iteration is now output. It
856: helps to forecast when convergence will be reached. Elapsed time
857: is stamped in powell. We created a new html file for the graphs
858: concerning matrix of covariance. It has extension -cov.htm.
859:
860: Revision 1.90 2003/06/24 12:34:15 brouard
861: (Module): Some bugs corrected for windows. Also, when
862: mle=-1 a template is output in file "or"mypar.txt with the design
863: of the covariance matrix to be input.
864:
865: Revision 1.89 2003/06/24 12:30:52 brouard
866: (Module): Some bugs corrected for windows. Also, when
867: mle=-1 a template is output in file "or"mypar.txt with the design
868: of the covariance matrix to be input.
869:
870: Revision 1.88 2003/06/23 17:54:56 brouard
871: * 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.
872:
873: Revision 1.87 2003/06/18 12:26:01 brouard
874: Version 0.96
875:
876: Revision 1.86 2003/06/17 20:04:08 brouard
877: (Module): Change position of html and gnuplot routines and added
878: routine fileappend.
879:
880: Revision 1.85 2003/06/17 13:12:43 brouard
881: * imach.c (Repository): Check when date of death was earlier that
882: current date of interview. It may happen when the death was just
883: prior to the death. In this case, dh was negative and likelihood
884: was wrong (infinity). We still send an "Error" but patch by
885: assuming that the date of death was just one stepm after the
886: interview.
887: (Repository): Because some people have very long ID (first column)
888: we changed int to long in num[] and we added a new lvector for
889: memory allocation. But we also truncated to 8 characters (left
890: truncation)
891: (Repository): No more line truncation errors.
892:
893: Revision 1.84 2003/06/13 21:44:43 brouard
894: * imach.c (Repository): Replace "freqsummary" at a correct
895: place. It differs from routine "prevalence" which may be called
896: many times. Probs is memory consuming and must be used with
897: parcimony.
898: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
899:
900: Revision 1.83 2003/06/10 13:39:11 lievre
901: *** empty log message ***
902:
903: Revision 1.82 2003/06/05 15:57:20 brouard
904: Add log in imach.c and fullversion number is now printed.
905:
906: */
907: /*
908: Interpolated Markov Chain
909:
910: Short summary of the programme:
911:
1.227 brouard 912: This program computes Healthy Life Expectancies or State-specific
913: (if states aren't health statuses) Expectancies from
914: cross-longitudinal data. Cross-longitudinal data consist in:
915:
916: -1- a first survey ("cross") where individuals from different ages
917: are interviewed on their health status or degree of disability (in
918: the case of a health survey which is our main interest)
919:
920: -2- at least a second wave of interviews ("longitudinal") which
921: measure each change (if any) in individual health status. Health
922: expectancies are computed from the time spent in each health state
923: according to a model. More health states you consider, more time is
924: necessary to reach the Maximum Likelihood of the parameters involved
925: in the model. The simplest model is the multinomial logistic model
926: where pij is the probability to be observed in state j at the second
927: wave conditional to be observed in state i at the first
928: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
929: etc , where 'age' is age and 'sex' is a covariate. If you want to
930: have a more complex model than "constant and age", you should modify
931: the program where the markup *Covariates have to be included here
932: again* invites you to do it. More covariates you add, slower the
1.126 brouard 933: convergence.
934:
935: The advantage of this computer programme, compared to a simple
936: multinomial logistic model, is clear when the delay between waves is not
937: identical for each individual. Also, if a individual missed an
938: intermediate interview, the information is lost, but taken into
939: account using an interpolation or extrapolation.
940:
941: hPijx is the probability to be observed in state i at age x+h
942: conditional to the observed state i at age x. The delay 'h' can be
943: split into an exact number (nh*stepm) of unobserved intermediate
944: states. This elementary transition (by month, quarter,
945: semester or year) is modelled as a multinomial logistic. The hPx
946: matrix is simply the matrix product of nh*stepm elementary matrices
947: and the contribution of each individual to the likelihood is simply
948: hPijx.
949:
950: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 951: of the life expectancies. It also computes the period (stable) prevalence.
952:
953: Back prevalence and projections:
1.227 brouard 954:
955: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
956: double agemaxpar, double ftolpl, int *ncvyearp, double
957: dateprev1,double dateprev2, int firstpass, int lastpass, int
958: mobilavproj)
959:
960: Computes the back prevalence limit for any combination of
961: covariate values k at any age between ageminpar and agemaxpar and
962: returns it in **bprlim. In the loops,
963:
964: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
965: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
966:
967: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 968: Computes for any combination of covariates k and any age between bage and fage
969: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
970: oldm=oldms;savm=savms;
1.227 brouard 971:
1.267 brouard 972: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 973: Computes the transition matrix starting at age 'age' over
974: 'nhstepm*hstepm*stepm' months (i.e. until
975: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 976: nhstepm*hstepm matrices.
977:
978: Returns p3mat[i][j][h] after calling
979: p3mat[i][j][h]=matprod2(newm,
980: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
981: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
982: oldm);
1.226 brouard 983:
984: Important routines
985:
986: - func (or funcone), computes logit (pij) distinguishing
987: o fixed variables (single or product dummies or quantitative);
988: o varying variables by:
989: (1) wave (single, product dummies, quantitative),
990: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
991: % fixed dummy (treated) or quantitative (not done because time-consuming);
992: % varying dummy (not done) or quantitative (not done);
993: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
994: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
995: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
996: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
997: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 998:
1.226 brouard 999:
1000:
1.133 brouard 1001: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
1002: Institut national d'études démographiques, Paris.
1.126 brouard 1003: This software have been partly granted by Euro-REVES, a concerted action
1004: from the European Union.
1005: It is copyrighted identically to a GNU software product, ie programme and
1006: software can be distributed freely for non commercial use. Latest version
1007: can be accessed at http://euroreves.ined.fr/imach .
1008:
1009: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
1010: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
1011:
1012: **********************************************************************/
1013: /*
1014: main
1015: read parameterfile
1016: read datafile
1017: concatwav
1018: freqsummary
1019: if (mle >= 1)
1020: mlikeli
1021: print results files
1022: if mle==1
1023: computes hessian
1024: read end of parameter file: agemin, agemax, bage, fage, estepm
1025: begin-prev-date,...
1026: open gnuplot file
1027: open html file
1.145 brouard 1028: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1029: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1030: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1031: freexexit2 possible for memory heap.
1032:
1033: h Pij x | pij_nom ficrestpij
1034: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1035: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1036: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1037:
1038: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1039: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1040: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1041: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1042: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1043:
1.126 brouard 1044: forecasting if prevfcast==1 prevforecast call prevalence()
1045: health expectancies
1046: Variance-covariance of DFLE
1047: prevalence()
1048: movingaverage()
1049: varevsij()
1050: if popbased==1 varevsij(,popbased)
1051: total life expectancies
1052: Variance of period (stable) prevalence
1053: end
1054: */
1055:
1.187 brouard 1056: /* #define DEBUG */
1057: /* #define DEBUGBRENT */
1.203 brouard 1058: /* #define DEBUGLINMIN */
1059: /* #define DEBUGHESS */
1060: #define DEBUGHESSIJ
1.224 brouard 1061: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1062: #define POWELL /* Instead of NLOPT */
1.224 brouard 1063: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1064: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1065: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1066:
1067: #include <math.h>
1068: #include <stdio.h>
1069: #include <stdlib.h>
1070: #include <string.h>
1.226 brouard 1071: #include <ctype.h>
1.159 brouard 1072:
1073: #ifdef _WIN32
1074: #include <io.h>
1.172 brouard 1075: #include <windows.h>
1076: #include <tchar.h>
1.159 brouard 1077: #else
1.126 brouard 1078: #include <unistd.h>
1.159 brouard 1079: #endif
1.126 brouard 1080:
1081: #include <limits.h>
1082: #include <sys/types.h>
1.171 brouard 1083:
1084: #if defined(__GNUC__)
1085: #include <sys/utsname.h> /* Doesn't work on Windows */
1086: #endif
1087:
1.126 brouard 1088: #include <sys/stat.h>
1089: #include <errno.h>
1.159 brouard 1090: /* extern int errno; */
1.126 brouard 1091:
1.157 brouard 1092: /* #ifdef LINUX */
1093: /* #include <time.h> */
1094: /* #include "timeval.h" */
1095: /* #else */
1096: /* #include <sys/time.h> */
1097: /* #endif */
1098:
1.126 brouard 1099: #include <time.h>
1100:
1.136 brouard 1101: #ifdef GSL
1102: #include <gsl/gsl_errno.h>
1103: #include <gsl/gsl_multimin.h>
1104: #endif
1105:
1.167 brouard 1106:
1.162 brouard 1107: #ifdef NLOPT
1108: #include <nlopt.h>
1109: typedef struct {
1110: double (* function)(double [] );
1111: } myfunc_data ;
1112: #endif
1113:
1.126 brouard 1114: /* #include <libintl.h> */
1115: /* #define _(String) gettext (String) */
1116:
1.251 brouard 1117: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1118:
1119: #define GNUPLOTPROGRAM "gnuplot"
1120: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1121: #define FILENAMELENGTH 132
1122:
1123: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1124: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1125:
1.144 brouard 1126: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1127: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1128:
1129: #define NINTERVMAX 8
1.144 brouard 1130: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1131: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1132: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1133: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1134: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1135: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1136: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1137: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1138: /* #define AGESUP 130 */
1.288 brouard 1139: /* #define AGESUP 150 */
1140: #define AGESUP 200
1.268 brouard 1141: #define AGEINF 0
1.218 brouard 1142: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1143: #define AGEBASE 40
1.194 brouard 1144: #define AGEOVERFLOW 1.e20
1.164 brouard 1145: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1146: #ifdef _WIN32
1147: #define DIRSEPARATOR '\\'
1148: #define CHARSEPARATOR "\\"
1149: #define ODIRSEPARATOR '/'
1150: #else
1.126 brouard 1151: #define DIRSEPARATOR '/'
1152: #define CHARSEPARATOR "/"
1153: #define ODIRSEPARATOR '\\'
1154: #endif
1155:
1.310 ! brouard 1156: /* $Id: imach.c,v 1.309 2021/05/20 12:39:14 brouard Exp $ */
1.126 brouard 1157: /* $State: Exp $ */
1.196 brouard 1158: #include "version.h"
1159: char version[]=__IMACH_VERSION__;
1.308 brouard 1160: char copyright[]="March 2021,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, INED 2000-2021";
1.310 ! brouard 1161: char fullversion[]="$Revision: 1.309 $ $Date: 2021/05/20 12:39:14 $";
1.126 brouard 1162: char strstart[80];
1163: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1164: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1165: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1166: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1167: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1168: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1169: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1170: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1171: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1172: int cptcovprodnoage=0; /**< Number of covariate products without age */
1173: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1174: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1175: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1176: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1177: int nsd=0; /**< Total number of single dummy variables (output) */
1178: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1179: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1180: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1181: int ntveff=0; /**< ntveff number of effective time varying variables */
1182: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1183: int cptcov=0; /* Working variable */
1.290 brouard 1184: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1185: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1186: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1187: int nlstate=2; /* Number of live states */
1188: int ndeath=1; /* Number of dead states */
1.130 brouard 1189: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1190: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1191: int popbased=0;
1192:
1193: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1194: int maxwav=0; /* Maxim number of waves */
1195: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1196: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1197: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1198: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1199: int mle=1, weightopt=0;
1.126 brouard 1200: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1201: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1202: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1203: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1204: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1205: int selected(int kvar); /* Is covariate kvar selected for printing results */
1206:
1.130 brouard 1207: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1208: double **matprod2(); /* test */
1.126 brouard 1209: double **oldm, **newm, **savm; /* Working pointers to matrices */
1210: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1211: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1212:
1.136 brouard 1213: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1214: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1215: FILE *ficlog, *ficrespow;
1.130 brouard 1216: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1217: double fretone; /* Only one call to likelihood */
1.130 brouard 1218: long ipmx=0; /* Number of contributions */
1.126 brouard 1219: double sw; /* Sum of weights */
1220: char filerespow[FILENAMELENGTH];
1221: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1222: FILE *ficresilk;
1223: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1224: FILE *ficresprobmorprev;
1225: FILE *fichtm, *fichtmcov; /* Html File */
1226: FILE *ficreseij;
1227: char filerese[FILENAMELENGTH];
1228: FILE *ficresstdeij;
1229: char fileresstde[FILENAMELENGTH];
1230: FILE *ficrescveij;
1231: char filerescve[FILENAMELENGTH];
1232: FILE *ficresvij;
1233: char fileresv[FILENAMELENGTH];
1.269 brouard 1234:
1.126 brouard 1235: char title[MAXLINE];
1.234 brouard 1236: char model[MAXLINE]; /**< The model line */
1.217 brouard 1237: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1238: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1239: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1240: char command[FILENAMELENGTH];
1241: int outcmd=0;
1242:
1.217 brouard 1243: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1244: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1245: char filelog[FILENAMELENGTH]; /* Log file */
1246: char filerest[FILENAMELENGTH];
1247: char fileregp[FILENAMELENGTH];
1248: char popfile[FILENAMELENGTH];
1249:
1250: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1251:
1.157 brouard 1252: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1253: /* struct timezone tzp; */
1254: /* extern int gettimeofday(); */
1255: struct tm tml, *gmtime(), *localtime();
1256:
1257: extern time_t time();
1258:
1259: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1260: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1261: struct tm tm;
1262:
1.126 brouard 1263: char strcurr[80], strfor[80];
1264:
1265: char *endptr;
1266: long lval;
1267: double dval;
1268:
1269: #define NR_END 1
1270: #define FREE_ARG char*
1271: #define FTOL 1.0e-10
1272:
1273: #define NRANSI
1.240 brouard 1274: #define ITMAX 200
1275: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1276:
1277: #define TOL 2.0e-4
1278:
1279: #define CGOLD 0.3819660
1280: #define ZEPS 1.0e-10
1281: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1282:
1283: #define GOLD 1.618034
1284: #define GLIMIT 100.0
1285: #define TINY 1.0e-20
1286:
1287: static double maxarg1,maxarg2;
1288: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1289: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1290:
1291: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1292: #define rint(a) floor(a+0.5)
1.166 brouard 1293: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1294: #define mytinydouble 1.0e-16
1.166 brouard 1295: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1296: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1297: /* static double dsqrarg; */
1298: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1299: static double sqrarg;
1300: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1301: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1302: int agegomp= AGEGOMP;
1303:
1304: int imx;
1305: int stepm=1;
1306: /* Stepm, step in month: minimum step interpolation*/
1307:
1308: int estepm;
1309: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1310:
1311: int m,nb;
1312: long *num;
1.197 brouard 1313: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1314: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1315: covariate for which somebody answered excluding
1316: undefined. Usually 2: 0 and 1. */
1317: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1318: covariate for which somebody answered including
1319: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1320: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1321: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1322: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1323: double *ageexmed,*agecens;
1324: double dateintmean=0;
1.296 brouard 1325: double anprojd, mprojd, jprojd; /* For eventual projections */
1326: double anprojf, mprojf, jprojf;
1.126 brouard 1327:
1.296 brouard 1328: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1329: double anbackf, mbackf, jbackf;
1330: double jintmean,mintmean,aintmean;
1.126 brouard 1331: double *weight;
1332: int **s; /* Status */
1.141 brouard 1333: double *agedc;
1.145 brouard 1334: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1335: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1336: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1337: double **coqvar; /* Fixed quantitative covariate nqv */
1338: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1339: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1340: double idx;
1341: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1342: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1343: /*k 1 2 3 4 5 6 7 8 9 */
1344: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1345: /* Tndvar[k] 1 2 3 4 5 */
1346: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1347: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1348: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1349: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1350: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1351: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1352: /* Tprod[i]=k 4 7 */
1353: /* Tage[i]=k 5 8 */
1354: /* */
1355: /* Type */
1356: /* V 1 2 3 4 5 */
1357: /* F F V V V */
1358: /* D Q D D Q */
1359: /* */
1360: int *TvarsD;
1361: int *TvarsDind;
1362: int *TvarsQ;
1363: int *TvarsQind;
1364:
1.235 brouard 1365: #define MAXRESULTLINES 10
1366: int nresult=0;
1.258 brouard 1367: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1368: int TKresult[MAXRESULTLINES];
1.237 brouard 1369: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1370: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1371: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1372: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1373: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1374: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1375:
1.234 brouard 1376: /* 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 1377: 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 */
1378: 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 */
1379: 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 */
1380: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1381: 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 */
1382: 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 1383: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1384: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1385: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1386: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1387: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1388: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1389: 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 */
1390: 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 */
1391:
1.230 brouard 1392: int *Tvarsel; /**< Selected covariates for output */
1393: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1394: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1395: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1396: 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 1397: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1398: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1399: int *Tage;
1.227 brouard 1400: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1401: 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 1402: 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*/
1403: 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 1404: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1405: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1406: int **Tvard;
1407: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1408: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1409: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1410: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1411: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1412: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1413: double *lsurv, *lpop, *tpop;
1414:
1.231 brouard 1415: #define FD 1; /* Fixed dummy covariate */
1416: #define FQ 2; /* Fixed quantitative covariate */
1417: #define FP 3; /* Fixed product covariate */
1418: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1419: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1420: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1421: #define VD 10; /* Varying dummy covariate */
1422: #define VQ 11; /* Varying quantitative covariate */
1423: #define VP 12; /* Varying product covariate */
1424: #define VPDD 13; /* Varying product dummy*dummy covariate */
1425: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1426: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1427: #define APFD 16; /* Age product * fixed dummy covariate */
1428: #define APFQ 17; /* Age product * fixed quantitative covariate */
1429: #define APVD 18; /* Age product * varying dummy covariate */
1430: #define APVQ 19; /* Age product * varying quantitative covariate */
1431:
1432: #define FTYPE 1; /* Fixed covariate */
1433: #define VTYPE 2; /* Varying covariate (loop in wave) */
1434: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1435:
1436: struct kmodel{
1437: int maintype; /* main type */
1438: int subtype; /* subtype */
1439: };
1440: struct kmodel modell[NCOVMAX];
1441:
1.143 brouard 1442: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1443: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1444:
1445: /**************** split *************************/
1446: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1447: {
1448: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1449: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1450: */
1451: char *ss; /* pointer */
1.186 brouard 1452: int l1=0, l2=0; /* length counters */
1.126 brouard 1453:
1454: l1 = strlen(path ); /* length of path */
1455: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1456: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1457: if ( ss == NULL ) { /* no directory, so determine current directory */
1458: strcpy( name, path ); /* we got the fullname name because no directory */
1459: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1460: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1461: /* get current working directory */
1462: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1463: #ifdef WIN32
1464: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1465: #else
1466: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1467: #endif
1.126 brouard 1468: return( GLOCK_ERROR_GETCWD );
1469: }
1470: /* got dirc from getcwd*/
1471: printf(" DIRC = %s \n",dirc);
1.205 brouard 1472: } else { /* strip directory from path */
1.126 brouard 1473: ss++; /* after this, the filename */
1474: l2 = strlen( ss ); /* length of filename */
1475: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1476: strcpy( name, ss ); /* save file name */
1477: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1478: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1479: printf(" DIRC2 = %s \n",dirc);
1480: }
1481: /* We add a separator at the end of dirc if not exists */
1482: l1 = strlen( dirc ); /* length of directory */
1483: if( dirc[l1-1] != DIRSEPARATOR ){
1484: dirc[l1] = DIRSEPARATOR;
1485: dirc[l1+1] = 0;
1486: printf(" DIRC3 = %s \n",dirc);
1487: }
1488: ss = strrchr( name, '.' ); /* find last / */
1489: if (ss >0){
1490: ss++;
1491: strcpy(ext,ss); /* save extension */
1492: l1= strlen( name);
1493: l2= strlen(ss)+1;
1494: strncpy( finame, name, l1-l2);
1495: finame[l1-l2]= 0;
1496: }
1497:
1498: return( 0 ); /* we're done */
1499: }
1500:
1501:
1502: /******************************************/
1503:
1504: void replace_back_to_slash(char *s, char*t)
1505: {
1506: int i;
1507: int lg=0;
1508: i=0;
1509: lg=strlen(t);
1510: for(i=0; i<= lg; i++) {
1511: (s[i] = t[i]);
1512: if (t[i]== '\\') s[i]='/';
1513: }
1514: }
1515:
1.132 brouard 1516: char *trimbb(char *out, char *in)
1.137 brouard 1517: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1518: char *s;
1519: s=out;
1520: while (*in != '\0'){
1.137 brouard 1521: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1522: in++;
1523: }
1524: *out++ = *in++;
1525: }
1526: *out='\0';
1527: return s;
1528: }
1529:
1.187 brouard 1530: /* char *substrchaine(char *out, char *in, char *chain) */
1531: /* { */
1532: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1533: /* char *s, *t; */
1534: /* t=in;s=out; */
1535: /* while ((*in != *chain) && (*in != '\0')){ */
1536: /* *out++ = *in++; */
1537: /* } */
1538:
1539: /* /\* *in matches *chain *\/ */
1540: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1541: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1542: /* } */
1543: /* in--; chain--; */
1544: /* while ( (*in != '\0')){ */
1545: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1546: /* *out++ = *in++; */
1547: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1548: /* } */
1549: /* *out='\0'; */
1550: /* out=s; */
1551: /* return out; */
1552: /* } */
1553: char *substrchaine(char *out, char *in, char *chain)
1554: {
1555: /* Substract chain 'chain' from 'in', return and output 'out' */
1556: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1557:
1558: char *strloc;
1559:
1560: strcpy (out, in);
1561: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1562: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1563: if(strloc != NULL){
1564: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1565: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1566: /* strcpy (strloc, strloc +strlen(chain));*/
1567: }
1568: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1569: return out;
1570: }
1571:
1572:
1.145 brouard 1573: char *cutl(char *blocc, char *alocc, char *in, char occ)
1574: {
1.187 brouard 1575: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1576: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.310 ! brouard 1577: gives alocc="abcdef" and blocc="ghi2j".
1.145 brouard 1578: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1579: */
1.160 brouard 1580: char *s, *t;
1.145 brouard 1581: t=in;s=in;
1582: while ((*in != occ) && (*in != '\0')){
1583: *alocc++ = *in++;
1584: }
1585: if( *in == occ){
1586: *(alocc)='\0';
1587: s=++in;
1588: }
1589:
1590: if (s == t) {/* occ not found */
1591: *(alocc-(in-s))='\0';
1592: in=s;
1593: }
1594: while ( *in != '\0'){
1595: *blocc++ = *in++;
1596: }
1597:
1598: *blocc='\0';
1599: return t;
1600: }
1.137 brouard 1601: char *cutv(char *blocc, char *alocc, char *in, char occ)
1602: {
1.187 brouard 1603: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1604: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1605: gives blocc="abcdef2ghi" and alocc="j".
1606: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1607: */
1608: char *s, *t;
1609: t=in;s=in;
1610: while (*in != '\0'){
1611: while( *in == occ){
1612: *blocc++ = *in++;
1613: s=in;
1614: }
1615: *blocc++ = *in++;
1616: }
1617: if (s == t) /* occ not found */
1618: *(blocc-(in-s))='\0';
1619: else
1620: *(blocc-(in-s)-1)='\0';
1621: in=s;
1622: while ( *in != '\0'){
1623: *alocc++ = *in++;
1624: }
1625:
1626: *alocc='\0';
1627: return s;
1628: }
1629:
1.126 brouard 1630: int nbocc(char *s, char occ)
1631: {
1632: int i,j=0;
1633: int lg=20;
1634: i=0;
1635: lg=strlen(s);
1636: for(i=0; i<= lg; i++) {
1.234 brouard 1637: if (s[i] == occ ) j++;
1.126 brouard 1638: }
1639: return j;
1640: }
1641:
1.137 brouard 1642: /* void cutv(char *u,char *v, char*t, char occ) */
1643: /* { */
1644: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1645: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1646: /* gives u="abcdef2ghi" and v="j" *\/ */
1647: /* int i,lg,j,p=0; */
1648: /* i=0; */
1649: /* lg=strlen(t); */
1650: /* for(j=0; j<=lg-1; j++) { */
1651: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1652: /* } */
1.126 brouard 1653:
1.137 brouard 1654: /* for(j=0; j<p; j++) { */
1655: /* (u[j] = t[j]); */
1656: /* } */
1657: /* u[p]='\0'; */
1.126 brouard 1658:
1.137 brouard 1659: /* for(j=0; j<= lg; j++) { */
1660: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1661: /* } */
1662: /* } */
1.126 brouard 1663:
1.160 brouard 1664: #ifdef _WIN32
1665: char * strsep(char **pp, const char *delim)
1666: {
1667: char *p, *q;
1668:
1669: if ((p = *pp) == NULL)
1670: return 0;
1671: if ((q = strpbrk (p, delim)) != NULL)
1672: {
1673: *pp = q + 1;
1674: *q = '\0';
1675: }
1676: else
1677: *pp = 0;
1678: return p;
1679: }
1680: #endif
1681:
1.126 brouard 1682: /********************** nrerror ********************/
1683:
1684: void nrerror(char error_text[])
1685: {
1686: fprintf(stderr,"ERREUR ...\n");
1687: fprintf(stderr,"%s\n",error_text);
1688: exit(EXIT_FAILURE);
1689: }
1690: /*********************** vector *******************/
1691: double *vector(int nl, int nh)
1692: {
1693: double *v;
1694: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1695: if (!v) nrerror("allocation failure in vector");
1696: return v-nl+NR_END;
1697: }
1698:
1699: /************************ free vector ******************/
1700: void free_vector(double*v, int nl, int nh)
1701: {
1702: free((FREE_ARG)(v+nl-NR_END));
1703: }
1704:
1705: /************************ivector *******************************/
1706: int *ivector(long nl,long nh)
1707: {
1708: int *v;
1709: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1710: if (!v) nrerror("allocation failure in ivector");
1711: return v-nl+NR_END;
1712: }
1713:
1714: /******************free ivector **************************/
1715: void free_ivector(int *v, long nl, long nh)
1716: {
1717: free((FREE_ARG)(v+nl-NR_END));
1718: }
1719:
1720: /************************lvector *******************************/
1721: long *lvector(long nl,long nh)
1722: {
1723: long *v;
1724: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1725: if (!v) nrerror("allocation failure in ivector");
1726: return v-nl+NR_END;
1727: }
1728:
1729: /******************free lvector **************************/
1730: void free_lvector(long *v, long nl, long nh)
1731: {
1732: free((FREE_ARG)(v+nl-NR_END));
1733: }
1734:
1735: /******************* imatrix *******************************/
1736: int **imatrix(long nrl, long nrh, long ncl, long nch)
1737: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1738: {
1739: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1740: int **m;
1741:
1742: /* allocate pointers to rows */
1743: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1744: if (!m) nrerror("allocation failure 1 in matrix()");
1745: m += NR_END;
1746: m -= nrl;
1747:
1748:
1749: /* allocate rows and set pointers to them */
1750: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1751: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1752: m[nrl] += NR_END;
1753: m[nrl] -= ncl;
1754:
1755: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1756:
1757: /* return pointer to array of pointers to rows */
1758: return m;
1759: }
1760:
1761: /****************** free_imatrix *************************/
1762: void free_imatrix(m,nrl,nrh,ncl,nch)
1763: int **m;
1764: long nch,ncl,nrh,nrl;
1765: /* free an int matrix allocated by imatrix() */
1766: {
1767: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1768: free((FREE_ARG) (m+nrl-NR_END));
1769: }
1770:
1771: /******************* matrix *******************************/
1772: double **matrix(long nrl, long nrh, long ncl, long nch)
1773: {
1774: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1775: double **m;
1776:
1777: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1778: if (!m) nrerror("allocation failure 1 in matrix()");
1779: m += NR_END;
1780: m -= nrl;
1781:
1782: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1783: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1784: m[nrl] += NR_END;
1785: m[nrl] -= ncl;
1786:
1787: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1788: return m;
1.145 brouard 1789: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1790: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1791: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1792: */
1793: }
1794:
1795: /*************************free matrix ************************/
1796: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1797: {
1798: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1799: free((FREE_ARG)(m+nrl-NR_END));
1800: }
1801:
1802: /******************* ma3x *******************************/
1803: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1804: {
1805: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1806: double ***m;
1807:
1808: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1809: if (!m) nrerror("allocation failure 1 in matrix()");
1810: m += NR_END;
1811: m -= nrl;
1812:
1813: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1814: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1815: m[nrl] += NR_END;
1816: m[nrl] -= ncl;
1817:
1818: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1819:
1820: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1821: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1822: m[nrl][ncl] += NR_END;
1823: m[nrl][ncl] -= nll;
1824: for (j=ncl+1; j<=nch; j++)
1825: m[nrl][j]=m[nrl][j-1]+nlay;
1826:
1827: for (i=nrl+1; i<=nrh; i++) {
1828: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1829: for (j=ncl+1; j<=nch; j++)
1830: m[i][j]=m[i][j-1]+nlay;
1831: }
1832: return m;
1833: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1834: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1835: */
1836: }
1837:
1838: /*************************free ma3x ************************/
1839: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1840: {
1841: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1842: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1843: free((FREE_ARG)(m+nrl-NR_END));
1844: }
1845:
1846: /*************** function subdirf ***********/
1847: char *subdirf(char fileres[])
1848: {
1849: /* Caution optionfilefiname is hidden */
1850: strcpy(tmpout,optionfilefiname);
1851: strcat(tmpout,"/"); /* Add to the right */
1852: strcat(tmpout,fileres);
1853: return tmpout;
1854: }
1855:
1856: /*************** function subdirf2 ***********/
1857: char *subdirf2(char fileres[], char *preop)
1858: {
1859:
1860: /* Caution optionfilefiname is hidden */
1861: strcpy(tmpout,optionfilefiname);
1862: strcat(tmpout,"/");
1863: strcat(tmpout,preop);
1864: strcat(tmpout,fileres);
1865: return tmpout;
1866: }
1867:
1868: /*************** function subdirf3 ***********/
1869: char *subdirf3(char fileres[], char *preop, char *preop2)
1870: {
1871:
1872: /* Caution optionfilefiname is hidden */
1873: strcpy(tmpout,optionfilefiname);
1874: strcat(tmpout,"/");
1875: strcat(tmpout,preop);
1876: strcat(tmpout,preop2);
1877: strcat(tmpout,fileres);
1878: return tmpout;
1879: }
1.213 brouard 1880:
1881: /*************** function subdirfext ***********/
1882: char *subdirfext(char fileres[], char *preop, char *postop)
1883: {
1884:
1885: strcpy(tmpout,preop);
1886: strcat(tmpout,fileres);
1887: strcat(tmpout,postop);
1888: return tmpout;
1889: }
1.126 brouard 1890:
1.213 brouard 1891: /*************** function subdirfext3 ***********/
1892: char *subdirfext3(char fileres[], char *preop, char *postop)
1893: {
1894:
1895: /* Caution optionfilefiname is hidden */
1896: strcpy(tmpout,optionfilefiname);
1897: strcat(tmpout,"/");
1898: strcat(tmpout,preop);
1899: strcat(tmpout,fileres);
1900: strcat(tmpout,postop);
1901: return tmpout;
1902: }
1903:
1.162 brouard 1904: char *asc_diff_time(long time_sec, char ascdiff[])
1905: {
1906: long sec_left, days, hours, minutes;
1907: days = (time_sec) / (60*60*24);
1908: sec_left = (time_sec) % (60*60*24);
1909: hours = (sec_left) / (60*60) ;
1910: sec_left = (sec_left) %(60*60);
1911: minutes = (sec_left) /60;
1912: sec_left = (sec_left) % (60);
1913: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1914: return ascdiff;
1915: }
1916:
1.126 brouard 1917: /***************** f1dim *************************/
1918: extern int ncom;
1919: extern double *pcom,*xicom;
1920: extern double (*nrfunc)(double []);
1921:
1922: double f1dim(double x)
1923: {
1924: int j;
1925: double f;
1926: double *xt;
1927:
1928: xt=vector(1,ncom);
1929: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1930: f=(*nrfunc)(xt);
1931: free_vector(xt,1,ncom);
1932: return f;
1933: }
1934:
1935: /*****************brent *************************/
1936: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1937: {
1938: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1939: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1940: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1941: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1942: * returned function value.
1943: */
1.126 brouard 1944: int iter;
1945: double a,b,d,etemp;
1.159 brouard 1946: double fu=0,fv,fw,fx;
1.164 brouard 1947: double ftemp=0.;
1.126 brouard 1948: double p,q,r,tol1,tol2,u,v,w,x,xm;
1949: double e=0.0;
1950:
1951: a=(ax < cx ? ax : cx);
1952: b=(ax > cx ? ax : cx);
1953: x=w=v=bx;
1954: fw=fv=fx=(*f)(x);
1955: for (iter=1;iter<=ITMAX;iter++) {
1956: xm=0.5*(a+b);
1957: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1958: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1959: printf(".");fflush(stdout);
1960: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1961: #ifdef DEBUGBRENT
1.126 brouard 1962: 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);
1963: 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);
1964: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1965: #endif
1966: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1967: *xmin=x;
1968: return fx;
1969: }
1970: ftemp=fu;
1971: if (fabs(e) > tol1) {
1972: r=(x-w)*(fx-fv);
1973: q=(x-v)*(fx-fw);
1974: p=(x-v)*q-(x-w)*r;
1975: q=2.0*(q-r);
1976: if (q > 0.0) p = -p;
1977: q=fabs(q);
1978: etemp=e;
1979: e=d;
1980: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1981: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1982: else {
1.224 brouard 1983: d=p/q;
1984: u=x+d;
1985: if (u-a < tol2 || b-u < tol2)
1986: d=SIGN(tol1,xm-x);
1.126 brouard 1987: }
1988: } else {
1989: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1990: }
1991: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1992: fu=(*f)(u);
1993: if (fu <= fx) {
1994: if (u >= x) a=x; else b=x;
1995: SHFT(v,w,x,u)
1.183 brouard 1996: SHFT(fv,fw,fx,fu)
1997: } else {
1998: if (u < x) a=u; else b=u;
1999: if (fu <= fw || w == x) {
1.224 brouard 2000: v=w;
2001: w=u;
2002: fv=fw;
2003: fw=fu;
1.183 brouard 2004: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 2005: v=u;
2006: fv=fu;
1.183 brouard 2007: }
2008: }
1.126 brouard 2009: }
2010: nrerror("Too many iterations in brent");
2011: *xmin=x;
2012: return fx;
2013: }
2014:
2015: /****************** mnbrak ***********************/
2016:
2017: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2018: double (*func)(double))
1.183 brouard 2019: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2020: the downhill direction (defined by the function as evaluated at the initial points) and returns
2021: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2022: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2023: */
1.126 brouard 2024: double ulim,u,r,q, dum;
2025: double fu;
1.187 brouard 2026:
2027: double scale=10.;
2028: int iterscale=0;
2029:
2030: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2031: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2032:
2033:
2034: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2035: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2036: /* *bx = *ax - (*ax - *bx)/scale; */
2037: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2038: /* } */
2039:
1.126 brouard 2040: if (*fb > *fa) {
2041: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2042: SHFT(dum,*fb,*fa,dum)
2043: }
1.126 brouard 2044: *cx=(*bx)+GOLD*(*bx-*ax);
2045: *fc=(*func)(*cx);
1.183 brouard 2046: #ifdef DEBUG
1.224 brouard 2047: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2048: 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 2049: #endif
1.224 brouard 2050: 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 2051: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2052: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2053: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2054: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2055: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2056: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2057: fu=(*func)(u);
1.163 brouard 2058: #ifdef DEBUG
2059: /* f(x)=A(x-u)**2+f(u) */
2060: double A, fparabu;
2061: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2062: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2063: 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);
2064: 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 2065: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2066: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2067: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2068: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2069: #endif
1.184 brouard 2070: #ifdef MNBRAKORIGINAL
1.183 brouard 2071: #else
1.191 brouard 2072: /* if (fu > *fc) { */
2073: /* #ifdef DEBUG */
2074: /* printf("mnbrak4 fu > fc \n"); */
2075: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2076: /* #endif */
2077: /* /\* 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 *\\/ *\/ */
2078: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2079: /* dum=u; /\* Shifting c and u *\/ */
2080: /* u = *cx; */
2081: /* *cx = dum; */
2082: /* dum = fu; */
2083: /* fu = *fc; */
2084: /* *fc =dum; */
2085: /* } else { /\* end *\/ */
2086: /* #ifdef DEBUG */
2087: /* printf("mnbrak3 fu < fc \n"); */
2088: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2089: /* #endif */
2090: /* dum=u; /\* Shifting c and u *\/ */
2091: /* u = *cx; */
2092: /* *cx = dum; */
2093: /* dum = fu; */
2094: /* fu = *fc; */
2095: /* *fc =dum; */
2096: /* } */
1.224 brouard 2097: #ifdef DEBUGMNBRAK
2098: double A, fparabu;
2099: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2100: fparabu= *fa - A*(*ax-u)*(*ax-u);
2101: 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);
2102: 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 2103: #endif
1.191 brouard 2104: dum=u; /* Shifting c and u */
2105: u = *cx;
2106: *cx = dum;
2107: dum = fu;
2108: fu = *fc;
2109: *fc =dum;
1.183 brouard 2110: #endif
1.162 brouard 2111: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2112: #ifdef DEBUG
1.224 brouard 2113: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2114: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2115: #endif
1.126 brouard 2116: fu=(*func)(u);
2117: if (fu < *fc) {
1.183 brouard 2118: #ifdef DEBUG
1.224 brouard 2119: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2120: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2121: #endif
2122: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2123: SHFT(*fb,*fc,fu,(*func)(u))
2124: #ifdef DEBUG
2125: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2126: #endif
2127: }
1.162 brouard 2128: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2129: #ifdef DEBUG
1.224 brouard 2130: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2131: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2132: #endif
1.126 brouard 2133: u=ulim;
2134: fu=(*func)(u);
1.183 brouard 2135: } else { /* u could be left to b (if r > q parabola has a maximum) */
2136: #ifdef DEBUG
1.224 brouard 2137: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2138: 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 2139: #endif
1.126 brouard 2140: u=(*cx)+GOLD*(*cx-*bx);
2141: fu=(*func)(u);
1.224 brouard 2142: #ifdef DEBUG
2143: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2144: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2145: #endif
1.183 brouard 2146: } /* end tests */
1.126 brouard 2147: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2148: SHFT(*fa,*fb,*fc,fu)
2149: #ifdef DEBUG
1.224 brouard 2150: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2151: 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 2152: #endif
2153: } /* 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 2154: }
2155:
2156: /*************** linmin ************************/
1.162 brouard 2157: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2158: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2159: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2160: the value of func at the returned location p . This is actually all accomplished by calling the
2161: routines mnbrak and brent .*/
1.126 brouard 2162: int ncom;
2163: double *pcom,*xicom;
2164: double (*nrfunc)(double []);
2165:
1.224 brouard 2166: #ifdef LINMINORIGINAL
1.126 brouard 2167: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2168: #else
2169: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2170: #endif
1.126 brouard 2171: {
2172: double brent(double ax, double bx, double cx,
2173: double (*f)(double), double tol, double *xmin);
2174: double f1dim(double x);
2175: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2176: double *fc, double (*func)(double));
2177: int j;
2178: double xx,xmin,bx,ax;
2179: double fx,fb,fa;
1.187 brouard 2180:
1.203 brouard 2181: #ifdef LINMINORIGINAL
2182: #else
2183: double scale=10., axs, xxs; /* Scale added for infinity */
2184: #endif
2185:
1.126 brouard 2186: ncom=n;
2187: pcom=vector(1,n);
2188: xicom=vector(1,n);
2189: nrfunc=func;
2190: for (j=1;j<=n;j++) {
2191: pcom[j]=p[j];
1.202 brouard 2192: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2193: }
1.187 brouard 2194:
1.203 brouard 2195: #ifdef LINMINORIGINAL
2196: xx=1.;
2197: #else
2198: axs=0.0;
2199: xxs=1.;
2200: do{
2201: xx= xxs;
2202: #endif
1.187 brouard 2203: ax=0.;
2204: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2205: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2206: /* 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)) */
2207: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2208: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2209: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2210: /* 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 2211: #ifdef LINMINORIGINAL
2212: #else
2213: if (fx != fx){
1.224 brouard 2214: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2215: printf("|");
2216: fprintf(ficlog,"|");
1.203 brouard 2217: #ifdef DEBUGLINMIN
1.224 brouard 2218: 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 2219: #endif
2220: }
1.224 brouard 2221: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2222: #endif
2223:
1.191 brouard 2224: #ifdef DEBUGLINMIN
2225: 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 2226: 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 2227: #endif
1.224 brouard 2228: #ifdef LINMINORIGINAL
2229: #else
2230: if(fb == fx){ /* Flat function in the direction */
2231: xmin=xx;
2232: *flat=1;
2233: }else{
2234: *flat=0;
2235: #endif
2236: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2237: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2238: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2239: /* fmin = f(p[j] + xmin * xi[j]) */
2240: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2241: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2242: #ifdef DEBUG
1.224 brouard 2243: 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);
2244: 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);
2245: #endif
2246: #ifdef LINMINORIGINAL
2247: #else
2248: }
1.126 brouard 2249: #endif
1.191 brouard 2250: #ifdef DEBUGLINMIN
2251: printf("linmin end ");
1.202 brouard 2252: fprintf(ficlog,"linmin end ");
1.191 brouard 2253: #endif
1.126 brouard 2254: for (j=1;j<=n;j++) {
1.203 brouard 2255: #ifdef LINMINORIGINAL
2256: xi[j] *= xmin;
2257: #else
2258: #ifdef DEBUGLINMIN
2259: if(xxs <1.0)
2260: printf(" before xi[%d]=%12.8f", j,xi[j]);
2261: #endif
2262: 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) */
2263: #ifdef DEBUGLINMIN
2264: if(xxs <1.0)
2265: 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 );
2266: #endif
2267: #endif
1.187 brouard 2268: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2269: }
1.191 brouard 2270: #ifdef DEBUGLINMIN
1.203 brouard 2271: printf("\n");
1.191 brouard 2272: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2273: 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 2274: for (j=1;j<=n;j++) {
1.202 brouard 2275: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2276: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2277: if(j % ncovmodel == 0){
1.191 brouard 2278: printf("\n");
1.202 brouard 2279: fprintf(ficlog,"\n");
2280: }
1.191 brouard 2281: }
1.203 brouard 2282: #else
1.191 brouard 2283: #endif
1.126 brouard 2284: free_vector(xicom,1,n);
2285: free_vector(pcom,1,n);
2286: }
2287:
2288:
2289: /*************** powell ************************/
1.162 brouard 2290: /*
2291: Minimization of a function func of n variables. Input consists of an initial starting point
2292: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2293: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2294: such that failure to decrease by more than this amount on one iteration signals doneness. On
2295: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2296: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2297: */
1.224 brouard 2298: #ifdef LINMINORIGINAL
2299: #else
2300: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2301: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2302: #endif
1.126 brouard 2303: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2304: double (*func)(double []))
2305: {
1.224 brouard 2306: #ifdef LINMINORIGINAL
2307: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2308: double (*func)(double []));
1.224 brouard 2309: #else
1.241 brouard 2310: void linmin(double p[], double xi[], int n, double *fret,
2311: double (*func)(double []),int *flat);
1.224 brouard 2312: #endif
1.239 brouard 2313: int i,ibig,j,jk,k;
1.126 brouard 2314: double del,t,*pt,*ptt,*xit;
1.181 brouard 2315: double directest;
1.126 brouard 2316: double fp,fptt;
2317: double *xits;
2318: int niterf, itmp;
1.224 brouard 2319: #ifdef LINMINORIGINAL
2320: #else
2321:
2322: flatdir=ivector(1,n);
2323: for (j=1;j<=n;j++) flatdir[j]=0;
2324: #endif
1.126 brouard 2325:
2326: pt=vector(1,n);
2327: ptt=vector(1,n);
2328: xit=vector(1,n);
2329: xits=vector(1,n);
2330: *fret=(*func)(p);
2331: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2332: rcurr_time = time(NULL);
1.126 brouard 2333: for (*iter=1;;++(*iter)) {
1.187 brouard 2334: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2335: ibig=0;
2336: del=0.0;
1.157 brouard 2337: rlast_time=rcurr_time;
2338: /* (void) gettimeofday(&curr_time,&tzp); */
2339: rcurr_time = time(NULL);
2340: curr_time = *localtime(&rcurr_time);
2341: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2342: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2343: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2344: for (i=1;i<=n;i++) {
1.126 brouard 2345: fprintf(ficrespow," %.12lf", p[i]);
2346: }
1.239 brouard 2347: fprintf(ficrespow,"\n");fflush(ficrespow);
2348: printf("\n#model= 1 + age ");
2349: fprintf(ficlog,"\n#model= 1 + age ");
2350: if(nagesqr==1){
1.241 brouard 2351: printf(" + age*age ");
2352: fprintf(ficlog," + age*age ");
1.239 brouard 2353: }
2354: for(j=1;j <=ncovmodel-2;j++){
2355: if(Typevar[j]==0) {
2356: printf(" + V%d ",Tvar[j]);
2357: fprintf(ficlog," + V%d ",Tvar[j]);
2358: }else if(Typevar[j]==1) {
2359: printf(" + V%d*age ",Tvar[j]);
2360: fprintf(ficlog," + V%d*age ",Tvar[j]);
2361: }else if(Typevar[j]==2) {
2362: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2363: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2364: }
2365: }
1.126 brouard 2366: printf("\n");
1.239 brouard 2367: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2368: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2369: fprintf(ficlog,"\n");
1.239 brouard 2370: for(i=1,jk=1; i <=nlstate; i++){
2371: for(k=1; k <=(nlstate+ndeath); k++){
2372: if (k != i) {
2373: printf("%d%d ",i,k);
2374: fprintf(ficlog,"%d%d ",i,k);
2375: for(j=1; j <=ncovmodel; j++){
2376: printf("%12.7f ",p[jk]);
2377: fprintf(ficlog,"%12.7f ",p[jk]);
2378: jk++;
2379: }
2380: printf("\n");
2381: fprintf(ficlog,"\n");
2382: }
2383: }
2384: }
1.241 brouard 2385: if(*iter <=3 && *iter >1){
1.157 brouard 2386: tml = *localtime(&rcurr_time);
2387: strcpy(strcurr,asctime(&tml));
2388: rforecast_time=rcurr_time;
1.126 brouard 2389: itmp = strlen(strcurr);
2390: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2391: strcurr[itmp-1]='\0';
1.162 brouard 2392: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2393: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2394: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2395: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2396: forecast_time = *localtime(&rforecast_time);
2397: strcpy(strfor,asctime(&forecast_time));
2398: itmp = strlen(strfor);
2399: if(strfor[itmp-1]=='\n')
2400: strfor[itmp-1]='\0';
2401: 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);
2402: 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 2403: }
2404: }
1.187 brouard 2405: for (i=1;i<=n;i++) { /* For each direction i */
2406: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2407: fptt=(*fret);
2408: #ifdef DEBUG
1.203 brouard 2409: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2410: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2411: #endif
1.203 brouard 2412: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2413: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2414: #ifdef LINMINORIGINAL
1.188 brouard 2415: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2416: #else
2417: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2418: flatdir[i]=flat; /* Function is vanishing in that direction i */
2419: #endif
2420: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2421: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2422: /* because that direction will be replaced unless the gain del is small */
2423: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2424: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2425: /* with the new direction. */
2426: del=fabs(fptt-(*fret));
2427: ibig=i;
1.126 brouard 2428: }
2429: #ifdef DEBUG
2430: printf("%d %.12e",i,(*fret));
2431: fprintf(ficlog,"%d %.12e",i,(*fret));
2432: for (j=1;j<=n;j++) {
1.224 brouard 2433: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2434: printf(" x(%d)=%.12e",j,xit[j]);
2435: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2436: }
2437: for(j=1;j<=n;j++) {
1.225 brouard 2438: printf(" p(%d)=%.12e",j,p[j]);
2439: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2440: }
2441: printf("\n");
2442: fprintf(ficlog,"\n");
2443: #endif
1.187 brouard 2444: } /* end loop on each direction i */
2445: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2446: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2447: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2448: for(j=1;j<=n;j++) {
1.302 brouard 2449: if(flatdir[j] >0){
2450: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2451: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2452: }
2453: /* printf("\n"); */
2454: /* fprintf(ficlog,"\n"); */
2455: }
1.243 brouard 2456: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2457: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2458: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2459: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2460: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2461: /* decreased of more than 3.84 */
2462: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2463: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2464: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2465:
1.188 brouard 2466: /* Starting the program with initial values given by a former maximization will simply change */
2467: /* the scales of the directions and the directions, because the are reset to canonical directions */
2468: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2469: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2470: #ifdef DEBUG
2471: int k[2],l;
2472: k[0]=1;
2473: k[1]=-1;
2474: printf("Max: %.12e",(*func)(p));
2475: fprintf(ficlog,"Max: %.12e",(*func)(p));
2476: for (j=1;j<=n;j++) {
2477: printf(" %.12e",p[j]);
2478: fprintf(ficlog," %.12e",p[j]);
2479: }
2480: printf("\n");
2481: fprintf(ficlog,"\n");
2482: for(l=0;l<=1;l++) {
2483: for (j=1;j<=n;j++) {
2484: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2485: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2486: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2487: }
2488: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2489: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2490: }
2491: #endif
2492:
1.224 brouard 2493: #ifdef LINMINORIGINAL
2494: #else
2495: free_ivector(flatdir,1,n);
2496: #endif
1.126 brouard 2497: free_vector(xit,1,n);
2498: free_vector(xits,1,n);
2499: free_vector(ptt,1,n);
2500: free_vector(pt,1,n);
2501: return;
1.192 brouard 2502: } /* enough precision */
1.240 brouard 2503: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2504: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2505: ptt[j]=2.0*p[j]-pt[j];
2506: xit[j]=p[j]-pt[j];
2507: pt[j]=p[j];
2508: }
1.181 brouard 2509: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2510: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2511: if (*iter <=4) {
1.225 brouard 2512: #else
2513: #endif
1.224 brouard 2514: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2515: #else
1.161 brouard 2516: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2517: #endif
1.162 brouard 2518: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2519: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2520: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2521: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2522: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2523: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2524: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2525: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2526: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2527: /* Even if f3 <f1, directest can be negative and t >0 */
2528: /* mu² and del² are equal when f3=f1 */
2529: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2530: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2531: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2532: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2533: #ifdef NRCORIGINAL
2534: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2535: #else
2536: 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 2537: t= t- del*SQR(fp-fptt);
1.183 brouard 2538: #endif
1.202 brouard 2539: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2540: #ifdef DEBUG
1.181 brouard 2541: 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);
2542: 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 2543: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2544: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2545: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2546: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2547: 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);
2548: 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);
2549: #endif
1.183 brouard 2550: #ifdef POWELLORIGINAL
2551: if (t < 0.0) { /* Then we use it for new direction */
2552: #else
1.182 brouard 2553: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2554: 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 2555: 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 2556: 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 2557: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2558: }
1.181 brouard 2559: if (directest < 0.0) { /* Then we use it for new direction */
2560: #endif
1.191 brouard 2561: #ifdef DEBUGLINMIN
1.234 brouard 2562: printf("Before linmin in direction P%d-P0\n",n);
2563: for (j=1;j<=n;j++) {
2564: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2565: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2566: if(j % ncovmodel == 0){
2567: printf("\n");
2568: fprintf(ficlog,"\n");
2569: }
2570: }
1.224 brouard 2571: #endif
2572: #ifdef LINMINORIGINAL
1.234 brouard 2573: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2574: #else
1.234 brouard 2575: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2576: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2577: #endif
1.234 brouard 2578:
1.191 brouard 2579: #ifdef DEBUGLINMIN
1.234 brouard 2580: for (j=1;j<=n;j++) {
2581: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2582: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2583: if(j % ncovmodel == 0){
2584: printf("\n");
2585: fprintf(ficlog,"\n");
2586: }
2587: }
1.224 brouard 2588: #endif
1.234 brouard 2589: for (j=1;j<=n;j++) {
2590: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2591: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2592: }
1.224 brouard 2593: #ifdef LINMINORIGINAL
2594: #else
1.234 brouard 2595: for (j=1, flatd=0;j<=n;j++) {
2596: if(flatdir[j]>0)
2597: flatd++;
2598: }
2599: if(flatd >0){
1.255 brouard 2600: printf("%d flat directions: ",flatd);
2601: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2602: for (j=1;j<=n;j++) {
2603: if(flatdir[j]>0){
2604: printf("%d ",j);
2605: fprintf(ficlog,"%d ",j);
2606: }
2607: }
2608: printf("\n");
2609: fprintf(ficlog,"\n");
2610: }
1.191 brouard 2611: #endif
1.234 brouard 2612: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2613: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2614:
1.126 brouard 2615: #ifdef DEBUG
1.234 brouard 2616: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2617: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2618: for(j=1;j<=n;j++){
2619: printf(" %lf",xit[j]);
2620: fprintf(ficlog," %lf",xit[j]);
2621: }
2622: printf("\n");
2623: fprintf(ficlog,"\n");
1.126 brouard 2624: #endif
1.192 brouard 2625: } /* end of t or directest negative */
1.224 brouard 2626: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2627: #else
1.234 brouard 2628: } /* end if (fptt < fp) */
1.192 brouard 2629: #endif
1.225 brouard 2630: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2631: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2632: #else
1.224 brouard 2633: #endif
1.234 brouard 2634: } /* loop iteration */
1.126 brouard 2635: }
1.234 brouard 2636:
1.126 brouard 2637: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2638:
1.235 brouard 2639: 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 2640: {
1.279 brouard 2641: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2642: * (and selected quantitative values in nres)
2643: * by left multiplying the unit
2644: * matrix by transitions matrix until convergence is reached with precision ftolpl
2645: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2646: * Wx is row vector: population in state 1, population in state 2, population dead
2647: * or prevalence in state 1, prevalence in state 2, 0
2648: * newm is the matrix after multiplications, its rows are identical at a factor.
2649: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2650: * Output is prlim.
2651: * Initial matrix pimij
2652: */
1.206 brouard 2653: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2654: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2655: /* 0, 0 , 1} */
2656: /*
2657: * and after some iteration: */
2658: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2659: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2660: /* 0, 0 , 1} */
2661: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2662: /* {0.51571254859325999, 0.4842874514067399, */
2663: /* 0.51326036147820708, 0.48673963852179264} */
2664: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2665:
1.126 brouard 2666: int i, ii,j,k;
1.209 brouard 2667: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2668: /* double **matprod2(); */ /* test */
1.218 brouard 2669: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2670: double **newm;
1.209 brouard 2671: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2672: int ncvloop=0;
1.288 brouard 2673: int first=0;
1.169 brouard 2674:
1.209 brouard 2675: min=vector(1,nlstate);
2676: max=vector(1,nlstate);
2677: meandiff=vector(1,nlstate);
2678:
1.218 brouard 2679: /* Starting with matrix unity */
1.126 brouard 2680: for (ii=1;ii<=nlstate+ndeath;ii++)
2681: for (j=1;j<=nlstate+ndeath;j++){
2682: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2683: }
1.169 brouard 2684:
2685: cov[1]=1.;
2686:
2687: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2688: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2689: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2690: ncvloop++;
1.126 brouard 2691: newm=savm;
2692: /* Covariates have to be included here again */
1.138 brouard 2693: cov[2]=agefin;
1.187 brouard 2694: if(nagesqr==1)
2695: cov[3]= agefin*agefin;;
1.234 brouard 2696: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2697: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2698: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2699: /* 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 2700: }
2701: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2702: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2703: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2704: /* 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 2705: }
1.237 brouard 2706: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2707: if(Dummy[Tvar[Tage[k]]]){
2708: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2709: } else{
1.235 brouard 2710: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2711: }
1.235 brouard 2712: /* 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 2713: }
1.237 brouard 2714: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2715: /* 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 2716: if(Dummy[Tvard[k][1]==0]){
2717: if(Dummy[Tvard[k][2]==0]){
2718: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2719: }else{
2720: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2721: }
2722: }else{
2723: if(Dummy[Tvard[k][2]==0]){
2724: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2725: }else{
2726: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2727: }
2728: }
1.234 brouard 2729: }
1.138 brouard 2730: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2731: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2732: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2733: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2734: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2735: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2736: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2737:
1.126 brouard 2738: savm=oldm;
2739: oldm=newm;
1.209 brouard 2740:
2741: for(j=1; j<=nlstate; j++){
2742: max[j]=0.;
2743: min[j]=1.;
2744: }
2745: for(i=1;i<=nlstate;i++){
2746: sumnew=0;
2747: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2748: for(j=1; j<=nlstate; j++){
2749: prlim[i][j]= newm[i][j]/(1-sumnew);
2750: max[j]=FMAX(max[j],prlim[i][j]);
2751: min[j]=FMIN(min[j],prlim[i][j]);
2752: }
2753: }
2754:
1.126 brouard 2755: maxmax=0.;
1.209 brouard 2756: for(j=1; j<=nlstate; j++){
2757: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2758: maxmax=FMAX(maxmax,meandiff[j]);
2759: /* 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 2760: } /* j loop */
1.203 brouard 2761: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2762: /* 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 2763: if(maxmax < ftolpl){
1.209 brouard 2764: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2765: free_vector(min,1,nlstate);
2766: free_vector(max,1,nlstate);
2767: free_vector(meandiff,1,nlstate);
1.126 brouard 2768: return prlim;
2769: }
1.288 brouard 2770: } /* agefin loop */
1.208 brouard 2771: /* After some age loop it doesn't converge */
1.288 brouard 2772: if(!first){
2773: first=1;
2774: 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);
2775: }
2776: 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);
2777:
1.209 brouard 2778: /* 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); */
2779: free_vector(min,1,nlstate);
2780: free_vector(max,1,nlstate);
2781: free_vector(meandiff,1,nlstate);
1.208 brouard 2782:
1.169 brouard 2783: return prlim; /* should not reach here */
1.126 brouard 2784: }
2785:
1.217 brouard 2786:
2787: /**** Back Prevalence limit (stable or period prevalence) ****************/
2788:
1.218 brouard 2789: /* 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) */
2790: /* 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 2791: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2792: {
1.264 brouard 2793: /* 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 2794: matrix by transitions matrix until convergence is reached with precision ftolpl */
2795: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2796: /* Wx is row vector: population in state 1, population in state 2, population dead */
2797: /* or prevalence in state 1, prevalence in state 2, 0 */
2798: /* newm is the matrix after multiplications, its rows are identical at a factor */
2799: /* Initial matrix pimij */
2800: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2801: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2802: /* 0, 0 , 1} */
2803: /*
2804: * and after some iteration: */
2805: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2806: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2807: /* 0, 0 , 1} */
2808: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2809: /* {0.51571254859325999, 0.4842874514067399, */
2810: /* 0.51326036147820708, 0.48673963852179264} */
2811: /* If we start from prlim again, prlim tends to a constant matrix */
2812:
2813: int i, ii,j,k;
1.247 brouard 2814: int first=0;
1.217 brouard 2815: double *min, *max, *meandiff, maxmax,sumnew=0.;
2816: /* double **matprod2(); */ /* test */
2817: double **out, cov[NCOVMAX+1], **bmij();
2818: double **newm;
1.218 brouard 2819: double **dnewm, **doldm, **dsavm; /* for use */
2820: double **oldm, **savm; /* for use */
2821:
1.217 brouard 2822: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2823: int ncvloop=0;
2824:
2825: min=vector(1,nlstate);
2826: max=vector(1,nlstate);
2827: meandiff=vector(1,nlstate);
2828:
1.266 brouard 2829: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2830: oldm=oldms; savm=savms;
2831:
2832: /* Starting with matrix unity */
2833: for (ii=1;ii<=nlstate+ndeath;ii++)
2834: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2835: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2836: }
2837:
2838: cov[1]=1.;
2839:
2840: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2841: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2842: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2843: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2844: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2845: ncvloop++;
1.218 brouard 2846: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2847: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2848: /* Covariates have to be included here again */
2849: cov[2]=agefin;
2850: if(nagesqr==1)
2851: cov[3]= agefin*agefin;;
1.242 brouard 2852: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2853: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2854: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2855: /* 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 2856: }
2857: /* for (k=1; k<=cptcovn;k++) { */
2858: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2859: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2860: /* /\* 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])]); *\/ */
2861: /* } */
2862: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2863: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2864: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2865: /* 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]); */
2866: }
2867: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2868: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2869: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2870: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2871: for (k=1; k<=cptcovage;k++){ /* For product with age */
2872: if(Dummy[Tvar[Tage[k]]]){
2873: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2874: } else{
2875: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2876: }
2877: /* 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]); */
2878: }
2879: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2880: /* 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]); */
2881: if(Dummy[Tvard[k][1]==0]){
2882: if(Dummy[Tvard[k][2]==0]){
2883: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2884: }else{
2885: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2886: }
2887: }else{
2888: if(Dummy[Tvard[k][2]==0]){
2889: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2890: }else{
2891: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2892: }
2893: }
1.217 brouard 2894: }
2895:
2896: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2897: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2898: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2899: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2900: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2901: /* ij should be linked to the correct index of cov */
2902: /* age and covariate values ij are in 'cov', but we need to pass
2903: * ij for the observed prevalence at age and status and covariate
2904: * number: prevacurrent[(int)agefin][ii][ij]
2905: */
2906: /* 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 *\/ */
2907: /* 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 *\/ */
2908: 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 2909: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2910: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2911: /* for(i=1; i<=nlstate+ndeath; i++) { */
2912: /* printf("%d newm= ",i); */
2913: /* for(j=1;j<=nlstate+ndeath;j++) { */
2914: /* printf("%f ",newm[i][j]); */
2915: /* } */
2916: /* printf("oldm * "); */
2917: /* for(j=1;j<=nlstate+ndeath;j++) { */
2918: /* printf("%f ",oldm[i][j]); */
2919: /* } */
1.268 brouard 2920: /* printf(" bmmij "); */
1.266 brouard 2921: /* for(j=1;j<=nlstate+ndeath;j++) { */
2922: /* printf("%f ",pmmij[i][j]); */
2923: /* } */
2924: /* printf("\n"); */
2925: /* } */
2926: /* } */
1.217 brouard 2927: savm=oldm;
2928: oldm=newm;
1.266 brouard 2929:
1.217 brouard 2930: for(j=1; j<=nlstate; j++){
2931: max[j]=0.;
2932: min[j]=1.;
2933: }
2934: for(j=1; j<=nlstate; j++){
2935: for(i=1;i<=nlstate;i++){
1.234 brouard 2936: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2937: bprlim[i][j]= newm[i][j];
2938: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2939: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2940: }
2941: }
1.218 brouard 2942:
1.217 brouard 2943: maxmax=0.;
2944: for(i=1; i<=nlstate; i++){
2945: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2946: maxmax=FMAX(maxmax,meandiff[i]);
2947: /* 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 2948: } /* i loop */
1.217 brouard 2949: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2950: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2951: if(maxmax < ftolpl){
1.220 brouard 2952: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2953: free_vector(min,1,nlstate);
2954: free_vector(max,1,nlstate);
2955: free_vector(meandiff,1,nlstate);
2956: return bprlim;
2957: }
1.288 brouard 2958: } /* agefin loop */
1.217 brouard 2959: /* After some age loop it doesn't converge */
1.288 brouard 2960: if(!first){
1.247 brouard 2961: first=1;
2962: 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\
2963: 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);
2964: }
2965: 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 2966: 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);
2967: /* 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); */
2968: free_vector(min,1,nlstate);
2969: free_vector(max,1,nlstate);
2970: free_vector(meandiff,1,nlstate);
2971:
2972: return bprlim; /* should not reach here */
2973: }
2974:
1.126 brouard 2975: /*************** transition probabilities ***************/
2976:
2977: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2978: {
1.138 brouard 2979: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2980: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2981: model to the ncovmodel covariates (including constant and age).
2982: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2983: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2984: ncth covariate in the global vector x is given by the formula:
2985: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2986: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2987: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2988: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2989: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2990: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2991: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2992: */
2993: double s1, lnpijopii;
1.126 brouard 2994: /*double t34;*/
1.164 brouard 2995: int i,j, nc, ii, jj;
1.126 brouard 2996:
1.223 brouard 2997: for(i=1; i<= nlstate; i++){
2998: for(j=1; j<i;j++){
2999: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3000: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3001: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3002: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3003: }
3004: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3005: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3006: }
3007: for(j=i+1; j<=nlstate+ndeath;j++){
3008: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3009: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3010: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3011: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3012: }
3013: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3014: }
3015: }
1.218 brouard 3016:
1.223 brouard 3017: for(i=1; i<= nlstate; i++){
3018: s1=0;
3019: for(j=1; j<i; j++){
3020: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3021: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3022: }
3023: for(j=i+1; j<=nlstate+ndeath; j++){
3024: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3025: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3026: }
3027: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3028: ps[i][i]=1./(s1+1.);
3029: /* Computing other pijs */
3030: for(j=1; j<i; j++)
3031: ps[i][j]= exp(ps[i][j])*ps[i][i];
3032: for(j=i+1; j<=nlstate+ndeath; j++)
3033: ps[i][j]= exp(ps[i][j])*ps[i][i];
3034: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3035: } /* end i */
1.218 brouard 3036:
1.223 brouard 3037: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3038: for(jj=1; jj<= nlstate+ndeath; jj++){
3039: ps[ii][jj]=0;
3040: ps[ii][ii]=1;
3041: }
3042: }
1.294 brouard 3043:
3044:
1.223 brouard 3045: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3046: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3047: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3048: /* } */
3049: /* printf("\n "); */
3050: /* } */
3051: /* printf("\n ");printf("%lf ",cov[2]);*/
3052: /*
3053: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3054: goto end;*/
1.266 brouard 3055: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3056: }
3057:
1.218 brouard 3058: /*************** backward transition probabilities ***************/
3059:
3060: /* 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 ) */
3061: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3062: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3063: {
1.302 brouard 3064: /* 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 3065: * 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 3066: */
1.218 brouard 3067: int i, ii, j,k;
1.222 brouard 3068:
3069: double **out, **pmij();
3070: double sumnew=0.;
1.218 brouard 3071: double agefin;
1.292 brouard 3072: 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 3073: double **dnewm, **dsavm, **doldm;
3074: double **bbmij;
3075:
1.218 brouard 3076: doldm=ddoldms; /* global pointers */
1.222 brouard 3077: dnewm=ddnewms;
3078: dsavm=ddsavms;
3079:
3080: agefin=cov[2];
1.268 brouard 3081: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3082: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3083: the observed prevalence (with this covariate ij) at beginning of transition */
3084: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3085:
3086: /* P_x */
1.266 brouard 3087: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3088: /* outputs pmmij which is a stochastic matrix in row */
3089:
3090: /* Diag(w_x) */
1.292 brouard 3091: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3092: sumnew=0.;
1.269 brouard 3093: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3094: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3095: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3096: sumnew+=prevacurrent[(int)agefin][ii][ij];
3097: }
3098: if(sumnew >0.01){ /* At least some value in the prevalence */
3099: for (ii=1;ii<=nlstate+ndeath;ii++){
3100: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3101: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3102: }
3103: }else{
3104: for (ii=1;ii<=nlstate+ndeath;ii++){
3105: for (j=1;j<=nlstate+ndeath;j++)
3106: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3107: }
3108: /* if(sumnew <0.9){ */
3109: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3110: /* } */
3111: }
3112: k3=0.0; /* We put the last diagonal to 0 */
3113: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3114: doldm[ii][ii]= k3;
3115: }
3116: /* End doldm, At the end doldm is diag[(w_i)] */
3117:
1.292 brouard 3118: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3119: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3120:
1.292 brouard 3121: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3122: /* 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 3123: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3124: sumnew=0.;
1.222 brouard 3125: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3126: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3127: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3128: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3129: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3130: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3131: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3132: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3133: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3134: /* }else */
1.268 brouard 3135: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3136: } /*End ii */
3137: } /* 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 */
3138:
1.292 brouard 3139: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3140: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3141: /* end bmij */
1.266 brouard 3142: return ps; /*pointer is unchanged */
1.218 brouard 3143: }
1.217 brouard 3144: /*************** transition probabilities ***************/
3145:
1.218 brouard 3146: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3147: {
3148: /* According to parameters values stored in x and the covariate's values stored in cov,
3149: computes the probability to be observed in state j being in state i by appying the
3150: model to the ncovmodel covariates (including constant and age).
3151: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3152: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3153: ncth covariate in the global vector x is given by the formula:
3154: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3155: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3156: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3157: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3158: Outputs ps[i][j] the probability to be observed in j being in j according to
3159: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3160: */
3161: double s1, lnpijopii;
3162: /*double t34;*/
3163: int i,j, nc, ii, jj;
3164:
1.234 brouard 3165: for(i=1; i<= nlstate; i++){
3166: for(j=1; j<i;j++){
3167: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3168: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3169: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3170: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3171: }
3172: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3173: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3174: }
3175: for(j=i+1; j<=nlstate+ndeath;j++){
3176: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3177: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3178: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3179: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3180: }
3181: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3182: }
3183: }
3184:
3185: for(i=1; i<= nlstate; i++){
3186: s1=0;
3187: for(j=1; j<i; j++){
3188: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3189: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3190: }
3191: for(j=i+1; j<=nlstate+ndeath; j++){
3192: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3193: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3194: }
3195: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3196: ps[i][i]=1./(s1+1.);
3197: /* Computing other pijs */
3198: for(j=1; j<i; j++)
3199: ps[i][j]= exp(ps[i][j])*ps[i][i];
3200: for(j=i+1; j<=nlstate+ndeath; j++)
3201: ps[i][j]= exp(ps[i][j])*ps[i][i];
3202: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3203: } /* end i */
3204:
3205: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3206: for(jj=1; jj<= nlstate+ndeath; jj++){
3207: ps[ii][jj]=0;
3208: ps[ii][ii]=1;
3209: }
3210: }
1.296 brouard 3211: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3212: for(jj=1; jj<= nlstate+ndeath; jj++){
3213: s1=0.;
3214: for(ii=1; ii<= nlstate+ndeath; ii++){
3215: s1+=ps[ii][jj];
3216: }
3217: for(ii=1; ii<= nlstate; ii++){
3218: ps[ii][jj]=ps[ii][jj]/s1;
3219: }
3220: }
3221: /* Transposition */
3222: for(jj=1; jj<= nlstate+ndeath; jj++){
3223: for(ii=jj; ii<= nlstate+ndeath; ii++){
3224: s1=ps[ii][jj];
3225: ps[ii][jj]=ps[jj][ii];
3226: ps[jj][ii]=s1;
3227: }
3228: }
3229: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3230: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3231: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3232: /* } */
3233: /* printf("\n "); */
3234: /* } */
3235: /* printf("\n ");printf("%lf ",cov[2]);*/
3236: /*
3237: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3238: goto end;*/
3239: return ps;
1.217 brouard 3240: }
3241:
3242:
1.126 brouard 3243: /**************** Product of 2 matrices ******************/
3244:
1.145 brouard 3245: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3246: {
3247: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3248: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3249: /* in, b, out are matrice of pointers which should have been initialized
3250: before: only the contents of out is modified. The function returns
3251: a pointer to pointers identical to out */
1.145 brouard 3252: int i, j, k;
1.126 brouard 3253: for(i=nrl; i<= nrh; i++)
1.145 brouard 3254: for(k=ncolol; k<=ncoloh; k++){
3255: out[i][k]=0.;
3256: for(j=ncl; j<=nch; j++)
3257: out[i][k] +=in[i][j]*b[j][k];
3258: }
1.126 brouard 3259: return out;
3260: }
3261:
3262:
3263: /************* Higher Matrix Product ***************/
3264:
1.235 brouard 3265: 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 3266: {
1.218 brouard 3267: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3268: 'nhstepm*hstepm*stepm' months (i.e. until
3269: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3270: nhstepm*hstepm matrices.
3271: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3272: (typically every 2 years instead of every month which is too big
3273: for the memory).
3274: Model is determined by parameters x and covariates have to be
3275: included manually here.
3276:
3277: */
3278:
3279: int i, j, d, h, k;
1.131 brouard 3280: double **out, cov[NCOVMAX+1];
1.126 brouard 3281: double **newm;
1.187 brouard 3282: double agexact;
1.214 brouard 3283: double agebegin, ageend;
1.126 brouard 3284:
3285: /* Hstepm could be zero and should return the unit matrix */
3286: for (i=1;i<=nlstate+ndeath;i++)
3287: for (j=1;j<=nlstate+ndeath;j++){
3288: oldm[i][j]=(i==j ? 1.0 : 0.0);
3289: po[i][j][0]=(i==j ? 1.0 : 0.0);
3290: }
3291: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3292: for(h=1; h <=nhstepm; h++){
3293: for(d=1; d <=hstepm; d++){
3294: newm=savm;
3295: /* Covariates have to be included here again */
3296: cov[1]=1.;
1.214 brouard 3297: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3298: cov[2]=agexact;
3299: if(nagesqr==1)
1.227 brouard 3300: cov[3]= agexact*agexact;
1.235 brouard 3301: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3302: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3303: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3304: /* 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)); */
3305: }
3306: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3307: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3308: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3309: /* 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]); */
3310: }
3311: for (k=1; k<=cptcovage;k++){
3312: if(Dummy[Tvar[Tage[k]]]){
3313: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3314: } else{
3315: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3316: }
3317: /* 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]); */
3318: }
3319: for (k=1; k<=cptcovprod;k++){ /* */
3320: /* 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]); */
3321: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3322: }
3323: /* for (k=1; k<=cptcovn;k++) */
3324: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3325: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3326: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3327: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3328: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3329:
3330:
1.126 brouard 3331: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3332: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3333: /* right multiplication of oldm by the current matrix */
1.126 brouard 3334: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3335: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3336: /* if((int)age == 70){ */
3337: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3338: /* for(i=1; i<=nlstate+ndeath; i++) { */
3339: /* printf("%d pmmij ",i); */
3340: /* for(j=1;j<=nlstate+ndeath;j++) { */
3341: /* printf("%f ",pmmij[i][j]); */
3342: /* } */
3343: /* printf(" oldm "); */
3344: /* for(j=1;j<=nlstate+ndeath;j++) { */
3345: /* printf("%f ",oldm[i][j]); */
3346: /* } */
3347: /* printf("\n"); */
3348: /* } */
3349: /* } */
1.126 brouard 3350: savm=oldm;
3351: oldm=newm;
3352: }
3353: for(i=1; i<=nlstate+ndeath; i++)
3354: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3355: po[i][j][h]=newm[i][j];
3356: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3357: }
1.128 brouard 3358: /*printf("h=%d ",h);*/
1.126 brouard 3359: } /* end h */
1.267 brouard 3360: /* printf("\n H=%d \n",h); */
1.126 brouard 3361: return po;
3362: }
3363:
1.217 brouard 3364: /************* Higher Back Matrix Product ***************/
1.218 brouard 3365: /* 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 3366: 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 3367: {
1.266 brouard 3368: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3369: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3370: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3371: nhstepm*hstepm matrices.
3372: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3373: (typically every 2 years instead of every month which is too big
1.217 brouard 3374: for the memory).
1.218 brouard 3375: Model is determined by parameters x and covariates have to be
1.266 brouard 3376: included manually here. Then we use a call to bmij(x and cov)
3377: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3378: */
1.217 brouard 3379:
3380: int i, j, d, h, k;
1.266 brouard 3381: double **out, cov[NCOVMAX+1], **bmij();
3382: double **newm, ***newmm;
1.217 brouard 3383: double agexact;
3384: double agebegin, ageend;
1.222 brouard 3385: double **oldm, **savm;
1.217 brouard 3386:
1.266 brouard 3387: newmm=po; /* To be saved */
3388: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3389: /* Hstepm could be zero and should return the unit matrix */
3390: for (i=1;i<=nlstate+ndeath;i++)
3391: for (j=1;j<=nlstate+ndeath;j++){
3392: oldm[i][j]=(i==j ? 1.0 : 0.0);
3393: po[i][j][0]=(i==j ? 1.0 : 0.0);
3394: }
3395: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3396: for(h=1; h <=nhstepm; h++){
3397: for(d=1; d <=hstepm; d++){
3398: newm=savm;
3399: /* Covariates have to be included here again */
3400: cov[1]=1.;
1.271 brouard 3401: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3402: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3403: cov[2]=agexact;
3404: if(nagesqr==1)
1.222 brouard 3405: cov[3]= agexact*agexact;
1.266 brouard 3406: for (k=1; k<=cptcovn;k++){
3407: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3408: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3409: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3410: /* 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)); */
3411: }
1.267 brouard 3412: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3413: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3414: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3415: /* 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]); */
3416: }
3417: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3418: if(Dummy[Tvar[Tage[k]]]){
3419: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3420: } else{
3421: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3422: }
3423: /* 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]); */
3424: }
3425: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3426: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3427: }
1.217 brouard 3428: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3429: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3430:
1.218 brouard 3431: /* Careful transposed matrix */
1.266 brouard 3432: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3433: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3434: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3435: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3436: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3437: /* if((int)age == 70){ */
3438: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3439: /* for(i=1; i<=nlstate+ndeath; i++) { */
3440: /* printf("%d pmmij ",i); */
3441: /* for(j=1;j<=nlstate+ndeath;j++) { */
3442: /* printf("%f ",pmmij[i][j]); */
3443: /* } */
3444: /* printf(" oldm "); */
3445: /* for(j=1;j<=nlstate+ndeath;j++) { */
3446: /* printf("%f ",oldm[i][j]); */
3447: /* } */
3448: /* printf("\n"); */
3449: /* } */
3450: /* } */
3451: savm=oldm;
3452: oldm=newm;
3453: }
3454: for(i=1; i<=nlstate+ndeath; i++)
3455: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3456: po[i][j][h]=newm[i][j];
1.268 brouard 3457: /* if(h==nhstepm) */
3458: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3459: }
1.268 brouard 3460: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3461: } /* end h */
1.268 brouard 3462: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3463: return po;
3464: }
3465:
3466:
1.162 brouard 3467: #ifdef NLOPT
3468: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3469: double fret;
3470: double *xt;
3471: int j;
3472: myfunc_data *d2 = (myfunc_data *) pd;
3473: /* xt = (p1-1); */
3474: xt=vector(1,n);
3475: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3476:
3477: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3478: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3479: printf("Function = %.12lf ",fret);
3480: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3481: printf("\n");
3482: free_vector(xt,1,n);
3483: return fret;
3484: }
3485: #endif
1.126 brouard 3486:
3487: /*************** log-likelihood *************/
3488: double func( double *x)
3489: {
1.226 brouard 3490: int i, ii, j, k, mi, d, kk;
3491: int ioffset=0;
3492: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3493: double **out;
3494: double lli; /* Individual log likelihood */
3495: int s1, s2;
1.228 brouard 3496: 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 3497: double bbh, survp;
3498: long ipmx;
3499: double agexact;
3500: /*extern weight */
3501: /* We are differentiating ll according to initial status */
3502: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3503: /*for(i=1;i<imx;i++)
3504: printf(" %d\n",s[4][i]);
3505: */
1.162 brouard 3506:
1.226 brouard 3507: ++countcallfunc;
1.162 brouard 3508:
1.226 brouard 3509: cov[1]=1.;
1.126 brouard 3510:
1.226 brouard 3511: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3512: ioffset=0;
1.226 brouard 3513: if(mle==1){
3514: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3515: /* Computes the values of the ncovmodel covariates of the model
3516: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3517: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3518: to be observed in j being in i according to the model.
3519: */
1.243 brouard 3520: ioffset=2+nagesqr ;
1.233 brouard 3521: /* Fixed */
1.234 brouard 3522: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3523: 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)*/
3524: }
1.226 brouard 3525: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3526: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3527: has been calculated etc */
3528: /* For an individual i, wav[i] gives the number of effective waves */
3529: /* We compute the contribution to Likelihood of each effective transition
3530: mw[mi][i] is real wave of the mi th effectve wave */
3531: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3532: s2=s[mw[mi+1][i]][i];
3533: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3534: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3535: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3536: */
3537: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3538: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3539: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3540: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3541: }
3542: for (ii=1;ii<=nlstate+ndeath;ii++)
3543: for (j=1;j<=nlstate+ndeath;j++){
3544: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3545: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3546: }
3547: for(d=0; d<dh[mi][i]; d++){
3548: newm=savm;
3549: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3550: cov[2]=agexact;
3551: if(nagesqr==1)
3552: cov[3]= agexact*agexact; /* Should be changed here */
3553: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3554: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3555: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3556: else
3557: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3558: }
3559: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3560: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3561: savm=oldm;
3562: oldm=newm;
3563: } /* end mult */
3564:
3565: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3566: /* But now since version 0.9 we anticipate for bias at large stepm.
3567: * If stepm is larger than one month (smallest stepm) and if the exact delay
3568: * (in months) between two waves is not a multiple of stepm, we rounded to
3569: * the nearest (and in case of equal distance, to the lowest) interval but now
3570: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3571: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3572: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3573: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3574: * -stepm/2 to stepm/2 .
3575: * For stepm=1 the results are the same as for previous versions of Imach.
3576: * For stepm > 1 the results are less biased than in previous versions.
3577: */
1.234 brouard 3578: s1=s[mw[mi][i]][i];
3579: s2=s[mw[mi+1][i]][i];
3580: bbh=(double)bh[mi][i]/(double)stepm;
3581: /* bias bh is positive if real duration
3582: * is higher than the multiple of stepm and negative otherwise.
3583: */
3584: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3585: if( s2 > nlstate){
3586: /* i.e. if s2 is a death state and if the date of death is known
3587: then the contribution to the likelihood is the probability to
3588: die between last step unit time and current step unit time,
3589: which is also equal to probability to die before dh
3590: minus probability to die before dh-stepm .
3591: In version up to 0.92 likelihood was computed
3592: as if date of death was unknown. Death was treated as any other
3593: health state: the date of the interview describes the actual state
3594: and not the date of a change in health state. The former idea was
3595: to consider that at each interview the state was recorded
3596: (healthy, disable or death) and IMaCh was corrected; but when we
3597: introduced the exact date of death then we should have modified
3598: the contribution of an exact death to the likelihood. This new
3599: contribution is smaller and very dependent of the step unit
3600: stepm. It is no more the probability to die between last interview
3601: and month of death but the probability to survive from last
3602: interview up to one month before death multiplied by the
3603: probability to die within a month. Thanks to Chris
3604: Jackson for correcting this bug. Former versions increased
3605: mortality artificially. The bad side is that we add another loop
3606: which slows down the processing. The difference can be up to 10%
3607: lower mortality.
3608: */
3609: /* If, at the beginning of the maximization mostly, the
3610: cumulative probability or probability to be dead is
3611: constant (ie = 1) over time d, the difference is equal to
3612: 0. out[s1][3] = savm[s1][3]: probability, being at state
3613: s1 at precedent wave, to be dead a month before current
3614: wave is equal to probability, being at state s1 at
3615: precedent wave, to be dead at mont of the current
3616: wave. Then the observed probability (that this person died)
3617: is null according to current estimated parameter. In fact,
3618: it should be very low but not zero otherwise the log go to
3619: infinity.
3620: */
1.183 brouard 3621: /* #ifdef INFINITYORIGINAL */
3622: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3623: /* #else */
3624: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3625: /* lli=log(mytinydouble); */
3626: /* else */
3627: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3628: /* #endif */
1.226 brouard 3629: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3630:
1.226 brouard 3631: } else if ( s2==-1 ) { /* alive */
3632: for (j=1,survp=0. ; j<=nlstate; j++)
3633: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3634: /*survp += out[s1][j]; */
3635: lli= log(survp);
3636: }
3637: else if (s2==-4) {
3638: for (j=3,survp=0. ; j<=nlstate; j++)
3639: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3640: lli= log(survp);
3641: }
3642: else if (s2==-5) {
3643: for (j=1,survp=0. ; j<=2; j++)
3644: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3645: lli= log(survp);
3646: }
3647: else{
3648: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3649: /* 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 */
3650: }
3651: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3652: /*if(lli ==000.0)*/
3653: /*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); */
3654: ipmx +=1;
3655: sw += weight[i];
3656: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3657: /* if (lli < log(mytinydouble)){ */
3658: /* 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); */
3659: /* 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]); */
3660: /* } */
3661: } /* end of wave */
3662: } /* end of individual */
3663: } else if(mle==2){
3664: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3665: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3666: for(mi=1; mi<= wav[i]-1; mi++){
3667: for (ii=1;ii<=nlstate+ndeath;ii++)
3668: for (j=1;j<=nlstate+ndeath;j++){
3669: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3670: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3671: }
3672: for(d=0; d<=dh[mi][i]; d++){
3673: newm=savm;
3674: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3675: cov[2]=agexact;
3676: if(nagesqr==1)
3677: cov[3]= agexact*agexact;
3678: for (kk=1; kk<=cptcovage;kk++) {
3679: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3680: }
3681: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3682: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3683: savm=oldm;
3684: oldm=newm;
3685: } /* end mult */
3686:
3687: s1=s[mw[mi][i]][i];
3688: s2=s[mw[mi+1][i]][i];
3689: bbh=(double)bh[mi][i]/(double)stepm;
3690: 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 */
3691: ipmx +=1;
3692: sw += weight[i];
3693: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3694: } /* end of wave */
3695: } /* end of individual */
3696: } else if(mle==3){ /* exponential inter-extrapolation */
3697: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3698: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3699: for(mi=1; mi<= wav[i]-1; mi++){
3700: for (ii=1;ii<=nlstate+ndeath;ii++)
3701: for (j=1;j<=nlstate+ndeath;j++){
3702: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3703: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3704: }
3705: for(d=0; d<dh[mi][i]; d++){
3706: newm=savm;
3707: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3708: cov[2]=agexact;
3709: if(nagesqr==1)
3710: cov[3]= agexact*agexact;
3711: for (kk=1; kk<=cptcovage;kk++) {
3712: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3713: }
3714: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3715: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3716: savm=oldm;
3717: oldm=newm;
3718: } /* end mult */
3719:
3720: s1=s[mw[mi][i]][i];
3721: s2=s[mw[mi+1][i]][i];
3722: bbh=(double)bh[mi][i]/(double)stepm;
3723: 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 */
3724: ipmx +=1;
3725: sw += weight[i];
3726: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3727: } /* end of wave */
3728: } /* end of individual */
3729: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3730: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3731: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3732: for(mi=1; mi<= wav[i]-1; mi++){
3733: for (ii=1;ii<=nlstate+ndeath;ii++)
3734: for (j=1;j<=nlstate+ndeath;j++){
3735: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3736: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3737: }
3738: for(d=0; d<dh[mi][i]; d++){
3739: newm=savm;
3740: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3741: cov[2]=agexact;
3742: if(nagesqr==1)
3743: cov[3]= agexact*agexact;
3744: for (kk=1; kk<=cptcovage;kk++) {
3745: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3746: }
1.126 brouard 3747:
1.226 brouard 3748: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3749: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3750: savm=oldm;
3751: oldm=newm;
3752: } /* end mult */
3753:
3754: s1=s[mw[mi][i]][i];
3755: s2=s[mw[mi+1][i]][i];
3756: if( s2 > nlstate){
3757: lli=log(out[s1][s2] - savm[s1][s2]);
3758: } else if ( s2==-1 ) { /* alive */
3759: for (j=1,survp=0. ; j<=nlstate; j++)
3760: survp += out[s1][j];
3761: lli= log(survp);
3762: }else{
3763: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3764: }
3765: ipmx +=1;
3766: sw += weight[i];
3767: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3768: /* 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 3769: } /* end of wave */
3770: } /* end of individual */
3771: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3772: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3773: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3774: for(mi=1; mi<= wav[i]-1; mi++){
3775: for (ii=1;ii<=nlstate+ndeath;ii++)
3776: for (j=1;j<=nlstate+ndeath;j++){
3777: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3778: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3779: }
3780: for(d=0; d<dh[mi][i]; d++){
3781: newm=savm;
3782: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3783: cov[2]=agexact;
3784: if(nagesqr==1)
3785: cov[3]= agexact*agexact;
3786: for (kk=1; kk<=cptcovage;kk++) {
3787: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3788: }
1.126 brouard 3789:
1.226 brouard 3790: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3791: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3792: savm=oldm;
3793: oldm=newm;
3794: } /* end mult */
3795:
3796: s1=s[mw[mi][i]][i];
3797: s2=s[mw[mi+1][i]][i];
3798: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3799: ipmx +=1;
3800: sw += weight[i];
3801: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3802: /*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]);*/
3803: } /* end of wave */
3804: } /* end of individual */
3805: } /* End of if */
3806: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3807: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3808: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3809: return -l;
1.126 brouard 3810: }
3811:
3812: /*************** log-likelihood *************/
3813: double funcone( double *x)
3814: {
1.228 brouard 3815: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3816: int i, ii, j, k, mi, d, kk;
1.228 brouard 3817: int ioffset=0;
1.131 brouard 3818: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3819: double **out;
3820: double lli; /* Individual log likelihood */
3821: double llt;
3822: int s1, s2;
1.228 brouard 3823: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3824:
1.126 brouard 3825: double bbh, survp;
1.187 brouard 3826: double agexact;
1.214 brouard 3827: double agebegin, ageend;
1.126 brouard 3828: /*extern weight */
3829: /* We are differentiating ll according to initial status */
3830: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3831: /*for(i=1;i<imx;i++)
3832: printf(" %d\n",s[4][i]);
3833: */
3834: cov[1]=1.;
3835:
3836: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3837: ioffset=0;
3838: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3839: /* ioffset=2+nagesqr+cptcovage; */
3840: ioffset=2+nagesqr;
1.232 brouard 3841: /* Fixed */
1.224 brouard 3842: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3843: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3844: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3845: 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)*/
3846: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3847: /* cov[2+6]=covar[Tvar[6]][i]; */
3848: /* cov[2+6]=covar[2][i]; V2 */
3849: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3850: /* cov[2+7]=covar[Tvar[7]][i]; */
3851: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3852: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3853: /* cov[2+9]=covar[Tvar[9]][i]; */
3854: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3855: }
1.232 brouard 3856: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3857: /* 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?)*\/ */
3858: /* } */
1.231 brouard 3859: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3860: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3861: /* } */
1.225 brouard 3862:
1.233 brouard 3863:
3864: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3865: /* Wave varying (but not age varying) */
3866: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3867: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3868: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3869: }
1.232 brouard 3870: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3871: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3872: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3873: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3874: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3875: /* 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 3876: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3877: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3878: /* /\* 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]); *\/ */
3879: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3880: /* } */
1.126 brouard 3881: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3882: for (j=1;j<=nlstate+ndeath;j++){
3883: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3884: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3885: }
1.214 brouard 3886:
3887: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3888: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3889: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3890: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3891: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3892: and mw[mi+1][i]. dh depends on stepm.*/
3893: newm=savm;
1.247 brouard 3894: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3895: cov[2]=agexact;
3896: if(nagesqr==1)
3897: cov[3]= agexact*agexact;
3898: for (kk=1; kk<=cptcovage;kk++) {
3899: if(!FixedV[Tvar[Tage[kk]]])
3900: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3901: else
3902: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3903: }
3904: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3905: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3906: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3907: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3908: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3909: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3910: savm=oldm;
3911: oldm=newm;
1.126 brouard 3912: } /* end mult */
3913:
3914: s1=s[mw[mi][i]][i];
3915: s2=s[mw[mi+1][i]][i];
1.217 brouard 3916: /* if(s2==-1){ */
1.268 brouard 3917: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3918: /* /\* exit(1); *\/ */
3919: /* } */
1.126 brouard 3920: bbh=(double)bh[mi][i]/(double)stepm;
3921: /* bias is positive if real duration
3922: * is higher than the multiple of stepm and negative otherwise.
3923: */
3924: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3925: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3926: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3927: for (j=1,survp=0. ; j<=nlstate; j++)
3928: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3929: lli= log(survp);
1.126 brouard 3930: }else if (mle==1){
1.242 brouard 3931: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3932: } else if(mle==2){
1.242 brouard 3933: 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 3934: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3935: 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 3936: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3937: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3938: } else{ /* mle=0 back to 1 */
1.242 brouard 3939: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3940: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3941: } /* End of if */
3942: ipmx +=1;
3943: sw += weight[i];
3944: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3945: /*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 3946: if(globpr){
1.246 brouard 3947: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3948: %11.6f %11.6f %11.6f ", \
1.242 brouard 3949: 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 3950: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3951: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3952: llt +=ll[k]*gipmx/gsw;
3953: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3954: }
3955: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3956: }
1.232 brouard 3957: } /* end of wave */
3958: } /* end of individual */
3959: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3960: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3961: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3962: if(globpr==0){ /* First time we count the contributions and weights */
3963: gipmx=ipmx;
3964: gsw=sw;
3965: }
3966: return -l;
1.126 brouard 3967: }
3968:
3969:
3970: /*************** function likelione ***********/
1.292 brouard 3971: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3972: {
3973: /* This routine should help understanding what is done with
3974: the selection of individuals/waves and
3975: to check the exact contribution to the likelihood.
3976: Plotting could be done.
3977: */
3978: int k;
3979:
3980: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3981: strcpy(fileresilk,"ILK_");
1.202 brouard 3982: strcat(fileresilk,fileresu);
1.126 brouard 3983: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3984: printf("Problem with resultfile: %s\n", fileresilk);
3985: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3986: }
1.214 brouard 3987: 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");
3988: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3989: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3990: for(k=1; k<=nlstate; k++)
3991: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3992: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3993: }
3994:
1.292 brouard 3995: *fretone=(*func)(p);
1.126 brouard 3996: if(*globpri !=0){
3997: fclose(ficresilk);
1.205 brouard 3998: if (mle ==0)
3999: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
4000: else if(mle >=1)
4001: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
4002: 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 4003: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 4004:
4005: for (k=1; k<= nlstate ; k++) {
1.211 brouard 4006: 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 4007: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
4008: }
1.207 brouard 4009: 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 4010: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4011: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 4012: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4013: fflush(fichtm);
1.205 brouard 4014: }
1.126 brouard 4015: return;
4016: }
4017:
4018:
4019: /*********** Maximum Likelihood Estimation ***************/
4020:
4021: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4022: {
1.165 brouard 4023: int i,j, iter=0;
1.126 brouard 4024: double **xi;
4025: double fret;
4026: double fretone; /* Only one call to likelihood */
4027: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4028:
4029: #ifdef NLOPT
4030: int creturn;
4031: nlopt_opt opt;
4032: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4033: double *lb;
4034: double minf; /* the minimum objective value, upon return */
4035: double * p1; /* Shifted parameters from 0 instead of 1 */
4036: myfunc_data dinst, *d = &dinst;
4037: #endif
4038:
4039:
1.126 brouard 4040: xi=matrix(1,npar,1,npar);
4041: for (i=1;i<=npar;i++)
4042: for (j=1;j<=npar;j++)
4043: xi[i][j]=(i==j ? 1.0 : 0.0);
4044: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4045: strcpy(filerespow,"POW_");
1.126 brouard 4046: strcat(filerespow,fileres);
4047: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4048: printf("Problem with resultfile: %s\n", filerespow);
4049: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4050: }
4051: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4052: for (i=1;i<=nlstate;i++)
4053: for(j=1;j<=nlstate+ndeath;j++)
4054: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4055: fprintf(ficrespow,"\n");
1.162 brouard 4056: #ifdef POWELL
1.126 brouard 4057: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4058: #endif
1.126 brouard 4059:
1.162 brouard 4060: #ifdef NLOPT
4061: #ifdef NEWUOA
4062: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4063: #else
4064: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4065: #endif
4066: lb=vector(0,npar-1);
4067: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4068: nlopt_set_lower_bounds(opt, lb);
4069: nlopt_set_initial_step1(opt, 0.1);
4070:
4071: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4072: d->function = func;
4073: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4074: nlopt_set_min_objective(opt, myfunc, d);
4075: nlopt_set_xtol_rel(opt, ftol);
4076: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4077: printf("nlopt failed! %d\n",creturn);
4078: }
4079: else {
4080: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4081: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4082: iter=1; /* not equal */
4083: }
4084: nlopt_destroy(opt);
4085: #endif
1.126 brouard 4086: free_matrix(xi,1,npar,1,npar);
4087: fclose(ficrespow);
1.203 brouard 4088: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4089: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4090: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4091:
4092: }
4093:
4094: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4095: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4096: {
4097: double **a,**y,*x,pd;
1.203 brouard 4098: /* double **hess; */
1.164 brouard 4099: int i, j;
1.126 brouard 4100: int *indx;
4101:
4102: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4103: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4104: void lubksb(double **a, int npar, int *indx, double b[]) ;
4105: void ludcmp(double **a, int npar, int *indx, double *d) ;
4106: double gompertz(double p[]);
1.203 brouard 4107: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4108:
4109: printf("\nCalculation of the hessian matrix. Wait...\n");
4110: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4111: for (i=1;i<=npar;i++){
1.203 brouard 4112: printf("%d-",i);fflush(stdout);
4113: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4114:
4115: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4116:
4117: /* printf(" %f ",p[i]);
4118: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4119: }
4120:
4121: for (i=1;i<=npar;i++) {
4122: for (j=1;j<=npar;j++) {
4123: if (j>i) {
1.203 brouard 4124: printf(".%d-%d",i,j);fflush(stdout);
4125: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4126: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4127:
4128: hess[j][i]=hess[i][j];
4129: /*printf(" %lf ",hess[i][j]);*/
4130: }
4131: }
4132: }
4133: printf("\n");
4134: fprintf(ficlog,"\n");
4135:
4136: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4137: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4138:
4139: a=matrix(1,npar,1,npar);
4140: y=matrix(1,npar,1,npar);
4141: x=vector(1,npar);
4142: indx=ivector(1,npar);
4143: for (i=1;i<=npar;i++)
4144: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4145: ludcmp(a,npar,indx,&pd);
4146:
4147: for (j=1;j<=npar;j++) {
4148: for (i=1;i<=npar;i++) x[i]=0;
4149: x[j]=1;
4150: lubksb(a,npar,indx,x);
4151: for (i=1;i<=npar;i++){
4152: matcov[i][j]=x[i];
4153: }
4154: }
4155:
4156: printf("\n#Hessian matrix#\n");
4157: fprintf(ficlog,"\n#Hessian matrix#\n");
4158: for (i=1;i<=npar;i++) {
4159: for (j=1;j<=npar;j++) {
1.203 brouard 4160: printf("%.6e ",hess[i][j]);
4161: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4162: }
4163: printf("\n");
4164: fprintf(ficlog,"\n");
4165: }
4166:
1.203 brouard 4167: /* printf("\n#Covariance matrix#\n"); */
4168: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4169: /* for (i=1;i<=npar;i++) { */
4170: /* for (j=1;j<=npar;j++) { */
4171: /* printf("%.6e ",matcov[i][j]); */
4172: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4173: /* } */
4174: /* printf("\n"); */
4175: /* fprintf(ficlog,"\n"); */
4176: /* } */
4177:
1.126 brouard 4178: /* Recompute Inverse */
1.203 brouard 4179: /* for (i=1;i<=npar;i++) */
4180: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4181: /* ludcmp(a,npar,indx,&pd); */
4182:
4183: /* printf("\n#Hessian matrix recomputed#\n"); */
4184:
4185: /* for (j=1;j<=npar;j++) { */
4186: /* for (i=1;i<=npar;i++) x[i]=0; */
4187: /* x[j]=1; */
4188: /* lubksb(a,npar,indx,x); */
4189: /* for (i=1;i<=npar;i++){ */
4190: /* y[i][j]=x[i]; */
4191: /* printf("%.3e ",y[i][j]); */
4192: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4193: /* } */
4194: /* printf("\n"); */
4195: /* fprintf(ficlog,"\n"); */
4196: /* } */
4197:
4198: /* Verifying the inverse matrix */
4199: #ifdef DEBUGHESS
4200: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4201:
1.203 brouard 4202: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4203: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4204:
4205: for (j=1;j<=npar;j++) {
4206: for (i=1;i<=npar;i++){
1.203 brouard 4207: printf("%.2f ",y[i][j]);
4208: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4209: }
4210: printf("\n");
4211: fprintf(ficlog,"\n");
4212: }
1.203 brouard 4213: #endif
1.126 brouard 4214:
4215: free_matrix(a,1,npar,1,npar);
4216: free_matrix(y,1,npar,1,npar);
4217: free_vector(x,1,npar);
4218: free_ivector(indx,1,npar);
1.203 brouard 4219: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4220:
4221:
4222: }
4223:
4224: /*************** hessian matrix ****************/
4225: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4226: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4227: int i;
4228: int l=1, lmax=20;
1.203 brouard 4229: double k1,k2, res, fx;
1.132 brouard 4230: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4231: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4232: int k=0,kmax=10;
4233: double l1;
4234:
4235: fx=func(x);
4236: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4237: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4238: l1=pow(10,l);
4239: delts=delt;
4240: for(k=1 ; k <kmax; k=k+1){
4241: delt = delta*(l1*k);
4242: p2[theta]=x[theta] +delt;
1.145 brouard 4243: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4244: p2[theta]=x[theta]-delt;
4245: k2=func(p2)-fx;
4246: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4247: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4248:
1.203 brouard 4249: #ifdef DEBUGHESSII
1.126 brouard 4250: 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);
4251: 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);
4252: #endif
4253: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4254: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4255: k=kmax;
4256: }
4257: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4258: k=kmax; l=lmax*10;
1.126 brouard 4259: }
4260: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4261: delts=delt;
4262: }
1.203 brouard 4263: } /* End loop k */
1.126 brouard 4264: }
4265: delti[theta]=delts;
4266: return res;
4267:
4268: }
4269:
1.203 brouard 4270: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4271: {
4272: int i;
1.164 brouard 4273: int l=1, lmax=20;
1.126 brouard 4274: double k1,k2,k3,k4,res,fx;
1.132 brouard 4275: double p2[MAXPARM+1];
1.203 brouard 4276: int k, kmax=1;
4277: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4278:
4279: int firstime=0;
1.203 brouard 4280:
1.126 brouard 4281: fx=func(x);
1.203 brouard 4282: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4283: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4284: p2[thetai]=x[thetai]+delti[thetai]*k;
4285: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4286: k1=func(p2)-fx;
4287:
1.203 brouard 4288: p2[thetai]=x[thetai]+delti[thetai]*k;
4289: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4290: k2=func(p2)-fx;
4291:
1.203 brouard 4292: p2[thetai]=x[thetai]-delti[thetai]*k;
4293: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4294: k3=func(p2)-fx;
4295:
1.203 brouard 4296: p2[thetai]=x[thetai]-delti[thetai]*k;
4297: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4298: k4=func(p2)-fx;
1.203 brouard 4299: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4300: if(k1*k2*k3*k4 <0.){
1.208 brouard 4301: firstime=1;
1.203 brouard 4302: kmax=kmax+10;
1.208 brouard 4303: }
4304: if(kmax >=10 || firstime ==1){
1.246 brouard 4305: 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);
4306: 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 4307: 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);
4308: 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);
4309: }
4310: #ifdef DEBUGHESSIJ
4311: v1=hess[thetai][thetai];
4312: v2=hess[thetaj][thetaj];
4313: cv12=res;
4314: /* Computing eigen value of Hessian matrix */
4315: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4316: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4317: if ((lc2 <0) || (lc1 <0) ){
4318: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4319: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4320: 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);
4321: 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);
4322: }
1.126 brouard 4323: #endif
4324: }
4325: return res;
4326: }
4327:
1.203 brouard 4328: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4329: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4330: /* { */
4331: /* int i; */
4332: /* int l=1, lmax=20; */
4333: /* double k1,k2,k3,k4,res,fx; */
4334: /* double p2[MAXPARM+1]; */
4335: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4336: /* int k=0,kmax=10; */
4337: /* double l1; */
4338:
4339: /* fx=func(x); */
4340: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4341: /* l1=pow(10,l); */
4342: /* delts=delt; */
4343: /* for(k=1 ; k <kmax; k=k+1){ */
4344: /* delt = delti*(l1*k); */
4345: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4346: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4347: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4348: /* k1=func(p2)-fx; */
4349:
4350: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4351: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4352: /* k2=func(p2)-fx; */
4353:
4354: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4355: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4356: /* k3=func(p2)-fx; */
4357:
4358: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4359: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4360: /* k4=func(p2)-fx; */
4361: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4362: /* #ifdef DEBUGHESSIJ */
4363: /* 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); */
4364: /* 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); */
4365: /* #endif */
4366: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4367: /* k=kmax; */
4368: /* } */
4369: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4370: /* k=kmax; l=lmax*10; */
4371: /* } */
4372: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4373: /* delts=delt; */
4374: /* } */
4375: /* } /\* End loop k *\/ */
4376: /* } */
4377: /* delti[theta]=delts; */
4378: /* return res; */
4379: /* } */
4380:
4381:
1.126 brouard 4382: /************** Inverse of matrix **************/
4383: void ludcmp(double **a, int n, int *indx, double *d)
4384: {
4385: int i,imax,j,k;
4386: double big,dum,sum,temp;
4387: double *vv;
4388:
4389: vv=vector(1,n);
4390: *d=1.0;
4391: for (i=1;i<=n;i++) {
4392: big=0.0;
4393: for (j=1;j<=n;j++)
4394: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4395: if (big == 0.0){
4396: printf(" Singular Hessian matrix at row %d:\n",i);
4397: for (j=1;j<=n;j++) {
4398: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4399: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4400: }
4401: fflush(ficlog);
4402: fclose(ficlog);
4403: nrerror("Singular matrix in routine ludcmp");
4404: }
1.126 brouard 4405: vv[i]=1.0/big;
4406: }
4407: for (j=1;j<=n;j++) {
4408: for (i=1;i<j;i++) {
4409: sum=a[i][j];
4410: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4411: a[i][j]=sum;
4412: }
4413: big=0.0;
4414: for (i=j;i<=n;i++) {
4415: sum=a[i][j];
4416: for (k=1;k<j;k++)
4417: sum -= a[i][k]*a[k][j];
4418: a[i][j]=sum;
4419: if ( (dum=vv[i]*fabs(sum)) >= big) {
4420: big=dum;
4421: imax=i;
4422: }
4423: }
4424: if (j != imax) {
4425: for (k=1;k<=n;k++) {
4426: dum=a[imax][k];
4427: a[imax][k]=a[j][k];
4428: a[j][k]=dum;
4429: }
4430: *d = -(*d);
4431: vv[imax]=vv[j];
4432: }
4433: indx[j]=imax;
4434: if (a[j][j] == 0.0) a[j][j]=TINY;
4435: if (j != n) {
4436: dum=1.0/(a[j][j]);
4437: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4438: }
4439: }
4440: free_vector(vv,1,n); /* Doesn't work */
4441: ;
4442: }
4443:
4444: void lubksb(double **a, int n, int *indx, double b[])
4445: {
4446: int i,ii=0,ip,j;
4447: double sum;
4448:
4449: for (i=1;i<=n;i++) {
4450: ip=indx[i];
4451: sum=b[ip];
4452: b[ip]=b[i];
4453: if (ii)
4454: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4455: else if (sum) ii=i;
4456: b[i]=sum;
4457: }
4458: for (i=n;i>=1;i--) {
4459: sum=b[i];
4460: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4461: b[i]=sum/a[i][i];
4462: }
4463: }
4464:
4465: void pstamp(FILE *fichier)
4466: {
1.196 brouard 4467: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4468: }
4469:
1.297 brouard 4470: void date2dmy(double date,double *day, double *month, double *year){
4471: double yp=0., yp1=0., yp2=0.;
4472:
4473: yp1=modf(date,&yp);/* extracts integral of date in yp and
4474: fractional in yp1 */
4475: *year=yp;
4476: yp2=modf((yp1*12),&yp);
4477: *month=yp;
4478: yp1=modf((yp2*30.5),&yp);
4479: *day=yp;
4480: if(*day==0) *day=1;
4481: if(*month==0) *month=1;
4482: }
4483:
1.253 brouard 4484:
4485:
1.126 brouard 4486: /************ Frequencies ********************/
1.251 brouard 4487: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4488: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4489: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4490: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4491:
1.265 brouard 4492: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4493: int iind=0, iage=0;
4494: int mi; /* Effective wave */
4495: int first;
4496: double ***freq; /* Frequencies */
1.268 brouard 4497: 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 */
4498: 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 4499: double *meanq, *stdq, *idq;
1.226 brouard 4500: double **meanqt;
4501: double *pp, **prop, *posprop, *pospropt;
4502: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4503: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4504: double agebegin, ageend;
4505:
4506: pp=vector(1,nlstate);
1.251 brouard 4507: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4508: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4509: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4510: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4511: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4512: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4513: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4514: meanqt=matrix(1,lastpass,1,nqtveff);
4515: strcpy(fileresp,"P_");
4516: strcat(fileresp,fileresu);
4517: /*strcat(fileresphtm,fileresu);*/
4518: if((ficresp=fopen(fileresp,"w"))==NULL) {
4519: printf("Problem with prevalence resultfile: %s\n", fileresp);
4520: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4521: exit(0);
4522: }
1.240 brouard 4523:
1.226 brouard 4524: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4525: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4526: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4527: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4528: fflush(ficlog);
4529: exit(70);
4530: }
4531: else{
4532: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4533: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4534: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4535: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4536: }
1.237 brouard 4537: 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 4538:
1.226 brouard 4539: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4540: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4541: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4542: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4543: fflush(ficlog);
4544: exit(70);
1.240 brouard 4545: } else{
1.226 brouard 4546: 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 4547: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4548: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4549: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4550: }
1.240 brouard 4551: 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);
4552:
1.253 brouard 4553: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4554: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4555: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4556: j1=0;
1.126 brouard 4557:
1.227 brouard 4558: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4559: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4560: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4561:
4562:
1.226 brouard 4563: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4564: reference=low_education V1=0,V2=0
4565: med_educ V1=1 V2=0,
4566: high_educ V1=0 V2=1
4567: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4568: */
1.249 brouard 4569: dateintsum=0;
4570: k2cpt=0;
4571:
1.253 brouard 4572: if(cptcoveff == 0 )
1.265 brouard 4573: nl=1; /* Constant and age model only */
1.253 brouard 4574: else
4575: nl=2;
1.265 brouard 4576:
4577: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4578: /* Loop on nj=1 or 2 if dummy covariates j!=0
4579: * Loop on j1(1 to 2**cptcoveff) covariate combination
4580: * freq[s1][s2][iage] =0.
4581: * Loop on iind
4582: * ++freq[s1][s2][iage] weighted
4583: * end iind
4584: * if covariate and j!0
4585: * headers Variable on one line
4586: * endif cov j!=0
4587: * header of frequency table by age
4588: * Loop on age
4589: * pp[s1]+=freq[s1][s2][iage] weighted
4590: * pos+=freq[s1][s2][iage] weighted
4591: * Loop on s1 initial state
4592: * fprintf(ficresp
4593: * end s1
4594: * end age
4595: * if j!=0 computes starting values
4596: * end compute starting values
4597: * end j1
4598: * end nl
4599: */
1.253 brouard 4600: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4601: if(nj==1)
4602: j=0; /* First pass for the constant */
1.265 brouard 4603: else{
1.253 brouard 4604: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4605: }
1.251 brouard 4606: first=1;
1.265 brouard 4607: 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 4608: posproptt=0.;
4609: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4610: scanf("%d", i);*/
4611: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4612: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4613: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4614: freq[i][s2][m]=0;
1.251 brouard 4615:
4616: for (i=1; i<=nlstate; i++) {
1.240 brouard 4617: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4618: prop[i][m]=0;
4619: posprop[i]=0;
4620: pospropt[i]=0;
4621: }
1.283 brouard 4622: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4623: idq[z1]=0.;
4624: meanq[z1]=0.;
4625: stdq[z1]=0.;
1.283 brouard 4626: }
4627: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4628: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4629: /* meanqt[m][z1]=0.; */
4630: /* } */
4631: /* } */
1.251 brouard 4632: /* dateintsum=0; */
4633: /* k2cpt=0; */
4634:
1.265 brouard 4635: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4636: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4637: bool=1;
4638: if(j !=0){
4639: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4640: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4641: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4642: /* if(Tvaraff[z1] ==-20){ */
4643: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4644: /* }else if(Tvaraff[z1] ==-10){ */
4645: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4646: /* }else */
4647: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4648: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4649: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4650: /* 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",
4651: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4652: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4653: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4654: } /* Onlyf fixed */
4655: } /* end z1 */
4656: } /* cptcovn > 0 */
4657: } /* end any */
4658: }/* end j==0 */
1.265 brouard 4659: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4660: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4661: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4662: m=mw[mi][iind];
4663: if(j!=0){
4664: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4665: for (z1=1; z1<=cptcoveff; z1++) {
4666: if( Fixed[Tmodelind[z1]]==1){
4667: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4668: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4669: value is -1, we don't select. It differs from the
4670: constant and age model which counts them. */
4671: bool=0; /* not selected */
4672: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4673: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4674: bool=0;
4675: }
4676: }
4677: }
4678: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4679: } /* end j==0 */
4680: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4681: if(bool==1){ /*Selected */
1.251 brouard 4682: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4683: and mw[mi+1][iind]. dh depends on stepm. */
4684: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4685: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4686: if(m >=firstpass && m <=lastpass){
4687: k2=anint[m][iind]+(mint[m][iind]/12.);
4688: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4689: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4690: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4691: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4692: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4693: if (m<lastpass) {
4694: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4695: /* 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]); */
4696: if(s[m][iind]==-1)
4697: 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.));
4698: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
1.284 brouard 4699: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4700: idq[z1]=idq[z1]+weight[iind];
4701: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4702: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4703: }
1.251 brouard 4704: /* if((int)agev[m][iind] == 55) */
4705: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4706: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4707: 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 4708: }
1.251 brouard 4709: } /* end if between passes */
4710: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4711: dateintsum=dateintsum+k2; /* on all covariates ?*/
4712: k2cpt++;
4713: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4714: }
1.251 brouard 4715: }else{
4716: bool=1;
4717: }/* end bool 2 */
4718: } /* end m */
1.284 brouard 4719: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4720: /* idq[z1]=idq[z1]+weight[iind]; */
4721: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4722: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4723: /* } */
1.251 brouard 4724: } /* end bool */
4725: } /* end iind = 1 to imx */
4726: /* prop[s][age] is feeded for any initial and valid live state as well as
4727: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4728:
4729:
4730: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4731: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4732: pstamp(ficresp);
1.251 brouard 4733: if (cptcoveff>0 && j!=0){
1.265 brouard 4734: pstamp(ficresp);
1.251 brouard 4735: printf( "\n#********** Variable ");
4736: fprintf(ficresp, "\n#********** Variable ");
4737: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4738: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4739: fprintf(ficlog, "\n#********** Variable ");
4740: for (z1=1; z1<=cptcoveff; z1++){
4741: if(!FixedV[Tvaraff[z1]]){
4742: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4743: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4744: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4745: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4746: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4747: }else{
1.251 brouard 4748: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4749: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4750: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4751: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4752: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4753: }
4754: }
4755: printf( "**********\n#");
4756: fprintf(ficresp, "**********\n#");
4757: fprintf(ficresphtm, "**********</h3>\n");
4758: fprintf(ficresphtmfr, "**********</h3>\n");
4759: fprintf(ficlog, "**********\n");
4760: }
1.284 brouard 4761: /*
4762: Printing means of quantitative variables if any
4763: */
4764: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4765: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4766: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4767: if(weightopt==1){
4768: printf(" Weighted mean and standard deviation of");
4769: fprintf(ficlog," Weighted mean and standard deviation of");
4770: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4771: }
1.285 brouard 4772: printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
4773: fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
4774: fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
1.284 brouard 4775: }
4776: /* for (z1=1; z1<= nqtveff; z1++) { */
4777: /* for(m=1;m<=lastpass;m++){ */
4778: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4779: /* } */
4780: /* } */
1.283 brouard 4781:
1.251 brouard 4782: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4783: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4784: fprintf(ficresp, " Age");
4785: 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 4786: for(i=1; i<=nlstate;i++) {
1.265 brouard 4787: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4788: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4789: }
1.265 brouard 4790: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4791: fprintf(ficresphtm, "\n");
4792:
4793: /* Header of frequency table by age */
4794: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4795: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4796: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4797: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4798: if(s2!=0 && m!=0)
4799: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4800: }
1.226 brouard 4801: }
1.251 brouard 4802: fprintf(ficresphtmfr, "\n");
4803:
4804: /* For each age */
4805: for(iage=iagemin; iage <= iagemax+3; iage++){
4806: fprintf(ficresphtm,"<tr>");
4807: if(iage==iagemax+1){
4808: fprintf(ficlog,"1");
4809: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4810: }else if(iage==iagemax+2){
4811: fprintf(ficlog,"0");
4812: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4813: }else if(iage==iagemax+3){
4814: fprintf(ficlog,"Total");
4815: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4816: }else{
1.240 brouard 4817: if(first==1){
1.251 brouard 4818: first=0;
4819: printf("See log file for details...\n");
4820: }
4821: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4822: fprintf(ficlog,"Age %d", iage);
4823: }
1.265 brouard 4824: for(s1=1; s1 <=nlstate ; s1++){
4825: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4826: pp[s1] += freq[s1][m][iage];
1.251 brouard 4827: }
1.265 brouard 4828: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4829: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4830: pos += freq[s1][m][iage];
4831: if(pp[s1]>=1.e-10){
1.251 brouard 4832: if(first==1){
1.265 brouard 4833: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4834: }
1.265 brouard 4835: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4836: }else{
4837: if(first==1)
1.265 brouard 4838: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4839: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4840: }
4841: }
4842:
1.265 brouard 4843: for(s1=1; s1 <=nlstate ; s1++){
4844: /* posprop[s1]=0; */
4845: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4846: pp[s1] += freq[s1][m][iage];
4847: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4848:
4849: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4850: pos += pp[s1]; /* pos is the total number of transitions until this age */
4851: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4852: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4853: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4854: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4855: }
4856:
4857: /* Writing ficresp */
4858: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4859: if( iage <= iagemax){
4860: fprintf(ficresp," %d",iage);
4861: }
4862: }else if( nj==2){
4863: if( iage <= iagemax){
4864: fprintf(ficresp," %d",iage);
4865: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4866: }
1.240 brouard 4867: }
1.265 brouard 4868: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4869: if(pos>=1.e-5){
1.251 brouard 4870: if(first==1)
1.265 brouard 4871: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4872: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4873: }else{
4874: if(first==1)
1.265 brouard 4875: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4876: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4877: }
4878: if( iage <= iagemax){
4879: if(pos>=1.e-5){
1.265 brouard 4880: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4881: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4882: }else if( nj==2){
4883: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4884: }
4885: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4886: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4887: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4888: } else{
4889: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4890: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4891: }
1.240 brouard 4892: }
1.265 brouard 4893: pospropt[s1] +=posprop[s1];
4894: } /* end loop s1 */
1.251 brouard 4895: /* pospropt=0.; */
1.265 brouard 4896: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4897: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4898: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4899: if(first==1){
1.265 brouard 4900: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4901: }
1.265 brouard 4902: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4903: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4904: }
1.265 brouard 4905: if(s1!=0 && m!=0)
4906: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4907: }
1.265 brouard 4908: } /* end loop s1 */
1.251 brouard 4909: posproptt=0.;
1.265 brouard 4910: for(s1=1; s1 <=nlstate; s1++){
4911: posproptt += pospropt[s1];
1.251 brouard 4912: }
4913: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4914: fprintf(ficresphtm,"</tr>\n");
4915: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4916: if(iage <= iagemax)
4917: fprintf(ficresp,"\n");
1.240 brouard 4918: }
1.251 brouard 4919: if(first==1)
4920: printf("Others in log...\n");
4921: fprintf(ficlog,"\n");
4922: } /* end loop age iage */
1.265 brouard 4923:
1.251 brouard 4924: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4925: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4926: if(posproptt < 1.e-5){
1.265 brouard 4927: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4928: }else{
1.265 brouard 4929: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4930: }
1.226 brouard 4931: }
1.251 brouard 4932: fprintf(ficresphtm,"</tr>\n");
4933: fprintf(ficresphtm,"</table>\n");
4934: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4935: if(posproptt < 1.e-5){
1.251 brouard 4936: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4937: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4938: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4939: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4940: invalidvarcomb[j1]=1;
1.226 brouard 4941: }else{
1.251 brouard 4942: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4943: invalidvarcomb[j1]=0;
1.226 brouard 4944: }
1.251 brouard 4945: fprintf(ficresphtmfr,"</table>\n");
4946: fprintf(ficlog,"\n");
4947: if(j!=0){
4948: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4949: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4950: for(k=1; k <=(nlstate+ndeath); k++){
4951: if (k != i) {
1.265 brouard 4952: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4953: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4954: if(j1==1){ /* All dummy covariates to zero */
4955: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4956: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4957: printf("%d%d ",i,k);
4958: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4959: 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]));
4960: 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]));
4961: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4962: }
1.253 brouard 4963: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4964: for(iage=iagemin; iage <= iagemax+3; iage++){
4965: x[iage]= (double)iage;
4966: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4967: /* 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 4968: }
1.268 brouard 4969: /* Some are not finite, but linreg will ignore these ages */
4970: no=0;
1.253 brouard 4971: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4972: pstart[s1]=b;
4973: pstart[s1-1]=a;
1.252 brouard 4974: }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 */
4975: 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]);
4976: 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 4977: 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 4978: printf("%d%d ",i,k);
4979: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4980: 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 4981: }else{ /* Other cases, like quantitative fixed or varying covariates */
4982: ;
4983: }
4984: /* printf("%12.7f )", param[i][jj][k]); */
4985: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4986: s1++;
1.251 brouard 4987: } /* end jj */
4988: } /* end k!= i */
4989: } /* end k */
1.265 brouard 4990: } /* end i, s1 */
1.251 brouard 4991: } /* end j !=0 */
4992: } /* end selected combination of covariate j1 */
4993: if(j==0){ /* We can estimate starting values from the occurences in each case */
4994: printf("#Freqsummary: Starting values for the constants:\n");
4995: fprintf(ficlog,"\n");
1.265 brouard 4996: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4997: for(k=1; k <=(nlstate+ndeath); k++){
4998: if (k != i) {
4999: printf("%d%d ",i,k);
5000: fprintf(ficlog,"%d%d ",i,k);
5001: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 5002: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 5003: if(jj==1){ /* Age has to be done */
1.265 brouard 5004: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
5005: 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]));
5006: 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 5007: }
5008: /* printf("%12.7f )", param[i][jj][k]); */
5009: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5010: s1++;
1.250 brouard 5011: }
1.251 brouard 5012: printf("\n");
5013: fprintf(ficlog,"\n");
1.250 brouard 5014: }
5015: }
1.284 brouard 5016: } /* end of state i */
1.251 brouard 5017: printf("#Freqsummary\n");
5018: fprintf(ficlog,"\n");
1.265 brouard 5019: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5020: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5021: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5022: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5023: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5024: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5025: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5026: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5027: /* } */
5028: }
1.265 brouard 5029: } /* end loop s1 */
1.251 brouard 5030:
5031: printf("\n");
5032: fprintf(ficlog,"\n");
5033: } /* end j=0 */
1.249 brouard 5034: } /* end j */
1.252 brouard 5035:
1.253 brouard 5036: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5037: for(i=1, jk=1; i <=nlstate; i++){
5038: for(j=1; j <=nlstate+ndeath; j++){
5039: if(j!=i){
5040: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5041: printf("%1d%1d",i,j);
5042: fprintf(ficparo,"%1d%1d",i,j);
5043: for(k=1; k<=ncovmodel;k++){
5044: /* printf(" %lf",param[i][j][k]); */
5045: /* fprintf(ficparo," %lf",param[i][j][k]); */
5046: p[jk]=pstart[jk];
5047: printf(" %f ",pstart[jk]);
5048: fprintf(ficparo," %f ",pstart[jk]);
5049: jk++;
5050: }
5051: printf("\n");
5052: fprintf(ficparo,"\n");
5053: }
5054: }
5055: }
5056: } /* end mle=-2 */
1.226 brouard 5057: dateintmean=dateintsum/k2cpt;
1.296 brouard 5058: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5059:
1.226 brouard 5060: fclose(ficresp);
5061: fclose(ficresphtm);
5062: fclose(ficresphtmfr);
1.283 brouard 5063: free_vector(idq,1,nqfveff);
1.226 brouard 5064: free_vector(meanq,1,nqfveff);
1.284 brouard 5065: free_vector(stdq,1,nqfveff);
1.226 brouard 5066: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5067: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5068: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5069: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5070: free_vector(pospropt,1,nlstate);
5071: free_vector(posprop,1,nlstate);
1.251 brouard 5072: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5073: free_vector(pp,1,nlstate);
5074: /* End of freqsummary */
5075: }
1.126 brouard 5076:
1.268 brouard 5077: /* Simple linear regression */
5078: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5079:
5080: /* y=a+bx regression */
5081: double sumx = 0.0; /* sum of x */
5082: double sumx2 = 0.0; /* sum of x**2 */
5083: double sumxy = 0.0; /* sum of x * y */
5084: double sumy = 0.0; /* sum of y */
5085: double sumy2 = 0.0; /* sum of y**2 */
5086: double sume2 = 0.0; /* sum of square or residuals */
5087: double yhat;
5088:
5089: double denom=0;
5090: int i;
5091: int ne=*no;
5092:
5093: for ( i=ifi, ne=0;i<=ila;i++) {
5094: if(!isfinite(x[i]) || !isfinite(y[i])){
5095: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5096: continue;
5097: }
5098: ne=ne+1;
5099: sumx += x[i];
5100: sumx2 += x[i]*x[i];
5101: sumxy += x[i] * y[i];
5102: sumy += y[i];
5103: sumy2 += y[i]*y[i];
5104: denom = (ne * sumx2 - sumx*sumx);
5105: /* 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); */
5106: }
5107:
5108: denom = (ne * sumx2 - sumx*sumx);
5109: if (denom == 0) {
5110: // vertical, slope m is infinity
5111: *b = INFINITY;
5112: *a = 0;
5113: if (r) *r = 0;
5114: return 1;
5115: }
5116:
5117: *b = (ne * sumxy - sumx * sumy) / denom;
5118: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5119: if (r!=NULL) {
5120: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5121: sqrt((sumx2 - sumx*sumx/ne) *
5122: (sumy2 - sumy*sumy/ne));
5123: }
5124: *no=ne;
5125: for ( i=ifi, ne=0;i<=ila;i++) {
5126: if(!isfinite(x[i]) || !isfinite(y[i])){
5127: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5128: continue;
5129: }
5130: ne=ne+1;
5131: yhat = y[i] - *a -*b* x[i];
5132: sume2 += yhat * yhat ;
5133:
5134: denom = (ne * sumx2 - sumx*sumx);
5135: /* 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); */
5136: }
5137: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5138: *sa= *sb * sqrt(sumx2/ne);
5139:
5140: return 0;
5141: }
5142:
1.126 brouard 5143: /************ Prevalence ********************/
1.227 brouard 5144: 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)
5145: {
5146: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5147: in each health status at the date of interview (if between dateprev1 and dateprev2).
5148: We still use firstpass and lastpass as another selection.
5149: */
1.126 brouard 5150:
1.227 brouard 5151: int i, m, jk, j1, bool, z1,j, iv;
5152: int mi; /* Effective wave */
5153: int iage;
5154: double agebegin, ageend;
5155:
5156: double **prop;
5157: double posprop;
5158: double y2; /* in fractional years */
5159: int iagemin, iagemax;
5160: int first; /** to stop verbosity which is redirected to log file */
5161:
5162: iagemin= (int) agemin;
5163: iagemax= (int) agemax;
5164: /*pp=vector(1,nlstate);*/
1.251 brouard 5165: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5166: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5167: j1=0;
1.222 brouard 5168:
1.227 brouard 5169: /*j=cptcoveff;*/
5170: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5171:
1.288 brouard 5172: first=0;
1.227 brouard 5173: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5174: for (i=1; i<=nlstate; i++)
1.251 brouard 5175: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5176: prop[i][iage]=0.0;
5177: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5178: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5179: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5180:
5181: for (i=1; i<=imx; i++) { /* Each individual */
5182: bool=1;
5183: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5184: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5185: m=mw[mi][i];
5186: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5187: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5188: for (z1=1; z1<=cptcoveff; z1++){
5189: if( Fixed[Tmodelind[z1]]==1){
5190: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5191: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5192: bool=0;
5193: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5194: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5195: bool=0;
5196: }
5197: }
5198: if(bool==1){ /* Otherwise we skip that wave/person */
5199: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5200: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5201: if(m >=firstpass && m <=lastpass){
5202: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5203: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5204: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5205: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5206: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5207: 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);
5208: exit(1);
5209: }
5210: if (s[m][i]>0 && s[m][i]<=nlstate) {
5211: /*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]]);*/
5212: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5213: prop[s[m][i]][iagemax+3] += weight[i];
5214: } /* end valid statuses */
5215: } /* end selection of dates */
5216: } /* end selection of waves */
5217: } /* end bool */
5218: } /* end wave */
5219: } /* end individual */
5220: for(i=iagemin; i <= iagemax+3; i++){
5221: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5222: posprop += prop[jk][i];
5223: }
5224:
5225: for(jk=1; jk <=nlstate ; jk++){
5226: if( i <= iagemax){
5227: if(posprop>=1.e-5){
5228: probs[i][jk][j1]= prop[jk][i]/posprop;
5229: } else{
1.288 brouard 5230: if(!first){
5231: first=1;
1.266 brouard 5232: 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]);
5233: }else{
1.288 brouard 5234: 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 5235: }
5236: }
5237: }
5238: }/* end jk */
5239: }/* end i */
1.222 brouard 5240: /*} *//* end i1 */
1.227 brouard 5241: } /* end j1 */
1.222 brouard 5242:
1.227 brouard 5243: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5244: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5245: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5246: } /* End of prevalence */
1.126 brouard 5247:
5248: /************* Waves Concatenation ***************/
5249:
5250: 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)
5251: {
1.298 brouard 5252: /* 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 5253: Death is a valid wave (if date is known).
5254: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5255: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5256: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5257: */
1.126 brouard 5258:
1.224 brouard 5259: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5260: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5261: double sum=0., jmean=0.;*/
1.224 brouard 5262: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5263: int j, k=0,jk, ju, jl;
5264: double sum=0.;
5265: first=0;
1.214 brouard 5266: firstwo=0;
1.217 brouard 5267: firsthree=0;
1.218 brouard 5268: firstfour=0;
1.164 brouard 5269: jmin=100000;
1.126 brouard 5270: jmax=-1;
5271: jmean=0.;
1.224 brouard 5272:
5273: /* Treating live states */
1.214 brouard 5274: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5275: mi=0; /* First valid wave */
1.227 brouard 5276: mli=0; /* Last valid wave */
1.309 brouard 5277: m=firstpass; /* Loop on waves */
5278: while(s[m][i] <= nlstate){ /* a live state or unknown state */
1.227 brouard 5279: 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 */
5280: mli=m-1;/* mw[++mi][i]=m-1; */
5281: }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 5282: 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 5283: mli=m;
1.224 brouard 5284: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5285: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5286: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5287: }
1.309 brouard 5288: else{ /* m = lastpass, eventual special issue with warning */
1.224 brouard 5289: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5290: break;
1.224 brouard 5291: #else
1.309 brouard 5292: 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 5293: if(firsthree == 0){
1.302 brouard 5294: 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 5295: firsthree=1;
5296: }
1.302 brouard 5297: 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 5298: mw[++mi][i]=m; /* Valid transition with unknown status */
1.227 brouard 5299: mli=m;
5300: }
5301: if(s[m][i]==-2){ /* Vital status is really unknown */
5302: nbwarn++;
1.309 brouard 5303: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */
1.227 brouard 5304: 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);
5305: 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);
5306: }
5307: break;
5308: }
5309: break;
1.224 brouard 5310: #endif
1.227 brouard 5311: }/* End m >= lastpass */
1.126 brouard 5312: }/* end while */
1.224 brouard 5313:
1.227 brouard 5314: /* 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 5315: /* After last pass */
1.224 brouard 5316: /* Treating death states */
1.214 brouard 5317: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5318: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5319: /* } */
1.126 brouard 5320: mi++; /* Death is another wave */
5321: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5322: /* Only death is a correct wave */
1.126 brouard 5323: mw[mi][i]=m;
1.257 brouard 5324: } /* else not in a death state */
1.224 brouard 5325: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5326: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5327: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.309 brouard 5328: 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 5329: nbwarn++;
5330: if(firstfiv==0){
1.309 brouard 5331: 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 5332: firstfiv=1;
5333: }else{
1.309 brouard 5334: 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 5335: }
1.309 brouard 5336: s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
5337: }else{ /* Month of Death occured afer last wave month, potential bias */
1.227 brouard 5338: nberr++;
5339: if(firstwo==0){
1.309 brouard 5340: 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 5341: firstwo=1;
5342: }
1.309 brouard 5343: 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 5344: }
1.257 brouard 5345: }else{ /* if date of interview is unknown */
1.227 brouard 5346: /* death is known but not confirmed by death status at any wave */
5347: if(firstfour==0){
1.309 brouard 5348: 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 5349: firstfour=1;
5350: }
1.309 brouard 5351: 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 5352: }
1.224 brouard 5353: } /* end if date of death is known */
5354: #endif
1.309 brouard 5355: wav[i]=mi; /* mi should be the last effective wave (or mli), */
5356: /* wav[i]=mw[mi][i]; */
1.126 brouard 5357: if(mi==0){
5358: nbwarn++;
5359: if(first==0){
1.227 brouard 5360: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5361: first=1;
1.126 brouard 5362: }
5363: if(first==1){
1.227 brouard 5364: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5365: }
5366: } /* end mi==0 */
5367: } /* End individuals */
1.214 brouard 5368: /* wav and mw are no more changed */
1.223 brouard 5369:
1.214 brouard 5370:
1.126 brouard 5371: for(i=1; i<=imx; i++){
5372: for(mi=1; mi<wav[i];mi++){
5373: if (stepm <=0)
1.227 brouard 5374: dh[mi][i]=1;
1.126 brouard 5375: else{
1.260 brouard 5376: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5377: if (agedc[i] < 2*AGESUP) {
5378: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5379: if(j==0) j=1; /* Survives at least one month after exam */
5380: else if(j<0){
5381: nberr++;
5382: 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]);
5383: j=1; /* Temporary Dangerous patch */
5384: 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);
5385: 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]);
5386: 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);
5387: }
5388: k=k+1;
5389: if (j >= jmax){
5390: jmax=j;
5391: ijmax=i;
5392: }
5393: if (j <= jmin){
5394: jmin=j;
5395: ijmin=i;
5396: }
5397: sum=sum+j;
5398: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5399: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5400: }
5401: }
5402: else{
5403: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5404: /* 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 5405:
1.227 brouard 5406: k=k+1;
5407: if (j >= jmax) {
5408: jmax=j;
5409: ijmax=i;
5410: }
5411: else if (j <= jmin){
5412: jmin=j;
5413: ijmin=i;
5414: }
5415: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5416: /*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]);*/
5417: if(j<0){
5418: nberr++;
5419: 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]);
5420: 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]);
5421: }
5422: sum=sum+j;
5423: }
5424: jk= j/stepm;
5425: jl= j -jk*stepm;
5426: ju= j -(jk+1)*stepm;
5427: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5428: if(jl==0){
5429: dh[mi][i]=jk;
5430: bh[mi][i]=0;
5431: }else{ /* We want a negative bias in order to only have interpolation ie
5432: * to avoid the price of an extra matrix product in likelihood */
5433: dh[mi][i]=jk+1;
5434: bh[mi][i]=ju;
5435: }
5436: }else{
5437: if(jl <= -ju){
5438: dh[mi][i]=jk;
5439: bh[mi][i]=jl; /* bias is positive if real duration
5440: * is higher than the multiple of stepm and negative otherwise.
5441: */
5442: }
5443: else{
5444: dh[mi][i]=jk+1;
5445: bh[mi][i]=ju;
5446: }
5447: if(dh[mi][i]==0){
5448: dh[mi][i]=1; /* At least one step */
5449: bh[mi][i]=ju; /* At least one step */
5450: /* 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);*/
5451: }
5452: } /* end if mle */
1.126 brouard 5453: }
5454: } /* end wave */
5455: }
5456: jmean=sum/k;
5457: 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 5458: 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 5459: }
1.126 brouard 5460:
5461: /*********** Tricode ****************************/
1.220 brouard 5462: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5463: {
5464: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5465: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5466: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5467: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5468: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5469: */
1.130 brouard 5470:
1.242 brouard 5471: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5472: int modmaxcovj=0; /* Modality max of covariates j */
5473: int cptcode=0; /* Modality max of covariates j */
5474: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5475:
5476:
1.242 brouard 5477: /* cptcoveff=0; */
5478: /* *cptcov=0; */
1.126 brouard 5479:
1.242 brouard 5480: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5481: for (k=1; k <= maxncov; k++)
5482: for(j=1; j<=2; j++)
5483: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5484:
1.242 brouard 5485: /* Loop on covariates without age and products and no quantitative variable */
5486: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5487: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5488: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5489: switch(Fixed[k]) {
5490: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5491: 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*/
5492: ij=(int)(covar[Tvar[k]][i]);
5493: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5494: * If product of Vn*Vm, still boolean *:
5495: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5496: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5497: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5498: modality of the nth covariate of individual i. */
5499: if (ij > modmaxcovj)
5500: modmaxcovj=ij;
5501: else if (ij < modmincovj)
5502: modmincovj=ij;
1.287 brouard 5503: if (ij <0 || ij >1 ){
5504: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5505: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5506: }
5507: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5508: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5509: exit(1);
5510: }else
5511: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5512: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5513: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5514: /* getting the maximum value of the modality of the covariate
5515: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5516: female ies 1, then modmaxcovj=1.
5517: */
5518: } /* end for loop on individuals i */
5519: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5520: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5521: cptcode=modmaxcovj;
5522: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5523: /*for (i=0; i<=cptcode; i++) {*/
5524: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5525: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5526: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5527: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5528: if( j != -1){
5529: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5530: covariate for which somebody answered excluding
5531: undefined. Usually 2: 0 and 1. */
5532: }
5533: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5534: covariate for which somebody answered including
5535: undefined. Usually 3: -1, 0 and 1. */
5536: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5537: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5538: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5539:
1.242 brouard 5540: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5541: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5542: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5543: /* modmincovj=3; modmaxcovj = 7; */
5544: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5545: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5546: /* defining two dummy variables: variables V1_1 and V1_2.*/
5547: /* nbcode[Tvar[j]][ij]=k; */
5548: /* nbcode[Tvar[j]][1]=0; */
5549: /* nbcode[Tvar[j]][2]=1; */
5550: /* nbcode[Tvar[j]][3]=2; */
5551: /* To be continued (not working yet). */
5552: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5553:
5554: /* 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*/
5555: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5556: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5557: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5558: /*, could be restored in the future */
5559: 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 5560: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5561: break;
5562: }
5563: ij++;
1.287 brouard 5564: 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 5565: cptcode = ij; /* New max modality for covar j */
5566: } /* end of loop on modality i=-1 to 1 or more */
5567: break;
5568: case 1: /* Testing on varying covariate, could be simple and
5569: * should look at waves or product of fixed *
5570: * varying. No time to test -1, assuming 0 and 1 only */
5571: ij=0;
5572: for(i=0; i<=1;i++){
5573: nbcode[Tvar[k]][++ij]=i;
5574: }
5575: break;
5576: default:
5577: break;
5578: } /* end switch */
5579: } /* end dummy test */
1.287 brouard 5580: } /* 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 5581:
5582: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5583: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5584: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5585: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5586: 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 */
5587: 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 */
5588: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5589: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5590:
5591: ij=0;
5592: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5593: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5594: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5595: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5596: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5597: /* If product not in single variable we don't print results */
5598: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5599: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5600: 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*/
5601: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5602: 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 */
5603: if(Fixed[k]!=0)
5604: anyvaryingduminmodel=1;
5605: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5606: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5607: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5608: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5609: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5610: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5611: }
5612: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5613: /* ij--; */
5614: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5615: *cptcov=ij; /*Number of total real effective covariates: effective
5616: * because they can be excluded from the model and real
5617: * if in the model but excluded because missing values, but how to get k from ij?*/
5618: for(j=ij+1; j<= cptcovt; j++){
5619: Tvaraff[j]=0;
5620: Tmodelind[j]=0;
5621: }
5622: for(j=ntveff+1; j<= cptcovt; j++){
5623: TmodelInvind[j]=0;
5624: }
5625: /* To be sorted */
5626: ;
5627: }
1.126 brouard 5628:
1.145 brouard 5629:
1.126 brouard 5630: /*********** Health Expectancies ****************/
5631:
1.235 brouard 5632: 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 5633:
5634: {
5635: /* Health expectancies, no variances */
1.164 brouard 5636: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5637: int nhstepma, nstepma; /* Decreasing with age */
5638: double age, agelim, hf;
5639: double ***p3mat;
5640: double eip;
5641:
1.238 brouard 5642: /* pstamp(ficreseij); */
1.126 brouard 5643: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5644: fprintf(ficreseij,"# Age");
5645: for(i=1; i<=nlstate;i++){
5646: for(j=1; j<=nlstate;j++){
5647: fprintf(ficreseij," e%1d%1d ",i,j);
5648: }
5649: fprintf(ficreseij," e%1d. ",i);
5650: }
5651: fprintf(ficreseij,"\n");
5652:
5653:
5654: if(estepm < stepm){
5655: printf ("Problem %d lower than %d\n",estepm, stepm);
5656: }
5657: else hstepm=estepm;
5658: /* We compute the life expectancy from trapezoids spaced every estepm months
5659: * This is mainly to measure the difference between two models: for example
5660: * if stepm=24 months pijx are given only every 2 years and by summing them
5661: * we are calculating an estimate of the Life Expectancy assuming a linear
5662: * progression in between and thus overestimating or underestimating according
5663: * to the curvature of the survival function. If, for the same date, we
5664: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5665: * to compare the new estimate of Life expectancy with the same linear
5666: * hypothesis. A more precise result, taking into account a more precise
5667: * curvature will be obtained if estepm is as small as stepm. */
5668:
5669: /* For example we decided to compute the life expectancy with the smallest unit */
5670: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5671: nhstepm is the number of hstepm from age to agelim
5672: nstepm is the number of stepm from age to agelin.
1.270 brouard 5673: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5674: and note for a fixed period like estepm months */
5675: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5676: survival function given by stepm (the optimization length). Unfortunately it
5677: means that if the survival funtion is printed only each two years of age and if
5678: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5679: results. So we changed our mind and took the option of the best precision.
5680: */
5681: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5682:
5683: agelim=AGESUP;
5684: /* If stepm=6 months */
5685: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5686: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5687:
5688: /* nhstepm age range expressed in number of stepm */
5689: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5690: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5691: /* if (stepm >= YEARM) hstepm=1;*/
5692: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5693: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5694:
5695: for (age=bage; age<=fage; age ++){
5696: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5697: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5698: /* if (stepm >= YEARM) hstepm=1;*/
5699: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5700:
5701: /* If stepm=6 months */
5702: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5703: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5704:
1.235 brouard 5705: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5706:
5707: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5708:
5709: printf("%d|",(int)age);fflush(stdout);
5710: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5711:
5712: /* Computing expectancies */
5713: for(i=1; i<=nlstate;i++)
5714: for(j=1; j<=nlstate;j++)
5715: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5716: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5717:
5718: /* 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]);*/
5719:
5720: }
5721:
5722: fprintf(ficreseij,"%3.0f",age );
5723: for(i=1; i<=nlstate;i++){
5724: eip=0;
5725: for(j=1; j<=nlstate;j++){
5726: eip +=eij[i][j][(int)age];
5727: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5728: }
5729: fprintf(ficreseij,"%9.4f", eip );
5730: }
5731: fprintf(ficreseij,"\n");
5732:
5733: }
5734: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5735: printf("\n");
5736: fprintf(ficlog,"\n");
5737:
5738: }
5739:
1.235 brouard 5740: 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 5741:
5742: {
5743: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5744: to initial status i, ei. .
1.126 brouard 5745: */
5746: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5747: int nhstepma, nstepma; /* Decreasing with age */
5748: double age, agelim, hf;
5749: double ***p3matp, ***p3matm, ***varhe;
5750: double **dnewm,**doldm;
5751: double *xp, *xm;
5752: double **gp, **gm;
5753: double ***gradg, ***trgradg;
5754: int theta;
5755:
5756: double eip, vip;
5757:
5758: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5759: xp=vector(1,npar);
5760: xm=vector(1,npar);
5761: dnewm=matrix(1,nlstate*nlstate,1,npar);
5762: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5763:
5764: pstamp(ficresstdeij);
5765: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5766: fprintf(ficresstdeij,"# Age");
5767: for(i=1; i<=nlstate;i++){
5768: for(j=1; j<=nlstate;j++)
5769: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5770: fprintf(ficresstdeij," e%1d. ",i);
5771: }
5772: fprintf(ficresstdeij,"\n");
5773:
5774: pstamp(ficrescveij);
5775: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5776: fprintf(ficrescveij,"# Age");
5777: for(i=1; i<=nlstate;i++)
5778: for(j=1; j<=nlstate;j++){
5779: cptj= (j-1)*nlstate+i;
5780: for(i2=1; i2<=nlstate;i2++)
5781: for(j2=1; j2<=nlstate;j2++){
5782: cptj2= (j2-1)*nlstate+i2;
5783: if(cptj2 <= cptj)
5784: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5785: }
5786: }
5787: fprintf(ficrescveij,"\n");
5788:
5789: if(estepm < stepm){
5790: printf ("Problem %d lower than %d\n",estepm, stepm);
5791: }
5792: else hstepm=estepm;
5793: /* We compute the life expectancy from trapezoids spaced every estepm months
5794: * This is mainly to measure the difference between two models: for example
5795: * if stepm=24 months pijx are given only every 2 years and by summing them
5796: * we are calculating an estimate of the Life Expectancy assuming a linear
5797: * progression in between and thus overestimating or underestimating according
5798: * to the curvature of the survival function. If, for the same date, we
5799: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5800: * to compare the new estimate of Life expectancy with the same linear
5801: * hypothesis. A more precise result, taking into account a more precise
5802: * curvature will be obtained if estepm is as small as stepm. */
5803:
5804: /* For example we decided to compute the life expectancy with the smallest unit */
5805: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5806: nhstepm is the number of hstepm from age to agelim
5807: nstepm is the number of stepm from age to agelin.
5808: Look at hpijx to understand the reason of that which relies in memory size
5809: and note for a fixed period like estepm months */
5810: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5811: survival function given by stepm (the optimization length). Unfortunately it
5812: means that if the survival funtion is printed only each two years of age and if
5813: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5814: results. So we changed our mind and took the option of the best precision.
5815: */
5816: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5817:
5818: /* If stepm=6 months */
5819: /* nhstepm age range expressed in number of stepm */
5820: agelim=AGESUP;
5821: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5822: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5823: /* if (stepm >= YEARM) hstepm=1;*/
5824: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5825:
5826: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5827: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5828: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5829: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5830: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5831: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5832:
5833: for (age=bage; age<=fage; age ++){
5834: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5835: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5836: /* if (stepm >= YEARM) hstepm=1;*/
5837: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5838:
1.126 brouard 5839: /* If stepm=6 months */
5840: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5841: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5842:
5843: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5844:
1.126 brouard 5845: /* Computing Variances of health expectancies */
5846: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5847: decrease memory allocation */
5848: for(theta=1; theta <=npar; theta++){
5849: for(i=1; i<=npar; i++){
1.222 brouard 5850: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5851: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5852: }
1.235 brouard 5853: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5854: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5855:
1.126 brouard 5856: for(j=1; j<= nlstate; j++){
1.222 brouard 5857: for(i=1; i<=nlstate; i++){
5858: for(h=0; h<=nhstepm-1; h++){
5859: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5860: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5861: }
5862: }
1.126 brouard 5863: }
1.218 brouard 5864:
1.126 brouard 5865: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5866: for(h=0; h<=nhstepm-1; h++){
5867: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5868: }
1.126 brouard 5869: }/* End theta */
5870:
5871:
5872: for(h=0; h<=nhstepm-1; h++)
5873: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5874: for(theta=1; theta <=npar; theta++)
5875: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5876:
1.218 brouard 5877:
1.222 brouard 5878: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5879: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5880: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5881:
1.222 brouard 5882: printf("%d|",(int)age);fflush(stdout);
5883: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5884: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5885: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5886: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5887: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5888: for(ij=1;ij<=nlstate*nlstate;ij++)
5889: for(ji=1;ji<=nlstate*nlstate;ji++)
5890: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5891: }
5892: }
1.218 brouard 5893:
1.126 brouard 5894: /* Computing expectancies */
1.235 brouard 5895: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5896: for(i=1; i<=nlstate;i++)
5897: for(j=1; j<=nlstate;j++)
1.222 brouard 5898: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5899: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5900:
1.222 brouard 5901: /* 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 5902:
1.222 brouard 5903: }
1.269 brouard 5904:
5905: /* Standard deviation of expectancies ij */
1.126 brouard 5906: fprintf(ficresstdeij,"%3.0f",age );
5907: for(i=1; i<=nlstate;i++){
5908: eip=0.;
5909: vip=0.;
5910: for(j=1; j<=nlstate;j++){
1.222 brouard 5911: eip += eij[i][j][(int)age];
5912: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5913: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5914: 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 5915: }
5916: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5917: }
5918: fprintf(ficresstdeij,"\n");
1.218 brouard 5919:
1.269 brouard 5920: /* Variance of expectancies ij */
1.126 brouard 5921: fprintf(ficrescveij,"%3.0f",age );
5922: for(i=1; i<=nlstate;i++)
5923: for(j=1; j<=nlstate;j++){
1.222 brouard 5924: cptj= (j-1)*nlstate+i;
5925: for(i2=1; i2<=nlstate;i2++)
5926: for(j2=1; j2<=nlstate;j2++){
5927: cptj2= (j2-1)*nlstate+i2;
5928: if(cptj2 <= cptj)
5929: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5930: }
1.126 brouard 5931: }
5932: fprintf(ficrescveij,"\n");
1.218 brouard 5933:
1.126 brouard 5934: }
5935: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5936: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5937: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5938: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5939: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5940: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5941: printf("\n");
5942: fprintf(ficlog,"\n");
1.218 brouard 5943:
1.126 brouard 5944: free_vector(xm,1,npar);
5945: free_vector(xp,1,npar);
5946: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5947: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5948: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5949: }
1.218 brouard 5950:
1.126 brouard 5951: /************ Variance ******************/
1.235 brouard 5952: 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 5953: {
1.279 brouard 5954: /** Variance of health expectancies
5955: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5956: * double **newm;
5957: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5958: */
1.218 brouard 5959:
5960: /* int movingaverage(); */
5961: double **dnewm,**doldm;
5962: double **dnewmp,**doldmp;
5963: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5964: int first=0;
1.218 brouard 5965: int k;
5966: double *xp;
1.279 brouard 5967: double **gp, **gm; /**< for var eij */
5968: double ***gradg, ***trgradg; /**< for var eij */
5969: double **gradgp, **trgradgp; /**< for var p point j */
5970: double *gpp, *gmp; /**< for var p point j */
5971: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5972: double ***p3mat;
5973: double age,agelim, hf;
5974: /* double ***mobaverage; */
5975: int theta;
5976: char digit[4];
5977: char digitp[25];
5978:
5979: char fileresprobmorprev[FILENAMELENGTH];
5980:
5981: if(popbased==1){
5982: if(mobilav!=0)
5983: strcpy(digitp,"-POPULBASED-MOBILAV_");
5984: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5985: }
5986: else
5987: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5988:
1.218 brouard 5989: /* if (mobilav!=0) { */
5990: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5991: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5992: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5993: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5994: /* } */
5995: /* } */
5996:
5997: strcpy(fileresprobmorprev,"PRMORPREV-");
5998: sprintf(digit,"%-d",ij);
5999: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
6000: strcat(fileresprobmorprev,digit); /* Tvar to be done */
6001: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
6002: strcat(fileresprobmorprev,fileresu);
6003: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
6004: printf("Problem with resultfile: %s\n", fileresprobmorprev);
6005: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
6006: }
6007: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6008: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
6009: pstamp(ficresprobmorprev);
6010: 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 6011: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
6012: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
6013: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
6014: }
6015: for(j=1;j<=cptcoveff;j++)
6016: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
6017: fprintf(ficresprobmorprev,"\n");
6018:
1.218 brouard 6019: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6020: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6021: fprintf(ficresprobmorprev," p.%-d SE",j);
6022: for(i=1; i<=nlstate;i++)
6023: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6024: }
6025: fprintf(ficresprobmorprev,"\n");
6026:
6027: fprintf(ficgp,"\n# Routine varevsij");
6028: fprintf(ficgp,"\nunset title \n");
6029: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6030: 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");
6031: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6032:
1.218 brouard 6033: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6034: pstamp(ficresvij);
6035: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6036: if(popbased==1)
6037: 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);
6038: else
6039: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6040: fprintf(ficresvij,"# Age");
6041: for(i=1; i<=nlstate;i++)
6042: for(j=1; j<=nlstate;j++)
6043: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6044: fprintf(ficresvij,"\n");
6045:
6046: xp=vector(1,npar);
6047: dnewm=matrix(1,nlstate,1,npar);
6048: doldm=matrix(1,nlstate,1,nlstate);
6049: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6050: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6051:
6052: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6053: gpp=vector(nlstate+1,nlstate+ndeath);
6054: gmp=vector(nlstate+1,nlstate+ndeath);
6055: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6056:
1.218 brouard 6057: if(estepm < stepm){
6058: printf ("Problem %d lower than %d\n",estepm, stepm);
6059: }
6060: else hstepm=estepm;
6061: /* For example we decided to compute the life expectancy with the smallest unit */
6062: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6063: nhstepm is the number of hstepm from age to agelim
6064: nstepm is the number of stepm from age to agelim.
6065: Look at function hpijx to understand why because of memory size limitations,
6066: we decided (b) to get a life expectancy respecting the most precise curvature of the
6067: survival function given by stepm (the optimization length). Unfortunately it
6068: means that if the survival funtion is printed every two years of age and if
6069: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6070: results. So we changed our mind and took the option of the best precision.
6071: */
6072: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6073: agelim = AGESUP;
6074: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6075: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6076: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6077: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6078: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6079: gp=matrix(0,nhstepm,1,nlstate);
6080: gm=matrix(0,nhstepm,1,nlstate);
6081:
6082:
6083: for(theta=1; theta <=npar; theta++){
6084: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6085: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6086: }
1.279 brouard 6087: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6088: * returns into prlim .
1.288 brouard 6089: */
1.242 brouard 6090: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6091:
6092: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6093: if (popbased==1) {
6094: if(mobilav ==0){
6095: for(i=1; i<=nlstate;i++)
6096: prlim[i][i]=probs[(int)age][i][ij];
6097: }else{ /* mobilav */
6098: for(i=1; i<=nlstate;i++)
6099: prlim[i][i]=mobaverage[(int)age][i][ij];
6100: }
6101: }
1.295 brouard 6102: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6103: */
6104: 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 6105: /**< 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 6106: * at horizon h in state j including mortality.
6107: */
1.218 brouard 6108: for(j=1; j<= nlstate; j++){
6109: for(h=0; h<=nhstepm; h++){
6110: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6111: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6112: }
6113: }
1.279 brouard 6114: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6115: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6116: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6117: */
6118: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6119: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6120: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6121: }
6122:
6123: /* Again with minus shift */
1.218 brouard 6124:
6125: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6126: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6127:
1.242 brouard 6128: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6129:
6130: if (popbased==1) {
6131: if(mobilav ==0){
6132: for(i=1; i<=nlstate;i++)
6133: prlim[i][i]=probs[(int)age][i][ij];
6134: }else{ /* mobilav */
6135: for(i=1; i<=nlstate;i++)
6136: prlim[i][i]=mobaverage[(int)age][i][ij];
6137: }
6138: }
6139:
1.235 brouard 6140: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6141:
6142: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6143: for(h=0; h<=nhstepm; h++){
6144: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6145: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6146: }
6147: }
6148: /* This for computing probability of death (h=1 means
6149: computed over hstepm matrices product = hstepm*stepm months)
6150: as a weighted average of prlim.
6151: */
6152: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6153: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6154: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6155: }
1.279 brouard 6156: /* end shifting computations */
6157:
6158: /**< Computing gradient matrix at horizon h
6159: */
1.218 brouard 6160: for(j=1; j<= nlstate; j++) /* vareij */
6161: for(h=0; h<=nhstepm; h++){
6162: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6163: }
1.279 brouard 6164: /**< Gradient of overall mortality p.3 (or p.j)
6165: */
6166: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6167: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6168: }
6169:
6170: } /* End theta */
1.279 brouard 6171:
6172: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6173: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6174:
6175: for(h=0; h<=nhstepm; h++) /* veij */
6176: for(j=1; j<=nlstate;j++)
6177: for(theta=1; theta <=npar; theta++)
6178: trgradg[h][j][theta]=gradg[h][theta][j];
6179:
6180: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6181: for(theta=1; theta <=npar; theta++)
6182: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6183: /**< as well as its transposed matrix
6184: */
1.218 brouard 6185:
6186: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6187: for(i=1;i<=nlstate;i++)
6188: for(j=1;j<=nlstate;j++)
6189: vareij[i][j][(int)age] =0.;
1.279 brouard 6190:
6191: /* Computing trgradg by matcov by gradg at age and summing over h
6192: * and k (nhstepm) formula 15 of article
6193: * Lievre-Brouard-Heathcote
6194: */
6195:
1.218 brouard 6196: for(h=0;h<=nhstepm;h++){
6197: for(k=0;k<=nhstepm;k++){
6198: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6199: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6200: for(i=1;i<=nlstate;i++)
6201: for(j=1;j<=nlstate;j++)
6202: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6203: }
6204: }
6205:
1.279 brouard 6206: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6207: * p.j overall mortality formula 49 but computed directly because
6208: * we compute the grad (wix pijx) instead of grad (pijx),even if
6209: * wix is independent of theta.
6210: */
1.218 brouard 6211: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6212: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6213: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6214: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6215: varppt[j][i]=doldmp[j][i];
6216: /* end ppptj */
6217: /* x centered again */
6218:
1.242 brouard 6219: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6220:
6221: if (popbased==1) {
6222: if(mobilav ==0){
6223: for(i=1; i<=nlstate;i++)
6224: prlim[i][i]=probs[(int)age][i][ij];
6225: }else{ /* mobilav */
6226: for(i=1; i<=nlstate;i++)
6227: prlim[i][i]=mobaverage[(int)age][i][ij];
6228: }
6229: }
6230:
6231: /* This for computing probability of death (h=1 means
6232: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6233: as a weighted average of prlim.
6234: */
1.235 brouard 6235: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6236: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6237: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6238: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6239: }
6240: /* end probability of death */
6241:
6242: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6243: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6244: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6245: for(i=1; i<=nlstate;i++){
6246: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6247: }
6248: }
6249: fprintf(ficresprobmorprev,"\n");
6250:
6251: fprintf(ficresvij,"%.0f ",age );
6252: for(i=1; i<=nlstate;i++)
6253: for(j=1; j<=nlstate;j++){
6254: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6255: }
6256: fprintf(ficresvij,"\n");
6257: free_matrix(gp,0,nhstepm,1,nlstate);
6258: free_matrix(gm,0,nhstepm,1,nlstate);
6259: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6260: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6261: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6262: } /* End age */
6263: free_vector(gpp,nlstate+1,nlstate+ndeath);
6264: free_vector(gmp,nlstate+1,nlstate+ndeath);
6265: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6266: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6267: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6268: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6269: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6270: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6271: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6272: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6273: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6274: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6275: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6276: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6277: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6278: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6279: 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);
6280: /* 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 6281: */
1.218 brouard 6282: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6283: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6284:
1.218 brouard 6285: free_vector(xp,1,npar);
6286: free_matrix(doldm,1,nlstate,1,nlstate);
6287: free_matrix(dnewm,1,nlstate,1,npar);
6288: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6289: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6290: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6291: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6292: fclose(ficresprobmorprev);
6293: fflush(ficgp);
6294: fflush(fichtm);
6295: } /* end varevsij */
1.126 brouard 6296:
6297: /************ Variance of prevlim ******************/
1.269 brouard 6298: 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 6299: {
1.205 brouard 6300: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6301: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6302:
1.268 brouard 6303: double **dnewmpar,**doldm;
1.126 brouard 6304: int i, j, nhstepm, hstepm;
6305: double *xp;
6306: double *gp, *gm;
6307: double **gradg, **trgradg;
1.208 brouard 6308: double **mgm, **mgp;
1.126 brouard 6309: double age,agelim;
6310: int theta;
6311:
6312: pstamp(ficresvpl);
1.288 brouard 6313: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6314: fprintf(ficresvpl,"# Age ");
6315: if(nresult >=1)
6316: fprintf(ficresvpl," Result# ");
1.126 brouard 6317: for(i=1; i<=nlstate;i++)
6318: fprintf(ficresvpl," %1d-%1d",i,i);
6319: fprintf(ficresvpl,"\n");
6320:
6321: xp=vector(1,npar);
1.268 brouard 6322: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6323: doldm=matrix(1,nlstate,1,nlstate);
6324:
6325: hstepm=1*YEARM; /* Every year of age */
6326: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6327: agelim = AGESUP;
6328: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6329: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6330: if (stepm >= YEARM) hstepm=1;
6331: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6332: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6333: mgp=matrix(1,npar,1,nlstate);
6334: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6335: gp=vector(1,nlstate);
6336: gm=vector(1,nlstate);
6337:
6338: for(theta=1; theta <=npar; theta++){
6339: for(i=1; i<=npar; i++){ /* Computes gradient */
6340: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6341: }
1.288 brouard 6342: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6343: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6344: /* else */
6345: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6346: for(i=1;i<=nlstate;i++){
1.126 brouard 6347: gp[i] = prlim[i][i];
1.208 brouard 6348: mgp[theta][i] = prlim[i][i];
6349: }
1.126 brouard 6350: for(i=1; i<=npar; i++) /* Computes gradient */
6351: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6352: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6353: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6354: /* else */
6355: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6356: for(i=1;i<=nlstate;i++){
1.126 brouard 6357: gm[i] = prlim[i][i];
1.208 brouard 6358: mgm[theta][i] = prlim[i][i];
6359: }
1.126 brouard 6360: for(i=1;i<=nlstate;i++)
6361: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6362: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6363: } /* End theta */
6364:
6365: trgradg =matrix(1,nlstate,1,npar);
6366:
6367: for(j=1; j<=nlstate;j++)
6368: for(theta=1; theta <=npar; theta++)
6369: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6370: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6371: /* printf("\nmgm mgp %d ",(int)age); */
6372: /* for(j=1; j<=nlstate;j++){ */
6373: /* printf(" %d ",j); */
6374: /* for(theta=1; theta <=npar; theta++) */
6375: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6376: /* printf("\n "); */
6377: /* } */
6378: /* } */
6379: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6380: /* printf("\n gradg %d ",(int)age); */
6381: /* for(j=1; j<=nlstate;j++){ */
6382: /* printf("%d ",j); */
6383: /* for(theta=1; theta <=npar; theta++) */
6384: /* printf("%d %lf ",theta,gradg[theta][j]); */
6385: /* printf("\n "); */
6386: /* } */
6387: /* } */
1.126 brouard 6388:
6389: for(i=1;i<=nlstate;i++)
6390: varpl[i][(int)age] =0.;
1.209 brouard 6391: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6392: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6393: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6394: }else{
1.268 brouard 6395: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6396: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6397: }
1.126 brouard 6398: for(i=1;i<=nlstate;i++)
6399: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6400:
6401: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6402: if(nresult >=1)
6403: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6404: for(i=1; i<=nlstate;i++){
1.126 brouard 6405: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6406: /* for(j=1;j<=nlstate;j++) */
6407: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6408: }
1.126 brouard 6409: fprintf(ficresvpl,"\n");
6410: free_vector(gp,1,nlstate);
6411: free_vector(gm,1,nlstate);
1.208 brouard 6412: free_matrix(mgm,1,npar,1,nlstate);
6413: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6414: free_matrix(gradg,1,npar,1,nlstate);
6415: free_matrix(trgradg,1,nlstate,1,npar);
6416: } /* End age */
6417:
6418: free_vector(xp,1,npar);
6419: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6420: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6421:
6422: }
6423:
6424:
6425: /************ Variance of backprevalence limit ******************/
1.269 brouard 6426: 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 6427: {
6428: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6429: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6430:
6431: double **dnewmpar,**doldm;
6432: int i, j, nhstepm, hstepm;
6433: double *xp;
6434: double *gp, *gm;
6435: double **gradg, **trgradg;
6436: double **mgm, **mgp;
6437: double age,agelim;
6438: int theta;
6439:
6440: pstamp(ficresvbl);
6441: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6442: fprintf(ficresvbl,"# Age ");
6443: if(nresult >=1)
6444: fprintf(ficresvbl," Result# ");
6445: for(i=1; i<=nlstate;i++)
6446: fprintf(ficresvbl," %1d-%1d",i,i);
6447: fprintf(ficresvbl,"\n");
6448:
6449: xp=vector(1,npar);
6450: dnewmpar=matrix(1,nlstate,1,npar);
6451: doldm=matrix(1,nlstate,1,nlstate);
6452:
6453: hstepm=1*YEARM; /* Every year of age */
6454: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6455: agelim = AGEINF;
6456: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6457: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6458: if (stepm >= YEARM) hstepm=1;
6459: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6460: gradg=matrix(1,npar,1,nlstate);
6461: mgp=matrix(1,npar,1,nlstate);
6462: mgm=matrix(1,npar,1,nlstate);
6463: gp=vector(1,nlstate);
6464: gm=vector(1,nlstate);
6465:
6466: for(theta=1; theta <=npar; theta++){
6467: for(i=1; i<=npar; i++){ /* Computes gradient */
6468: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6469: }
6470: if(mobilavproj > 0 )
6471: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6472: else
6473: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6474: for(i=1;i<=nlstate;i++){
6475: gp[i] = bprlim[i][i];
6476: mgp[theta][i] = bprlim[i][i];
6477: }
6478: for(i=1; i<=npar; i++) /* Computes gradient */
6479: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6480: if(mobilavproj > 0 )
6481: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6482: else
6483: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6484: for(i=1;i<=nlstate;i++){
6485: gm[i] = bprlim[i][i];
6486: mgm[theta][i] = bprlim[i][i];
6487: }
6488: for(i=1;i<=nlstate;i++)
6489: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6490: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6491: } /* End theta */
6492:
6493: trgradg =matrix(1,nlstate,1,npar);
6494:
6495: for(j=1; j<=nlstate;j++)
6496: for(theta=1; theta <=npar; theta++)
6497: trgradg[j][theta]=gradg[theta][j];
6498: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6499: /* printf("\nmgm mgp %d ",(int)age); */
6500: /* for(j=1; j<=nlstate;j++){ */
6501: /* printf(" %d ",j); */
6502: /* for(theta=1; theta <=npar; theta++) */
6503: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6504: /* printf("\n "); */
6505: /* } */
6506: /* } */
6507: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6508: /* printf("\n gradg %d ",(int)age); */
6509: /* for(j=1; j<=nlstate;j++){ */
6510: /* printf("%d ",j); */
6511: /* for(theta=1; theta <=npar; theta++) */
6512: /* printf("%d %lf ",theta,gradg[theta][j]); */
6513: /* printf("\n "); */
6514: /* } */
6515: /* } */
6516:
6517: for(i=1;i<=nlstate;i++)
6518: varbpl[i][(int)age] =0.;
6519: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6520: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6521: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6522: }else{
6523: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6524: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6525: }
6526: for(i=1;i<=nlstate;i++)
6527: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6528:
6529: fprintf(ficresvbl,"%.0f ",age );
6530: if(nresult >=1)
6531: fprintf(ficresvbl,"%d ",nres );
6532: for(i=1; i<=nlstate;i++)
6533: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6534: fprintf(ficresvbl,"\n");
6535: free_vector(gp,1,nlstate);
6536: free_vector(gm,1,nlstate);
6537: free_matrix(mgm,1,npar,1,nlstate);
6538: free_matrix(mgp,1,npar,1,nlstate);
6539: free_matrix(gradg,1,npar,1,nlstate);
6540: free_matrix(trgradg,1,nlstate,1,npar);
6541: } /* End age */
6542:
6543: free_vector(xp,1,npar);
6544: free_matrix(doldm,1,nlstate,1,npar);
6545: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6546:
6547: }
6548:
6549: /************ Variance of one-step probabilities ******************/
6550: 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 6551: {
6552: int i, j=0, k1, l1, tj;
6553: int k2, l2, j1, z1;
6554: int k=0, l;
6555: int first=1, first1, first2;
6556: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6557: double **dnewm,**doldm;
6558: double *xp;
6559: double *gp, *gm;
6560: double **gradg, **trgradg;
6561: double **mu;
6562: double age, cov[NCOVMAX+1];
6563: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6564: int theta;
6565: char fileresprob[FILENAMELENGTH];
6566: char fileresprobcov[FILENAMELENGTH];
6567: char fileresprobcor[FILENAMELENGTH];
6568: double ***varpij;
6569:
6570: strcpy(fileresprob,"PROB_");
6571: strcat(fileresprob,fileres);
6572: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6573: printf("Problem with resultfile: %s\n", fileresprob);
6574: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6575: }
6576: strcpy(fileresprobcov,"PROBCOV_");
6577: strcat(fileresprobcov,fileresu);
6578: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6579: printf("Problem with resultfile: %s\n", fileresprobcov);
6580: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6581: }
6582: strcpy(fileresprobcor,"PROBCOR_");
6583: strcat(fileresprobcor,fileresu);
6584: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6585: printf("Problem with resultfile: %s\n", fileresprobcor);
6586: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6587: }
6588: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6589: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6590: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6591: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6592: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6593: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6594: pstamp(ficresprob);
6595: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6596: fprintf(ficresprob,"# Age");
6597: pstamp(ficresprobcov);
6598: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6599: fprintf(ficresprobcov,"# Age");
6600: pstamp(ficresprobcor);
6601: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6602: fprintf(ficresprobcor,"# Age");
1.126 brouard 6603:
6604:
1.222 brouard 6605: for(i=1; i<=nlstate;i++)
6606: for(j=1; j<=(nlstate+ndeath);j++){
6607: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6608: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6609: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6610: }
6611: /* fprintf(ficresprob,"\n");
6612: fprintf(ficresprobcov,"\n");
6613: fprintf(ficresprobcor,"\n");
6614: */
6615: xp=vector(1,npar);
6616: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6617: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6618: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6619: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6620: first=1;
6621: fprintf(ficgp,"\n# Routine varprob");
6622: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6623: fprintf(fichtm,"\n");
6624:
1.288 brouard 6625: 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 6626: 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);
6627: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6628: and drawn. It helps understanding how is the covariance between two incidences.\
6629: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6630: 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 6631: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6632: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6633: standard deviations wide on each axis. <br>\
6634: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6635: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6636: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6637:
1.222 brouard 6638: cov[1]=1;
6639: /* tj=cptcoveff; */
1.225 brouard 6640: tj = (int) pow(2,cptcoveff);
1.222 brouard 6641: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6642: j1=0;
1.224 brouard 6643: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6644: if (cptcovn>0) {
6645: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6646: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6647: fprintf(ficresprob, "**********\n#\n");
6648: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6649: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6650: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6651:
1.222 brouard 6652: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6653: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6654: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6655:
6656:
1.222 brouard 6657: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6658: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6659: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6660:
1.222 brouard 6661: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6662: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6663: fprintf(ficresprobcor, "**********\n#");
6664: if(invalidvarcomb[j1]){
6665: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6666: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6667: continue;
6668: }
6669: }
6670: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6671: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6672: gp=vector(1,(nlstate)*(nlstate+ndeath));
6673: gm=vector(1,(nlstate)*(nlstate+ndeath));
6674: for (age=bage; age<=fage; age ++){
6675: cov[2]=age;
6676: if(nagesqr==1)
6677: cov[3]= age*age;
6678: for (k=1; k<=cptcovn;k++) {
6679: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6680: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6681: * 1 1 1 1 1
6682: * 2 2 1 1 1
6683: * 3 1 2 1 1
6684: */
6685: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6686: }
6687: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6688: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6689: for (k=1; k<=cptcovprod;k++)
6690: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6691:
6692:
1.222 brouard 6693: for(theta=1; theta <=npar; theta++){
6694: for(i=1; i<=npar; i++)
6695: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6696:
1.222 brouard 6697: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6698:
1.222 brouard 6699: k=0;
6700: for(i=1; i<= (nlstate); i++){
6701: for(j=1; j<=(nlstate+ndeath);j++){
6702: k=k+1;
6703: gp[k]=pmmij[i][j];
6704: }
6705: }
1.220 brouard 6706:
1.222 brouard 6707: for(i=1; i<=npar; i++)
6708: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6709:
1.222 brouard 6710: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6711: k=0;
6712: for(i=1; i<=(nlstate); i++){
6713: for(j=1; j<=(nlstate+ndeath);j++){
6714: k=k+1;
6715: gm[k]=pmmij[i][j];
6716: }
6717: }
1.220 brouard 6718:
1.222 brouard 6719: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6720: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6721: }
1.126 brouard 6722:
1.222 brouard 6723: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6724: for(theta=1; theta <=npar; theta++)
6725: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6726:
1.222 brouard 6727: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6728: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6729:
1.222 brouard 6730: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6731:
1.222 brouard 6732: k=0;
6733: for(i=1; i<=(nlstate); i++){
6734: for(j=1; j<=(nlstate+ndeath);j++){
6735: k=k+1;
6736: mu[k][(int) age]=pmmij[i][j];
6737: }
6738: }
6739: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6740: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6741: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6742:
1.222 brouard 6743: /*printf("\n%d ",(int)age);
6744: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6745: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6746: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6747: }*/
1.220 brouard 6748:
1.222 brouard 6749: fprintf(ficresprob,"\n%d ",(int)age);
6750: fprintf(ficresprobcov,"\n%d ",(int)age);
6751: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6752:
1.222 brouard 6753: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6754: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6755: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6756: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6757: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6758: }
6759: i=0;
6760: for (k=1; k<=(nlstate);k++){
6761: for (l=1; l<=(nlstate+ndeath);l++){
6762: i++;
6763: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6764: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6765: for (j=1; j<=i;j++){
6766: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6767: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6768: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6769: }
6770: }
6771: }/* end of loop for state */
6772: } /* end of loop for age */
6773: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6774: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6775: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6776: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6777:
6778: /* Confidence intervalle of pij */
6779: /*
6780: fprintf(ficgp,"\nunset parametric;unset label");
6781: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6782: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6783: 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);
6784: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6785: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6786: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6787: */
6788:
6789: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6790: first1=1;first2=2;
6791: for (k2=1; k2<=(nlstate);k2++){
6792: for (l2=1; l2<=(nlstate+ndeath);l2++){
6793: if(l2==k2) continue;
6794: j=(k2-1)*(nlstate+ndeath)+l2;
6795: for (k1=1; k1<=(nlstate);k1++){
6796: for (l1=1; l1<=(nlstate+ndeath);l1++){
6797: if(l1==k1) continue;
6798: i=(k1-1)*(nlstate+ndeath)+l1;
6799: if(i<=j) continue;
6800: for (age=bage; age<=fage; age ++){
6801: if ((int)age %5==0){
6802: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6803: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6804: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6805: mu1=mu[i][(int) age]/stepm*YEARM ;
6806: mu2=mu[j][(int) age]/stepm*YEARM;
6807: c12=cv12/sqrt(v1*v2);
6808: /* Computing eigen value of matrix of covariance */
6809: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6810: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6811: if ((lc2 <0) || (lc1 <0) ){
6812: if(first2==1){
6813: first1=0;
6814: 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);
6815: }
6816: 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);
6817: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6818: /* lc2=fabs(lc2); */
6819: }
1.220 brouard 6820:
1.222 brouard 6821: /* Eigen vectors */
1.280 brouard 6822: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6823: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6824: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6825: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6826: }else
6827: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6828: /*v21=sqrt(1.-v11*v11); *//* error */
6829: v21=(lc1-v1)/cv12*v11;
6830: v12=-v21;
6831: v22=v11;
6832: tnalp=v21/v11;
6833: if(first1==1){
6834: first1=0;
6835: 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);
6836: }
6837: 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);
6838: /*printf(fignu*/
6839: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6840: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6841: if(first==1){
6842: first=0;
6843: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6844: fprintf(ficgp,"\nset parametric;unset label");
6845: 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);
6846: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6847: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6848: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6849: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6850: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6851: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6852: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6853: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6854: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6855: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6856: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6857: 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 6858: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6859: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6860: }else{
6861: first=0;
6862: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6863: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6864: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6865: 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 6866: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6867: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6868: }/* if first */
6869: } /* age mod 5 */
6870: } /* end loop age */
6871: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6872: first=1;
6873: } /*l12 */
6874: } /* k12 */
6875: } /*l1 */
6876: }/* k1 */
6877: } /* loop on combination of covariates j1 */
6878: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6879: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6880: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6881: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6882: free_vector(xp,1,npar);
6883: fclose(ficresprob);
6884: fclose(ficresprobcov);
6885: fclose(ficresprobcor);
6886: fflush(ficgp);
6887: fflush(fichtmcov);
6888: }
1.126 brouard 6889:
6890:
6891: /******************* Printing html file ***********/
1.201 brouard 6892: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6893: int lastpass, int stepm, int weightopt, char model[],\
6894: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6895: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6896: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6897: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6898: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6899:
6900: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6901: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6902: </ul>");
1.237 brouard 6903: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6904: </ul>", model);
1.214 brouard 6905: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6906: 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",
6907: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6908: 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 6909: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6910: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6911: fprintf(fichtm,"\
6912: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6913: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6914: fprintf(fichtm,"\
1.217 brouard 6915: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6916: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6917: fprintf(fichtm,"\
1.288 brouard 6918: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6919: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6920: fprintf(fichtm,"\
1.288 brouard 6921: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6922: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6923: fprintf(fichtm,"\
1.211 brouard 6924: - (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 6925: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6926: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6927: if(prevfcast==1){
6928: fprintf(fichtm,"\
6929: - Prevalence projections by age and states: \
1.201 brouard 6930: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6931: }
1.126 brouard 6932:
6933:
1.225 brouard 6934: m=pow(2,cptcoveff);
1.222 brouard 6935: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6936:
1.264 brouard 6937: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6938:
6939: jj1=0;
6940:
6941: fprintf(fichtm," \n<ul>");
6942: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6943: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6944: if(m != 1 && TKresult[nres]!= k1)
6945: continue;
6946: jj1++;
6947: if (cptcovn > 0) {
6948: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6949: for (cpt=1; cpt<=cptcoveff;cpt++){
6950: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6951: }
6952: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6953: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6954: }
6955: fprintf(fichtm,"\">");
6956:
6957: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6958: fprintf(fichtm,"************ Results for covariates");
6959: for (cpt=1; cpt<=cptcoveff;cpt++){
6960: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6961: }
6962: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6963: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6964: }
6965: if(invalidvarcomb[k1]){
6966: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6967: continue;
6968: }
6969: fprintf(fichtm,"</a></li>");
6970: } /* cptcovn >0 */
6971: }
6972: fprintf(fichtm," \n</ul>");
6973:
1.222 brouard 6974: jj1=0;
1.237 brouard 6975:
6976: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6977: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6978: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6979: continue;
1.220 brouard 6980:
1.222 brouard 6981: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6982: jj1++;
6983: if (cptcovn > 0) {
1.264 brouard 6984: fprintf(fichtm,"\n<p><a name=\"rescov");
6985: for (cpt=1; cpt<=cptcoveff;cpt++){
6986: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6987: }
6988: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6989: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6990: }
6991: fprintf(fichtm,"\"</a>");
6992:
1.222 brouard 6993: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6994: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6995: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6996: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6997: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6998: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6999: }
1.237 brouard 7000: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7001: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7002: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
7003: }
7004:
1.230 brouard 7005: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 7006: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
7007: if(invalidvarcomb[k1]){
7008: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
7009: printf("\nCombination (%d) ignored because no cases \n",k1);
7010: continue;
7011: }
7012: }
7013: /* aij, bij */
1.259 brouard 7014: 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 7015: <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 7016: /* Pij */
1.241 brouard 7017: 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> \
7018: <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 7019: /* Quasi-incidences */
7020: 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 7021: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7022: 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 7023: 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> \
7024: <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 7025: /* Survival functions (period) in state j */
7026: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7027: 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 7028: <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 7029: }
7030: /* State specific survival functions (period) */
7031: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7032: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7033: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7034: <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 7035: }
1.288 brouard 7036: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7037: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7038: 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> \
7039: <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 7040: }
1.296 brouard 7041: if(prevbcast==1){
1.288 brouard 7042: /* Backward prevalence in each health state */
1.222 brouard 7043: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7044: 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 7045: <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 7046: }
1.217 brouard 7047: }
1.222 brouard 7048: if(prevfcast==1){
1.288 brouard 7049: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7050: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7051: 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><br> \
1.296 brouard 7052: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 7053: }
7054: }
1.296 brouard 7055: if(prevbcast==1){
1.268 brouard 7056: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7057: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7058: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7059: 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 \
7060: 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) \
7061: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7062: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
1.268 brouard 7063: }
7064: }
1.220 brouard 7065:
1.222 brouard 7066: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7067: 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> <br> \
7068: <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.222 brouard 7069: }
7070: /* } /\* end i1 *\/ */
7071: }/* End k1 */
7072: fprintf(fichtm,"</ul>");
1.126 brouard 7073:
1.222 brouard 7074: fprintf(fichtm,"\
1.126 brouard 7075: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7076: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7077: - 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 7078: But because parameters are usually highly correlated (a higher incidence of disability \
7079: and a higher incidence of recovery can give very close observed transition) it might \
7080: be very useful to look not only at linear confidence intervals estimated from the \
7081: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7082: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7083: covariance matrix of the one-step probabilities. \
7084: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7085:
1.222 brouard 7086: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7087: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7088: fprintf(fichtm,"\
1.126 brouard 7089: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7090: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7091:
1.222 brouard 7092: fprintf(fichtm,"\
1.126 brouard 7093: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7094: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7095: fprintf(fichtm,"\
1.126 brouard 7096: - 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): \
7097: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7098: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7099: fprintf(fichtm,"\
1.126 brouard 7100: - (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): \
7101: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7102: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7103: fprintf(fichtm,"\
1.288 brouard 7104: - 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 7105: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7106: fprintf(fichtm,"\
1.128 brouard 7107: - 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 7108: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7109: fprintf(fichtm,"\
1.288 brouard 7110: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7111: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7112:
7113: /* if(popforecast==1) fprintf(fichtm,"\n */
7114: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7115: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7116: /* <br>",fileres,fileres,fileres,fileres); */
7117: /* else */
7118: /* 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 7119: fflush(fichtm);
7120: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7121:
1.225 brouard 7122: m=pow(2,cptcoveff);
1.222 brouard 7123: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7124:
1.222 brouard 7125: jj1=0;
1.237 brouard 7126:
1.241 brouard 7127: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7128: for(k1=1; k1<=m;k1++){
1.253 brouard 7129: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7130: continue;
1.222 brouard 7131: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7132: jj1++;
1.126 brouard 7133: if (cptcovn > 0) {
7134: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7135: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7136: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7137: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7138: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7139: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7140: }
7141:
1.126 brouard 7142: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7143:
1.222 brouard 7144: if(invalidvarcomb[k1]){
7145: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7146: continue;
7147: }
1.126 brouard 7148: }
7149: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7150: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7151: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
1.258 brouard 7152: <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
1.126 brouard 7153: }
7154: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7155: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7156: true period expectancies (those weighted with period prevalences are also\
7157: drawn in addition to the population based expectancies computed using\
1.241 brouard 7158: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7159: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7160: /* } /\* end i1 *\/ */
7161: }/* End k1 */
1.241 brouard 7162: }/* End nres */
1.222 brouard 7163: fprintf(fichtm,"</ul>");
7164: fflush(fichtm);
1.126 brouard 7165: }
7166:
7167: /******************* Gnuplot file **************/
1.296 brouard 7168: 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 7169:
7170: char dirfileres[132],optfileres[132];
1.264 brouard 7171: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7172: 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 7173: int lv=0, vlv=0, kl=0;
1.130 brouard 7174: int ng=0;
1.201 brouard 7175: int vpopbased;
1.223 brouard 7176: int ioffset; /* variable offset for columns */
1.270 brouard 7177: int iyearc=1; /* variable column for year of projection */
7178: int iagec=1; /* variable column for age of projection */
1.235 brouard 7179: int nres=0; /* Index of resultline */
1.266 brouard 7180: int istart=1; /* For starting graphs in projections */
1.219 brouard 7181:
1.126 brouard 7182: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7183: /* printf("Problem with file %s",optionfilegnuplot); */
7184: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7185: /* } */
7186:
7187: /*#ifdef windows */
7188: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7189: /*#endif */
1.225 brouard 7190: m=pow(2,cptcoveff);
1.126 brouard 7191:
1.274 brouard 7192: /* diagram of the model */
7193: fprintf(ficgp,"\n#Diagram of the model \n");
7194: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7195: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7196: 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);
7197:
7198: 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);
7199: fprintf(ficgp,"\n#show arrow\nunset label\n");
7200: 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);
7201: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7202: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7203: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7204: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7205:
1.202 brouard 7206: /* Contribution to likelihood */
7207: /* Plot the probability implied in the likelihood */
1.223 brouard 7208: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7209: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7210: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7211: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7212: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7213: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7214: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7215: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7216: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7217: 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));
7218: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7219: 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));
7220: for (i=1; i<= nlstate ; i ++) {
7221: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7222: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7223: 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);
7224: for (j=2; j<= nlstate+ndeath ; j ++) {
7225: 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);
7226: }
7227: fprintf(ficgp,";\nset out; unset ylabel;\n");
7228: }
7229: /* 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 */
7230: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7231: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7232: fprintf(ficgp,"\nset out;unset log\n");
7233: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7234:
1.126 brouard 7235: strcpy(dirfileres,optionfilefiname);
7236: strcpy(optfileres,"vpl");
1.223 brouard 7237: /* 1eme*/
1.238 brouard 7238: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7239: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7240: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7241: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7242: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7243: continue;
7244: /* We are interested in selected combination by the resultline */
1.246 brouard 7245: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7246: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7247: strcpy(gplotlabel,"(");
1.238 brouard 7248: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7249: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7250: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7251: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7252: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7253: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7254: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7255: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7256: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7257: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7258: }
7259: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7260: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7261: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7262: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7263: }
7264: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7265: /* printf("\n#\n"); */
1.238 brouard 7266: fprintf(ficgp,"\n#\n");
7267: if(invalidvarcomb[k1]){
1.260 brouard 7268: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7269: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7270: continue;
7271: }
1.235 brouard 7272:
1.241 brouard 7273: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7274: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7275: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7276: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7277: 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);
7278: /* 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); */
7279: /* k1-1 error should be nres-1*/
1.238 brouard 7280: for (i=1; i<= nlstate ; i ++) {
7281: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7282: else fprintf(ficgp," %%*lf (%%*lf)");
7283: }
1.288 brouard 7284: 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 7285: for (i=1; i<= nlstate ; i ++) {
7286: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7287: else fprintf(ficgp," %%*lf (%%*lf)");
7288: }
1.260 brouard 7289: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7290: for (i=1; i<= nlstate ; i ++) {
7291: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7292: else fprintf(ficgp," %%*lf (%%*lf)");
7293: }
1.265 brouard 7294: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7295:
7296: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7297: if(cptcoveff ==0){
1.271 brouard 7298: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7299: }else{
7300: kl=0;
7301: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7302: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7303: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7304: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7305: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7306: vlv= nbcode[Tvaraff[k]][lv];
7307: kl++;
7308: /* 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 *\/ */
7309: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7310: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7311: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7312: if(k==cptcoveff){
7313: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7314: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7315: }else{
7316: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7317: kl++;
7318: }
7319: } /* end covariate */
7320: } /* end if no covariate */
7321:
1.296 brouard 7322: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7323: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7324: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7325: if(cptcoveff ==0){
1.245 brouard 7326: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7327: }else{
7328: kl=0;
7329: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7330: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7331: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7332: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7333: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7334: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7335: kl++;
1.238 brouard 7336: /* 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 *\/ */
7337: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7338: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7339: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7340: if(k==cptcoveff){
1.245 brouard 7341: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7342: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7343: }else{
7344: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7345: kl++;
7346: }
7347: } /* end covariate */
7348: } /* end if no covariate */
1.296 brouard 7349: if(prevbcast == 1){
1.268 brouard 7350: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7351: /* k1-1 error should be nres-1*/
7352: for (i=1; i<= nlstate ; i ++) {
7353: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7354: else fprintf(ficgp," %%*lf (%%*lf)");
7355: }
1.271 brouard 7356: 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 7357: for (i=1; i<= nlstate ; i ++) {
7358: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7359: else fprintf(ficgp," %%*lf (%%*lf)");
7360: }
1.276 brouard 7361: 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 7362: for (i=1; i<= nlstate ; i ++) {
7363: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7364: else fprintf(ficgp," %%*lf (%%*lf)");
7365: }
1.274 brouard 7366: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7367: } /* end if backprojcast */
1.296 brouard 7368: } /* end if prevbcast */
1.276 brouard 7369: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7370: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7371: } /* nres */
1.201 brouard 7372: } /* k1 */
7373: } /* cpt */
1.235 brouard 7374:
7375:
1.126 brouard 7376: /*2 eme*/
1.238 brouard 7377: for (k1=1; k1<= m ; k1 ++){
7378: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7379: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7380: continue;
7381: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7382: strcpy(gplotlabel,"(");
1.238 brouard 7383: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7384: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7385: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7386: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7387: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7388: vlv= nbcode[Tvaraff[k]][lv];
7389: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7390: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7391: }
1.237 brouard 7392: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7393: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7394: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7395: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7396: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7397: }
1.264 brouard 7398: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7399: fprintf(ficgp,"\n#\n");
1.223 brouard 7400: if(invalidvarcomb[k1]){
7401: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7402: continue;
7403: }
1.219 brouard 7404:
1.241 brouard 7405: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7406: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7407: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7408: if(vpopbased==0){
1.238 brouard 7409: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7410: }else
1.238 brouard 7411: fprintf(ficgp,"\nreplot ");
7412: for (i=1; i<= nlstate+1 ; i ++) {
7413: k=2*i;
1.261 brouard 7414: 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 7415: for (j=1; j<= nlstate+1 ; j ++) {
7416: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7417: else fprintf(ficgp," %%*lf (%%*lf)");
7418: }
7419: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7420: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7421: 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 7422: for (j=1; j<= nlstate+1 ; j ++) {
7423: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7424: else fprintf(ficgp," %%*lf (%%*lf)");
7425: }
7426: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7427: 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 7428: for (j=1; j<= nlstate+1 ; j ++) {
7429: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7430: else fprintf(ficgp," %%*lf (%%*lf)");
7431: }
7432: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7433: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7434: } /* state */
7435: } /* vpopbased */
1.264 brouard 7436: 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 7437: } /* end nres */
7438: } /* k1 end 2 eme*/
7439:
7440:
7441: /*3eme*/
7442: for (k1=1; k1<= m ; k1 ++){
7443: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7444: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7445: continue;
7446:
7447: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7448: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7449: strcpy(gplotlabel,"(");
1.238 brouard 7450: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7451: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7452: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7453: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7454: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7455: vlv= nbcode[Tvaraff[k]][lv];
7456: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7457: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7458: }
7459: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7460: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7461: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7462: }
1.264 brouard 7463: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7464: fprintf(ficgp,"\n#\n");
7465: if(invalidvarcomb[k1]){
7466: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7467: continue;
7468: }
7469:
7470: /* k=2+nlstate*(2*cpt-2); */
7471: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7472: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7473: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7474: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7475: 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 7476: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7477: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7478: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7479: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7480: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7481: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7482:
1.238 brouard 7483: */
7484: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7485: 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 7486: /* 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 7487:
1.238 brouard 7488: }
1.261 brouard 7489: 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 7490: }
1.264 brouard 7491: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7492: } /* end nres */
7493: } /* end kl 3eme */
1.126 brouard 7494:
1.223 brouard 7495: /* 4eme */
1.201 brouard 7496: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7497: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7498: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7499: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7500: continue;
1.238 brouard 7501: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7502: strcpy(gplotlabel,"(");
1.238 brouard 7503: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7504: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7505: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7506: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7507: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7508: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7509: vlv= nbcode[Tvaraff[k]][lv];
7510: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7511: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7512: }
7513: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7514: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7515: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7516: }
1.264 brouard 7517: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7518: fprintf(ficgp,"\n#\n");
7519: if(invalidvarcomb[k1]){
7520: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7521: continue;
1.223 brouard 7522: }
1.238 brouard 7523:
1.241 brouard 7524: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7525: 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 7526: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7527: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7528: k=3;
7529: for (i=1; i<= nlstate ; i ++){
7530: if(i==1){
7531: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7532: }else{
7533: fprintf(ficgp,", '' ");
7534: }
7535: l=(nlstate+ndeath)*(i-1)+1;
7536: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7537: for (j=2; j<= nlstate+ndeath ; j ++)
7538: fprintf(ficgp,"+$%d",k+l+j-1);
7539: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7540: } /* nlstate */
1.264 brouard 7541: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7542: } /* end cpt state*/
7543: } /* end nres */
7544: } /* end covariate k1 */
7545:
1.220 brouard 7546: /* 5eme */
1.201 brouard 7547: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7548: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7549: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7550: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7551: continue;
1.238 brouard 7552: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7553: strcpy(gplotlabel,"(");
1.238 brouard 7554: 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);
7555: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7556: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7557: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7558: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7559: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7560: vlv= nbcode[Tvaraff[k]][lv];
7561: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7562: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7563: }
7564: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7565: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7566: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7567: }
1.264 brouard 7568: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7569: fprintf(ficgp,"\n#\n");
7570: if(invalidvarcomb[k1]){
7571: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7572: continue;
7573: }
1.227 brouard 7574:
1.241 brouard 7575: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7576: 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 7577: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7578: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7579: k=3;
7580: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7581: if(j==1)
7582: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7583: else
7584: fprintf(ficgp,", '' ");
7585: l=(nlstate+ndeath)*(cpt-1) +j;
7586: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7587: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7588: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7589: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7590: } /* nlstate */
7591: fprintf(ficgp,", '' ");
7592: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7593: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7594: l=(nlstate+ndeath)*(cpt-1) +j;
7595: if(j < nlstate)
7596: fprintf(ficgp,"$%d +",k+l);
7597: else
7598: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7599: }
1.264 brouard 7600: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7601: } /* end cpt state*/
7602: } /* end covariate */
7603: } /* end nres */
1.227 brouard 7604:
1.220 brouard 7605: /* 6eme */
1.202 brouard 7606: /* CV preval stable (period) for each covariate */
1.237 brouard 7607: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7608: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7609: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7610: continue;
1.255 brouard 7611: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7612: strcpy(gplotlabel,"(");
1.288 brouard 7613: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7614: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7615: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7616: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7617: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7618: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7619: vlv= nbcode[Tvaraff[k]][lv];
7620: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7621: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7622: }
1.237 brouard 7623: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7624: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7625: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7626: }
1.264 brouard 7627: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7628: fprintf(ficgp,"\n#\n");
1.223 brouard 7629: if(invalidvarcomb[k1]){
1.227 brouard 7630: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7631: continue;
1.223 brouard 7632: }
1.227 brouard 7633:
1.241 brouard 7634: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7635: 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 7636: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7637: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7638: k=3; /* Offset */
1.255 brouard 7639: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7640: if(i==1)
7641: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7642: else
7643: fprintf(ficgp,", '' ");
1.255 brouard 7644: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7645: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7646: for (j=2; j<= nlstate ; j ++)
7647: fprintf(ficgp,"+$%d",k+l+j-1);
7648: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7649: } /* nlstate */
1.264 brouard 7650: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7651: } /* end cpt state*/
7652: } /* end covariate */
1.227 brouard 7653:
7654:
1.220 brouard 7655: /* 7eme */
1.296 brouard 7656: if(prevbcast == 1){
1.288 brouard 7657: /* CV backward prevalence for each covariate */
1.237 brouard 7658: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7659: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7660: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7661: continue;
1.268 brouard 7662: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7663: strcpy(gplotlabel,"(");
1.288 brouard 7664: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7665: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7666: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7667: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7668: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7669: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7670: vlv= nbcode[Tvaraff[k]][lv];
7671: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7672: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7673: }
1.237 brouard 7674: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7675: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7676: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7677: }
1.264 brouard 7678: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7679: fprintf(ficgp,"\n#\n");
7680: if(invalidvarcomb[k1]){
7681: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7682: continue;
7683: }
7684:
1.241 brouard 7685: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7686: 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 7687: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7688: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7689: k=3; /* Offset */
1.268 brouard 7690: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7691: if(i==1)
7692: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7693: else
7694: fprintf(ficgp,", '' ");
7695: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7696: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7697: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7698: /* 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 7699: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7700: /* for (j=2; j<= nlstate ; j ++) */
7701: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7702: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7703: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7704: } /* nlstate */
1.264 brouard 7705: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7706: } /* end cpt state*/
7707: } /* end covariate */
1.296 brouard 7708: } /* End if prevbcast */
1.218 brouard 7709:
1.223 brouard 7710: /* 8eme */
1.218 brouard 7711: if(prevfcast==1){
1.288 brouard 7712: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7713:
1.237 brouard 7714: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7715: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7716: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7717: continue;
1.211 brouard 7718: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7719: strcpy(gplotlabel,"(");
1.288 brouard 7720: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7721: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7722: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7723: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7724: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7725: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7726: vlv= nbcode[Tvaraff[k]][lv];
7727: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7728: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7729: }
1.237 brouard 7730: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7731: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7732: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7733: }
1.264 brouard 7734: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7735: fprintf(ficgp,"\n#\n");
7736: if(invalidvarcomb[k1]){
7737: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7738: continue;
7739: }
7740:
7741: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7742: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7743: 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 7744: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7745: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7746:
7747: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7748: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7749: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7750: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7751: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7752: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7753: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7754: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7755: if(i==istart){
1.227 brouard 7756: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7757: }else{
7758: fprintf(ficgp,",\\\n '' ");
7759: }
7760: if(cptcoveff ==0){ /* No covariate */
7761: ioffset=2; /* Age is in 2 */
7762: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7763: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7764: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7765: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7766: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7767: if(i==nlstate+1){
1.270 brouard 7768: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7769: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7770: fprintf(ficgp,",\\\n '' ");
7771: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7772: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7773: offyear, \
1.268 brouard 7774: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7775: }else
1.227 brouard 7776: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7777: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7778: }else{ /* more than 2 covariates */
1.270 brouard 7779: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7780: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7781: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7782: iyearc=ioffset-1;
7783: iagec=ioffset;
1.227 brouard 7784: fprintf(ficgp," u %d:(",ioffset);
7785: kl=0;
7786: strcpy(gplotcondition,"(");
7787: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7788: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7789: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7790: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7791: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7792: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7793: kl++;
7794: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7795: kl++;
7796: if(k <cptcoveff && cptcoveff>1)
7797: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7798: }
7799: strcpy(gplotcondition+strlen(gplotcondition),")");
7800: /* 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 *\/ */
7801: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7802: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7803: /* '' 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*/
7804: if(i==nlstate+1){
1.270 brouard 7805: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7806: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7807: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7808: fprintf(ficgp," u %d:(",iagec);
7809: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7810: iyearc, iagec, offyear, \
7811: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7812: /* '' 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 7813: }else{
7814: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7815: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7816: }
7817: } /* end if covariate */
7818: } /* nlstate */
1.264 brouard 7819: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7820: } /* end cpt state*/
7821: } /* end covariate */
7822: } /* End if prevfcast */
1.227 brouard 7823:
1.296 brouard 7824: if(prevbcast==1){
1.268 brouard 7825: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7826:
7827: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7828: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7829: if(m != 1 && TKresult[nres]!= k1)
7830: continue;
7831: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7832: strcpy(gplotlabel,"(");
7833: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7834: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7835: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7836: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7837: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7838: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7839: vlv= nbcode[Tvaraff[k]][lv];
7840: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7841: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7842: }
7843: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7844: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7845: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7846: }
7847: strcpy(gplotlabel+strlen(gplotlabel),")");
7848: fprintf(ficgp,"\n#\n");
7849: if(invalidvarcomb[k1]){
7850: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7851: continue;
7852: }
7853:
7854: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7855: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7856: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7857: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7858: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7859:
7860: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7861: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7862: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7863: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7864: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7865: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7866: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7867: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7868: if(i==istart){
7869: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7870: }else{
7871: fprintf(ficgp,",\\\n '' ");
7872: }
7873: if(cptcoveff ==0){ /* No covariate */
7874: ioffset=2; /* Age is in 2 */
7875: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7876: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7877: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7878: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7879: fprintf(ficgp," u %d:(", ioffset);
7880: if(i==nlstate+1){
1.270 brouard 7881: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7882: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7883: fprintf(ficgp,",\\\n '' ");
7884: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7885: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7886: offbyear, \
7887: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7888: }else
7889: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7890: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7891: }else{ /* more than 2 covariates */
1.270 brouard 7892: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7893: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7894: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7895: iyearc=ioffset-1;
7896: iagec=ioffset;
1.268 brouard 7897: fprintf(ficgp," u %d:(",ioffset);
7898: kl=0;
7899: strcpy(gplotcondition,"(");
7900: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7901: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7902: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7903: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7904: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7905: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7906: kl++;
7907: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7908: kl++;
7909: if(k <cptcoveff && cptcoveff>1)
7910: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7911: }
7912: strcpy(gplotcondition+strlen(gplotcondition),")");
7913: /* 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 *\/ */
7914: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7915: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7916: /* '' 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*/
7917: if(i==nlstate+1){
1.270 brouard 7918: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7919: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7920: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7921: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7922: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7923: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7924: iyearc,iagec,offbyear, \
7925: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7926: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7927: }else{
7928: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7929: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7930: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7931: }
7932: } /* end if covariate */
7933: } /* nlstate */
7934: fprintf(ficgp,"\nset out; unset label;\n");
7935: } /* end cpt state*/
7936: } /* end covariate */
1.296 brouard 7937: } /* End if prevbcast */
1.268 brouard 7938:
1.227 brouard 7939:
1.238 brouard 7940: /* 9eme writing MLE parameters */
7941: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7942: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7943: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7944: for(k=1; k <=(nlstate+ndeath); k++){
7945: if (k != i) {
1.227 brouard 7946: fprintf(ficgp,"# current state %d\n",k);
7947: for(j=1; j <=ncovmodel; j++){
7948: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7949: jk++;
7950: }
7951: fprintf(ficgp,"\n");
1.126 brouard 7952: }
7953: }
1.223 brouard 7954: }
1.187 brouard 7955: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7956:
1.145 brouard 7957: /*goto avoid;*/
1.238 brouard 7958: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7959: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7960: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7961: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7962: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7963: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7964: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7965: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7966: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7967: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7968: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7969: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7970: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7971: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7972: fprintf(ficgp,"#\n");
1.223 brouard 7973: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7974: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7975: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7976: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7977: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7978: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7979: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7980: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7981: continue;
1.264 brouard 7982: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7983: strcpy(gplotlabel,"(");
1.276 brouard 7984: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7985: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7986: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7987: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7988: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7989: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7990: vlv= nbcode[Tvaraff[k]][lv];
7991: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7992: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7993: }
1.237 brouard 7994: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7995: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7996: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7997: }
1.264 brouard 7998: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7999: fprintf(ficgp,"\n#\n");
1.264 brouard 8000: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 8001: fprintf(ficgp,"\nset key outside ");
8002: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
8003: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 8004: fprintf(ficgp,"\nset ter svg size 640, 480 ");
8005: if (ng==1){
8006: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
8007: fprintf(ficgp,"\nunset log y");
8008: }else if (ng==2){
8009: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
8010: fprintf(ficgp,"\nset log y");
8011: }else if (ng==3){
8012: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
8013: fprintf(ficgp,"\nset log y");
8014: }else
8015: fprintf(ficgp,"\nunset title ");
8016: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
8017: i=1;
8018: for(k2=1; k2<=nlstate; k2++) {
8019: k3=i;
8020: for(k=1; k<=(nlstate+ndeath); k++) {
8021: if (k != k2){
8022: switch( ng) {
8023: case 1:
8024: if(nagesqr==0)
8025: fprintf(ficgp," p%d+p%d*x",i,i+1);
8026: else /* nagesqr =1 */
8027: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8028: break;
8029: case 2: /* ng=2 */
8030: if(nagesqr==0)
8031: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8032: else /* nagesqr =1 */
8033: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8034: break;
8035: case 3:
8036: if(nagesqr==0)
8037: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8038: else /* nagesqr =1 */
8039: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8040: break;
8041: }
8042: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8043: ijp=1; /* product no age */
8044: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8045: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8046: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8047: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8048: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8049: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8050: if(DummyV[j]==0){
8051: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8052: }else{ /* quantitative */
8053: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8054: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8055: }
8056: ij++;
1.237 brouard 8057: }
1.268 brouard 8058: }
8059: }else if(cptcovprod >0){
8060: if(j==Tprod[ijp]) { /* */
8061: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8062: if(ijp <=cptcovprod) { /* Product */
8063: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8064: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8065: /* 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)]); */
8066: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8067: }else{ /* Vn is dummy and Vm is quanti */
8068: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8069: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8070: }
8071: }else{ /* Vn*Vm Vn is quanti */
8072: if(DummyV[Tvard[ijp][2]]==0){
8073: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8074: }else{ /* Both quanti */
8075: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8076: }
1.237 brouard 8077: }
1.268 brouard 8078: ijp++;
1.237 brouard 8079: }
1.268 brouard 8080: } /* end Tprod */
1.237 brouard 8081: } else{ /* simple covariate */
1.264 brouard 8082: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8083: if(Dummy[j]==0){
8084: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8085: }else{ /* quantitative */
8086: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8087: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8088: }
1.237 brouard 8089: } /* end simple */
8090: } /* end j */
1.223 brouard 8091: }else{
8092: i=i-ncovmodel;
8093: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8094: fprintf(ficgp," (1.");
8095: }
1.227 brouard 8096:
1.223 brouard 8097: if(ng != 1){
8098: fprintf(ficgp,")/(1");
1.227 brouard 8099:
1.264 brouard 8100: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8101: if(nagesqr==0)
1.264 brouard 8102: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8103: else /* nagesqr =1 */
1.264 brouard 8104: 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 8105:
1.223 brouard 8106: ij=1;
8107: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8108: if(cptcovage >0){
8109: if((j-2)==Tage[ij]) { /* Bug valgrind */
8110: if(ij <=cptcovage) { /* Bug valgrind */
8111: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8112: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8113: ij++;
8114: }
8115: }
8116: }else
8117: 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 8118: }
8119: fprintf(ficgp,")");
8120: }
8121: fprintf(ficgp,")");
8122: if(ng ==2)
1.276 brouard 8123: 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 8124: else /* ng= 3 */
1.276 brouard 8125: 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 8126: }else{ /* end ng <> 1 */
8127: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8128: 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 8129: }
8130: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8131: fprintf(ficgp,",");
8132: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8133: fprintf(ficgp,",");
8134: i=i+ncovmodel;
8135: } /* end k */
8136: } /* end k2 */
1.276 brouard 8137: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8138: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8139: } /* end k1 */
1.223 brouard 8140: } /* end ng */
8141: /* avoid: */
8142: fflush(ficgp);
1.126 brouard 8143: } /* end gnuplot */
8144:
8145:
8146: /*************** Moving average **************/
1.219 brouard 8147: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8148: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8149:
1.222 brouard 8150: int i, cpt, cptcod;
8151: int modcovmax =1;
8152: int mobilavrange, mob;
8153: int iage=0;
1.288 brouard 8154: int firstA1=0, firstA2=0;
1.222 brouard 8155:
1.266 brouard 8156: double sum=0., sumr=0.;
1.222 brouard 8157: double age;
1.266 brouard 8158: double *sumnewp, *sumnewm, *sumnewmr;
8159: double *agemingood, *agemaxgood;
8160: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8161:
8162:
1.278 brouard 8163: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8164: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8165:
8166: sumnewp = vector(1,ncovcombmax);
8167: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8168: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8169: agemingood = vector(1,ncovcombmax);
1.266 brouard 8170: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8171: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8172: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8173:
8174: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8175: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8176: sumnewp[cptcod]=0.;
1.266 brouard 8177: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8178: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8179: }
8180: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8181:
1.266 brouard 8182: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8183: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8184: else mobilavrange=mobilav;
8185: for (age=bage; age<=fage; age++)
8186: for (i=1; i<=nlstate;i++)
8187: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8188: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8189: /* We keep the original values on the extreme ages bage, fage and for
8190: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8191: we use a 5 terms etc. until the borders are no more concerned.
8192: */
8193: for (mob=3;mob <=mobilavrange;mob=mob+2){
8194: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8195: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8196: sumnewm[cptcod]=0.;
8197: for (i=1; i<=nlstate;i++){
1.222 brouard 8198: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8199: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8200: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8201: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8202: }
8203: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8204: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8205: } /* end i */
8206: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8207: } /* end cptcod */
1.222 brouard 8208: }/* end age */
8209: }/* end mob */
1.266 brouard 8210: }else{
8211: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8212: return -1;
1.266 brouard 8213: }
8214:
8215: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8216: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8217: if(invalidvarcomb[cptcod]){
8218: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8219: continue;
8220: }
1.219 brouard 8221:
1.266 brouard 8222: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8223: sumnewm[cptcod]=0.;
8224: sumnewmr[cptcod]=0.;
8225: for (i=1; i<=nlstate;i++){
8226: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8227: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8228: }
8229: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8230: agemingoodr[cptcod]=age;
8231: }
8232: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8233: agemingood[cptcod]=age;
8234: }
8235: } /* age */
8236: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8237: sumnewm[cptcod]=0.;
1.266 brouard 8238: sumnewmr[cptcod]=0.;
1.222 brouard 8239: for (i=1; i<=nlstate;i++){
8240: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8241: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8242: }
8243: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8244: agemaxgoodr[cptcod]=age;
1.222 brouard 8245: }
8246: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8247: agemaxgood[cptcod]=age;
8248: }
8249: } /* age */
8250: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8251: /* but they will change */
1.288 brouard 8252: firstA1=0;firstA2=0;
1.266 brouard 8253: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8254: sumnewm[cptcod]=0.;
8255: sumnewmr[cptcod]=0.;
8256: for (i=1; i<=nlstate;i++){
8257: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8258: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8259: }
8260: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8261: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8262: agemaxgoodr[cptcod]=age; /* age min */
8263: for (i=1; i<=nlstate;i++)
8264: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8265: }else{ /* bad we change the value with the values of good ages */
8266: for (i=1; i<=nlstate;i++){
8267: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8268: } /* i */
8269: } /* end bad */
8270: }else{
8271: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8272: agemaxgood[cptcod]=age;
8273: }else{ /* bad we change the value with the values of good ages */
8274: for (i=1; i<=nlstate;i++){
8275: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8276: } /* i */
8277: } /* end bad */
8278: }/* end else */
8279: sum=0.;sumr=0.;
8280: for (i=1; i<=nlstate;i++){
8281: sum+=mobaverage[(int)age][i][cptcod];
8282: sumr+=probs[(int)age][i][cptcod];
8283: }
8284: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8285: if(!firstA1){
8286: firstA1=1;
8287: 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);
8288: }
8289: 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 8290: } /* end bad */
8291: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8292: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8293: if(!firstA2){
8294: firstA2=1;
8295: 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);
8296: }
8297: 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 8298: } /* end bad */
8299: }/* age */
1.266 brouard 8300:
8301: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8302: sumnewm[cptcod]=0.;
1.266 brouard 8303: sumnewmr[cptcod]=0.;
1.222 brouard 8304: for (i=1; i<=nlstate;i++){
8305: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8306: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8307: }
8308: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8309: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8310: agemingoodr[cptcod]=age;
8311: for (i=1; i<=nlstate;i++)
8312: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8313: }else{ /* bad we change the value with the values of good ages */
8314: for (i=1; i<=nlstate;i++){
8315: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8316: } /* i */
8317: } /* end bad */
8318: }else{
8319: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8320: agemingood[cptcod]=age;
8321: }else{ /* bad */
8322: for (i=1; i<=nlstate;i++){
8323: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8324: } /* i */
8325: } /* end bad */
8326: }/* end else */
8327: sum=0.;sumr=0.;
8328: for (i=1; i<=nlstate;i++){
8329: sum+=mobaverage[(int)age][i][cptcod];
8330: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8331: }
1.266 brouard 8332: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8333: 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 8334: } /* end bad */
8335: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8336: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8337: 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 8338: } /* end bad */
8339: }/* age */
1.266 brouard 8340:
1.222 brouard 8341:
8342: for (age=bage; age<=fage; age++){
1.235 brouard 8343: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8344: sumnewp[cptcod]=0.;
8345: sumnewm[cptcod]=0.;
8346: for (i=1; i<=nlstate;i++){
8347: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8348: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8349: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8350: }
8351: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8352: }
8353: /* printf("\n"); */
8354: /* } */
1.266 brouard 8355:
1.222 brouard 8356: /* brutal averaging */
1.266 brouard 8357: /* for (i=1; i<=nlstate;i++){ */
8358: /* for (age=1; age<=bage; age++){ */
8359: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8360: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8361: /* } */
8362: /* for (age=fage; age<=AGESUP; age++){ */
8363: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8364: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8365: /* } */
8366: /* } /\* end i status *\/ */
8367: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8368: /* for (age=1; age<=AGESUP; age++){ */
8369: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8370: /* mobaverage[(int)age][i][cptcod]=0.; */
8371: /* } */
8372: /* } */
1.222 brouard 8373: }/* end cptcod */
1.266 brouard 8374: free_vector(agemaxgoodr,1, ncovcombmax);
8375: free_vector(agemaxgood,1, ncovcombmax);
8376: free_vector(agemingood,1, ncovcombmax);
8377: free_vector(agemingoodr,1, ncovcombmax);
8378: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8379: free_vector(sumnewm,1, ncovcombmax);
8380: free_vector(sumnewp,1, ncovcombmax);
8381: return 0;
8382: }/* End movingaverage */
1.218 brouard 8383:
1.126 brouard 8384:
1.296 brouard 8385:
1.126 brouard 8386: /************** Forecasting ******************/
1.296 brouard 8387: /* 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)*/
8388: 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){
8389: /* dateintemean, mean date of interviews
8390: dateprojd, year, month, day of starting projection
8391: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8392: agemin, agemax range of age
8393: dateprev1 dateprev2 range of dates during which prevalence is computed
8394: */
1.296 brouard 8395: /* double anprojd, mprojd, jprojd; */
8396: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8397: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8398: double agec; /* generic age */
1.296 brouard 8399: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8400: double *popeffectif,*popcount;
8401: double ***p3mat;
1.218 brouard 8402: /* double ***mobaverage; */
1.126 brouard 8403: char fileresf[FILENAMELENGTH];
8404:
8405: agelim=AGESUP;
1.211 brouard 8406: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8407: in each health status at the date of interview (if between dateprev1 and dateprev2).
8408: We still use firstpass and lastpass as another selection.
8409: */
1.214 brouard 8410: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8411: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8412:
1.201 brouard 8413: strcpy(fileresf,"F_");
8414: strcat(fileresf,fileresu);
1.126 brouard 8415: if((ficresf=fopen(fileresf,"w"))==NULL) {
8416: printf("Problem with forecast resultfile: %s\n", fileresf);
8417: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8418: }
1.235 brouard 8419: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8420: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8421:
1.225 brouard 8422: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8423:
8424:
8425: stepsize=(int) (stepm+YEARM-1)/YEARM;
8426: if (stepm<=12) stepsize=1;
8427: if(estepm < stepm){
8428: printf ("Problem %d lower than %d\n",estepm, stepm);
8429: }
1.270 brouard 8430: else{
8431: hstepm=estepm;
8432: }
8433: if(estepm > stepm){ /* Yes every two year */
8434: stepsize=2;
8435: }
1.296 brouard 8436: hstepm=hstepm/stepm;
1.126 brouard 8437:
1.296 brouard 8438:
8439: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8440: /* fractional in yp1 *\/ */
8441: /* aintmean=yp; */
8442: /* yp2=modf((yp1*12),&yp); */
8443: /* mintmean=yp; */
8444: /* yp1=modf((yp2*30.5),&yp); */
8445: /* jintmean=yp; */
8446: /* if(jintmean==0) jintmean=1; */
8447: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8448:
1.296 brouard 8449:
8450: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8451: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8452: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8453: i1=pow(2,cptcoveff);
1.126 brouard 8454: if (cptcovn < 1){i1=1;}
8455:
1.296 brouard 8456: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8457:
8458: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8459:
1.126 brouard 8460: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8461: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8462: for(k=1; k<=i1;k++){
1.253 brouard 8463: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8464: continue;
1.227 brouard 8465: if(invalidvarcomb[k]){
8466: printf("\nCombination (%d) projection ignored because no cases \n",k);
8467: continue;
8468: }
8469: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8470: for(j=1;j<=cptcoveff;j++) {
8471: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8472: }
1.235 brouard 8473: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8474: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8475: }
1.227 brouard 8476: fprintf(ficresf," yearproj age");
8477: for(j=1; j<=nlstate+ndeath;j++){
8478: for(i=1; i<=nlstate;i++)
8479: fprintf(ficresf," p%d%d",i,j);
8480: fprintf(ficresf," wp.%d",j);
8481: }
1.296 brouard 8482: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8483: fprintf(ficresf,"\n");
1.296 brouard 8484: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8485: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8486: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8487: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8488: nhstepm = nhstepm/hstepm;
8489: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8490: oldm=oldms;savm=savms;
1.268 brouard 8491: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8492: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8493: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8494: for (h=0; h<=nhstepm; h++){
8495: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8496: break;
8497: }
8498: }
8499: fprintf(ficresf,"\n");
8500: for(j=1;j<=cptcoveff;j++)
8501: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8502: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8503:
8504: for(j=1; j<=nlstate+ndeath;j++) {
8505: ppij=0.;
8506: for(i=1; i<=nlstate;i++) {
1.278 brouard 8507: if (mobilav>=1)
8508: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8509: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8510: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8511: }
1.268 brouard 8512: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8513: } /* end i */
8514: fprintf(ficresf," %.3f", ppij);
8515: }/* end j */
1.227 brouard 8516: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8517: } /* end agec */
1.266 brouard 8518: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8519: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8520: } /* end yearp */
8521: } /* end k */
1.219 brouard 8522:
1.126 brouard 8523: fclose(ficresf);
1.215 brouard 8524: printf("End of Computing forecasting \n");
8525: fprintf(ficlog,"End of Computing forecasting\n");
8526:
1.126 brouard 8527: }
8528:
1.269 brouard 8529: /************** Back Forecasting ******************/
1.296 brouard 8530: /* 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){ */
8531: 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){
8532: /* back1, year, month, day of starting backprojection
1.267 brouard 8533: agemin, agemax range of age
8534: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8535: anback2 year of end of backprojection (same day and month as back1).
8536: prevacurrent and prev are prevalences.
1.267 brouard 8537: */
8538: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8539: double agec; /* generic age */
1.302 brouard 8540: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8541: double *popeffectif,*popcount;
8542: double ***p3mat;
8543: /* double ***mobaverage; */
8544: char fileresfb[FILENAMELENGTH];
8545:
1.268 brouard 8546: agelim=AGEINF;
1.267 brouard 8547: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8548: in each health status at the date of interview (if between dateprev1 and dateprev2).
8549: We still use firstpass and lastpass as another selection.
8550: */
8551: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8552: /* firstpass, lastpass, stepm, weightopt, model); */
8553:
8554: /*Do we need to compute prevalence again?*/
8555:
8556: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8557:
8558: strcpy(fileresfb,"FB_");
8559: strcat(fileresfb,fileresu);
8560: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8561: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8562: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8563: }
8564: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8565: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8566:
8567: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8568:
8569:
8570: stepsize=(int) (stepm+YEARM-1)/YEARM;
8571: if (stepm<=12) stepsize=1;
8572: if(estepm < stepm){
8573: printf ("Problem %d lower than %d\n",estepm, stepm);
8574: }
1.270 brouard 8575: else{
8576: hstepm=estepm;
8577: }
8578: if(estepm >= stepm){ /* Yes every two year */
8579: stepsize=2;
8580: }
1.267 brouard 8581:
8582: hstepm=hstepm/stepm;
1.296 brouard 8583: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8584: /* fractional in yp1 *\/ */
8585: /* aintmean=yp; */
8586: /* yp2=modf((yp1*12),&yp); */
8587: /* mintmean=yp; */
8588: /* yp1=modf((yp2*30.5),&yp); */
8589: /* jintmean=yp; */
8590: /* if(jintmean==0) jintmean=1; */
8591: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8592:
8593: i1=pow(2,cptcoveff);
8594: if (cptcovn < 1){i1=1;}
8595:
1.296 brouard 8596: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8597: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8598:
8599: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8600:
8601: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8602: for(k=1; k<=i1;k++){
8603: if(i1 != 1 && TKresult[nres]!= k)
8604: continue;
8605: if(invalidvarcomb[k]){
8606: printf("\nCombination (%d) projection ignored because no cases \n",k);
8607: continue;
8608: }
1.268 brouard 8609: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8610: for(j=1;j<=cptcoveff;j++) {
8611: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8612: }
8613: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8614: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8615: }
8616: fprintf(ficresfb," yearbproj age");
8617: for(j=1; j<=nlstate+ndeath;j++){
8618: for(i=1; i<=nlstate;i++)
1.268 brouard 8619: fprintf(ficresfb," b%d%d",i,j);
8620: fprintf(ficresfb," b.%d",j);
1.267 brouard 8621: }
1.296 brouard 8622: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8623: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8624: fprintf(ficresfb,"\n");
1.296 brouard 8625: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8626: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8627: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8628: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8629: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8630: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8631: nhstepm = nhstepm/hstepm;
8632: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8633: oldm=oldms;savm=savms;
1.268 brouard 8634: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8635: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8636: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8637: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8638: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8639: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8640: for (h=0; h<=nhstepm; h++){
1.268 brouard 8641: if (h*hstepm/YEARM*stepm ==-yearp) {
8642: break;
8643: }
8644: }
8645: fprintf(ficresfb,"\n");
8646: for(j=1;j<=cptcoveff;j++)
8647: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8648: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8649: for(i=1; i<=nlstate+ndeath;i++) {
8650: ppij=0.;ppi=0.;
8651: for(j=1; j<=nlstate;j++) {
8652: /* if (mobilav==1) */
1.269 brouard 8653: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8654: ppi=ppi+prevacurrent[(int)agec][j][k];
8655: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8656: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8657: /* else { */
8658: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8659: /* } */
1.268 brouard 8660: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8661: } /* end j */
8662: if(ppi <0.99){
8663: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8664: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8665: }
8666: fprintf(ficresfb," %.3f", ppij);
8667: }/* end j */
1.267 brouard 8668: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8669: } /* end agec */
8670: } /* end yearp */
8671: } /* end k */
1.217 brouard 8672:
1.267 brouard 8673: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8674:
1.267 brouard 8675: fclose(ficresfb);
8676: printf("End of Computing Back forecasting \n");
8677: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8678:
1.267 brouard 8679: }
1.217 brouard 8680:
1.269 brouard 8681: /* Variance of prevalence limit: varprlim */
8682: 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 8683: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8684:
8685: char fileresvpl[FILENAMELENGTH];
8686: FILE *ficresvpl;
8687: double **oldm, **savm;
8688: double **varpl; /* Variances of prevalence limits by age */
8689: int i1, k, nres, j ;
8690:
8691: strcpy(fileresvpl,"VPL_");
8692: strcat(fileresvpl,fileresu);
8693: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8694: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8695: exit(0);
8696: }
1.288 brouard 8697: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8698: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8699:
8700: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8701: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8702:
8703: i1=pow(2,cptcoveff);
8704: if (cptcovn < 1){i1=1;}
8705:
8706: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8707: for(k=1; k<=i1;k++){
8708: if(i1 != 1 && TKresult[nres]!= k)
8709: continue;
8710: fprintf(ficresvpl,"\n#****** ");
8711: printf("\n#****** ");
8712: fprintf(ficlog,"\n#****** ");
8713: for(j=1;j<=cptcoveff;j++) {
8714: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8715: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8716: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8717: }
8718: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8719: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8720: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8721: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8722: }
8723: fprintf(ficresvpl,"******\n");
8724: printf("******\n");
8725: fprintf(ficlog,"******\n");
8726:
8727: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8728: oldm=oldms;savm=savms;
8729: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8730: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8731: /*}*/
8732: }
8733:
8734: fclose(ficresvpl);
1.288 brouard 8735: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8736: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8737:
8738: }
8739: /* Variance of back prevalence: varbprlim */
8740: 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){
8741: /*------- Variance of back (stable) prevalence------*/
8742:
8743: char fileresvbl[FILENAMELENGTH];
8744: FILE *ficresvbl;
8745:
8746: double **oldm, **savm;
8747: double **varbpl; /* Variances of back prevalence limits by age */
8748: int i1, k, nres, j ;
8749:
8750: strcpy(fileresvbl,"VBL_");
8751: strcat(fileresvbl,fileresu);
8752: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8753: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8754: exit(0);
8755: }
8756: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8757: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8758:
8759:
8760: i1=pow(2,cptcoveff);
8761: if (cptcovn < 1){i1=1;}
8762:
8763: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8764: for(k=1; k<=i1;k++){
8765: if(i1 != 1 && TKresult[nres]!= k)
8766: continue;
8767: fprintf(ficresvbl,"\n#****** ");
8768: printf("\n#****** ");
8769: fprintf(ficlog,"\n#****** ");
8770: for(j=1;j<=cptcoveff;j++) {
8771: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8772: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8773: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8774: }
8775: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8776: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8777: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8778: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8779: }
8780: fprintf(ficresvbl,"******\n");
8781: printf("******\n");
8782: fprintf(ficlog,"******\n");
8783:
8784: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8785: oldm=oldms;savm=savms;
8786:
8787: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8788: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8789: /*}*/
8790: }
8791:
8792: fclose(ficresvbl);
8793: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8794: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8795:
8796: } /* End of varbprlim */
8797:
1.126 brouard 8798: /************** Forecasting *****not tested NB*************/
1.227 brouard 8799: /* 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 8800:
1.227 brouard 8801: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8802: /* int *popage; */
8803: /* double calagedatem, agelim, kk1, kk2; */
8804: /* double *popeffectif,*popcount; */
8805: /* double ***p3mat,***tabpop,***tabpopprev; */
8806: /* /\* double ***mobaverage; *\/ */
8807: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8808:
1.227 brouard 8809: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8810: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8811: /* agelim=AGESUP; */
8812: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8813:
1.227 brouard 8814: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8815:
8816:
1.227 brouard 8817: /* strcpy(filerespop,"POP_"); */
8818: /* strcat(filerespop,fileresu); */
8819: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8820: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8821: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8822: /* } */
8823: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8824: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8825:
1.227 brouard 8826: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8827:
1.227 brouard 8828: /* /\* if (mobilav!=0) { *\/ */
8829: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8830: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8831: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8832: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8833: /* /\* } *\/ */
8834: /* /\* } *\/ */
1.126 brouard 8835:
1.227 brouard 8836: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8837: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8838:
1.227 brouard 8839: /* agelim=AGESUP; */
1.126 brouard 8840:
1.227 brouard 8841: /* hstepm=1; */
8842: /* hstepm=hstepm/stepm; */
1.218 brouard 8843:
1.227 brouard 8844: /* if (popforecast==1) { */
8845: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8846: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8847: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8848: /* } */
8849: /* popage=ivector(0,AGESUP); */
8850: /* popeffectif=vector(0,AGESUP); */
8851: /* popcount=vector(0,AGESUP); */
1.126 brouard 8852:
1.227 brouard 8853: /* i=1; */
8854: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8855:
1.227 brouard 8856: /* imx=i; */
8857: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8858: /* } */
1.218 brouard 8859:
1.227 brouard 8860: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8861: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8862: /* k=k+1; */
8863: /* fprintf(ficrespop,"\n#******"); */
8864: /* for(j=1;j<=cptcoveff;j++) { */
8865: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8866: /* } */
8867: /* fprintf(ficrespop,"******\n"); */
8868: /* fprintf(ficrespop,"# Age"); */
8869: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8870: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8871:
1.227 brouard 8872: /* for (cpt=0; cpt<=0;cpt++) { */
8873: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8874:
1.227 brouard 8875: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8876: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8877: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8878:
1.227 brouard 8879: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8880: /* oldm=oldms;savm=savms; */
8881: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8882:
1.227 brouard 8883: /* for (h=0; h<=nhstepm; h++){ */
8884: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8885: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8886: /* } */
8887: /* for(j=1; j<=nlstate+ndeath;j++) { */
8888: /* kk1=0.;kk2=0; */
8889: /* for(i=1; i<=nlstate;i++) { */
8890: /* if (mobilav==1) */
8891: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8892: /* else { */
8893: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8894: /* } */
8895: /* } */
8896: /* if (h==(int)(calagedatem+12*cpt)){ */
8897: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8898: /* /\*fprintf(ficrespop," %.3f", kk1); */
8899: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8900: /* } */
8901: /* } */
8902: /* for(i=1; i<=nlstate;i++){ */
8903: /* kk1=0.; */
8904: /* for(j=1; j<=nlstate;j++){ */
8905: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8906: /* } */
8907: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8908: /* } */
1.218 brouard 8909:
1.227 brouard 8910: /* if (h==(int)(calagedatem+12*cpt)) */
8911: /* for(j=1; j<=nlstate;j++) */
8912: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8913: /* } */
8914: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8915: /* } */
8916: /* } */
1.218 brouard 8917:
1.227 brouard 8918: /* /\******\/ */
1.218 brouard 8919:
1.227 brouard 8920: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8921: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8922: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8923: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8924: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8925:
1.227 brouard 8926: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8927: /* oldm=oldms;savm=savms; */
8928: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8929: /* for (h=0; h<=nhstepm; h++){ */
8930: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8931: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8932: /* } */
8933: /* for(j=1; j<=nlstate+ndeath;j++) { */
8934: /* kk1=0.;kk2=0; */
8935: /* for(i=1; i<=nlstate;i++) { */
8936: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8937: /* } */
8938: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8939: /* } */
8940: /* } */
8941: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8942: /* } */
8943: /* } */
8944: /* } */
8945: /* } */
1.218 brouard 8946:
1.227 brouard 8947: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8948:
1.227 brouard 8949: /* if (popforecast==1) { */
8950: /* free_ivector(popage,0,AGESUP); */
8951: /* free_vector(popeffectif,0,AGESUP); */
8952: /* free_vector(popcount,0,AGESUP); */
8953: /* } */
8954: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8955: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8956: /* fclose(ficrespop); */
8957: /* } /\* End of popforecast *\/ */
1.218 brouard 8958:
1.126 brouard 8959: int fileappend(FILE *fichier, char *optionfich)
8960: {
8961: if((fichier=fopen(optionfich,"a"))==NULL) {
8962: printf("Problem with file: %s\n", optionfich);
8963: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8964: return (0);
8965: }
8966: fflush(fichier);
8967: return (1);
8968: }
8969:
8970:
8971: /**************** function prwizard **********************/
8972: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8973: {
8974:
8975: /* Wizard to print covariance matrix template */
8976:
1.164 brouard 8977: char ca[32], cb[32];
8978: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8979: int numlinepar;
8980:
8981: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8982: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8983: for(i=1; i <=nlstate; i++){
8984: jj=0;
8985: for(j=1; j <=nlstate+ndeath; j++){
8986: if(j==i) continue;
8987: jj++;
8988: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8989: printf("%1d%1d",i,j);
8990: fprintf(ficparo,"%1d%1d",i,j);
8991: for(k=1; k<=ncovmodel;k++){
8992: /* printf(" %lf",param[i][j][k]); */
8993: /* fprintf(ficparo," %lf",param[i][j][k]); */
8994: printf(" 0.");
8995: fprintf(ficparo," 0.");
8996: }
8997: printf("\n");
8998: fprintf(ficparo,"\n");
8999: }
9000: }
9001: printf("# Scales (for hessian or gradient estimation)\n");
9002: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
9003: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
9004: for(i=1; i <=nlstate; i++){
9005: jj=0;
9006: for(j=1; j <=nlstate+ndeath; j++){
9007: if(j==i) continue;
9008: jj++;
9009: fprintf(ficparo,"%1d%1d",i,j);
9010: printf("%1d%1d",i,j);
9011: fflush(stdout);
9012: for(k=1; k<=ncovmodel;k++){
9013: /* printf(" %le",delti3[i][j][k]); */
9014: /* fprintf(ficparo," %le",delti3[i][j][k]); */
9015: printf(" 0.");
9016: fprintf(ficparo," 0.");
9017: }
9018: numlinepar++;
9019: printf("\n");
9020: fprintf(ficparo,"\n");
9021: }
9022: }
9023: printf("# Covariance matrix\n");
9024: /* # 121 Var(a12)\n\ */
9025: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9026: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9027: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9028: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9029: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9030: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9031: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9032: fflush(stdout);
9033: fprintf(ficparo,"# Covariance matrix\n");
9034: /* # 121 Var(a12)\n\ */
9035: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9036: /* # ...\n\ */
9037: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9038:
9039: for(itimes=1;itimes<=2;itimes++){
9040: jj=0;
9041: for(i=1; i <=nlstate; i++){
9042: for(j=1; j <=nlstate+ndeath; j++){
9043: if(j==i) continue;
9044: for(k=1; k<=ncovmodel;k++){
9045: jj++;
9046: ca[0]= k+'a'-1;ca[1]='\0';
9047: if(itimes==1){
9048: printf("#%1d%1d%d",i,j,k);
9049: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9050: }else{
9051: printf("%1d%1d%d",i,j,k);
9052: fprintf(ficparo,"%1d%1d%d",i,j,k);
9053: /* printf(" %.5le",matcov[i][j]); */
9054: }
9055: ll=0;
9056: for(li=1;li <=nlstate; li++){
9057: for(lj=1;lj <=nlstate+ndeath; lj++){
9058: if(lj==li) continue;
9059: for(lk=1;lk<=ncovmodel;lk++){
9060: ll++;
9061: if(ll<=jj){
9062: cb[0]= lk +'a'-1;cb[1]='\0';
9063: if(ll<jj){
9064: if(itimes==1){
9065: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9066: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9067: }else{
9068: printf(" 0.");
9069: fprintf(ficparo," 0.");
9070: }
9071: }else{
9072: if(itimes==1){
9073: printf(" Var(%s%1d%1d)",ca,i,j);
9074: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9075: }else{
9076: printf(" 0.");
9077: fprintf(ficparo," 0.");
9078: }
9079: }
9080: }
9081: } /* end lk */
9082: } /* end lj */
9083: } /* end li */
9084: printf("\n");
9085: fprintf(ficparo,"\n");
9086: numlinepar++;
9087: } /* end k*/
9088: } /*end j */
9089: } /* end i */
9090: } /* end itimes */
9091:
9092: } /* end of prwizard */
9093: /******************* Gompertz Likelihood ******************************/
9094: double gompertz(double x[])
9095: {
1.302 brouard 9096: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9097: int i,n=0; /* n is the size of the sample */
9098:
1.220 brouard 9099: for (i=1;i<=imx ; i++) {
1.126 brouard 9100: sump=sump+weight[i];
9101: /* sump=sump+1;*/
9102: num=num+1;
9103: }
1.302 brouard 9104: L=0.0;
9105: /* agegomp=AGEGOMP; */
1.126 brouard 9106: /* for (i=0; i<=imx; i++)
9107: 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]);*/
9108:
1.302 brouard 9109: for (i=1;i<=imx ; i++) {
9110: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9111: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9112: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9113: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9114: * +
9115: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9116: */
9117: if (wav[i] > 1 || agedc[i] < AGESUP) {
9118: if (cens[i] == 1){
9119: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9120: } else if (cens[i] == 0){
1.126 brouard 9121: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9122: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9123: } else
9124: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9125: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9126: L=L+A*weight[i];
1.126 brouard 9127: /* 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 9128: }
9129: }
1.126 brouard 9130:
1.302 brouard 9131: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9132:
9133: return -2*L*num/sump;
9134: }
9135:
1.136 brouard 9136: #ifdef GSL
9137: /******************* Gompertz_f Likelihood ******************************/
9138: double gompertz_f(const gsl_vector *v, void *params)
9139: {
1.302 brouard 9140: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9141: double *x= (double *) v->data;
9142: int i,n=0; /* n is the size of the sample */
9143:
9144: for (i=0;i<=imx-1 ; i++) {
9145: sump=sump+weight[i];
9146: /* sump=sump+1;*/
9147: num=num+1;
9148: }
9149:
9150:
9151: /* for (i=0; i<=imx; i++)
9152: 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]);*/
9153: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9154: for (i=1;i<=imx ; i++)
9155: {
9156: if (cens[i] == 1 && wav[i]>1)
9157: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9158:
9159: if (cens[i] == 0 && wav[i]>1)
9160: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9161: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9162:
9163: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9164: if (wav[i] > 1 ) { /* ??? */
9165: LL=LL+A*weight[i];
9166: /* 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]);*/
9167: }
9168: }
9169:
9170: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9171: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9172:
9173: return -2*LL*num/sump;
9174: }
9175: #endif
9176:
1.126 brouard 9177: /******************* Printing html file ***********/
1.201 brouard 9178: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9179: int lastpass, int stepm, int weightopt, char model[],\
9180: int imx, double p[],double **matcov,double agemortsup){
9181: int i,k;
9182:
9183: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9184: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9185: for (i=1;i<=2;i++)
9186: 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 9187: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9188: fprintf(fichtm,"</ul>");
9189:
9190: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9191:
9192: 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>");
9193:
9194: for (k=agegomp;k<(agemortsup-2);k++)
9195: 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]);
9196:
9197:
9198: fflush(fichtm);
9199: }
9200:
9201: /******************* Gnuplot file **************/
1.201 brouard 9202: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9203:
9204: char dirfileres[132],optfileres[132];
1.164 brouard 9205:
1.126 brouard 9206: int ng;
9207:
9208:
9209: /*#ifdef windows */
9210: fprintf(ficgp,"cd \"%s\" \n",pathc);
9211: /*#endif */
9212:
9213:
9214: strcpy(dirfileres,optionfilefiname);
9215: strcpy(optfileres,"vpl");
1.199 brouard 9216: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9217: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9218: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9219: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9220: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9221:
9222: }
9223:
1.136 brouard 9224: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9225: {
1.126 brouard 9226:
1.136 brouard 9227: /*-------- data file ----------*/
9228: FILE *fic;
9229: char dummy[]=" ";
1.240 brouard 9230: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9231: int lstra;
1.136 brouard 9232: int linei, month, year,iout;
1.302 brouard 9233: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9234: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9235: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9236: char *stratrunc;
1.223 brouard 9237:
1.240 brouard 9238: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9239: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9240:
1.240 brouard 9241: for(v=1; v <=ncovcol;v++){
9242: DummyV[v]=0;
9243: FixedV[v]=0;
9244: }
9245: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9246: DummyV[v]=1;
9247: FixedV[v]=0;
9248: }
9249: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9250: DummyV[v]=0;
9251: FixedV[v]=1;
9252: }
9253: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9254: DummyV[v]=1;
9255: FixedV[v]=1;
9256: }
9257: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9258: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9259: 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]);
9260: }
1.126 brouard 9261:
1.136 brouard 9262: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9263: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9264: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9265: }
1.126 brouard 9266:
1.302 brouard 9267: /* Is it a BOM UTF-8 Windows file? */
9268: /* First data line */
9269: linei=0;
9270: while(fgets(line, MAXLINE, fic)) {
9271: noffset=0;
9272: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9273: {
9274: noffset=noffset+3;
9275: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9276: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9277: fflush(ficlog); return 1;
9278: }
9279: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9280: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9281: {
9282: noffset=noffset+2;
1.304 brouard 9283: 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);
9284: 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 9285: fflush(ficlog); return 1;
9286: }
9287: else if( line[0] == 0 && line[1] == 0)
9288: {
9289: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9290: noffset=noffset+4;
1.304 brouard 9291: 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);
9292: 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 9293: fflush(ficlog); return 1;
9294: }
9295: } else{
9296: ;/*printf(" Not a BOM file\n");*/
9297: }
9298: /* If line starts with a # it is a comment */
9299: if (line[noffset] == '#') {
9300: linei=linei+1;
9301: break;
9302: }else{
9303: break;
9304: }
9305: }
9306: fclose(fic);
9307: if((fic=fopen(datafile,"r"))==NULL) {
9308: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9309: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9310: }
9311: /* Not a Bom file */
9312:
1.136 brouard 9313: i=1;
9314: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9315: linei=linei+1;
9316: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9317: if(line[j] == '\t')
9318: line[j] = ' ';
9319: }
9320: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9321: ;
9322: };
9323: line[j+1]=0; /* Trims blanks at end of line */
9324: if(line[0]=='#'){
9325: fprintf(ficlog,"Comment line\n%s\n",line);
9326: printf("Comment line\n%s\n",line);
9327: continue;
9328: }
9329: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9330: strcpy(line, linetmp);
1.223 brouard 9331:
9332: /* Loops on waves */
9333: for (j=maxwav;j>=1;j--){
9334: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9335: cutv(stra, strb, line, ' ');
9336: if(strb[0]=='.') { /* Missing value */
9337: lval=-1;
9338: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9339: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9340: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9341: 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);
9342: 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);
9343: return 1;
9344: }
9345: }else{
9346: errno=0;
9347: /* what_kind_of_number(strb); */
9348: dval=strtod(strb,&endptr);
9349: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9350: /* if(strb != endptr && *endptr == '\0') */
9351: /* dval=dlval; */
9352: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9353: if( strb[0]=='\0' || (*endptr != '\0')){
9354: 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);
9355: 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);
9356: return 1;
9357: }
9358: cotqvar[j][iv][i]=dval;
9359: cotvar[j][ntv+iv][i]=dval;
9360: }
9361: strcpy(line,stra);
1.223 brouard 9362: }/* end loop ntqv */
1.225 brouard 9363:
1.223 brouard 9364: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9365: cutv(stra, strb, line, ' ');
9366: if(strb[0]=='.') { /* Missing value */
9367: lval=-1;
9368: }else{
9369: errno=0;
9370: lval=strtol(strb,&endptr,10);
9371: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9372: if( strb[0]=='\0' || (*endptr != '\0')){
9373: 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);
9374: 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);
9375: return 1;
9376: }
9377: }
9378: if(lval <-1 || lval >1){
9379: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9380: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9381: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9382: For example, for multinomial values like 1, 2 and 3,\n \
9383: build V1=0 V2=0 for the reference value (1),\n \
9384: V1=1 V2=0 for (2) \n \
1.223 brouard 9385: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9386: output of IMaCh is often meaningless.\n \
1.223 brouard 9387: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9388: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9389: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9390: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9391: For example, for multinomial values like 1, 2 and 3,\n \
9392: build V1=0 V2=0 for the reference value (1),\n \
9393: V1=1 V2=0 for (2) \n \
1.223 brouard 9394: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9395: output of IMaCh is often meaningless.\n \
1.223 brouard 9396: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9397: return 1;
9398: }
9399: cotvar[j][iv][i]=(double)(lval);
9400: strcpy(line,stra);
1.223 brouard 9401: }/* end loop ntv */
1.225 brouard 9402:
1.223 brouard 9403: /* Statuses at wave */
1.137 brouard 9404: cutv(stra, strb, line, ' ');
1.223 brouard 9405: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9406: lval=-1;
1.136 brouard 9407: }else{
1.238 brouard 9408: errno=0;
9409: lval=strtol(strb,&endptr,10);
9410: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9411: if( strb[0]=='\0' || (*endptr != '\0')){
9412: 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);
9413: 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);
9414: return 1;
9415: }
1.136 brouard 9416: }
1.225 brouard 9417:
1.136 brouard 9418: s[j][i]=lval;
1.225 brouard 9419:
1.223 brouard 9420: /* Date of Interview */
1.136 brouard 9421: strcpy(line,stra);
9422: cutv(stra, strb,line,' ');
1.169 brouard 9423: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9424: }
1.169 brouard 9425: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9426: month=99;
9427: year=9999;
1.136 brouard 9428: }else{
1.225 brouard 9429: 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);
9430: 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);
9431: return 1;
1.136 brouard 9432: }
9433: anint[j][i]= (double) year;
1.302 brouard 9434: mint[j][i]= (double)month;
9435: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9436: /* 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]); */
9437: /* 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]); */
9438: /* } */
1.136 brouard 9439: strcpy(line,stra);
1.223 brouard 9440: } /* End loop on waves */
1.225 brouard 9441:
1.223 brouard 9442: /* Date of death */
1.136 brouard 9443: cutv(stra, strb,line,' ');
1.169 brouard 9444: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9445: }
1.169 brouard 9446: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9447: month=99;
9448: year=9999;
9449: }else{
1.141 brouard 9450: 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 9451: 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);
9452: return 1;
1.136 brouard 9453: }
9454: andc[i]=(double) year;
9455: moisdc[i]=(double) month;
9456: strcpy(line,stra);
9457:
1.223 brouard 9458: /* Date of birth */
1.136 brouard 9459: cutv(stra, strb,line,' ');
1.169 brouard 9460: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9461: }
1.169 brouard 9462: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9463: month=99;
9464: year=9999;
9465: }else{
1.141 brouard 9466: 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);
9467: 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 9468: return 1;
1.136 brouard 9469: }
9470: if (year==9999) {
1.141 brouard 9471: 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);
9472: 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 9473: return 1;
9474:
1.136 brouard 9475: }
9476: annais[i]=(double)(year);
1.302 brouard 9477: moisnais[i]=(double)(month);
9478: for (j=1;j<=maxwav;j++){
9479: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9480: 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]);
9481: 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]);
9482: }
9483: }
9484:
1.136 brouard 9485: strcpy(line,stra);
1.225 brouard 9486:
1.223 brouard 9487: /* Sample weight */
1.136 brouard 9488: cutv(stra, strb,line,' ');
9489: errno=0;
9490: dval=strtod(strb,&endptr);
9491: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9492: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9493: 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 9494: fflush(ficlog);
9495: return 1;
9496: }
9497: weight[i]=dval;
9498: strcpy(line,stra);
1.225 brouard 9499:
1.223 brouard 9500: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9501: cutv(stra, strb, line, ' ');
9502: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9503: lval=-1;
1.223 brouard 9504: }else{
1.225 brouard 9505: errno=0;
9506: /* what_kind_of_number(strb); */
9507: dval=strtod(strb,&endptr);
9508: /* if(strb != endptr && *endptr == '\0') */
9509: /* dval=dlval; */
9510: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9511: if( strb[0]=='\0' || (*endptr != '\0')){
9512: 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);
9513: 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);
9514: return 1;
9515: }
9516: coqvar[iv][i]=dval;
1.226 brouard 9517: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9518: }
9519: strcpy(line,stra);
9520: }/* end loop nqv */
1.136 brouard 9521:
1.223 brouard 9522: /* Covariate values */
1.136 brouard 9523: for (j=ncovcol;j>=1;j--){
9524: cutv(stra, strb,line,' ');
1.223 brouard 9525: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9526: lval=-1;
1.136 brouard 9527: }else{
1.225 brouard 9528: errno=0;
9529: lval=strtol(strb,&endptr,10);
9530: if( strb[0]=='\0' || (*endptr != '\0')){
9531: 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);
9532: 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);
9533: return 1;
9534: }
1.136 brouard 9535: }
9536: if(lval <-1 || lval >1){
1.225 brouard 9537: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9538: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9539: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9540: For example, for multinomial values like 1, 2 and 3,\n \
9541: build V1=0 V2=0 for the reference value (1),\n \
9542: V1=1 V2=0 for (2) \n \
1.136 brouard 9543: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9544: output of IMaCh is often meaningless.\n \
1.136 brouard 9545: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9546: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9547: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9548: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9549: For example, for multinomial values like 1, 2 and 3,\n \
9550: build V1=0 V2=0 for the reference value (1),\n \
9551: V1=1 V2=0 for (2) \n \
1.136 brouard 9552: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9553: output of IMaCh is often meaningless.\n \
1.136 brouard 9554: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9555: return 1;
1.136 brouard 9556: }
9557: covar[j][i]=(double)(lval);
9558: strcpy(line,stra);
9559: }
9560: lstra=strlen(stra);
1.225 brouard 9561:
1.136 brouard 9562: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9563: stratrunc = &(stra[lstra-9]);
9564: num[i]=atol(stratrunc);
9565: }
9566: else
9567: num[i]=atol(stra);
9568: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9569: 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;}*/
9570:
9571: i=i+1;
9572: } /* End loop reading data */
1.225 brouard 9573:
1.136 brouard 9574: *imax=i-1; /* Number of individuals */
9575: fclose(fic);
1.225 brouard 9576:
1.136 brouard 9577: return (0);
1.164 brouard 9578: /* endread: */
1.225 brouard 9579: printf("Exiting readdata: ");
9580: fclose(fic);
9581: return (1);
1.223 brouard 9582: }
1.126 brouard 9583:
1.234 brouard 9584: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9585: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9586: while (*p2 == ' ')
1.234 brouard 9587: p2++;
9588: /* while ((*p1++ = *p2++) !=0) */
9589: /* ; */
9590: /* do */
9591: /* while (*p2 == ' ') */
9592: /* p2++; */
9593: /* while (*p1++ == *p2++); */
9594: *stri=p2;
1.145 brouard 9595: }
9596:
1.235 brouard 9597: int decoderesult ( char resultline[], int nres)
1.230 brouard 9598: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9599: {
1.235 brouard 9600: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9601: char resultsav[MAXLINE];
1.234 brouard 9602: int resultmodel[MAXLINE];
9603: int modelresult[MAXLINE];
1.230 brouard 9604: char stra[80], strb[80], strc[80], strd[80],stre[80];
9605:
1.234 brouard 9606: removefirstspace(&resultline);
1.230 brouard 9607:
9608: if (strstr(resultline,"v") !=0){
9609: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9610: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9611: return 1;
9612: }
9613: trimbb(resultsav, resultline);
9614: if (strlen(resultsav) >1){
9615: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9616: }
1.253 brouard 9617: if(j == 0){ /* Resultline but no = */
9618: TKresult[nres]=0; /* Combination for the nresult and the model */
9619: return (0);
9620: }
1.234 brouard 9621: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
1.310 ! brouard 9622: 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);
! 9623: 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 9624: }
9625: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9626: if(nbocc(resultsav,'=') >1){
9627: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
1.310 ! brouard 9628: resultsav= V4=1 V5=25.1 V3=0 stra= V5=25.1 V3=0 strb= V4=1 */
1.234 brouard 9629: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9630: }else
9631: cutl(strc,strd,resultsav,'=');
1.230 brouard 9632: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9633:
1.230 brouard 9634: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9635: Tvarsel[k]=atoi(strc);
9636: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9637: /* cptcovsel++; */
9638: if (nbocc(stra,'=') >0)
9639: strcpy(resultsav,stra); /* and analyzes it */
9640: }
1.235 brouard 9641: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9642: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9643: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9644: match=0;
1.236 brouard 9645: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9646: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9647: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9648: match=1;
9649: break;
9650: }
9651: }
9652: if(match == 0){
1.310 ! brouard 9653: printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
! 9654: fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);
! 9655: return 1;
1.234 brouard 9656: }
9657: }
9658: }
1.235 brouard 9659: /* Checking for missing or useless values in comparison of current model needs */
9660: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9661: match=0;
1.235 brouard 9662: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9663: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9664: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9665: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9666: ++match;
9667: }
9668: }
9669: }
9670: if(match == 0){
9671: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
1.310 ! brouard 9672: fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
! 9673: return 1;
1.234 brouard 9674: }else if(match > 1){
9675: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
1.310 ! brouard 9676: fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
! 9677: return 1;
1.234 brouard 9678: }
9679: }
1.235 brouard 9680:
1.234 brouard 9681: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9682: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9683: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9684: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9685: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9686: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9687: /* 1 0 0 0 */
9688: /* 2 1 0 0 */
9689: /* 3 0 1 0 */
9690: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9691: /* 5 0 0 1 */
9692: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9693: /* 7 0 1 1 */
9694: /* 8 1 1 1 */
1.237 brouard 9695: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9696: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9697: /* V5*age V5 known which value for nres? */
9698: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9699: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9700: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9701: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9702: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9703: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9704: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9705: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9706: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9707: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9708: k4++;;
9709: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9710: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9711: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9712: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9713: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9714: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9715: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9716: k4q++;;
9717: }
9718: }
1.234 brouard 9719:
1.235 brouard 9720: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9721: return (0);
9722: }
1.235 brouard 9723:
1.230 brouard 9724: int decodemodel( char model[], int lastobs)
9725: /**< This routine decodes the model and returns:
1.224 brouard 9726: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9727: * - nagesqr = 1 if age*age in the model, otherwise 0.
9728: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9729: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9730: * - cptcovage number of covariates with age*products =2
9731: * - cptcovs number of simple covariates
9732: * - 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
9733: * which is a new column after the 9 (ncovcol) variables.
9734: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9735: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9736: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9737: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9738: */
1.136 brouard 9739: {
1.238 brouard 9740: int i, j, k, ks, v;
1.227 brouard 9741: int j1, k1, k2, k3, k4;
1.136 brouard 9742: char modelsav[80];
1.145 brouard 9743: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9744: char *strpt;
1.136 brouard 9745:
1.145 brouard 9746: /*removespace(model);*/
1.136 brouard 9747: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9748: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9749: if (strstr(model,"AGE") !=0){
1.192 brouard 9750: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9751: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9752: return 1;
9753: }
1.141 brouard 9754: if (strstr(model,"v") !=0){
9755: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9756: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9757: return 1;
9758: }
1.187 brouard 9759: strcpy(modelsav,model);
9760: if ((strpt=strstr(model,"age*age")) !=0){
9761: printf(" strpt=%s, model=%s\n",strpt, model);
9762: if(strpt != model){
1.234 brouard 9763: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9764: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9765: corresponding column of parameters.\n",model);
1.234 brouard 9766: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9767: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9768: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9769: return 1;
1.225 brouard 9770: }
1.187 brouard 9771: nagesqr=1;
9772: if (strstr(model,"+age*age") !=0)
1.234 brouard 9773: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9774: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9775: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9776: else
1.234 brouard 9777: substrchaine(modelsav, model, "age*age");
1.187 brouard 9778: }else
9779: nagesqr=0;
9780: if (strlen(modelsav) >1){
9781: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9782: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9783: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9784: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9785: * cst, age and age*age
9786: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9787: /* including age products which are counted in cptcovage.
9788: * but the covariates which are products must be treated
9789: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9790: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9791: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9792:
9793:
1.187 brouard 9794: /* Design
9795: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9796: * < ncovcol=8 >
9797: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9798: * k= 1 2 3 4 5 6 7 8
9799: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9800: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9801: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9802: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9803: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9804: * Tage[++cptcovage]=k
9805: * if products, new covar are created after ncovcol with k1
9806: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9807: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9808: * 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
9809: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9810: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9811: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9812: * < ncovcol=8 >
9813: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9814: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9815: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9816: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9817: * p Tprod[1]@2={ 6, 5}
9818: *p Tvard[1][1]@4= {7, 8, 5, 6}
9819: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9820: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9821: *How to reorganize?
9822: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9823: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9824: * {2, 1, 4, 8, 5, 6, 3, 7}
9825: * Struct []
9826: */
1.225 brouard 9827:
1.187 brouard 9828: /* This loop fills the array Tvar from the string 'model'.*/
9829: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9830: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9831: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9832: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9833: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9834: /* k=1 Tvar[1]=2 (from V2) */
9835: /* k=5 Tvar[5] */
9836: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9837: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9838: /* } */
1.198 brouard 9839: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9840: /*
9841: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9842: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9843: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9844: }
1.187 brouard 9845: cptcovage=0;
9846: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9847: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9848: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9849: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9850: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9851: /*scanf("%d",i);*/
9852: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9853: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9854: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9855: /* covar is not filled and then is empty */
9856: cptcovprod--;
9857: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9858: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9859: Typevar[k]=1; /* 1 for age product */
9860: cptcovage++; /* Sums the number of covariates which include age as a product */
9861: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9862: /*printf("stre=%s ", stre);*/
9863: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9864: cptcovprod--;
9865: cutl(stre,strb,strc,'V');
9866: Tvar[k]=atoi(stre);
9867: Typevar[k]=1; /* 1 for age product */
9868: cptcovage++;
9869: Tage[cptcovage]=k;
9870: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9871: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9872: cptcovn++;
9873: cptcovprodnoage++;k1++;
9874: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9875: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9876: because this model-covariate is a construction we invent a new column
9877: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9878: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9879: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9880: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9881: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9882: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9883: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9884: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9885: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9886: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9887: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9888: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9889: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9890: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9891: for (i=1; i<=lastobs;i++){
9892: /* Computes the new covariate which is a product of
9893: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9894: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9895: }
9896: } /* End age is not in the model */
9897: } /* End if model includes a product */
9898: else { /* no more sum */
9899: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9900: /* scanf("%d",i);*/
9901: cutl(strd,strc,strb,'V');
9902: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9903: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9904: Tvar[k]=atoi(strd);
9905: Typevar[k]=0; /* 0 for simple covariates */
9906: }
9907: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9908: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9909: scanf("%d",i);*/
1.187 brouard 9910: } /* end of loop + on total covariates */
9911: } /* end if strlen(modelsave == 0) age*age might exist */
9912: } /* end if strlen(model == 0) */
1.136 brouard 9913:
9914: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9915: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9916:
1.136 brouard 9917: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9918: printf("cptcovprod=%d ", cptcovprod);
9919: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9920: scanf("%d ",i);*/
9921:
9922:
1.230 brouard 9923: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9924: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9925: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9926: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9927: k = 1 2 3 4 5 6 7 8 9
9928: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9929: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9930: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9931: Dummy[k] 1 0 0 0 3 1 1 2 3
9932: Tmodelind[combination of covar]=k;
1.225 brouard 9933: */
9934: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9935: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9936: /* 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 9937: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9938: printf("Model=%s\n\
9939: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9940: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9941: 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);
9942: fprintf(ficlog,"Model=%s\n\
9943: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9944: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9945: 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 9946: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9947: 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 */
9948: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9949: Fixed[k]= 0;
9950: Dummy[k]= 0;
1.225 brouard 9951: ncoveff++;
1.232 brouard 9952: ncovf++;
1.234 brouard 9953: nsd++;
9954: modell[k].maintype= FTYPE;
9955: TvarsD[nsd]=Tvar[k];
9956: TvarsDind[nsd]=k;
9957: TvarF[ncovf]=Tvar[k];
9958: TvarFind[ncovf]=k;
9959: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9960: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9961: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9962: Fixed[k]= 0;
9963: Dummy[k]= 0;
9964: ncoveff++;
9965: ncovf++;
9966: modell[k].maintype= FTYPE;
9967: TvarF[ncovf]=Tvar[k];
9968: TvarFind[ncovf]=k;
1.230 brouard 9969: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9970: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9971: }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 9972: Fixed[k]= 0;
9973: Dummy[k]= 1;
1.230 brouard 9974: nqfveff++;
1.234 brouard 9975: modell[k].maintype= FTYPE;
9976: modell[k].subtype= FQ;
9977: nsq++;
9978: TvarsQ[nsq]=Tvar[k];
9979: TvarsQind[nsq]=k;
1.232 brouard 9980: ncovf++;
1.234 brouard 9981: TvarF[ncovf]=Tvar[k];
9982: TvarFind[ncovf]=k;
1.231 brouard 9983: 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 9984: 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 9985: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9986: Fixed[k]= 1;
9987: Dummy[k]= 0;
1.225 brouard 9988: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9989: modell[k].maintype= VTYPE;
9990: modell[k].subtype= VD;
9991: nsd++;
9992: TvarsD[nsd]=Tvar[k];
9993: TvarsDind[nsd]=k;
9994: ncovv++; /* Only simple time varying variables */
9995: TvarV[ncovv]=Tvar[k];
1.242 brouard 9996: 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 9997: 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 */
9998: 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 9999: 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);
10000: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 10001: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 10002: Fixed[k]= 1;
10003: Dummy[k]= 1;
10004: nqtveff++;
10005: modell[k].maintype= VTYPE;
10006: modell[k].subtype= VQ;
10007: ncovv++; /* Only simple time varying variables */
10008: nsq++;
10009: TvarsQ[nsq]=Tvar[k];
10010: TvarsQind[nsq]=k;
10011: TvarV[ncovv]=Tvar[k];
1.242 brouard 10012: 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 10013: 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 */
10014: 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 10015: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
10016: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
10017: 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 10018: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 10019: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 10020: ncova++;
10021: TvarA[ncova]=Tvar[k];
10022: TvarAind[ncova]=k;
1.231 brouard 10023: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10024: Fixed[k]= 2;
10025: Dummy[k]= 2;
10026: modell[k].maintype= ATYPE;
10027: modell[k].subtype= APFD;
10028: /* ncoveff++; */
1.227 brouard 10029: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10030: Fixed[k]= 2;
10031: Dummy[k]= 3;
10032: modell[k].maintype= ATYPE;
10033: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10034: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10035: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10036: Fixed[k]= 3;
10037: Dummy[k]= 2;
10038: modell[k].maintype= ATYPE;
10039: modell[k].subtype= APVD; /* Product age * varying dummy */
10040: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10041: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10042: Fixed[k]= 3;
10043: Dummy[k]= 3;
10044: modell[k].maintype= ATYPE;
10045: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10046: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10047: }
10048: }else if (Typevar[k] == 2) { /* product without age */
10049: k1=Tposprod[k];
10050: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10051: if(Tvard[k1][2] <=ncovcol){
10052: Fixed[k]= 1;
10053: Dummy[k]= 0;
10054: modell[k].maintype= FTYPE;
10055: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10056: ncovf++; /* Fixed variables without age */
10057: TvarF[ncovf]=Tvar[k];
10058: TvarFind[ncovf]=k;
10059: }else if(Tvard[k1][2] <=ncovcol+nqv){
10060: Fixed[k]= 0; /* or 2 ?*/
10061: Dummy[k]= 1;
10062: modell[k].maintype= FTYPE;
10063: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10064: ncovf++; /* Varying variables without age */
10065: TvarF[ncovf]=Tvar[k];
10066: TvarFind[ncovf]=k;
10067: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10068: Fixed[k]= 1;
10069: Dummy[k]= 0;
10070: modell[k].maintype= VTYPE;
10071: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10072: ncovv++; /* Varying variables without age */
10073: TvarV[ncovv]=Tvar[k];
10074: TvarVind[ncovv]=k;
10075: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10076: Fixed[k]= 1;
10077: Dummy[k]= 1;
10078: modell[k].maintype= VTYPE;
10079: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10080: ncovv++; /* Varying variables without age */
10081: TvarV[ncovv]=Tvar[k];
10082: TvarVind[ncovv]=k;
10083: }
1.227 brouard 10084: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10085: if(Tvard[k1][2] <=ncovcol){
10086: Fixed[k]= 0; /* or 2 ?*/
10087: Dummy[k]= 1;
10088: modell[k].maintype= FTYPE;
10089: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10090: ncovf++; /* Fixed variables without age */
10091: TvarF[ncovf]=Tvar[k];
10092: TvarFind[ncovf]=k;
10093: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10094: Fixed[k]= 1;
10095: Dummy[k]= 1;
10096: modell[k].maintype= VTYPE;
10097: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10098: ncovv++; /* Varying variables without age */
10099: TvarV[ncovv]=Tvar[k];
10100: TvarVind[ncovv]=k;
10101: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10102: Fixed[k]= 1;
10103: Dummy[k]= 1;
10104: modell[k].maintype= VTYPE;
10105: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10106: ncovv++; /* Varying variables without age */
10107: TvarV[ncovv]=Tvar[k];
10108: TvarVind[ncovv]=k;
10109: ncovv++; /* Varying variables without age */
10110: TvarV[ncovv]=Tvar[k];
10111: TvarVind[ncovv]=k;
10112: }
1.227 brouard 10113: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10114: if(Tvard[k1][2] <=ncovcol){
10115: Fixed[k]= 1;
10116: Dummy[k]= 1;
10117: modell[k].maintype= VTYPE;
10118: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10119: ncovv++; /* Varying variables without age */
10120: TvarV[ncovv]=Tvar[k];
10121: TvarVind[ncovv]=k;
10122: }else if(Tvard[k1][2] <=ncovcol+nqv){
10123: Fixed[k]= 1;
10124: Dummy[k]= 1;
10125: modell[k].maintype= VTYPE;
10126: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10127: ncovv++; /* Varying variables without age */
10128: TvarV[ncovv]=Tvar[k];
10129: TvarVind[ncovv]=k;
10130: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10131: Fixed[k]= 1;
10132: Dummy[k]= 0;
10133: modell[k].maintype= VTYPE;
10134: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10135: ncovv++; /* Varying variables without age */
10136: TvarV[ncovv]=Tvar[k];
10137: TvarVind[ncovv]=k;
10138: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10139: Fixed[k]= 1;
10140: Dummy[k]= 1;
10141: modell[k].maintype= VTYPE;
10142: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10143: ncovv++; /* Varying variables without age */
10144: TvarV[ncovv]=Tvar[k];
10145: TvarVind[ncovv]=k;
10146: }
1.227 brouard 10147: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10148: if(Tvard[k1][2] <=ncovcol){
10149: Fixed[k]= 1;
10150: Dummy[k]= 1;
10151: modell[k].maintype= VTYPE;
10152: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10153: ncovv++; /* Varying variables without age */
10154: TvarV[ncovv]=Tvar[k];
10155: TvarVind[ncovv]=k;
10156: }else if(Tvard[k1][2] <=ncovcol+nqv){
10157: Fixed[k]= 1;
10158: Dummy[k]= 1;
10159: modell[k].maintype= VTYPE;
10160: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10161: ncovv++; /* Varying variables without age */
10162: TvarV[ncovv]=Tvar[k];
10163: TvarVind[ncovv]=k;
10164: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10165: Fixed[k]= 1;
10166: Dummy[k]= 1;
10167: modell[k].maintype= VTYPE;
10168: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10169: ncovv++; /* Varying variables without age */
10170: TvarV[ncovv]=Tvar[k];
10171: TvarVind[ncovv]=k;
10172: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10173: Fixed[k]= 1;
10174: Dummy[k]= 1;
10175: modell[k].maintype= VTYPE;
10176: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10177: ncovv++; /* Varying variables without age */
10178: TvarV[ncovv]=Tvar[k];
10179: TvarVind[ncovv]=k;
10180: }
1.227 brouard 10181: }else{
1.240 brouard 10182: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10183: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10184: } /*end k1*/
1.225 brouard 10185: }else{
1.226 brouard 10186: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10187: 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 10188: }
1.227 brouard 10189: 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 10190: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10191: 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]);
10192: }
10193: /* Searching for doublons in the model */
10194: for(k1=1; k1<= cptcovt;k1++){
10195: for(k2=1; k2 <k1;k2++){
1.285 brouard 10196: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10197: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10198: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10199: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10200: 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]);
10201: 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 10202: return(1);
10203: }
10204: }else if (Typevar[k1] ==2){
10205: k3=Tposprod[k1];
10206: k4=Tposprod[k2];
10207: 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])) ){
10208: 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]]);
10209: 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);
10210: return(1);
10211: }
10212: }
1.227 brouard 10213: }
10214: }
1.225 brouard 10215: }
10216: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10217: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10218: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10219: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10220: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10221: /*endread:*/
1.225 brouard 10222: printf("Exiting decodemodel: ");
10223: return (1);
1.136 brouard 10224: }
10225:
1.169 brouard 10226: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10227: {/* Check ages at death */
1.136 brouard 10228: int i, m;
1.218 brouard 10229: int firstone=0;
10230:
1.136 brouard 10231: for (i=1; i<=imx; i++) {
10232: for(m=2; (m<= maxwav); m++) {
10233: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10234: anint[m][i]=9999;
1.216 brouard 10235: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10236: s[m][i]=-1;
1.136 brouard 10237: }
10238: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10239: *nberr = *nberr + 1;
1.218 brouard 10240: if(firstone == 0){
10241: firstone=1;
1.260 brouard 10242: 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 10243: }
1.262 brouard 10244: 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 10245: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10246: }
10247: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10248: (*nberr)++;
1.259 brouard 10249: 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 10250: 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 10251: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10252: }
10253: }
10254: }
10255:
10256: for (i=1; i<=imx; i++) {
10257: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10258: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10259: 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 10260: if (s[m][i] >= nlstate+1) {
1.169 brouard 10261: if(agedc[i]>0){
10262: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10263: agev[m][i]=agedc[i];
1.214 brouard 10264: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10265: }else {
1.136 brouard 10266: if ((int)andc[i]!=9999){
10267: nbwarn++;
10268: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10269: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10270: agev[m][i]=-1;
10271: }
10272: }
1.169 brouard 10273: } /* agedc > 0 */
1.214 brouard 10274: } /* end if */
1.136 brouard 10275: else if(s[m][i] !=9){ /* Standard case, age in fractional
10276: years but with the precision of a month */
10277: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10278: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10279: agev[m][i]=1;
10280: else if(agev[m][i] < *agemin){
10281: *agemin=agev[m][i];
10282: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10283: }
10284: else if(agev[m][i] >*agemax){
10285: *agemax=agev[m][i];
1.156 brouard 10286: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10287: }
10288: /*agev[m][i]=anint[m][i]-annais[i];*/
10289: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10290: } /* en if 9*/
1.136 brouard 10291: else { /* =9 */
1.214 brouard 10292: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10293: agev[m][i]=1;
10294: s[m][i]=-1;
10295: }
10296: }
1.214 brouard 10297: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10298: agev[m][i]=1;
1.214 brouard 10299: else{
10300: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10301: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10302: agev[m][i]=0;
10303: }
10304: } /* End for lastpass */
10305: }
1.136 brouard 10306:
10307: for (i=1; i<=imx; i++) {
10308: for(m=firstpass; (m<=lastpass); m++){
10309: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10310: (*nberr)++;
1.136 brouard 10311: 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);
10312: 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);
10313: return 1;
10314: }
10315: }
10316: }
10317:
10318: /*for (i=1; i<=imx; i++){
10319: for (m=firstpass; (m<lastpass); m++){
10320: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10321: }
10322:
10323: }*/
10324:
10325:
1.139 brouard 10326: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10327: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10328:
10329: return (0);
1.164 brouard 10330: /* endread:*/
1.136 brouard 10331: printf("Exiting calandcheckages: ");
10332: return (1);
10333: }
10334:
1.172 brouard 10335: #if defined(_MSC_VER)
10336: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10337: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10338: //#include "stdafx.h"
10339: //#include <stdio.h>
10340: //#include <tchar.h>
10341: //#include <windows.h>
10342: //#include <iostream>
10343: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10344:
10345: LPFN_ISWOW64PROCESS fnIsWow64Process;
10346:
10347: BOOL IsWow64()
10348: {
10349: BOOL bIsWow64 = FALSE;
10350:
10351: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10352: // (HANDLE, PBOOL);
10353:
10354: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10355:
10356: HMODULE module = GetModuleHandle(_T("kernel32"));
10357: const char funcName[] = "IsWow64Process";
10358: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10359: GetProcAddress(module, funcName);
10360:
10361: if (NULL != fnIsWow64Process)
10362: {
10363: if (!fnIsWow64Process(GetCurrentProcess(),
10364: &bIsWow64))
10365: //throw std::exception("Unknown error");
10366: printf("Unknown error\n");
10367: }
10368: return bIsWow64 != FALSE;
10369: }
10370: #endif
1.177 brouard 10371:
1.191 brouard 10372: void syscompilerinfo(int logged)
1.292 brouard 10373: {
10374: #include <stdint.h>
10375:
10376: /* #include "syscompilerinfo.h"*/
1.185 brouard 10377: /* command line Intel compiler 32bit windows, XP compatible:*/
10378: /* /GS /W3 /Gy
10379: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10380: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10381: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10382: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10383: */
10384: /* 64 bits */
1.185 brouard 10385: /*
10386: /GS /W3 /Gy
10387: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10388: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10389: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10390: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10391: /* Optimization are useless and O3 is slower than O2 */
10392: /*
10393: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10394: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10395: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10396: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10397: */
1.186 brouard 10398: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10399: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10400: /PDB:"visual studio
10401: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10402: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10403: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10404: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10405: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10406: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10407: uiAccess='false'"
10408: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10409: /NOLOGO /TLBID:1
10410: */
1.292 brouard 10411:
10412:
1.177 brouard 10413: #if defined __INTEL_COMPILER
1.178 brouard 10414: #if defined(__GNUC__)
10415: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10416: #endif
1.177 brouard 10417: #elif defined(__GNUC__)
1.179 brouard 10418: #ifndef __APPLE__
1.174 brouard 10419: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10420: #endif
1.177 brouard 10421: struct utsname sysInfo;
1.178 brouard 10422: int cross = CROSS;
10423: if (cross){
10424: printf("Cross-");
1.191 brouard 10425: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10426: }
1.174 brouard 10427: #endif
10428:
1.191 brouard 10429: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10430: #if defined(__clang__)
1.191 brouard 10431: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10432: #endif
10433: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10434: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10435: #endif
10436: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10437: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10438: #endif
10439: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10440: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10441: #endif
10442: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10443: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10444: #endif
10445: #if defined(_MSC_VER)
1.191 brouard 10446: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10447: #endif
10448: #if defined(__PGI)
1.191 brouard 10449: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10450: #endif
10451: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10452: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10453: #endif
1.191 brouard 10454: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10455:
1.167 brouard 10456: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10457: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10458: // Windows (x64 and x86)
1.191 brouard 10459: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10460: #elif __unix__ // all unices, not all compilers
10461: // Unix
1.191 brouard 10462: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10463: #elif __linux__
10464: // linux
1.191 brouard 10465: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10466: #elif __APPLE__
1.174 brouard 10467: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10468: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10469: #endif
10470:
10471: /* __MINGW32__ */
10472: /* __CYGWIN__ */
10473: /* __MINGW64__ */
10474: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10475: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10476: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10477: /* _WIN64 // Defined for applications for Win64. */
10478: /* _M_X64 // Defined for compilations that target x64 processors. */
10479: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10480:
1.167 brouard 10481: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10482: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10483: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10484: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10485: #else
1.191 brouard 10486: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10487: #endif
10488:
1.169 brouard 10489: #if defined(__GNUC__)
10490: # if defined(__GNUC_PATCHLEVEL__)
10491: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10492: + __GNUC_MINOR__ * 100 \
10493: + __GNUC_PATCHLEVEL__)
10494: # else
10495: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10496: + __GNUC_MINOR__ * 100)
10497: # endif
1.174 brouard 10498: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10499: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10500:
10501: if (uname(&sysInfo) != -1) {
10502: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10503: 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 10504: }
10505: else
10506: perror("uname() error");
1.179 brouard 10507: //#ifndef __INTEL_COMPILER
10508: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10509: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10510: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10511: #endif
1.169 brouard 10512: #endif
1.172 brouard 10513:
1.286 brouard 10514: // void main ()
1.172 brouard 10515: // {
1.169 brouard 10516: #if defined(_MSC_VER)
1.174 brouard 10517: if (IsWow64()){
1.191 brouard 10518: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10519: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10520: }
10521: else{
1.191 brouard 10522: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10523: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10524: }
1.172 brouard 10525: // printf("\nPress Enter to continue...");
10526: // getchar();
10527: // }
10528:
1.169 brouard 10529: #endif
10530:
1.167 brouard 10531:
1.219 brouard 10532: }
1.136 brouard 10533:
1.219 brouard 10534: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10535: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10536: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10537: /* double ftolpl = 1.e-10; */
1.180 brouard 10538: double age, agebase, agelim;
1.203 brouard 10539: double tot;
1.180 brouard 10540:
1.202 brouard 10541: strcpy(filerespl,"PL_");
10542: strcat(filerespl,fileresu);
10543: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10544: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10545: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10546: }
1.288 brouard 10547: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10548: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10549: pstamp(ficrespl);
1.288 brouard 10550: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10551: fprintf(ficrespl,"#Age ");
10552: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10553: fprintf(ficrespl,"\n");
1.180 brouard 10554:
1.219 brouard 10555: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10556:
1.219 brouard 10557: agebase=ageminpar;
10558: agelim=agemaxpar;
1.180 brouard 10559:
1.227 brouard 10560: /* i1=pow(2,ncoveff); */
1.234 brouard 10561: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10562: if (cptcovn < 1){i1=1;}
1.180 brouard 10563:
1.238 brouard 10564: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10565: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10566: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10567: continue;
1.235 brouard 10568:
1.238 brouard 10569: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10570: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10571: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10572: /* k=k+1; */
10573: /* to clean */
10574: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10575: fprintf(ficrespl,"#******");
10576: printf("#******");
10577: fprintf(ficlog,"#******");
10578: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10579: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10580: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10581: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10582: }
10583: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10584: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10585: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10586: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10587: }
10588: fprintf(ficrespl,"******\n");
10589: printf("******\n");
10590: fprintf(ficlog,"******\n");
10591: if(invalidvarcomb[k]){
10592: printf("\nCombination (%d) ignored because no case \n",k);
10593: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10594: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10595: continue;
10596: }
1.219 brouard 10597:
1.238 brouard 10598: fprintf(ficrespl,"#Age ");
10599: for(j=1;j<=cptcoveff;j++) {
10600: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10601: }
10602: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10603: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10604:
1.238 brouard 10605: for (age=agebase; age<=agelim; age++){
10606: /* for (age=agebase; age<=agebase; age++){ */
10607: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10608: fprintf(ficrespl,"%.0f ",age );
10609: for(j=1;j<=cptcoveff;j++)
10610: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10611: tot=0.;
10612: for(i=1; i<=nlstate;i++){
10613: tot += prlim[i][i];
10614: fprintf(ficrespl," %.5f", prlim[i][i]);
10615: }
10616: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10617: } /* Age */
10618: /* was end of cptcod */
10619: } /* cptcov */
10620: } /* nres */
1.219 brouard 10621: return 0;
1.180 brouard 10622: }
10623:
1.218 brouard 10624: 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 10625: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10626:
10627: /* Computes the back prevalence limit for any combination of covariate values
10628: * at any age between ageminpar and agemaxpar
10629: */
1.235 brouard 10630: int i, j, k, i1, nres=0 ;
1.217 brouard 10631: /* double ftolpl = 1.e-10; */
10632: double age, agebase, agelim;
10633: double tot;
1.218 brouard 10634: /* double ***mobaverage; */
10635: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10636:
10637: strcpy(fileresplb,"PLB_");
10638: strcat(fileresplb,fileresu);
10639: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10640: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10641: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10642: }
1.288 brouard 10643: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10644: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10645: pstamp(ficresplb);
1.288 brouard 10646: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10647: fprintf(ficresplb,"#Age ");
10648: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10649: fprintf(ficresplb,"\n");
10650:
1.218 brouard 10651:
10652: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10653:
10654: agebase=ageminpar;
10655: agelim=agemaxpar;
10656:
10657:
1.227 brouard 10658: i1=pow(2,cptcoveff);
1.218 brouard 10659: if (cptcovn < 1){i1=1;}
1.227 brouard 10660:
1.238 brouard 10661: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10662: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10663: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10664: continue;
10665: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10666: fprintf(ficresplb,"#******");
10667: printf("#******");
10668: fprintf(ficlog,"#******");
10669: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10670: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10671: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10672: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10673: }
10674: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10675: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10676: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10677: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10678: }
10679: fprintf(ficresplb,"******\n");
10680: printf("******\n");
10681: fprintf(ficlog,"******\n");
10682: if(invalidvarcomb[k]){
10683: printf("\nCombination (%d) ignored because no cases \n",k);
10684: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10685: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10686: continue;
10687: }
1.218 brouard 10688:
1.238 brouard 10689: fprintf(ficresplb,"#Age ");
10690: for(j=1;j<=cptcoveff;j++) {
10691: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10692: }
10693: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10694: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10695:
10696:
1.238 brouard 10697: for (age=agebase; age<=agelim; age++){
10698: /* for (age=agebase; age<=agebase; age++){ */
10699: if(mobilavproj > 0){
10700: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10701: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10702: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10703: }else if (mobilavproj == 0){
10704: 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);
10705: 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);
10706: exit(1);
10707: }else{
10708: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10709: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10710: /* printf("TOTOT\n"); */
10711: /* exit(1); */
1.238 brouard 10712: }
10713: fprintf(ficresplb,"%.0f ",age );
10714: for(j=1;j<=cptcoveff;j++)
10715: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10716: tot=0.;
10717: for(i=1; i<=nlstate;i++){
10718: tot += bprlim[i][i];
10719: fprintf(ficresplb," %.5f", bprlim[i][i]);
10720: }
10721: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10722: } /* Age */
10723: /* was end of cptcod */
1.255 brouard 10724: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10725: } /* end of any combination */
10726: } /* end of nres */
1.218 brouard 10727: /* hBijx(p, bage, fage); */
10728: /* fclose(ficrespijb); */
10729:
10730: return 0;
1.217 brouard 10731: }
1.218 brouard 10732:
1.180 brouard 10733: int hPijx(double *p, int bage, int fage){
10734: /*------------- h Pij x at various ages ------------*/
10735:
10736: int stepsize;
10737: int agelim;
10738: int hstepm;
10739: int nhstepm;
1.235 brouard 10740: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10741:
10742: double agedeb;
10743: double ***p3mat;
10744:
1.201 brouard 10745: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10746: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10747: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10748: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10749: }
10750: printf("Computing pij: result on file '%s' \n", filerespij);
10751: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10752:
10753: stepsize=(int) (stepm+YEARM-1)/YEARM;
10754: /*if (stepm<=24) stepsize=2;*/
10755:
10756: agelim=AGESUP;
10757: hstepm=stepsize*YEARM; /* Every year of age */
10758: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10759:
1.180 brouard 10760: /* hstepm=1; aff par mois*/
10761: pstamp(ficrespij);
10762: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10763: i1= pow(2,cptcoveff);
1.218 brouard 10764: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10765: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10766: /* k=k+1; */
1.235 brouard 10767: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10768: for(k=1; k<=i1;k++){
1.253 brouard 10769: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10770: continue;
1.183 brouard 10771: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10772: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10773: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10774: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10775: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10776: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10777: }
1.183 brouard 10778: fprintf(ficrespij,"******\n");
10779:
10780: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10781: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10782: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10783:
10784: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10785:
1.183 brouard 10786: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10787: oldm=oldms;savm=savms;
1.235 brouard 10788: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10789: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10790: for(i=1; i<=nlstate;i++)
10791: for(j=1; j<=nlstate+ndeath;j++)
10792: fprintf(ficrespij," %1d-%1d",i,j);
10793: fprintf(ficrespij,"\n");
10794: for (h=0; h<=nhstepm; h++){
10795: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10796: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10797: for(i=1; i<=nlstate;i++)
10798: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10799: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10800: fprintf(ficrespij,"\n");
10801: }
1.183 brouard 10802: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10803: fprintf(ficrespij,"\n");
10804: }
1.180 brouard 10805: /*}*/
10806: }
1.218 brouard 10807: return 0;
1.180 brouard 10808: }
1.218 brouard 10809:
10810: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10811: /*------------- h Bij x at various ages ------------*/
10812:
10813: int stepsize;
1.218 brouard 10814: /* int agelim; */
10815: int ageminl;
1.217 brouard 10816: int hstepm;
10817: int nhstepm;
1.238 brouard 10818: int h, i, i1, j, k, nres;
1.218 brouard 10819:
1.217 brouard 10820: double agedeb;
10821: double ***p3mat;
1.218 brouard 10822:
10823: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10824: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10825: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10826: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10827: }
10828: printf("Computing pij back: result on file '%s' \n", filerespijb);
10829: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10830:
10831: stepsize=(int) (stepm+YEARM-1)/YEARM;
10832: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10833:
1.218 brouard 10834: /* agelim=AGESUP; */
1.289 brouard 10835: ageminl=AGEINF; /* was 30 */
1.218 brouard 10836: hstepm=stepsize*YEARM; /* Every year of age */
10837: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10838:
10839: /* hstepm=1; aff par mois*/
10840: pstamp(ficrespijb);
1.255 brouard 10841: 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 10842: i1= pow(2,cptcoveff);
1.218 brouard 10843: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10844: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10845: /* k=k+1; */
1.238 brouard 10846: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10847: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10848: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10849: continue;
10850: fprintf(ficrespijb,"\n#****** ");
10851: for(j=1;j<=cptcoveff;j++)
10852: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10853: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10854: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10855: }
10856: fprintf(ficrespijb,"******\n");
1.264 brouard 10857: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10858: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10859: continue;
10860: }
10861:
10862: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10863: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10864: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10865: 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 */
10866: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10867:
10868: /* nhstepm=nhstepm*YEARM; aff par mois*/
10869:
1.266 brouard 10870: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10871: /* and memory limitations if stepm is small */
10872:
1.238 brouard 10873: /* oldm=oldms;savm=savms; */
10874: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10875: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10876: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10877: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10878: for(i=1; i<=nlstate;i++)
10879: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10880: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10881: fprintf(ficrespijb,"\n");
1.238 brouard 10882: for (h=0; h<=nhstepm; h++){
10883: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10884: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10885: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10886: for(i=1; i<=nlstate;i++)
10887: for(j=1; j<=nlstate+ndeath;j++)
10888: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10889: fprintf(ficrespijb,"\n");
10890: }
10891: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10892: fprintf(ficrespijb,"\n");
10893: } /* end age deb */
10894: } /* end combination */
10895: } /* end nres */
1.218 brouard 10896: return 0;
10897: } /* hBijx */
1.217 brouard 10898:
1.180 brouard 10899:
1.136 brouard 10900: /***********************************************/
10901: /**************** Main Program *****************/
10902: /***********************************************/
10903:
10904: int main(int argc, char *argv[])
10905: {
10906: #ifdef GSL
10907: const gsl_multimin_fminimizer_type *T;
10908: size_t iteri = 0, it;
10909: int rval = GSL_CONTINUE;
10910: int status = GSL_SUCCESS;
10911: double ssval;
10912: #endif
10913: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10914: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10915: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10916: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10917: int jj, ll, li, lj, lk;
1.136 brouard 10918: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10919: int num_filled;
1.136 brouard 10920: int itimes;
10921: int NDIM=2;
10922: int vpopbased=0;
1.235 brouard 10923: int nres=0;
1.258 brouard 10924: int endishere=0;
1.277 brouard 10925: int noffset=0;
1.274 brouard 10926: int ncurrv=0; /* Temporary variable */
10927:
1.164 brouard 10928: char ca[32], cb[32];
1.136 brouard 10929: /* FILE *fichtm; *//* Html File */
10930: /* FILE *ficgp;*/ /*Gnuplot File */
10931: struct stat info;
1.191 brouard 10932: double agedeb=0.;
1.194 brouard 10933:
10934: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10935: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10936:
1.165 brouard 10937: double fret;
1.191 brouard 10938: double dum=0.; /* Dummy variable */
1.136 brouard 10939: double ***p3mat;
1.218 brouard 10940: /* double ***mobaverage; */
1.164 brouard 10941:
10942: char line[MAXLINE];
1.197 brouard 10943: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10944:
1.234 brouard 10945: char modeltemp[MAXLINE];
1.230 brouard 10946: char resultline[MAXLINE];
10947:
1.136 brouard 10948: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10949: char *tok, *val; /* pathtot */
1.290 brouard 10950: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10951: int c, h , cpt, c2;
1.191 brouard 10952: int jl=0;
10953: int i1, j1, jk, stepsize=0;
1.194 brouard 10954: int count=0;
10955:
1.164 brouard 10956: int *tab;
1.136 brouard 10957: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10958: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10959: /* double anprojf, mprojf, jprojf; */
10960: /* double jintmean,mintmean,aintmean; */
10961: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10962: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10963: double yrfproj= 10.0; /* Number of years of forward projections */
10964: double yrbproj= 10.0; /* Number of years of backward projections */
10965: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10966: int mobilav=0,popforecast=0;
1.191 brouard 10967: int hstepm=0, nhstepm=0;
1.136 brouard 10968: int agemortsup;
10969: float sumlpop=0.;
10970: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10971: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10972:
1.191 brouard 10973: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10974: double ftolpl=FTOL;
10975: double **prlim;
1.217 brouard 10976: double **bprlim;
1.136 brouard 10977: double ***param; /* Matrix of parameters */
1.251 brouard 10978: double ***paramstart; /* Matrix of starting parameter values */
10979: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10980: double **matcov; /* Matrix of covariance */
1.203 brouard 10981: double **hess; /* Hessian matrix */
1.136 brouard 10982: double ***delti3; /* Scale */
10983: double *delti; /* Scale */
10984: double ***eij, ***vareij;
10985: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10986:
1.136 brouard 10987: double *epj, vepp;
1.164 brouard 10988:
1.273 brouard 10989: double dateprev1, dateprev2;
1.296 brouard 10990: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10991: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10992:
1.217 brouard 10993:
1.136 brouard 10994: double **ximort;
1.145 brouard 10995: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10996: int *dcwave;
10997:
1.164 brouard 10998: char z[1]="c";
1.136 brouard 10999:
11000: /*char *strt;*/
11001: char strtend[80];
1.126 brouard 11002:
1.164 brouard 11003:
1.126 brouard 11004: /* setlocale (LC_ALL, ""); */
11005: /* bindtextdomain (PACKAGE, LOCALEDIR); */
11006: /* textdomain (PACKAGE); */
11007: /* setlocale (LC_CTYPE, ""); */
11008: /* setlocale (LC_MESSAGES, ""); */
11009:
11010: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 11011: rstart_time = time(NULL);
11012: /* (void) gettimeofday(&start_time,&tzp);*/
11013: start_time = *localtime(&rstart_time);
1.126 brouard 11014: curr_time=start_time;
1.157 brouard 11015: /*tml = *localtime(&start_time.tm_sec);*/
11016: /* strcpy(strstart,asctime(&tml)); */
11017: strcpy(strstart,asctime(&start_time));
1.126 brouard 11018:
11019: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 11020: /* tp.tm_sec = tp.tm_sec +86400; */
11021: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 11022: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11023: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11024: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11025: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11026: /* strt=asctime(&tmg); */
11027: /* printf("Time(after) =%s",strstart); */
11028: /* (void) time (&time_value);
11029: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11030: * tm = *localtime(&time_value);
11031: * strstart=asctime(&tm);
11032: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11033: */
11034:
11035: nberr=0; /* Number of errors and warnings */
11036: nbwarn=0;
1.184 brouard 11037: #ifdef WIN32
11038: _getcwd(pathcd, size);
11039: #else
1.126 brouard 11040: getcwd(pathcd, size);
1.184 brouard 11041: #endif
1.191 brouard 11042: syscompilerinfo(0);
1.196 brouard 11043: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11044: if(argc <=1){
11045: printf("\nEnter the parameter file name: ");
1.205 brouard 11046: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11047: printf("ERROR Empty parameter file name\n");
11048: goto end;
11049: }
1.126 brouard 11050: i=strlen(pathr);
11051: if(pathr[i-1]=='\n')
11052: pathr[i-1]='\0';
1.156 brouard 11053: i=strlen(pathr);
1.205 brouard 11054: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11055: pathr[i-1]='\0';
1.205 brouard 11056: }
11057: i=strlen(pathr);
11058: if( i==0 ){
11059: printf("ERROR Empty parameter file name\n");
11060: goto end;
11061: }
11062: for (tok = pathr; tok != NULL; ){
1.126 brouard 11063: printf("Pathr |%s|\n",pathr);
11064: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11065: printf("val= |%s| pathr=%s\n",val,pathr);
11066: strcpy (pathtot, val);
11067: if(pathr[0] == '\0') break; /* Dirty */
11068: }
11069: }
1.281 brouard 11070: else if (argc<=2){
11071: strcpy(pathtot,argv[1]);
11072: }
1.126 brouard 11073: else{
11074: strcpy(pathtot,argv[1]);
1.281 brouard 11075: strcpy(z,argv[2]);
11076: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11077: }
11078: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11079: /*cygwin_split_path(pathtot,path,optionfile);
11080: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11081: /* cutv(path,optionfile,pathtot,'\\');*/
11082:
11083: /* Split argv[0], imach program to get pathimach */
11084: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11085: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11086: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11087: /* strcpy(pathimach,argv[0]); */
11088: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11089: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11090: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11091: #ifdef WIN32
11092: _chdir(path); /* Can be a relative path */
11093: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11094: #else
1.126 brouard 11095: chdir(path); /* Can be a relative path */
1.184 brouard 11096: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11097: #endif
11098: printf("Current directory %s!\n",pathcd);
1.126 brouard 11099: strcpy(command,"mkdir ");
11100: strcat(command,optionfilefiname);
11101: if((outcmd=system(command)) != 0){
1.169 brouard 11102: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11103: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11104: /* fclose(ficlog); */
11105: /* exit(1); */
11106: }
11107: /* if((imk=mkdir(optionfilefiname))<0){ */
11108: /* perror("mkdir"); */
11109: /* } */
11110:
11111: /*-------- arguments in the command line --------*/
11112:
1.186 brouard 11113: /* Main Log file */
1.126 brouard 11114: strcat(filelog, optionfilefiname);
11115: strcat(filelog,".log"); /* */
11116: if((ficlog=fopen(filelog,"w"))==NULL) {
11117: printf("Problem with logfile %s\n",filelog);
11118: goto end;
11119: }
11120: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11121: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11122: fprintf(ficlog,"\nEnter the parameter file name: \n");
11123: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11124: path=%s \n\
11125: optionfile=%s\n\
11126: optionfilext=%s\n\
1.156 brouard 11127: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11128:
1.197 brouard 11129: syscompilerinfo(1);
1.167 brouard 11130:
1.126 brouard 11131: printf("Local time (at start):%s",strstart);
11132: fprintf(ficlog,"Local time (at start): %s",strstart);
11133: fflush(ficlog);
11134: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11135: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11136:
11137: /* */
11138: strcpy(fileres,"r");
11139: strcat(fileres, optionfilefiname);
1.201 brouard 11140: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11141: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11142: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11143:
1.186 brouard 11144: /* Main ---------arguments file --------*/
1.126 brouard 11145:
11146: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11147: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11148: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11149: fflush(ficlog);
1.149 brouard 11150: /* goto end; */
11151: exit(70);
1.126 brouard 11152: }
11153:
11154: strcpy(filereso,"o");
1.201 brouard 11155: strcat(filereso,fileresu);
1.126 brouard 11156: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11157: printf("Problem with Output resultfile: %s\n", filereso);
11158: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11159: fflush(ficlog);
11160: goto end;
11161: }
1.278 brouard 11162: /*-------- Rewriting parameter file ----------*/
11163: strcpy(rfileres,"r"); /* "Rparameterfile */
11164: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11165: strcat(rfileres,"."); /* */
11166: strcat(rfileres,optionfilext); /* Other files have txt extension */
11167: if((ficres =fopen(rfileres,"w"))==NULL) {
11168: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11169: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11170: fflush(ficlog);
11171: goto end;
11172: }
11173: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11174:
1.278 brouard 11175:
1.126 brouard 11176: /* Reads comments: lines beginning with '#' */
11177: numlinepar=0;
1.277 brouard 11178: /* Is it a BOM UTF-8 Windows file? */
11179: /* First parameter line */
1.197 brouard 11180: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11181: noffset=0;
11182: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11183: {
11184: noffset=noffset+3;
11185: printf("# File is an UTF8 Bom.\n"); // 0xBF
11186: }
1.302 brouard 11187: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11188: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11189: {
11190: noffset=noffset+2;
11191: printf("# File is an UTF16BE BOM file\n");
11192: }
11193: else if( line[0] == 0 && line[1] == 0)
11194: {
11195: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11196: noffset=noffset+4;
11197: printf("# File is an UTF16BE BOM file\n");
11198: }
11199: } else{
11200: ;/*printf(" Not a BOM file\n");*/
11201: }
11202:
1.197 brouard 11203: /* If line starts with a # it is a comment */
1.277 brouard 11204: if (line[noffset] == '#') {
1.197 brouard 11205: numlinepar++;
11206: fputs(line,stdout);
11207: fputs(line,ficparo);
1.278 brouard 11208: fputs(line,ficres);
1.197 brouard 11209: fputs(line,ficlog);
11210: continue;
11211: }else
11212: break;
11213: }
11214: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11215: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11216: if (num_filled != 5) {
11217: printf("Should be 5 parameters\n");
1.283 brouard 11218: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11219: }
1.126 brouard 11220: numlinepar++;
1.197 brouard 11221: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11222: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11223: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11224: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11225: }
11226: /* Second parameter line */
11227: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11228: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11229: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11230: if (line[0] == '#') {
11231: numlinepar++;
1.283 brouard 11232: printf("%s",line);
11233: fprintf(ficres,"%s",line);
11234: fprintf(ficparo,"%s",line);
11235: fprintf(ficlog,"%s",line);
1.197 brouard 11236: continue;
11237: }else
11238: break;
11239: }
1.223 brouard 11240: 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", \
11241: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11242: if (num_filled != 11) {
11243: 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 11244: printf("but line=%s\n",line);
1.283 brouard 11245: 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");
11246: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11247: }
1.286 brouard 11248: if( lastpass > maxwav){
11249: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11250: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11251: fflush(ficlog);
11252: goto end;
11253: }
11254: 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 11255: 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 11256: 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 11257: 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 11258: }
1.203 brouard 11259: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11260: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11261: /* Third parameter line */
11262: while(fgets(line, MAXLINE, ficpar)) {
11263: /* If line starts with a # it is a comment */
11264: if (line[0] == '#') {
11265: numlinepar++;
1.283 brouard 11266: printf("%s",line);
11267: fprintf(ficres,"%s",line);
11268: fprintf(ficparo,"%s",line);
11269: fprintf(ficlog,"%s",line);
1.197 brouard 11270: continue;
11271: }else
11272: break;
11273: }
1.201 brouard 11274: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11275: if (num_filled != 1){
1.302 brouard 11276: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11277: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11278: model[0]='\0';
11279: goto end;
11280: }
11281: else{
11282: if (model[0]=='+'){
11283: for(i=1; i<=strlen(model);i++)
11284: modeltemp[i-1]=model[i];
1.201 brouard 11285: strcpy(model,modeltemp);
1.197 brouard 11286: }
11287: }
1.199 brouard 11288: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11289: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11290: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11291: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11292: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11293: }
11294: /* 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); */
11295: /* numlinepar=numlinepar+3; /\* In general *\/ */
11296: /* 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 11297: /* 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); */
11298: /* 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 11299: fflush(ficlog);
1.190 brouard 11300: /* if(model[0]=='#'|| model[0]== '\0'){ */
11301: if(model[0]=='#'){
1.279 brouard 11302: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11303: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11304: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11305: if(mle != -1){
1.279 brouard 11306: 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 11307: exit(1);
11308: }
11309: }
1.126 brouard 11310: while((c=getc(ficpar))=='#' && c!= EOF){
11311: ungetc(c,ficpar);
11312: fgets(line, MAXLINE, ficpar);
11313: numlinepar++;
1.195 brouard 11314: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11315: z[0]=line[1];
11316: }
11317: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11318: fputs(line, stdout);
11319: //puts(line);
1.126 brouard 11320: fputs(line,ficparo);
11321: fputs(line,ficlog);
11322: }
11323: ungetc(c,ficpar);
11324:
11325:
1.290 brouard 11326: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11327: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11328: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11329: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11330: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11331: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11332: v1+v2*age+v2*v3 makes cptcovn = 3
11333: */
11334: if (strlen(model)>1)
1.187 brouard 11335: 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 11336: else
1.187 brouard 11337: ncovmodel=2; /* Constant and age */
1.133 brouard 11338: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11339: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11340: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11341: 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);
11342: 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);
11343: fflush(stdout);
11344: fclose (ficlog);
11345: goto end;
11346: }
1.126 brouard 11347: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11348: delti=delti3[1][1];
11349: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11350: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11351: /* We could also provide initial parameters values giving by simple logistic regression
11352: * only one way, that is without matrix product. We will have nlstate maximizations */
11353: /* for(i=1;i<nlstate;i++){ */
11354: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11355: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11356: /* } */
1.126 brouard 11357: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11358: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11359: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11360: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11361: fclose (ficparo);
11362: fclose (ficlog);
11363: goto end;
11364: exit(0);
1.220 brouard 11365: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11366: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11367: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11368: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11369: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11370: matcov=matrix(1,npar,1,npar);
1.203 brouard 11371: hess=matrix(1,npar,1,npar);
1.220 brouard 11372: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11373: /* Read guessed parameters */
1.126 brouard 11374: /* Reads comments: lines beginning with '#' */
11375: while((c=getc(ficpar))=='#' && c!= EOF){
11376: ungetc(c,ficpar);
11377: fgets(line, MAXLINE, ficpar);
11378: numlinepar++;
1.141 brouard 11379: fputs(line,stdout);
1.126 brouard 11380: fputs(line,ficparo);
11381: fputs(line,ficlog);
11382: }
11383: ungetc(c,ficpar);
11384:
11385: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11386: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11387: for(i=1; i <=nlstate; i++){
1.234 brouard 11388: j=0;
1.126 brouard 11389: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11390: if(jj==i) continue;
11391: j++;
1.292 brouard 11392: while((c=getc(ficpar))=='#' && c!= EOF){
11393: ungetc(c,ficpar);
11394: fgets(line, MAXLINE, ficpar);
11395: numlinepar++;
11396: fputs(line,stdout);
11397: fputs(line,ficparo);
11398: fputs(line,ficlog);
11399: }
11400: ungetc(c,ficpar);
1.234 brouard 11401: fscanf(ficpar,"%1d%1d",&i1,&j1);
11402: if ((i1 != i) || (j1 != jj)){
11403: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11404: It might be a problem of design; if ncovcol and the model are correct\n \
11405: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11406: exit(1);
11407: }
11408: fprintf(ficparo,"%1d%1d",i1,j1);
11409: if(mle==1)
11410: printf("%1d%1d",i,jj);
11411: fprintf(ficlog,"%1d%1d",i,jj);
11412: for(k=1; k<=ncovmodel;k++){
11413: fscanf(ficpar," %lf",¶m[i][j][k]);
11414: if(mle==1){
11415: printf(" %lf",param[i][j][k]);
11416: fprintf(ficlog," %lf",param[i][j][k]);
11417: }
11418: else
11419: fprintf(ficlog," %lf",param[i][j][k]);
11420: fprintf(ficparo," %lf",param[i][j][k]);
11421: }
11422: fscanf(ficpar,"\n");
11423: numlinepar++;
11424: if(mle==1)
11425: printf("\n");
11426: fprintf(ficlog,"\n");
11427: fprintf(ficparo,"\n");
1.126 brouard 11428: }
11429: }
11430: fflush(ficlog);
1.234 brouard 11431:
1.251 brouard 11432: /* Reads parameters values */
1.126 brouard 11433: p=param[1][1];
1.251 brouard 11434: pstart=paramstart[1][1];
1.126 brouard 11435:
11436: /* Reads comments: lines beginning with '#' */
11437: while((c=getc(ficpar))=='#' && c!= EOF){
11438: ungetc(c,ficpar);
11439: fgets(line, MAXLINE, ficpar);
11440: numlinepar++;
1.141 brouard 11441: fputs(line,stdout);
1.126 brouard 11442: fputs(line,ficparo);
11443: fputs(line,ficlog);
11444: }
11445: ungetc(c,ficpar);
11446:
11447: for(i=1; i <=nlstate; i++){
11448: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11449: fscanf(ficpar,"%1d%1d",&i1,&j1);
11450: if ( (i1-i) * (j1-j) != 0){
11451: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11452: exit(1);
11453: }
11454: printf("%1d%1d",i,j);
11455: fprintf(ficparo,"%1d%1d",i1,j1);
11456: fprintf(ficlog,"%1d%1d",i1,j1);
11457: for(k=1; k<=ncovmodel;k++){
11458: fscanf(ficpar,"%le",&delti3[i][j][k]);
11459: printf(" %le",delti3[i][j][k]);
11460: fprintf(ficparo," %le",delti3[i][j][k]);
11461: fprintf(ficlog," %le",delti3[i][j][k]);
11462: }
11463: fscanf(ficpar,"\n");
11464: numlinepar++;
11465: printf("\n");
11466: fprintf(ficparo,"\n");
11467: fprintf(ficlog,"\n");
1.126 brouard 11468: }
11469: }
11470: fflush(ficlog);
1.234 brouard 11471:
1.145 brouard 11472: /* Reads covariance matrix */
1.126 brouard 11473: delti=delti3[1][1];
1.220 brouard 11474:
11475:
1.126 brouard 11476: /* 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 11477:
1.126 brouard 11478: /* Reads comments: lines beginning with '#' */
11479: while((c=getc(ficpar))=='#' && c!= EOF){
11480: ungetc(c,ficpar);
11481: fgets(line, MAXLINE, ficpar);
11482: numlinepar++;
1.141 brouard 11483: fputs(line,stdout);
1.126 brouard 11484: fputs(line,ficparo);
11485: fputs(line,ficlog);
11486: }
11487: ungetc(c,ficpar);
1.220 brouard 11488:
1.126 brouard 11489: matcov=matrix(1,npar,1,npar);
1.203 brouard 11490: hess=matrix(1,npar,1,npar);
1.131 brouard 11491: for(i=1; i <=npar; i++)
11492: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11493:
1.194 brouard 11494: /* Scans npar lines */
1.126 brouard 11495: for(i=1; i <=npar; i++){
1.226 brouard 11496: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11497: if(count != 3){
1.226 brouard 11498: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11499: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11500: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11501: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11502: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11503: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11504: exit(1);
1.220 brouard 11505: }else{
1.226 brouard 11506: if(mle==1)
11507: printf("%1d%1d%d",i1,j1,jk);
11508: }
11509: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11510: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11511: for(j=1; j <=i; j++){
1.226 brouard 11512: fscanf(ficpar," %le",&matcov[i][j]);
11513: if(mle==1){
11514: printf(" %.5le",matcov[i][j]);
11515: }
11516: fprintf(ficlog," %.5le",matcov[i][j]);
11517: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11518: }
11519: fscanf(ficpar,"\n");
11520: numlinepar++;
11521: if(mle==1)
1.220 brouard 11522: printf("\n");
1.126 brouard 11523: fprintf(ficlog,"\n");
11524: fprintf(ficparo,"\n");
11525: }
1.194 brouard 11526: /* End of read covariance matrix npar lines */
1.126 brouard 11527: for(i=1; i <=npar; i++)
11528: for(j=i+1;j<=npar;j++)
1.226 brouard 11529: matcov[i][j]=matcov[j][i];
1.126 brouard 11530:
11531: if(mle==1)
11532: printf("\n");
11533: fprintf(ficlog,"\n");
11534:
11535: fflush(ficlog);
11536:
11537: } /* End of mle != -3 */
1.218 brouard 11538:
1.186 brouard 11539: /* Main data
11540: */
1.290 brouard 11541: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11542: /* num=lvector(1,n); */
11543: /* moisnais=vector(1,n); */
11544: /* annais=vector(1,n); */
11545: /* moisdc=vector(1,n); */
11546: /* andc=vector(1,n); */
11547: /* weight=vector(1,n); */
11548: /* agedc=vector(1,n); */
11549: /* cod=ivector(1,n); */
11550: /* for(i=1;i<=n;i++){ */
11551: num=lvector(firstobs,lastobs);
11552: moisnais=vector(firstobs,lastobs);
11553: annais=vector(firstobs,lastobs);
11554: moisdc=vector(firstobs,lastobs);
11555: andc=vector(firstobs,lastobs);
11556: weight=vector(firstobs,lastobs);
11557: agedc=vector(firstobs,lastobs);
11558: cod=ivector(firstobs,lastobs);
11559: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11560: num[i]=0;
11561: moisnais[i]=0;
11562: annais[i]=0;
11563: moisdc[i]=0;
11564: andc[i]=0;
11565: agedc[i]=0;
11566: cod[i]=0;
11567: weight[i]=1.0; /* Equal weights, 1 by default */
11568: }
1.290 brouard 11569: mint=matrix(1,maxwav,firstobs,lastobs);
11570: anint=matrix(1,maxwav,firstobs,lastobs);
11571: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11572: tab=ivector(1,NCOVMAX);
1.144 brouard 11573: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11574: 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 11575:
1.136 brouard 11576: /* Reads data from file datafile */
11577: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11578: goto end;
11579:
11580: /* Calculation of the number of parameters from char model */
1.234 brouard 11581: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11582: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11583: k=3 V4 Tvar[k=3]= 4 (from V4)
11584: k=2 V1 Tvar[k=2]= 1 (from V1)
11585: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11586: */
11587:
11588: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11589: TvarsDind=ivector(1,NCOVMAX); /* */
11590: TvarsD=ivector(1,NCOVMAX); /* */
11591: TvarsQind=ivector(1,NCOVMAX); /* */
11592: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11593: TvarF=ivector(1,NCOVMAX); /* */
11594: TvarFind=ivector(1,NCOVMAX); /* */
11595: TvarV=ivector(1,NCOVMAX); /* */
11596: TvarVind=ivector(1,NCOVMAX); /* */
11597: TvarA=ivector(1,NCOVMAX); /* */
11598: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11599: TvarFD=ivector(1,NCOVMAX); /* */
11600: TvarFDind=ivector(1,NCOVMAX); /* */
11601: TvarFQ=ivector(1,NCOVMAX); /* */
11602: TvarFQind=ivector(1,NCOVMAX); /* */
11603: TvarVD=ivector(1,NCOVMAX); /* */
11604: TvarVDind=ivector(1,NCOVMAX); /* */
11605: TvarVQ=ivector(1,NCOVMAX); /* */
11606: TvarVQind=ivector(1,NCOVMAX); /* */
11607:
1.230 brouard 11608: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11609: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11610: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11611: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11612: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11613: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11614: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11615: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11616: */
11617: /* For model-covariate k tells which data-covariate to use but
11618: because this model-covariate is a construction we invent a new column
11619: ncovcol + k1
11620: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11621: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11622: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11623: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11624: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11625: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11626: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11627: */
1.145 brouard 11628: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11629: 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 11630: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11631: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11632: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11633: 4 covariates (3 plus signs)
11634: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11635: */
1.230 brouard 11636: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11637: * individual dummy, fixed or varying:
11638: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11639: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11640: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11641: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11642: * Tmodelind[1]@9={9,0,3,2,}*/
11643: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11644: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11645: * individual quantitative, fixed or varying:
11646: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11647: * 3, 1, 0, 0, 0, 0, 0, 0},
11648: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11649: /* Main decodemodel */
11650:
1.187 brouard 11651:
1.223 brouard 11652: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11653: goto end;
11654:
1.137 brouard 11655: if((double)(lastobs-imx)/(double)imx > 1.10){
11656: nbwarn++;
11657: 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);
11658: 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);
11659: }
1.136 brouard 11660: /* if(mle==1){*/
1.137 brouard 11661: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11662: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11663: }
11664:
11665: /*-calculation of age at interview from date of interview and age at death -*/
11666: agev=matrix(1,maxwav,1,imx);
11667:
11668: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11669: goto end;
11670:
1.126 brouard 11671:
1.136 brouard 11672: agegomp=(int)agemin;
1.290 brouard 11673: free_vector(moisnais,firstobs,lastobs);
11674: free_vector(annais,firstobs,lastobs);
1.126 brouard 11675: /* free_matrix(mint,1,maxwav,1,n);
11676: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11677: /* free_vector(moisdc,1,n); */
11678: /* free_vector(andc,1,n); */
1.145 brouard 11679: /* */
11680:
1.126 brouard 11681: wav=ivector(1,imx);
1.214 brouard 11682: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11683: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11684: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11685: 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.*/
11686: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11687: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11688:
11689: /* Concatenates waves */
1.214 brouard 11690: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11691: Death is a valid wave (if date is known).
11692: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11693: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11694: and mw[mi+1][i]. dh depends on stepm.
11695: */
11696:
1.126 brouard 11697: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11698: /* Concatenates waves */
1.145 brouard 11699:
1.290 brouard 11700: free_vector(moisdc,firstobs,lastobs);
11701: free_vector(andc,firstobs,lastobs);
1.215 brouard 11702:
1.126 brouard 11703: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11704: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11705: ncodemax[1]=1;
1.145 brouard 11706: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11707: cptcoveff=0;
1.220 brouard 11708: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11709: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11710: }
11711:
11712: ncovcombmax=pow(2,cptcoveff);
11713: invalidvarcomb=ivector(1, ncovcombmax);
11714: for(i=1;i<ncovcombmax;i++)
11715: invalidvarcomb[i]=0;
11716:
1.211 brouard 11717: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11718: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11719: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11720:
1.200 brouard 11721: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11722: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11723: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11724: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11725: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11726: * (currently 0 or 1) in the data.
11727: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11728: * corresponding modality (h,j).
11729: */
11730:
1.145 brouard 11731: h=0;
11732: /*if (cptcovn > 0) */
1.126 brouard 11733: m=pow(2,cptcoveff);
11734:
1.144 brouard 11735: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11736: * For k=4 covariates, h goes from 1 to m=2**k
11737: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11738: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11739: * h\k 1 2 3 4
1.143 brouard 11740: *______________________________
11741: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11742: * 2 2 1 1 1
11743: * 3 i=2 1 2 1 1
11744: * 4 2 2 1 1
11745: * 5 i=3 1 i=2 1 2 1
11746: * 6 2 1 2 1
11747: * 7 i=4 1 2 2 1
11748: * 8 2 2 2 1
1.197 brouard 11749: * 9 i=5 1 i=3 1 i=2 1 2
11750: * 10 2 1 1 2
11751: * 11 i=6 1 2 1 2
11752: * 12 2 2 1 2
11753: * 13 i=7 1 i=4 1 2 2
11754: * 14 2 1 2 2
11755: * 15 i=8 1 2 2 2
11756: * 16 2 2 2 2
1.143 brouard 11757: */
1.212 brouard 11758: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11759: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11760: * and the value of each covariate?
11761: * V1=1, V2=1, V3=2, V4=1 ?
11762: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11763: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11764: * In order to get the real value in the data, we use nbcode
11765: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11766: * We are keeping this crazy system in order to be able (in the future?)
11767: * to have more than 2 values (0 or 1) for a covariate.
11768: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11769: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11770: * bbbbbbbb
11771: * 76543210
11772: * h-1 00000101 (6-1=5)
1.219 brouard 11773: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11774: * &
11775: * 1 00000001 (1)
1.219 brouard 11776: * 00000000 = 1 & ((h-1) >> (k-1))
11777: * +1= 00000001 =1
1.211 brouard 11778: *
11779: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11780: * h' 1101 =2^3+2^2+0x2^1+2^0
11781: * >>k' 11
11782: * & 00000001
11783: * = 00000001
11784: * +1 = 00000010=2 = codtabm(14,3)
11785: * Reverse h=6 and m=16?
11786: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11787: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11788: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11789: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11790: * V3=decodtabm(14,3,2**4)=2
11791: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11792: *(h-1) >> (j-1) 0011 =13 >> 2
11793: * &1 000000001
11794: * = 000000001
11795: * +1= 000000010 =2
11796: * 2211
11797: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11798: * V3=2
1.220 brouard 11799: * codtabm and decodtabm are identical
1.211 brouard 11800: */
11801:
1.145 brouard 11802:
11803: free_ivector(Ndum,-1,NCOVMAX);
11804:
11805:
1.126 brouard 11806:
1.186 brouard 11807: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11808: strcpy(optionfilegnuplot,optionfilefiname);
11809: if(mle==-3)
1.201 brouard 11810: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11811: strcat(optionfilegnuplot,".gp");
11812:
11813: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11814: printf("Problem with file %s",optionfilegnuplot);
11815: }
11816: else{
1.204 brouard 11817: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11818: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11819: //fprintf(ficgp,"set missing 'NaNq'\n");
11820: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11821: }
11822: /* fclose(ficgp);*/
1.186 brouard 11823:
11824:
11825: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11826:
11827: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11828: if(mle==-3)
1.201 brouard 11829: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11830: strcat(optionfilehtm,".htm");
11831: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11832: printf("Problem with %s \n",optionfilehtm);
11833: exit(0);
1.126 brouard 11834: }
11835:
11836: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11837: strcat(optionfilehtmcov,"-cov.htm");
11838: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11839: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11840: }
11841: else{
11842: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11843: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11844: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11845: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11846: }
11847:
1.213 brouard 11848: 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 日本学術振興会 (<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 11849: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11850: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11851: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11852: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11853: \n\
11854: <hr size=\"2\" color=\"#EC5E5E\">\
11855: <ul><li><h4>Parameter files</h4>\n\
11856: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11857: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11858: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11859: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11860: - Date and time at start: %s</ul>\n",\
11861: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11862: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11863: fileres,fileres,\
11864: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11865: fflush(fichtm);
11866:
11867: strcpy(pathr,path);
11868: strcat(pathr,optionfilefiname);
1.184 brouard 11869: #ifdef WIN32
11870: _chdir(optionfilefiname); /* Move to directory named optionfile */
11871: #else
1.126 brouard 11872: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11873: #endif
11874:
1.126 brouard 11875:
1.220 brouard 11876: /* Calculates basic frequencies. Computes observed prevalence at single age
11877: and for any valid combination of covariates
1.126 brouard 11878: and prints on file fileres'p'. */
1.251 brouard 11879: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11880: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11881:
11882: fprintf(fichtm,"\n");
1.286 brouard 11883: 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 11884: ftol, stepm);
11885: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11886: ncurrv=1;
11887: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11888: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11889: ncurrv=i;
11890: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11891: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11892: ncurrv=i;
11893: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11894: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11895: ncurrv=i;
11896: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11897: 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", \
11898: nlstate, ndeath, maxwav, mle, weightopt);
11899:
11900: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11901: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11902:
11903:
11904: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11905: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11906: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11907: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11908: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11909: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11910: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11911: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11912: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11913:
1.126 brouard 11914: /* For Powell, parameters are in a vector p[] starting at p[1]
11915: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11916: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11917:
11918: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11919: /* For mortality only */
1.126 brouard 11920: if (mle==-3){
1.136 brouard 11921: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11922: for(i=1;i<=NDIM;i++)
11923: for(j=1;j<=NDIM;j++)
11924: ximort[i][j]=0.;
1.186 brouard 11925: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11926: cens=ivector(firstobs,lastobs);
11927: ageexmed=vector(firstobs,lastobs);
11928: agecens=vector(firstobs,lastobs);
11929: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11930:
1.126 brouard 11931: for (i=1; i<=imx; i++){
11932: dcwave[i]=-1;
11933: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11934: if (s[m][i]>nlstate) {
11935: dcwave[i]=m;
11936: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11937: break;
11938: }
1.126 brouard 11939: }
1.226 brouard 11940:
1.126 brouard 11941: for (i=1; i<=imx; i++) {
11942: if (wav[i]>0){
1.226 brouard 11943: ageexmed[i]=agev[mw[1][i]][i];
11944: j=wav[i];
11945: agecens[i]=1.;
11946:
11947: if (ageexmed[i]> 1 && wav[i] > 0){
11948: agecens[i]=agev[mw[j][i]][i];
11949: cens[i]= 1;
11950: }else if (ageexmed[i]< 1)
11951: cens[i]= -1;
11952: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11953: cens[i]=0 ;
1.126 brouard 11954: }
11955: else cens[i]=-1;
11956: }
11957:
11958: for (i=1;i<=NDIM;i++) {
11959: for (j=1;j<=NDIM;j++)
1.226 brouard 11960: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11961: }
11962:
1.302 brouard 11963: p[1]=0.0268; p[NDIM]=0.083;
11964: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 11965:
11966:
1.136 brouard 11967: #ifdef GSL
11968: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11969: #else
1.126 brouard 11970: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11971: #endif
1.201 brouard 11972: strcpy(filerespow,"POW-MORT_");
11973: strcat(filerespow,fileresu);
1.126 brouard 11974: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11975: printf("Problem with resultfile: %s\n", filerespow);
11976: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11977: }
1.136 brouard 11978: #ifdef GSL
11979: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11980: #else
1.126 brouard 11981: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11982: #endif
1.126 brouard 11983: /* for (i=1;i<=nlstate;i++)
11984: for(j=1;j<=nlstate+ndeath;j++)
11985: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11986: */
11987: fprintf(ficrespow,"\n");
1.136 brouard 11988: #ifdef GSL
11989: /* gsl starts here */
11990: T = gsl_multimin_fminimizer_nmsimplex;
11991: gsl_multimin_fminimizer *sfm = NULL;
11992: gsl_vector *ss, *x;
11993: gsl_multimin_function minex_func;
11994:
11995: /* Initial vertex size vector */
11996: ss = gsl_vector_alloc (NDIM);
11997:
11998: if (ss == NULL){
11999: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
12000: }
12001: /* Set all step sizes to 1 */
12002: gsl_vector_set_all (ss, 0.001);
12003:
12004: /* Starting point */
1.126 brouard 12005:
1.136 brouard 12006: x = gsl_vector_alloc (NDIM);
12007:
12008: if (x == NULL){
12009: gsl_vector_free(ss);
12010: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
12011: }
12012:
12013: /* Initialize method and iterate */
12014: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 12015: /* gsl_vector_set(x, 0, 0.0268); */
12016: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 12017: gsl_vector_set(x, 0, p[1]);
12018: gsl_vector_set(x, 1, p[2]);
12019:
12020: minex_func.f = &gompertz_f;
12021: minex_func.n = NDIM;
12022: minex_func.params = (void *)&p; /* ??? */
12023:
12024: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12025: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12026:
12027: printf("Iterations beginning .....\n\n");
12028: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12029:
12030: iteri=0;
12031: while (rval == GSL_CONTINUE){
12032: iteri++;
12033: status = gsl_multimin_fminimizer_iterate(sfm);
12034:
12035: if (status) printf("error: %s\n", gsl_strerror (status));
12036: fflush(0);
12037:
12038: if (status)
12039: break;
12040:
12041: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12042: ssval = gsl_multimin_fminimizer_size (sfm);
12043:
12044: if (rval == GSL_SUCCESS)
12045: printf ("converged to a local maximum at\n");
12046:
12047: printf("%5d ", iteri);
12048: for (it = 0; it < NDIM; it++){
12049: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12050: }
12051: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12052: }
12053:
12054: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12055:
12056: gsl_vector_free(x); /* initial values */
12057: gsl_vector_free(ss); /* inital step size */
12058: for (it=0; it<NDIM; it++){
12059: p[it+1]=gsl_vector_get(sfm->x,it);
12060: fprintf(ficrespow," %.12lf", p[it]);
12061: }
12062: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12063: #endif
12064: #ifdef POWELL
12065: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12066: #endif
1.126 brouard 12067: fclose(ficrespow);
12068:
1.203 brouard 12069: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12070:
12071: for(i=1; i <=NDIM; i++)
12072: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12073: matcov[i][j]=matcov[j][i];
1.126 brouard 12074:
12075: printf("\nCovariance matrix\n ");
1.203 brouard 12076: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12077: for(i=1; i <=NDIM; i++) {
12078: for(j=1;j<=NDIM;j++){
1.220 brouard 12079: printf("%f ",matcov[i][j]);
12080: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12081: }
1.203 brouard 12082: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12083: }
12084:
12085: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12086: for (i=1;i<=NDIM;i++) {
1.126 brouard 12087: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12088: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12089: }
1.302 brouard 12090: lsurv=vector(agegomp,AGESUP);
12091: lpop=vector(agegomp,AGESUP);
12092: tpop=vector(agegomp,AGESUP);
1.126 brouard 12093: lsurv[agegomp]=100000;
12094:
12095: for (k=agegomp;k<=AGESUP;k++) {
12096: agemortsup=k;
12097: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12098: }
12099:
12100: for (k=agegomp;k<agemortsup;k++)
12101: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12102:
12103: for (k=agegomp;k<agemortsup;k++){
12104: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12105: sumlpop=sumlpop+lpop[k];
12106: }
12107:
12108: tpop[agegomp]=sumlpop;
12109: for (k=agegomp;k<(agemortsup-3);k++){
12110: /* tpop[k+1]=2;*/
12111: tpop[k+1]=tpop[k]-lpop[k];
12112: }
12113:
12114:
12115: printf("\nAge lx qx dx Lx Tx e(x)\n");
12116: for (k=agegomp;k<(agemortsup-2);k++)
12117: 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]);
12118:
12119:
12120: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12121: ageminpar=50;
12122: agemaxpar=100;
1.194 brouard 12123: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12124: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12125: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12126: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12127: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12128: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12129: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12130: }else{
12131: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12132: 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 12133: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12134: }
1.201 brouard 12135: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12136: stepm, weightopt,\
12137: model,imx,p,matcov,agemortsup);
12138:
1.302 brouard 12139: free_vector(lsurv,agegomp,AGESUP);
12140: free_vector(lpop,agegomp,AGESUP);
12141: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12142: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12143: free_ivector(dcwave,firstobs,lastobs);
12144: free_vector(agecens,firstobs,lastobs);
12145: free_vector(ageexmed,firstobs,lastobs);
12146: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12147: #ifdef GSL
1.136 brouard 12148: #endif
1.186 brouard 12149: } /* Endof if mle==-3 mortality only */
1.205 brouard 12150: /* Standard */
12151: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12152: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12153: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12154: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12155: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12156: for (k=1; k<=npar;k++)
12157: printf(" %d %8.5f",k,p[k]);
12158: printf("\n");
1.205 brouard 12159: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12160: /* mlikeli uses func not funcone */
1.247 brouard 12161: /* for(i=1;i<nlstate;i++){ */
12162: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12163: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12164: /* } */
1.205 brouard 12165: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12166: }
12167: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12168: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12169: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12170: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12171: }
12172: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12173: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12174: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12175: for (k=1; k<=npar;k++)
12176: printf(" %d %8.5f",k,p[k]);
12177: printf("\n");
12178:
12179: /*--------- results files --------------*/
1.283 brouard 12180: /* 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 12181:
12182:
12183: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12184: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12185: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12186: for(i=1,jk=1; i <=nlstate; i++){
12187: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12188: if (k != i) {
12189: printf("%d%d ",i,k);
12190: fprintf(ficlog,"%d%d ",i,k);
12191: fprintf(ficres,"%1d%1d ",i,k);
12192: for(j=1; j <=ncovmodel; j++){
12193: printf("%12.7f ",p[jk]);
12194: fprintf(ficlog,"%12.7f ",p[jk]);
12195: fprintf(ficres,"%12.7f ",p[jk]);
12196: jk++;
12197: }
12198: printf("\n");
12199: fprintf(ficlog,"\n");
12200: fprintf(ficres,"\n");
12201: }
1.126 brouard 12202: }
12203: }
1.203 brouard 12204: if(mle != 0){
12205: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12206: ftolhess=ftol; /* Usually correct */
1.203 brouard 12207: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12208: 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");
12209: 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");
12210: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12211: for(k=1; k <=(nlstate+ndeath); k++){
12212: if (k != i) {
12213: printf("%d%d ",i,k);
12214: fprintf(ficlog,"%d%d ",i,k);
12215: for(j=1; j <=ncovmodel; j++){
12216: 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]));
12217: 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]));
12218: jk++;
12219: }
12220: printf("\n");
12221: fprintf(ficlog,"\n");
12222: }
12223: }
1.193 brouard 12224: }
1.203 brouard 12225: } /* end of hesscov and Wald tests */
1.225 brouard 12226:
1.203 brouard 12227: /* */
1.126 brouard 12228: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12229: printf("# Scales (for hessian or gradient estimation)\n");
12230: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12231: for(i=1,jk=1; i <=nlstate; i++){
12232: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12233: if (j!=i) {
12234: fprintf(ficres,"%1d%1d",i,j);
12235: printf("%1d%1d",i,j);
12236: fprintf(ficlog,"%1d%1d",i,j);
12237: for(k=1; k<=ncovmodel;k++){
12238: printf(" %.5e",delti[jk]);
12239: fprintf(ficlog," %.5e",delti[jk]);
12240: fprintf(ficres," %.5e",delti[jk]);
12241: jk++;
12242: }
12243: printf("\n");
12244: fprintf(ficlog,"\n");
12245: fprintf(ficres,"\n");
12246: }
1.126 brouard 12247: }
12248: }
12249:
12250: 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 12251: if(mle >= 1) /* To big for the screen */
1.126 brouard 12252: 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");
12253: 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");
12254: /* # 121 Var(a12)\n\ */
12255: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12256: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12257: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12258: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12259: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12260: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12261: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12262:
12263:
12264: /* Just to have a covariance matrix which will be more understandable
12265: even is we still don't want to manage dictionary of variables
12266: */
12267: for(itimes=1;itimes<=2;itimes++){
12268: jj=0;
12269: for(i=1; i <=nlstate; i++){
1.225 brouard 12270: for(j=1; j <=nlstate+ndeath; j++){
12271: if(j==i) continue;
12272: for(k=1; k<=ncovmodel;k++){
12273: jj++;
12274: ca[0]= k+'a'-1;ca[1]='\0';
12275: if(itimes==1){
12276: if(mle>=1)
12277: printf("#%1d%1d%d",i,j,k);
12278: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12279: fprintf(ficres,"#%1d%1d%d",i,j,k);
12280: }else{
12281: if(mle>=1)
12282: printf("%1d%1d%d",i,j,k);
12283: fprintf(ficlog,"%1d%1d%d",i,j,k);
12284: fprintf(ficres,"%1d%1d%d",i,j,k);
12285: }
12286: ll=0;
12287: for(li=1;li <=nlstate; li++){
12288: for(lj=1;lj <=nlstate+ndeath; lj++){
12289: if(lj==li) continue;
12290: for(lk=1;lk<=ncovmodel;lk++){
12291: ll++;
12292: if(ll<=jj){
12293: cb[0]= lk +'a'-1;cb[1]='\0';
12294: if(ll<jj){
12295: if(itimes==1){
12296: if(mle>=1)
12297: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12298: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12299: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12300: }else{
12301: if(mle>=1)
12302: printf(" %.5e",matcov[jj][ll]);
12303: fprintf(ficlog," %.5e",matcov[jj][ll]);
12304: fprintf(ficres," %.5e",matcov[jj][ll]);
12305: }
12306: }else{
12307: if(itimes==1){
12308: if(mle>=1)
12309: printf(" Var(%s%1d%1d)",ca,i,j);
12310: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12311: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12312: }else{
12313: if(mle>=1)
12314: printf(" %.7e",matcov[jj][ll]);
12315: fprintf(ficlog," %.7e",matcov[jj][ll]);
12316: fprintf(ficres," %.7e",matcov[jj][ll]);
12317: }
12318: }
12319: }
12320: } /* end lk */
12321: } /* end lj */
12322: } /* end li */
12323: if(mle>=1)
12324: printf("\n");
12325: fprintf(ficlog,"\n");
12326: fprintf(ficres,"\n");
12327: numlinepar++;
12328: } /* end k*/
12329: } /*end j */
1.126 brouard 12330: } /* end i */
12331: } /* end itimes */
12332:
12333: fflush(ficlog);
12334: fflush(ficres);
1.225 brouard 12335: while(fgets(line, MAXLINE, ficpar)) {
12336: /* If line starts with a # it is a comment */
12337: if (line[0] == '#') {
12338: numlinepar++;
12339: fputs(line,stdout);
12340: fputs(line,ficparo);
12341: fputs(line,ficlog);
1.299 brouard 12342: fputs(line,ficres);
1.225 brouard 12343: continue;
12344: }else
12345: break;
12346: }
12347:
1.209 brouard 12348: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12349: /* ungetc(c,ficpar); */
12350: /* fgets(line, MAXLINE, ficpar); */
12351: /* fputs(line,stdout); */
12352: /* fputs(line,ficparo); */
12353: /* } */
12354: /* ungetc(c,ficpar); */
1.126 brouard 12355:
12356: estepm=0;
1.209 brouard 12357: 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 12358:
12359: if (num_filled != 6) {
12360: 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);
12361: 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);
12362: goto end;
12363: }
12364: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12365: }
12366: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12367: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12368:
1.209 brouard 12369: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12370: if (estepm==0 || estepm < stepm) estepm=stepm;
12371: if (fage <= 2) {
12372: bage = ageminpar;
12373: fage = agemaxpar;
12374: }
12375:
12376: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12377: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12378: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12379:
1.186 brouard 12380: /* Other stuffs, more or less useful */
1.254 brouard 12381: while(fgets(line, MAXLINE, ficpar)) {
12382: /* If line starts with a # it is a comment */
12383: if (line[0] == '#') {
12384: numlinepar++;
12385: fputs(line,stdout);
12386: fputs(line,ficparo);
12387: fputs(line,ficlog);
1.299 brouard 12388: fputs(line,ficres);
1.254 brouard 12389: continue;
12390: }else
12391: break;
12392: }
12393:
12394: 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){
12395:
12396: if (num_filled != 7) {
12397: 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);
12398: 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);
12399: goto end;
12400: }
12401: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12402: 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);
12403: 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);
12404: 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 12405: }
1.254 brouard 12406:
12407: while(fgets(line, MAXLINE, ficpar)) {
12408: /* If line starts with a # it is a comment */
12409: if (line[0] == '#') {
12410: numlinepar++;
12411: fputs(line,stdout);
12412: fputs(line,ficparo);
12413: fputs(line,ficlog);
1.299 brouard 12414: fputs(line,ficres);
1.254 brouard 12415: continue;
12416: }else
12417: break;
1.126 brouard 12418: }
12419:
12420:
12421: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12422: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12423:
1.254 brouard 12424: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12425: if (num_filled != 1) {
12426: 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);
12427: 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);
12428: goto end;
12429: }
12430: printf("pop_based=%d\n",popbased);
12431: fprintf(ficlog,"pop_based=%d\n",popbased);
12432: fprintf(ficparo,"pop_based=%d\n",popbased);
12433: fprintf(ficres,"pop_based=%d\n",popbased);
12434: }
12435:
1.258 brouard 12436: /* Results */
1.307 brouard 12437: endishere=0;
1.258 brouard 12438: nresult=0;
1.308 brouard 12439: parameterline=0;
1.258 brouard 12440: do{
12441: if(!fgets(line, MAXLINE, ficpar)){
12442: endishere=1;
1.308 brouard 12443: parameterline=15;
1.258 brouard 12444: }else if (line[0] == '#') {
12445: /* If line starts with a # it is a comment */
1.254 brouard 12446: numlinepar++;
12447: fputs(line,stdout);
12448: fputs(line,ficparo);
12449: fputs(line,ficlog);
1.299 brouard 12450: fputs(line,ficres);
1.254 brouard 12451: continue;
1.258 brouard 12452: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12453: parameterline=11;
1.296 brouard 12454: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12455: parameterline=12;
1.307 brouard 12456: else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258 brouard 12457: parameterline=13;
1.307 brouard 12458: }
1.258 brouard 12459: else{
12460: parameterline=14;
1.254 brouard 12461: }
1.308 brouard 12462: switch (parameterline){ /* =0 only if only comments */
1.258 brouard 12463: case 11:
1.296 brouard 12464: 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)){
12465: 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 12466: 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);
12467: 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);
12468: 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);
12469: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12470: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12471: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12472: prvforecast = 1;
12473: }
12474: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.302 brouard 12475: printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12476: fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12477: fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12478: prvforecast = 2;
12479: }
12480: else {
12481: 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);
12482: 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);
12483: goto end;
1.258 brouard 12484: }
1.254 brouard 12485: break;
1.258 brouard 12486: case 12:
1.296 brouard 12487: 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)){
12488: 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);
12489: 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);
12490: 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);
12491: 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);
12492: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12493: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12494: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12495: prvbackcast = 1;
12496: }
12497: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.302 brouard 12498: printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12499: fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12500: fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12501: prvbackcast = 2;
12502: }
12503: else {
12504: 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);
12505: 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);
12506: goto end;
1.258 brouard 12507: }
1.230 brouard 12508: break;
1.258 brouard 12509: case 13:
1.307 brouard 12510: num_filled=sscanf(line,"result:%[^\n]\n",resultline);
12511: nresult++; /* Sum of resultlines */
12512: printf("Result %d: result:%s\n",nresult, resultline);
12513: if(nresult > MAXRESULTLINES){
12514: 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);
12515: 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);
12516: goto end;
12517: }
1.310 ! brouard 12518: if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.307 brouard 12519: fprintf(ficparo,"result: %s\n",resultline);
12520: fprintf(ficres,"result: %s\n",resultline);
12521: fprintf(ficlog,"result: %s\n",resultline);
1.310 ! brouard 12522: } else
! 12523: goto end;
1.307 brouard 12524: break;
12525: case 14:
12526: printf("Error: Unknown command '%s'\n",line);
12527: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
12528: if(ncovmodel >=2 && nresult==0 ){
12529: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
12530: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12531: }
1.307 brouard 12532: /* goto end; */
12533: break;
1.308 brouard 12534: case 15:
12535: printf("End of resultlines.\n");
12536: fprintf(ficlog,"End of resultlines.\n");
12537: break;
12538: default: /* parameterline =0 */
1.307 brouard 12539: nresult=1;
12540: decoderesult(".",nresult ); /* No covariate */
1.258 brouard 12541: } /* End switch parameterline */
12542: }while(endishere==0); /* End do */
1.126 brouard 12543:
1.230 brouard 12544: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12545: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12546:
12547: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12548: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12549: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12550: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12551: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12552: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12553: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12554: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12555: }else{
1.270 brouard 12556: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12557: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12558: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12559: if(prvforecast==1){
12560: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12561: jprojd=jproj1;
12562: mprojd=mproj1;
12563: anprojd=anproj1;
12564: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12565: jprojf=jproj2;
12566: mprojf=mproj2;
12567: anprojf=anproj2;
12568: } else if(prvforecast == 2){
12569: dateprojd=dateintmean;
12570: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12571: dateprojf=dateintmean+yrfproj;
12572: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12573: }
12574: if(prvbackcast==1){
12575: datebackd=(jback1+12*mback1+365*anback1)/365;
12576: jbackd=jback1;
12577: mbackd=mback1;
12578: anbackd=anback1;
12579: datebackf=(jback2+12*mback2+365*anback2)/365;
12580: jbackf=jback2;
12581: mbackf=mback2;
12582: anbackf=anback2;
12583: } else if(prvbackcast == 2){
12584: datebackd=dateintmean;
12585: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12586: datebackf=dateintmean-yrbproj;
12587: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12588: }
12589:
12590: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12591: }
12592: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12593: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12594: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12595:
1.225 brouard 12596: /*------------ free_vector -------------*/
12597: /* chdir(path); */
1.220 brouard 12598:
1.215 brouard 12599: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12600: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12601: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12602: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12603: free_lvector(num,firstobs,lastobs);
12604: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12605: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12606: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12607: fclose(ficparo);
12608: fclose(ficres);
1.220 brouard 12609:
12610:
1.186 brouard 12611: /* Other results (useful)*/
1.220 brouard 12612:
12613:
1.126 brouard 12614: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12615: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12616: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12617: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12618: fclose(ficrespl);
12619:
12620: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12621: /*#include "hpijx.h"*/
12622: hPijx(p, bage, fage);
1.145 brouard 12623: fclose(ficrespij);
1.227 brouard 12624:
1.220 brouard 12625: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12626: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12627: k=1;
1.126 brouard 12628: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12629:
1.269 brouard 12630: /* Prevalence for each covariate combination in probs[age][status][cov] */
12631: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12632: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12633: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12634: for(k=1;k<=ncovcombmax;k++)
12635: probs[i][j][k]=0.;
1.269 brouard 12636: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12637: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12638: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12639: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12640: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12641: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12642: for(k=1;k<=ncovcombmax;k++)
12643: mobaverages[i][j][k]=0.;
1.219 brouard 12644: mobaverage=mobaverages;
12645: if (mobilav!=0) {
1.235 brouard 12646: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12647: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12648: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12649: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12650: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12651: }
1.269 brouard 12652: } else if (mobilavproj !=0) {
1.235 brouard 12653: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12654: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12655: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12656: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12657: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12658: }
1.269 brouard 12659: }else{
12660: printf("Internal error moving average\n");
12661: fflush(stdout);
12662: exit(1);
1.219 brouard 12663: }
12664: }/* end if moving average */
1.227 brouard 12665:
1.126 brouard 12666: /*---------- Forecasting ------------------*/
1.296 brouard 12667: if(prevfcast==1){
12668: /* /\* if(stepm ==1){*\/ */
12669: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12670: /*This done previously after freqsummary.*/
12671: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12672: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12673:
12674: /* } else if (prvforecast==2){ */
12675: /* /\* if(stepm ==1){*\/ */
12676: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12677: /* } */
12678: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12679: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12680: }
1.269 brouard 12681:
1.296 brouard 12682: /* Prevbcasting */
12683: if(prevbcast==1){
1.219 brouard 12684: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12685: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12686: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12687:
12688: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12689:
12690: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12691:
1.219 brouard 12692: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12693: fclose(ficresplb);
12694:
1.222 brouard 12695: hBijx(p, bage, fage, mobaverage);
12696: fclose(ficrespijb);
1.219 brouard 12697:
1.296 brouard 12698: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12699: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12700: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12701: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12702: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12703: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12704:
12705:
1.269 brouard 12706: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12707:
12708:
1.269 brouard 12709: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12710: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12711: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12712: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12713: } /* end Prevbcasting */
1.268 brouard 12714:
1.186 brouard 12715:
12716: /* ------ Other prevalence ratios------------ */
1.126 brouard 12717:
1.215 brouard 12718: free_ivector(wav,1,imx);
12719: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12720: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12721: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12722:
12723:
1.127 brouard 12724: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12725:
1.201 brouard 12726: strcpy(filerese,"E_");
12727: strcat(filerese,fileresu);
1.126 brouard 12728: if((ficreseij=fopen(filerese,"w"))==NULL) {
12729: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12730: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12731: }
1.208 brouard 12732: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12733: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12734:
12735: pstamp(ficreseij);
1.219 brouard 12736:
1.235 brouard 12737: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12738: if (cptcovn < 1){i1=1;}
12739:
12740: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12741: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12742: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12743: continue;
1.219 brouard 12744: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12745: printf("\n#****** ");
1.225 brouard 12746: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12747: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12748: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12749: }
12750: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12751: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12752: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12753: }
12754: fprintf(ficreseij,"******\n");
1.235 brouard 12755: printf("******\n");
1.219 brouard 12756:
12757: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12758: oldm=oldms;savm=savms;
1.235 brouard 12759: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12760:
1.219 brouard 12761: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12762: }
12763: fclose(ficreseij);
1.208 brouard 12764: printf("done evsij\n");fflush(stdout);
12765: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12766:
1.218 brouard 12767:
1.227 brouard 12768: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12769:
1.201 brouard 12770: strcpy(filerest,"T_");
12771: strcat(filerest,fileresu);
1.127 brouard 12772: if((ficrest=fopen(filerest,"w"))==NULL) {
12773: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12774: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12775: }
1.208 brouard 12776: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12777: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12778: strcpy(fileresstde,"STDE_");
12779: strcat(fileresstde,fileresu);
1.126 brouard 12780: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12781: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12782: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12783: }
1.227 brouard 12784: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12785: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12786:
1.201 brouard 12787: strcpy(filerescve,"CVE_");
12788: strcat(filerescve,fileresu);
1.126 brouard 12789: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12790: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12791: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12792: }
1.227 brouard 12793: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12794: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12795:
1.201 brouard 12796: strcpy(fileresv,"V_");
12797: strcat(fileresv,fileresu);
1.126 brouard 12798: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12799: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12800: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12801: }
1.227 brouard 12802: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12803: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12804:
1.235 brouard 12805: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12806: if (cptcovn < 1){i1=1;}
12807:
12808: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12809: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12810: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12811: continue;
1.242 brouard 12812: printf("\n#****** Result for:");
12813: fprintf(ficrest,"\n#****** Result for:");
12814: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12815: for(j=1;j<=cptcoveff;j++){
12816: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12817: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12818: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12819: }
1.235 brouard 12820: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12821: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12822: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12823: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12824: }
1.208 brouard 12825: fprintf(ficrest,"******\n");
1.227 brouard 12826: fprintf(ficlog,"******\n");
12827: printf("******\n");
1.208 brouard 12828:
12829: fprintf(ficresstdeij,"\n#****** ");
12830: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12831: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12832: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12833: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12834: }
1.235 brouard 12835: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12836: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12837: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12838: }
1.208 brouard 12839: fprintf(ficresstdeij,"******\n");
12840: fprintf(ficrescveij,"******\n");
12841:
12842: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12843: /* pstamp(ficresvij); */
1.225 brouard 12844: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12845: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12846: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12847: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12848: }
1.208 brouard 12849: fprintf(ficresvij,"******\n");
12850:
12851: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12852: oldm=oldms;savm=savms;
1.235 brouard 12853: printf(" cvevsij ");
12854: fprintf(ficlog, " cvevsij ");
12855: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12856: printf(" end cvevsij \n ");
12857: fprintf(ficlog, " end cvevsij \n ");
12858:
12859: /*
12860: */
12861: /* goto endfree; */
12862:
12863: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12864: pstamp(ficrest);
12865:
1.269 brouard 12866: epj=vector(1,nlstate+1);
1.208 brouard 12867: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12868: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12869: cptcod= 0; /* To be deleted */
12870: printf("varevsij vpopbased=%d \n",vpopbased);
12871: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12872: 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 12873: 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 ");
12874: if(vpopbased==1)
12875: 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);
12876: else
1.288 brouard 12877: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12878: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12879: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12880: fprintf(ficrest,"\n");
12881: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12882: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12883: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12884: for(age=bage; age <=fage ;age++){
1.235 brouard 12885: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12886: if (vpopbased==1) {
12887: if(mobilav ==0){
12888: for(i=1; i<=nlstate;i++)
12889: prlim[i][i]=probs[(int)age][i][k];
12890: }else{ /* mobilav */
12891: for(i=1; i<=nlstate;i++)
12892: prlim[i][i]=mobaverage[(int)age][i][k];
12893: }
12894: }
1.219 brouard 12895:
1.227 brouard 12896: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12897: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12898: /* printf(" age %4.0f ",age); */
12899: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12900: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12901: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12902: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12903: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12904: }
12905: epj[nlstate+1] +=epj[j];
12906: }
12907: /* printf(" age %4.0f \n",age); */
1.219 brouard 12908:
1.227 brouard 12909: for(i=1, vepp=0.;i <=nlstate;i++)
12910: for(j=1;j <=nlstate;j++)
12911: vepp += vareij[i][j][(int)age];
12912: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12913: for(j=1;j <=nlstate;j++){
12914: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12915: }
12916: fprintf(ficrest,"\n");
12917: }
1.208 brouard 12918: } /* End vpopbased */
1.269 brouard 12919: free_vector(epj,1,nlstate+1);
1.208 brouard 12920: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12921: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12922: printf("done selection\n");fflush(stdout);
12923: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12924:
1.235 brouard 12925: } /* End k selection */
1.227 brouard 12926:
12927: printf("done State-specific expectancies\n");fflush(stdout);
12928: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12929:
1.288 brouard 12930: /* variance-covariance of forward period prevalence*/
1.269 brouard 12931: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12932:
1.227 brouard 12933:
1.290 brouard 12934: free_vector(weight,firstobs,lastobs);
1.227 brouard 12935: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12936: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12937: free_matrix(anint,1,maxwav,firstobs,lastobs);
12938: free_matrix(mint,1,maxwav,firstobs,lastobs);
12939: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12940: free_ivector(tab,1,NCOVMAX);
12941: fclose(ficresstdeij);
12942: fclose(ficrescveij);
12943: fclose(ficresvij);
12944: fclose(ficrest);
12945: fclose(ficpar);
12946:
12947:
1.126 brouard 12948: /*---------- End : free ----------------*/
1.219 brouard 12949: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12950: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12951: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12952: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12953: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12954: } /* mle==-3 arrives here for freeing */
1.227 brouard 12955: /* endfree:*/
12956: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12957: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12958: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12959: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12960: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12961: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12962: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12963: free_matrix(matcov,1,npar,1,npar);
12964: free_matrix(hess,1,npar,1,npar);
12965: /*free_vector(delti,1,npar);*/
12966: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12967: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12968: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12969: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12970:
12971: free_ivector(ncodemax,1,NCOVMAX);
12972: free_ivector(ncodemaxwundef,1,NCOVMAX);
12973: free_ivector(Dummy,-1,NCOVMAX);
12974: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12975: free_ivector(DummyV,1,NCOVMAX);
12976: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12977: free_ivector(Typevar,-1,NCOVMAX);
12978: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12979: free_ivector(TvarsQ,1,NCOVMAX);
12980: free_ivector(TvarsQind,1,NCOVMAX);
12981: free_ivector(TvarsD,1,NCOVMAX);
12982: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12983: free_ivector(TvarFD,1,NCOVMAX);
12984: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12985: free_ivector(TvarF,1,NCOVMAX);
12986: free_ivector(TvarFind,1,NCOVMAX);
12987: free_ivector(TvarV,1,NCOVMAX);
12988: free_ivector(TvarVind,1,NCOVMAX);
12989: free_ivector(TvarA,1,NCOVMAX);
12990: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12991: free_ivector(TvarFQ,1,NCOVMAX);
12992: free_ivector(TvarFQind,1,NCOVMAX);
12993: free_ivector(TvarVD,1,NCOVMAX);
12994: free_ivector(TvarVDind,1,NCOVMAX);
12995: free_ivector(TvarVQ,1,NCOVMAX);
12996: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12997: free_ivector(Tvarsel,1,NCOVMAX);
12998: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12999: free_ivector(Tposprod,1,NCOVMAX);
13000: free_ivector(Tprod,1,NCOVMAX);
13001: free_ivector(Tvaraff,1,NCOVMAX);
13002: free_ivector(invalidvarcomb,1,ncovcombmax);
13003: free_ivector(Tage,1,NCOVMAX);
13004: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 13005: free_ivector(TmodelInvind,1,NCOVMAX);
13006: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 13007:
13008: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
13009: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 13010: fflush(fichtm);
13011: fflush(ficgp);
13012:
1.227 brouard 13013:
1.126 brouard 13014: if((nberr >0) || (nbwarn>0)){
1.216 brouard 13015: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
13016: 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 13017: }else{
13018: printf("End of Imach\n");
13019: fprintf(ficlog,"End of Imach\n");
13020: }
13021: printf("See log file on %s\n",filelog);
13022: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 13023: /*(void) gettimeofday(&end_time,&tzp);*/
13024: rend_time = time(NULL);
13025: end_time = *localtime(&rend_time);
13026: /* tml = *localtime(&end_time.tm_sec); */
13027: strcpy(strtend,asctime(&end_time));
1.126 brouard 13028: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13029: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13030: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13031:
1.157 brouard 13032: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13033: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13034: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13035: /* printf("Total time was %d uSec.\n", total_usecs);*/
13036: /* if(fileappend(fichtm,optionfilehtm)){ */
13037: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13038: fclose(fichtm);
13039: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13040: fclose(fichtmcov);
13041: fclose(ficgp);
13042: fclose(ficlog);
13043: /*------ End -----------*/
1.227 brouard 13044:
1.281 brouard 13045:
13046: /* Executes gnuplot */
1.227 brouard 13047:
13048: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13049: #ifdef WIN32
1.227 brouard 13050: if (_chdir(pathcd) != 0)
13051: printf("Can't move to directory %s!\n",path);
13052: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13053: #else
1.227 brouard 13054: if(chdir(pathcd) != 0)
13055: printf("Can't move to directory %s!\n", path);
13056: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13057: #endif
1.126 brouard 13058: printf("Current directory %s!\n",pathcd);
13059: /*strcat(plotcmd,CHARSEPARATOR);*/
13060: sprintf(plotcmd,"gnuplot");
1.157 brouard 13061: #ifdef _WIN32
1.126 brouard 13062: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13063: #endif
13064: if(!stat(plotcmd,&info)){
1.158 brouard 13065: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13066: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13067: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13068: }else
13069: strcpy(pplotcmd,plotcmd);
1.157 brouard 13070: #ifdef __unix
1.126 brouard 13071: strcpy(plotcmd,GNUPLOTPROGRAM);
13072: if(!stat(plotcmd,&info)){
1.158 brouard 13073: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13074: }else
13075: strcpy(pplotcmd,plotcmd);
13076: #endif
13077: }else
13078: strcpy(pplotcmd,plotcmd);
13079:
13080: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13081: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13082: strcpy(pplotcmd,plotcmd);
1.227 brouard 13083:
1.126 brouard 13084: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13085: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13086: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13087: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13088: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13089: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13090: strcpy(plotcmd,pplotcmd);
13091: }
1.126 brouard 13092: }
1.158 brouard 13093: printf(" Successful, please wait...");
1.126 brouard 13094: while (z[0] != 'q') {
13095: /* chdir(path); */
1.154 brouard 13096: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13097: scanf("%s",z);
13098: /* if (z[0] == 'c') system("./imach"); */
13099: if (z[0] == 'e') {
1.158 brouard 13100: #ifdef __APPLE__
1.152 brouard 13101: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13102: #elif __linux
13103: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13104: #else
1.152 brouard 13105: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13106: #endif
13107: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13108: system(pplotcmd);
1.126 brouard 13109: }
13110: else if (z[0] == 'g') system(plotcmd);
13111: else if (z[0] == 'q') exit(0);
13112: }
1.227 brouard 13113: end:
1.126 brouard 13114: while (z[0] != 'q') {
1.195 brouard 13115: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13116: scanf("%s",z);
13117: }
1.283 brouard 13118: printf("End\n");
1.282 brouard 13119: exit(0);
1.126 brouard 13120: }
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