Annotation of imach/src/imach.c, revision 1.307
1.307 ! brouard 1: /* $Id: imach.c,v 1.306 2021/02/20 15:44:02 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.307 ! brouard 4: Revision 1.306 2021/02/20 15:44:02 brouard
! 5: Summary: Version 0.99r21
! 6:
! 7: * imach.c (Module): Fix bug on quitting after result lines!
! 8: (Module): Version 0.99r21
! 9:
1.306 brouard 10: Revision 1.305 2021/02/20 15:28:30 brouard
11: * imach.c (Module): Fix bug on quitting after result lines!
12:
1.305 brouard 13: Revision 1.304 2021/02/12 11:34:20 brouard
14: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
15:
1.304 brouard 16: Revision 1.303 2021/02/11 19:50:15 brouard
17: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
18:
1.303 brouard 19: Revision 1.302 2020/02/22 21:00:05 brouard
20: * (Module): imach.c Update mle=-3 (for computing Life expectancy
21: and life table from the data without any state)
22:
1.302 brouard 23: Revision 1.301 2019/06/04 13:51:20 brouard
24: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
25:
1.301 brouard 26: Revision 1.300 2019/05/22 19:09:45 brouard
27: Summary: version 0.99r19 of May 2019
28:
1.300 brouard 29: Revision 1.299 2019/05/22 18:37:08 brouard
30: Summary: Cleaned 0.99r19
31:
1.299 brouard 32: Revision 1.298 2019/05/22 18:19:56 brouard
33: *** empty log message ***
34:
1.298 brouard 35: Revision 1.297 2019/05/22 17:56:10 brouard
36: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
37:
1.297 brouard 38: Revision 1.296 2019/05/20 13:03:18 brouard
39: Summary: Projection syntax simplified
40:
41:
42: We can now start projections, forward or backward, from the mean date
43: of inteviews up to or down to a number of years of projection:
44: prevforecast=1 yearsfproj=15.3 mobil_average=0
45: or
46: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
47: or
48: prevbackcast=1 yearsbproj=12.3 mobil_average=1
49: or
50: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
51:
1.296 brouard 52: Revision 1.295 2019/05/18 09:52:50 brouard
53: Summary: doxygen tex bug
54:
1.295 brouard 55: Revision 1.294 2019/05/16 14:54:33 brouard
56: Summary: There was some wrong lines added
57:
1.294 brouard 58: Revision 1.293 2019/05/09 15:17:34 brouard
59: *** empty log message ***
60:
1.293 brouard 61: Revision 1.292 2019/05/09 14:17:20 brouard
62: Summary: Some updates
63:
1.292 brouard 64: Revision 1.291 2019/05/09 13:44:18 brouard
65: Summary: Before ncovmax
66:
1.291 brouard 67: Revision 1.290 2019/05/09 13:39:37 brouard
68: Summary: 0.99r18 unlimited number of individuals
69:
70: 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.
71:
1.290 brouard 72: Revision 1.289 2018/12/13 09:16:26 brouard
73: Summary: Bug for young ages (<-30) will be in r17
74:
1.289 brouard 75: Revision 1.288 2018/05/02 20:58:27 brouard
76: Summary: Some bugs fixed
77:
1.288 brouard 78: Revision 1.287 2018/05/01 17:57:25 brouard
79: Summary: Bug fixed by providing frequencies only for non missing covariates
80:
1.287 brouard 81: Revision 1.286 2018/04/27 14:27:04 brouard
82: Summary: some minor bugs
83:
1.286 brouard 84: Revision 1.285 2018/04/21 21:02:16 brouard
85: Summary: Some bugs fixed, valgrind tested
86:
1.285 brouard 87: Revision 1.284 2018/04/20 05:22:13 brouard
88: Summary: Computing mean and stdeviation of fixed quantitative variables
89:
1.284 brouard 90: Revision 1.283 2018/04/19 14:49:16 brouard
91: Summary: Some minor bugs fixed
92:
1.283 brouard 93: Revision 1.282 2018/02/27 22:50:02 brouard
94: *** empty log message ***
95:
1.282 brouard 96: Revision 1.281 2018/02/27 19:25:23 brouard
97: Summary: Adding second argument for quitting
98:
1.281 brouard 99: Revision 1.280 2018/02/21 07:58:13 brouard
100: Summary: 0.99r15
101:
102: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
103:
1.280 brouard 104: Revision 1.279 2017/07/20 13:35:01 brouard
105: Summary: temporary working
106:
1.279 brouard 107: Revision 1.278 2017/07/19 14:09:02 brouard
108: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
109:
1.278 brouard 110: Revision 1.277 2017/07/17 08:53:49 brouard
111: Summary: BOM files can be read now
112:
1.277 brouard 113: Revision 1.276 2017/06/30 15:48:31 brouard
114: Summary: Graphs improvements
115:
1.276 brouard 116: Revision 1.275 2017/06/30 13:39:33 brouard
117: Summary: Saito's color
118:
1.275 brouard 119: Revision 1.274 2017/06/29 09:47:08 brouard
120: Summary: Version 0.99r14
121:
1.274 brouard 122: Revision 1.273 2017/06/27 11:06:02 brouard
123: Summary: More documentation on projections
124:
1.273 brouard 125: Revision 1.272 2017/06/27 10:22:40 brouard
126: Summary: Color of backprojection changed from 6 to 5(yellow)
127:
1.272 brouard 128: Revision 1.271 2017/06/27 10:17:50 brouard
129: Summary: Some bug with rint
130:
1.271 brouard 131: Revision 1.270 2017/05/24 05:45:29 brouard
132: *** empty log message ***
133:
1.270 brouard 134: Revision 1.269 2017/05/23 08:39:25 brouard
135: Summary: Code into subroutine, cleanings
136:
1.269 brouard 137: Revision 1.268 2017/05/18 20:09:32 brouard
138: Summary: backprojection and confidence intervals of backprevalence
139:
1.268 brouard 140: Revision 1.267 2017/05/13 10:25:05 brouard
141: Summary: temporary save for backprojection
142:
1.267 brouard 143: Revision 1.266 2017/05/13 07:26:12 brouard
144: Summary: Version 0.99r13 (improvements and bugs fixed)
145:
1.266 brouard 146: Revision 1.265 2017/04/26 16:22:11 brouard
147: Summary: imach 0.99r13 Some bugs fixed
148:
1.265 brouard 149: Revision 1.264 2017/04/26 06:01:29 brouard
150: Summary: Labels in graphs
151:
1.264 brouard 152: Revision 1.263 2017/04/24 15:23:15 brouard
153: Summary: to save
154:
1.263 brouard 155: Revision 1.262 2017/04/18 16:48:12 brouard
156: *** empty log message ***
157:
1.262 brouard 158: Revision 1.261 2017/04/05 10:14:09 brouard
159: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
160:
1.261 brouard 161: Revision 1.260 2017/04/04 17:46:59 brouard
162: Summary: Gnuplot indexations fixed (humm)
163:
1.260 brouard 164: Revision 1.259 2017/04/04 13:01:16 brouard
165: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
166:
1.259 brouard 167: Revision 1.258 2017/04/03 10:17:47 brouard
168: Summary: Version 0.99r12
169:
170: Some cleanings, conformed with updated documentation.
171:
1.258 brouard 172: Revision 1.257 2017/03/29 16:53:30 brouard
173: Summary: Temp
174:
1.257 brouard 175: Revision 1.256 2017/03/27 05:50:23 brouard
176: Summary: Temporary
177:
1.256 brouard 178: Revision 1.255 2017/03/08 16:02:28 brouard
179: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
180:
1.255 brouard 181: Revision 1.254 2017/03/08 07:13:00 brouard
182: Summary: Fixing data parameter line
183:
1.254 brouard 184: Revision 1.253 2016/12/15 11:59:41 brouard
185: Summary: 0.99 in progress
186:
1.253 brouard 187: Revision 1.252 2016/09/15 21:15:37 brouard
188: *** empty log message ***
189:
1.252 brouard 190: Revision 1.251 2016/09/15 15:01:13 brouard
191: Summary: not working
192:
1.251 brouard 193: Revision 1.250 2016/09/08 16:07:27 brouard
194: Summary: continue
195:
1.250 brouard 196: Revision 1.249 2016/09/07 17:14:18 brouard
197: Summary: Starting values from frequencies
198:
1.249 brouard 199: Revision 1.248 2016/09/07 14:10:18 brouard
200: *** empty log message ***
201:
1.248 brouard 202: Revision 1.247 2016/09/02 11:11:21 brouard
203: *** empty log message ***
204:
1.247 brouard 205: Revision 1.246 2016/09/02 08:49:22 brouard
206: *** empty log message ***
207:
1.246 brouard 208: Revision 1.245 2016/09/02 07:25:01 brouard
209: *** empty log message ***
210:
1.245 brouard 211: Revision 1.244 2016/09/02 07:17:34 brouard
212: *** empty log message ***
213:
1.244 brouard 214: Revision 1.243 2016/09/02 06:45:35 brouard
215: *** empty log message ***
216:
1.243 brouard 217: Revision 1.242 2016/08/30 15:01:20 brouard
218: Summary: Fixing a lots
219:
1.242 brouard 220: Revision 1.241 2016/08/29 17:17:25 brouard
221: Summary: gnuplot problem in Back projection to fix
222:
1.241 brouard 223: Revision 1.240 2016/08/29 07:53:18 brouard
224: Summary: Better
225:
1.240 brouard 226: Revision 1.239 2016/08/26 15:51:03 brouard
227: Summary: Improvement in Powell output in order to copy and paste
228:
229: Author:
230:
1.239 brouard 231: Revision 1.238 2016/08/26 14:23:35 brouard
232: Summary: Starting tests of 0.99
233:
1.238 brouard 234: Revision 1.237 2016/08/26 09:20:19 brouard
235: Summary: to valgrind
236:
1.237 brouard 237: Revision 1.236 2016/08/25 10:50:18 brouard
238: *** empty log message ***
239:
1.236 brouard 240: Revision 1.235 2016/08/25 06:59:23 brouard
241: *** empty log message ***
242:
1.235 brouard 243: Revision 1.234 2016/08/23 16:51:20 brouard
244: *** empty log message ***
245:
1.234 brouard 246: Revision 1.233 2016/08/23 07:40:50 brouard
247: Summary: not working
248:
1.233 brouard 249: Revision 1.232 2016/08/22 14:20:21 brouard
250: Summary: not working
251:
1.232 brouard 252: Revision 1.231 2016/08/22 07:17:15 brouard
253: Summary: not working
254:
1.231 brouard 255: Revision 1.230 2016/08/22 06:55:53 brouard
256: Summary: Not working
257:
1.230 brouard 258: Revision 1.229 2016/07/23 09:45:53 brouard
259: Summary: Completing for func too
260:
1.229 brouard 261: Revision 1.228 2016/07/22 17:45:30 brouard
262: Summary: Fixing some arrays, still debugging
263:
1.227 brouard 264: Revision 1.226 2016/07/12 18:42:34 brouard
265: Summary: temp
266:
1.226 brouard 267: Revision 1.225 2016/07/12 08:40:03 brouard
268: Summary: saving but not running
269:
1.225 brouard 270: Revision 1.224 2016/07/01 13:16:01 brouard
271: Summary: Fixes
272:
1.224 brouard 273: Revision 1.223 2016/02/19 09:23:35 brouard
274: Summary: temporary
275:
1.223 brouard 276: Revision 1.222 2016/02/17 08:14:50 brouard
277: Summary: Probably last 0.98 stable version 0.98r6
278:
1.222 brouard 279: Revision 1.221 2016/02/15 23:35:36 brouard
280: Summary: minor bug
281:
1.220 brouard 282: Revision 1.219 2016/02/15 00:48:12 brouard
283: *** empty log message ***
284:
1.219 brouard 285: Revision 1.218 2016/02/12 11:29:23 brouard
286: Summary: 0.99 Back projections
287:
1.218 brouard 288: Revision 1.217 2015/12/23 17:18:31 brouard
289: Summary: Experimental backcast
290:
1.217 brouard 291: Revision 1.216 2015/12/18 17:32:11 brouard
292: Summary: 0.98r4 Warning and status=-2
293:
294: Version 0.98r4 is now:
295: - displaying an error when status is -1, date of interview unknown and date of death known;
296: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
297: Older changes concerning s=-2, dating from 2005 have been supersed.
298:
1.216 brouard 299: Revision 1.215 2015/12/16 08:52:24 brouard
300: Summary: 0.98r4 working
301:
1.215 brouard 302: Revision 1.214 2015/12/16 06:57:54 brouard
303: Summary: temporary not working
304:
1.214 brouard 305: Revision 1.213 2015/12/11 18:22:17 brouard
306: Summary: 0.98r4
307:
1.213 brouard 308: Revision 1.212 2015/11/21 12:47:24 brouard
309: Summary: minor typo
310:
1.212 brouard 311: Revision 1.211 2015/11/21 12:41:11 brouard
312: Summary: 0.98r3 with some graph of projected cross-sectional
313:
314: Author: Nicolas Brouard
315:
1.211 brouard 316: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 317: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 318: Summary: Adding ftolpl parameter
319: Author: N Brouard
320:
321: We had difficulties to get smoothed confidence intervals. It was due
322: to the period prevalence which wasn't computed accurately. The inner
323: parameter ftolpl is now an outer parameter of the .imach parameter
324: file after estepm. If ftolpl is small 1.e-4 and estepm too,
325: computation are long.
326:
1.209 brouard 327: Revision 1.208 2015/11/17 14:31:57 brouard
328: Summary: temporary
329:
1.208 brouard 330: Revision 1.207 2015/10/27 17:36:57 brouard
331: *** empty log message ***
332:
1.207 brouard 333: Revision 1.206 2015/10/24 07:14:11 brouard
334: *** empty log message ***
335:
1.206 brouard 336: Revision 1.205 2015/10/23 15:50:53 brouard
337: Summary: 0.98r3 some clarification for graphs on likelihood contributions
338:
1.205 brouard 339: Revision 1.204 2015/10/01 16:20:26 brouard
340: Summary: Some new graphs of contribution to likelihood
341:
1.204 brouard 342: Revision 1.203 2015/09/30 17:45:14 brouard
343: Summary: looking at better estimation of the hessian
344:
345: Also a better criteria for convergence to the period prevalence And
346: therefore adding the number of years needed to converge. (The
347: prevalence in any alive state shold sum to one
348:
1.203 brouard 349: Revision 1.202 2015/09/22 19:45:16 brouard
350: Summary: Adding some overall graph on contribution to likelihood. Might change
351:
1.202 brouard 352: Revision 1.201 2015/09/15 17:34:58 brouard
353: Summary: 0.98r0
354:
355: - Some new graphs like suvival functions
356: - Some bugs fixed like model=1+age+V2.
357:
1.201 brouard 358: Revision 1.200 2015/09/09 16:53:55 brouard
359: Summary: Big bug thanks to Flavia
360:
361: Even model=1+age+V2. did not work anymore
362:
1.200 brouard 363: Revision 1.199 2015/09/07 14:09:23 brouard
364: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
365:
1.199 brouard 366: Revision 1.198 2015/09/03 07:14:39 brouard
367: Summary: 0.98q5 Flavia
368:
1.198 brouard 369: Revision 1.197 2015/09/01 18:24:39 brouard
370: *** empty log message ***
371:
1.197 brouard 372: Revision 1.196 2015/08/18 23:17:52 brouard
373: Summary: 0.98q5
374:
1.196 brouard 375: Revision 1.195 2015/08/18 16:28:39 brouard
376: Summary: Adding a hack for testing purpose
377:
378: After reading the title, ftol and model lines, if the comment line has
379: a q, starting with #q, the answer at the end of the run is quit. It
380: permits to run test files in batch with ctest. The former workaround was
381: $ echo q | imach foo.imach
382:
1.195 brouard 383: Revision 1.194 2015/08/18 13:32:00 brouard
384: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
385:
1.194 brouard 386: Revision 1.193 2015/08/04 07:17:42 brouard
387: Summary: 0.98q4
388:
1.193 brouard 389: Revision 1.192 2015/07/16 16:49:02 brouard
390: Summary: Fixing some outputs
391:
1.192 brouard 392: Revision 1.191 2015/07/14 10:00:33 brouard
393: Summary: Some fixes
394:
1.191 brouard 395: Revision 1.190 2015/05/05 08:51:13 brouard
396: Summary: Adding digits in output parameters (7 digits instead of 6)
397:
398: Fix 1+age+.
399:
1.190 brouard 400: Revision 1.189 2015/04/30 14:45:16 brouard
401: Summary: 0.98q2
402:
1.189 brouard 403: Revision 1.188 2015/04/30 08:27:53 brouard
404: *** empty log message ***
405:
1.188 brouard 406: Revision 1.187 2015/04/29 09:11:15 brouard
407: *** empty log message ***
408:
1.187 brouard 409: Revision 1.186 2015/04/23 12:01:52 brouard
410: Summary: V1*age is working now, version 0.98q1
411:
412: Some codes had been disabled in order to simplify and Vn*age was
413: working in the optimization phase, ie, giving correct MLE parameters,
414: but, as usual, outputs were not correct and program core dumped.
415:
1.186 brouard 416: Revision 1.185 2015/03/11 13:26:42 brouard
417: Summary: Inclusion of compile and links command line for Intel Compiler
418:
1.185 brouard 419: Revision 1.184 2015/03/11 11:52:39 brouard
420: Summary: Back from Windows 8. Intel Compiler
421:
1.184 brouard 422: Revision 1.183 2015/03/10 20:34:32 brouard
423: Summary: 0.98q0, trying with directest, mnbrak fixed
424:
425: We use directest instead of original Powell test; probably no
426: incidence on the results, but better justifications;
427: We fixed Numerical Recipes mnbrak routine which was wrong and gave
428: wrong results.
429:
1.183 brouard 430: Revision 1.182 2015/02/12 08:19:57 brouard
431: Summary: Trying to keep directest which seems simpler and more general
432: Author: Nicolas Brouard
433:
1.182 brouard 434: Revision 1.181 2015/02/11 23:22:24 brouard
435: Summary: Comments on Powell added
436:
437: Author:
438:
1.181 brouard 439: Revision 1.180 2015/02/11 17:33:45 brouard
440: Summary: Finishing move from main to function (hpijx and prevalence_limit)
441:
1.180 brouard 442: Revision 1.179 2015/01/04 09:57:06 brouard
443: Summary: back to OS/X
444:
1.179 brouard 445: Revision 1.178 2015/01/04 09:35:48 brouard
446: *** empty log message ***
447:
1.178 brouard 448: Revision 1.177 2015/01/03 18:40:56 brouard
449: Summary: Still testing ilc32 on OSX
450:
1.177 brouard 451: Revision 1.176 2015/01/03 16:45:04 brouard
452: *** empty log message ***
453:
1.176 brouard 454: Revision 1.175 2015/01/03 16:33:42 brouard
455: *** empty log message ***
456:
1.175 brouard 457: Revision 1.174 2015/01/03 16:15:49 brouard
458: Summary: Still in cross-compilation
459:
1.174 brouard 460: Revision 1.173 2015/01/03 12:06:26 brouard
461: Summary: trying to detect cross-compilation
462:
1.173 brouard 463: Revision 1.172 2014/12/27 12:07:47 brouard
464: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
465:
1.172 brouard 466: Revision 1.171 2014/12/23 13:26:59 brouard
467: Summary: Back from Visual C
468:
469: Still problem with utsname.h on Windows
470:
1.171 brouard 471: Revision 1.170 2014/12/23 11:17:12 brouard
472: Summary: Cleaning some \%% back to %%
473:
474: The escape was mandatory for a specific compiler (which one?), but too many warnings.
475:
1.170 brouard 476: Revision 1.169 2014/12/22 23:08:31 brouard
477: Summary: 0.98p
478:
479: Outputs some informations on compiler used, OS etc. Testing on different platforms.
480:
1.169 brouard 481: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 482: Summary: update
1.169 brouard 483:
1.168 brouard 484: Revision 1.167 2014/12/22 13:50:56 brouard
485: Summary: Testing uname and compiler version and if compiled 32 or 64
486:
487: Testing on Linux 64
488:
1.167 brouard 489: Revision 1.166 2014/12/22 11:40:47 brouard
490: *** empty log message ***
491:
1.166 brouard 492: Revision 1.165 2014/12/16 11:20:36 brouard
493: Summary: After compiling on Visual C
494:
495: * imach.c (Module): Merging 1.61 to 1.162
496:
1.165 brouard 497: Revision 1.164 2014/12/16 10:52:11 brouard
498: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
499:
500: * imach.c (Module): Merging 1.61 to 1.162
501:
1.164 brouard 502: Revision 1.163 2014/12/16 10:30:11 brouard
503: * imach.c (Module): Merging 1.61 to 1.162
504:
1.163 brouard 505: Revision 1.162 2014/09/25 11:43:39 brouard
506: Summary: temporary backup 0.99!
507:
1.162 brouard 508: Revision 1.1 2014/09/16 11:06:58 brouard
509: Summary: With some code (wrong) for nlopt
510:
511: Author:
512:
513: Revision 1.161 2014/09/15 20:41:41 brouard
514: Summary: Problem with macro SQR on Intel compiler
515:
1.161 brouard 516: Revision 1.160 2014/09/02 09:24:05 brouard
517: *** empty log message ***
518:
1.160 brouard 519: Revision 1.159 2014/09/01 10:34:10 brouard
520: Summary: WIN32
521: Author: Brouard
522:
1.159 brouard 523: Revision 1.158 2014/08/27 17:11:51 brouard
524: *** empty log message ***
525:
1.158 brouard 526: Revision 1.157 2014/08/27 16:26:55 brouard
527: Summary: Preparing windows Visual studio version
528: Author: Brouard
529:
530: In order to compile on Visual studio, time.h is now correct and time_t
531: and tm struct should be used. difftime should be used but sometimes I
532: just make the differences in raw time format (time(&now).
533: Trying to suppress #ifdef LINUX
534: Add xdg-open for __linux in order to open default browser.
535:
1.157 brouard 536: Revision 1.156 2014/08/25 20:10:10 brouard
537: *** empty log message ***
538:
1.156 brouard 539: Revision 1.155 2014/08/25 18:32:34 brouard
540: Summary: New compile, minor changes
541: Author: Brouard
542:
1.155 brouard 543: Revision 1.154 2014/06/20 17:32:08 brouard
544: Summary: Outputs now all graphs of convergence to period prevalence
545:
1.154 brouard 546: Revision 1.153 2014/06/20 16:45:46 brouard
547: Summary: If 3 live state, convergence to period prevalence on same graph
548: Author: Brouard
549:
1.153 brouard 550: Revision 1.152 2014/06/18 17:54:09 brouard
551: Summary: open browser, use gnuplot on same dir than imach if not found in the path
552:
1.152 brouard 553: Revision 1.151 2014/06/18 16:43:30 brouard
554: *** empty log message ***
555:
1.151 brouard 556: Revision 1.150 2014/06/18 16:42:35 brouard
557: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
558: Author: brouard
559:
1.150 brouard 560: Revision 1.149 2014/06/18 15:51:14 brouard
561: Summary: Some fixes in parameter files errors
562: Author: Nicolas Brouard
563:
1.149 brouard 564: Revision 1.148 2014/06/17 17:38:48 brouard
565: Summary: Nothing new
566: Author: Brouard
567:
568: Just a new packaging for OS/X version 0.98nS
569:
1.148 brouard 570: Revision 1.147 2014/06/16 10:33:11 brouard
571: *** empty log message ***
572:
1.147 brouard 573: Revision 1.146 2014/06/16 10:20:28 brouard
574: Summary: Merge
575: Author: Brouard
576:
577: Merge, before building revised version.
578:
1.146 brouard 579: Revision 1.145 2014/06/10 21:23:15 brouard
580: Summary: Debugging with valgrind
581: Author: Nicolas Brouard
582:
583: Lot of changes in order to output the results with some covariates
584: After the Edimburgh REVES conference 2014, it seems mandatory to
585: improve the code.
586: No more memory valgrind error but a lot has to be done in order to
587: continue the work of splitting the code into subroutines.
588: Also, decodemodel has been improved. Tricode is still not
589: optimal. nbcode should be improved. Documentation has been added in
590: the source code.
591:
1.144 brouard 592: Revision 1.143 2014/01/26 09:45:38 brouard
593: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
594:
595: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
596: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
597:
1.143 brouard 598: Revision 1.142 2014/01/26 03:57:36 brouard
599: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
600:
601: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
602:
1.142 brouard 603: Revision 1.141 2014/01/26 02:42:01 brouard
604: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
605:
1.141 brouard 606: Revision 1.140 2011/09/02 10:37:54 brouard
607: Summary: times.h is ok with mingw32 now.
608:
1.140 brouard 609: Revision 1.139 2010/06/14 07:50:17 brouard
610: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
611: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
612:
1.139 brouard 613: Revision 1.138 2010/04/30 18:19:40 brouard
614: *** empty log message ***
615:
1.138 brouard 616: Revision 1.137 2010/04/29 18:11:38 brouard
617: (Module): Checking covariates for more complex models
618: than V1+V2. A lot of change to be done. Unstable.
619:
1.137 brouard 620: Revision 1.136 2010/04/26 20:30:53 brouard
621: (Module): merging some libgsl code. Fixing computation
622: of likelione (using inter/intrapolation if mle = 0) in order to
623: get same likelihood as if mle=1.
624: Some cleaning of code and comments added.
625:
1.136 brouard 626: Revision 1.135 2009/10/29 15:33:14 brouard
627: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
628:
1.135 brouard 629: Revision 1.134 2009/10/29 13:18:53 brouard
630: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
631:
1.134 brouard 632: Revision 1.133 2009/07/06 10:21:25 brouard
633: just nforces
634:
1.133 brouard 635: Revision 1.132 2009/07/06 08:22:05 brouard
636: Many tings
637:
1.132 brouard 638: Revision 1.131 2009/06/20 16:22:47 brouard
639: Some dimensions resccaled
640:
1.131 brouard 641: Revision 1.130 2009/05/26 06:44:34 brouard
642: (Module): Max Covariate is now set to 20 instead of 8. A
643: lot of cleaning with variables initialized to 0. Trying to make
644: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
645:
1.130 brouard 646: Revision 1.129 2007/08/31 13:49:27 lievre
647: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
648:
1.129 lievre 649: Revision 1.128 2006/06/30 13:02:05 brouard
650: (Module): Clarifications on computing e.j
651:
1.128 brouard 652: Revision 1.127 2006/04/28 18:11:50 brouard
653: (Module): Yes the sum of survivors was wrong since
654: imach-114 because nhstepm was no more computed in the age
655: loop. Now we define nhstepma in the age loop.
656: (Module): In order to speed up (in case of numerous covariates) we
657: compute health expectancies (without variances) in a first step
658: and then all the health expectancies with variances or standard
659: deviation (needs data from the Hessian matrices) which slows the
660: computation.
661: In the future we should be able to stop the program is only health
662: expectancies and graph are needed without standard deviations.
663:
1.127 brouard 664: Revision 1.126 2006/04/28 17:23:28 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: Version 0.98h
669:
1.126 brouard 670: Revision 1.125 2006/04/04 15:20:31 lievre
671: Errors in calculation of health expectancies. Age was not initialized.
672: Forecasting file added.
673:
674: Revision 1.124 2006/03/22 17:13:53 lievre
675: Parameters are printed with %lf instead of %f (more numbers after the comma).
676: The log-likelihood is printed in the log file
677:
678: Revision 1.123 2006/03/20 10:52:43 brouard
679: * imach.c (Module): <title> changed, corresponds to .htm file
680: name. <head> headers where missing.
681:
682: * imach.c (Module): Weights can have a decimal point as for
683: English (a comma might work with a correct LC_NUMERIC environment,
684: otherwise the weight is truncated).
685: Modification of warning when the covariates values are not 0 or
686: 1.
687: Version 0.98g
688:
689: Revision 1.122 2006/03/20 09:45:41 brouard
690: (Module): Weights can have a decimal point as for
691: English (a comma might work with a correct LC_NUMERIC environment,
692: otherwise the weight is truncated).
693: Modification of warning when the covariates values are not 0 or
694: 1.
695: Version 0.98g
696:
697: Revision 1.121 2006/03/16 17:45:01 lievre
698: * imach.c (Module): Comments concerning covariates added
699:
700: * imach.c (Module): refinements in the computation of lli if
701: status=-2 in order to have more reliable computation if stepm is
702: not 1 month. Version 0.98f
703:
704: Revision 1.120 2006/03/16 15:10:38 lievre
705: (Module): refinements in the computation of lli if
706: status=-2 in order to have more reliable computation if stepm is
707: not 1 month. Version 0.98f
708:
709: Revision 1.119 2006/03/15 17:42:26 brouard
710: (Module): Bug if status = -2, the loglikelihood was
711: computed as likelihood omitting the logarithm. Version O.98e
712:
713: Revision 1.118 2006/03/14 18:20:07 brouard
714: (Module): varevsij Comments added explaining the second
715: table of variances if popbased=1 .
716: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
717: (Module): Function pstamp added
718: (Module): Version 0.98d
719:
720: Revision 1.117 2006/03/14 17:16:22 brouard
721: (Module): varevsij Comments added explaining the second
722: table of variances if popbased=1 .
723: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
724: (Module): Function pstamp added
725: (Module): Version 0.98d
726:
727: Revision 1.116 2006/03/06 10:29:27 brouard
728: (Module): Variance-covariance wrong links and
729: varian-covariance of ej. is needed (Saito).
730:
731: Revision 1.115 2006/02/27 12:17:45 brouard
732: (Module): One freematrix added in mlikeli! 0.98c
733:
734: Revision 1.114 2006/02/26 12:57:58 brouard
735: (Module): Some improvements in processing parameter
736: filename with strsep.
737:
738: Revision 1.113 2006/02/24 14:20:24 brouard
739: (Module): Memory leaks checks with valgrind and:
740: datafile was not closed, some imatrix were not freed and on matrix
741: allocation too.
742:
743: Revision 1.112 2006/01/30 09:55:26 brouard
744: (Module): Back to gnuplot.exe instead of wgnuplot.exe
745:
746: Revision 1.111 2006/01/25 20:38:18 brouard
747: (Module): Lots of cleaning and bugs added (Gompertz)
748: (Module): Comments can be added in data file. Missing date values
749: can be a simple dot '.'.
750:
751: Revision 1.110 2006/01/25 00:51:50 brouard
752: (Module): Lots of cleaning and bugs added (Gompertz)
753:
754: Revision 1.109 2006/01/24 19:37:15 brouard
755: (Module): Comments (lines starting with a #) are allowed in data.
756:
757: Revision 1.108 2006/01/19 18:05:42 lievre
758: Gnuplot problem appeared...
759: To be fixed
760:
761: Revision 1.107 2006/01/19 16:20:37 brouard
762: Test existence of gnuplot in imach path
763:
764: Revision 1.106 2006/01/19 13:24:36 brouard
765: Some cleaning and links added in html output
766:
767: Revision 1.105 2006/01/05 20:23:19 lievre
768: *** empty log message ***
769:
770: Revision 1.104 2005/09/30 16:11:43 lievre
771: (Module): sump fixed, loop imx fixed, and simplifications.
772: (Module): If the status is missing at the last wave but we know
773: that the person is alive, then we can code his/her status as -2
774: (instead of missing=-1 in earlier versions) and his/her
775: contributions to the likelihood is 1 - Prob of dying from last
776: health status (= 1-p13= p11+p12 in the easiest case of somebody in
777: the healthy state at last known wave). Version is 0.98
778:
779: Revision 1.103 2005/09/30 15:54:49 lievre
780: (Module): sump fixed, loop imx fixed, and simplifications.
781:
782: Revision 1.102 2004/09/15 17:31:30 brouard
783: Add the possibility to read data file including tab characters.
784:
785: Revision 1.101 2004/09/15 10:38:38 brouard
786: Fix on curr_time
787:
788: Revision 1.100 2004/07/12 18:29:06 brouard
789: Add version for Mac OS X. Just define UNIX in Makefile
790:
791: Revision 1.99 2004/06/05 08:57:40 brouard
792: *** empty log message ***
793:
794: Revision 1.98 2004/05/16 15:05:56 brouard
795: New version 0.97 . First attempt to estimate force of mortality
796: directly from the data i.e. without the need of knowing the health
797: state at each age, but using a Gompertz model: log u =a + b*age .
798: This is the basic analysis of mortality and should be done before any
799: other analysis, in order to test if the mortality estimated from the
800: cross-longitudinal survey is different from the mortality estimated
801: from other sources like vital statistic data.
802:
803: The same imach parameter file can be used but the option for mle should be -3.
804:
1.133 brouard 805: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 806: former routines in order to include the new code within the former code.
807:
808: The output is very simple: only an estimate of the intercept and of
809: the slope with 95% confident intervals.
810:
811: Current limitations:
812: A) Even if you enter covariates, i.e. with the
813: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
814: B) There is no computation of Life Expectancy nor Life Table.
815:
816: Revision 1.97 2004/02/20 13:25:42 lievre
817: Version 0.96d. Population forecasting command line is (temporarily)
818: suppressed.
819:
820: Revision 1.96 2003/07/15 15:38:55 brouard
821: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
822: rewritten within the same printf. Workaround: many printfs.
823:
824: Revision 1.95 2003/07/08 07:54:34 brouard
825: * imach.c (Repository):
826: (Repository): Using imachwizard code to output a more meaningful covariance
827: matrix (cov(a12,c31) instead of numbers.
828:
829: Revision 1.94 2003/06/27 13:00:02 brouard
830: Just cleaning
831:
832: Revision 1.93 2003/06/25 16:33:55 brouard
833: (Module): On windows (cygwin) function asctime_r doesn't
834: exist so I changed back to asctime which exists.
835: (Module): Version 0.96b
836:
837: Revision 1.92 2003/06/25 16:30:45 brouard
838: (Module): On windows (cygwin) function asctime_r doesn't
839: exist so I changed back to asctime which exists.
840:
841: Revision 1.91 2003/06/25 15:30:29 brouard
842: * imach.c (Repository): Duplicated warning errors corrected.
843: (Repository): Elapsed time after each iteration is now output. It
844: helps to forecast when convergence will be reached. Elapsed time
845: is stamped in powell. We created a new html file for the graphs
846: concerning matrix of covariance. It has extension -cov.htm.
847:
848: Revision 1.90 2003/06/24 12:34:15 brouard
849: (Module): Some bugs corrected for windows. Also, when
850: mle=-1 a template is output in file "or"mypar.txt with the design
851: of the covariance matrix to be input.
852:
853: Revision 1.89 2003/06/24 12:30:52 brouard
854: (Module): Some bugs corrected for windows. Also, when
855: mle=-1 a template is output in file "or"mypar.txt with the design
856: of the covariance matrix to be input.
857:
858: Revision 1.88 2003/06/23 17:54:56 brouard
859: * 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.
860:
861: Revision 1.87 2003/06/18 12:26:01 brouard
862: Version 0.96
863:
864: Revision 1.86 2003/06/17 20:04:08 brouard
865: (Module): Change position of html and gnuplot routines and added
866: routine fileappend.
867:
868: Revision 1.85 2003/06/17 13:12:43 brouard
869: * imach.c (Repository): Check when date of death was earlier that
870: current date of interview. It may happen when the death was just
871: prior to the death. In this case, dh was negative and likelihood
872: was wrong (infinity). We still send an "Error" but patch by
873: assuming that the date of death was just one stepm after the
874: interview.
875: (Repository): Because some people have very long ID (first column)
876: we changed int to long in num[] and we added a new lvector for
877: memory allocation. But we also truncated to 8 characters (left
878: truncation)
879: (Repository): No more line truncation errors.
880:
881: Revision 1.84 2003/06/13 21:44:43 brouard
882: * imach.c (Repository): Replace "freqsummary" at a correct
883: place. It differs from routine "prevalence" which may be called
884: many times. Probs is memory consuming and must be used with
885: parcimony.
886: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
887:
888: Revision 1.83 2003/06/10 13:39:11 lievre
889: *** empty log message ***
890:
891: Revision 1.82 2003/06/05 15:57:20 brouard
892: Add log in imach.c and fullversion number is now printed.
893:
894: */
895: /*
896: Interpolated Markov Chain
897:
898: Short summary of the programme:
899:
1.227 brouard 900: This program computes Healthy Life Expectancies or State-specific
901: (if states aren't health statuses) Expectancies from
902: cross-longitudinal data. Cross-longitudinal data consist in:
903:
904: -1- a first survey ("cross") where individuals from different ages
905: are interviewed on their health status or degree of disability (in
906: the case of a health survey which is our main interest)
907:
908: -2- at least a second wave of interviews ("longitudinal") which
909: measure each change (if any) in individual health status. Health
910: expectancies are computed from the time spent in each health state
911: according to a model. More health states you consider, more time is
912: necessary to reach the Maximum Likelihood of the parameters involved
913: in the model. The simplest model is the multinomial logistic model
914: where pij is the probability to be observed in state j at the second
915: wave conditional to be observed in state i at the first
916: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
917: etc , where 'age' is age and 'sex' is a covariate. If you want to
918: have a more complex model than "constant and age", you should modify
919: the program where the markup *Covariates have to be included here
920: again* invites you to do it. More covariates you add, slower the
1.126 brouard 921: convergence.
922:
923: The advantage of this computer programme, compared to a simple
924: multinomial logistic model, is clear when the delay between waves is not
925: identical for each individual. Also, if a individual missed an
926: intermediate interview, the information is lost, but taken into
927: account using an interpolation or extrapolation.
928:
929: hPijx is the probability to be observed in state i at age x+h
930: conditional to the observed state i at age x. The delay 'h' can be
931: split into an exact number (nh*stepm) of unobserved intermediate
932: states. This elementary transition (by month, quarter,
933: semester or year) is modelled as a multinomial logistic. The hPx
934: matrix is simply the matrix product of nh*stepm elementary matrices
935: and the contribution of each individual to the likelihood is simply
936: hPijx.
937:
938: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 939: of the life expectancies. It also computes the period (stable) prevalence.
940:
941: Back prevalence and projections:
1.227 brouard 942:
943: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
944: double agemaxpar, double ftolpl, int *ncvyearp, double
945: dateprev1,double dateprev2, int firstpass, int lastpass, int
946: mobilavproj)
947:
948: Computes the back prevalence limit for any combination of
949: covariate values k at any age between ageminpar and agemaxpar and
950: returns it in **bprlim. In the loops,
951:
952: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
953: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
954:
955: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 956: Computes for any combination of covariates k and any age between bage and fage
957: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
958: oldm=oldms;savm=savms;
1.227 brouard 959:
1.267 brouard 960: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 961: Computes the transition matrix starting at age 'age' over
962: 'nhstepm*hstepm*stepm' months (i.e. until
963: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 964: nhstepm*hstepm matrices.
965:
966: Returns p3mat[i][j][h] after calling
967: p3mat[i][j][h]=matprod2(newm,
968: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
969: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
970: oldm);
1.226 brouard 971:
972: Important routines
973:
974: - func (or funcone), computes logit (pij) distinguishing
975: o fixed variables (single or product dummies or quantitative);
976: o varying variables by:
977: (1) wave (single, product dummies, quantitative),
978: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
979: % fixed dummy (treated) or quantitative (not done because time-consuming);
980: % varying dummy (not done) or quantitative (not done);
981: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
982: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
983: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
984: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
985: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 986:
1.226 brouard 987:
988:
1.133 brouard 989: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
990: Institut national d'études démographiques, Paris.
1.126 brouard 991: This software have been partly granted by Euro-REVES, a concerted action
992: from the European Union.
993: It is copyrighted identically to a GNU software product, ie programme and
994: software can be distributed freely for non commercial use. Latest version
995: can be accessed at http://euroreves.ined.fr/imach .
996:
997: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
998: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
999:
1000: **********************************************************************/
1001: /*
1002: main
1003: read parameterfile
1004: read datafile
1005: concatwav
1006: freqsummary
1007: if (mle >= 1)
1008: mlikeli
1009: print results files
1010: if mle==1
1011: computes hessian
1012: read end of parameter file: agemin, agemax, bage, fage, estepm
1013: begin-prev-date,...
1014: open gnuplot file
1015: open html file
1.145 brouard 1016: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1017: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1018: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1019: freexexit2 possible for memory heap.
1020:
1021: h Pij x | pij_nom ficrestpij
1022: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1023: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1024: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1025:
1026: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1027: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1028: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1029: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1030: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1031:
1.126 brouard 1032: forecasting if prevfcast==1 prevforecast call prevalence()
1033: health expectancies
1034: Variance-covariance of DFLE
1035: prevalence()
1036: movingaverage()
1037: varevsij()
1038: if popbased==1 varevsij(,popbased)
1039: total life expectancies
1040: Variance of period (stable) prevalence
1041: end
1042: */
1043:
1.187 brouard 1044: /* #define DEBUG */
1045: /* #define DEBUGBRENT */
1.203 brouard 1046: /* #define DEBUGLINMIN */
1047: /* #define DEBUGHESS */
1048: #define DEBUGHESSIJ
1.224 brouard 1049: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1050: #define POWELL /* Instead of NLOPT */
1.224 brouard 1051: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1052: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1053: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1054:
1055: #include <math.h>
1056: #include <stdio.h>
1057: #include <stdlib.h>
1058: #include <string.h>
1.226 brouard 1059: #include <ctype.h>
1.159 brouard 1060:
1061: #ifdef _WIN32
1062: #include <io.h>
1.172 brouard 1063: #include <windows.h>
1064: #include <tchar.h>
1.159 brouard 1065: #else
1.126 brouard 1066: #include <unistd.h>
1.159 brouard 1067: #endif
1.126 brouard 1068:
1069: #include <limits.h>
1070: #include <sys/types.h>
1.171 brouard 1071:
1072: #if defined(__GNUC__)
1073: #include <sys/utsname.h> /* Doesn't work on Windows */
1074: #endif
1075:
1.126 brouard 1076: #include <sys/stat.h>
1077: #include <errno.h>
1.159 brouard 1078: /* extern int errno; */
1.126 brouard 1079:
1.157 brouard 1080: /* #ifdef LINUX */
1081: /* #include <time.h> */
1082: /* #include "timeval.h" */
1083: /* #else */
1084: /* #include <sys/time.h> */
1085: /* #endif */
1086:
1.126 brouard 1087: #include <time.h>
1088:
1.136 brouard 1089: #ifdef GSL
1090: #include <gsl/gsl_errno.h>
1091: #include <gsl/gsl_multimin.h>
1092: #endif
1093:
1.167 brouard 1094:
1.162 brouard 1095: #ifdef NLOPT
1096: #include <nlopt.h>
1097: typedef struct {
1098: double (* function)(double [] );
1099: } myfunc_data ;
1100: #endif
1101:
1.126 brouard 1102: /* #include <libintl.h> */
1103: /* #define _(String) gettext (String) */
1104:
1.251 brouard 1105: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1106:
1107: #define GNUPLOTPROGRAM "gnuplot"
1108: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1109: #define FILENAMELENGTH 132
1110:
1111: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1112: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1113:
1.144 brouard 1114: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1115: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1116:
1117: #define NINTERVMAX 8
1.144 brouard 1118: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1119: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1120: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1121: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1122: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1123: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1124: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1125: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1126: /* #define AGESUP 130 */
1.288 brouard 1127: /* #define AGESUP 150 */
1128: #define AGESUP 200
1.268 brouard 1129: #define AGEINF 0
1.218 brouard 1130: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1131: #define AGEBASE 40
1.194 brouard 1132: #define AGEOVERFLOW 1.e20
1.164 brouard 1133: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1134: #ifdef _WIN32
1135: #define DIRSEPARATOR '\\'
1136: #define CHARSEPARATOR "\\"
1137: #define ODIRSEPARATOR '/'
1138: #else
1.126 brouard 1139: #define DIRSEPARATOR '/'
1140: #define CHARSEPARATOR "/"
1141: #define ODIRSEPARATOR '\\'
1142: #endif
1143:
1.307 ! brouard 1144: /* $Id: imach.c,v 1.306 2021/02/20 15:44:02 brouard Exp $ */
1.126 brouard 1145: /* $State: Exp $ */
1.196 brouard 1146: #include "version.h"
1147: char version[]=__IMACH_VERSION__;
1.306 brouard 1148: char copyright[]="Feb 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, INED 2000-2021";
1.307 ! brouard 1149: char fullversion[]="$Revision: 1.306 $ $Date: 2021/02/20 15:44:02 $";
1.126 brouard 1150: char strstart[80];
1151: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1152: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1153: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1154: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1155: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1156: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1157: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1158: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1159: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1160: int cptcovprodnoage=0; /**< Number of covariate products without age */
1161: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1162: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1163: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1164: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1165: int nsd=0; /**< Total number of single dummy variables (output) */
1166: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1167: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1168: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1169: int ntveff=0; /**< ntveff number of effective time varying variables */
1170: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1171: int cptcov=0; /* Working variable */
1.290 brouard 1172: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1173: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1174: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1175: int nlstate=2; /* Number of live states */
1176: int ndeath=1; /* Number of dead states */
1.130 brouard 1177: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1178: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1179: int popbased=0;
1180:
1181: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1182: int maxwav=0; /* Maxim number of waves */
1183: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1184: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1185: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1186: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1187: int mle=1, weightopt=0;
1.126 brouard 1188: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1189: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1190: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1191: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1192: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1193: int selected(int kvar); /* Is covariate kvar selected for printing results */
1194:
1.130 brouard 1195: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1196: double **matprod2(); /* test */
1.126 brouard 1197: double **oldm, **newm, **savm; /* Working pointers to matrices */
1198: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1199: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1200:
1.136 brouard 1201: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1202: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1203: FILE *ficlog, *ficrespow;
1.130 brouard 1204: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1205: double fretone; /* Only one call to likelihood */
1.130 brouard 1206: long ipmx=0; /* Number of contributions */
1.126 brouard 1207: double sw; /* Sum of weights */
1208: char filerespow[FILENAMELENGTH];
1209: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1210: FILE *ficresilk;
1211: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1212: FILE *ficresprobmorprev;
1213: FILE *fichtm, *fichtmcov; /* Html File */
1214: FILE *ficreseij;
1215: char filerese[FILENAMELENGTH];
1216: FILE *ficresstdeij;
1217: char fileresstde[FILENAMELENGTH];
1218: FILE *ficrescveij;
1219: char filerescve[FILENAMELENGTH];
1220: FILE *ficresvij;
1221: char fileresv[FILENAMELENGTH];
1.269 brouard 1222:
1.126 brouard 1223: char title[MAXLINE];
1.234 brouard 1224: char model[MAXLINE]; /**< The model line */
1.217 brouard 1225: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1226: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1227: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1228: char command[FILENAMELENGTH];
1229: int outcmd=0;
1230:
1.217 brouard 1231: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1232: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1233: char filelog[FILENAMELENGTH]; /* Log file */
1234: char filerest[FILENAMELENGTH];
1235: char fileregp[FILENAMELENGTH];
1236: char popfile[FILENAMELENGTH];
1237:
1238: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1239:
1.157 brouard 1240: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1241: /* struct timezone tzp; */
1242: /* extern int gettimeofday(); */
1243: struct tm tml, *gmtime(), *localtime();
1244:
1245: extern time_t time();
1246:
1247: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1248: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1249: struct tm tm;
1250:
1.126 brouard 1251: char strcurr[80], strfor[80];
1252:
1253: char *endptr;
1254: long lval;
1255: double dval;
1256:
1257: #define NR_END 1
1258: #define FREE_ARG char*
1259: #define FTOL 1.0e-10
1260:
1261: #define NRANSI
1.240 brouard 1262: #define ITMAX 200
1263: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1264:
1265: #define TOL 2.0e-4
1266:
1267: #define CGOLD 0.3819660
1268: #define ZEPS 1.0e-10
1269: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1270:
1271: #define GOLD 1.618034
1272: #define GLIMIT 100.0
1273: #define TINY 1.0e-20
1274:
1275: static double maxarg1,maxarg2;
1276: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1277: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1278:
1279: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1280: #define rint(a) floor(a+0.5)
1.166 brouard 1281: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1282: #define mytinydouble 1.0e-16
1.166 brouard 1283: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1284: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1285: /* static double dsqrarg; */
1286: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1287: static double sqrarg;
1288: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1289: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1290: int agegomp= AGEGOMP;
1291:
1292: int imx;
1293: int stepm=1;
1294: /* Stepm, step in month: minimum step interpolation*/
1295:
1296: int estepm;
1297: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1298:
1299: int m,nb;
1300: long *num;
1.197 brouard 1301: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1302: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1303: covariate for which somebody answered excluding
1304: undefined. Usually 2: 0 and 1. */
1305: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1306: covariate for which somebody answered including
1307: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1308: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1309: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1310: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1311: double *ageexmed,*agecens;
1312: double dateintmean=0;
1.296 brouard 1313: double anprojd, mprojd, jprojd; /* For eventual projections */
1314: double anprojf, mprojf, jprojf;
1.126 brouard 1315:
1.296 brouard 1316: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1317: double anbackf, mbackf, jbackf;
1318: double jintmean,mintmean,aintmean;
1.126 brouard 1319: double *weight;
1320: int **s; /* Status */
1.141 brouard 1321: double *agedc;
1.145 brouard 1322: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1323: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1324: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1325: double **coqvar; /* Fixed quantitative covariate nqv */
1326: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1327: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1328: double idx;
1329: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1330: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1331: /*k 1 2 3 4 5 6 7 8 9 */
1332: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1333: /* Tndvar[k] 1 2 3 4 5 */
1334: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1335: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1336: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1337: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1338: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1339: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1340: /* Tprod[i]=k 4 7 */
1341: /* Tage[i]=k 5 8 */
1342: /* */
1343: /* Type */
1344: /* V 1 2 3 4 5 */
1345: /* F F V V V */
1346: /* D Q D D Q */
1347: /* */
1348: int *TvarsD;
1349: int *TvarsDind;
1350: int *TvarsQ;
1351: int *TvarsQind;
1352:
1.235 brouard 1353: #define MAXRESULTLINES 10
1354: int nresult=0;
1.258 brouard 1355: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1356: int TKresult[MAXRESULTLINES];
1.237 brouard 1357: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1358: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1359: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1360: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1361: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1362: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1363:
1.234 brouard 1364: /* 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 1365: 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 */
1366: 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 */
1367: 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 */
1368: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1369: 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 */
1370: 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 1371: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1372: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1373: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1374: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1375: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1376: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1377: 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 */
1378: 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 */
1379:
1.230 brouard 1380: int *Tvarsel; /**< Selected covariates for output */
1381: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1382: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1383: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1384: 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 1385: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1386: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1387: int *Tage;
1.227 brouard 1388: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1389: 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 1390: 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*/
1391: 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 1392: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1393: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1394: int **Tvard;
1395: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1396: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1397: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1398: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1399: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1400: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1401: double *lsurv, *lpop, *tpop;
1402:
1.231 brouard 1403: #define FD 1; /* Fixed dummy covariate */
1404: #define FQ 2; /* Fixed quantitative covariate */
1405: #define FP 3; /* Fixed product covariate */
1406: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1407: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1408: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1409: #define VD 10; /* Varying dummy covariate */
1410: #define VQ 11; /* Varying quantitative covariate */
1411: #define VP 12; /* Varying product covariate */
1412: #define VPDD 13; /* Varying product dummy*dummy covariate */
1413: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1414: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1415: #define APFD 16; /* Age product * fixed dummy covariate */
1416: #define APFQ 17; /* Age product * fixed quantitative covariate */
1417: #define APVD 18; /* Age product * varying dummy covariate */
1418: #define APVQ 19; /* Age product * varying quantitative covariate */
1419:
1420: #define FTYPE 1; /* Fixed covariate */
1421: #define VTYPE 2; /* Varying covariate (loop in wave) */
1422: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1423:
1424: struct kmodel{
1425: int maintype; /* main type */
1426: int subtype; /* subtype */
1427: };
1428: struct kmodel modell[NCOVMAX];
1429:
1.143 brouard 1430: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1431: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1432:
1433: /**************** split *************************/
1434: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1435: {
1436: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1437: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1438: */
1439: char *ss; /* pointer */
1.186 brouard 1440: int l1=0, l2=0; /* length counters */
1.126 brouard 1441:
1442: l1 = strlen(path ); /* length of path */
1443: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1444: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1445: if ( ss == NULL ) { /* no directory, so determine current directory */
1446: strcpy( name, path ); /* we got the fullname name because no directory */
1447: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1448: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1449: /* get current working directory */
1450: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1451: #ifdef WIN32
1452: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1453: #else
1454: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1455: #endif
1.126 brouard 1456: return( GLOCK_ERROR_GETCWD );
1457: }
1458: /* got dirc from getcwd*/
1459: printf(" DIRC = %s \n",dirc);
1.205 brouard 1460: } else { /* strip directory from path */
1.126 brouard 1461: ss++; /* after this, the filename */
1462: l2 = strlen( ss ); /* length of filename */
1463: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1464: strcpy( name, ss ); /* save file name */
1465: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1466: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1467: printf(" DIRC2 = %s \n",dirc);
1468: }
1469: /* We add a separator at the end of dirc if not exists */
1470: l1 = strlen( dirc ); /* length of directory */
1471: if( dirc[l1-1] != DIRSEPARATOR ){
1472: dirc[l1] = DIRSEPARATOR;
1473: dirc[l1+1] = 0;
1474: printf(" DIRC3 = %s \n",dirc);
1475: }
1476: ss = strrchr( name, '.' ); /* find last / */
1477: if (ss >0){
1478: ss++;
1479: strcpy(ext,ss); /* save extension */
1480: l1= strlen( name);
1481: l2= strlen(ss)+1;
1482: strncpy( finame, name, l1-l2);
1483: finame[l1-l2]= 0;
1484: }
1485:
1486: return( 0 ); /* we're done */
1487: }
1488:
1489:
1490: /******************************************/
1491:
1492: void replace_back_to_slash(char *s, char*t)
1493: {
1494: int i;
1495: int lg=0;
1496: i=0;
1497: lg=strlen(t);
1498: for(i=0; i<= lg; i++) {
1499: (s[i] = t[i]);
1500: if (t[i]== '\\') s[i]='/';
1501: }
1502: }
1503:
1.132 brouard 1504: char *trimbb(char *out, char *in)
1.137 brouard 1505: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1506: char *s;
1507: s=out;
1508: while (*in != '\0'){
1.137 brouard 1509: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1510: in++;
1511: }
1512: *out++ = *in++;
1513: }
1514: *out='\0';
1515: return s;
1516: }
1517:
1.187 brouard 1518: /* char *substrchaine(char *out, char *in, char *chain) */
1519: /* { */
1520: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1521: /* char *s, *t; */
1522: /* t=in;s=out; */
1523: /* while ((*in != *chain) && (*in != '\0')){ */
1524: /* *out++ = *in++; */
1525: /* } */
1526:
1527: /* /\* *in matches *chain *\/ */
1528: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1529: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1530: /* } */
1531: /* in--; chain--; */
1532: /* while ( (*in != '\0')){ */
1533: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1534: /* *out++ = *in++; */
1535: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1536: /* } */
1537: /* *out='\0'; */
1538: /* out=s; */
1539: /* return out; */
1540: /* } */
1541: char *substrchaine(char *out, char *in, char *chain)
1542: {
1543: /* Substract chain 'chain' from 'in', return and output 'out' */
1544: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1545:
1546: char *strloc;
1547:
1548: strcpy (out, in);
1549: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1550: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1551: if(strloc != NULL){
1552: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1553: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1554: /* strcpy (strloc, strloc +strlen(chain));*/
1555: }
1556: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1557: return out;
1558: }
1559:
1560:
1.145 brouard 1561: char *cutl(char *blocc, char *alocc, char *in, char occ)
1562: {
1.187 brouard 1563: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1564: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1565: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1566: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1567: */
1.160 brouard 1568: char *s, *t;
1.145 brouard 1569: t=in;s=in;
1570: while ((*in != occ) && (*in != '\0')){
1571: *alocc++ = *in++;
1572: }
1573: if( *in == occ){
1574: *(alocc)='\0';
1575: s=++in;
1576: }
1577:
1578: if (s == t) {/* occ not found */
1579: *(alocc-(in-s))='\0';
1580: in=s;
1581: }
1582: while ( *in != '\0'){
1583: *blocc++ = *in++;
1584: }
1585:
1586: *blocc='\0';
1587: return t;
1588: }
1.137 brouard 1589: char *cutv(char *blocc, char *alocc, char *in, char occ)
1590: {
1.187 brouard 1591: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1592: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1593: gives blocc="abcdef2ghi" and alocc="j".
1594: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1595: */
1596: char *s, *t;
1597: t=in;s=in;
1598: while (*in != '\0'){
1599: while( *in == occ){
1600: *blocc++ = *in++;
1601: s=in;
1602: }
1603: *blocc++ = *in++;
1604: }
1605: if (s == t) /* occ not found */
1606: *(blocc-(in-s))='\0';
1607: else
1608: *(blocc-(in-s)-1)='\0';
1609: in=s;
1610: while ( *in != '\0'){
1611: *alocc++ = *in++;
1612: }
1613:
1614: *alocc='\0';
1615: return s;
1616: }
1617:
1.126 brouard 1618: int nbocc(char *s, char occ)
1619: {
1620: int i,j=0;
1621: int lg=20;
1622: i=0;
1623: lg=strlen(s);
1624: for(i=0; i<= lg; i++) {
1.234 brouard 1625: if (s[i] == occ ) j++;
1.126 brouard 1626: }
1627: return j;
1628: }
1629:
1.137 brouard 1630: /* void cutv(char *u,char *v, char*t, char occ) */
1631: /* { */
1632: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1633: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1634: /* gives u="abcdef2ghi" and v="j" *\/ */
1635: /* int i,lg,j,p=0; */
1636: /* i=0; */
1637: /* lg=strlen(t); */
1638: /* for(j=0; j<=lg-1; j++) { */
1639: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1640: /* } */
1.126 brouard 1641:
1.137 brouard 1642: /* for(j=0; j<p; j++) { */
1643: /* (u[j] = t[j]); */
1644: /* } */
1645: /* u[p]='\0'; */
1.126 brouard 1646:
1.137 brouard 1647: /* for(j=0; j<= lg; j++) { */
1648: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1649: /* } */
1650: /* } */
1.126 brouard 1651:
1.160 brouard 1652: #ifdef _WIN32
1653: char * strsep(char **pp, const char *delim)
1654: {
1655: char *p, *q;
1656:
1657: if ((p = *pp) == NULL)
1658: return 0;
1659: if ((q = strpbrk (p, delim)) != NULL)
1660: {
1661: *pp = q + 1;
1662: *q = '\0';
1663: }
1664: else
1665: *pp = 0;
1666: return p;
1667: }
1668: #endif
1669:
1.126 brouard 1670: /********************** nrerror ********************/
1671:
1672: void nrerror(char error_text[])
1673: {
1674: fprintf(stderr,"ERREUR ...\n");
1675: fprintf(stderr,"%s\n",error_text);
1676: exit(EXIT_FAILURE);
1677: }
1678: /*********************** vector *******************/
1679: double *vector(int nl, int nh)
1680: {
1681: double *v;
1682: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1683: if (!v) nrerror("allocation failure in vector");
1684: return v-nl+NR_END;
1685: }
1686:
1687: /************************ free vector ******************/
1688: void free_vector(double*v, int nl, int nh)
1689: {
1690: free((FREE_ARG)(v+nl-NR_END));
1691: }
1692:
1693: /************************ivector *******************************/
1694: int *ivector(long nl,long nh)
1695: {
1696: int *v;
1697: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1698: if (!v) nrerror("allocation failure in ivector");
1699: return v-nl+NR_END;
1700: }
1701:
1702: /******************free ivector **************************/
1703: void free_ivector(int *v, long nl, long nh)
1704: {
1705: free((FREE_ARG)(v+nl-NR_END));
1706: }
1707:
1708: /************************lvector *******************************/
1709: long *lvector(long nl,long nh)
1710: {
1711: long *v;
1712: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1713: if (!v) nrerror("allocation failure in ivector");
1714: return v-nl+NR_END;
1715: }
1716:
1717: /******************free lvector **************************/
1718: void free_lvector(long *v, long nl, long nh)
1719: {
1720: free((FREE_ARG)(v+nl-NR_END));
1721: }
1722:
1723: /******************* imatrix *******************************/
1724: int **imatrix(long nrl, long nrh, long ncl, long nch)
1725: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1726: {
1727: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1728: int **m;
1729:
1730: /* allocate pointers to rows */
1731: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1732: if (!m) nrerror("allocation failure 1 in matrix()");
1733: m += NR_END;
1734: m -= nrl;
1735:
1736:
1737: /* allocate rows and set pointers to them */
1738: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1739: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1740: m[nrl] += NR_END;
1741: m[nrl] -= ncl;
1742:
1743: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1744:
1745: /* return pointer to array of pointers to rows */
1746: return m;
1747: }
1748:
1749: /****************** free_imatrix *************************/
1750: void free_imatrix(m,nrl,nrh,ncl,nch)
1751: int **m;
1752: long nch,ncl,nrh,nrl;
1753: /* free an int matrix allocated by imatrix() */
1754: {
1755: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1756: free((FREE_ARG) (m+nrl-NR_END));
1757: }
1758:
1759: /******************* matrix *******************************/
1760: double **matrix(long nrl, long nrh, long ncl, long nch)
1761: {
1762: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1763: double **m;
1764:
1765: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1766: if (!m) nrerror("allocation failure 1 in matrix()");
1767: m += NR_END;
1768: m -= nrl;
1769:
1770: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1771: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1772: m[nrl] += NR_END;
1773: m[nrl] -= ncl;
1774:
1775: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1776: return m;
1.145 brouard 1777: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1778: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1779: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1780: */
1781: }
1782:
1783: /*************************free matrix ************************/
1784: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1785: {
1786: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1787: free((FREE_ARG)(m+nrl-NR_END));
1788: }
1789:
1790: /******************* ma3x *******************************/
1791: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1792: {
1793: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1794: double ***m;
1795:
1796: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1797: if (!m) nrerror("allocation failure 1 in matrix()");
1798: m += NR_END;
1799: m -= nrl;
1800:
1801: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1802: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1803: m[nrl] += NR_END;
1804: m[nrl] -= ncl;
1805:
1806: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1807:
1808: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1809: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1810: m[nrl][ncl] += NR_END;
1811: m[nrl][ncl] -= nll;
1812: for (j=ncl+1; j<=nch; j++)
1813: m[nrl][j]=m[nrl][j-1]+nlay;
1814:
1815: for (i=nrl+1; i<=nrh; i++) {
1816: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1817: for (j=ncl+1; j<=nch; j++)
1818: m[i][j]=m[i][j-1]+nlay;
1819: }
1820: return m;
1821: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1822: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1823: */
1824: }
1825:
1826: /*************************free ma3x ************************/
1827: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1828: {
1829: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1830: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1831: free((FREE_ARG)(m+nrl-NR_END));
1832: }
1833:
1834: /*************** function subdirf ***********/
1835: char *subdirf(char fileres[])
1836: {
1837: /* Caution optionfilefiname is hidden */
1838: strcpy(tmpout,optionfilefiname);
1839: strcat(tmpout,"/"); /* Add to the right */
1840: strcat(tmpout,fileres);
1841: return tmpout;
1842: }
1843:
1844: /*************** function subdirf2 ***********/
1845: char *subdirf2(char fileres[], char *preop)
1846: {
1847:
1848: /* Caution optionfilefiname is hidden */
1849: strcpy(tmpout,optionfilefiname);
1850: strcat(tmpout,"/");
1851: strcat(tmpout,preop);
1852: strcat(tmpout,fileres);
1853: return tmpout;
1854: }
1855:
1856: /*************** function subdirf3 ***********/
1857: char *subdirf3(char fileres[], char *preop, char *preop2)
1858: {
1859:
1860: /* Caution optionfilefiname is hidden */
1861: strcpy(tmpout,optionfilefiname);
1862: strcat(tmpout,"/");
1863: strcat(tmpout,preop);
1864: strcat(tmpout,preop2);
1865: strcat(tmpout,fileres);
1866: return tmpout;
1867: }
1.213 brouard 1868:
1869: /*************** function subdirfext ***********/
1870: char *subdirfext(char fileres[], char *preop, char *postop)
1871: {
1872:
1873: strcpy(tmpout,preop);
1874: strcat(tmpout,fileres);
1875: strcat(tmpout,postop);
1876: return tmpout;
1877: }
1.126 brouard 1878:
1.213 brouard 1879: /*************** function subdirfext3 ***********/
1880: char *subdirfext3(char fileres[], char *preop, char *postop)
1881: {
1882:
1883: /* Caution optionfilefiname is hidden */
1884: strcpy(tmpout,optionfilefiname);
1885: strcat(tmpout,"/");
1886: strcat(tmpout,preop);
1887: strcat(tmpout,fileres);
1888: strcat(tmpout,postop);
1889: return tmpout;
1890: }
1891:
1.162 brouard 1892: char *asc_diff_time(long time_sec, char ascdiff[])
1893: {
1894: long sec_left, days, hours, minutes;
1895: days = (time_sec) / (60*60*24);
1896: sec_left = (time_sec) % (60*60*24);
1897: hours = (sec_left) / (60*60) ;
1898: sec_left = (sec_left) %(60*60);
1899: minutes = (sec_left) /60;
1900: sec_left = (sec_left) % (60);
1901: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1902: return ascdiff;
1903: }
1904:
1.126 brouard 1905: /***************** f1dim *************************/
1906: extern int ncom;
1907: extern double *pcom,*xicom;
1908: extern double (*nrfunc)(double []);
1909:
1910: double f1dim(double x)
1911: {
1912: int j;
1913: double f;
1914: double *xt;
1915:
1916: xt=vector(1,ncom);
1917: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1918: f=(*nrfunc)(xt);
1919: free_vector(xt,1,ncom);
1920: return f;
1921: }
1922:
1923: /*****************brent *************************/
1924: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1925: {
1926: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1927: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1928: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1929: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1930: * returned function value.
1931: */
1.126 brouard 1932: int iter;
1933: double a,b,d,etemp;
1.159 brouard 1934: double fu=0,fv,fw,fx;
1.164 brouard 1935: double ftemp=0.;
1.126 brouard 1936: double p,q,r,tol1,tol2,u,v,w,x,xm;
1937: double e=0.0;
1938:
1939: a=(ax < cx ? ax : cx);
1940: b=(ax > cx ? ax : cx);
1941: x=w=v=bx;
1942: fw=fv=fx=(*f)(x);
1943: for (iter=1;iter<=ITMAX;iter++) {
1944: xm=0.5*(a+b);
1945: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1946: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1947: printf(".");fflush(stdout);
1948: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1949: #ifdef DEBUGBRENT
1.126 brouard 1950: 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);
1951: 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);
1952: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1953: #endif
1954: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1955: *xmin=x;
1956: return fx;
1957: }
1958: ftemp=fu;
1959: if (fabs(e) > tol1) {
1960: r=(x-w)*(fx-fv);
1961: q=(x-v)*(fx-fw);
1962: p=(x-v)*q-(x-w)*r;
1963: q=2.0*(q-r);
1964: if (q > 0.0) p = -p;
1965: q=fabs(q);
1966: etemp=e;
1967: e=d;
1968: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1969: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1970: else {
1.224 brouard 1971: d=p/q;
1972: u=x+d;
1973: if (u-a < tol2 || b-u < tol2)
1974: d=SIGN(tol1,xm-x);
1.126 brouard 1975: }
1976: } else {
1977: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1978: }
1979: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1980: fu=(*f)(u);
1981: if (fu <= fx) {
1982: if (u >= x) a=x; else b=x;
1983: SHFT(v,w,x,u)
1.183 brouard 1984: SHFT(fv,fw,fx,fu)
1985: } else {
1986: if (u < x) a=u; else b=u;
1987: if (fu <= fw || w == x) {
1.224 brouard 1988: v=w;
1989: w=u;
1990: fv=fw;
1991: fw=fu;
1.183 brouard 1992: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1993: v=u;
1994: fv=fu;
1.183 brouard 1995: }
1996: }
1.126 brouard 1997: }
1998: nrerror("Too many iterations in brent");
1999: *xmin=x;
2000: return fx;
2001: }
2002:
2003: /****************** mnbrak ***********************/
2004:
2005: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2006: double (*func)(double))
1.183 brouard 2007: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2008: the downhill direction (defined by the function as evaluated at the initial points) and returns
2009: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2010: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2011: */
1.126 brouard 2012: double ulim,u,r,q, dum;
2013: double fu;
1.187 brouard 2014:
2015: double scale=10.;
2016: int iterscale=0;
2017:
2018: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2019: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2020:
2021:
2022: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2023: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2024: /* *bx = *ax - (*ax - *bx)/scale; */
2025: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2026: /* } */
2027:
1.126 brouard 2028: if (*fb > *fa) {
2029: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2030: SHFT(dum,*fb,*fa,dum)
2031: }
1.126 brouard 2032: *cx=(*bx)+GOLD*(*bx-*ax);
2033: *fc=(*func)(*cx);
1.183 brouard 2034: #ifdef DEBUG
1.224 brouard 2035: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2036: 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 2037: #endif
1.224 brouard 2038: 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 2039: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2040: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2041: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2042: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2043: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2044: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2045: fu=(*func)(u);
1.163 brouard 2046: #ifdef DEBUG
2047: /* f(x)=A(x-u)**2+f(u) */
2048: double A, fparabu;
2049: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2050: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2051: 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);
2052: 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 2053: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2054: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2055: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2056: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2057: #endif
1.184 brouard 2058: #ifdef MNBRAKORIGINAL
1.183 brouard 2059: #else
1.191 brouard 2060: /* if (fu > *fc) { */
2061: /* #ifdef DEBUG */
2062: /* printf("mnbrak4 fu > fc \n"); */
2063: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2064: /* #endif */
2065: /* /\* 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 *\\/ *\/ */
2066: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2067: /* dum=u; /\* Shifting c and u *\/ */
2068: /* u = *cx; */
2069: /* *cx = dum; */
2070: /* dum = fu; */
2071: /* fu = *fc; */
2072: /* *fc =dum; */
2073: /* } else { /\* end *\/ */
2074: /* #ifdef DEBUG */
2075: /* printf("mnbrak3 fu < fc \n"); */
2076: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2077: /* #endif */
2078: /* dum=u; /\* Shifting c and u *\/ */
2079: /* u = *cx; */
2080: /* *cx = dum; */
2081: /* dum = fu; */
2082: /* fu = *fc; */
2083: /* *fc =dum; */
2084: /* } */
1.224 brouard 2085: #ifdef DEBUGMNBRAK
2086: double A, fparabu;
2087: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2088: fparabu= *fa - A*(*ax-u)*(*ax-u);
2089: 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);
2090: 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 2091: #endif
1.191 brouard 2092: dum=u; /* Shifting c and u */
2093: u = *cx;
2094: *cx = dum;
2095: dum = fu;
2096: fu = *fc;
2097: *fc =dum;
1.183 brouard 2098: #endif
1.162 brouard 2099: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2100: #ifdef DEBUG
1.224 brouard 2101: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2102: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2103: #endif
1.126 brouard 2104: fu=(*func)(u);
2105: if (fu < *fc) {
1.183 brouard 2106: #ifdef DEBUG
1.224 brouard 2107: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2108: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2109: #endif
2110: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2111: SHFT(*fb,*fc,fu,(*func)(u))
2112: #ifdef DEBUG
2113: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2114: #endif
2115: }
1.162 brouard 2116: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2117: #ifdef DEBUG
1.224 brouard 2118: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2119: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2120: #endif
1.126 brouard 2121: u=ulim;
2122: fu=(*func)(u);
1.183 brouard 2123: } else { /* u could be left to b (if r > q parabola has a maximum) */
2124: #ifdef DEBUG
1.224 brouard 2125: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2126: 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 2127: #endif
1.126 brouard 2128: u=(*cx)+GOLD*(*cx-*bx);
2129: fu=(*func)(u);
1.224 brouard 2130: #ifdef DEBUG
2131: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2132: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2133: #endif
1.183 brouard 2134: } /* end tests */
1.126 brouard 2135: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2136: SHFT(*fa,*fb,*fc,fu)
2137: #ifdef DEBUG
1.224 brouard 2138: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2139: 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 2140: #endif
2141: } /* 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 2142: }
2143:
2144: /*************** linmin ************************/
1.162 brouard 2145: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2146: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2147: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2148: the value of func at the returned location p . This is actually all accomplished by calling the
2149: routines mnbrak and brent .*/
1.126 brouard 2150: int ncom;
2151: double *pcom,*xicom;
2152: double (*nrfunc)(double []);
2153:
1.224 brouard 2154: #ifdef LINMINORIGINAL
1.126 brouard 2155: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2156: #else
2157: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2158: #endif
1.126 brouard 2159: {
2160: double brent(double ax, double bx, double cx,
2161: double (*f)(double), double tol, double *xmin);
2162: double f1dim(double x);
2163: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2164: double *fc, double (*func)(double));
2165: int j;
2166: double xx,xmin,bx,ax;
2167: double fx,fb,fa;
1.187 brouard 2168:
1.203 brouard 2169: #ifdef LINMINORIGINAL
2170: #else
2171: double scale=10., axs, xxs; /* Scale added for infinity */
2172: #endif
2173:
1.126 brouard 2174: ncom=n;
2175: pcom=vector(1,n);
2176: xicom=vector(1,n);
2177: nrfunc=func;
2178: for (j=1;j<=n;j++) {
2179: pcom[j]=p[j];
1.202 brouard 2180: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2181: }
1.187 brouard 2182:
1.203 brouard 2183: #ifdef LINMINORIGINAL
2184: xx=1.;
2185: #else
2186: axs=0.0;
2187: xxs=1.;
2188: do{
2189: xx= xxs;
2190: #endif
1.187 brouard 2191: ax=0.;
2192: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2193: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2194: /* 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)) */
2195: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2196: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2197: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2198: /* 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 2199: #ifdef LINMINORIGINAL
2200: #else
2201: if (fx != fx){
1.224 brouard 2202: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2203: printf("|");
2204: fprintf(ficlog,"|");
1.203 brouard 2205: #ifdef DEBUGLINMIN
1.224 brouard 2206: 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 2207: #endif
2208: }
1.224 brouard 2209: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2210: #endif
2211:
1.191 brouard 2212: #ifdef DEBUGLINMIN
2213: 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 2214: 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 2215: #endif
1.224 brouard 2216: #ifdef LINMINORIGINAL
2217: #else
2218: if(fb == fx){ /* Flat function in the direction */
2219: xmin=xx;
2220: *flat=1;
2221: }else{
2222: *flat=0;
2223: #endif
2224: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2225: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2226: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2227: /* fmin = f(p[j] + xmin * xi[j]) */
2228: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2229: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2230: #ifdef DEBUG
1.224 brouard 2231: 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);
2232: 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);
2233: #endif
2234: #ifdef LINMINORIGINAL
2235: #else
2236: }
1.126 brouard 2237: #endif
1.191 brouard 2238: #ifdef DEBUGLINMIN
2239: printf("linmin end ");
1.202 brouard 2240: fprintf(ficlog,"linmin end ");
1.191 brouard 2241: #endif
1.126 brouard 2242: for (j=1;j<=n;j++) {
1.203 brouard 2243: #ifdef LINMINORIGINAL
2244: xi[j] *= xmin;
2245: #else
2246: #ifdef DEBUGLINMIN
2247: if(xxs <1.0)
2248: printf(" before xi[%d]=%12.8f", j,xi[j]);
2249: #endif
2250: 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) */
2251: #ifdef DEBUGLINMIN
2252: if(xxs <1.0)
2253: 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 );
2254: #endif
2255: #endif
1.187 brouard 2256: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2257: }
1.191 brouard 2258: #ifdef DEBUGLINMIN
1.203 brouard 2259: printf("\n");
1.191 brouard 2260: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2261: 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 2262: for (j=1;j<=n;j++) {
1.202 brouard 2263: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2264: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2265: if(j % ncovmodel == 0){
1.191 brouard 2266: printf("\n");
1.202 brouard 2267: fprintf(ficlog,"\n");
2268: }
1.191 brouard 2269: }
1.203 brouard 2270: #else
1.191 brouard 2271: #endif
1.126 brouard 2272: free_vector(xicom,1,n);
2273: free_vector(pcom,1,n);
2274: }
2275:
2276:
2277: /*************** powell ************************/
1.162 brouard 2278: /*
2279: Minimization of a function func of n variables. Input consists of an initial starting point
2280: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2281: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2282: such that failure to decrease by more than this amount on one iteration signals doneness. On
2283: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2284: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2285: */
1.224 brouard 2286: #ifdef LINMINORIGINAL
2287: #else
2288: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2289: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2290: #endif
1.126 brouard 2291: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2292: double (*func)(double []))
2293: {
1.224 brouard 2294: #ifdef LINMINORIGINAL
2295: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2296: double (*func)(double []));
1.224 brouard 2297: #else
1.241 brouard 2298: void linmin(double p[], double xi[], int n, double *fret,
2299: double (*func)(double []),int *flat);
1.224 brouard 2300: #endif
1.239 brouard 2301: int i,ibig,j,jk,k;
1.126 brouard 2302: double del,t,*pt,*ptt,*xit;
1.181 brouard 2303: double directest;
1.126 brouard 2304: double fp,fptt;
2305: double *xits;
2306: int niterf, itmp;
1.224 brouard 2307: #ifdef LINMINORIGINAL
2308: #else
2309:
2310: flatdir=ivector(1,n);
2311: for (j=1;j<=n;j++) flatdir[j]=0;
2312: #endif
1.126 brouard 2313:
2314: pt=vector(1,n);
2315: ptt=vector(1,n);
2316: xit=vector(1,n);
2317: xits=vector(1,n);
2318: *fret=(*func)(p);
2319: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2320: rcurr_time = time(NULL);
1.126 brouard 2321: for (*iter=1;;++(*iter)) {
1.187 brouard 2322: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2323: ibig=0;
2324: del=0.0;
1.157 brouard 2325: rlast_time=rcurr_time;
2326: /* (void) gettimeofday(&curr_time,&tzp); */
2327: rcurr_time = time(NULL);
2328: curr_time = *localtime(&rcurr_time);
2329: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2330: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2331: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2332: for (i=1;i<=n;i++) {
1.126 brouard 2333: fprintf(ficrespow," %.12lf", p[i]);
2334: }
1.239 brouard 2335: fprintf(ficrespow,"\n");fflush(ficrespow);
2336: printf("\n#model= 1 + age ");
2337: fprintf(ficlog,"\n#model= 1 + age ");
2338: if(nagesqr==1){
1.241 brouard 2339: printf(" + age*age ");
2340: fprintf(ficlog," + age*age ");
1.239 brouard 2341: }
2342: for(j=1;j <=ncovmodel-2;j++){
2343: if(Typevar[j]==0) {
2344: printf(" + V%d ",Tvar[j]);
2345: fprintf(ficlog," + V%d ",Tvar[j]);
2346: }else if(Typevar[j]==1) {
2347: printf(" + V%d*age ",Tvar[j]);
2348: fprintf(ficlog," + V%d*age ",Tvar[j]);
2349: }else if(Typevar[j]==2) {
2350: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2351: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2352: }
2353: }
1.126 brouard 2354: printf("\n");
1.239 brouard 2355: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2356: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2357: fprintf(ficlog,"\n");
1.239 brouard 2358: for(i=1,jk=1; i <=nlstate; i++){
2359: for(k=1; k <=(nlstate+ndeath); k++){
2360: if (k != i) {
2361: printf("%d%d ",i,k);
2362: fprintf(ficlog,"%d%d ",i,k);
2363: for(j=1; j <=ncovmodel; j++){
2364: printf("%12.7f ",p[jk]);
2365: fprintf(ficlog,"%12.7f ",p[jk]);
2366: jk++;
2367: }
2368: printf("\n");
2369: fprintf(ficlog,"\n");
2370: }
2371: }
2372: }
1.241 brouard 2373: if(*iter <=3 && *iter >1){
1.157 brouard 2374: tml = *localtime(&rcurr_time);
2375: strcpy(strcurr,asctime(&tml));
2376: rforecast_time=rcurr_time;
1.126 brouard 2377: itmp = strlen(strcurr);
2378: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2379: strcurr[itmp-1]='\0';
1.162 brouard 2380: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2381: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2382: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2383: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2384: forecast_time = *localtime(&rforecast_time);
2385: strcpy(strfor,asctime(&forecast_time));
2386: itmp = strlen(strfor);
2387: if(strfor[itmp-1]=='\n')
2388: strfor[itmp-1]='\0';
2389: 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);
2390: 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 2391: }
2392: }
1.187 brouard 2393: for (i=1;i<=n;i++) { /* For each direction i */
2394: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2395: fptt=(*fret);
2396: #ifdef DEBUG
1.203 brouard 2397: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2398: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2399: #endif
1.203 brouard 2400: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2401: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2402: #ifdef LINMINORIGINAL
1.188 brouard 2403: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2404: #else
2405: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2406: flatdir[i]=flat; /* Function is vanishing in that direction i */
2407: #endif
2408: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2409: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2410: /* because that direction will be replaced unless the gain del is small */
2411: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2412: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2413: /* with the new direction. */
2414: del=fabs(fptt-(*fret));
2415: ibig=i;
1.126 brouard 2416: }
2417: #ifdef DEBUG
2418: printf("%d %.12e",i,(*fret));
2419: fprintf(ficlog,"%d %.12e",i,(*fret));
2420: for (j=1;j<=n;j++) {
1.224 brouard 2421: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2422: printf(" x(%d)=%.12e",j,xit[j]);
2423: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2424: }
2425: for(j=1;j<=n;j++) {
1.225 brouard 2426: printf(" p(%d)=%.12e",j,p[j]);
2427: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2428: }
2429: printf("\n");
2430: fprintf(ficlog,"\n");
2431: #endif
1.187 brouard 2432: } /* end loop on each direction i */
2433: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2434: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2435: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2436: for(j=1;j<=n;j++) {
1.302 brouard 2437: if(flatdir[j] >0){
2438: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2439: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2440: }
2441: /* printf("\n"); */
2442: /* fprintf(ficlog,"\n"); */
2443: }
1.243 brouard 2444: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2445: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2446: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2447: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2448: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2449: /* decreased of more than 3.84 */
2450: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2451: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2452: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2453:
1.188 brouard 2454: /* Starting the program with initial values given by a former maximization will simply change */
2455: /* the scales of the directions and the directions, because the are reset to canonical directions */
2456: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2457: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2458: #ifdef DEBUG
2459: int k[2],l;
2460: k[0]=1;
2461: k[1]=-1;
2462: printf("Max: %.12e",(*func)(p));
2463: fprintf(ficlog,"Max: %.12e",(*func)(p));
2464: for (j=1;j<=n;j++) {
2465: printf(" %.12e",p[j]);
2466: fprintf(ficlog," %.12e",p[j]);
2467: }
2468: printf("\n");
2469: fprintf(ficlog,"\n");
2470: for(l=0;l<=1;l++) {
2471: for (j=1;j<=n;j++) {
2472: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2473: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2474: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2475: }
2476: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2477: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2478: }
2479: #endif
2480:
1.224 brouard 2481: #ifdef LINMINORIGINAL
2482: #else
2483: free_ivector(flatdir,1,n);
2484: #endif
1.126 brouard 2485: free_vector(xit,1,n);
2486: free_vector(xits,1,n);
2487: free_vector(ptt,1,n);
2488: free_vector(pt,1,n);
2489: return;
1.192 brouard 2490: } /* enough precision */
1.240 brouard 2491: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2492: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2493: ptt[j]=2.0*p[j]-pt[j];
2494: xit[j]=p[j]-pt[j];
2495: pt[j]=p[j];
2496: }
1.181 brouard 2497: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2498: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2499: if (*iter <=4) {
1.225 brouard 2500: #else
2501: #endif
1.224 brouard 2502: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2503: #else
1.161 brouard 2504: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2505: #endif
1.162 brouard 2506: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2507: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2508: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2509: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2510: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2511: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2512: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2513: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2514: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2515: /* Even if f3 <f1, directest can be negative and t >0 */
2516: /* mu² and del² are equal when f3=f1 */
2517: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2518: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2519: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2520: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2521: #ifdef NRCORIGINAL
2522: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2523: #else
2524: 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 2525: t= t- del*SQR(fp-fptt);
1.183 brouard 2526: #endif
1.202 brouard 2527: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2528: #ifdef DEBUG
1.181 brouard 2529: 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);
2530: 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 2531: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2532: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2533: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2534: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2535: 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);
2536: 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);
2537: #endif
1.183 brouard 2538: #ifdef POWELLORIGINAL
2539: if (t < 0.0) { /* Then we use it for new direction */
2540: #else
1.182 brouard 2541: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2542: 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 2543: 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 2544: 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 2545: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2546: }
1.181 brouard 2547: if (directest < 0.0) { /* Then we use it for new direction */
2548: #endif
1.191 brouard 2549: #ifdef DEBUGLINMIN
1.234 brouard 2550: printf("Before linmin in direction P%d-P0\n",n);
2551: for (j=1;j<=n;j++) {
2552: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2553: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2554: if(j % ncovmodel == 0){
2555: printf("\n");
2556: fprintf(ficlog,"\n");
2557: }
2558: }
1.224 brouard 2559: #endif
2560: #ifdef LINMINORIGINAL
1.234 brouard 2561: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2562: #else
1.234 brouard 2563: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2564: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2565: #endif
1.234 brouard 2566:
1.191 brouard 2567: #ifdef DEBUGLINMIN
1.234 brouard 2568: for (j=1;j<=n;j++) {
2569: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2570: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2571: if(j % ncovmodel == 0){
2572: printf("\n");
2573: fprintf(ficlog,"\n");
2574: }
2575: }
1.224 brouard 2576: #endif
1.234 brouard 2577: for (j=1;j<=n;j++) {
2578: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2579: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2580: }
1.224 brouard 2581: #ifdef LINMINORIGINAL
2582: #else
1.234 brouard 2583: for (j=1, flatd=0;j<=n;j++) {
2584: if(flatdir[j]>0)
2585: flatd++;
2586: }
2587: if(flatd >0){
1.255 brouard 2588: printf("%d flat directions: ",flatd);
2589: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2590: for (j=1;j<=n;j++) {
2591: if(flatdir[j]>0){
2592: printf("%d ",j);
2593: fprintf(ficlog,"%d ",j);
2594: }
2595: }
2596: printf("\n");
2597: fprintf(ficlog,"\n");
2598: }
1.191 brouard 2599: #endif
1.234 brouard 2600: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2601: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2602:
1.126 brouard 2603: #ifdef DEBUG
1.234 brouard 2604: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2605: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2606: for(j=1;j<=n;j++){
2607: printf(" %lf",xit[j]);
2608: fprintf(ficlog," %lf",xit[j]);
2609: }
2610: printf("\n");
2611: fprintf(ficlog,"\n");
1.126 brouard 2612: #endif
1.192 brouard 2613: } /* end of t or directest negative */
1.224 brouard 2614: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2615: #else
1.234 brouard 2616: } /* end if (fptt < fp) */
1.192 brouard 2617: #endif
1.225 brouard 2618: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2619: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2620: #else
1.224 brouard 2621: #endif
1.234 brouard 2622: } /* loop iteration */
1.126 brouard 2623: }
1.234 brouard 2624:
1.126 brouard 2625: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2626:
1.235 brouard 2627: 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 2628: {
1.279 brouard 2629: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2630: * (and selected quantitative values in nres)
2631: * by left multiplying the unit
2632: * matrix by transitions matrix until convergence is reached with precision ftolpl
2633: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2634: * Wx is row vector: population in state 1, population in state 2, population dead
2635: * or prevalence in state 1, prevalence in state 2, 0
2636: * newm is the matrix after multiplications, its rows are identical at a factor.
2637: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2638: * Output is prlim.
2639: * Initial matrix pimij
2640: */
1.206 brouard 2641: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2642: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2643: /* 0, 0 , 1} */
2644: /*
2645: * and after some iteration: */
2646: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2647: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2648: /* 0, 0 , 1} */
2649: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2650: /* {0.51571254859325999, 0.4842874514067399, */
2651: /* 0.51326036147820708, 0.48673963852179264} */
2652: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2653:
1.126 brouard 2654: int i, ii,j,k;
1.209 brouard 2655: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2656: /* double **matprod2(); */ /* test */
1.218 brouard 2657: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2658: double **newm;
1.209 brouard 2659: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2660: int ncvloop=0;
1.288 brouard 2661: int first=0;
1.169 brouard 2662:
1.209 brouard 2663: min=vector(1,nlstate);
2664: max=vector(1,nlstate);
2665: meandiff=vector(1,nlstate);
2666:
1.218 brouard 2667: /* Starting with matrix unity */
1.126 brouard 2668: for (ii=1;ii<=nlstate+ndeath;ii++)
2669: for (j=1;j<=nlstate+ndeath;j++){
2670: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2671: }
1.169 brouard 2672:
2673: cov[1]=1.;
2674:
2675: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2676: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2677: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2678: ncvloop++;
1.126 brouard 2679: newm=savm;
2680: /* Covariates have to be included here again */
1.138 brouard 2681: cov[2]=agefin;
1.187 brouard 2682: if(nagesqr==1)
2683: cov[3]= agefin*agefin;;
1.234 brouard 2684: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2685: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2686: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2687: /* 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 2688: }
2689: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2690: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2691: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2692: /* 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 2693: }
1.237 brouard 2694: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2695: if(Dummy[Tvar[Tage[k]]]){
2696: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2697: } else{
1.235 brouard 2698: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2699: }
1.235 brouard 2700: /* 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 2701: }
1.237 brouard 2702: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2703: /* 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 2704: if(Dummy[Tvard[k][1]==0]){
2705: if(Dummy[Tvard[k][2]==0]){
2706: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2707: }else{
2708: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2709: }
2710: }else{
2711: if(Dummy[Tvard[k][2]==0]){
2712: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2713: }else{
2714: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2715: }
2716: }
1.234 brouard 2717: }
1.138 brouard 2718: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2719: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2720: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2721: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2722: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2723: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2724: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2725:
1.126 brouard 2726: savm=oldm;
2727: oldm=newm;
1.209 brouard 2728:
2729: for(j=1; j<=nlstate; j++){
2730: max[j]=0.;
2731: min[j]=1.;
2732: }
2733: for(i=1;i<=nlstate;i++){
2734: sumnew=0;
2735: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2736: for(j=1; j<=nlstate; j++){
2737: prlim[i][j]= newm[i][j]/(1-sumnew);
2738: max[j]=FMAX(max[j],prlim[i][j]);
2739: min[j]=FMIN(min[j],prlim[i][j]);
2740: }
2741: }
2742:
1.126 brouard 2743: maxmax=0.;
1.209 brouard 2744: for(j=1; j<=nlstate; j++){
2745: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2746: maxmax=FMAX(maxmax,meandiff[j]);
2747: /* 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 2748: } /* j loop */
1.203 brouard 2749: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2750: /* 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 2751: if(maxmax < ftolpl){
1.209 brouard 2752: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2753: free_vector(min,1,nlstate);
2754: free_vector(max,1,nlstate);
2755: free_vector(meandiff,1,nlstate);
1.126 brouard 2756: return prlim;
2757: }
1.288 brouard 2758: } /* agefin loop */
1.208 brouard 2759: /* After some age loop it doesn't converge */
1.288 brouard 2760: if(!first){
2761: first=1;
2762: 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);
2763: }
2764: 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);
2765:
1.209 brouard 2766: /* 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); */
2767: free_vector(min,1,nlstate);
2768: free_vector(max,1,nlstate);
2769: free_vector(meandiff,1,nlstate);
1.208 brouard 2770:
1.169 brouard 2771: return prlim; /* should not reach here */
1.126 brouard 2772: }
2773:
1.217 brouard 2774:
2775: /**** Back Prevalence limit (stable or period prevalence) ****************/
2776:
1.218 brouard 2777: /* 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) */
2778: /* 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 2779: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2780: {
1.264 brouard 2781: /* 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 2782: matrix by transitions matrix until convergence is reached with precision ftolpl */
2783: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2784: /* Wx is row vector: population in state 1, population in state 2, population dead */
2785: /* or prevalence in state 1, prevalence in state 2, 0 */
2786: /* newm is the matrix after multiplications, its rows are identical at a factor */
2787: /* Initial matrix pimij */
2788: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2789: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2790: /* 0, 0 , 1} */
2791: /*
2792: * and after some iteration: */
2793: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2794: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2795: /* 0, 0 , 1} */
2796: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2797: /* {0.51571254859325999, 0.4842874514067399, */
2798: /* 0.51326036147820708, 0.48673963852179264} */
2799: /* If we start from prlim again, prlim tends to a constant matrix */
2800:
2801: int i, ii,j,k;
1.247 brouard 2802: int first=0;
1.217 brouard 2803: double *min, *max, *meandiff, maxmax,sumnew=0.;
2804: /* double **matprod2(); */ /* test */
2805: double **out, cov[NCOVMAX+1], **bmij();
2806: double **newm;
1.218 brouard 2807: double **dnewm, **doldm, **dsavm; /* for use */
2808: double **oldm, **savm; /* for use */
2809:
1.217 brouard 2810: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2811: int ncvloop=0;
2812:
2813: min=vector(1,nlstate);
2814: max=vector(1,nlstate);
2815: meandiff=vector(1,nlstate);
2816:
1.266 brouard 2817: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2818: oldm=oldms; savm=savms;
2819:
2820: /* Starting with matrix unity */
2821: for (ii=1;ii<=nlstate+ndeath;ii++)
2822: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2823: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2824: }
2825:
2826: cov[1]=1.;
2827:
2828: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2829: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2830: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2831: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2832: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2833: ncvloop++;
1.218 brouard 2834: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2835: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2836: /* Covariates have to be included here again */
2837: cov[2]=agefin;
2838: if(nagesqr==1)
2839: cov[3]= agefin*agefin;;
1.242 brouard 2840: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2841: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2842: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2843: /* 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 2844: }
2845: /* for (k=1; k<=cptcovn;k++) { */
2846: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2847: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2848: /* /\* 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])]); *\/ */
2849: /* } */
2850: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2851: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2852: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2853: /* 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]); */
2854: }
2855: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2856: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2857: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2858: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2859: for (k=1; k<=cptcovage;k++){ /* For product with age */
2860: if(Dummy[Tvar[Tage[k]]]){
2861: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2862: } else{
2863: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2864: }
2865: /* 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]); */
2866: }
2867: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2868: /* 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]); */
2869: if(Dummy[Tvard[k][1]==0]){
2870: if(Dummy[Tvard[k][2]==0]){
2871: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2872: }else{
2873: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2874: }
2875: }else{
2876: if(Dummy[Tvard[k][2]==0]){
2877: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2878: }else{
2879: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2880: }
2881: }
1.217 brouard 2882: }
2883:
2884: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2885: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2886: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2887: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2888: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2889: /* ij should be linked to the correct index of cov */
2890: /* age and covariate values ij are in 'cov', but we need to pass
2891: * ij for the observed prevalence at age and status and covariate
2892: * number: prevacurrent[(int)agefin][ii][ij]
2893: */
2894: /* 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 *\/ */
2895: /* 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 *\/ */
2896: 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 2897: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2898: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2899: /* for(i=1; i<=nlstate+ndeath; i++) { */
2900: /* printf("%d newm= ",i); */
2901: /* for(j=1;j<=nlstate+ndeath;j++) { */
2902: /* printf("%f ",newm[i][j]); */
2903: /* } */
2904: /* printf("oldm * "); */
2905: /* for(j=1;j<=nlstate+ndeath;j++) { */
2906: /* printf("%f ",oldm[i][j]); */
2907: /* } */
1.268 brouard 2908: /* printf(" bmmij "); */
1.266 brouard 2909: /* for(j=1;j<=nlstate+ndeath;j++) { */
2910: /* printf("%f ",pmmij[i][j]); */
2911: /* } */
2912: /* printf("\n"); */
2913: /* } */
2914: /* } */
1.217 brouard 2915: savm=oldm;
2916: oldm=newm;
1.266 brouard 2917:
1.217 brouard 2918: for(j=1; j<=nlstate; j++){
2919: max[j]=0.;
2920: min[j]=1.;
2921: }
2922: for(j=1; j<=nlstate; j++){
2923: for(i=1;i<=nlstate;i++){
1.234 brouard 2924: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2925: bprlim[i][j]= newm[i][j];
2926: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2927: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2928: }
2929: }
1.218 brouard 2930:
1.217 brouard 2931: maxmax=0.;
2932: for(i=1; i<=nlstate; i++){
2933: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2934: maxmax=FMAX(maxmax,meandiff[i]);
2935: /* 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 2936: } /* i loop */
1.217 brouard 2937: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2938: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2939: if(maxmax < ftolpl){
1.220 brouard 2940: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2941: free_vector(min,1,nlstate);
2942: free_vector(max,1,nlstate);
2943: free_vector(meandiff,1,nlstate);
2944: return bprlim;
2945: }
1.288 brouard 2946: } /* agefin loop */
1.217 brouard 2947: /* After some age loop it doesn't converge */
1.288 brouard 2948: if(!first){
1.247 brouard 2949: first=1;
2950: 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\
2951: 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);
2952: }
2953: 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 2954: 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);
2955: /* 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); */
2956: free_vector(min,1,nlstate);
2957: free_vector(max,1,nlstate);
2958: free_vector(meandiff,1,nlstate);
2959:
2960: return bprlim; /* should not reach here */
2961: }
2962:
1.126 brouard 2963: /*************** transition probabilities ***************/
2964:
2965: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2966: {
1.138 brouard 2967: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2968: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2969: model to the ncovmodel covariates (including constant and age).
2970: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2971: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2972: ncth covariate in the global vector x is given by the formula:
2973: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2974: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2975: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2976: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2977: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2978: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2979: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2980: */
2981: double s1, lnpijopii;
1.126 brouard 2982: /*double t34;*/
1.164 brouard 2983: int i,j, nc, ii, jj;
1.126 brouard 2984:
1.223 brouard 2985: for(i=1; i<= nlstate; i++){
2986: for(j=1; j<i;j++){
2987: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2988: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2989: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2990: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2991: }
2992: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2993: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2994: }
2995: for(j=i+1; j<=nlstate+ndeath;j++){
2996: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2997: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2998: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2999: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3000: }
3001: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3002: }
3003: }
1.218 brouard 3004:
1.223 brouard 3005: for(i=1; i<= nlstate; i++){
3006: s1=0;
3007: for(j=1; j<i; j++){
3008: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3009: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3010: }
3011: for(j=i+1; j<=nlstate+ndeath; j++){
3012: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3013: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3014: }
3015: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3016: ps[i][i]=1./(s1+1.);
3017: /* Computing other pijs */
3018: for(j=1; j<i; j++)
3019: ps[i][j]= exp(ps[i][j])*ps[i][i];
3020: for(j=i+1; j<=nlstate+ndeath; j++)
3021: ps[i][j]= exp(ps[i][j])*ps[i][i];
3022: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3023: } /* end i */
1.218 brouard 3024:
1.223 brouard 3025: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3026: for(jj=1; jj<= nlstate+ndeath; jj++){
3027: ps[ii][jj]=0;
3028: ps[ii][ii]=1;
3029: }
3030: }
1.294 brouard 3031:
3032:
1.223 brouard 3033: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3034: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3035: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3036: /* } */
3037: /* printf("\n "); */
3038: /* } */
3039: /* printf("\n ");printf("%lf ",cov[2]);*/
3040: /*
3041: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3042: goto end;*/
1.266 brouard 3043: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3044: }
3045:
1.218 brouard 3046: /*************** backward transition probabilities ***************/
3047:
3048: /* 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 ) */
3049: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3050: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3051: {
1.302 brouard 3052: /* 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 3053: * 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 3054: */
1.218 brouard 3055: int i, ii, j,k;
1.222 brouard 3056:
3057: double **out, **pmij();
3058: double sumnew=0.;
1.218 brouard 3059: double agefin;
1.292 brouard 3060: 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 3061: double **dnewm, **dsavm, **doldm;
3062: double **bbmij;
3063:
1.218 brouard 3064: doldm=ddoldms; /* global pointers */
1.222 brouard 3065: dnewm=ddnewms;
3066: dsavm=ddsavms;
3067:
3068: agefin=cov[2];
1.268 brouard 3069: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3070: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3071: the observed prevalence (with this covariate ij) at beginning of transition */
3072: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3073:
3074: /* P_x */
1.266 brouard 3075: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3076: /* outputs pmmij which is a stochastic matrix in row */
3077:
3078: /* Diag(w_x) */
1.292 brouard 3079: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3080: sumnew=0.;
1.269 brouard 3081: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3082: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3083: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3084: sumnew+=prevacurrent[(int)agefin][ii][ij];
3085: }
3086: if(sumnew >0.01){ /* At least some value in the prevalence */
3087: for (ii=1;ii<=nlstate+ndeath;ii++){
3088: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3089: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3090: }
3091: }else{
3092: for (ii=1;ii<=nlstate+ndeath;ii++){
3093: for (j=1;j<=nlstate+ndeath;j++)
3094: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3095: }
3096: /* if(sumnew <0.9){ */
3097: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3098: /* } */
3099: }
3100: k3=0.0; /* We put the last diagonal to 0 */
3101: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3102: doldm[ii][ii]= k3;
3103: }
3104: /* End doldm, At the end doldm is diag[(w_i)] */
3105:
1.292 brouard 3106: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3107: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3108:
1.292 brouard 3109: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3110: /* 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 3111: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3112: sumnew=0.;
1.222 brouard 3113: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3114: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3115: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3116: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3117: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3118: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3119: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3120: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3121: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3122: /* }else */
1.268 brouard 3123: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3124: } /*End ii */
3125: } /* 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 */
3126:
1.292 brouard 3127: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3128: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3129: /* end bmij */
1.266 brouard 3130: return ps; /*pointer is unchanged */
1.218 brouard 3131: }
1.217 brouard 3132: /*************** transition probabilities ***************/
3133:
1.218 brouard 3134: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3135: {
3136: /* According to parameters values stored in x and the covariate's values stored in cov,
3137: computes the probability to be observed in state j being in state i by appying the
3138: model to the ncovmodel covariates (including constant and age).
3139: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3140: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3141: ncth covariate in the global vector x is given by the formula:
3142: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3143: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3144: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3145: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3146: Outputs ps[i][j] the probability to be observed in j being in j according to
3147: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3148: */
3149: double s1, lnpijopii;
3150: /*double t34;*/
3151: int i,j, nc, ii, jj;
3152:
1.234 brouard 3153: for(i=1; i<= nlstate; i++){
3154: for(j=1; j<i;j++){
3155: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3156: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3157: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3158: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3159: }
3160: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3161: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3162: }
3163: for(j=i+1; j<=nlstate+ndeath;j++){
3164: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3165: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3166: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3167: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3168: }
3169: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3170: }
3171: }
3172:
3173: for(i=1; i<= nlstate; i++){
3174: s1=0;
3175: for(j=1; j<i; j++){
3176: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3177: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3178: }
3179: for(j=i+1; j<=nlstate+ndeath; j++){
3180: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3181: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3182: }
3183: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3184: ps[i][i]=1./(s1+1.);
3185: /* Computing other pijs */
3186: for(j=1; j<i; j++)
3187: ps[i][j]= exp(ps[i][j])*ps[i][i];
3188: for(j=i+1; j<=nlstate+ndeath; j++)
3189: ps[i][j]= exp(ps[i][j])*ps[i][i];
3190: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3191: } /* end i */
3192:
3193: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3194: for(jj=1; jj<= nlstate+ndeath; jj++){
3195: ps[ii][jj]=0;
3196: ps[ii][ii]=1;
3197: }
3198: }
1.296 brouard 3199: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3200: for(jj=1; jj<= nlstate+ndeath; jj++){
3201: s1=0.;
3202: for(ii=1; ii<= nlstate+ndeath; ii++){
3203: s1+=ps[ii][jj];
3204: }
3205: for(ii=1; ii<= nlstate; ii++){
3206: ps[ii][jj]=ps[ii][jj]/s1;
3207: }
3208: }
3209: /* Transposition */
3210: for(jj=1; jj<= nlstate+ndeath; jj++){
3211: for(ii=jj; ii<= nlstate+ndeath; ii++){
3212: s1=ps[ii][jj];
3213: ps[ii][jj]=ps[jj][ii];
3214: ps[jj][ii]=s1;
3215: }
3216: }
3217: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3218: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3219: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3220: /* } */
3221: /* printf("\n "); */
3222: /* } */
3223: /* printf("\n ");printf("%lf ",cov[2]);*/
3224: /*
3225: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3226: goto end;*/
3227: return ps;
1.217 brouard 3228: }
3229:
3230:
1.126 brouard 3231: /**************** Product of 2 matrices ******************/
3232:
1.145 brouard 3233: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3234: {
3235: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3236: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3237: /* in, b, out are matrice of pointers which should have been initialized
3238: before: only the contents of out is modified. The function returns
3239: a pointer to pointers identical to out */
1.145 brouard 3240: int i, j, k;
1.126 brouard 3241: for(i=nrl; i<= nrh; i++)
1.145 brouard 3242: for(k=ncolol; k<=ncoloh; k++){
3243: out[i][k]=0.;
3244: for(j=ncl; j<=nch; j++)
3245: out[i][k] +=in[i][j]*b[j][k];
3246: }
1.126 brouard 3247: return out;
3248: }
3249:
3250:
3251: /************* Higher Matrix Product ***************/
3252:
1.235 brouard 3253: 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 3254: {
1.218 brouard 3255: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3256: 'nhstepm*hstepm*stepm' months (i.e. until
3257: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3258: nhstepm*hstepm matrices.
3259: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3260: (typically every 2 years instead of every month which is too big
3261: for the memory).
3262: Model is determined by parameters x and covariates have to be
3263: included manually here.
3264:
3265: */
3266:
3267: int i, j, d, h, k;
1.131 brouard 3268: double **out, cov[NCOVMAX+1];
1.126 brouard 3269: double **newm;
1.187 brouard 3270: double agexact;
1.214 brouard 3271: double agebegin, ageend;
1.126 brouard 3272:
3273: /* Hstepm could be zero and should return the unit matrix */
3274: for (i=1;i<=nlstate+ndeath;i++)
3275: for (j=1;j<=nlstate+ndeath;j++){
3276: oldm[i][j]=(i==j ? 1.0 : 0.0);
3277: po[i][j][0]=(i==j ? 1.0 : 0.0);
3278: }
3279: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3280: for(h=1; h <=nhstepm; h++){
3281: for(d=1; d <=hstepm; d++){
3282: newm=savm;
3283: /* Covariates have to be included here again */
3284: cov[1]=1.;
1.214 brouard 3285: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3286: cov[2]=agexact;
3287: if(nagesqr==1)
1.227 brouard 3288: cov[3]= agexact*agexact;
1.235 brouard 3289: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3290: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3291: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3292: /* 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)); */
3293: }
3294: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3295: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3296: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3297: /* 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]); */
3298: }
3299: for (k=1; k<=cptcovage;k++){
3300: if(Dummy[Tvar[Tage[k]]]){
3301: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3302: } else{
3303: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3304: }
3305: /* 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]); */
3306: }
3307: for (k=1; k<=cptcovprod;k++){ /* */
3308: /* 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]); */
3309: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3310: }
3311: /* for (k=1; k<=cptcovn;k++) */
3312: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3313: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3314: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3315: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3316: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3317:
3318:
1.126 brouard 3319: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3320: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3321: /* right multiplication of oldm by the current matrix */
1.126 brouard 3322: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3323: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3324: /* if((int)age == 70){ */
3325: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3326: /* for(i=1; i<=nlstate+ndeath; i++) { */
3327: /* printf("%d pmmij ",i); */
3328: /* for(j=1;j<=nlstate+ndeath;j++) { */
3329: /* printf("%f ",pmmij[i][j]); */
3330: /* } */
3331: /* printf(" oldm "); */
3332: /* for(j=1;j<=nlstate+ndeath;j++) { */
3333: /* printf("%f ",oldm[i][j]); */
3334: /* } */
3335: /* printf("\n"); */
3336: /* } */
3337: /* } */
1.126 brouard 3338: savm=oldm;
3339: oldm=newm;
3340: }
3341: for(i=1; i<=nlstate+ndeath; i++)
3342: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3343: po[i][j][h]=newm[i][j];
3344: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3345: }
1.128 brouard 3346: /*printf("h=%d ",h);*/
1.126 brouard 3347: } /* end h */
1.267 brouard 3348: /* printf("\n H=%d \n",h); */
1.126 brouard 3349: return po;
3350: }
3351:
1.217 brouard 3352: /************* Higher Back Matrix Product ***************/
1.218 brouard 3353: /* 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 3354: 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 3355: {
1.266 brouard 3356: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3357: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3358: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3359: nhstepm*hstepm matrices.
3360: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3361: (typically every 2 years instead of every month which is too big
1.217 brouard 3362: for the memory).
1.218 brouard 3363: Model is determined by parameters x and covariates have to be
1.266 brouard 3364: included manually here. Then we use a call to bmij(x and cov)
3365: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3366: */
1.217 brouard 3367:
3368: int i, j, d, h, k;
1.266 brouard 3369: double **out, cov[NCOVMAX+1], **bmij();
3370: double **newm, ***newmm;
1.217 brouard 3371: double agexact;
3372: double agebegin, ageend;
1.222 brouard 3373: double **oldm, **savm;
1.217 brouard 3374:
1.266 brouard 3375: newmm=po; /* To be saved */
3376: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3377: /* Hstepm could be zero and should return the unit matrix */
3378: for (i=1;i<=nlstate+ndeath;i++)
3379: for (j=1;j<=nlstate+ndeath;j++){
3380: oldm[i][j]=(i==j ? 1.0 : 0.0);
3381: po[i][j][0]=(i==j ? 1.0 : 0.0);
3382: }
3383: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3384: for(h=1; h <=nhstepm; h++){
3385: for(d=1; d <=hstepm; d++){
3386: newm=savm;
3387: /* Covariates have to be included here again */
3388: cov[1]=1.;
1.271 brouard 3389: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3390: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3391: cov[2]=agexact;
3392: if(nagesqr==1)
1.222 brouard 3393: cov[3]= agexact*agexact;
1.266 brouard 3394: for (k=1; k<=cptcovn;k++){
3395: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3396: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3397: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3398: /* 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)); */
3399: }
1.267 brouard 3400: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3401: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3402: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3403: /* 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]); */
3404: }
3405: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3406: if(Dummy[Tvar[Tage[k]]]){
3407: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3408: } else{
3409: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3410: }
3411: /* 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]); */
3412: }
3413: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3414: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3415: }
1.217 brouard 3416: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3417: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3418:
1.218 brouard 3419: /* Careful transposed matrix */
1.266 brouard 3420: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3421: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3422: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3423: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3424: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3425: /* if((int)age == 70){ */
3426: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3427: /* for(i=1; i<=nlstate+ndeath; i++) { */
3428: /* printf("%d pmmij ",i); */
3429: /* for(j=1;j<=nlstate+ndeath;j++) { */
3430: /* printf("%f ",pmmij[i][j]); */
3431: /* } */
3432: /* printf(" oldm "); */
3433: /* for(j=1;j<=nlstate+ndeath;j++) { */
3434: /* printf("%f ",oldm[i][j]); */
3435: /* } */
3436: /* printf("\n"); */
3437: /* } */
3438: /* } */
3439: savm=oldm;
3440: oldm=newm;
3441: }
3442: for(i=1; i<=nlstate+ndeath; i++)
3443: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3444: po[i][j][h]=newm[i][j];
1.268 brouard 3445: /* if(h==nhstepm) */
3446: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3447: }
1.268 brouard 3448: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3449: } /* end h */
1.268 brouard 3450: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3451: return po;
3452: }
3453:
3454:
1.162 brouard 3455: #ifdef NLOPT
3456: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3457: double fret;
3458: double *xt;
3459: int j;
3460: myfunc_data *d2 = (myfunc_data *) pd;
3461: /* xt = (p1-1); */
3462: xt=vector(1,n);
3463: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3464:
3465: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3466: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3467: printf("Function = %.12lf ",fret);
3468: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3469: printf("\n");
3470: free_vector(xt,1,n);
3471: return fret;
3472: }
3473: #endif
1.126 brouard 3474:
3475: /*************** log-likelihood *************/
3476: double func( double *x)
3477: {
1.226 brouard 3478: int i, ii, j, k, mi, d, kk;
3479: int ioffset=0;
3480: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3481: double **out;
3482: double lli; /* Individual log likelihood */
3483: int s1, s2;
1.228 brouard 3484: 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 3485: double bbh, survp;
3486: long ipmx;
3487: double agexact;
3488: /*extern weight */
3489: /* We are differentiating ll according to initial status */
3490: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3491: /*for(i=1;i<imx;i++)
3492: printf(" %d\n",s[4][i]);
3493: */
1.162 brouard 3494:
1.226 brouard 3495: ++countcallfunc;
1.162 brouard 3496:
1.226 brouard 3497: cov[1]=1.;
1.126 brouard 3498:
1.226 brouard 3499: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3500: ioffset=0;
1.226 brouard 3501: if(mle==1){
3502: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3503: /* Computes the values of the ncovmodel covariates of the model
3504: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3505: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3506: to be observed in j being in i according to the model.
3507: */
1.243 brouard 3508: ioffset=2+nagesqr ;
1.233 brouard 3509: /* Fixed */
1.234 brouard 3510: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3511: 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)*/
3512: }
1.226 brouard 3513: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3514: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3515: has been calculated etc */
3516: /* For an individual i, wav[i] gives the number of effective waves */
3517: /* We compute the contribution to Likelihood of each effective transition
3518: mw[mi][i] is real wave of the mi th effectve wave */
3519: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3520: s2=s[mw[mi+1][i]][i];
3521: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3522: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3523: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3524: */
3525: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3526: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3527: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3528: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3529: }
3530: for (ii=1;ii<=nlstate+ndeath;ii++)
3531: for (j=1;j<=nlstate+ndeath;j++){
3532: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3533: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3534: }
3535: for(d=0; d<dh[mi][i]; d++){
3536: newm=savm;
3537: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3538: cov[2]=agexact;
3539: if(nagesqr==1)
3540: cov[3]= agexact*agexact; /* Should be changed here */
3541: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3542: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3543: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3544: else
3545: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3546: }
3547: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3548: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3549: savm=oldm;
3550: oldm=newm;
3551: } /* end mult */
3552:
3553: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3554: /* But now since version 0.9 we anticipate for bias at large stepm.
3555: * If stepm is larger than one month (smallest stepm) and if the exact delay
3556: * (in months) between two waves is not a multiple of stepm, we rounded to
3557: * the nearest (and in case of equal distance, to the lowest) interval but now
3558: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3559: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3560: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3561: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3562: * -stepm/2 to stepm/2 .
3563: * For stepm=1 the results are the same as for previous versions of Imach.
3564: * For stepm > 1 the results are less biased than in previous versions.
3565: */
1.234 brouard 3566: s1=s[mw[mi][i]][i];
3567: s2=s[mw[mi+1][i]][i];
3568: bbh=(double)bh[mi][i]/(double)stepm;
3569: /* bias bh is positive if real duration
3570: * is higher than the multiple of stepm and negative otherwise.
3571: */
3572: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3573: if( s2 > nlstate){
3574: /* i.e. if s2 is a death state and if the date of death is known
3575: then the contribution to the likelihood is the probability to
3576: die between last step unit time and current step unit time,
3577: which is also equal to probability to die before dh
3578: minus probability to die before dh-stepm .
3579: In version up to 0.92 likelihood was computed
3580: as if date of death was unknown. Death was treated as any other
3581: health state: the date of the interview describes the actual state
3582: and not the date of a change in health state. The former idea was
3583: to consider that at each interview the state was recorded
3584: (healthy, disable or death) and IMaCh was corrected; but when we
3585: introduced the exact date of death then we should have modified
3586: the contribution of an exact death to the likelihood. This new
3587: contribution is smaller and very dependent of the step unit
3588: stepm. It is no more the probability to die between last interview
3589: and month of death but the probability to survive from last
3590: interview up to one month before death multiplied by the
3591: probability to die within a month. Thanks to Chris
3592: Jackson for correcting this bug. Former versions increased
3593: mortality artificially. The bad side is that we add another loop
3594: which slows down the processing. The difference can be up to 10%
3595: lower mortality.
3596: */
3597: /* If, at the beginning of the maximization mostly, the
3598: cumulative probability or probability to be dead is
3599: constant (ie = 1) over time d, the difference is equal to
3600: 0. out[s1][3] = savm[s1][3]: probability, being at state
3601: s1 at precedent wave, to be dead a month before current
3602: wave is equal to probability, being at state s1 at
3603: precedent wave, to be dead at mont of the current
3604: wave. Then the observed probability (that this person died)
3605: is null according to current estimated parameter. In fact,
3606: it should be very low but not zero otherwise the log go to
3607: infinity.
3608: */
1.183 brouard 3609: /* #ifdef INFINITYORIGINAL */
3610: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3611: /* #else */
3612: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3613: /* lli=log(mytinydouble); */
3614: /* else */
3615: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3616: /* #endif */
1.226 brouard 3617: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3618:
1.226 brouard 3619: } else if ( s2==-1 ) { /* alive */
3620: for (j=1,survp=0. ; j<=nlstate; j++)
3621: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3622: /*survp += out[s1][j]; */
3623: lli= log(survp);
3624: }
3625: else if (s2==-4) {
3626: for (j=3,survp=0. ; j<=nlstate; j++)
3627: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3628: lli= log(survp);
3629: }
3630: else if (s2==-5) {
3631: for (j=1,survp=0. ; j<=2; j++)
3632: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3633: lli= log(survp);
3634: }
3635: else{
3636: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3637: /* 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 */
3638: }
3639: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3640: /*if(lli ==000.0)*/
3641: /*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); */
3642: ipmx +=1;
3643: sw += weight[i];
3644: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3645: /* if (lli < log(mytinydouble)){ */
3646: /* 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); */
3647: /* 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]); */
3648: /* } */
3649: } /* end of wave */
3650: } /* end of individual */
3651: } else if(mle==2){
3652: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3653: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3654: for(mi=1; mi<= wav[i]-1; mi++){
3655: for (ii=1;ii<=nlstate+ndeath;ii++)
3656: for (j=1;j<=nlstate+ndeath;j++){
3657: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3658: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3659: }
3660: for(d=0; d<=dh[mi][i]; d++){
3661: newm=savm;
3662: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3663: cov[2]=agexact;
3664: if(nagesqr==1)
3665: cov[3]= agexact*agexact;
3666: for (kk=1; kk<=cptcovage;kk++) {
3667: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3668: }
3669: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3670: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3671: savm=oldm;
3672: oldm=newm;
3673: } /* end mult */
3674:
3675: s1=s[mw[mi][i]][i];
3676: s2=s[mw[mi+1][i]][i];
3677: bbh=(double)bh[mi][i]/(double)stepm;
3678: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
3679: ipmx +=1;
3680: sw += weight[i];
3681: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3682: } /* end of wave */
3683: } /* end of individual */
3684: } else if(mle==3){ /* exponential inter-extrapolation */
3685: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3686: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3687: for(mi=1; mi<= wav[i]-1; mi++){
3688: for (ii=1;ii<=nlstate+ndeath;ii++)
3689: for (j=1;j<=nlstate+ndeath;j++){
3690: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3691: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3692: }
3693: for(d=0; d<dh[mi][i]; d++){
3694: newm=savm;
3695: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3696: cov[2]=agexact;
3697: if(nagesqr==1)
3698: cov[3]= agexact*agexact;
3699: for (kk=1; kk<=cptcovage;kk++) {
3700: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3701: }
3702: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3703: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3704: savm=oldm;
3705: oldm=newm;
3706: } /* end mult */
3707:
3708: s1=s[mw[mi][i]][i];
3709: s2=s[mw[mi+1][i]][i];
3710: bbh=(double)bh[mi][i]/(double)stepm;
3711: 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 */
3712: ipmx +=1;
3713: sw += weight[i];
3714: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3715: } /* end of wave */
3716: } /* end of individual */
3717: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3718: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3719: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3720: for(mi=1; mi<= wav[i]-1; mi++){
3721: for (ii=1;ii<=nlstate+ndeath;ii++)
3722: for (j=1;j<=nlstate+ndeath;j++){
3723: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3724: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3725: }
3726: for(d=0; d<dh[mi][i]; d++){
3727: newm=savm;
3728: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3729: cov[2]=agexact;
3730: if(nagesqr==1)
3731: cov[3]= agexact*agexact;
3732: for (kk=1; kk<=cptcovage;kk++) {
3733: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3734: }
1.126 brouard 3735:
1.226 brouard 3736: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3737: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3738: savm=oldm;
3739: oldm=newm;
3740: } /* end mult */
3741:
3742: s1=s[mw[mi][i]][i];
3743: s2=s[mw[mi+1][i]][i];
3744: if( s2 > nlstate){
3745: lli=log(out[s1][s2] - savm[s1][s2]);
3746: } else if ( s2==-1 ) { /* alive */
3747: for (j=1,survp=0. ; j<=nlstate; j++)
3748: survp += out[s1][j];
3749: lli= log(survp);
3750: }else{
3751: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3752: }
3753: ipmx +=1;
3754: sw += weight[i];
3755: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3756: /* 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 3757: } /* end of wave */
3758: } /* end of individual */
3759: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3760: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3761: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3762: for(mi=1; mi<= wav[i]-1; mi++){
3763: for (ii=1;ii<=nlstate+ndeath;ii++)
3764: for (j=1;j<=nlstate+ndeath;j++){
3765: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3766: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3767: }
3768: for(d=0; d<dh[mi][i]; d++){
3769: newm=savm;
3770: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3771: cov[2]=agexact;
3772: if(nagesqr==1)
3773: cov[3]= agexact*agexact;
3774: for (kk=1; kk<=cptcovage;kk++) {
3775: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3776: }
1.126 brouard 3777:
1.226 brouard 3778: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3779: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3780: savm=oldm;
3781: oldm=newm;
3782: } /* end mult */
3783:
3784: s1=s[mw[mi][i]][i];
3785: s2=s[mw[mi+1][i]][i];
3786: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3787: ipmx +=1;
3788: sw += weight[i];
3789: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3790: /*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]);*/
3791: } /* end of wave */
3792: } /* end of individual */
3793: } /* End of if */
3794: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3795: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3796: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3797: return -l;
1.126 brouard 3798: }
3799:
3800: /*************** log-likelihood *************/
3801: double funcone( double *x)
3802: {
1.228 brouard 3803: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3804: int i, ii, j, k, mi, d, kk;
1.228 brouard 3805: int ioffset=0;
1.131 brouard 3806: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3807: double **out;
3808: double lli; /* Individual log likelihood */
3809: double llt;
3810: int s1, s2;
1.228 brouard 3811: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3812:
1.126 brouard 3813: double bbh, survp;
1.187 brouard 3814: double agexact;
1.214 brouard 3815: double agebegin, ageend;
1.126 brouard 3816: /*extern weight */
3817: /* We are differentiating ll according to initial status */
3818: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3819: /*for(i=1;i<imx;i++)
3820: printf(" %d\n",s[4][i]);
3821: */
3822: cov[1]=1.;
3823:
3824: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3825: ioffset=0;
3826: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3827: /* ioffset=2+nagesqr+cptcovage; */
3828: ioffset=2+nagesqr;
1.232 brouard 3829: /* Fixed */
1.224 brouard 3830: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3831: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3832: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3833: 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)*/
3834: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3835: /* cov[2+6]=covar[Tvar[6]][i]; */
3836: /* cov[2+6]=covar[2][i]; V2 */
3837: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3838: /* cov[2+7]=covar[Tvar[7]][i]; */
3839: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3840: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3841: /* cov[2+9]=covar[Tvar[9]][i]; */
3842: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3843: }
1.232 brouard 3844: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3845: /* 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?)*\/ */
3846: /* } */
1.231 brouard 3847: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3848: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3849: /* } */
1.225 brouard 3850:
1.233 brouard 3851:
3852: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3853: /* Wave varying (but not age varying) */
3854: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3855: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3856: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3857: }
1.232 brouard 3858: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3859: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3860: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3861: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3862: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3863: /* 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 3864: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3865: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3866: /* /\* 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]); *\/ */
3867: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3868: /* } */
1.126 brouard 3869: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3870: for (j=1;j<=nlstate+ndeath;j++){
3871: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3872: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3873: }
1.214 brouard 3874:
3875: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3876: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3877: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3878: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3879: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3880: and mw[mi+1][i]. dh depends on stepm.*/
3881: newm=savm;
1.247 brouard 3882: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3883: cov[2]=agexact;
3884: if(nagesqr==1)
3885: cov[3]= agexact*agexact;
3886: for (kk=1; kk<=cptcovage;kk++) {
3887: if(!FixedV[Tvar[Tage[kk]]])
3888: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3889: else
3890: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3891: }
3892: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3893: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3894: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3895: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3896: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3897: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3898: savm=oldm;
3899: oldm=newm;
1.126 brouard 3900: } /* end mult */
3901:
3902: s1=s[mw[mi][i]][i];
3903: s2=s[mw[mi+1][i]][i];
1.217 brouard 3904: /* if(s2==-1){ */
1.268 brouard 3905: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3906: /* /\* exit(1); *\/ */
3907: /* } */
1.126 brouard 3908: bbh=(double)bh[mi][i]/(double)stepm;
3909: /* bias is positive if real duration
3910: * is higher than the multiple of stepm and negative otherwise.
3911: */
3912: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3913: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3914: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3915: for (j=1,survp=0. ; j<=nlstate; j++)
3916: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3917: lli= log(survp);
1.126 brouard 3918: }else if (mle==1){
1.242 brouard 3919: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3920: } else if(mle==2){
1.242 brouard 3921: 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 3922: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3923: 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 3924: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3925: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3926: } else{ /* mle=0 back to 1 */
1.242 brouard 3927: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3928: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3929: } /* End of if */
3930: ipmx +=1;
3931: sw += weight[i];
3932: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3933: /*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 3934: if(globpr){
1.246 brouard 3935: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3936: %11.6f %11.6f %11.6f ", \
1.242 brouard 3937: 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 3938: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3939: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3940: llt +=ll[k]*gipmx/gsw;
3941: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3942: }
3943: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3944: }
1.232 brouard 3945: } /* end of wave */
3946: } /* end of individual */
3947: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3948: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3949: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3950: if(globpr==0){ /* First time we count the contributions and weights */
3951: gipmx=ipmx;
3952: gsw=sw;
3953: }
3954: return -l;
1.126 brouard 3955: }
3956:
3957:
3958: /*************** function likelione ***********/
1.292 brouard 3959: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3960: {
3961: /* This routine should help understanding what is done with
3962: the selection of individuals/waves and
3963: to check the exact contribution to the likelihood.
3964: Plotting could be done.
3965: */
3966: int k;
3967:
3968: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3969: strcpy(fileresilk,"ILK_");
1.202 brouard 3970: strcat(fileresilk,fileresu);
1.126 brouard 3971: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3972: printf("Problem with resultfile: %s\n", fileresilk);
3973: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3974: }
1.214 brouard 3975: 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");
3976: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3977: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3978: for(k=1; k<=nlstate; k++)
3979: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3980: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3981: }
3982:
1.292 brouard 3983: *fretone=(*func)(p);
1.126 brouard 3984: if(*globpri !=0){
3985: fclose(ficresilk);
1.205 brouard 3986: if (mle ==0)
3987: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3988: else if(mle >=1)
3989: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3990: 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 3991: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3992:
3993: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3994: 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 3995: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3996: }
1.207 brouard 3997: 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 3998: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3999: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 4000: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4001: fflush(fichtm);
1.205 brouard 4002: }
1.126 brouard 4003: return;
4004: }
4005:
4006:
4007: /*********** Maximum Likelihood Estimation ***************/
4008:
4009: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4010: {
1.165 brouard 4011: int i,j, iter=0;
1.126 brouard 4012: double **xi;
4013: double fret;
4014: double fretone; /* Only one call to likelihood */
4015: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4016:
4017: #ifdef NLOPT
4018: int creturn;
4019: nlopt_opt opt;
4020: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4021: double *lb;
4022: double minf; /* the minimum objective value, upon return */
4023: double * p1; /* Shifted parameters from 0 instead of 1 */
4024: myfunc_data dinst, *d = &dinst;
4025: #endif
4026:
4027:
1.126 brouard 4028: xi=matrix(1,npar,1,npar);
4029: for (i=1;i<=npar;i++)
4030: for (j=1;j<=npar;j++)
4031: xi[i][j]=(i==j ? 1.0 : 0.0);
4032: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4033: strcpy(filerespow,"POW_");
1.126 brouard 4034: strcat(filerespow,fileres);
4035: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4036: printf("Problem with resultfile: %s\n", filerespow);
4037: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4038: }
4039: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4040: for (i=1;i<=nlstate;i++)
4041: for(j=1;j<=nlstate+ndeath;j++)
4042: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4043: fprintf(ficrespow,"\n");
1.162 brouard 4044: #ifdef POWELL
1.126 brouard 4045: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4046: #endif
1.126 brouard 4047:
1.162 brouard 4048: #ifdef NLOPT
4049: #ifdef NEWUOA
4050: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4051: #else
4052: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4053: #endif
4054: lb=vector(0,npar-1);
4055: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4056: nlopt_set_lower_bounds(opt, lb);
4057: nlopt_set_initial_step1(opt, 0.1);
4058:
4059: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4060: d->function = func;
4061: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4062: nlopt_set_min_objective(opt, myfunc, d);
4063: nlopt_set_xtol_rel(opt, ftol);
4064: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4065: printf("nlopt failed! %d\n",creturn);
4066: }
4067: else {
4068: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4069: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4070: iter=1; /* not equal */
4071: }
4072: nlopt_destroy(opt);
4073: #endif
1.126 brouard 4074: free_matrix(xi,1,npar,1,npar);
4075: fclose(ficrespow);
1.203 brouard 4076: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4077: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4078: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4079:
4080: }
4081:
4082: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4083: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4084: {
4085: double **a,**y,*x,pd;
1.203 brouard 4086: /* double **hess; */
1.164 brouard 4087: int i, j;
1.126 brouard 4088: int *indx;
4089:
4090: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4091: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4092: void lubksb(double **a, int npar, int *indx, double b[]) ;
4093: void ludcmp(double **a, int npar, int *indx, double *d) ;
4094: double gompertz(double p[]);
1.203 brouard 4095: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4096:
4097: printf("\nCalculation of the hessian matrix. Wait...\n");
4098: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4099: for (i=1;i<=npar;i++){
1.203 brouard 4100: printf("%d-",i);fflush(stdout);
4101: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4102:
4103: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4104:
4105: /* printf(" %f ",p[i]);
4106: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4107: }
4108:
4109: for (i=1;i<=npar;i++) {
4110: for (j=1;j<=npar;j++) {
4111: if (j>i) {
1.203 brouard 4112: printf(".%d-%d",i,j);fflush(stdout);
4113: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4114: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4115:
4116: hess[j][i]=hess[i][j];
4117: /*printf(" %lf ",hess[i][j]);*/
4118: }
4119: }
4120: }
4121: printf("\n");
4122: fprintf(ficlog,"\n");
4123:
4124: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4125: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4126:
4127: a=matrix(1,npar,1,npar);
4128: y=matrix(1,npar,1,npar);
4129: x=vector(1,npar);
4130: indx=ivector(1,npar);
4131: for (i=1;i<=npar;i++)
4132: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4133: ludcmp(a,npar,indx,&pd);
4134:
4135: for (j=1;j<=npar;j++) {
4136: for (i=1;i<=npar;i++) x[i]=0;
4137: x[j]=1;
4138: lubksb(a,npar,indx,x);
4139: for (i=1;i<=npar;i++){
4140: matcov[i][j]=x[i];
4141: }
4142: }
4143:
4144: printf("\n#Hessian matrix#\n");
4145: fprintf(ficlog,"\n#Hessian matrix#\n");
4146: for (i=1;i<=npar;i++) {
4147: for (j=1;j<=npar;j++) {
1.203 brouard 4148: printf("%.6e ",hess[i][j]);
4149: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4150: }
4151: printf("\n");
4152: fprintf(ficlog,"\n");
4153: }
4154:
1.203 brouard 4155: /* printf("\n#Covariance matrix#\n"); */
4156: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4157: /* for (i=1;i<=npar;i++) { */
4158: /* for (j=1;j<=npar;j++) { */
4159: /* printf("%.6e ",matcov[i][j]); */
4160: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4161: /* } */
4162: /* printf("\n"); */
4163: /* fprintf(ficlog,"\n"); */
4164: /* } */
4165:
1.126 brouard 4166: /* Recompute Inverse */
1.203 brouard 4167: /* for (i=1;i<=npar;i++) */
4168: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4169: /* ludcmp(a,npar,indx,&pd); */
4170:
4171: /* printf("\n#Hessian matrix recomputed#\n"); */
4172:
4173: /* for (j=1;j<=npar;j++) { */
4174: /* for (i=1;i<=npar;i++) x[i]=0; */
4175: /* x[j]=1; */
4176: /* lubksb(a,npar,indx,x); */
4177: /* for (i=1;i<=npar;i++){ */
4178: /* y[i][j]=x[i]; */
4179: /* printf("%.3e ",y[i][j]); */
4180: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4181: /* } */
4182: /* printf("\n"); */
4183: /* fprintf(ficlog,"\n"); */
4184: /* } */
4185:
4186: /* Verifying the inverse matrix */
4187: #ifdef DEBUGHESS
4188: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4189:
1.203 brouard 4190: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4191: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4192:
4193: for (j=1;j<=npar;j++) {
4194: for (i=1;i<=npar;i++){
1.203 brouard 4195: printf("%.2f ",y[i][j]);
4196: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4197: }
4198: printf("\n");
4199: fprintf(ficlog,"\n");
4200: }
1.203 brouard 4201: #endif
1.126 brouard 4202:
4203: free_matrix(a,1,npar,1,npar);
4204: free_matrix(y,1,npar,1,npar);
4205: free_vector(x,1,npar);
4206: free_ivector(indx,1,npar);
1.203 brouard 4207: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4208:
4209:
4210: }
4211:
4212: /*************** hessian matrix ****************/
4213: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4214: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4215: int i;
4216: int l=1, lmax=20;
1.203 brouard 4217: double k1,k2, res, fx;
1.132 brouard 4218: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4219: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4220: int k=0,kmax=10;
4221: double l1;
4222:
4223: fx=func(x);
4224: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4225: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4226: l1=pow(10,l);
4227: delts=delt;
4228: for(k=1 ; k <kmax; k=k+1){
4229: delt = delta*(l1*k);
4230: p2[theta]=x[theta] +delt;
1.145 brouard 4231: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4232: p2[theta]=x[theta]-delt;
4233: k2=func(p2)-fx;
4234: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4235: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4236:
1.203 brouard 4237: #ifdef DEBUGHESSII
1.126 brouard 4238: 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);
4239: 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);
4240: #endif
4241: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4242: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4243: k=kmax;
4244: }
4245: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4246: k=kmax; l=lmax*10;
1.126 brouard 4247: }
4248: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4249: delts=delt;
4250: }
1.203 brouard 4251: } /* End loop k */
1.126 brouard 4252: }
4253: delti[theta]=delts;
4254: return res;
4255:
4256: }
4257:
1.203 brouard 4258: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4259: {
4260: int i;
1.164 brouard 4261: int l=1, lmax=20;
1.126 brouard 4262: double k1,k2,k3,k4,res,fx;
1.132 brouard 4263: double p2[MAXPARM+1];
1.203 brouard 4264: int k, kmax=1;
4265: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4266:
4267: int firstime=0;
1.203 brouard 4268:
1.126 brouard 4269: fx=func(x);
1.203 brouard 4270: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4271: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4272: p2[thetai]=x[thetai]+delti[thetai]*k;
4273: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4274: k1=func(p2)-fx;
4275:
1.203 brouard 4276: p2[thetai]=x[thetai]+delti[thetai]*k;
4277: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4278: k2=func(p2)-fx;
4279:
1.203 brouard 4280: p2[thetai]=x[thetai]-delti[thetai]*k;
4281: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4282: k3=func(p2)-fx;
4283:
1.203 brouard 4284: p2[thetai]=x[thetai]-delti[thetai]*k;
4285: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4286: k4=func(p2)-fx;
1.203 brouard 4287: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4288: if(k1*k2*k3*k4 <0.){
1.208 brouard 4289: firstime=1;
1.203 brouard 4290: kmax=kmax+10;
1.208 brouard 4291: }
4292: if(kmax >=10 || firstime ==1){
1.246 brouard 4293: 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);
4294: 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 4295: 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);
4296: 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);
4297: }
4298: #ifdef DEBUGHESSIJ
4299: v1=hess[thetai][thetai];
4300: v2=hess[thetaj][thetaj];
4301: cv12=res;
4302: /* Computing eigen value of Hessian matrix */
4303: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4304: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4305: if ((lc2 <0) || (lc1 <0) ){
4306: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4307: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4308: 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);
4309: 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);
4310: }
1.126 brouard 4311: #endif
4312: }
4313: return res;
4314: }
4315:
1.203 brouard 4316: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4317: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4318: /* { */
4319: /* int i; */
4320: /* int l=1, lmax=20; */
4321: /* double k1,k2,k3,k4,res,fx; */
4322: /* double p2[MAXPARM+1]; */
4323: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4324: /* int k=0,kmax=10; */
4325: /* double l1; */
4326:
4327: /* fx=func(x); */
4328: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4329: /* l1=pow(10,l); */
4330: /* delts=delt; */
4331: /* for(k=1 ; k <kmax; k=k+1){ */
4332: /* delt = delti*(l1*k); */
4333: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4334: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4335: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4336: /* k1=func(p2)-fx; */
4337:
4338: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4339: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4340: /* k2=func(p2)-fx; */
4341:
4342: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4343: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4344: /* k3=func(p2)-fx; */
4345:
4346: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4347: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4348: /* k4=func(p2)-fx; */
4349: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4350: /* #ifdef DEBUGHESSIJ */
4351: /* 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); */
4352: /* 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); */
4353: /* #endif */
4354: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4355: /* k=kmax; */
4356: /* } */
4357: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4358: /* k=kmax; l=lmax*10; */
4359: /* } */
4360: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4361: /* delts=delt; */
4362: /* } */
4363: /* } /\* End loop k *\/ */
4364: /* } */
4365: /* delti[theta]=delts; */
4366: /* return res; */
4367: /* } */
4368:
4369:
1.126 brouard 4370: /************** Inverse of matrix **************/
4371: void ludcmp(double **a, int n, int *indx, double *d)
4372: {
4373: int i,imax,j,k;
4374: double big,dum,sum,temp;
4375: double *vv;
4376:
4377: vv=vector(1,n);
4378: *d=1.0;
4379: for (i=1;i<=n;i++) {
4380: big=0.0;
4381: for (j=1;j<=n;j++)
4382: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4383: if (big == 0.0){
4384: printf(" Singular Hessian matrix at row %d:\n",i);
4385: for (j=1;j<=n;j++) {
4386: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4387: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4388: }
4389: fflush(ficlog);
4390: fclose(ficlog);
4391: nrerror("Singular matrix in routine ludcmp");
4392: }
1.126 brouard 4393: vv[i]=1.0/big;
4394: }
4395: for (j=1;j<=n;j++) {
4396: for (i=1;i<j;i++) {
4397: sum=a[i][j];
4398: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4399: a[i][j]=sum;
4400: }
4401: big=0.0;
4402: for (i=j;i<=n;i++) {
4403: sum=a[i][j];
4404: for (k=1;k<j;k++)
4405: sum -= a[i][k]*a[k][j];
4406: a[i][j]=sum;
4407: if ( (dum=vv[i]*fabs(sum)) >= big) {
4408: big=dum;
4409: imax=i;
4410: }
4411: }
4412: if (j != imax) {
4413: for (k=1;k<=n;k++) {
4414: dum=a[imax][k];
4415: a[imax][k]=a[j][k];
4416: a[j][k]=dum;
4417: }
4418: *d = -(*d);
4419: vv[imax]=vv[j];
4420: }
4421: indx[j]=imax;
4422: if (a[j][j] == 0.0) a[j][j]=TINY;
4423: if (j != n) {
4424: dum=1.0/(a[j][j]);
4425: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4426: }
4427: }
4428: free_vector(vv,1,n); /* Doesn't work */
4429: ;
4430: }
4431:
4432: void lubksb(double **a, int n, int *indx, double b[])
4433: {
4434: int i,ii=0,ip,j;
4435: double sum;
4436:
4437: for (i=1;i<=n;i++) {
4438: ip=indx[i];
4439: sum=b[ip];
4440: b[ip]=b[i];
4441: if (ii)
4442: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4443: else if (sum) ii=i;
4444: b[i]=sum;
4445: }
4446: for (i=n;i>=1;i--) {
4447: sum=b[i];
4448: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4449: b[i]=sum/a[i][i];
4450: }
4451: }
4452:
4453: void pstamp(FILE *fichier)
4454: {
1.196 brouard 4455: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4456: }
4457:
1.297 brouard 4458: void date2dmy(double date,double *day, double *month, double *year){
4459: double yp=0., yp1=0., yp2=0.;
4460:
4461: yp1=modf(date,&yp);/* extracts integral of date in yp and
4462: fractional in yp1 */
4463: *year=yp;
4464: yp2=modf((yp1*12),&yp);
4465: *month=yp;
4466: yp1=modf((yp2*30.5),&yp);
4467: *day=yp;
4468: if(*day==0) *day=1;
4469: if(*month==0) *month=1;
4470: }
4471:
1.253 brouard 4472:
4473:
1.126 brouard 4474: /************ Frequencies ********************/
1.251 brouard 4475: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4476: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4477: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4478: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4479:
1.265 brouard 4480: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4481: int iind=0, iage=0;
4482: int mi; /* Effective wave */
4483: int first;
4484: double ***freq; /* Frequencies */
1.268 brouard 4485: 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 */
4486: 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 4487: double *meanq, *stdq, *idq;
1.226 brouard 4488: double **meanqt;
4489: double *pp, **prop, *posprop, *pospropt;
4490: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4491: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4492: double agebegin, ageend;
4493:
4494: pp=vector(1,nlstate);
1.251 brouard 4495: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4496: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4497: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4498: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4499: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4500: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4501: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4502: meanqt=matrix(1,lastpass,1,nqtveff);
4503: strcpy(fileresp,"P_");
4504: strcat(fileresp,fileresu);
4505: /*strcat(fileresphtm,fileresu);*/
4506: if((ficresp=fopen(fileresp,"w"))==NULL) {
4507: printf("Problem with prevalence resultfile: %s\n", fileresp);
4508: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4509: exit(0);
4510: }
1.240 brouard 4511:
1.226 brouard 4512: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4513: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4514: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4515: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4516: fflush(ficlog);
4517: exit(70);
4518: }
4519: else{
4520: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4521: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4522: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4523: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4524: }
1.237 brouard 4525: 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 4526:
1.226 brouard 4527: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4528: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4529: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4530: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4531: fflush(ficlog);
4532: exit(70);
1.240 brouard 4533: } else{
1.226 brouard 4534: 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 4535: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4536: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4537: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4538: }
1.240 brouard 4539: 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);
4540:
1.253 brouard 4541: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4542: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4543: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4544: j1=0;
1.126 brouard 4545:
1.227 brouard 4546: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4547: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4548: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4549:
4550:
1.226 brouard 4551: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4552: reference=low_education V1=0,V2=0
4553: med_educ V1=1 V2=0,
4554: high_educ V1=0 V2=1
4555: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4556: */
1.249 brouard 4557: dateintsum=0;
4558: k2cpt=0;
4559:
1.253 brouard 4560: if(cptcoveff == 0 )
1.265 brouard 4561: nl=1; /* Constant and age model only */
1.253 brouard 4562: else
4563: nl=2;
1.265 brouard 4564:
4565: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4566: /* Loop on nj=1 or 2 if dummy covariates j!=0
4567: * Loop on j1(1 to 2**cptcoveff) covariate combination
4568: * freq[s1][s2][iage] =0.
4569: * Loop on iind
4570: * ++freq[s1][s2][iage] weighted
4571: * end iind
4572: * if covariate and j!0
4573: * headers Variable on one line
4574: * endif cov j!=0
4575: * header of frequency table by age
4576: * Loop on age
4577: * pp[s1]+=freq[s1][s2][iage] weighted
4578: * pos+=freq[s1][s2][iage] weighted
4579: * Loop on s1 initial state
4580: * fprintf(ficresp
4581: * end s1
4582: * end age
4583: * if j!=0 computes starting values
4584: * end compute starting values
4585: * end j1
4586: * end nl
4587: */
1.253 brouard 4588: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4589: if(nj==1)
4590: j=0; /* First pass for the constant */
1.265 brouard 4591: else{
1.253 brouard 4592: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4593: }
1.251 brouard 4594: first=1;
1.265 brouard 4595: 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 4596: posproptt=0.;
4597: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4598: scanf("%d", i);*/
4599: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4600: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4601: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4602: freq[i][s2][m]=0;
1.251 brouard 4603:
4604: for (i=1; i<=nlstate; i++) {
1.240 brouard 4605: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4606: prop[i][m]=0;
4607: posprop[i]=0;
4608: pospropt[i]=0;
4609: }
1.283 brouard 4610: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4611: idq[z1]=0.;
4612: meanq[z1]=0.;
4613: stdq[z1]=0.;
1.283 brouard 4614: }
4615: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4616: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4617: /* meanqt[m][z1]=0.; */
4618: /* } */
4619: /* } */
1.251 brouard 4620: /* dateintsum=0; */
4621: /* k2cpt=0; */
4622:
1.265 brouard 4623: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4624: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4625: bool=1;
4626: if(j !=0){
4627: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4628: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4629: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4630: /* if(Tvaraff[z1] ==-20){ */
4631: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4632: /* }else if(Tvaraff[z1] ==-10){ */
4633: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4634: /* }else */
4635: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4636: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4637: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4638: /* 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",
4639: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4640: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4641: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4642: } /* Onlyf fixed */
4643: } /* end z1 */
4644: } /* cptcovn > 0 */
4645: } /* end any */
4646: }/* end j==0 */
1.265 brouard 4647: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4648: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4649: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4650: m=mw[mi][iind];
4651: if(j!=0){
4652: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4653: for (z1=1; z1<=cptcoveff; z1++) {
4654: if( Fixed[Tmodelind[z1]]==1){
4655: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4656: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4657: value is -1, we don't select. It differs from the
4658: constant and age model which counts them. */
4659: bool=0; /* not selected */
4660: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4661: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4662: bool=0;
4663: }
4664: }
4665: }
4666: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4667: } /* end j==0 */
4668: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4669: if(bool==1){ /*Selected */
1.251 brouard 4670: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4671: and mw[mi+1][iind]. dh depends on stepm. */
4672: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4673: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4674: if(m >=firstpass && m <=lastpass){
4675: k2=anint[m][iind]+(mint[m][iind]/12.);
4676: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4677: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4678: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4679: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4680: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4681: if (m<lastpass) {
4682: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4683: /* 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]); */
4684: if(s[m][iind]==-1)
4685: 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.));
4686: 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 4687: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4688: idq[z1]=idq[z1]+weight[iind];
4689: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4690: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4691: }
1.251 brouard 4692: /* if((int)agev[m][iind] == 55) */
4693: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4694: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4695: 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 4696: }
1.251 brouard 4697: } /* end if between passes */
4698: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4699: dateintsum=dateintsum+k2; /* on all covariates ?*/
4700: k2cpt++;
4701: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4702: }
1.251 brouard 4703: }else{
4704: bool=1;
4705: }/* end bool 2 */
4706: } /* end m */
1.284 brouard 4707: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4708: /* idq[z1]=idq[z1]+weight[iind]; */
4709: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4710: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4711: /* } */
1.251 brouard 4712: } /* end bool */
4713: } /* end iind = 1 to imx */
4714: /* prop[s][age] is feeded for any initial and valid live state as well as
4715: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4716:
4717:
4718: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4719: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4720: pstamp(ficresp);
1.251 brouard 4721: if (cptcoveff>0 && j!=0){
1.265 brouard 4722: pstamp(ficresp);
1.251 brouard 4723: printf( "\n#********** Variable ");
4724: fprintf(ficresp, "\n#********** Variable ");
4725: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4726: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4727: fprintf(ficlog, "\n#********** Variable ");
4728: for (z1=1; z1<=cptcoveff; z1++){
4729: if(!FixedV[Tvaraff[z1]]){
4730: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4731: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4732: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4733: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4734: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4735: }else{
1.251 brouard 4736: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4737: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4738: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4739: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4740: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4741: }
4742: }
4743: printf( "**********\n#");
4744: fprintf(ficresp, "**********\n#");
4745: fprintf(ficresphtm, "**********</h3>\n");
4746: fprintf(ficresphtmfr, "**********</h3>\n");
4747: fprintf(ficlog, "**********\n");
4748: }
1.284 brouard 4749: /*
4750: Printing means of quantitative variables if any
4751: */
4752: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4753: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4754: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4755: if(weightopt==1){
4756: printf(" Weighted mean and standard deviation of");
4757: fprintf(ficlog," Weighted mean and standard deviation of");
4758: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4759: }
1.285 brouard 4760: 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]));
4761: 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]));
4762: 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 4763: }
4764: /* for (z1=1; z1<= nqtveff; z1++) { */
4765: /* for(m=1;m<=lastpass;m++){ */
4766: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4767: /* } */
4768: /* } */
1.283 brouard 4769:
1.251 brouard 4770: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4771: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4772: fprintf(ficresp, " Age");
4773: 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 4774: for(i=1; i<=nlstate;i++) {
1.265 brouard 4775: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4776: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4777: }
1.265 brouard 4778: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4779: fprintf(ficresphtm, "\n");
4780:
4781: /* Header of frequency table by age */
4782: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4783: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4784: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4785: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4786: if(s2!=0 && m!=0)
4787: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4788: }
1.226 brouard 4789: }
1.251 brouard 4790: fprintf(ficresphtmfr, "\n");
4791:
4792: /* For each age */
4793: for(iage=iagemin; iage <= iagemax+3; iage++){
4794: fprintf(ficresphtm,"<tr>");
4795: if(iage==iagemax+1){
4796: fprintf(ficlog,"1");
4797: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4798: }else if(iage==iagemax+2){
4799: fprintf(ficlog,"0");
4800: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4801: }else if(iage==iagemax+3){
4802: fprintf(ficlog,"Total");
4803: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4804: }else{
1.240 brouard 4805: if(first==1){
1.251 brouard 4806: first=0;
4807: printf("See log file for details...\n");
4808: }
4809: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4810: fprintf(ficlog,"Age %d", iage);
4811: }
1.265 brouard 4812: for(s1=1; s1 <=nlstate ; s1++){
4813: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4814: pp[s1] += freq[s1][m][iage];
1.251 brouard 4815: }
1.265 brouard 4816: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4817: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4818: pos += freq[s1][m][iage];
4819: if(pp[s1]>=1.e-10){
1.251 brouard 4820: if(first==1){
1.265 brouard 4821: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4822: }
1.265 brouard 4823: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4824: }else{
4825: if(first==1)
1.265 brouard 4826: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4827: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4828: }
4829: }
4830:
1.265 brouard 4831: for(s1=1; s1 <=nlstate ; s1++){
4832: /* posprop[s1]=0; */
4833: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4834: pp[s1] += freq[s1][m][iage];
4835: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4836:
4837: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4838: pos += pp[s1]; /* pos is the total number of transitions until this age */
4839: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4840: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4841: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4842: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4843: }
4844:
4845: /* Writing ficresp */
4846: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4847: if( iage <= iagemax){
4848: fprintf(ficresp," %d",iage);
4849: }
4850: }else if( nj==2){
4851: if( iage <= iagemax){
4852: fprintf(ficresp," %d",iage);
4853: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4854: }
1.240 brouard 4855: }
1.265 brouard 4856: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4857: if(pos>=1.e-5){
1.251 brouard 4858: if(first==1)
1.265 brouard 4859: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4860: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4861: }else{
4862: if(first==1)
1.265 brouard 4863: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4864: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4865: }
4866: if( iage <= iagemax){
4867: if(pos>=1.e-5){
1.265 brouard 4868: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4869: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4870: }else if( nj==2){
4871: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4872: }
4873: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4874: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4875: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4876: } else{
4877: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4878: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4879: }
1.240 brouard 4880: }
1.265 brouard 4881: pospropt[s1] +=posprop[s1];
4882: } /* end loop s1 */
1.251 brouard 4883: /* pospropt=0.; */
1.265 brouard 4884: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4885: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4886: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4887: if(first==1){
1.265 brouard 4888: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4889: }
1.265 brouard 4890: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4891: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4892: }
1.265 brouard 4893: if(s1!=0 && m!=0)
4894: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4895: }
1.265 brouard 4896: } /* end loop s1 */
1.251 brouard 4897: posproptt=0.;
1.265 brouard 4898: for(s1=1; s1 <=nlstate; s1++){
4899: posproptt += pospropt[s1];
1.251 brouard 4900: }
4901: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4902: fprintf(ficresphtm,"</tr>\n");
4903: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4904: if(iage <= iagemax)
4905: fprintf(ficresp,"\n");
1.240 brouard 4906: }
1.251 brouard 4907: if(first==1)
4908: printf("Others in log...\n");
4909: fprintf(ficlog,"\n");
4910: } /* end loop age iage */
1.265 brouard 4911:
1.251 brouard 4912: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4913: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4914: if(posproptt < 1.e-5){
1.265 brouard 4915: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4916: }else{
1.265 brouard 4917: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4918: }
1.226 brouard 4919: }
1.251 brouard 4920: fprintf(ficresphtm,"</tr>\n");
4921: fprintf(ficresphtm,"</table>\n");
4922: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4923: if(posproptt < 1.e-5){
1.251 brouard 4924: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4925: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4926: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4927: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4928: invalidvarcomb[j1]=1;
1.226 brouard 4929: }else{
1.251 brouard 4930: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4931: invalidvarcomb[j1]=0;
1.226 brouard 4932: }
1.251 brouard 4933: fprintf(ficresphtmfr,"</table>\n");
4934: fprintf(ficlog,"\n");
4935: if(j!=0){
4936: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4937: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4938: for(k=1; k <=(nlstate+ndeath); k++){
4939: if (k != i) {
1.265 brouard 4940: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4941: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4942: if(j1==1){ /* All dummy covariates to zero */
4943: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4944: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4945: printf("%d%d ",i,k);
4946: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4947: 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]));
4948: 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]));
4949: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4950: }
1.253 brouard 4951: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4952: for(iage=iagemin; iage <= iagemax+3; iage++){
4953: x[iage]= (double)iage;
4954: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4955: /* 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 4956: }
1.268 brouard 4957: /* Some are not finite, but linreg will ignore these ages */
4958: no=0;
1.253 brouard 4959: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4960: pstart[s1]=b;
4961: pstart[s1-1]=a;
1.252 brouard 4962: }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 */
4963: 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]);
4964: 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 4965: 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 4966: printf("%d%d ",i,k);
4967: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4968: 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 4969: }else{ /* Other cases, like quantitative fixed or varying covariates */
4970: ;
4971: }
4972: /* printf("%12.7f )", param[i][jj][k]); */
4973: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4974: s1++;
1.251 brouard 4975: } /* end jj */
4976: } /* end k!= i */
4977: } /* end k */
1.265 brouard 4978: } /* end i, s1 */
1.251 brouard 4979: } /* end j !=0 */
4980: } /* end selected combination of covariate j1 */
4981: if(j==0){ /* We can estimate starting values from the occurences in each case */
4982: printf("#Freqsummary: Starting values for the constants:\n");
4983: fprintf(ficlog,"\n");
1.265 brouard 4984: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4985: for(k=1; k <=(nlstate+ndeath); k++){
4986: if (k != i) {
4987: printf("%d%d ",i,k);
4988: fprintf(ficlog,"%d%d ",i,k);
4989: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4990: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4991: if(jj==1){ /* Age has to be done */
1.265 brouard 4992: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4993: 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]));
4994: 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 4995: }
4996: /* printf("%12.7f )", param[i][jj][k]); */
4997: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4998: s1++;
1.250 brouard 4999: }
1.251 brouard 5000: printf("\n");
5001: fprintf(ficlog,"\n");
1.250 brouard 5002: }
5003: }
1.284 brouard 5004: } /* end of state i */
1.251 brouard 5005: printf("#Freqsummary\n");
5006: fprintf(ficlog,"\n");
1.265 brouard 5007: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5008: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5009: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5010: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5011: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5012: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5013: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5014: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5015: /* } */
5016: }
1.265 brouard 5017: } /* end loop s1 */
1.251 brouard 5018:
5019: printf("\n");
5020: fprintf(ficlog,"\n");
5021: } /* end j=0 */
1.249 brouard 5022: } /* end j */
1.252 brouard 5023:
1.253 brouard 5024: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5025: for(i=1, jk=1; i <=nlstate; i++){
5026: for(j=1; j <=nlstate+ndeath; j++){
5027: if(j!=i){
5028: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5029: printf("%1d%1d",i,j);
5030: fprintf(ficparo,"%1d%1d",i,j);
5031: for(k=1; k<=ncovmodel;k++){
5032: /* printf(" %lf",param[i][j][k]); */
5033: /* fprintf(ficparo," %lf",param[i][j][k]); */
5034: p[jk]=pstart[jk];
5035: printf(" %f ",pstart[jk]);
5036: fprintf(ficparo," %f ",pstart[jk]);
5037: jk++;
5038: }
5039: printf("\n");
5040: fprintf(ficparo,"\n");
5041: }
5042: }
5043: }
5044: } /* end mle=-2 */
1.226 brouard 5045: dateintmean=dateintsum/k2cpt;
1.296 brouard 5046: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5047:
1.226 brouard 5048: fclose(ficresp);
5049: fclose(ficresphtm);
5050: fclose(ficresphtmfr);
1.283 brouard 5051: free_vector(idq,1,nqfveff);
1.226 brouard 5052: free_vector(meanq,1,nqfveff);
1.284 brouard 5053: free_vector(stdq,1,nqfveff);
1.226 brouard 5054: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5055: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5056: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5057: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5058: free_vector(pospropt,1,nlstate);
5059: free_vector(posprop,1,nlstate);
1.251 brouard 5060: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5061: free_vector(pp,1,nlstate);
5062: /* End of freqsummary */
5063: }
1.126 brouard 5064:
1.268 brouard 5065: /* Simple linear regression */
5066: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5067:
5068: /* y=a+bx regression */
5069: double sumx = 0.0; /* sum of x */
5070: double sumx2 = 0.0; /* sum of x**2 */
5071: double sumxy = 0.0; /* sum of x * y */
5072: double sumy = 0.0; /* sum of y */
5073: double sumy2 = 0.0; /* sum of y**2 */
5074: double sume2 = 0.0; /* sum of square or residuals */
5075: double yhat;
5076:
5077: double denom=0;
5078: int i;
5079: int ne=*no;
5080:
5081: for ( i=ifi, ne=0;i<=ila;i++) {
5082: if(!isfinite(x[i]) || !isfinite(y[i])){
5083: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5084: continue;
5085: }
5086: ne=ne+1;
5087: sumx += x[i];
5088: sumx2 += x[i]*x[i];
5089: sumxy += x[i] * y[i];
5090: sumy += y[i];
5091: sumy2 += y[i]*y[i];
5092: denom = (ne * sumx2 - sumx*sumx);
5093: /* 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); */
5094: }
5095:
5096: denom = (ne * sumx2 - sumx*sumx);
5097: if (denom == 0) {
5098: // vertical, slope m is infinity
5099: *b = INFINITY;
5100: *a = 0;
5101: if (r) *r = 0;
5102: return 1;
5103: }
5104:
5105: *b = (ne * sumxy - sumx * sumy) / denom;
5106: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5107: if (r!=NULL) {
5108: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5109: sqrt((sumx2 - sumx*sumx/ne) *
5110: (sumy2 - sumy*sumy/ne));
5111: }
5112: *no=ne;
5113: for ( i=ifi, ne=0;i<=ila;i++) {
5114: if(!isfinite(x[i]) || !isfinite(y[i])){
5115: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5116: continue;
5117: }
5118: ne=ne+1;
5119: yhat = y[i] - *a -*b* x[i];
5120: sume2 += yhat * yhat ;
5121:
5122: denom = (ne * sumx2 - sumx*sumx);
5123: /* 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); */
5124: }
5125: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5126: *sa= *sb * sqrt(sumx2/ne);
5127:
5128: return 0;
5129: }
5130:
1.126 brouard 5131: /************ Prevalence ********************/
1.227 brouard 5132: 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)
5133: {
5134: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5135: in each health status at the date of interview (if between dateprev1 and dateprev2).
5136: We still use firstpass and lastpass as another selection.
5137: */
1.126 brouard 5138:
1.227 brouard 5139: int i, m, jk, j1, bool, z1,j, iv;
5140: int mi; /* Effective wave */
5141: int iage;
5142: double agebegin, ageend;
5143:
5144: double **prop;
5145: double posprop;
5146: double y2; /* in fractional years */
5147: int iagemin, iagemax;
5148: int first; /** to stop verbosity which is redirected to log file */
5149:
5150: iagemin= (int) agemin;
5151: iagemax= (int) agemax;
5152: /*pp=vector(1,nlstate);*/
1.251 brouard 5153: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5154: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5155: j1=0;
1.222 brouard 5156:
1.227 brouard 5157: /*j=cptcoveff;*/
5158: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5159:
1.288 brouard 5160: first=0;
1.227 brouard 5161: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5162: for (i=1; i<=nlstate; i++)
1.251 brouard 5163: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5164: prop[i][iage]=0.0;
5165: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5166: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5167: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5168:
5169: for (i=1; i<=imx; i++) { /* Each individual */
5170: bool=1;
5171: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5172: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5173: m=mw[mi][i];
5174: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5175: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5176: for (z1=1; z1<=cptcoveff; z1++){
5177: if( Fixed[Tmodelind[z1]]==1){
5178: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5179: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5180: bool=0;
5181: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5182: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5183: bool=0;
5184: }
5185: }
5186: if(bool==1){ /* Otherwise we skip that wave/person */
5187: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5188: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5189: if(m >=firstpass && m <=lastpass){
5190: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5191: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5192: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5193: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5194: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5195: 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);
5196: exit(1);
5197: }
5198: if (s[m][i]>0 && s[m][i]<=nlstate) {
5199: /*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]]);*/
5200: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5201: prop[s[m][i]][iagemax+3] += weight[i];
5202: } /* end valid statuses */
5203: } /* end selection of dates */
5204: } /* end selection of waves */
5205: } /* end bool */
5206: } /* end wave */
5207: } /* end individual */
5208: for(i=iagemin; i <= iagemax+3; i++){
5209: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5210: posprop += prop[jk][i];
5211: }
5212:
5213: for(jk=1; jk <=nlstate ; jk++){
5214: if( i <= iagemax){
5215: if(posprop>=1.e-5){
5216: probs[i][jk][j1]= prop[jk][i]/posprop;
5217: } else{
1.288 brouard 5218: if(!first){
5219: first=1;
1.266 brouard 5220: 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]);
5221: }else{
1.288 brouard 5222: 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 5223: }
5224: }
5225: }
5226: }/* end jk */
5227: }/* end i */
1.222 brouard 5228: /*} *//* end i1 */
1.227 brouard 5229: } /* end j1 */
1.222 brouard 5230:
1.227 brouard 5231: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5232: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5233: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5234: } /* End of prevalence */
1.126 brouard 5235:
5236: /************* Waves Concatenation ***************/
5237:
5238: 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)
5239: {
1.298 brouard 5240: /* 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 5241: Death is a valid wave (if date is known).
5242: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5243: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5244: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5245: */
1.126 brouard 5246:
1.224 brouard 5247: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5248: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5249: double sum=0., jmean=0.;*/
1.224 brouard 5250: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5251: int j, k=0,jk, ju, jl;
5252: double sum=0.;
5253: first=0;
1.214 brouard 5254: firstwo=0;
1.217 brouard 5255: firsthree=0;
1.218 brouard 5256: firstfour=0;
1.164 brouard 5257: jmin=100000;
1.126 brouard 5258: jmax=-1;
5259: jmean=0.;
1.224 brouard 5260:
5261: /* Treating live states */
1.214 brouard 5262: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5263: mi=0; /* First valid wave */
1.227 brouard 5264: mli=0; /* Last valid wave */
1.126 brouard 5265: m=firstpass;
1.214 brouard 5266: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5267: 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 */
5268: mli=m-1;/* mw[++mi][i]=m-1; */
5269: }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 */
5270: mw[++mi][i]=m;
5271: mli=m;
1.224 brouard 5272: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5273: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5274: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5275: }
1.227 brouard 5276: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5277: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5278: break;
1.224 brouard 5279: #else
1.227 brouard 5280: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5281: if(firsthree == 0){
1.302 brouard 5282: 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 5283: firsthree=1;
5284: }
1.302 brouard 5285: 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);
1.227 brouard 5286: mw[++mi][i]=m;
5287: mli=m;
5288: }
5289: if(s[m][i]==-2){ /* Vital status is really unknown */
5290: nbwarn++;
5291: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5292: 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);
5293: 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);
5294: }
5295: break;
5296: }
5297: break;
1.224 brouard 5298: #endif
1.227 brouard 5299: }/* End m >= lastpass */
1.126 brouard 5300: }/* end while */
1.224 brouard 5301:
1.227 brouard 5302: /* 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 5303: /* After last pass */
1.224 brouard 5304: /* Treating death states */
1.214 brouard 5305: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5306: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5307: /* } */
1.126 brouard 5308: mi++; /* Death is another wave */
5309: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5310: /* Only death is a correct wave */
1.126 brouard 5311: mw[mi][i]=m;
1.257 brouard 5312: } /* else not in a death state */
1.224 brouard 5313: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5314: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5315: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5316: if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
5317: nbwarn++;
5318: if(firstfiv==0){
5319: printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
5320: firstfiv=1;
5321: }else{
5322: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %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 );
5323: }
5324: }else{ /* Death occured afer last wave potential bias */
5325: nberr++;
5326: if(firstwo==0){
1.257 brouard 5327: printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). 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], i,m );
1.227 brouard 5328: firstwo=1;
5329: }
1.257 brouard 5330: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%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. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
1.227 brouard 5331: }
1.257 brouard 5332: }else{ /* if date of interview is unknown */
1.227 brouard 5333: /* death is known but not confirmed by death status at any wave */
5334: if(firstfour==0){
5335: 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. 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], i,m );
5336: firstfour=1;
5337: }
5338: 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. 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], i,m );
1.214 brouard 5339: }
1.224 brouard 5340: } /* end if date of death is known */
5341: #endif
5342: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5343: /* wav[i]=mw[mi][i]; */
1.126 brouard 5344: if(mi==0){
5345: nbwarn++;
5346: if(first==0){
1.227 brouard 5347: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5348: first=1;
1.126 brouard 5349: }
5350: if(first==1){
1.227 brouard 5351: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5352: }
5353: } /* end mi==0 */
5354: } /* End individuals */
1.214 brouard 5355: /* wav and mw are no more changed */
1.223 brouard 5356:
1.214 brouard 5357:
1.126 brouard 5358: for(i=1; i<=imx; i++){
5359: for(mi=1; mi<wav[i];mi++){
5360: if (stepm <=0)
1.227 brouard 5361: dh[mi][i]=1;
1.126 brouard 5362: else{
1.260 brouard 5363: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5364: if (agedc[i] < 2*AGESUP) {
5365: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5366: if(j==0) j=1; /* Survives at least one month after exam */
5367: else if(j<0){
5368: nberr++;
5369: 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]);
5370: j=1; /* Temporary Dangerous patch */
5371: 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);
5372: 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]);
5373: 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);
5374: }
5375: k=k+1;
5376: if (j >= jmax){
5377: jmax=j;
5378: ijmax=i;
5379: }
5380: if (j <= jmin){
5381: jmin=j;
5382: ijmin=i;
5383: }
5384: sum=sum+j;
5385: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5386: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5387: }
5388: }
5389: else{
5390: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5391: /* 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 5392:
1.227 brouard 5393: k=k+1;
5394: if (j >= jmax) {
5395: jmax=j;
5396: ijmax=i;
5397: }
5398: else if (j <= jmin){
5399: jmin=j;
5400: ijmin=i;
5401: }
5402: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5403: /*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]);*/
5404: if(j<0){
5405: nberr++;
5406: 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]);
5407: 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]);
5408: }
5409: sum=sum+j;
5410: }
5411: jk= j/stepm;
5412: jl= j -jk*stepm;
5413: ju= j -(jk+1)*stepm;
5414: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5415: if(jl==0){
5416: dh[mi][i]=jk;
5417: bh[mi][i]=0;
5418: }else{ /* We want a negative bias in order to only have interpolation ie
5419: * to avoid the price of an extra matrix product in likelihood */
5420: dh[mi][i]=jk+1;
5421: bh[mi][i]=ju;
5422: }
5423: }else{
5424: if(jl <= -ju){
5425: dh[mi][i]=jk;
5426: bh[mi][i]=jl; /* bias is positive if real duration
5427: * is higher than the multiple of stepm and negative otherwise.
5428: */
5429: }
5430: else{
5431: dh[mi][i]=jk+1;
5432: bh[mi][i]=ju;
5433: }
5434: if(dh[mi][i]==0){
5435: dh[mi][i]=1; /* At least one step */
5436: bh[mi][i]=ju; /* At least one step */
5437: /* 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);*/
5438: }
5439: } /* end if mle */
1.126 brouard 5440: }
5441: } /* end wave */
5442: }
5443: jmean=sum/k;
5444: 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 5445: 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 5446: }
1.126 brouard 5447:
5448: /*********** Tricode ****************************/
1.220 brouard 5449: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5450: {
5451: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5452: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5453: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5454: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5455: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5456: */
1.130 brouard 5457:
1.242 brouard 5458: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5459: int modmaxcovj=0; /* Modality max of covariates j */
5460: int cptcode=0; /* Modality max of covariates j */
5461: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5462:
5463:
1.242 brouard 5464: /* cptcoveff=0; */
5465: /* *cptcov=0; */
1.126 brouard 5466:
1.242 brouard 5467: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5468: for (k=1; k <= maxncov; k++)
5469: for(j=1; j<=2; j++)
5470: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5471:
1.242 brouard 5472: /* Loop on covariates without age and products and no quantitative variable */
5473: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5474: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5475: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5476: switch(Fixed[k]) {
5477: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5478: 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*/
5479: ij=(int)(covar[Tvar[k]][i]);
5480: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5481: * If product of Vn*Vm, still boolean *:
5482: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5483: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5484: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5485: modality of the nth covariate of individual i. */
5486: if (ij > modmaxcovj)
5487: modmaxcovj=ij;
5488: else if (ij < modmincovj)
5489: modmincovj=ij;
1.287 brouard 5490: if (ij <0 || ij >1 ){
5491: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5492: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5493: }
5494: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5495: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5496: exit(1);
5497: }else
5498: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5499: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5500: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5501: /* getting the maximum value of the modality of the covariate
5502: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5503: female ies 1, then modmaxcovj=1.
5504: */
5505: } /* end for loop on individuals i */
5506: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5507: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5508: cptcode=modmaxcovj;
5509: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5510: /*for (i=0; i<=cptcode; i++) {*/
5511: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5512: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5513: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5514: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5515: if( j != -1){
5516: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5517: covariate for which somebody answered excluding
5518: undefined. Usually 2: 0 and 1. */
5519: }
5520: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5521: covariate for which somebody answered including
5522: undefined. Usually 3: -1, 0 and 1. */
5523: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5524: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5525: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5526:
1.242 brouard 5527: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5528: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5529: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5530: /* modmincovj=3; modmaxcovj = 7; */
5531: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5532: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5533: /* defining two dummy variables: variables V1_1 and V1_2.*/
5534: /* nbcode[Tvar[j]][ij]=k; */
5535: /* nbcode[Tvar[j]][1]=0; */
5536: /* nbcode[Tvar[j]][2]=1; */
5537: /* nbcode[Tvar[j]][3]=2; */
5538: /* To be continued (not working yet). */
5539: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5540:
5541: /* 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*/
5542: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5543: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5544: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5545: /*, could be restored in the future */
5546: 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 5547: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5548: break;
5549: }
5550: ij++;
1.287 brouard 5551: 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 5552: cptcode = ij; /* New max modality for covar j */
5553: } /* end of loop on modality i=-1 to 1 or more */
5554: break;
5555: case 1: /* Testing on varying covariate, could be simple and
5556: * should look at waves or product of fixed *
5557: * varying. No time to test -1, assuming 0 and 1 only */
5558: ij=0;
5559: for(i=0; i<=1;i++){
5560: nbcode[Tvar[k]][++ij]=i;
5561: }
5562: break;
5563: default:
5564: break;
5565: } /* end switch */
5566: } /* end dummy test */
1.287 brouard 5567: } /* 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 5568:
5569: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5570: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5571: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5572: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5573: 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 */
5574: 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 */
5575: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5576: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5577:
5578: ij=0;
5579: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5580: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5581: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5582: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5583: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5584: /* If product not in single variable we don't print results */
5585: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5586: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5587: 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*/
5588: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5589: 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 */
5590: if(Fixed[k]!=0)
5591: anyvaryingduminmodel=1;
5592: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5593: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5594: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5595: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5596: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5597: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5598: }
5599: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5600: /* ij--; */
5601: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5602: *cptcov=ij; /*Number of total real effective covariates: effective
5603: * because they can be excluded from the model and real
5604: * if in the model but excluded because missing values, but how to get k from ij?*/
5605: for(j=ij+1; j<= cptcovt; j++){
5606: Tvaraff[j]=0;
5607: Tmodelind[j]=0;
5608: }
5609: for(j=ntveff+1; j<= cptcovt; j++){
5610: TmodelInvind[j]=0;
5611: }
5612: /* To be sorted */
5613: ;
5614: }
1.126 brouard 5615:
1.145 brouard 5616:
1.126 brouard 5617: /*********** Health Expectancies ****************/
5618:
1.235 brouard 5619: 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 5620:
5621: {
5622: /* Health expectancies, no variances */
1.164 brouard 5623: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5624: int nhstepma, nstepma; /* Decreasing with age */
5625: double age, agelim, hf;
5626: double ***p3mat;
5627: double eip;
5628:
1.238 brouard 5629: /* pstamp(ficreseij); */
1.126 brouard 5630: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5631: fprintf(ficreseij,"# Age");
5632: for(i=1; i<=nlstate;i++){
5633: for(j=1; j<=nlstate;j++){
5634: fprintf(ficreseij," e%1d%1d ",i,j);
5635: }
5636: fprintf(ficreseij," e%1d. ",i);
5637: }
5638: fprintf(ficreseij,"\n");
5639:
5640:
5641: if(estepm < stepm){
5642: printf ("Problem %d lower than %d\n",estepm, stepm);
5643: }
5644: else hstepm=estepm;
5645: /* We compute the life expectancy from trapezoids spaced every estepm months
5646: * This is mainly to measure the difference between two models: for example
5647: * if stepm=24 months pijx are given only every 2 years and by summing them
5648: * we are calculating an estimate of the Life Expectancy assuming a linear
5649: * progression in between and thus overestimating or underestimating according
5650: * to the curvature of the survival function. If, for the same date, we
5651: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5652: * to compare the new estimate of Life expectancy with the same linear
5653: * hypothesis. A more precise result, taking into account a more precise
5654: * curvature will be obtained if estepm is as small as stepm. */
5655:
5656: /* For example we decided to compute the life expectancy with the smallest unit */
5657: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5658: nhstepm is the number of hstepm from age to agelim
5659: nstepm is the number of stepm from age to agelin.
1.270 brouard 5660: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5661: and note for a fixed period like estepm months */
5662: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5663: survival function given by stepm (the optimization length). Unfortunately it
5664: means that if the survival funtion is printed only each two years of age and if
5665: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5666: results. So we changed our mind and took the option of the best precision.
5667: */
5668: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5669:
5670: agelim=AGESUP;
5671: /* If stepm=6 months */
5672: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5673: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5674:
5675: /* nhstepm age range expressed in number of stepm */
5676: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5677: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5678: /* if (stepm >= YEARM) hstepm=1;*/
5679: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5680: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5681:
5682: for (age=bage; age<=fage; age ++){
5683: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5684: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5685: /* if (stepm >= YEARM) hstepm=1;*/
5686: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5687:
5688: /* If stepm=6 months */
5689: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5690: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5691:
1.235 brouard 5692: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5693:
5694: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5695:
5696: printf("%d|",(int)age);fflush(stdout);
5697: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5698:
5699: /* Computing expectancies */
5700: for(i=1; i<=nlstate;i++)
5701: for(j=1; j<=nlstate;j++)
5702: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5703: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5704:
5705: /* 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]);*/
5706:
5707: }
5708:
5709: fprintf(ficreseij,"%3.0f",age );
5710: for(i=1; i<=nlstate;i++){
5711: eip=0;
5712: for(j=1; j<=nlstate;j++){
5713: eip +=eij[i][j][(int)age];
5714: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5715: }
5716: fprintf(ficreseij,"%9.4f", eip );
5717: }
5718: fprintf(ficreseij,"\n");
5719:
5720: }
5721: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5722: printf("\n");
5723: fprintf(ficlog,"\n");
5724:
5725: }
5726:
1.235 brouard 5727: 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 5728:
5729: {
5730: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5731: to initial status i, ei. .
1.126 brouard 5732: */
5733: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5734: int nhstepma, nstepma; /* Decreasing with age */
5735: double age, agelim, hf;
5736: double ***p3matp, ***p3matm, ***varhe;
5737: double **dnewm,**doldm;
5738: double *xp, *xm;
5739: double **gp, **gm;
5740: double ***gradg, ***trgradg;
5741: int theta;
5742:
5743: double eip, vip;
5744:
5745: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5746: xp=vector(1,npar);
5747: xm=vector(1,npar);
5748: dnewm=matrix(1,nlstate*nlstate,1,npar);
5749: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5750:
5751: pstamp(ficresstdeij);
5752: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5753: fprintf(ficresstdeij,"# Age");
5754: for(i=1; i<=nlstate;i++){
5755: for(j=1; j<=nlstate;j++)
5756: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5757: fprintf(ficresstdeij," e%1d. ",i);
5758: }
5759: fprintf(ficresstdeij,"\n");
5760:
5761: pstamp(ficrescveij);
5762: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5763: fprintf(ficrescveij,"# Age");
5764: for(i=1; i<=nlstate;i++)
5765: for(j=1; j<=nlstate;j++){
5766: cptj= (j-1)*nlstate+i;
5767: for(i2=1; i2<=nlstate;i2++)
5768: for(j2=1; j2<=nlstate;j2++){
5769: cptj2= (j2-1)*nlstate+i2;
5770: if(cptj2 <= cptj)
5771: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5772: }
5773: }
5774: fprintf(ficrescveij,"\n");
5775:
5776: if(estepm < stepm){
5777: printf ("Problem %d lower than %d\n",estepm, stepm);
5778: }
5779: else hstepm=estepm;
5780: /* We compute the life expectancy from trapezoids spaced every estepm months
5781: * This is mainly to measure the difference between two models: for example
5782: * if stepm=24 months pijx are given only every 2 years and by summing them
5783: * we are calculating an estimate of the Life Expectancy assuming a linear
5784: * progression in between and thus overestimating or underestimating according
5785: * to the curvature of the survival function. If, for the same date, we
5786: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5787: * to compare the new estimate of Life expectancy with the same linear
5788: * hypothesis. A more precise result, taking into account a more precise
5789: * curvature will be obtained if estepm is as small as stepm. */
5790:
5791: /* For example we decided to compute the life expectancy with the smallest unit */
5792: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5793: nhstepm is the number of hstepm from age to agelim
5794: nstepm is the number of stepm from age to agelin.
5795: Look at hpijx to understand the reason of that which relies in memory size
5796: and note for a fixed period like estepm months */
5797: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5798: survival function given by stepm (the optimization length). Unfortunately it
5799: means that if the survival funtion is printed only each two years of age and if
5800: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5801: results. So we changed our mind and took the option of the best precision.
5802: */
5803: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5804:
5805: /* If stepm=6 months */
5806: /* nhstepm age range expressed in number of stepm */
5807: agelim=AGESUP;
5808: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5809: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5810: /* if (stepm >= YEARM) hstepm=1;*/
5811: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5812:
5813: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5814: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5815: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5816: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5817: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5818: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5819:
5820: for (age=bage; age<=fage; age ++){
5821: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5822: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5823: /* if (stepm >= YEARM) hstepm=1;*/
5824: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5825:
1.126 brouard 5826: /* If stepm=6 months */
5827: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5828: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5829:
5830: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5831:
1.126 brouard 5832: /* Computing Variances of health expectancies */
5833: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5834: decrease memory allocation */
5835: for(theta=1; theta <=npar; theta++){
5836: for(i=1; i<=npar; i++){
1.222 brouard 5837: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5838: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5839: }
1.235 brouard 5840: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5841: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5842:
1.126 brouard 5843: for(j=1; j<= nlstate; j++){
1.222 brouard 5844: for(i=1; i<=nlstate; i++){
5845: for(h=0; h<=nhstepm-1; h++){
5846: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5847: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5848: }
5849: }
1.126 brouard 5850: }
1.218 brouard 5851:
1.126 brouard 5852: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5853: for(h=0; h<=nhstepm-1; h++){
5854: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5855: }
1.126 brouard 5856: }/* End theta */
5857:
5858:
5859: for(h=0; h<=nhstepm-1; h++)
5860: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5861: for(theta=1; theta <=npar; theta++)
5862: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5863:
1.218 brouard 5864:
1.222 brouard 5865: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5866: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5867: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5868:
1.222 brouard 5869: printf("%d|",(int)age);fflush(stdout);
5870: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5871: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5872: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5873: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5874: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5875: for(ij=1;ij<=nlstate*nlstate;ij++)
5876: for(ji=1;ji<=nlstate*nlstate;ji++)
5877: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5878: }
5879: }
1.218 brouard 5880:
1.126 brouard 5881: /* Computing expectancies */
1.235 brouard 5882: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5883: for(i=1; i<=nlstate;i++)
5884: for(j=1; j<=nlstate;j++)
1.222 brouard 5885: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5886: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5887:
1.222 brouard 5888: /* 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 5889:
1.222 brouard 5890: }
1.269 brouard 5891:
5892: /* Standard deviation of expectancies ij */
1.126 brouard 5893: fprintf(ficresstdeij,"%3.0f",age );
5894: for(i=1; i<=nlstate;i++){
5895: eip=0.;
5896: vip=0.;
5897: for(j=1; j<=nlstate;j++){
1.222 brouard 5898: eip += eij[i][j][(int)age];
5899: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5900: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5901: 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 5902: }
5903: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5904: }
5905: fprintf(ficresstdeij,"\n");
1.218 brouard 5906:
1.269 brouard 5907: /* Variance of expectancies ij */
1.126 brouard 5908: fprintf(ficrescveij,"%3.0f",age );
5909: for(i=1; i<=nlstate;i++)
5910: for(j=1; j<=nlstate;j++){
1.222 brouard 5911: cptj= (j-1)*nlstate+i;
5912: for(i2=1; i2<=nlstate;i2++)
5913: for(j2=1; j2<=nlstate;j2++){
5914: cptj2= (j2-1)*nlstate+i2;
5915: if(cptj2 <= cptj)
5916: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5917: }
1.126 brouard 5918: }
5919: fprintf(ficrescveij,"\n");
1.218 brouard 5920:
1.126 brouard 5921: }
5922: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5923: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5924: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5925: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5926: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5927: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5928: printf("\n");
5929: fprintf(ficlog,"\n");
1.218 brouard 5930:
1.126 brouard 5931: free_vector(xm,1,npar);
5932: free_vector(xp,1,npar);
5933: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5934: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5935: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5936: }
1.218 brouard 5937:
1.126 brouard 5938: /************ Variance ******************/
1.235 brouard 5939: 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 5940: {
1.279 brouard 5941: /** Variance of health expectancies
5942: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5943: * double **newm;
5944: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5945: */
1.218 brouard 5946:
5947: /* int movingaverage(); */
5948: double **dnewm,**doldm;
5949: double **dnewmp,**doldmp;
5950: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5951: int first=0;
1.218 brouard 5952: int k;
5953: double *xp;
1.279 brouard 5954: double **gp, **gm; /**< for var eij */
5955: double ***gradg, ***trgradg; /**< for var eij */
5956: double **gradgp, **trgradgp; /**< for var p point j */
5957: double *gpp, *gmp; /**< for var p point j */
5958: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5959: double ***p3mat;
5960: double age,agelim, hf;
5961: /* double ***mobaverage; */
5962: int theta;
5963: char digit[4];
5964: char digitp[25];
5965:
5966: char fileresprobmorprev[FILENAMELENGTH];
5967:
5968: if(popbased==1){
5969: if(mobilav!=0)
5970: strcpy(digitp,"-POPULBASED-MOBILAV_");
5971: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5972: }
5973: else
5974: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5975:
1.218 brouard 5976: /* if (mobilav!=0) { */
5977: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5978: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5979: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5980: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5981: /* } */
5982: /* } */
5983:
5984: strcpy(fileresprobmorprev,"PRMORPREV-");
5985: sprintf(digit,"%-d",ij);
5986: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5987: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5988: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5989: strcat(fileresprobmorprev,fileresu);
5990: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5991: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5992: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5993: }
5994: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5995: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5996: pstamp(ficresprobmorprev);
5997: 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 5998: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5999: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
6000: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
6001: }
6002: for(j=1;j<=cptcoveff;j++)
6003: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
6004: fprintf(ficresprobmorprev,"\n");
6005:
1.218 brouard 6006: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6007: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6008: fprintf(ficresprobmorprev," p.%-d SE",j);
6009: for(i=1; i<=nlstate;i++)
6010: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6011: }
6012: fprintf(ficresprobmorprev,"\n");
6013:
6014: fprintf(ficgp,"\n# Routine varevsij");
6015: fprintf(ficgp,"\nunset title \n");
6016: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6017: 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");
6018: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6019:
1.218 brouard 6020: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6021: pstamp(ficresvij);
6022: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6023: if(popbased==1)
6024: 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);
6025: else
6026: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6027: fprintf(ficresvij,"# Age");
6028: for(i=1; i<=nlstate;i++)
6029: for(j=1; j<=nlstate;j++)
6030: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6031: fprintf(ficresvij,"\n");
6032:
6033: xp=vector(1,npar);
6034: dnewm=matrix(1,nlstate,1,npar);
6035: doldm=matrix(1,nlstate,1,nlstate);
6036: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6037: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6038:
6039: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6040: gpp=vector(nlstate+1,nlstate+ndeath);
6041: gmp=vector(nlstate+1,nlstate+ndeath);
6042: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6043:
1.218 brouard 6044: if(estepm < stepm){
6045: printf ("Problem %d lower than %d\n",estepm, stepm);
6046: }
6047: else hstepm=estepm;
6048: /* For example we decided to compute the life expectancy with the smallest unit */
6049: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6050: nhstepm is the number of hstepm from age to agelim
6051: nstepm is the number of stepm from age to agelim.
6052: Look at function hpijx to understand why because of memory size limitations,
6053: we decided (b) to get a life expectancy respecting the most precise curvature of the
6054: survival function given by stepm (the optimization length). Unfortunately it
6055: means that if the survival funtion is printed every two years of age and if
6056: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6057: results. So we changed our mind and took the option of the best precision.
6058: */
6059: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6060: agelim = AGESUP;
6061: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6062: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6063: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6064: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6065: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6066: gp=matrix(0,nhstepm,1,nlstate);
6067: gm=matrix(0,nhstepm,1,nlstate);
6068:
6069:
6070: for(theta=1; theta <=npar; theta++){
6071: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6072: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6073: }
1.279 brouard 6074: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6075: * returns into prlim .
1.288 brouard 6076: */
1.242 brouard 6077: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6078:
6079: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6080: if (popbased==1) {
6081: if(mobilav ==0){
6082: for(i=1; i<=nlstate;i++)
6083: prlim[i][i]=probs[(int)age][i][ij];
6084: }else{ /* mobilav */
6085: for(i=1; i<=nlstate;i++)
6086: prlim[i][i]=mobaverage[(int)age][i][ij];
6087: }
6088: }
1.295 brouard 6089: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6090: */
6091: 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 6092: /**< 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 6093: * at horizon h in state j including mortality.
6094: */
1.218 brouard 6095: for(j=1; j<= nlstate; j++){
6096: for(h=0; h<=nhstepm; h++){
6097: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6098: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6099: }
6100: }
1.279 brouard 6101: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6102: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6103: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6104: */
6105: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6106: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6107: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6108: }
6109:
6110: /* Again with minus shift */
1.218 brouard 6111:
6112: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6113: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6114:
1.242 brouard 6115: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6116:
6117: if (popbased==1) {
6118: if(mobilav ==0){
6119: for(i=1; i<=nlstate;i++)
6120: prlim[i][i]=probs[(int)age][i][ij];
6121: }else{ /* mobilav */
6122: for(i=1; i<=nlstate;i++)
6123: prlim[i][i]=mobaverage[(int)age][i][ij];
6124: }
6125: }
6126:
1.235 brouard 6127: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6128:
6129: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6130: for(h=0; h<=nhstepm; h++){
6131: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6132: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6133: }
6134: }
6135: /* This for computing probability of death (h=1 means
6136: computed over hstepm matrices product = hstepm*stepm months)
6137: as a weighted average of prlim.
6138: */
6139: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6140: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6141: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6142: }
1.279 brouard 6143: /* end shifting computations */
6144:
6145: /**< Computing gradient matrix at horizon h
6146: */
1.218 brouard 6147: for(j=1; j<= nlstate; j++) /* vareij */
6148: for(h=0; h<=nhstepm; h++){
6149: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6150: }
1.279 brouard 6151: /**< Gradient of overall mortality p.3 (or p.j)
6152: */
6153: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6154: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6155: }
6156:
6157: } /* End theta */
1.279 brouard 6158:
6159: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6160: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6161:
6162: for(h=0; h<=nhstepm; h++) /* veij */
6163: for(j=1; j<=nlstate;j++)
6164: for(theta=1; theta <=npar; theta++)
6165: trgradg[h][j][theta]=gradg[h][theta][j];
6166:
6167: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6168: for(theta=1; theta <=npar; theta++)
6169: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6170: /**< as well as its transposed matrix
6171: */
1.218 brouard 6172:
6173: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6174: for(i=1;i<=nlstate;i++)
6175: for(j=1;j<=nlstate;j++)
6176: vareij[i][j][(int)age] =0.;
1.279 brouard 6177:
6178: /* Computing trgradg by matcov by gradg at age and summing over h
6179: * and k (nhstepm) formula 15 of article
6180: * Lievre-Brouard-Heathcote
6181: */
6182:
1.218 brouard 6183: for(h=0;h<=nhstepm;h++){
6184: for(k=0;k<=nhstepm;k++){
6185: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6186: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6187: for(i=1;i<=nlstate;i++)
6188: for(j=1;j<=nlstate;j++)
6189: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6190: }
6191: }
6192:
1.279 brouard 6193: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6194: * p.j overall mortality formula 49 but computed directly because
6195: * we compute the grad (wix pijx) instead of grad (pijx),even if
6196: * wix is independent of theta.
6197: */
1.218 brouard 6198: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6199: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6200: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6201: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6202: varppt[j][i]=doldmp[j][i];
6203: /* end ppptj */
6204: /* x centered again */
6205:
1.242 brouard 6206: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6207:
6208: if (popbased==1) {
6209: if(mobilav ==0){
6210: for(i=1; i<=nlstate;i++)
6211: prlim[i][i]=probs[(int)age][i][ij];
6212: }else{ /* mobilav */
6213: for(i=1; i<=nlstate;i++)
6214: prlim[i][i]=mobaverage[(int)age][i][ij];
6215: }
6216: }
6217:
6218: /* This for computing probability of death (h=1 means
6219: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6220: as a weighted average of prlim.
6221: */
1.235 brouard 6222: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6223: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6224: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6225: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6226: }
6227: /* end probability of death */
6228:
6229: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6230: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6231: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6232: for(i=1; i<=nlstate;i++){
6233: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6234: }
6235: }
6236: fprintf(ficresprobmorprev,"\n");
6237:
6238: fprintf(ficresvij,"%.0f ",age );
6239: for(i=1; i<=nlstate;i++)
6240: for(j=1; j<=nlstate;j++){
6241: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6242: }
6243: fprintf(ficresvij,"\n");
6244: free_matrix(gp,0,nhstepm,1,nlstate);
6245: free_matrix(gm,0,nhstepm,1,nlstate);
6246: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6247: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6248: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6249: } /* End age */
6250: free_vector(gpp,nlstate+1,nlstate+ndeath);
6251: free_vector(gmp,nlstate+1,nlstate+ndeath);
6252: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6253: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6254: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6255: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6256: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6257: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6258: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6259: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6260: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6261: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6262: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6263: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6264: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6265: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6266: 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);
6267: /* 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 6268: */
1.218 brouard 6269: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6270: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6271:
1.218 brouard 6272: free_vector(xp,1,npar);
6273: free_matrix(doldm,1,nlstate,1,nlstate);
6274: free_matrix(dnewm,1,nlstate,1,npar);
6275: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6276: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6277: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6278: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6279: fclose(ficresprobmorprev);
6280: fflush(ficgp);
6281: fflush(fichtm);
6282: } /* end varevsij */
1.126 brouard 6283:
6284: /************ Variance of prevlim ******************/
1.269 brouard 6285: 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 6286: {
1.205 brouard 6287: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6288: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6289:
1.268 brouard 6290: double **dnewmpar,**doldm;
1.126 brouard 6291: int i, j, nhstepm, hstepm;
6292: double *xp;
6293: double *gp, *gm;
6294: double **gradg, **trgradg;
1.208 brouard 6295: double **mgm, **mgp;
1.126 brouard 6296: double age,agelim;
6297: int theta;
6298:
6299: pstamp(ficresvpl);
1.288 brouard 6300: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6301: fprintf(ficresvpl,"# Age ");
6302: if(nresult >=1)
6303: fprintf(ficresvpl," Result# ");
1.126 brouard 6304: for(i=1; i<=nlstate;i++)
6305: fprintf(ficresvpl," %1d-%1d",i,i);
6306: fprintf(ficresvpl,"\n");
6307:
6308: xp=vector(1,npar);
1.268 brouard 6309: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6310: doldm=matrix(1,nlstate,1,nlstate);
6311:
6312: hstepm=1*YEARM; /* Every year of age */
6313: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6314: agelim = AGESUP;
6315: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6316: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6317: if (stepm >= YEARM) hstepm=1;
6318: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6319: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6320: mgp=matrix(1,npar,1,nlstate);
6321: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6322: gp=vector(1,nlstate);
6323: gm=vector(1,nlstate);
6324:
6325: for(theta=1; theta <=npar; theta++){
6326: for(i=1; i<=npar; i++){ /* Computes gradient */
6327: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6328: }
1.288 brouard 6329: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6330: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6331: /* else */
6332: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6333: for(i=1;i<=nlstate;i++){
1.126 brouard 6334: gp[i] = prlim[i][i];
1.208 brouard 6335: mgp[theta][i] = prlim[i][i];
6336: }
1.126 brouard 6337: for(i=1; i<=npar; i++) /* Computes gradient */
6338: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6339: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6340: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6341: /* else */
6342: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6343: for(i=1;i<=nlstate;i++){
1.126 brouard 6344: gm[i] = prlim[i][i];
1.208 brouard 6345: mgm[theta][i] = prlim[i][i];
6346: }
1.126 brouard 6347: for(i=1;i<=nlstate;i++)
6348: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6349: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6350: } /* End theta */
6351:
6352: trgradg =matrix(1,nlstate,1,npar);
6353:
6354: for(j=1; j<=nlstate;j++)
6355: for(theta=1; theta <=npar; theta++)
6356: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6357: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6358: /* printf("\nmgm mgp %d ",(int)age); */
6359: /* for(j=1; j<=nlstate;j++){ */
6360: /* printf(" %d ",j); */
6361: /* for(theta=1; theta <=npar; theta++) */
6362: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6363: /* printf("\n "); */
6364: /* } */
6365: /* } */
6366: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6367: /* printf("\n gradg %d ",(int)age); */
6368: /* for(j=1; j<=nlstate;j++){ */
6369: /* printf("%d ",j); */
6370: /* for(theta=1; theta <=npar; theta++) */
6371: /* printf("%d %lf ",theta,gradg[theta][j]); */
6372: /* printf("\n "); */
6373: /* } */
6374: /* } */
1.126 brouard 6375:
6376: for(i=1;i<=nlstate;i++)
6377: varpl[i][(int)age] =0.;
1.209 brouard 6378: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6379: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6380: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6381: }else{
1.268 brouard 6382: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6383: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6384: }
1.126 brouard 6385: for(i=1;i<=nlstate;i++)
6386: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6387:
6388: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6389: if(nresult >=1)
6390: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6391: for(i=1; i<=nlstate;i++){
1.126 brouard 6392: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6393: /* for(j=1;j<=nlstate;j++) */
6394: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6395: }
1.126 brouard 6396: fprintf(ficresvpl,"\n");
6397: free_vector(gp,1,nlstate);
6398: free_vector(gm,1,nlstate);
1.208 brouard 6399: free_matrix(mgm,1,npar,1,nlstate);
6400: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6401: free_matrix(gradg,1,npar,1,nlstate);
6402: free_matrix(trgradg,1,nlstate,1,npar);
6403: } /* End age */
6404:
6405: free_vector(xp,1,npar);
6406: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6407: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6408:
6409: }
6410:
6411:
6412: /************ Variance of backprevalence limit ******************/
1.269 brouard 6413: 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 6414: {
6415: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6416: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6417:
6418: double **dnewmpar,**doldm;
6419: int i, j, nhstepm, hstepm;
6420: double *xp;
6421: double *gp, *gm;
6422: double **gradg, **trgradg;
6423: double **mgm, **mgp;
6424: double age,agelim;
6425: int theta;
6426:
6427: pstamp(ficresvbl);
6428: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6429: fprintf(ficresvbl,"# Age ");
6430: if(nresult >=1)
6431: fprintf(ficresvbl," Result# ");
6432: for(i=1; i<=nlstate;i++)
6433: fprintf(ficresvbl," %1d-%1d",i,i);
6434: fprintf(ficresvbl,"\n");
6435:
6436: xp=vector(1,npar);
6437: dnewmpar=matrix(1,nlstate,1,npar);
6438: doldm=matrix(1,nlstate,1,nlstate);
6439:
6440: hstepm=1*YEARM; /* Every year of age */
6441: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6442: agelim = AGEINF;
6443: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6444: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6445: if (stepm >= YEARM) hstepm=1;
6446: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6447: gradg=matrix(1,npar,1,nlstate);
6448: mgp=matrix(1,npar,1,nlstate);
6449: mgm=matrix(1,npar,1,nlstate);
6450: gp=vector(1,nlstate);
6451: gm=vector(1,nlstate);
6452:
6453: for(theta=1; theta <=npar; theta++){
6454: for(i=1; i<=npar; i++){ /* Computes gradient */
6455: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6456: }
6457: if(mobilavproj > 0 )
6458: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6459: else
6460: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6461: for(i=1;i<=nlstate;i++){
6462: gp[i] = bprlim[i][i];
6463: mgp[theta][i] = bprlim[i][i];
6464: }
6465: for(i=1; i<=npar; i++) /* Computes gradient */
6466: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6467: if(mobilavproj > 0 )
6468: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6469: else
6470: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6471: for(i=1;i<=nlstate;i++){
6472: gm[i] = bprlim[i][i];
6473: mgm[theta][i] = bprlim[i][i];
6474: }
6475: for(i=1;i<=nlstate;i++)
6476: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6477: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6478: } /* End theta */
6479:
6480: trgradg =matrix(1,nlstate,1,npar);
6481:
6482: for(j=1; j<=nlstate;j++)
6483: for(theta=1; theta <=npar; theta++)
6484: trgradg[j][theta]=gradg[theta][j];
6485: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6486: /* printf("\nmgm mgp %d ",(int)age); */
6487: /* for(j=1; j<=nlstate;j++){ */
6488: /* printf(" %d ",j); */
6489: /* for(theta=1; theta <=npar; theta++) */
6490: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6491: /* printf("\n "); */
6492: /* } */
6493: /* } */
6494: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6495: /* printf("\n gradg %d ",(int)age); */
6496: /* for(j=1; j<=nlstate;j++){ */
6497: /* printf("%d ",j); */
6498: /* for(theta=1; theta <=npar; theta++) */
6499: /* printf("%d %lf ",theta,gradg[theta][j]); */
6500: /* printf("\n "); */
6501: /* } */
6502: /* } */
6503:
6504: for(i=1;i<=nlstate;i++)
6505: varbpl[i][(int)age] =0.;
6506: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6507: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6508: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6509: }else{
6510: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6511: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6512: }
6513: for(i=1;i<=nlstate;i++)
6514: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6515:
6516: fprintf(ficresvbl,"%.0f ",age );
6517: if(nresult >=1)
6518: fprintf(ficresvbl,"%d ",nres );
6519: for(i=1; i<=nlstate;i++)
6520: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6521: fprintf(ficresvbl,"\n");
6522: free_vector(gp,1,nlstate);
6523: free_vector(gm,1,nlstate);
6524: free_matrix(mgm,1,npar,1,nlstate);
6525: free_matrix(mgp,1,npar,1,nlstate);
6526: free_matrix(gradg,1,npar,1,nlstate);
6527: free_matrix(trgradg,1,nlstate,1,npar);
6528: } /* End age */
6529:
6530: free_vector(xp,1,npar);
6531: free_matrix(doldm,1,nlstate,1,npar);
6532: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6533:
6534: }
6535:
6536: /************ Variance of one-step probabilities ******************/
6537: 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 6538: {
6539: int i, j=0, k1, l1, tj;
6540: int k2, l2, j1, z1;
6541: int k=0, l;
6542: int first=1, first1, first2;
6543: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6544: double **dnewm,**doldm;
6545: double *xp;
6546: double *gp, *gm;
6547: double **gradg, **trgradg;
6548: double **mu;
6549: double age, cov[NCOVMAX+1];
6550: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6551: int theta;
6552: char fileresprob[FILENAMELENGTH];
6553: char fileresprobcov[FILENAMELENGTH];
6554: char fileresprobcor[FILENAMELENGTH];
6555: double ***varpij;
6556:
6557: strcpy(fileresprob,"PROB_");
6558: strcat(fileresprob,fileres);
6559: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6560: printf("Problem with resultfile: %s\n", fileresprob);
6561: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6562: }
6563: strcpy(fileresprobcov,"PROBCOV_");
6564: strcat(fileresprobcov,fileresu);
6565: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6566: printf("Problem with resultfile: %s\n", fileresprobcov);
6567: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6568: }
6569: strcpy(fileresprobcor,"PROBCOR_");
6570: strcat(fileresprobcor,fileresu);
6571: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6572: printf("Problem with resultfile: %s\n", fileresprobcor);
6573: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6574: }
6575: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6576: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6577: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6578: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6579: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6580: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6581: pstamp(ficresprob);
6582: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6583: fprintf(ficresprob,"# Age");
6584: pstamp(ficresprobcov);
6585: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6586: fprintf(ficresprobcov,"# Age");
6587: pstamp(ficresprobcor);
6588: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6589: fprintf(ficresprobcor,"# Age");
1.126 brouard 6590:
6591:
1.222 brouard 6592: for(i=1; i<=nlstate;i++)
6593: for(j=1; j<=(nlstate+ndeath);j++){
6594: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6595: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6596: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6597: }
6598: /* fprintf(ficresprob,"\n");
6599: fprintf(ficresprobcov,"\n");
6600: fprintf(ficresprobcor,"\n");
6601: */
6602: xp=vector(1,npar);
6603: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6604: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6605: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6606: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6607: first=1;
6608: fprintf(ficgp,"\n# Routine varprob");
6609: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6610: fprintf(fichtm,"\n");
6611:
1.288 brouard 6612: 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 6613: 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);
6614: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6615: and drawn. It helps understanding how is the covariance between two incidences.\
6616: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6617: 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 6618: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6619: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6620: standard deviations wide on each axis. <br>\
6621: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6622: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6623: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6624:
1.222 brouard 6625: cov[1]=1;
6626: /* tj=cptcoveff; */
1.225 brouard 6627: tj = (int) pow(2,cptcoveff);
1.222 brouard 6628: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6629: j1=0;
1.224 brouard 6630: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6631: if (cptcovn>0) {
6632: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6633: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6634: fprintf(ficresprob, "**********\n#\n");
6635: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6636: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6637: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6638:
1.222 brouard 6639: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6640: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6641: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6642:
6643:
1.222 brouard 6644: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6645: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6646: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6647:
1.222 brouard 6648: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6649: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6650: fprintf(ficresprobcor, "**********\n#");
6651: if(invalidvarcomb[j1]){
6652: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6653: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6654: continue;
6655: }
6656: }
6657: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6658: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6659: gp=vector(1,(nlstate)*(nlstate+ndeath));
6660: gm=vector(1,(nlstate)*(nlstate+ndeath));
6661: for (age=bage; age<=fage; age ++){
6662: cov[2]=age;
6663: if(nagesqr==1)
6664: cov[3]= age*age;
6665: for (k=1; k<=cptcovn;k++) {
6666: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6667: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6668: * 1 1 1 1 1
6669: * 2 2 1 1 1
6670: * 3 1 2 1 1
6671: */
6672: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6673: }
6674: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6675: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6676: for (k=1; k<=cptcovprod;k++)
6677: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6678:
6679:
1.222 brouard 6680: for(theta=1; theta <=npar; theta++){
6681: for(i=1; i<=npar; i++)
6682: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6683:
1.222 brouard 6684: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6685:
1.222 brouard 6686: k=0;
6687: for(i=1; i<= (nlstate); i++){
6688: for(j=1; j<=(nlstate+ndeath);j++){
6689: k=k+1;
6690: gp[k]=pmmij[i][j];
6691: }
6692: }
1.220 brouard 6693:
1.222 brouard 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);
6698: k=0;
6699: for(i=1; i<=(nlstate); i++){
6700: for(j=1; j<=(nlstate+ndeath);j++){
6701: k=k+1;
6702: gm[k]=pmmij[i][j];
6703: }
6704: }
1.220 brouard 6705:
1.222 brouard 6706: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6707: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6708: }
1.126 brouard 6709:
1.222 brouard 6710: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6711: for(theta=1; theta <=npar; theta++)
6712: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6713:
1.222 brouard 6714: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6715: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6716:
1.222 brouard 6717: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6718:
1.222 brouard 6719: k=0;
6720: for(i=1; i<=(nlstate); i++){
6721: for(j=1; j<=(nlstate+ndeath);j++){
6722: k=k+1;
6723: mu[k][(int) age]=pmmij[i][j];
6724: }
6725: }
6726: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6727: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6728: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6729:
1.222 brouard 6730: /*printf("\n%d ",(int)age);
6731: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6732: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6733: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6734: }*/
1.220 brouard 6735:
1.222 brouard 6736: fprintf(ficresprob,"\n%d ",(int)age);
6737: fprintf(ficresprobcov,"\n%d ",(int)age);
6738: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6739:
1.222 brouard 6740: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6741: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6742: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6743: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6744: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6745: }
6746: i=0;
6747: for (k=1; k<=(nlstate);k++){
6748: for (l=1; l<=(nlstate+ndeath);l++){
6749: i++;
6750: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6751: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6752: for (j=1; j<=i;j++){
6753: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6754: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6755: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6756: }
6757: }
6758: }/* end of loop for state */
6759: } /* end of loop for age */
6760: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6761: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6762: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6763: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6764:
6765: /* Confidence intervalle of pij */
6766: /*
6767: fprintf(ficgp,"\nunset parametric;unset label");
6768: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6769: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6770: 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);
6771: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6772: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6773: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6774: */
6775:
6776: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6777: first1=1;first2=2;
6778: for (k2=1; k2<=(nlstate);k2++){
6779: for (l2=1; l2<=(nlstate+ndeath);l2++){
6780: if(l2==k2) continue;
6781: j=(k2-1)*(nlstate+ndeath)+l2;
6782: for (k1=1; k1<=(nlstate);k1++){
6783: for (l1=1; l1<=(nlstate+ndeath);l1++){
6784: if(l1==k1) continue;
6785: i=(k1-1)*(nlstate+ndeath)+l1;
6786: if(i<=j) continue;
6787: for (age=bage; age<=fage; age ++){
6788: if ((int)age %5==0){
6789: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6790: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6791: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6792: mu1=mu[i][(int) age]/stepm*YEARM ;
6793: mu2=mu[j][(int) age]/stepm*YEARM;
6794: c12=cv12/sqrt(v1*v2);
6795: /* Computing eigen value of matrix of covariance */
6796: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6797: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6798: if ((lc2 <0) || (lc1 <0) ){
6799: if(first2==1){
6800: first1=0;
6801: 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);
6802: }
6803: 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);
6804: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6805: /* lc2=fabs(lc2); */
6806: }
1.220 brouard 6807:
1.222 brouard 6808: /* Eigen vectors */
1.280 brouard 6809: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6810: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6811: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6812: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6813: }else
6814: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6815: /*v21=sqrt(1.-v11*v11); *//* error */
6816: v21=(lc1-v1)/cv12*v11;
6817: v12=-v21;
6818: v22=v11;
6819: tnalp=v21/v11;
6820: if(first1==1){
6821: first1=0;
6822: 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);
6823: }
6824: 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);
6825: /*printf(fignu*/
6826: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6827: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6828: if(first==1){
6829: first=0;
6830: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6831: fprintf(ficgp,"\nset parametric;unset label");
6832: 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);
6833: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6834: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6835: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6836: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6837: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6838: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6839: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6840: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6841: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6842: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6843: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6844: 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 6845: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6846: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6847: }else{
6848: first=0;
6849: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6850: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6851: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6852: 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 6853: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6854: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6855: }/* if first */
6856: } /* age mod 5 */
6857: } /* end loop age */
6858: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6859: first=1;
6860: } /*l12 */
6861: } /* k12 */
6862: } /*l1 */
6863: }/* k1 */
6864: } /* loop on combination of covariates j1 */
6865: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6866: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6867: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6868: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6869: free_vector(xp,1,npar);
6870: fclose(ficresprob);
6871: fclose(ficresprobcov);
6872: fclose(ficresprobcor);
6873: fflush(ficgp);
6874: fflush(fichtmcov);
6875: }
1.126 brouard 6876:
6877:
6878: /******************* Printing html file ***********/
1.201 brouard 6879: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6880: int lastpass, int stepm, int weightopt, char model[],\
6881: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6882: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6883: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6884: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6885: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6886:
6887: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6888: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6889: </ul>");
1.237 brouard 6890: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6891: </ul>", model);
1.214 brouard 6892: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6893: 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",
6894: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6895: 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 6896: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6897: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6898: fprintf(fichtm,"\
6899: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6900: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6901: fprintf(fichtm,"\
1.217 brouard 6902: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6903: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6904: fprintf(fichtm,"\
1.288 brouard 6905: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6906: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6907: fprintf(fichtm,"\
1.288 brouard 6908: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6909: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6910: fprintf(fichtm,"\
1.211 brouard 6911: - (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 6912: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6913: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6914: if(prevfcast==1){
6915: fprintf(fichtm,"\
6916: - Prevalence projections by age and states: \
1.201 brouard 6917: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6918: }
1.126 brouard 6919:
6920:
1.225 brouard 6921: m=pow(2,cptcoveff);
1.222 brouard 6922: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6923:
1.264 brouard 6924: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6925:
6926: jj1=0;
6927:
6928: fprintf(fichtm," \n<ul>");
6929: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6930: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6931: if(m != 1 && TKresult[nres]!= k1)
6932: continue;
6933: jj1++;
6934: if (cptcovn > 0) {
6935: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6936: for (cpt=1; cpt<=cptcoveff;cpt++){
6937: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6938: }
6939: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6940: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6941: }
6942: fprintf(fichtm,"\">");
6943:
6944: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6945: fprintf(fichtm,"************ Results for covariates");
6946: for (cpt=1; cpt<=cptcoveff;cpt++){
6947: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6948: }
6949: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6950: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6951: }
6952: if(invalidvarcomb[k1]){
6953: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6954: continue;
6955: }
6956: fprintf(fichtm,"</a></li>");
6957: } /* cptcovn >0 */
6958: }
6959: fprintf(fichtm," \n</ul>");
6960:
1.222 brouard 6961: jj1=0;
1.237 brouard 6962:
6963: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6964: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6965: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6966: continue;
1.220 brouard 6967:
1.222 brouard 6968: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6969: jj1++;
6970: if (cptcovn > 0) {
1.264 brouard 6971: fprintf(fichtm,"\n<p><a name=\"rescov");
6972: for (cpt=1; cpt<=cptcoveff;cpt++){
6973: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6974: }
6975: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6976: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6977: }
6978: fprintf(fichtm,"\"</a>");
6979:
1.222 brouard 6980: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6981: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6982: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6983: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6984: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6985: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6986: }
1.237 brouard 6987: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6988: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6989: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6990: }
6991:
1.230 brouard 6992: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6993: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6994: if(invalidvarcomb[k1]){
6995: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6996: printf("\nCombination (%d) ignored because no cases \n",k1);
6997: continue;
6998: }
6999: }
7000: /* aij, bij */
1.259 brouard 7001: 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 7002: <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 7003: /* Pij */
1.241 brouard 7004: 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> \
7005: <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 7006: /* Quasi-incidences */
7007: 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 7008: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7009: 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 7010: 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> \
7011: <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 7012: /* Survival functions (period) in state j */
7013: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7014: 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 7015: <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 7016: }
7017: /* State specific survival functions (period) */
7018: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7019: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7020: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7021: <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 7022: }
1.288 brouard 7023: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7024: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7025: 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> \
7026: <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 7027: }
1.296 brouard 7028: if(prevbcast==1){
1.288 brouard 7029: /* Backward prevalence in each health state */
1.222 brouard 7030: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7031: 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 7032: <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 7033: }
1.217 brouard 7034: }
1.222 brouard 7035: if(prevfcast==1){
1.288 brouard 7036: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7037: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7038: 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 7039: <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 7040: }
7041: }
1.296 brouard 7042: if(prevbcast==1){
1.268 brouard 7043: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7044: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7045: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7046: 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 \
7047: 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) \
7048: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7049: <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 7050: }
7051: }
1.220 brouard 7052:
1.222 brouard 7053: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7054: 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> \
7055: <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 7056: }
7057: /* } /\* end i1 *\/ */
7058: }/* End k1 */
7059: fprintf(fichtm,"</ul>");
1.126 brouard 7060:
1.222 brouard 7061: fprintf(fichtm,"\
1.126 brouard 7062: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7063: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7064: - 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 7065: But because parameters are usually highly correlated (a higher incidence of disability \
7066: and a higher incidence of recovery can give very close observed transition) it might \
7067: be very useful to look not only at linear confidence intervals estimated from the \
7068: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7069: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7070: covariance matrix of the one-step probabilities. \
7071: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7072:
1.222 brouard 7073: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7074: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7075: fprintf(fichtm,"\
1.126 brouard 7076: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7077: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7078:
1.222 brouard 7079: fprintf(fichtm,"\
1.126 brouard 7080: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7081: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7082: fprintf(fichtm,"\
1.126 brouard 7083: - 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): \
7084: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7085: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7086: fprintf(fichtm,"\
1.126 brouard 7087: - (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): \
7088: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7089: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7090: fprintf(fichtm,"\
1.288 brouard 7091: - 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 7092: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7093: fprintf(fichtm,"\
1.128 brouard 7094: - 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 7095: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7096: fprintf(fichtm,"\
1.288 brouard 7097: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7098: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7099:
7100: /* if(popforecast==1) fprintf(fichtm,"\n */
7101: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7102: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7103: /* <br>",fileres,fileres,fileres,fileres); */
7104: /* else */
7105: /* 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 7106: fflush(fichtm);
7107: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7108:
1.225 brouard 7109: m=pow(2,cptcoveff);
1.222 brouard 7110: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7111:
1.222 brouard 7112: jj1=0;
1.237 brouard 7113:
1.241 brouard 7114: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7115: for(k1=1; k1<=m;k1++){
1.253 brouard 7116: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7117: continue;
1.222 brouard 7118: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7119: jj1++;
1.126 brouard 7120: if (cptcovn > 0) {
7121: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7122: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7123: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7124: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7125: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7126: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7127: }
7128:
1.126 brouard 7129: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7130:
1.222 brouard 7131: if(invalidvarcomb[k1]){
7132: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7133: continue;
7134: }
1.126 brouard 7135: }
7136: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7137: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7138: 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 7139: <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 7140: }
7141: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7142: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7143: true period expectancies (those weighted with period prevalences are also\
7144: drawn in addition to the population based expectancies computed using\
1.241 brouard 7145: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7146: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7147: /* } /\* end i1 *\/ */
7148: }/* End k1 */
1.241 brouard 7149: }/* End nres */
1.222 brouard 7150: fprintf(fichtm,"</ul>");
7151: fflush(fichtm);
1.126 brouard 7152: }
7153:
7154: /******************* Gnuplot file **************/
1.296 brouard 7155: 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 7156:
7157: char dirfileres[132],optfileres[132];
1.264 brouard 7158: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7159: 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 7160: int lv=0, vlv=0, kl=0;
1.130 brouard 7161: int ng=0;
1.201 brouard 7162: int vpopbased;
1.223 brouard 7163: int ioffset; /* variable offset for columns */
1.270 brouard 7164: int iyearc=1; /* variable column for year of projection */
7165: int iagec=1; /* variable column for age of projection */
1.235 brouard 7166: int nres=0; /* Index of resultline */
1.266 brouard 7167: int istart=1; /* For starting graphs in projections */
1.219 brouard 7168:
1.126 brouard 7169: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7170: /* printf("Problem with file %s",optionfilegnuplot); */
7171: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7172: /* } */
7173:
7174: /*#ifdef windows */
7175: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7176: /*#endif */
1.225 brouard 7177: m=pow(2,cptcoveff);
1.126 brouard 7178:
1.274 brouard 7179: /* diagram of the model */
7180: fprintf(ficgp,"\n#Diagram of the model \n");
7181: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7182: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7183: 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);
7184:
7185: 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);
7186: fprintf(ficgp,"\n#show arrow\nunset label\n");
7187: 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);
7188: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7189: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7190: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7191: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7192:
1.202 brouard 7193: /* Contribution to likelihood */
7194: /* Plot the probability implied in the likelihood */
1.223 brouard 7195: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7196: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7197: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7198: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7199: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7200: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7201: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7202: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7203: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7204: 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));
7205: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7206: 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));
7207: for (i=1; i<= nlstate ; i ++) {
7208: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7209: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7210: 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);
7211: for (j=2; j<= nlstate+ndeath ; j ++) {
7212: 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);
7213: }
7214: fprintf(ficgp,";\nset out; unset ylabel;\n");
7215: }
7216: /* 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 */
7217: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7218: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7219: fprintf(ficgp,"\nset out;unset log\n");
7220: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7221:
1.126 brouard 7222: strcpy(dirfileres,optionfilefiname);
7223: strcpy(optfileres,"vpl");
1.223 brouard 7224: /* 1eme*/
1.238 brouard 7225: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7226: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7227: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7228: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7229: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7230: continue;
7231: /* We are interested in selected combination by the resultline */
1.246 brouard 7232: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7233: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7234: strcpy(gplotlabel,"(");
1.238 brouard 7235: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7236: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7237: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7238: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7239: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7240: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7241: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7242: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7243: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7244: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7245: }
7246: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7247: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7248: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7249: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7250: }
7251: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7252: /* printf("\n#\n"); */
1.238 brouard 7253: fprintf(ficgp,"\n#\n");
7254: if(invalidvarcomb[k1]){
1.260 brouard 7255: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7256: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7257: continue;
7258: }
1.235 brouard 7259:
1.241 brouard 7260: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7261: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7262: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7263: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7264: 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);
7265: /* 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); */
7266: /* k1-1 error should be nres-1*/
1.238 brouard 7267: for (i=1; i<= nlstate ; i ++) {
7268: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7269: else fprintf(ficgp," %%*lf (%%*lf)");
7270: }
1.288 brouard 7271: 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 7272: for (i=1; i<= nlstate ; i ++) {
7273: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7274: else fprintf(ficgp," %%*lf (%%*lf)");
7275: }
1.260 brouard 7276: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7277: for (i=1; i<= nlstate ; i ++) {
7278: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7279: else fprintf(ficgp," %%*lf (%%*lf)");
7280: }
1.265 brouard 7281: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7282:
7283: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7284: if(cptcoveff ==0){
1.271 brouard 7285: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7286: }else{
7287: kl=0;
7288: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7289: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7290: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7291: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7292: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7293: vlv= nbcode[Tvaraff[k]][lv];
7294: kl++;
7295: /* 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 *\/ */
7296: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7297: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7298: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7299: if(k==cptcoveff){
7300: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7301: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7302: }else{
7303: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7304: kl++;
7305: }
7306: } /* end covariate */
7307: } /* end if no covariate */
7308:
1.296 brouard 7309: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7310: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7311: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7312: if(cptcoveff ==0){
1.245 brouard 7313: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7314: }else{
7315: kl=0;
7316: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7317: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7318: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7319: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7320: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7321: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7322: kl++;
1.238 brouard 7323: /* 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 *\/ */
7324: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7325: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7326: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7327: if(k==cptcoveff){
1.245 brouard 7328: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7329: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7330: }else{
7331: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7332: kl++;
7333: }
7334: } /* end covariate */
7335: } /* end if no covariate */
1.296 brouard 7336: if(prevbcast == 1){
1.268 brouard 7337: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7338: /* k1-1 error should be nres-1*/
7339: for (i=1; i<= nlstate ; i ++) {
7340: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7341: else fprintf(ficgp," %%*lf (%%*lf)");
7342: }
1.271 brouard 7343: 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 7344: for (i=1; i<= nlstate ; i ++) {
7345: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7346: else fprintf(ficgp," %%*lf (%%*lf)");
7347: }
1.276 brouard 7348: 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 7349: for (i=1; i<= nlstate ; i ++) {
7350: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7351: else fprintf(ficgp," %%*lf (%%*lf)");
7352: }
1.274 brouard 7353: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7354: } /* end if backprojcast */
1.296 brouard 7355: } /* end if prevbcast */
1.276 brouard 7356: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7357: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7358: } /* nres */
1.201 brouard 7359: } /* k1 */
7360: } /* cpt */
1.235 brouard 7361:
7362:
1.126 brouard 7363: /*2 eme*/
1.238 brouard 7364: for (k1=1; k1<= m ; k1 ++){
7365: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7366: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7367: continue;
7368: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7369: strcpy(gplotlabel,"(");
1.238 brouard 7370: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7371: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7372: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7373: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7374: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7375: vlv= nbcode[Tvaraff[k]][lv];
7376: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7377: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7378: }
1.237 brouard 7379: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7380: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7381: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7382: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7383: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7384: }
1.264 brouard 7385: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7386: fprintf(ficgp,"\n#\n");
1.223 brouard 7387: if(invalidvarcomb[k1]){
7388: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7389: continue;
7390: }
1.219 brouard 7391:
1.241 brouard 7392: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7393: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7394: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7395: if(vpopbased==0){
1.238 brouard 7396: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7397: }else
1.238 brouard 7398: fprintf(ficgp,"\nreplot ");
7399: for (i=1; i<= nlstate+1 ; i ++) {
7400: k=2*i;
1.261 brouard 7401: 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 7402: for (j=1; j<= nlstate+1 ; j ++) {
7403: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7404: else fprintf(ficgp," %%*lf (%%*lf)");
7405: }
7406: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7407: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7408: 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 7409: for (j=1; j<= nlstate+1 ; j ++) {
7410: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7411: else fprintf(ficgp," %%*lf (%%*lf)");
7412: }
7413: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7414: 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 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== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7420: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7421: } /* state */
7422: } /* vpopbased */
1.264 brouard 7423: 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 7424: } /* end nres */
7425: } /* k1 end 2 eme*/
7426:
7427:
7428: /*3eme*/
7429: for (k1=1; k1<= m ; k1 ++){
7430: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7431: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7432: continue;
7433:
7434: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7435: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7436: strcpy(gplotlabel,"(");
1.238 brouard 7437: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7438: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7439: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7440: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7441: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7442: vlv= nbcode[Tvaraff[k]][lv];
7443: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7444: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7445: }
7446: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7447: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7448: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7449: }
1.264 brouard 7450: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7451: fprintf(ficgp,"\n#\n");
7452: if(invalidvarcomb[k1]){
7453: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7454: continue;
7455: }
7456:
7457: /* k=2+nlstate*(2*cpt-2); */
7458: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7459: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7460: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7461: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7462: 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 7463: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7464: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7465: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7466: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7467: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7468: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7469:
1.238 brouard 7470: */
7471: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7472: 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 7473: /* 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 7474:
1.238 brouard 7475: }
1.261 brouard 7476: 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 7477: }
1.264 brouard 7478: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7479: } /* end nres */
7480: } /* end kl 3eme */
1.126 brouard 7481:
1.223 brouard 7482: /* 4eme */
1.201 brouard 7483: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7484: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7485: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7486: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7487: continue;
1.238 brouard 7488: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7489: strcpy(gplotlabel,"(");
1.238 brouard 7490: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7491: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7492: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7493: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7494: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7495: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7496: vlv= nbcode[Tvaraff[k]][lv];
7497: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7498: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7499: }
7500: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7501: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7502: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7503: }
1.264 brouard 7504: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7505: fprintf(ficgp,"\n#\n");
7506: if(invalidvarcomb[k1]){
7507: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7508: continue;
1.223 brouard 7509: }
1.238 brouard 7510:
1.241 brouard 7511: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7512: 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 7513: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7514: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7515: k=3;
7516: for (i=1; i<= nlstate ; i ++){
7517: if(i==1){
7518: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7519: }else{
7520: fprintf(ficgp,", '' ");
7521: }
7522: l=(nlstate+ndeath)*(i-1)+1;
7523: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7524: for (j=2; j<= nlstate+ndeath ; j ++)
7525: fprintf(ficgp,"+$%d",k+l+j-1);
7526: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7527: } /* nlstate */
1.264 brouard 7528: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7529: } /* end cpt state*/
7530: } /* end nres */
7531: } /* end covariate k1 */
7532:
1.220 brouard 7533: /* 5eme */
1.201 brouard 7534: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7535: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7536: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7537: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7538: continue;
1.238 brouard 7539: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7540: strcpy(gplotlabel,"(");
1.238 brouard 7541: 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);
7542: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7543: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7544: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7545: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7546: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7547: vlv= nbcode[Tvaraff[k]][lv];
7548: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7549: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7550: }
7551: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7552: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7553: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7554: }
1.264 brouard 7555: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7556: fprintf(ficgp,"\n#\n");
7557: if(invalidvarcomb[k1]){
7558: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7559: continue;
7560: }
1.227 brouard 7561:
1.241 brouard 7562: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7563: 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 7564: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7565: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7566: k=3;
7567: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7568: if(j==1)
7569: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7570: else
7571: fprintf(ficgp,", '' ");
7572: l=(nlstate+ndeath)*(cpt-1) +j;
7573: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7574: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7575: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7576: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7577: } /* nlstate */
7578: fprintf(ficgp,", '' ");
7579: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7580: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7581: l=(nlstate+ndeath)*(cpt-1) +j;
7582: if(j < nlstate)
7583: fprintf(ficgp,"$%d +",k+l);
7584: else
7585: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7586: }
1.264 brouard 7587: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7588: } /* end cpt state*/
7589: } /* end covariate */
7590: } /* end nres */
1.227 brouard 7591:
1.220 brouard 7592: /* 6eme */
1.202 brouard 7593: /* CV preval stable (period) for each covariate */
1.237 brouard 7594: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7595: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7596: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7597: continue;
1.255 brouard 7598: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7599: strcpy(gplotlabel,"(");
1.288 brouard 7600: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7601: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7602: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7603: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7604: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7605: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7606: vlv= nbcode[Tvaraff[k]][lv];
7607: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7608: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7609: }
1.237 brouard 7610: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7611: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7612: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7613: }
1.264 brouard 7614: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7615: fprintf(ficgp,"\n#\n");
1.223 brouard 7616: if(invalidvarcomb[k1]){
1.227 brouard 7617: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7618: continue;
1.223 brouard 7619: }
1.227 brouard 7620:
1.241 brouard 7621: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7622: 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 7623: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7624: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7625: k=3; /* Offset */
1.255 brouard 7626: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7627: if(i==1)
7628: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7629: else
7630: fprintf(ficgp,", '' ");
1.255 brouard 7631: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7632: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7633: for (j=2; j<= nlstate ; j ++)
7634: fprintf(ficgp,"+$%d",k+l+j-1);
7635: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7636: } /* nlstate */
1.264 brouard 7637: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7638: } /* end cpt state*/
7639: } /* end covariate */
1.227 brouard 7640:
7641:
1.220 brouard 7642: /* 7eme */
1.296 brouard 7643: if(prevbcast == 1){
1.288 brouard 7644: /* CV backward prevalence for each covariate */
1.237 brouard 7645: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7646: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7647: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7648: continue;
1.268 brouard 7649: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7650: strcpy(gplotlabel,"(");
1.288 brouard 7651: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7652: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7653: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7654: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7655: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7656: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7657: vlv= nbcode[Tvaraff[k]][lv];
7658: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7659: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7660: }
1.237 brouard 7661: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7662: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7663: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7664: }
1.264 brouard 7665: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7666: fprintf(ficgp,"\n#\n");
7667: if(invalidvarcomb[k1]){
7668: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7669: continue;
7670: }
7671:
1.241 brouard 7672: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7673: 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 7674: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7675: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7676: k=3; /* Offset */
1.268 brouard 7677: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7678: if(i==1)
7679: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7680: else
7681: fprintf(ficgp,", '' ");
7682: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7683: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7684: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7685: /* 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 7686: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7687: /* for (j=2; j<= nlstate ; j ++) */
7688: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7689: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7690: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7691: } /* nlstate */
1.264 brouard 7692: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7693: } /* end cpt state*/
7694: } /* end covariate */
1.296 brouard 7695: } /* End if prevbcast */
1.218 brouard 7696:
1.223 brouard 7697: /* 8eme */
1.218 brouard 7698: if(prevfcast==1){
1.288 brouard 7699: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7700:
1.237 brouard 7701: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7702: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7703: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7704: continue;
1.211 brouard 7705: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7706: strcpy(gplotlabel,"(");
1.288 brouard 7707: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7708: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7709: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7710: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7711: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7712: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7713: vlv= nbcode[Tvaraff[k]][lv];
7714: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7715: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7716: }
1.237 brouard 7717: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7718: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7719: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7720: }
1.264 brouard 7721: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7722: fprintf(ficgp,"\n#\n");
7723: if(invalidvarcomb[k1]){
7724: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7725: continue;
7726: }
7727:
7728: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7729: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7730: 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 7731: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7732: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7733:
7734: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7735: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7736: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7737: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7738: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7739: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7740: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7741: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7742: if(i==istart){
1.227 brouard 7743: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7744: }else{
7745: fprintf(ficgp,",\\\n '' ");
7746: }
7747: if(cptcoveff ==0){ /* No covariate */
7748: ioffset=2; /* Age is in 2 */
7749: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7750: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7751: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7752: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7753: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7754: if(i==nlstate+1){
1.270 brouard 7755: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7756: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7757: fprintf(ficgp,",\\\n '' ");
7758: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7759: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7760: offyear, \
1.268 brouard 7761: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7762: }else
1.227 brouard 7763: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7764: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7765: }else{ /* more than 2 covariates */
1.270 brouard 7766: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7767: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7768: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7769: iyearc=ioffset-1;
7770: iagec=ioffset;
1.227 brouard 7771: fprintf(ficgp," u %d:(",ioffset);
7772: kl=0;
7773: strcpy(gplotcondition,"(");
7774: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7775: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7776: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7777: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7778: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7779: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7780: kl++;
7781: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7782: kl++;
7783: if(k <cptcoveff && cptcoveff>1)
7784: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7785: }
7786: strcpy(gplotcondition+strlen(gplotcondition),")");
7787: /* 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 *\/ */
7788: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7789: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7790: /* '' 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*/
7791: if(i==nlstate+1){
1.270 brouard 7792: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7793: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7794: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7795: fprintf(ficgp," u %d:(",iagec);
7796: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7797: iyearc, iagec, offyear, \
7798: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7799: /* '' 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 7800: }else{
7801: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7802: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7803: }
7804: } /* end if covariate */
7805: } /* nlstate */
1.264 brouard 7806: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7807: } /* end cpt state*/
7808: } /* end covariate */
7809: } /* End if prevfcast */
1.227 brouard 7810:
1.296 brouard 7811: if(prevbcast==1){
1.268 brouard 7812: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7813:
7814: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7815: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7816: if(m != 1 && TKresult[nres]!= k1)
7817: continue;
7818: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7819: strcpy(gplotlabel,"(");
7820: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7821: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7822: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7823: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7824: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7825: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7826: vlv= nbcode[Tvaraff[k]][lv];
7827: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7828: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7829: }
7830: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7831: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7832: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7833: }
7834: strcpy(gplotlabel+strlen(gplotlabel),")");
7835: fprintf(ficgp,"\n#\n");
7836: if(invalidvarcomb[k1]){
7837: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7838: continue;
7839: }
7840:
7841: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7842: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7843: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7844: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7845: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7846:
7847: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7848: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7849: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7850: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7851: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7852: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7853: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7854: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7855: if(i==istart){
7856: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7857: }else{
7858: fprintf(ficgp,",\\\n '' ");
7859: }
7860: if(cptcoveff ==0){ /* No covariate */
7861: ioffset=2; /* Age is in 2 */
7862: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7863: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7864: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7865: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7866: fprintf(ficgp," u %d:(", ioffset);
7867: if(i==nlstate+1){
1.270 brouard 7868: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7869: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7870: fprintf(ficgp,",\\\n '' ");
7871: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7872: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7873: offbyear, \
7874: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7875: }else
7876: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7877: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7878: }else{ /* more than 2 covariates */
1.270 brouard 7879: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7880: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7881: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7882: iyearc=ioffset-1;
7883: iagec=ioffset;
1.268 brouard 7884: fprintf(ficgp," u %d:(",ioffset);
7885: kl=0;
7886: strcpy(gplotcondition,"(");
7887: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7888: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7889: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7890: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7891: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7892: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7893: kl++;
7894: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7895: kl++;
7896: if(k <cptcoveff && cptcoveff>1)
7897: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7898: }
7899: strcpy(gplotcondition+strlen(gplotcondition),")");
7900: /* 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 *\/ */
7901: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7902: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7903: /* '' 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*/
7904: if(i==nlstate+1){
1.270 brouard 7905: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7906: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7907: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7908: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7909: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7910: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7911: iyearc,iagec,offbyear, \
7912: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7913: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7914: }else{
7915: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7916: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7917: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7918: }
7919: } /* end if covariate */
7920: } /* nlstate */
7921: fprintf(ficgp,"\nset out; unset label;\n");
7922: } /* end cpt state*/
7923: } /* end covariate */
1.296 brouard 7924: } /* End if prevbcast */
1.268 brouard 7925:
1.227 brouard 7926:
1.238 brouard 7927: /* 9eme writing MLE parameters */
7928: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7929: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7930: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7931: for(k=1; k <=(nlstate+ndeath); k++){
7932: if (k != i) {
1.227 brouard 7933: fprintf(ficgp,"# current state %d\n",k);
7934: for(j=1; j <=ncovmodel; j++){
7935: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7936: jk++;
7937: }
7938: fprintf(ficgp,"\n");
1.126 brouard 7939: }
7940: }
1.223 brouard 7941: }
1.187 brouard 7942: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7943:
1.145 brouard 7944: /*goto avoid;*/
1.238 brouard 7945: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7946: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7947: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7948: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7949: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7950: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7951: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7952: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7953: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7954: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7955: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7956: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7957: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7958: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7959: fprintf(ficgp,"#\n");
1.223 brouard 7960: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7961: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7962: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7963: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7964: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7965: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7966: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7967: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7968: continue;
1.264 brouard 7969: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7970: strcpy(gplotlabel,"(");
1.276 brouard 7971: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7972: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7973: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7974: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7975: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7976: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7977: vlv= nbcode[Tvaraff[k]][lv];
7978: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7979: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7980: }
1.237 brouard 7981: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7982: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7983: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7984: }
1.264 brouard 7985: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7986: fprintf(ficgp,"\n#\n");
1.264 brouard 7987: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7988: fprintf(ficgp,"\nset key outside ");
7989: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7990: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7991: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7992: if (ng==1){
7993: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7994: fprintf(ficgp,"\nunset log y");
7995: }else if (ng==2){
7996: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7997: fprintf(ficgp,"\nset log y");
7998: }else if (ng==3){
7999: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
8000: fprintf(ficgp,"\nset log y");
8001: }else
8002: fprintf(ficgp,"\nunset title ");
8003: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
8004: i=1;
8005: for(k2=1; k2<=nlstate; k2++) {
8006: k3=i;
8007: for(k=1; k<=(nlstate+ndeath); k++) {
8008: if (k != k2){
8009: switch( ng) {
8010: case 1:
8011: if(nagesqr==0)
8012: fprintf(ficgp," p%d+p%d*x",i,i+1);
8013: else /* nagesqr =1 */
8014: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8015: break;
8016: case 2: /* ng=2 */
8017: if(nagesqr==0)
8018: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8019: else /* nagesqr =1 */
8020: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8021: break;
8022: case 3:
8023: if(nagesqr==0)
8024: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8025: else /* nagesqr =1 */
8026: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8027: break;
8028: }
8029: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8030: ijp=1; /* product no age */
8031: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8032: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8033: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8034: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8035: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8036: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8037: if(DummyV[j]==0){
8038: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8039: }else{ /* quantitative */
8040: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8041: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8042: }
8043: ij++;
1.237 brouard 8044: }
1.268 brouard 8045: }
8046: }else if(cptcovprod >0){
8047: if(j==Tprod[ijp]) { /* */
8048: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8049: if(ijp <=cptcovprod) { /* Product */
8050: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8051: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8052: /* 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)]); */
8053: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8054: }else{ /* Vn is dummy and Vm is quanti */
8055: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8056: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8057: }
8058: }else{ /* Vn*Vm Vn is quanti */
8059: if(DummyV[Tvard[ijp][2]]==0){
8060: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8061: }else{ /* Both quanti */
8062: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8063: }
1.237 brouard 8064: }
1.268 brouard 8065: ijp++;
1.237 brouard 8066: }
1.268 brouard 8067: } /* end Tprod */
1.237 brouard 8068: } else{ /* simple covariate */
1.264 brouard 8069: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8070: if(Dummy[j]==0){
8071: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8072: }else{ /* quantitative */
8073: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8074: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8075: }
1.237 brouard 8076: } /* end simple */
8077: } /* end j */
1.223 brouard 8078: }else{
8079: i=i-ncovmodel;
8080: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8081: fprintf(ficgp," (1.");
8082: }
1.227 brouard 8083:
1.223 brouard 8084: if(ng != 1){
8085: fprintf(ficgp,")/(1");
1.227 brouard 8086:
1.264 brouard 8087: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8088: if(nagesqr==0)
1.264 brouard 8089: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8090: else /* nagesqr =1 */
1.264 brouard 8091: 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 8092:
1.223 brouard 8093: ij=1;
8094: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8095: if(cptcovage >0){
8096: if((j-2)==Tage[ij]) { /* Bug valgrind */
8097: if(ij <=cptcovage) { /* Bug valgrind */
8098: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8099: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8100: ij++;
8101: }
8102: }
8103: }else
8104: 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 8105: }
8106: fprintf(ficgp,")");
8107: }
8108: fprintf(ficgp,")");
8109: if(ng ==2)
1.276 brouard 8110: 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 8111: else /* ng= 3 */
1.276 brouard 8112: 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 8113: }else{ /* end ng <> 1 */
8114: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8115: 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 8116: }
8117: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8118: fprintf(ficgp,",");
8119: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8120: fprintf(ficgp,",");
8121: i=i+ncovmodel;
8122: } /* end k */
8123: } /* end k2 */
1.276 brouard 8124: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8125: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8126: } /* end k1 */
1.223 brouard 8127: } /* end ng */
8128: /* avoid: */
8129: fflush(ficgp);
1.126 brouard 8130: } /* end gnuplot */
8131:
8132:
8133: /*************** Moving average **************/
1.219 brouard 8134: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8135: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8136:
1.222 brouard 8137: int i, cpt, cptcod;
8138: int modcovmax =1;
8139: int mobilavrange, mob;
8140: int iage=0;
1.288 brouard 8141: int firstA1=0, firstA2=0;
1.222 brouard 8142:
1.266 brouard 8143: double sum=0., sumr=0.;
1.222 brouard 8144: double age;
1.266 brouard 8145: double *sumnewp, *sumnewm, *sumnewmr;
8146: double *agemingood, *agemaxgood;
8147: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8148:
8149:
1.278 brouard 8150: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8151: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8152:
8153: sumnewp = vector(1,ncovcombmax);
8154: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8155: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8156: agemingood = vector(1,ncovcombmax);
1.266 brouard 8157: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8158: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8159: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8160:
8161: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8162: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8163: sumnewp[cptcod]=0.;
1.266 brouard 8164: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8165: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8166: }
8167: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8168:
1.266 brouard 8169: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8170: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8171: else mobilavrange=mobilav;
8172: for (age=bage; age<=fage; age++)
8173: for (i=1; i<=nlstate;i++)
8174: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8175: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8176: /* We keep the original values on the extreme ages bage, fage and for
8177: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8178: we use a 5 terms etc. until the borders are no more concerned.
8179: */
8180: for (mob=3;mob <=mobilavrange;mob=mob+2){
8181: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8182: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8183: sumnewm[cptcod]=0.;
8184: for (i=1; i<=nlstate;i++){
1.222 brouard 8185: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8186: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8187: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8188: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8189: }
8190: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8191: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8192: } /* end i */
8193: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8194: } /* end cptcod */
1.222 brouard 8195: }/* end age */
8196: }/* end mob */
1.266 brouard 8197: }else{
8198: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8199: return -1;
1.266 brouard 8200: }
8201:
8202: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8203: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8204: if(invalidvarcomb[cptcod]){
8205: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8206: continue;
8207: }
1.219 brouard 8208:
1.266 brouard 8209: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8210: sumnewm[cptcod]=0.;
8211: sumnewmr[cptcod]=0.;
8212: for (i=1; i<=nlstate;i++){
8213: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8214: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8215: }
8216: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8217: agemingoodr[cptcod]=age;
8218: }
8219: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8220: agemingood[cptcod]=age;
8221: }
8222: } /* age */
8223: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8224: sumnewm[cptcod]=0.;
1.266 brouard 8225: sumnewmr[cptcod]=0.;
1.222 brouard 8226: for (i=1; i<=nlstate;i++){
8227: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8228: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8229: }
8230: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8231: agemaxgoodr[cptcod]=age;
1.222 brouard 8232: }
8233: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8234: agemaxgood[cptcod]=age;
8235: }
8236: } /* age */
8237: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8238: /* but they will change */
1.288 brouard 8239: firstA1=0;firstA2=0;
1.266 brouard 8240: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8241: sumnewm[cptcod]=0.;
8242: sumnewmr[cptcod]=0.;
8243: for (i=1; i<=nlstate;i++){
8244: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8245: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8246: }
8247: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8248: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8249: agemaxgoodr[cptcod]=age; /* age min */
8250: for (i=1; i<=nlstate;i++)
8251: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8252: }else{ /* bad we change the value with the values of good ages */
8253: for (i=1; i<=nlstate;i++){
8254: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8255: } /* i */
8256: } /* end bad */
8257: }else{
8258: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8259: agemaxgood[cptcod]=age;
8260: }else{ /* bad we change the value with the values of good ages */
8261: for (i=1; i<=nlstate;i++){
8262: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8263: } /* i */
8264: } /* end bad */
8265: }/* end else */
8266: sum=0.;sumr=0.;
8267: for (i=1; i<=nlstate;i++){
8268: sum+=mobaverage[(int)age][i][cptcod];
8269: sumr+=probs[(int)age][i][cptcod];
8270: }
8271: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8272: if(!firstA1){
8273: firstA1=1;
8274: 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);
8275: }
8276: 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 8277: } /* end bad */
8278: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8279: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8280: if(!firstA2){
8281: firstA2=1;
8282: 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);
8283: }
8284: 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 8285: } /* end bad */
8286: }/* age */
1.266 brouard 8287:
8288: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8289: sumnewm[cptcod]=0.;
1.266 brouard 8290: sumnewmr[cptcod]=0.;
1.222 brouard 8291: for (i=1; i<=nlstate;i++){
8292: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8293: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8294: }
8295: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8296: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8297: agemingoodr[cptcod]=age;
8298: for (i=1; i<=nlstate;i++)
8299: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8300: }else{ /* bad we change the value with the values of good ages */
8301: for (i=1; i<=nlstate;i++){
8302: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8303: } /* i */
8304: } /* end bad */
8305: }else{
8306: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8307: agemingood[cptcod]=age;
8308: }else{ /* bad */
8309: for (i=1; i<=nlstate;i++){
8310: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8311: } /* i */
8312: } /* end bad */
8313: }/* end else */
8314: sum=0.;sumr=0.;
8315: for (i=1; i<=nlstate;i++){
8316: sum+=mobaverage[(int)age][i][cptcod];
8317: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8318: }
1.266 brouard 8319: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8320: 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 8321: } /* end bad */
8322: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8323: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8324: 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 8325: } /* end bad */
8326: }/* age */
1.266 brouard 8327:
1.222 brouard 8328:
8329: for (age=bage; age<=fage; age++){
1.235 brouard 8330: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8331: sumnewp[cptcod]=0.;
8332: sumnewm[cptcod]=0.;
8333: for (i=1; i<=nlstate;i++){
8334: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8335: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8336: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8337: }
8338: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8339: }
8340: /* printf("\n"); */
8341: /* } */
1.266 brouard 8342:
1.222 brouard 8343: /* brutal averaging */
1.266 brouard 8344: /* for (i=1; i<=nlstate;i++){ */
8345: /* for (age=1; age<=bage; age++){ */
8346: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8347: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8348: /* } */
8349: /* for (age=fage; age<=AGESUP; age++){ */
8350: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8351: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8352: /* } */
8353: /* } /\* end i status *\/ */
8354: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8355: /* for (age=1; age<=AGESUP; age++){ */
8356: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8357: /* mobaverage[(int)age][i][cptcod]=0.; */
8358: /* } */
8359: /* } */
1.222 brouard 8360: }/* end cptcod */
1.266 brouard 8361: free_vector(agemaxgoodr,1, ncovcombmax);
8362: free_vector(agemaxgood,1, ncovcombmax);
8363: free_vector(agemingood,1, ncovcombmax);
8364: free_vector(agemingoodr,1, ncovcombmax);
8365: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8366: free_vector(sumnewm,1, ncovcombmax);
8367: free_vector(sumnewp,1, ncovcombmax);
8368: return 0;
8369: }/* End movingaverage */
1.218 brouard 8370:
1.126 brouard 8371:
1.296 brouard 8372:
1.126 brouard 8373: /************** Forecasting ******************/
1.296 brouard 8374: /* 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)*/
8375: 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){
8376: /* dateintemean, mean date of interviews
8377: dateprojd, year, month, day of starting projection
8378: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8379: agemin, agemax range of age
8380: dateprev1 dateprev2 range of dates during which prevalence is computed
8381: */
1.296 brouard 8382: /* double anprojd, mprojd, jprojd; */
8383: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8384: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8385: double agec; /* generic age */
1.296 brouard 8386: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8387: double *popeffectif,*popcount;
8388: double ***p3mat;
1.218 brouard 8389: /* double ***mobaverage; */
1.126 brouard 8390: char fileresf[FILENAMELENGTH];
8391:
8392: agelim=AGESUP;
1.211 brouard 8393: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8394: in each health status at the date of interview (if between dateprev1 and dateprev2).
8395: We still use firstpass and lastpass as another selection.
8396: */
1.214 brouard 8397: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8398: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8399:
1.201 brouard 8400: strcpy(fileresf,"F_");
8401: strcat(fileresf,fileresu);
1.126 brouard 8402: if((ficresf=fopen(fileresf,"w"))==NULL) {
8403: printf("Problem with forecast resultfile: %s\n", fileresf);
8404: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8405: }
1.235 brouard 8406: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8407: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8408:
1.225 brouard 8409: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8410:
8411:
8412: stepsize=(int) (stepm+YEARM-1)/YEARM;
8413: if (stepm<=12) stepsize=1;
8414: if(estepm < stepm){
8415: printf ("Problem %d lower than %d\n",estepm, stepm);
8416: }
1.270 brouard 8417: else{
8418: hstepm=estepm;
8419: }
8420: if(estepm > stepm){ /* Yes every two year */
8421: stepsize=2;
8422: }
1.296 brouard 8423: hstepm=hstepm/stepm;
1.126 brouard 8424:
1.296 brouard 8425:
8426: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8427: /* fractional in yp1 *\/ */
8428: /* aintmean=yp; */
8429: /* yp2=modf((yp1*12),&yp); */
8430: /* mintmean=yp; */
8431: /* yp1=modf((yp2*30.5),&yp); */
8432: /* jintmean=yp; */
8433: /* if(jintmean==0) jintmean=1; */
8434: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8435:
1.296 brouard 8436:
8437: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8438: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8439: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8440: i1=pow(2,cptcoveff);
1.126 brouard 8441: if (cptcovn < 1){i1=1;}
8442:
1.296 brouard 8443: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8444:
8445: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8446:
1.126 brouard 8447: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8448: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8449: for(k=1; k<=i1;k++){
1.253 brouard 8450: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8451: continue;
1.227 brouard 8452: if(invalidvarcomb[k]){
8453: printf("\nCombination (%d) projection ignored because no cases \n",k);
8454: continue;
8455: }
8456: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8457: for(j=1;j<=cptcoveff;j++) {
8458: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8459: }
1.235 brouard 8460: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8461: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8462: }
1.227 brouard 8463: fprintf(ficresf," yearproj age");
8464: for(j=1; j<=nlstate+ndeath;j++){
8465: for(i=1; i<=nlstate;i++)
8466: fprintf(ficresf," p%d%d",i,j);
8467: fprintf(ficresf," wp.%d",j);
8468: }
1.296 brouard 8469: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8470: fprintf(ficresf,"\n");
1.296 brouard 8471: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8472: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8473: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8474: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8475: nhstepm = nhstepm/hstepm;
8476: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8477: oldm=oldms;savm=savms;
1.268 brouard 8478: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8479: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8480: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8481: for (h=0; h<=nhstepm; h++){
8482: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8483: break;
8484: }
8485: }
8486: fprintf(ficresf,"\n");
8487: for(j=1;j<=cptcoveff;j++)
8488: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8489: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8490:
8491: for(j=1; j<=nlstate+ndeath;j++) {
8492: ppij=0.;
8493: for(i=1; i<=nlstate;i++) {
1.278 brouard 8494: if (mobilav>=1)
8495: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8496: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8497: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8498: }
1.268 brouard 8499: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8500: } /* end i */
8501: fprintf(ficresf," %.3f", ppij);
8502: }/* end j */
1.227 brouard 8503: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8504: } /* end agec */
1.266 brouard 8505: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8506: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8507: } /* end yearp */
8508: } /* end k */
1.219 brouard 8509:
1.126 brouard 8510: fclose(ficresf);
1.215 brouard 8511: printf("End of Computing forecasting \n");
8512: fprintf(ficlog,"End of Computing forecasting\n");
8513:
1.126 brouard 8514: }
8515:
1.269 brouard 8516: /************** Back Forecasting ******************/
1.296 brouard 8517: /* 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){ */
8518: 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){
8519: /* back1, year, month, day of starting backprojection
1.267 brouard 8520: agemin, agemax range of age
8521: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8522: anback2 year of end of backprojection (same day and month as back1).
8523: prevacurrent and prev are prevalences.
1.267 brouard 8524: */
8525: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8526: double agec; /* generic age */
1.302 brouard 8527: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8528: double *popeffectif,*popcount;
8529: double ***p3mat;
8530: /* double ***mobaverage; */
8531: char fileresfb[FILENAMELENGTH];
8532:
1.268 brouard 8533: agelim=AGEINF;
1.267 brouard 8534: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8535: in each health status at the date of interview (if between dateprev1 and dateprev2).
8536: We still use firstpass and lastpass as another selection.
8537: */
8538: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8539: /* firstpass, lastpass, stepm, weightopt, model); */
8540:
8541: /*Do we need to compute prevalence again?*/
8542:
8543: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8544:
8545: strcpy(fileresfb,"FB_");
8546: strcat(fileresfb,fileresu);
8547: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8548: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8549: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8550: }
8551: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8552: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8553:
8554: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8555:
8556:
8557: stepsize=(int) (stepm+YEARM-1)/YEARM;
8558: if (stepm<=12) stepsize=1;
8559: if(estepm < stepm){
8560: printf ("Problem %d lower than %d\n",estepm, stepm);
8561: }
1.270 brouard 8562: else{
8563: hstepm=estepm;
8564: }
8565: if(estepm >= stepm){ /* Yes every two year */
8566: stepsize=2;
8567: }
1.267 brouard 8568:
8569: hstepm=hstepm/stepm;
1.296 brouard 8570: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8571: /* fractional in yp1 *\/ */
8572: /* aintmean=yp; */
8573: /* yp2=modf((yp1*12),&yp); */
8574: /* mintmean=yp; */
8575: /* yp1=modf((yp2*30.5),&yp); */
8576: /* jintmean=yp; */
8577: /* if(jintmean==0) jintmean=1; */
8578: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8579:
8580: i1=pow(2,cptcoveff);
8581: if (cptcovn < 1){i1=1;}
8582:
1.296 brouard 8583: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8584: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8585:
8586: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8587:
8588: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8589: for(k=1; k<=i1;k++){
8590: if(i1 != 1 && TKresult[nres]!= k)
8591: continue;
8592: if(invalidvarcomb[k]){
8593: printf("\nCombination (%d) projection ignored because no cases \n",k);
8594: continue;
8595: }
1.268 brouard 8596: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8597: for(j=1;j<=cptcoveff;j++) {
8598: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8599: }
8600: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8601: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8602: }
8603: fprintf(ficresfb," yearbproj age");
8604: for(j=1; j<=nlstate+ndeath;j++){
8605: for(i=1; i<=nlstate;i++)
1.268 brouard 8606: fprintf(ficresfb," b%d%d",i,j);
8607: fprintf(ficresfb," b.%d",j);
1.267 brouard 8608: }
1.296 brouard 8609: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8610: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8611: fprintf(ficresfb,"\n");
1.296 brouard 8612: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8613: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8614: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8615: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8616: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8617: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8618: nhstepm = nhstepm/hstepm;
8619: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8620: oldm=oldms;savm=savms;
1.268 brouard 8621: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8622: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8623: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8624: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8625: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8626: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8627: for (h=0; h<=nhstepm; h++){
1.268 brouard 8628: if (h*hstepm/YEARM*stepm ==-yearp) {
8629: break;
8630: }
8631: }
8632: fprintf(ficresfb,"\n");
8633: for(j=1;j<=cptcoveff;j++)
8634: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8635: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8636: for(i=1; i<=nlstate+ndeath;i++) {
8637: ppij=0.;ppi=0.;
8638: for(j=1; j<=nlstate;j++) {
8639: /* if (mobilav==1) */
1.269 brouard 8640: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8641: ppi=ppi+prevacurrent[(int)agec][j][k];
8642: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8643: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8644: /* else { */
8645: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8646: /* } */
1.268 brouard 8647: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8648: } /* end j */
8649: if(ppi <0.99){
8650: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8651: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8652: }
8653: fprintf(ficresfb," %.3f", ppij);
8654: }/* end j */
1.267 brouard 8655: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8656: } /* end agec */
8657: } /* end yearp */
8658: } /* end k */
1.217 brouard 8659:
1.267 brouard 8660: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8661:
1.267 brouard 8662: fclose(ficresfb);
8663: printf("End of Computing Back forecasting \n");
8664: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8665:
1.267 brouard 8666: }
1.217 brouard 8667:
1.269 brouard 8668: /* Variance of prevalence limit: varprlim */
8669: 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 8670: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8671:
8672: char fileresvpl[FILENAMELENGTH];
8673: FILE *ficresvpl;
8674: double **oldm, **savm;
8675: double **varpl; /* Variances of prevalence limits by age */
8676: int i1, k, nres, j ;
8677:
8678: strcpy(fileresvpl,"VPL_");
8679: strcat(fileresvpl,fileresu);
8680: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8681: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8682: exit(0);
8683: }
1.288 brouard 8684: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8685: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8686:
8687: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8688: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8689:
8690: i1=pow(2,cptcoveff);
8691: if (cptcovn < 1){i1=1;}
8692:
8693: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8694: for(k=1; k<=i1;k++){
8695: if(i1 != 1 && TKresult[nres]!= k)
8696: continue;
8697: fprintf(ficresvpl,"\n#****** ");
8698: printf("\n#****** ");
8699: fprintf(ficlog,"\n#****** ");
8700: for(j=1;j<=cptcoveff;j++) {
8701: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8702: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8703: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8704: }
8705: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8706: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8707: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8708: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8709: }
8710: fprintf(ficresvpl,"******\n");
8711: printf("******\n");
8712: fprintf(ficlog,"******\n");
8713:
8714: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8715: oldm=oldms;savm=savms;
8716: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8717: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8718: /*}*/
8719: }
8720:
8721: fclose(ficresvpl);
1.288 brouard 8722: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8723: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8724:
8725: }
8726: /* Variance of back prevalence: varbprlim */
8727: 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){
8728: /*------- Variance of back (stable) prevalence------*/
8729:
8730: char fileresvbl[FILENAMELENGTH];
8731: FILE *ficresvbl;
8732:
8733: double **oldm, **savm;
8734: double **varbpl; /* Variances of back prevalence limits by age */
8735: int i1, k, nres, j ;
8736:
8737: strcpy(fileresvbl,"VBL_");
8738: strcat(fileresvbl,fileresu);
8739: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8740: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8741: exit(0);
8742: }
8743: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8744: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8745:
8746:
8747: i1=pow(2,cptcoveff);
8748: if (cptcovn < 1){i1=1;}
8749:
8750: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8751: for(k=1; k<=i1;k++){
8752: if(i1 != 1 && TKresult[nres]!= k)
8753: continue;
8754: fprintf(ficresvbl,"\n#****** ");
8755: printf("\n#****** ");
8756: fprintf(ficlog,"\n#****** ");
8757: for(j=1;j<=cptcoveff;j++) {
8758: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8759: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8760: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8761: }
8762: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8763: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8764: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8765: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8766: }
8767: fprintf(ficresvbl,"******\n");
8768: printf("******\n");
8769: fprintf(ficlog,"******\n");
8770:
8771: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8772: oldm=oldms;savm=savms;
8773:
8774: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8775: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8776: /*}*/
8777: }
8778:
8779: fclose(ficresvbl);
8780: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8781: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8782:
8783: } /* End of varbprlim */
8784:
1.126 brouard 8785: /************** Forecasting *****not tested NB*************/
1.227 brouard 8786: /* 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 8787:
1.227 brouard 8788: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8789: /* int *popage; */
8790: /* double calagedatem, agelim, kk1, kk2; */
8791: /* double *popeffectif,*popcount; */
8792: /* double ***p3mat,***tabpop,***tabpopprev; */
8793: /* /\* double ***mobaverage; *\/ */
8794: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8795:
1.227 brouard 8796: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8797: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8798: /* agelim=AGESUP; */
8799: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8800:
1.227 brouard 8801: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8802:
8803:
1.227 brouard 8804: /* strcpy(filerespop,"POP_"); */
8805: /* strcat(filerespop,fileresu); */
8806: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8807: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8808: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8809: /* } */
8810: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8811: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8812:
1.227 brouard 8813: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8814:
1.227 brouard 8815: /* /\* if (mobilav!=0) { *\/ */
8816: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8817: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8818: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8819: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8820: /* /\* } *\/ */
8821: /* /\* } *\/ */
1.126 brouard 8822:
1.227 brouard 8823: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8824: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8825:
1.227 brouard 8826: /* agelim=AGESUP; */
1.126 brouard 8827:
1.227 brouard 8828: /* hstepm=1; */
8829: /* hstepm=hstepm/stepm; */
1.218 brouard 8830:
1.227 brouard 8831: /* if (popforecast==1) { */
8832: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8833: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8834: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8835: /* } */
8836: /* popage=ivector(0,AGESUP); */
8837: /* popeffectif=vector(0,AGESUP); */
8838: /* popcount=vector(0,AGESUP); */
1.126 brouard 8839:
1.227 brouard 8840: /* i=1; */
8841: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8842:
1.227 brouard 8843: /* imx=i; */
8844: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8845: /* } */
1.218 brouard 8846:
1.227 brouard 8847: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8848: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8849: /* k=k+1; */
8850: /* fprintf(ficrespop,"\n#******"); */
8851: /* for(j=1;j<=cptcoveff;j++) { */
8852: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8853: /* } */
8854: /* fprintf(ficrespop,"******\n"); */
8855: /* fprintf(ficrespop,"# Age"); */
8856: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8857: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8858:
1.227 brouard 8859: /* for (cpt=0; cpt<=0;cpt++) { */
8860: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8861:
1.227 brouard 8862: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8863: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8864: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8865:
1.227 brouard 8866: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8867: /* oldm=oldms;savm=savms; */
8868: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8869:
1.227 brouard 8870: /* for (h=0; h<=nhstepm; h++){ */
8871: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8872: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8873: /* } */
8874: /* for(j=1; j<=nlstate+ndeath;j++) { */
8875: /* kk1=0.;kk2=0; */
8876: /* for(i=1; i<=nlstate;i++) { */
8877: /* if (mobilav==1) */
8878: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8879: /* else { */
8880: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8881: /* } */
8882: /* } */
8883: /* if (h==(int)(calagedatem+12*cpt)){ */
8884: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8885: /* /\*fprintf(ficrespop," %.3f", kk1); */
8886: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8887: /* } */
8888: /* } */
8889: /* for(i=1; i<=nlstate;i++){ */
8890: /* kk1=0.; */
8891: /* for(j=1; j<=nlstate;j++){ */
8892: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8893: /* } */
8894: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8895: /* } */
1.218 brouard 8896:
1.227 brouard 8897: /* if (h==(int)(calagedatem+12*cpt)) */
8898: /* for(j=1; j<=nlstate;j++) */
8899: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8900: /* } */
8901: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8902: /* } */
8903: /* } */
1.218 brouard 8904:
1.227 brouard 8905: /* /\******\/ */
1.218 brouard 8906:
1.227 brouard 8907: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8908: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8909: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8910: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8911: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8912:
1.227 brouard 8913: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8914: /* oldm=oldms;savm=savms; */
8915: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8916: /* for (h=0; h<=nhstepm; h++){ */
8917: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8918: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8919: /* } */
8920: /* for(j=1; j<=nlstate+ndeath;j++) { */
8921: /* kk1=0.;kk2=0; */
8922: /* for(i=1; i<=nlstate;i++) { */
8923: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8924: /* } */
8925: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8926: /* } */
8927: /* } */
8928: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8929: /* } */
8930: /* } */
8931: /* } */
8932: /* } */
1.218 brouard 8933:
1.227 brouard 8934: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8935:
1.227 brouard 8936: /* if (popforecast==1) { */
8937: /* free_ivector(popage,0,AGESUP); */
8938: /* free_vector(popeffectif,0,AGESUP); */
8939: /* free_vector(popcount,0,AGESUP); */
8940: /* } */
8941: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8942: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8943: /* fclose(ficrespop); */
8944: /* } /\* End of popforecast *\/ */
1.218 brouard 8945:
1.126 brouard 8946: int fileappend(FILE *fichier, char *optionfich)
8947: {
8948: if((fichier=fopen(optionfich,"a"))==NULL) {
8949: printf("Problem with file: %s\n", optionfich);
8950: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8951: return (0);
8952: }
8953: fflush(fichier);
8954: return (1);
8955: }
8956:
8957:
8958: /**************** function prwizard **********************/
8959: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8960: {
8961:
8962: /* Wizard to print covariance matrix template */
8963:
1.164 brouard 8964: char ca[32], cb[32];
8965: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8966: int numlinepar;
8967:
8968: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8969: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8970: for(i=1; i <=nlstate; i++){
8971: jj=0;
8972: for(j=1; j <=nlstate+ndeath; j++){
8973: if(j==i) continue;
8974: jj++;
8975: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8976: printf("%1d%1d",i,j);
8977: fprintf(ficparo,"%1d%1d",i,j);
8978: for(k=1; k<=ncovmodel;k++){
8979: /* printf(" %lf",param[i][j][k]); */
8980: /* fprintf(ficparo," %lf",param[i][j][k]); */
8981: printf(" 0.");
8982: fprintf(ficparo," 0.");
8983: }
8984: printf("\n");
8985: fprintf(ficparo,"\n");
8986: }
8987: }
8988: printf("# Scales (for hessian or gradient estimation)\n");
8989: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8990: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8991: for(i=1; i <=nlstate; i++){
8992: jj=0;
8993: for(j=1; j <=nlstate+ndeath; j++){
8994: if(j==i) continue;
8995: jj++;
8996: fprintf(ficparo,"%1d%1d",i,j);
8997: printf("%1d%1d",i,j);
8998: fflush(stdout);
8999: for(k=1; k<=ncovmodel;k++){
9000: /* printf(" %le",delti3[i][j][k]); */
9001: /* fprintf(ficparo," %le",delti3[i][j][k]); */
9002: printf(" 0.");
9003: fprintf(ficparo," 0.");
9004: }
9005: numlinepar++;
9006: printf("\n");
9007: fprintf(ficparo,"\n");
9008: }
9009: }
9010: printf("# Covariance matrix\n");
9011: /* # 121 Var(a12)\n\ */
9012: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9013: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9014: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9015: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9016: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9017: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9018: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9019: fflush(stdout);
9020: fprintf(ficparo,"# Covariance matrix\n");
9021: /* # 121 Var(a12)\n\ */
9022: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9023: /* # ...\n\ */
9024: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9025:
9026: for(itimes=1;itimes<=2;itimes++){
9027: jj=0;
9028: for(i=1; i <=nlstate; i++){
9029: for(j=1; j <=nlstate+ndeath; j++){
9030: if(j==i) continue;
9031: for(k=1; k<=ncovmodel;k++){
9032: jj++;
9033: ca[0]= k+'a'-1;ca[1]='\0';
9034: if(itimes==1){
9035: printf("#%1d%1d%d",i,j,k);
9036: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9037: }else{
9038: printf("%1d%1d%d",i,j,k);
9039: fprintf(ficparo,"%1d%1d%d",i,j,k);
9040: /* printf(" %.5le",matcov[i][j]); */
9041: }
9042: ll=0;
9043: for(li=1;li <=nlstate; li++){
9044: for(lj=1;lj <=nlstate+ndeath; lj++){
9045: if(lj==li) continue;
9046: for(lk=1;lk<=ncovmodel;lk++){
9047: ll++;
9048: if(ll<=jj){
9049: cb[0]= lk +'a'-1;cb[1]='\0';
9050: if(ll<jj){
9051: if(itimes==1){
9052: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9053: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9054: }else{
9055: printf(" 0.");
9056: fprintf(ficparo," 0.");
9057: }
9058: }else{
9059: if(itimes==1){
9060: printf(" Var(%s%1d%1d)",ca,i,j);
9061: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9062: }else{
9063: printf(" 0.");
9064: fprintf(ficparo," 0.");
9065: }
9066: }
9067: }
9068: } /* end lk */
9069: } /* end lj */
9070: } /* end li */
9071: printf("\n");
9072: fprintf(ficparo,"\n");
9073: numlinepar++;
9074: } /* end k*/
9075: } /*end j */
9076: } /* end i */
9077: } /* end itimes */
9078:
9079: } /* end of prwizard */
9080: /******************* Gompertz Likelihood ******************************/
9081: double gompertz(double x[])
9082: {
1.302 brouard 9083: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9084: int i,n=0; /* n is the size of the sample */
9085:
1.220 brouard 9086: for (i=1;i<=imx ; i++) {
1.126 brouard 9087: sump=sump+weight[i];
9088: /* sump=sump+1;*/
9089: num=num+1;
9090: }
1.302 brouard 9091: L=0.0;
9092: /* agegomp=AGEGOMP; */
1.126 brouard 9093: /* for (i=0; i<=imx; i++)
9094: 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]);*/
9095:
1.302 brouard 9096: for (i=1;i<=imx ; i++) {
9097: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9098: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9099: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9100: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9101: * +
9102: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9103: */
9104: if (wav[i] > 1 || agedc[i] < AGESUP) {
9105: if (cens[i] == 1){
9106: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9107: } else if (cens[i] == 0){
1.126 brouard 9108: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9109: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9110: } else
9111: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9112: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9113: L=L+A*weight[i];
1.126 brouard 9114: /* 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 9115: }
9116: }
1.126 brouard 9117:
1.302 brouard 9118: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9119:
9120: return -2*L*num/sump;
9121: }
9122:
1.136 brouard 9123: #ifdef GSL
9124: /******************* Gompertz_f Likelihood ******************************/
9125: double gompertz_f(const gsl_vector *v, void *params)
9126: {
1.302 brouard 9127: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9128: double *x= (double *) v->data;
9129: int i,n=0; /* n is the size of the sample */
9130:
9131: for (i=0;i<=imx-1 ; i++) {
9132: sump=sump+weight[i];
9133: /* sump=sump+1;*/
9134: num=num+1;
9135: }
9136:
9137:
9138: /* for (i=0; i<=imx; i++)
9139: 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]);*/
9140: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9141: for (i=1;i<=imx ; i++)
9142: {
9143: if (cens[i] == 1 && wav[i]>1)
9144: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9145:
9146: if (cens[i] == 0 && wav[i]>1)
9147: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9148: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9149:
9150: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9151: if (wav[i] > 1 ) { /* ??? */
9152: LL=LL+A*weight[i];
9153: /* 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]);*/
9154: }
9155: }
9156:
9157: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9158: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9159:
9160: return -2*LL*num/sump;
9161: }
9162: #endif
9163:
1.126 brouard 9164: /******************* Printing html file ***********/
1.201 brouard 9165: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9166: int lastpass, int stepm, int weightopt, char model[],\
9167: int imx, double p[],double **matcov,double agemortsup){
9168: int i,k;
9169:
9170: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9171: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9172: for (i=1;i<=2;i++)
9173: 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 9174: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9175: fprintf(fichtm,"</ul>");
9176:
9177: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9178:
9179: 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>");
9180:
9181: for (k=agegomp;k<(agemortsup-2);k++)
9182: 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]);
9183:
9184:
9185: fflush(fichtm);
9186: }
9187:
9188: /******************* Gnuplot file **************/
1.201 brouard 9189: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9190:
9191: char dirfileres[132],optfileres[132];
1.164 brouard 9192:
1.126 brouard 9193: int ng;
9194:
9195:
9196: /*#ifdef windows */
9197: fprintf(ficgp,"cd \"%s\" \n",pathc);
9198: /*#endif */
9199:
9200:
9201: strcpy(dirfileres,optionfilefiname);
9202: strcpy(optfileres,"vpl");
1.199 brouard 9203: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9204: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9205: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9206: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9207: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9208:
9209: }
9210:
1.136 brouard 9211: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9212: {
1.126 brouard 9213:
1.136 brouard 9214: /*-------- data file ----------*/
9215: FILE *fic;
9216: char dummy[]=" ";
1.240 brouard 9217: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9218: int lstra;
1.136 brouard 9219: int linei, month, year,iout;
1.302 brouard 9220: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9221: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9222: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9223: char *stratrunc;
1.223 brouard 9224:
1.240 brouard 9225: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9226: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9227:
1.240 brouard 9228: for(v=1; v <=ncovcol;v++){
9229: DummyV[v]=0;
9230: FixedV[v]=0;
9231: }
9232: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9233: DummyV[v]=1;
9234: FixedV[v]=0;
9235: }
9236: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9237: DummyV[v]=0;
9238: FixedV[v]=1;
9239: }
9240: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9241: DummyV[v]=1;
9242: FixedV[v]=1;
9243: }
9244: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9245: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9246: 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]);
9247: }
1.126 brouard 9248:
1.136 brouard 9249: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9250: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9251: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9252: }
1.126 brouard 9253:
1.302 brouard 9254: /* Is it a BOM UTF-8 Windows file? */
9255: /* First data line */
9256: linei=0;
9257: while(fgets(line, MAXLINE, fic)) {
9258: noffset=0;
9259: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9260: {
9261: noffset=noffset+3;
9262: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9263: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9264: fflush(ficlog); return 1;
9265: }
9266: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9267: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9268: {
9269: noffset=noffset+2;
1.304 brouard 9270: 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);
9271: 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 9272: fflush(ficlog); return 1;
9273: }
9274: else if( line[0] == 0 && line[1] == 0)
9275: {
9276: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9277: noffset=noffset+4;
1.304 brouard 9278: 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);
9279: 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 9280: fflush(ficlog); return 1;
9281: }
9282: } else{
9283: ;/*printf(" Not a BOM file\n");*/
9284: }
9285: /* If line starts with a # it is a comment */
9286: if (line[noffset] == '#') {
9287: linei=linei+1;
9288: break;
9289: }else{
9290: break;
9291: }
9292: }
9293: fclose(fic);
9294: if((fic=fopen(datafile,"r"))==NULL) {
9295: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9296: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9297: }
9298: /* Not a Bom file */
9299:
1.136 brouard 9300: i=1;
9301: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9302: linei=linei+1;
9303: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9304: if(line[j] == '\t')
9305: line[j] = ' ';
9306: }
9307: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9308: ;
9309: };
9310: line[j+1]=0; /* Trims blanks at end of line */
9311: if(line[0]=='#'){
9312: fprintf(ficlog,"Comment line\n%s\n",line);
9313: printf("Comment line\n%s\n",line);
9314: continue;
9315: }
9316: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9317: strcpy(line, linetmp);
1.223 brouard 9318:
9319: /* Loops on waves */
9320: for (j=maxwav;j>=1;j--){
9321: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9322: cutv(stra, strb, line, ' ');
9323: if(strb[0]=='.') { /* Missing value */
9324: lval=-1;
9325: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9326: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9327: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9328: 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);
9329: 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);
9330: return 1;
9331: }
9332: }else{
9333: errno=0;
9334: /* what_kind_of_number(strb); */
9335: dval=strtod(strb,&endptr);
9336: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9337: /* if(strb != endptr && *endptr == '\0') */
9338: /* dval=dlval; */
9339: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9340: if( strb[0]=='\0' || (*endptr != '\0')){
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. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
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. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
9343: return 1;
9344: }
9345: cotqvar[j][iv][i]=dval;
9346: cotvar[j][ntv+iv][i]=dval;
9347: }
9348: strcpy(line,stra);
1.223 brouard 9349: }/* end loop ntqv */
1.225 brouard 9350:
1.223 brouard 9351: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9352: cutv(stra, strb, line, ' ');
9353: if(strb[0]=='.') { /* Missing value */
9354: lval=-1;
9355: }else{
9356: errno=0;
9357: lval=strtol(strb,&endptr,10);
9358: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9359: if( strb[0]=='\0' || (*endptr != '\0')){
9360: 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);
9361: 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);
9362: return 1;
9363: }
9364: }
9365: if(lval <-1 || lval >1){
9366: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9367: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9368: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9369: For example, for multinomial values like 1, 2 and 3,\n \
9370: build V1=0 V2=0 for the reference value (1),\n \
9371: V1=1 V2=0 for (2) \n \
1.223 brouard 9372: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9373: output of IMaCh is often meaningless.\n \
1.223 brouard 9374: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9375: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9376: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9377: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9378: For example, for multinomial values like 1, 2 and 3,\n \
9379: build V1=0 V2=0 for the reference value (1),\n \
9380: V1=1 V2=0 for (2) \n \
1.223 brouard 9381: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9382: output of IMaCh is often meaningless.\n \
1.223 brouard 9383: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9384: return 1;
9385: }
9386: cotvar[j][iv][i]=(double)(lval);
9387: strcpy(line,stra);
1.223 brouard 9388: }/* end loop ntv */
1.225 brouard 9389:
1.223 brouard 9390: /* Statuses at wave */
1.137 brouard 9391: cutv(stra, strb, line, ' ');
1.223 brouard 9392: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9393: lval=-1;
1.136 brouard 9394: }else{
1.238 brouard 9395: errno=0;
9396: lval=strtol(strb,&endptr,10);
9397: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9398: if( strb[0]=='\0' || (*endptr != '\0')){
9399: 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);
9400: 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);
9401: return 1;
9402: }
1.136 brouard 9403: }
1.225 brouard 9404:
1.136 brouard 9405: s[j][i]=lval;
1.225 brouard 9406:
1.223 brouard 9407: /* Date of Interview */
1.136 brouard 9408: strcpy(line,stra);
9409: cutv(stra, strb,line,' ');
1.169 brouard 9410: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9411: }
1.169 brouard 9412: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9413: month=99;
9414: year=9999;
1.136 brouard 9415: }else{
1.225 brouard 9416: 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);
9417: 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);
9418: return 1;
1.136 brouard 9419: }
9420: anint[j][i]= (double) year;
1.302 brouard 9421: mint[j][i]= (double)month;
9422: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9423: /* 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]); */
9424: /* 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]); */
9425: /* } */
1.136 brouard 9426: strcpy(line,stra);
1.223 brouard 9427: } /* End loop on waves */
1.225 brouard 9428:
1.223 brouard 9429: /* Date of death */
1.136 brouard 9430: cutv(stra, strb,line,' ');
1.169 brouard 9431: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9432: }
1.169 brouard 9433: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9434: month=99;
9435: year=9999;
9436: }else{
1.141 brouard 9437: 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 9438: 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);
9439: return 1;
1.136 brouard 9440: }
9441: andc[i]=(double) year;
9442: moisdc[i]=(double) month;
9443: strcpy(line,stra);
9444:
1.223 brouard 9445: /* Date of birth */
1.136 brouard 9446: cutv(stra, strb,line,' ');
1.169 brouard 9447: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9448: }
1.169 brouard 9449: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9450: month=99;
9451: year=9999;
9452: }else{
1.141 brouard 9453: 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);
9454: 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 9455: return 1;
1.136 brouard 9456: }
9457: if (year==9999) {
1.141 brouard 9458: 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);
9459: 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 9460: return 1;
9461:
1.136 brouard 9462: }
9463: annais[i]=(double)(year);
1.302 brouard 9464: moisnais[i]=(double)(month);
9465: for (j=1;j<=maxwav;j++){
9466: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9467: 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]);
9468: 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]);
9469: }
9470: }
9471:
1.136 brouard 9472: strcpy(line,stra);
1.225 brouard 9473:
1.223 brouard 9474: /* Sample weight */
1.136 brouard 9475: cutv(stra, strb,line,' ');
9476: errno=0;
9477: dval=strtod(strb,&endptr);
9478: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9479: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9480: 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 9481: fflush(ficlog);
9482: return 1;
9483: }
9484: weight[i]=dval;
9485: strcpy(line,stra);
1.225 brouard 9486:
1.223 brouard 9487: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9488: cutv(stra, strb, line, ' ');
9489: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9490: lval=-1;
1.223 brouard 9491: }else{
1.225 brouard 9492: errno=0;
9493: /* what_kind_of_number(strb); */
9494: dval=strtod(strb,&endptr);
9495: /* if(strb != endptr && *endptr == '\0') */
9496: /* dval=dlval; */
9497: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9498: if( strb[0]=='\0' || (*endptr != '\0')){
9499: 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);
9500: 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);
9501: return 1;
9502: }
9503: coqvar[iv][i]=dval;
1.226 brouard 9504: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9505: }
9506: strcpy(line,stra);
9507: }/* end loop nqv */
1.136 brouard 9508:
1.223 brouard 9509: /* Covariate values */
1.136 brouard 9510: for (j=ncovcol;j>=1;j--){
9511: cutv(stra, strb,line,' ');
1.223 brouard 9512: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9513: lval=-1;
1.136 brouard 9514: }else{
1.225 brouard 9515: errno=0;
9516: lval=strtol(strb,&endptr,10);
9517: if( strb[0]=='\0' || (*endptr != '\0')){
9518: 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);
9519: 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);
9520: return 1;
9521: }
1.136 brouard 9522: }
9523: if(lval <-1 || lval >1){
1.225 brouard 9524: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9525: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9526: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9527: For example, for multinomial values like 1, 2 and 3,\n \
9528: build V1=0 V2=0 for the reference value (1),\n \
9529: V1=1 V2=0 for (2) \n \
1.136 brouard 9530: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9531: output of IMaCh is often meaningless.\n \
1.136 brouard 9532: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9533: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9534: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9535: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9536: For example, for multinomial values like 1, 2 and 3,\n \
9537: build V1=0 V2=0 for the reference value (1),\n \
9538: V1=1 V2=0 for (2) \n \
1.136 brouard 9539: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9540: output of IMaCh is often meaningless.\n \
1.136 brouard 9541: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9542: return 1;
1.136 brouard 9543: }
9544: covar[j][i]=(double)(lval);
9545: strcpy(line,stra);
9546: }
9547: lstra=strlen(stra);
1.225 brouard 9548:
1.136 brouard 9549: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9550: stratrunc = &(stra[lstra-9]);
9551: num[i]=atol(stratrunc);
9552: }
9553: else
9554: num[i]=atol(stra);
9555: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9556: 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;}*/
9557:
9558: i=i+1;
9559: } /* End loop reading data */
1.225 brouard 9560:
1.136 brouard 9561: *imax=i-1; /* Number of individuals */
9562: fclose(fic);
1.225 brouard 9563:
1.136 brouard 9564: return (0);
1.164 brouard 9565: /* endread: */
1.225 brouard 9566: printf("Exiting readdata: ");
9567: fclose(fic);
9568: return (1);
1.223 brouard 9569: }
1.126 brouard 9570:
1.234 brouard 9571: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9572: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9573: while (*p2 == ' ')
1.234 brouard 9574: p2++;
9575: /* while ((*p1++ = *p2++) !=0) */
9576: /* ; */
9577: /* do */
9578: /* while (*p2 == ' ') */
9579: /* p2++; */
9580: /* while (*p1++ == *p2++); */
9581: *stri=p2;
1.145 brouard 9582: }
9583:
1.235 brouard 9584: int decoderesult ( char resultline[], int nres)
1.230 brouard 9585: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9586: {
1.235 brouard 9587: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9588: char resultsav[MAXLINE];
1.234 brouard 9589: int resultmodel[MAXLINE];
9590: int modelresult[MAXLINE];
1.230 brouard 9591: char stra[80], strb[80], strc[80], strd[80],stre[80];
9592:
1.234 brouard 9593: removefirstspace(&resultline);
1.230 brouard 9594:
9595: if (strstr(resultline,"v") !=0){
9596: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9597: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9598: return 1;
9599: }
9600: trimbb(resultsav, resultline);
9601: if (strlen(resultsav) >1){
9602: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9603: }
1.253 brouard 9604: if(j == 0){ /* Resultline but no = */
9605: TKresult[nres]=0; /* Combination for the nresult and the model */
9606: return (0);
9607: }
1.234 brouard 9608: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9609: printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
9610: fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
9611: }
9612: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9613: if(nbocc(resultsav,'=') >1){
9614: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9615: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9616: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9617: }else
9618: cutl(strc,strd,resultsav,'=');
1.230 brouard 9619: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9620:
1.230 brouard 9621: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9622: Tvarsel[k]=atoi(strc);
9623: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9624: /* cptcovsel++; */
9625: if (nbocc(stra,'=') >0)
9626: strcpy(resultsav,stra); /* and analyzes it */
9627: }
1.235 brouard 9628: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9629: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9630: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9631: match=0;
1.236 brouard 9632: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9633: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9634: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9635: match=1;
9636: break;
9637: }
9638: }
9639: if(match == 0){
9640: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9641: }
9642: }
9643: }
1.235 brouard 9644: /* Checking for missing or useless values in comparison of current model needs */
9645: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9646: match=0;
1.235 brouard 9647: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9648: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9649: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9650: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9651: ++match;
9652: }
9653: }
9654: }
9655: if(match == 0){
9656: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9657: }else if(match > 1){
9658: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9659: }
9660: }
1.235 brouard 9661:
1.234 brouard 9662: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9663: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9664: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9665: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9666: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9667: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9668: /* 1 0 0 0 */
9669: /* 2 1 0 0 */
9670: /* 3 0 1 0 */
9671: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9672: /* 5 0 0 1 */
9673: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9674: /* 7 0 1 1 */
9675: /* 8 1 1 1 */
1.237 brouard 9676: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9677: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9678: /* V5*age V5 known which value for nres? */
9679: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9680: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9681: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9682: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9683: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9684: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9685: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9686: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9687: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9688: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9689: k4++;;
9690: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9691: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9692: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9693: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9694: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9695: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9696: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9697: k4q++;;
9698: }
9699: }
1.234 brouard 9700:
1.235 brouard 9701: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9702: return (0);
9703: }
1.235 brouard 9704:
1.230 brouard 9705: int decodemodel( char model[], int lastobs)
9706: /**< This routine decodes the model and returns:
1.224 brouard 9707: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9708: * - nagesqr = 1 if age*age in the model, otherwise 0.
9709: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9710: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9711: * - cptcovage number of covariates with age*products =2
9712: * - cptcovs number of simple covariates
9713: * - 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
9714: * which is a new column after the 9 (ncovcol) variables.
9715: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9716: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9717: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9718: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9719: */
1.136 brouard 9720: {
1.238 brouard 9721: int i, j, k, ks, v;
1.227 brouard 9722: int j1, k1, k2, k3, k4;
1.136 brouard 9723: char modelsav[80];
1.145 brouard 9724: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9725: char *strpt;
1.136 brouard 9726:
1.145 brouard 9727: /*removespace(model);*/
1.136 brouard 9728: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9729: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9730: if (strstr(model,"AGE") !=0){
1.192 brouard 9731: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9732: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9733: return 1;
9734: }
1.141 brouard 9735: if (strstr(model,"v") !=0){
9736: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9737: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9738: return 1;
9739: }
1.187 brouard 9740: strcpy(modelsav,model);
9741: if ((strpt=strstr(model,"age*age")) !=0){
9742: printf(" strpt=%s, model=%s\n",strpt, model);
9743: if(strpt != model){
1.234 brouard 9744: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9745: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9746: corresponding column of parameters.\n",model);
1.234 brouard 9747: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9748: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9749: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9750: return 1;
1.225 brouard 9751: }
1.187 brouard 9752: nagesqr=1;
9753: if (strstr(model,"+age*age") !=0)
1.234 brouard 9754: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9755: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9756: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9757: else
1.234 brouard 9758: substrchaine(modelsav, model, "age*age");
1.187 brouard 9759: }else
9760: nagesqr=0;
9761: if (strlen(modelsav) >1){
9762: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9763: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9764: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9765: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9766: * cst, age and age*age
9767: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9768: /* including age products which are counted in cptcovage.
9769: * but the covariates which are products must be treated
9770: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9771: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9772: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9773:
9774:
1.187 brouard 9775: /* Design
9776: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9777: * < ncovcol=8 >
9778: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9779: * k= 1 2 3 4 5 6 7 8
9780: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9781: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9782: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9783: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9784: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9785: * Tage[++cptcovage]=k
9786: * if products, new covar are created after ncovcol with k1
9787: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9788: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9789: * 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
9790: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9791: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9792: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9793: * < ncovcol=8 >
9794: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9795: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9796: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9797: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9798: * p Tprod[1]@2={ 6, 5}
9799: *p Tvard[1][1]@4= {7, 8, 5, 6}
9800: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9801: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9802: *How to reorganize?
9803: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9804: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9805: * {2, 1, 4, 8, 5, 6, 3, 7}
9806: * Struct []
9807: */
1.225 brouard 9808:
1.187 brouard 9809: /* This loop fills the array Tvar from the string 'model'.*/
9810: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9811: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9812: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9813: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9814: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9815: /* k=1 Tvar[1]=2 (from V2) */
9816: /* k=5 Tvar[5] */
9817: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9818: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9819: /* } */
1.198 brouard 9820: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9821: /*
9822: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9823: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9824: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9825: }
1.187 brouard 9826: cptcovage=0;
9827: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9828: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9829: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9830: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9831: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9832: /*scanf("%d",i);*/
9833: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9834: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9835: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9836: /* covar is not filled and then is empty */
9837: cptcovprod--;
9838: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9839: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9840: Typevar[k]=1; /* 1 for age product */
9841: cptcovage++; /* Sums the number of covariates which include age as a product */
9842: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9843: /*printf("stre=%s ", stre);*/
9844: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9845: cptcovprod--;
9846: cutl(stre,strb,strc,'V');
9847: Tvar[k]=atoi(stre);
9848: Typevar[k]=1; /* 1 for age product */
9849: cptcovage++;
9850: Tage[cptcovage]=k;
9851: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9852: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9853: cptcovn++;
9854: cptcovprodnoage++;k1++;
9855: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9856: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9857: because this model-covariate is a construction we invent a new column
9858: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9859: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9860: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9861: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9862: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9863: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9864: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9865: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9866: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9867: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9868: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9869: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9870: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9871: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9872: for (i=1; i<=lastobs;i++){
9873: /* Computes the new covariate which is a product of
9874: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9875: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9876: }
9877: } /* End age is not in the model */
9878: } /* End if model includes a product */
9879: else { /* no more sum */
9880: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9881: /* scanf("%d",i);*/
9882: cutl(strd,strc,strb,'V');
9883: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9884: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9885: Tvar[k]=atoi(strd);
9886: Typevar[k]=0; /* 0 for simple covariates */
9887: }
9888: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9889: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9890: scanf("%d",i);*/
1.187 brouard 9891: } /* end of loop + on total covariates */
9892: } /* end if strlen(modelsave == 0) age*age might exist */
9893: } /* end if strlen(model == 0) */
1.136 brouard 9894:
9895: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9896: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9897:
1.136 brouard 9898: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9899: printf("cptcovprod=%d ", cptcovprod);
9900: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9901: scanf("%d ",i);*/
9902:
9903:
1.230 brouard 9904: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9905: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9906: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9907: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9908: k = 1 2 3 4 5 6 7 8 9
9909: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9910: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9911: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9912: Dummy[k] 1 0 0 0 3 1 1 2 3
9913: Tmodelind[combination of covar]=k;
1.225 brouard 9914: */
9915: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9916: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9917: /* 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 9918: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9919: printf("Model=%s\n\
9920: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9921: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9922: 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);
9923: fprintf(ficlog,"Model=%s\n\
9924: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9925: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9926: 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 9927: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9928: 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 */
9929: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9930: Fixed[k]= 0;
9931: Dummy[k]= 0;
1.225 brouard 9932: ncoveff++;
1.232 brouard 9933: ncovf++;
1.234 brouard 9934: nsd++;
9935: modell[k].maintype= FTYPE;
9936: TvarsD[nsd]=Tvar[k];
9937: TvarsDind[nsd]=k;
9938: TvarF[ncovf]=Tvar[k];
9939: TvarFind[ncovf]=k;
9940: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9941: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9942: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9943: Fixed[k]= 0;
9944: Dummy[k]= 0;
9945: ncoveff++;
9946: ncovf++;
9947: modell[k].maintype= FTYPE;
9948: TvarF[ncovf]=Tvar[k];
9949: TvarFind[ncovf]=k;
1.230 brouard 9950: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9951: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9952: }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 9953: Fixed[k]= 0;
9954: Dummy[k]= 1;
1.230 brouard 9955: nqfveff++;
1.234 brouard 9956: modell[k].maintype= FTYPE;
9957: modell[k].subtype= FQ;
9958: nsq++;
9959: TvarsQ[nsq]=Tvar[k];
9960: TvarsQind[nsq]=k;
1.232 brouard 9961: ncovf++;
1.234 brouard 9962: TvarF[ncovf]=Tvar[k];
9963: TvarFind[ncovf]=k;
1.231 brouard 9964: 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 9965: 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 9966: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9967: Fixed[k]= 1;
9968: Dummy[k]= 0;
1.225 brouard 9969: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9970: modell[k].maintype= VTYPE;
9971: modell[k].subtype= VD;
9972: nsd++;
9973: TvarsD[nsd]=Tvar[k];
9974: TvarsDind[nsd]=k;
9975: ncovv++; /* Only simple time varying variables */
9976: TvarV[ncovv]=Tvar[k];
1.242 brouard 9977: 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 9978: 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 */
9979: 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 9980: 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);
9981: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9982: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9983: Fixed[k]= 1;
9984: Dummy[k]= 1;
9985: nqtveff++;
9986: modell[k].maintype= VTYPE;
9987: modell[k].subtype= VQ;
9988: ncovv++; /* Only simple time varying variables */
9989: nsq++;
9990: TvarsQ[nsq]=Tvar[k];
9991: TvarsQind[nsq]=k;
9992: TvarV[ncovv]=Tvar[k];
1.242 brouard 9993: 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 9994: 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 */
9995: 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 9996: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9997: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9998: 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 9999: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 10000: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 10001: ncova++;
10002: TvarA[ncova]=Tvar[k];
10003: TvarAind[ncova]=k;
1.231 brouard 10004: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10005: Fixed[k]= 2;
10006: Dummy[k]= 2;
10007: modell[k].maintype= ATYPE;
10008: modell[k].subtype= APFD;
10009: /* ncoveff++; */
1.227 brouard 10010: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10011: Fixed[k]= 2;
10012: Dummy[k]= 3;
10013: modell[k].maintype= ATYPE;
10014: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10015: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10016: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10017: Fixed[k]= 3;
10018: Dummy[k]= 2;
10019: modell[k].maintype= ATYPE;
10020: modell[k].subtype= APVD; /* Product age * varying dummy */
10021: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10022: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10023: Fixed[k]= 3;
10024: Dummy[k]= 3;
10025: modell[k].maintype= ATYPE;
10026: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10027: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10028: }
10029: }else if (Typevar[k] == 2) { /* product without age */
10030: k1=Tposprod[k];
10031: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10032: if(Tvard[k1][2] <=ncovcol){
10033: Fixed[k]= 1;
10034: Dummy[k]= 0;
10035: modell[k].maintype= FTYPE;
10036: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10037: ncovf++; /* Fixed variables without age */
10038: TvarF[ncovf]=Tvar[k];
10039: TvarFind[ncovf]=k;
10040: }else if(Tvard[k1][2] <=ncovcol+nqv){
10041: Fixed[k]= 0; /* or 2 ?*/
10042: Dummy[k]= 1;
10043: modell[k].maintype= FTYPE;
10044: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10045: ncovf++; /* Varying variables without age */
10046: TvarF[ncovf]=Tvar[k];
10047: TvarFind[ncovf]=k;
10048: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10049: Fixed[k]= 1;
10050: Dummy[k]= 0;
10051: modell[k].maintype= VTYPE;
10052: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10053: ncovv++; /* Varying variables without age */
10054: TvarV[ncovv]=Tvar[k];
10055: TvarVind[ncovv]=k;
10056: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10057: Fixed[k]= 1;
10058: Dummy[k]= 1;
10059: modell[k].maintype= VTYPE;
10060: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10061: ncovv++; /* Varying variables without age */
10062: TvarV[ncovv]=Tvar[k];
10063: TvarVind[ncovv]=k;
10064: }
1.227 brouard 10065: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10066: if(Tvard[k1][2] <=ncovcol){
10067: Fixed[k]= 0; /* or 2 ?*/
10068: Dummy[k]= 1;
10069: modell[k].maintype= FTYPE;
10070: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10071: ncovf++; /* Fixed variables without age */
10072: TvarF[ncovf]=Tvar[k];
10073: TvarFind[ncovf]=k;
10074: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10075: Fixed[k]= 1;
10076: Dummy[k]= 1;
10077: modell[k].maintype= VTYPE;
10078: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10079: ncovv++; /* Varying variables without age */
10080: TvarV[ncovv]=Tvar[k];
10081: TvarVind[ncovv]=k;
10082: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10083: Fixed[k]= 1;
10084: Dummy[k]= 1;
10085: modell[k].maintype= VTYPE;
10086: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10087: ncovv++; /* Varying variables without age */
10088: TvarV[ncovv]=Tvar[k];
10089: TvarVind[ncovv]=k;
10090: ncovv++; /* Varying variables without age */
10091: TvarV[ncovv]=Tvar[k];
10092: TvarVind[ncovv]=k;
10093: }
1.227 brouard 10094: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10095: if(Tvard[k1][2] <=ncovcol){
10096: Fixed[k]= 1;
10097: Dummy[k]= 1;
10098: modell[k].maintype= VTYPE;
10099: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10100: ncovv++; /* Varying variables without age */
10101: TvarV[ncovv]=Tvar[k];
10102: TvarVind[ncovv]=k;
10103: }else if(Tvard[k1][2] <=ncovcol+nqv){
10104: Fixed[k]= 1;
10105: Dummy[k]= 1;
10106: modell[k].maintype= VTYPE;
10107: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10108: ncovv++; /* Varying variables without age */
10109: TvarV[ncovv]=Tvar[k];
10110: TvarVind[ncovv]=k;
10111: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10112: Fixed[k]= 1;
10113: Dummy[k]= 0;
10114: modell[k].maintype= VTYPE;
10115: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10116: ncovv++; /* Varying variables without age */
10117: TvarV[ncovv]=Tvar[k];
10118: TvarVind[ncovv]=k;
10119: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10120: Fixed[k]= 1;
10121: Dummy[k]= 1;
10122: modell[k].maintype= VTYPE;
10123: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10124: ncovv++; /* Varying variables without age */
10125: TvarV[ncovv]=Tvar[k];
10126: TvarVind[ncovv]=k;
10127: }
1.227 brouard 10128: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10129: if(Tvard[k1][2] <=ncovcol){
10130: Fixed[k]= 1;
10131: Dummy[k]= 1;
10132: modell[k].maintype= VTYPE;
10133: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10134: ncovv++; /* Varying variables without age */
10135: TvarV[ncovv]=Tvar[k];
10136: TvarVind[ncovv]=k;
10137: }else if(Tvard[k1][2] <=ncovcol+nqv){
10138: Fixed[k]= 1;
10139: Dummy[k]= 1;
10140: modell[k].maintype= VTYPE;
10141: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10142: ncovv++; /* Varying variables without age */
10143: TvarV[ncovv]=Tvar[k];
10144: TvarVind[ncovv]=k;
10145: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10146: Fixed[k]= 1;
10147: Dummy[k]= 1;
10148: modell[k].maintype= VTYPE;
10149: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10150: ncovv++; /* Varying variables without age */
10151: TvarV[ncovv]=Tvar[k];
10152: TvarVind[ncovv]=k;
10153: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10154: Fixed[k]= 1;
10155: Dummy[k]= 1;
10156: modell[k].maintype= VTYPE;
10157: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10158: ncovv++; /* Varying variables without age */
10159: TvarV[ncovv]=Tvar[k];
10160: TvarVind[ncovv]=k;
10161: }
1.227 brouard 10162: }else{
1.240 brouard 10163: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10164: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10165: } /*end k1*/
1.225 brouard 10166: }else{
1.226 brouard 10167: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10168: 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 10169: }
1.227 brouard 10170: 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 10171: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10172: 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]);
10173: }
10174: /* Searching for doublons in the model */
10175: for(k1=1; k1<= cptcovt;k1++){
10176: for(k2=1; k2 <k1;k2++){
1.285 brouard 10177: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10178: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10179: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10180: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10181: 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]);
10182: 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 10183: return(1);
10184: }
10185: }else if (Typevar[k1] ==2){
10186: k3=Tposprod[k1];
10187: k4=Tposprod[k2];
10188: 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])) ){
10189: 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]]);
10190: 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);
10191: return(1);
10192: }
10193: }
1.227 brouard 10194: }
10195: }
1.225 brouard 10196: }
10197: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10198: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10199: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10200: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10201: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10202: /*endread:*/
1.225 brouard 10203: printf("Exiting decodemodel: ");
10204: return (1);
1.136 brouard 10205: }
10206:
1.169 brouard 10207: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10208: {/* Check ages at death */
1.136 brouard 10209: int i, m;
1.218 brouard 10210: int firstone=0;
10211:
1.136 brouard 10212: for (i=1; i<=imx; i++) {
10213: for(m=2; (m<= maxwav); m++) {
10214: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10215: anint[m][i]=9999;
1.216 brouard 10216: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10217: s[m][i]=-1;
1.136 brouard 10218: }
10219: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10220: *nberr = *nberr + 1;
1.218 brouard 10221: if(firstone == 0){
10222: firstone=1;
1.260 brouard 10223: 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 10224: }
1.262 brouard 10225: 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 10226: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10227: }
10228: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10229: (*nberr)++;
1.259 brouard 10230: 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 10231: 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 10232: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10233: }
10234: }
10235: }
10236:
10237: for (i=1; i<=imx; i++) {
10238: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10239: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10240: 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 10241: if (s[m][i] >= nlstate+1) {
1.169 brouard 10242: if(agedc[i]>0){
10243: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10244: agev[m][i]=agedc[i];
1.214 brouard 10245: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10246: }else {
1.136 brouard 10247: if ((int)andc[i]!=9999){
10248: nbwarn++;
10249: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10250: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10251: agev[m][i]=-1;
10252: }
10253: }
1.169 brouard 10254: } /* agedc > 0 */
1.214 brouard 10255: } /* end if */
1.136 brouard 10256: else if(s[m][i] !=9){ /* Standard case, age in fractional
10257: years but with the precision of a month */
10258: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10259: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10260: agev[m][i]=1;
10261: else if(agev[m][i] < *agemin){
10262: *agemin=agev[m][i];
10263: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10264: }
10265: else if(agev[m][i] >*agemax){
10266: *agemax=agev[m][i];
1.156 brouard 10267: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10268: }
10269: /*agev[m][i]=anint[m][i]-annais[i];*/
10270: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10271: } /* en if 9*/
1.136 brouard 10272: else { /* =9 */
1.214 brouard 10273: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10274: agev[m][i]=1;
10275: s[m][i]=-1;
10276: }
10277: }
1.214 brouard 10278: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10279: agev[m][i]=1;
1.214 brouard 10280: else{
10281: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10282: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10283: agev[m][i]=0;
10284: }
10285: } /* End for lastpass */
10286: }
1.136 brouard 10287:
10288: for (i=1; i<=imx; i++) {
10289: for(m=firstpass; (m<=lastpass); m++){
10290: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10291: (*nberr)++;
1.136 brouard 10292: 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);
10293: 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);
10294: return 1;
10295: }
10296: }
10297: }
10298:
10299: /*for (i=1; i<=imx; i++){
10300: for (m=firstpass; (m<lastpass); m++){
10301: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10302: }
10303:
10304: }*/
10305:
10306:
1.139 brouard 10307: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10308: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10309:
10310: return (0);
1.164 brouard 10311: /* endread:*/
1.136 brouard 10312: printf("Exiting calandcheckages: ");
10313: return (1);
10314: }
10315:
1.172 brouard 10316: #if defined(_MSC_VER)
10317: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10318: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10319: //#include "stdafx.h"
10320: //#include <stdio.h>
10321: //#include <tchar.h>
10322: //#include <windows.h>
10323: //#include <iostream>
10324: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10325:
10326: LPFN_ISWOW64PROCESS fnIsWow64Process;
10327:
10328: BOOL IsWow64()
10329: {
10330: BOOL bIsWow64 = FALSE;
10331:
10332: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10333: // (HANDLE, PBOOL);
10334:
10335: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10336:
10337: HMODULE module = GetModuleHandle(_T("kernel32"));
10338: const char funcName[] = "IsWow64Process";
10339: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10340: GetProcAddress(module, funcName);
10341:
10342: if (NULL != fnIsWow64Process)
10343: {
10344: if (!fnIsWow64Process(GetCurrentProcess(),
10345: &bIsWow64))
10346: //throw std::exception("Unknown error");
10347: printf("Unknown error\n");
10348: }
10349: return bIsWow64 != FALSE;
10350: }
10351: #endif
1.177 brouard 10352:
1.191 brouard 10353: void syscompilerinfo(int logged)
1.292 brouard 10354: {
10355: #include <stdint.h>
10356:
10357: /* #include "syscompilerinfo.h"*/
1.185 brouard 10358: /* command line Intel compiler 32bit windows, XP compatible:*/
10359: /* /GS /W3 /Gy
10360: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10361: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10362: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10363: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10364: */
10365: /* 64 bits */
1.185 brouard 10366: /*
10367: /GS /W3 /Gy
10368: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10369: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10370: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10371: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10372: /* Optimization are useless and O3 is slower than O2 */
10373: /*
10374: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10375: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10376: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10377: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10378: */
1.186 brouard 10379: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10380: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10381: /PDB:"visual studio
10382: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10383: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10384: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10385: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10386: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10387: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10388: uiAccess='false'"
10389: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10390: /NOLOGO /TLBID:1
10391: */
1.292 brouard 10392:
10393:
1.177 brouard 10394: #if defined __INTEL_COMPILER
1.178 brouard 10395: #if defined(__GNUC__)
10396: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10397: #endif
1.177 brouard 10398: #elif defined(__GNUC__)
1.179 brouard 10399: #ifndef __APPLE__
1.174 brouard 10400: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10401: #endif
1.177 brouard 10402: struct utsname sysInfo;
1.178 brouard 10403: int cross = CROSS;
10404: if (cross){
10405: printf("Cross-");
1.191 brouard 10406: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10407: }
1.174 brouard 10408: #endif
10409:
1.191 brouard 10410: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10411: #if defined(__clang__)
1.191 brouard 10412: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10413: #endif
10414: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10415: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10416: #endif
10417: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10418: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10419: #endif
10420: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10421: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10422: #endif
10423: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10424: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10425: #endif
10426: #if defined(_MSC_VER)
1.191 brouard 10427: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10428: #endif
10429: #if defined(__PGI)
1.191 brouard 10430: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10431: #endif
10432: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10433: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10434: #endif
1.191 brouard 10435: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10436:
1.167 brouard 10437: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10438: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10439: // Windows (x64 and x86)
1.191 brouard 10440: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10441: #elif __unix__ // all unices, not all compilers
10442: // Unix
1.191 brouard 10443: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10444: #elif __linux__
10445: // linux
1.191 brouard 10446: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10447: #elif __APPLE__
1.174 brouard 10448: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10449: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10450: #endif
10451:
10452: /* __MINGW32__ */
10453: /* __CYGWIN__ */
10454: /* __MINGW64__ */
10455: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10456: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10457: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10458: /* _WIN64 // Defined for applications for Win64. */
10459: /* _M_X64 // Defined for compilations that target x64 processors. */
10460: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10461:
1.167 brouard 10462: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10463: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10464: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10465: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10466: #else
1.191 brouard 10467: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10468: #endif
10469:
1.169 brouard 10470: #if defined(__GNUC__)
10471: # if defined(__GNUC_PATCHLEVEL__)
10472: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10473: + __GNUC_MINOR__ * 100 \
10474: + __GNUC_PATCHLEVEL__)
10475: # else
10476: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10477: + __GNUC_MINOR__ * 100)
10478: # endif
1.174 brouard 10479: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10480: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10481:
10482: if (uname(&sysInfo) != -1) {
10483: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10484: 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 10485: }
10486: else
10487: perror("uname() error");
1.179 brouard 10488: //#ifndef __INTEL_COMPILER
10489: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10490: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10491: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10492: #endif
1.169 brouard 10493: #endif
1.172 brouard 10494:
1.286 brouard 10495: // void main ()
1.172 brouard 10496: // {
1.169 brouard 10497: #if defined(_MSC_VER)
1.174 brouard 10498: if (IsWow64()){
1.191 brouard 10499: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10500: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10501: }
10502: else{
1.191 brouard 10503: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10504: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10505: }
1.172 brouard 10506: // printf("\nPress Enter to continue...");
10507: // getchar();
10508: // }
10509:
1.169 brouard 10510: #endif
10511:
1.167 brouard 10512:
1.219 brouard 10513: }
1.136 brouard 10514:
1.219 brouard 10515: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10516: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10517: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10518: /* double ftolpl = 1.e-10; */
1.180 brouard 10519: double age, agebase, agelim;
1.203 brouard 10520: double tot;
1.180 brouard 10521:
1.202 brouard 10522: strcpy(filerespl,"PL_");
10523: strcat(filerespl,fileresu);
10524: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10525: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10526: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10527: }
1.288 brouard 10528: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10529: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10530: pstamp(ficrespl);
1.288 brouard 10531: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10532: fprintf(ficrespl,"#Age ");
10533: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10534: fprintf(ficrespl,"\n");
1.180 brouard 10535:
1.219 brouard 10536: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10537:
1.219 brouard 10538: agebase=ageminpar;
10539: agelim=agemaxpar;
1.180 brouard 10540:
1.227 brouard 10541: /* i1=pow(2,ncoveff); */
1.234 brouard 10542: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10543: if (cptcovn < 1){i1=1;}
1.180 brouard 10544:
1.238 brouard 10545: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10546: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10547: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10548: continue;
1.235 brouard 10549:
1.238 brouard 10550: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10551: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10552: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10553: /* k=k+1; */
10554: /* to clean */
10555: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10556: fprintf(ficrespl,"#******");
10557: printf("#******");
10558: fprintf(ficlog,"#******");
10559: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10560: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10561: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10562: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10563: }
10564: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10565: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10566: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10567: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10568: }
10569: fprintf(ficrespl,"******\n");
10570: printf("******\n");
10571: fprintf(ficlog,"******\n");
10572: if(invalidvarcomb[k]){
10573: printf("\nCombination (%d) ignored because no case \n",k);
10574: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10575: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10576: continue;
10577: }
1.219 brouard 10578:
1.238 brouard 10579: fprintf(ficrespl,"#Age ");
10580: for(j=1;j<=cptcoveff;j++) {
10581: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10582: }
10583: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10584: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10585:
1.238 brouard 10586: for (age=agebase; age<=agelim; age++){
10587: /* for (age=agebase; age<=agebase; age++){ */
10588: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10589: fprintf(ficrespl,"%.0f ",age );
10590: for(j=1;j<=cptcoveff;j++)
10591: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10592: tot=0.;
10593: for(i=1; i<=nlstate;i++){
10594: tot += prlim[i][i];
10595: fprintf(ficrespl," %.5f", prlim[i][i]);
10596: }
10597: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10598: } /* Age */
10599: /* was end of cptcod */
10600: } /* cptcov */
10601: } /* nres */
1.219 brouard 10602: return 0;
1.180 brouard 10603: }
10604:
1.218 brouard 10605: 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 10606: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10607:
10608: /* Computes the back prevalence limit for any combination of covariate values
10609: * at any age between ageminpar and agemaxpar
10610: */
1.235 brouard 10611: int i, j, k, i1, nres=0 ;
1.217 brouard 10612: /* double ftolpl = 1.e-10; */
10613: double age, agebase, agelim;
10614: double tot;
1.218 brouard 10615: /* double ***mobaverage; */
10616: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10617:
10618: strcpy(fileresplb,"PLB_");
10619: strcat(fileresplb,fileresu);
10620: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10621: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10622: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10623: }
1.288 brouard 10624: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10625: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10626: pstamp(ficresplb);
1.288 brouard 10627: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10628: fprintf(ficresplb,"#Age ");
10629: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10630: fprintf(ficresplb,"\n");
10631:
1.218 brouard 10632:
10633: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10634:
10635: agebase=ageminpar;
10636: agelim=agemaxpar;
10637:
10638:
1.227 brouard 10639: i1=pow(2,cptcoveff);
1.218 brouard 10640: if (cptcovn < 1){i1=1;}
1.227 brouard 10641:
1.238 brouard 10642: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10643: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10644: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10645: continue;
10646: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10647: fprintf(ficresplb,"#******");
10648: printf("#******");
10649: fprintf(ficlog,"#******");
10650: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10651: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10652: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10653: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10654: }
10655: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10656: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10657: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10658: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10659: }
10660: fprintf(ficresplb,"******\n");
10661: printf("******\n");
10662: fprintf(ficlog,"******\n");
10663: if(invalidvarcomb[k]){
10664: printf("\nCombination (%d) ignored because no cases \n",k);
10665: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10666: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10667: continue;
10668: }
1.218 brouard 10669:
1.238 brouard 10670: fprintf(ficresplb,"#Age ");
10671: for(j=1;j<=cptcoveff;j++) {
10672: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10673: }
10674: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10675: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10676:
10677:
1.238 brouard 10678: for (age=agebase; age<=agelim; age++){
10679: /* for (age=agebase; age<=agebase; age++){ */
10680: if(mobilavproj > 0){
10681: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10682: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10683: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10684: }else if (mobilavproj == 0){
10685: 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);
10686: 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);
10687: exit(1);
10688: }else{
10689: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10690: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10691: /* printf("TOTOT\n"); */
10692: /* exit(1); */
1.238 brouard 10693: }
10694: fprintf(ficresplb,"%.0f ",age );
10695: for(j=1;j<=cptcoveff;j++)
10696: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10697: tot=0.;
10698: for(i=1; i<=nlstate;i++){
10699: tot += bprlim[i][i];
10700: fprintf(ficresplb," %.5f", bprlim[i][i]);
10701: }
10702: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10703: } /* Age */
10704: /* was end of cptcod */
1.255 brouard 10705: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10706: } /* end of any combination */
10707: } /* end of nres */
1.218 brouard 10708: /* hBijx(p, bage, fage); */
10709: /* fclose(ficrespijb); */
10710:
10711: return 0;
1.217 brouard 10712: }
1.218 brouard 10713:
1.180 brouard 10714: int hPijx(double *p, int bage, int fage){
10715: /*------------- h Pij x at various ages ------------*/
10716:
10717: int stepsize;
10718: int agelim;
10719: int hstepm;
10720: int nhstepm;
1.235 brouard 10721: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10722:
10723: double agedeb;
10724: double ***p3mat;
10725:
1.201 brouard 10726: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10727: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10728: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10729: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10730: }
10731: printf("Computing pij: result on file '%s' \n", filerespij);
10732: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10733:
10734: stepsize=(int) (stepm+YEARM-1)/YEARM;
10735: /*if (stepm<=24) stepsize=2;*/
10736:
10737: agelim=AGESUP;
10738: hstepm=stepsize*YEARM; /* Every year of age */
10739: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10740:
1.180 brouard 10741: /* hstepm=1; aff par mois*/
10742: pstamp(ficrespij);
10743: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10744: i1= pow(2,cptcoveff);
1.218 brouard 10745: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10746: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10747: /* k=k+1; */
1.235 brouard 10748: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10749: for(k=1; k<=i1;k++){
1.253 brouard 10750: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10751: continue;
1.183 brouard 10752: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10753: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10754: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10755: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10756: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10757: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10758: }
1.183 brouard 10759: fprintf(ficrespij,"******\n");
10760:
10761: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10762: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10763: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10764:
10765: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10766:
1.183 brouard 10767: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10768: oldm=oldms;savm=savms;
1.235 brouard 10769: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10770: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10771: for(i=1; i<=nlstate;i++)
10772: for(j=1; j<=nlstate+ndeath;j++)
10773: fprintf(ficrespij," %1d-%1d",i,j);
10774: fprintf(ficrespij,"\n");
10775: for (h=0; h<=nhstepm; h++){
10776: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10777: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10778: for(i=1; i<=nlstate;i++)
10779: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10780: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10781: fprintf(ficrespij,"\n");
10782: }
1.183 brouard 10783: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10784: fprintf(ficrespij,"\n");
10785: }
1.180 brouard 10786: /*}*/
10787: }
1.218 brouard 10788: return 0;
1.180 brouard 10789: }
1.218 brouard 10790:
10791: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10792: /*------------- h Bij x at various ages ------------*/
10793:
10794: int stepsize;
1.218 brouard 10795: /* int agelim; */
10796: int ageminl;
1.217 brouard 10797: int hstepm;
10798: int nhstepm;
1.238 brouard 10799: int h, i, i1, j, k, nres;
1.218 brouard 10800:
1.217 brouard 10801: double agedeb;
10802: double ***p3mat;
1.218 brouard 10803:
10804: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10805: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10806: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10807: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10808: }
10809: printf("Computing pij back: result on file '%s' \n", filerespijb);
10810: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10811:
10812: stepsize=(int) (stepm+YEARM-1)/YEARM;
10813: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10814:
1.218 brouard 10815: /* agelim=AGESUP; */
1.289 brouard 10816: ageminl=AGEINF; /* was 30 */
1.218 brouard 10817: hstepm=stepsize*YEARM; /* Every year of age */
10818: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10819:
10820: /* hstepm=1; aff par mois*/
10821: pstamp(ficrespijb);
1.255 brouard 10822: 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 10823: i1= pow(2,cptcoveff);
1.218 brouard 10824: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10825: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10826: /* k=k+1; */
1.238 brouard 10827: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10828: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10829: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10830: continue;
10831: fprintf(ficrespijb,"\n#****** ");
10832: for(j=1;j<=cptcoveff;j++)
10833: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10834: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10835: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10836: }
10837: fprintf(ficrespijb,"******\n");
1.264 brouard 10838: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10839: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10840: continue;
10841: }
10842:
10843: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10844: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10845: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10846: 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 */
10847: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10848:
10849: /* nhstepm=nhstepm*YEARM; aff par mois*/
10850:
1.266 brouard 10851: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10852: /* and memory limitations if stepm is small */
10853:
1.238 brouard 10854: /* oldm=oldms;savm=savms; */
10855: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10856: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10857: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10858: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10859: for(i=1; i<=nlstate;i++)
10860: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10861: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10862: fprintf(ficrespijb,"\n");
1.238 brouard 10863: for (h=0; h<=nhstepm; h++){
10864: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10865: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10866: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10867: for(i=1; i<=nlstate;i++)
10868: for(j=1; j<=nlstate+ndeath;j++)
10869: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10870: fprintf(ficrespijb,"\n");
10871: }
10872: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10873: fprintf(ficrespijb,"\n");
10874: } /* end age deb */
10875: } /* end combination */
10876: } /* end nres */
1.218 brouard 10877: return 0;
10878: } /* hBijx */
1.217 brouard 10879:
1.180 brouard 10880:
1.136 brouard 10881: /***********************************************/
10882: /**************** Main Program *****************/
10883: /***********************************************/
10884:
10885: int main(int argc, char *argv[])
10886: {
10887: #ifdef GSL
10888: const gsl_multimin_fminimizer_type *T;
10889: size_t iteri = 0, it;
10890: int rval = GSL_CONTINUE;
10891: int status = GSL_SUCCESS;
10892: double ssval;
10893: #endif
10894: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10895: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10896: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10897: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10898: int jj, ll, li, lj, lk;
1.136 brouard 10899: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10900: int num_filled;
1.136 brouard 10901: int itimes;
10902: int NDIM=2;
10903: int vpopbased=0;
1.235 brouard 10904: int nres=0;
1.258 brouard 10905: int endishere=0;
1.277 brouard 10906: int noffset=0;
1.274 brouard 10907: int ncurrv=0; /* Temporary variable */
10908:
1.164 brouard 10909: char ca[32], cb[32];
1.136 brouard 10910: /* FILE *fichtm; *//* Html File */
10911: /* FILE *ficgp;*/ /*Gnuplot File */
10912: struct stat info;
1.191 brouard 10913: double agedeb=0.;
1.194 brouard 10914:
10915: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10916: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10917:
1.165 brouard 10918: double fret;
1.191 brouard 10919: double dum=0.; /* Dummy variable */
1.136 brouard 10920: double ***p3mat;
1.218 brouard 10921: /* double ***mobaverage; */
1.164 brouard 10922:
10923: char line[MAXLINE];
1.197 brouard 10924: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10925:
1.234 brouard 10926: char modeltemp[MAXLINE];
1.230 brouard 10927: char resultline[MAXLINE];
10928:
1.136 brouard 10929: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10930: char *tok, *val; /* pathtot */
1.290 brouard 10931: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10932: int c, h , cpt, c2;
1.191 brouard 10933: int jl=0;
10934: int i1, j1, jk, stepsize=0;
1.194 brouard 10935: int count=0;
10936:
1.164 brouard 10937: int *tab;
1.136 brouard 10938: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10939: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10940: /* double anprojf, mprojf, jprojf; */
10941: /* double jintmean,mintmean,aintmean; */
10942: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10943: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10944: double yrfproj= 10.0; /* Number of years of forward projections */
10945: double yrbproj= 10.0; /* Number of years of backward projections */
10946: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10947: int mobilav=0,popforecast=0;
1.191 brouard 10948: int hstepm=0, nhstepm=0;
1.136 brouard 10949: int agemortsup;
10950: float sumlpop=0.;
10951: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10952: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10953:
1.191 brouard 10954: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10955: double ftolpl=FTOL;
10956: double **prlim;
1.217 brouard 10957: double **bprlim;
1.136 brouard 10958: double ***param; /* Matrix of parameters */
1.251 brouard 10959: double ***paramstart; /* Matrix of starting parameter values */
10960: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10961: double **matcov; /* Matrix of covariance */
1.203 brouard 10962: double **hess; /* Hessian matrix */
1.136 brouard 10963: double ***delti3; /* Scale */
10964: double *delti; /* Scale */
10965: double ***eij, ***vareij;
10966: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10967:
1.136 brouard 10968: double *epj, vepp;
1.164 brouard 10969:
1.273 brouard 10970: double dateprev1, dateprev2;
1.296 brouard 10971: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10972: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10973:
1.217 brouard 10974:
1.136 brouard 10975: double **ximort;
1.145 brouard 10976: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10977: int *dcwave;
10978:
1.164 brouard 10979: char z[1]="c";
1.136 brouard 10980:
10981: /*char *strt;*/
10982: char strtend[80];
1.126 brouard 10983:
1.164 brouard 10984:
1.126 brouard 10985: /* setlocale (LC_ALL, ""); */
10986: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10987: /* textdomain (PACKAGE); */
10988: /* setlocale (LC_CTYPE, ""); */
10989: /* setlocale (LC_MESSAGES, ""); */
10990:
10991: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10992: rstart_time = time(NULL);
10993: /* (void) gettimeofday(&start_time,&tzp);*/
10994: start_time = *localtime(&rstart_time);
1.126 brouard 10995: curr_time=start_time;
1.157 brouard 10996: /*tml = *localtime(&start_time.tm_sec);*/
10997: /* strcpy(strstart,asctime(&tml)); */
10998: strcpy(strstart,asctime(&start_time));
1.126 brouard 10999:
11000: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 11001: /* tp.tm_sec = tp.tm_sec +86400; */
11002: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 11003: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11004: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11005: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11006: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11007: /* strt=asctime(&tmg); */
11008: /* printf("Time(after) =%s",strstart); */
11009: /* (void) time (&time_value);
11010: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11011: * tm = *localtime(&time_value);
11012: * strstart=asctime(&tm);
11013: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11014: */
11015:
11016: nberr=0; /* Number of errors and warnings */
11017: nbwarn=0;
1.184 brouard 11018: #ifdef WIN32
11019: _getcwd(pathcd, size);
11020: #else
1.126 brouard 11021: getcwd(pathcd, size);
1.184 brouard 11022: #endif
1.191 brouard 11023: syscompilerinfo(0);
1.196 brouard 11024: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11025: if(argc <=1){
11026: printf("\nEnter the parameter file name: ");
1.205 brouard 11027: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11028: printf("ERROR Empty parameter file name\n");
11029: goto end;
11030: }
1.126 brouard 11031: i=strlen(pathr);
11032: if(pathr[i-1]=='\n')
11033: pathr[i-1]='\0';
1.156 brouard 11034: i=strlen(pathr);
1.205 brouard 11035: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11036: pathr[i-1]='\0';
1.205 brouard 11037: }
11038: i=strlen(pathr);
11039: if( i==0 ){
11040: printf("ERROR Empty parameter file name\n");
11041: goto end;
11042: }
11043: for (tok = pathr; tok != NULL; ){
1.126 brouard 11044: printf("Pathr |%s|\n",pathr);
11045: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11046: printf("val= |%s| pathr=%s\n",val,pathr);
11047: strcpy (pathtot, val);
11048: if(pathr[0] == '\0') break; /* Dirty */
11049: }
11050: }
1.281 brouard 11051: else if (argc<=2){
11052: strcpy(pathtot,argv[1]);
11053: }
1.126 brouard 11054: else{
11055: strcpy(pathtot,argv[1]);
1.281 brouard 11056: strcpy(z,argv[2]);
11057: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11058: }
11059: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11060: /*cygwin_split_path(pathtot,path,optionfile);
11061: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11062: /* cutv(path,optionfile,pathtot,'\\');*/
11063:
11064: /* Split argv[0], imach program to get pathimach */
11065: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11066: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11067: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11068: /* strcpy(pathimach,argv[0]); */
11069: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11070: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11071: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11072: #ifdef WIN32
11073: _chdir(path); /* Can be a relative path */
11074: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11075: #else
1.126 brouard 11076: chdir(path); /* Can be a relative path */
1.184 brouard 11077: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11078: #endif
11079: printf("Current directory %s!\n",pathcd);
1.126 brouard 11080: strcpy(command,"mkdir ");
11081: strcat(command,optionfilefiname);
11082: if((outcmd=system(command)) != 0){
1.169 brouard 11083: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11084: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11085: /* fclose(ficlog); */
11086: /* exit(1); */
11087: }
11088: /* if((imk=mkdir(optionfilefiname))<0){ */
11089: /* perror("mkdir"); */
11090: /* } */
11091:
11092: /*-------- arguments in the command line --------*/
11093:
1.186 brouard 11094: /* Main Log file */
1.126 brouard 11095: strcat(filelog, optionfilefiname);
11096: strcat(filelog,".log"); /* */
11097: if((ficlog=fopen(filelog,"w"))==NULL) {
11098: printf("Problem with logfile %s\n",filelog);
11099: goto end;
11100: }
11101: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11102: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11103: fprintf(ficlog,"\nEnter the parameter file name: \n");
11104: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11105: path=%s \n\
11106: optionfile=%s\n\
11107: optionfilext=%s\n\
1.156 brouard 11108: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11109:
1.197 brouard 11110: syscompilerinfo(1);
1.167 brouard 11111:
1.126 brouard 11112: printf("Local time (at start):%s",strstart);
11113: fprintf(ficlog,"Local time (at start): %s",strstart);
11114: fflush(ficlog);
11115: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11116: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11117:
11118: /* */
11119: strcpy(fileres,"r");
11120: strcat(fileres, optionfilefiname);
1.201 brouard 11121: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11122: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11123: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11124:
1.186 brouard 11125: /* Main ---------arguments file --------*/
1.126 brouard 11126:
11127: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11128: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11129: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11130: fflush(ficlog);
1.149 brouard 11131: /* goto end; */
11132: exit(70);
1.126 brouard 11133: }
11134:
11135: strcpy(filereso,"o");
1.201 brouard 11136: strcat(filereso,fileresu);
1.126 brouard 11137: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11138: printf("Problem with Output resultfile: %s\n", filereso);
11139: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11140: fflush(ficlog);
11141: goto end;
11142: }
1.278 brouard 11143: /*-------- Rewriting parameter file ----------*/
11144: strcpy(rfileres,"r"); /* "Rparameterfile */
11145: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11146: strcat(rfileres,"."); /* */
11147: strcat(rfileres,optionfilext); /* Other files have txt extension */
11148: if((ficres =fopen(rfileres,"w"))==NULL) {
11149: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11150: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11151: fflush(ficlog);
11152: goto end;
11153: }
11154: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11155:
1.278 brouard 11156:
1.126 brouard 11157: /* Reads comments: lines beginning with '#' */
11158: numlinepar=0;
1.277 brouard 11159: /* Is it a BOM UTF-8 Windows file? */
11160: /* First parameter line */
1.197 brouard 11161: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11162: noffset=0;
11163: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11164: {
11165: noffset=noffset+3;
11166: printf("# File is an UTF8 Bom.\n"); // 0xBF
11167: }
1.302 brouard 11168: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11169: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11170: {
11171: noffset=noffset+2;
11172: printf("# File is an UTF16BE BOM file\n");
11173: }
11174: else if( line[0] == 0 && line[1] == 0)
11175: {
11176: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11177: noffset=noffset+4;
11178: printf("# File is an UTF16BE BOM file\n");
11179: }
11180: } else{
11181: ;/*printf(" Not a BOM file\n");*/
11182: }
11183:
1.197 brouard 11184: /* If line starts with a # it is a comment */
1.277 brouard 11185: if (line[noffset] == '#') {
1.197 brouard 11186: numlinepar++;
11187: fputs(line,stdout);
11188: fputs(line,ficparo);
1.278 brouard 11189: fputs(line,ficres);
1.197 brouard 11190: fputs(line,ficlog);
11191: continue;
11192: }else
11193: break;
11194: }
11195: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11196: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11197: if (num_filled != 5) {
11198: printf("Should be 5 parameters\n");
1.283 brouard 11199: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11200: }
1.126 brouard 11201: numlinepar++;
1.197 brouard 11202: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11203: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11204: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11205: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11206: }
11207: /* Second parameter line */
11208: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11209: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11210: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11211: if (line[0] == '#') {
11212: numlinepar++;
1.283 brouard 11213: printf("%s",line);
11214: fprintf(ficres,"%s",line);
11215: fprintf(ficparo,"%s",line);
11216: fprintf(ficlog,"%s",line);
1.197 brouard 11217: continue;
11218: }else
11219: break;
11220: }
1.223 brouard 11221: 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", \
11222: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11223: if (num_filled != 11) {
11224: 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 11225: printf("but line=%s\n",line);
1.283 brouard 11226: 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");
11227: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11228: }
1.286 brouard 11229: if( lastpass > maxwav){
11230: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11231: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11232: fflush(ficlog);
11233: goto end;
11234: }
11235: 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 11236: 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 11237: 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 11238: 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 11239: }
1.203 brouard 11240: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11241: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11242: /* Third parameter line */
11243: while(fgets(line, MAXLINE, ficpar)) {
11244: /* If line starts with a # it is a comment */
11245: if (line[0] == '#') {
11246: numlinepar++;
1.283 brouard 11247: printf("%s",line);
11248: fprintf(ficres,"%s",line);
11249: fprintf(ficparo,"%s",line);
11250: fprintf(ficlog,"%s",line);
1.197 brouard 11251: continue;
11252: }else
11253: break;
11254: }
1.201 brouard 11255: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11256: if (num_filled != 1){
1.302 brouard 11257: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11258: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11259: model[0]='\0';
11260: goto end;
11261: }
11262: else{
11263: if (model[0]=='+'){
11264: for(i=1; i<=strlen(model);i++)
11265: modeltemp[i-1]=model[i];
1.201 brouard 11266: strcpy(model,modeltemp);
1.197 brouard 11267: }
11268: }
1.199 brouard 11269: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11270: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11271: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11272: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11273: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11274: }
11275: /* 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); */
11276: /* numlinepar=numlinepar+3; /\* In general *\/ */
11277: /* 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 11278: /* 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); */
11279: /* 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 11280: fflush(ficlog);
1.190 brouard 11281: /* if(model[0]=='#'|| model[0]== '\0'){ */
11282: if(model[0]=='#'){
1.279 brouard 11283: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11284: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11285: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11286: if(mle != -1){
1.279 brouard 11287: 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 11288: exit(1);
11289: }
11290: }
1.126 brouard 11291: while((c=getc(ficpar))=='#' && c!= EOF){
11292: ungetc(c,ficpar);
11293: fgets(line, MAXLINE, ficpar);
11294: numlinepar++;
1.195 brouard 11295: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11296: z[0]=line[1];
11297: }
11298: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11299: fputs(line, stdout);
11300: //puts(line);
1.126 brouard 11301: fputs(line,ficparo);
11302: fputs(line,ficlog);
11303: }
11304: ungetc(c,ficpar);
11305:
11306:
1.290 brouard 11307: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11308: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11309: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11310: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11311: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11312: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11313: v1+v2*age+v2*v3 makes cptcovn = 3
11314: */
11315: if (strlen(model)>1)
1.187 brouard 11316: 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 11317: else
1.187 brouard 11318: ncovmodel=2; /* Constant and age */
1.133 brouard 11319: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11320: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11321: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11322: 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);
11323: 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);
11324: fflush(stdout);
11325: fclose (ficlog);
11326: goto end;
11327: }
1.126 brouard 11328: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11329: delti=delti3[1][1];
11330: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11331: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11332: /* We could also provide initial parameters values giving by simple logistic regression
11333: * only one way, that is without matrix product. We will have nlstate maximizations */
11334: /* for(i=1;i<nlstate;i++){ */
11335: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11336: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11337: /* } */
1.126 brouard 11338: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11339: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11340: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11341: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11342: fclose (ficparo);
11343: fclose (ficlog);
11344: goto end;
11345: exit(0);
1.220 brouard 11346: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11347: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11348: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11349: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11350: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11351: matcov=matrix(1,npar,1,npar);
1.203 brouard 11352: hess=matrix(1,npar,1,npar);
1.220 brouard 11353: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11354: /* Read guessed parameters */
1.126 brouard 11355: /* Reads comments: lines beginning with '#' */
11356: while((c=getc(ficpar))=='#' && c!= EOF){
11357: ungetc(c,ficpar);
11358: fgets(line, MAXLINE, ficpar);
11359: numlinepar++;
1.141 brouard 11360: fputs(line,stdout);
1.126 brouard 11361: fputs(line,ficparo);
11362: fputs(line,ficlog);
11363: }
11364: ungetc(c,ficpar);
11365:
11366: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11367: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11368: for(i=1; i <=nlstate; i++){
1.234 brouard 11369: j=0;
1.126 brouard 11370: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11371: if(jj==i) continue;
11372: j++;
1.292 brouard 11373: while((c=getc(ficpar))=='#' && c!= EOF){
11374: ungetc(c,ficpar);
11375: fgets(line, MAXLINE, ficpar);
11376: numlinepar++;
11377: fputs(line,stdout);
11378: fputs(line,ficparo);
11379: fputs(line,ficlog);
11380: }
11381: ungetc(c,ficpar);
1.234 brouard 11382: fscanf(ficpar,"%1d%1d",&i1,&j1);
11383: if ((i1 != i) || (j1 != jj)){
11384: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11385: It might be a problem of design; if ncovcol and the model are correct\n \
11386: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11387: exit(1);
11388: }
11389: fprintf(ficparo,"%1d%1d",i1,j1);
11390: if(mle==1)
11391: printf("%1d%1d",i,jj);
11392: fprintf(ficlog,"%1d%1d",i,jj);
11393: for(k=1; k<=ncovmodel;k++){
11394: fscanf(ficpar," %lf",¶m[i][j][k]);
11395: if(mle==1){
11396: printf(" %lf",param[i][j][k]);
11397: fprintf(ficlog," %lf",param[i][j][k]);
11398: }
11399: else
11400: fprintf(ficlog," %lf",param[i][j][k]);
11401: fprintf(ficparo," %lf",param[i][j][k]);
11402: }
11403: fscanf(ficpar,"\n");
11404: numlinepar++;
11405: if(mle==1)
11406: printf("\n");
11407: fprintf(ficlog,"\n");
11408: fprintf(ficparo,"\n");
1.126 brouard 11409: }
11410: }
11411: fflush(ficlog);
1.234 brouard 11412:
1.251 brouard 11413: /* Reads parameters values */
1.126 brouard 11414: p=param[1][1];
1.251 brouard 11415: pstart=paramstart[1][1];
1.126 brouard 11416:
11417: /* Reads comments: lines beginning with '#' */
11418: while((c=getc(ficpar))=='#' && c!= EOF){
11419: ungetc(c,ficpar);
11420: fgets(line, MAXLINE, ficpar);
11421: numlinepar++;
1.141 brouard 11422: fputs(line,stdout);
1.126 brouard 11423: fputs(line,ficparo);
11424: fputs(line,ficlog);
11425: }
11426: ungetc(c,ficpar);
11427:
11428: for(i=1; i <=nlstate; i++){
11429: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11430: fscanf(ficpar,"%1d%1d",&i1,&j1);
11431: if ( (i1-i) * (j1-j) != 0){
11432: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11433: exit(1);
11434: }
11435: printf("%1d%1d",i,j);
11436: fprintf(ficparo,"%1d%1d",i1,j1);
11437: fprintf(ficlog,"%1d%1d",i1,j1);
11438: for(k=1; k<=ncovmodel;k++){
11439: fscanf(ficpar,"%le",&delti3[i][j][k]);
11440: printf(" %le",delti3[i][j][k]);
11441: fprintf(ficparo," %le",delti3[i][j][k]);
11442: fprintf(ficlog," %le",delti3[i][j][k]);
11443: }
11444: fscanf(ficpar,"\n");
11445: numlinepar++;
11446: printf("\n");
11447: fprintf(ficparo,"\n");
11448: fprintf(ficlog,"\n");
1.126 brouard 11449: }
11450: }
11451: fflush(ficlog);
1.234 brouard 11452:
1.145 brouard 11453: /* Reads covariance matrix */
1.126 brouard 11454: delti=delti3[1][1];
1.220 brouard 11455:
11456:
1.126 brouard 11457: /* 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 11458:
1.126 brouard 11459: /* Reads comments: lines beginning with '#' */
11460: while((c=getc(ficpar))=='#' && c!= EOF){
11461: ungetc(c,ficpar);
11462: fgets(line, MAXLINE, ficpar);
11463: numlinepar++;
1.141 brouard 11464: fputs(line,stdout);
1.126 brouard 11465: fputs(line,ficparo);
11466: fputs(line,ficlog);
11467: }
11468: ungetc(c,ficpar);
1.220 brouard 11469:
1.126 brouard 11470: matcov=matrix(1,npar,1,npar);
1.203 brouard 11471: hess=matrix(1,npar,1,npar);
1.131 brouard 11472: for(i=1; i <=npar; i++)
11473: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11474:
1.194 brouard 11475: /* Scans npar lines */
1.126 brouard 11476: for(i=1; i <=npar; i++){
1.226 brouard 11477: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11478: if(count != 3){
1.226 brouard 11479: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11480: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11481: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11482: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11483: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11484: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11485: exit(1);
1.220 brouard 11486: }else{
1.226 brouard 11487: if(mle==1)
11488: printf("%1d%1d%d",i1,j1,jk);
11489: }
11490: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11491: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11492: for(j=1; j <=i; j++){
1.226 brouard 11493: fscanf(ficpar," %le",&matcov[i][j]);
11494: if(mle==1){
11495: printf(" %.5le",matcov[i][j]);
11496: }
11497: fprintf(ficlog," %.5le",matcov[i][j]);
11498: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11499: }
11500: fscanf(ficpar,"\n");
11501: numlinepar++;
11502: if(mle==1)
1.220 brouard 11503: printf("\n");
1.126 brouard 11504: fprintf(ficlog,"\n");
11505: fprintf(ficparo,"\n");
11506: }
1.194 brouard 11507: /* End of read covariance matrix npar lines */
1.126 brouard 11508: for(i=1; i <=npar; i++)
11509: for(j=i+1;j<=npar;j++)
1.226 brouard 11510: matcov[i][j]=matcov[j][i];
1.126 brouard 11511:
11512: if(mle==1)
11513: printf("\n");
11514: fprintf(ficlog,"\n");
11515:
11516: fflush(ficlog);
11517:
11518: } /* End of mle != -3 */
1.218 brouard 11519:
1.186 brouard 11520: /* Main data
11521: */
1.290 brouard 11522: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11523: /* num=lvector(1,n); */
11524: /* moisnais=vector(1,n); */
11525: /* annais=vector(1,n); */
11526: /* moisdc=vector(1,n); */
11527: /* andc=vector(1,n); */
11528: /* weight=vector(1,n); */
11529: /* agedc=vector(1,n); */
11530: /* cod=ivector(1,n); */
11531: /* for(i=1;i<=n;i++){ */
11532: num=lvector(firstobs,lastobs);
11533: moisnais=vector(firstobs,lastobs);
11534: annais=vector(firstobs,lastobs);
11535: moisdc=vector(firstobs,lastobs);
11536: andc=vector(firstobs,lastobs);
11537: weight=vector(firstobs,lastobs);
11538: agedc=vector(firstobs,lastobs);
11539: cod=ivector(firstobs,lastobs);
11540: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11541: num[i]=0;
11542: moisnais[i]=0;
11543: annais[i]=0;
11544: moisdc[i]=0;
11545: andc[i]=0;
11546: agedc[i]=0;
11547: cod[i]=0;
11548: weight[i]=1.0; /* Equal weights, 1 by default */
11549: }
1.290 brouard 11550: mint=matrix(1,maxwav,firstobs,lastobs);
11551: anint=matrix(1,maxwav,firstobs,lastobs);
11552: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11553: tab=ivector(1,NCOVMAX);
1.144 brouard 11554: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11555: 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 11556:
1.136 brouard 11557: /* Reads data from file datafile */
11558: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11559: goto end;
11560:
11561: /* Calculation of the number of parameters from char model */
1.234 brouard 11562: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11563: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11564: k=3 V4 Tvar[k=3]= 4 (from V4)
11565: k=2 V1 Tvar[k=2]= 1 (from V1)
11566: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11567: */
11568:
11569: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11570: TvarsDind=ivector(1,NCOVMAX); /* */
11571: TvarsD=ivector(1,NCOVMAX); /* */
11572: TvarsQind=ivector(1,NCOVMAX); /* */
11573: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11574: TvarF=ivector(1,NCOVMAX); /* */
11575: TvarFind=ivector(1,NCOVMAX); /* */
11576: TvarV=ivector(1,NCOVMAX); /* */
11577: TvarVind=ivector(1,NCOVMAX); /* */
11578: TvarA=ivector(1,NCOVMAX); /* */
11579: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11580: TvarFD=ivector(1,NCOVMAX); /* */
11581: TvarFDind=ivector(1,NCOVMAX); /* */
11582: TvarFQ=ivector(1,NCOVMAX); /* */
11583: TvarFQind=ivector(1,NCOVMAX); /* */
11584: TvarVD=ivector(1,NCOVMAX); /* */
11585: TvarVDind=ivector(1,NCOVMAX); /* */
11586: TvarVQ=ivector(1,NCOVMAX); /* */
11587: TvarVQind=ivector(1,NCOVMAX); /* */
11588:
1.230 brouard 11589: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11590: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11591: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11592: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11593: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11594: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11595: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11596: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11597: */
11598: /* For model-covariate k tells which data-covariate to use but
11599: because this model-covariate is a construction we invent a new column
11600: ncovcol + k1
11601: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11602: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11603: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11604: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11605: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11606: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11607: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11608: */
1.145 brouard 11609: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11610: 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 11611: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11612: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11613: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11614: 4 covariates (3 plus signs)
11615: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11616: */
1.230 brouard 11617: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11618: * individual dummy, fixed or varying:
11619: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11620: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11621: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11622: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11623: * Tmodelind[1]@9={9,0,3,2,}*/
11624: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11625: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11626: * individual quantitative, fixed or varying:
11627: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11628: * 3, 1, 0, 0, 0, 0, 0, 0},
11629: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11630: /* Main decodemodel */
11631:
1.187 brouard 11632:
1.223 brouard 11633: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11634: goto end;
11635:
1.137 brouard 11636: if((double)(lastobs-imx)/(double)imx > 1.10){
11637: nbwarn++;
11638: 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);
11639: 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);
11640: }
1.136 brouard 11641: /* if(mle==1){*/
1.137 brouard 11642: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11643: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11644: }
11645:
11646: /*-calculation of age at interview from date of interview and age at death -*/
11647: agev=matrix(1,maxwav,1,imx);
11648:
11649: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11650: goto end;
11651:
1.126 brouard 11652:
1.136 brouard 11653: agegomp=(int)agemin;
1.290 brouard 11654: free_vector(moisnais,firstobs,lastobs);
11655: free_vector(annais,firstobs,lastobs);
1.126 brouard 11656: /* free_matrix(mint,1,maxwav,1,n);
11657: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11658: /* free_vector(moisdc,1,n); */
11659: /* free_vector(andc,1,n); */
1.145 brouard 11660: /* */
11661:
1.126 brouard 11662: wav=ivector(1,imx);
1.214 brouard 11663: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11664: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11665: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11666: 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.*/
11667: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11668: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11669:
11670: /* Concatenates waves */
1.214 brouard 11671: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11672: Death is a valid wave (if date is known).
11673: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11674: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11675: and mw[mi+1][i]. dh depends on stepm.
11676: */
11677:
1.126 brouard 11678: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11679: /* Concatenates waves */
1.145 brouard 11680:
1.290 brouard 11681: free_vector(moisdc,firstobs,lastobs);
11682: free_vector(andc,firstobs,lastobs);
1.215 brouard 11683:
1.126 brouard 11684: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11685: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11686: ncodemax[1]=1;
1.145 brouard 11687: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11688: cptcoveff=0;
1.220 brouard 11689: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11690: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11691: }
11692:
11693: ncovcombmax=pow(2,cptcoveff);
11694: invalidvarcomb=ivector(1, ncovcombmax);
11695: for(i=1;i<ncovcombmax;i++)
11696: invalidvarcomb[i]=0;
11697:
1.211 brouard 11698: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11699: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11700: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11701:
1.200 brouard 11702: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11703: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11704: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11705: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11706: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11707: * (currently 0 or 1) in the data.
11708: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11709: * corresponding modality (h,j).
11710: */
11711:
1.145 brouard 11712: h=0;
11713: /*if (cptcovn > 0) */
1.126 brouard 11714: m=pow(2,cptcoveff);
11715:
1.144 brouard 11716: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11717: * For k=4 covariates, h goes from 1 to m=2**k
11718: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11719: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11720: * h\k 1 2 3 4
1.143 brouard 11721: *______________________________
11722: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11723: * 2 2 1 1 1
11724: * 3 i=2 1 2 1 1
11725: * 4 2 2 1 1
11726: * 5 i=3 1 i=2 1 2 1
11727: * 6 2 1 2 1
11728: * 7 i=4 1 2 2 1
11729: * 8 2 2 2 1
1.197 brouard 11730: * 9 i=5 1 i=3 1 i=2 1 2
11731: * 10 2 1 1 2
11732: * 11 i=6 1 2 1 2
11733: * 12 2 2 1 2
11734: * 13 i=7 1 i=4 1 2 2
11735: * 14 2 1 2 2
11736: * 15 i=8 1 2 2 2
11737: * 16 2 2 2 2
1.143 brouard 11738: */
1.212 brouard 11739: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11740: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11741: * and the value of each covariate?
11742: * V1=1, V2=1, V3=2, V4=1 ?
11743: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11744: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11745: * In order to get the real value in the data, we use nbcode
11746: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11747: * We are keeping this crazy system in order to be able (in the future?)
11748: * to have more than 2 values (0 or 1) for a covariate.
11749: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11750: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11751: * bbbbbbbb
11752: * 76543210
11753: * h-1 00000101 (6-1=5)
1.219 brouard 11754: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11755: * &
11756: * 1 00000001 (1)
1.219 brouard 11757: * 00000000 = 1 & ((h-1) >> (k-1))
11758: * +1= 00000001 =1
1.211 brouard 11759: *
11760: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11761: * h' 1101 =2^3+2^2+0x2^1+2^0
11762: * >>k' 11
11763: * & 00000001
11764: * = 00000001
11765: * +1 = 00000010=2 = codtabm(14,3)
11766: * Reverse h=6 and m=16?
11767: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11768: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11769: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11770: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11771: * V3=decodtabm(14,3,2**4)=2
11772: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11773: *(h-1) >> (j-1) 0011 =13 >> 2
11774: * &1 000000001
11775: * = 000000001
11776: * +1= 000000010 =2
11777: * 2211
11778: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11779: * V3=2
1.220 brouard 11780: * codtabm and decodtabm are identical
1.211 brouard 11781: */
11782:
1.145 brouard 11783:
11784: free_ivector(Ndum,-1,NCOVMAX);
11785:
11786:
1.126 brouard 11787:
1.186 brouard 11788: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11789: strcpy(optionfilegnuplot,optionfilefiname);
11790: if(mle==-3)
1.201 brouard 11791: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11792: strcat(optionfilegnuplot,".gp");
11793:
11794: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11795: printf("Problem with file %s",optionfilegnuplot);
11796: }
11797: else{
1.204 brouard 11798: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11799: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11800: //fprintf(ficgp,"set missing 'NaNq'\n");
11801: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11802: }
11803: /* fclose(ficgp);*/
1.186 brouard 11804:
11805:
11806: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11807:
11808: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11809: if(mle==-3)
1.201 brouard 11810: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11811: strcat(optionfilehtm,".htm");
11812: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11813: printf("Problem with %s \n",optionfilehtm);
11814: exit(0);
1.126 brouard 11815: }
11816:
11817: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11818: strcat(optionfilehtmcov,"-cov.htm");
11819: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11820: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11821: }
11822: else{
11823: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11824: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11825: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11826: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11827: }
11828:
1.213 brouard 11829: 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 11830: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11831: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11832: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11833: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11834: \n\
11835: <hr size=\"2\" color=\"#EC5E5E\">\
11836: <ul><li><h4>Parameter files</h4>\n\
11837: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11838: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11839: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11840: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11841: - Date and time at start: %s</ul>\n",\
11842: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11843: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11844: fileres,fileres,\
11845: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11846: fflush(fichtm);
11847:
11848: strcpy(pathr,path);
11849: strcat(pathr,optionfilefiname);
1.184 brouard 11850: #ifdef WIN32
11851: _chdir(optionfilefiname); /* Move to directory named optionfile */
11852: #else
1.126 brouard 11853: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11854: #endif
11855:
1.126 brouard 11856:
1.220 brouard 11857: /* Calculates basic frequencies. Computes observed prevalence at single age
11858: and for any valid combination of covariates
1.126 brouard 11859: and prints on file fileres'p'. */
1.251 brouard 11860: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11861: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11862:
11863: fprintf(fichtm,"\n");
1.286 brouard 11864: 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 11865: ftol, stepm);
11866: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11867: ncurrv=1;
11868: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11869: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11870: ncurrv=i;
11871: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11872: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11873: ncurrv=i;
11874: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11875: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11876: ncurrv=i;
11877: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11878: 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", \
11879: nlstate, ndeath, maxwav, mle, weightopt);
11880:
11881: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11882: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11883:
11884:
11885: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11886: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11887: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11888: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11889: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11890: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11891: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11892: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11893: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11894:
1.126 brouard 11895: /* For Powell, parameters are in a vector p[] starting at p[1]
11896: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11897: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11898:
11899: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11900: /* For mortality only */
1.126 brouard 11901: if (mle==-3){
1.136 brouard 11902: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11903: for(i=1;i<=NDIM;i++)
11904: for(j=1;j<=NDIM;j++)
11905: ximort[i][j]=0.;
1.186 brouard 11906: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11907: cens=ivector(firstobs,lastobs);
11908: ageexmed=vector(firstobs,lastobs);
11909: agecens=vector(firstobs,lastobs);
11910: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11911:
1.126 brouard 11912: for (i=1; i<=imx; i++){
11913: dcwave[i]=-1;
11914: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11915: if (s[m][i]>nlstate) {
11916: dcwave[i]=m;
11917: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11918: break;
11919: }
1.126 brouard 11920: }
1.226 brouard 11921:
1.126 brouard 11922: for (i=1; i<=imx; i++) {
11923: if (wav[i]>0){
1.226 brouard 11924: ageexmed[i]=agev[mw[1][i]][i];
11925: j=wav[i];
11926: agecens[i]=1.;
11927:
11928: if (ageexmed[i]> 1 && wav[i] > 0){
11929: agecens[i]=agev[mw[j][i]][i];
11930: cens[i]= 1;
11931: }else if (ageexmed[i]< 1)
11932: cens[i]= -1;
11933: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11934: cens[i]=0 ;
1.126 brouard 11935: }
11936: else cens[i]=-1;
11937: }
11938:
11939: for (i=1;i<=NDIM;i++) {
11940: for (j=1;j<=NDIM;j++)
1.226 brouard 11941: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11942: }
11943:
1.302 brouard 11944: p[1]=0.0268; p[NDIM]=0.083;
11945: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 11946:
11947:
1.136 brouard 11948: #ifdef GSL
11949: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11950: #else
1.126 brouard 11951: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11952: #endif
1.201 brouard 11953: strcpy(filerespow,"POW-MORT_");
11954: strcat(filerespow,fileresu);
1.126 brouard 11955: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11956: printf("Problem with resultfile: %s\n", filerespow);
11957: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11958: }
1.136 brouard 11959: #ifdef GSL
11960: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11961: #else
1.126 brouard 11962: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11963: #endif
1.126 brouard 11964: /* for (i=1;i<=nlstate;i++)
11965: for(j=1;j<=nlstate+ndeath;j++)
11966: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11967: */
11968: fprintf(ficrespow,"\n");
1.136 brouard 11969: #ifdef GSL
11970: /* gsl starts here */
11971: T = gsl_multimin_fminimizer_nmsimplex;
11972: gsl_multimin_fminimizer *sfm = NULL;
11973: gsl_vector *ss, *x;
11974: gsl_multimin_function minex_func;
11975:
11976: /* Initial vertex size vector */
11977: ss = gsl_vector_alloc (NDIM);
11978:
11979: if (ss == NULL){
11980: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11981: }
11982: /* Set all step sizes to 1 */
11983: gsl_vector_set_all (ss, 0.001);
11984:
11985: /* Starting point */
1.126 brouard 11986:
1.136 brouard 11987: x = gsl_vector_alloc (NDIM);
11988:
11989: if (x == NULL){
11990: gsl_vector_free(ss);
11991: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11992: }
11993:
11994: /* Initialize method and iterate */
11995: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11996: /* gsl_vector_set(x, 0, 0.0268); */
11997: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11998: gsl_vector_set(x, 0, p[1]);
11999: gsl_vector_set(x, 1, p[2]);
12000:
12001: minex_func.f = &gompertz_f;
12002: minex_func.n = NDIM;
12003: minex_func.params = (void *)&p; /* ??? */
12004:
12005: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12006: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12007:
12008: printf("Iterations beginning .....\n\n");
12009: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12010:
12011: iteri=0;
12012: while (rval == GSL_CONTINUE){
12013: iteri++;
12014: status = gsl_multimin_fminimizer_iterate(sfm);
12015:
12016: if (status) printf("error: %s\n", gsl_strerror (status));
12017: fflush(0);
12018:
12019: if (status)
12020: break;
12021:
12022: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12023: ssval = gsl_multimin_fminimizer_size (sfm);
12024:
12025: if (rval == GSL_SUCCESS)
12026: printf ("converged to a local maximum at\n");
12027:
12028: printf("%5d ", iteri);
12029: for (it = 0; it < NDIM; it++){
12030: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12031: }
12032: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12033: }
12034:
12035: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12036:
12037: gsl_vector_free(x); /* initial values */
12038: gsl_vector_free(ss); /* inital step size */
12039: for (it=0; it<NDIM; it++){
12040: p[it+1]=gsl_vector_get(sfm->x,it);
12041: fprintf(ficrespow," %.12lf", p[it]);
12042: }
12043: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12044: #endif
12045: #ifdef POWELL
12046: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12047: #endif
1.126 brouard 12048: fclose(ficrespow);
12049:
1.203 brouard 12050: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12051:
12052: for(i=1; i <=NDIM; i++)
12053: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12054: matcov[i][j]=matcov[j][i];
1.126 brouard 12055:
12056: printf("\nCovariance matrix\n ");
1.203 brouard 12057: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12058: for(i=1; i <=NDIM; i++) {
12059: for(j=1;j<=NDIM;j++){
1.220 brouard 12060: printf("%f ",matcov[i][j]);
12061: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12062: }
1.203 brouard 12063: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12064: }
12065:
12066: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12067: for (i=1;i<=NDIM;i++) {
1.126 brouard 12068: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12069: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12070: }
1.302 brouard 12071: lsurv=vector(agegomp,AGESUP);
12072: lpop=vector(agegomp,AGESUP);
12073: tpop=vector(agegomp,AGESUP);
1.126 brouard 12074: lsurv[agegomp]=100000;
12075:
12076: for (k=agegomp;k<=AGESUP;k++) {
12077: agemortsup=k;
12078: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12079: }
12080:
12081: for (k=agegomp;k<agemortsup;k++)
12082: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12083:
12084: for (k=agegomp;k<agemortsup;k++){
12085: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12086: sumlpop=sumlpop+lpop[k];
12087: }
12088:
12089: tpop[agegomp]=sumlpop;
12090: for (k=agegomp;k<(agemortsup-3);k++){
12091: /* tpop[k+1]=2;*/
12092: tpop[k+1]=tpop[k]-lpop[k];
12093: }
12094:
12095:
12096: printf("\nAge lx qx dx Lx Tx e(x)\n");
12097: for (k=agegomp;k<(agemortsup-2);k++)
12098: 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]);
12099:
12100:
12101: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12102: ageminpar=50;
12103: agemaxpar=100;
1.194 brouard 12104: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12105: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12106: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12107: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12108: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12109: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12110: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12111: }else{
12112: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12113: 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 12114: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12115: }
1.201 brouard 12116: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12117: stepm, weightopt,\
12118: model,imx,p,matcov,agemortsup);
12119:
1.302 brouard 12120: free_vector(lsurv,agegomp,AGESUP);
12121: free_vector(lpop,agegomp,AGESUP);
12122: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12123: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12124: free_ivector(dcwave,firstobs,lastobs);
12125: free_vector(agecens,firstobs,lastobs);
12126: free_vector(ageexmed,firstobs,lastobs);
12127: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12128: #ifdef GSL
1.136 brouard 12129: #endif
1.186 brouard 12130: } /* Endof if mle==-3 mortality only */
1.205 brouard 12131: /* Standard */
12132: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12133: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12134: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12135: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12136: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12137: for (k=1; k<=npar;k++)
12138: printf(" %d %8.5f",k,p[k]);
12139: printf("\n");
1.205 brouard 12140: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12141: /* mlikeli uses func not funcone */
1.247 brouard 12142: /* for(i=1;i<nlstate;i++){ */
12143: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12144: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12145: /* } */
1.205 brouard 12146: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12147: }
12148: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12149: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12150: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12151: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12152: }
12153: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12154: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12155: printf("Second 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");
12159:
12160: /*--------- results files --------------*/
1.283 brouard 12161: /* 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 12162:
12163:
12164: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12165: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12166: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12167: for(i=1,jk=1; i <=nlstate; i++){
12168: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12169: if (k != i) {
12170: printf("%d%d ",i,k);
12171: fprintf(ficlog,"%d%d ",i,k);
12172: fprintf(ficres,"%1d%1d ",i,k);
12173: for(j=1; j <=ncovmodel; j++){
12174: printf("%12.7f ",p[jk]);
12175: fprintf(ficlog,"%12.7f ",p[jk]);
12176: fprintf(ficres,"%12.7f ",p[jk]);
12177: jk++;
12178: }
12179: printf("\n");
12180: fprintf(ficlog,"\n");
12181: fprintf(ficres,"\n");
12182: }
1.126 brouard 12183: }
12184: }
1.203 brouard 12185: if(mle != 0){
12186: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12187: ftolhess=ftol; /* Usually correct */
1.203 brouard 12188: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12189: 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");
12190: 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");
12191: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12192: for(k=1; k <=(nlstate+ndeath); k++){
12193: if (k != i) {
12194: printf("%d%d ",i,k);
12195: fprintf(ficlog,"%d%d ",i,k);
12196: for(j=1; j <=ncovmodel; j++){
12197: 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]));
12198: 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]));
12199: jk++;
12200: }
12201: printf("\n");
12202: fprintf(ficlog,"\n");
12203: }
12204: }
1.193 brouard 12205: }
1.203 brouard 12206: } /* end of hesscov and Wald tests */
1.225 brouard 12207:
1.203 brouard 12208: /* */
1.126 brouard 12209: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12210: printf("# Scales (for hessian or gradient estimation)\n");
12211: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12212: for(i=1,jk=1; i <=nlstate; i++){
12213: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12214: if (j!=i) {
12215: fprintf(ficres,"%1d%1d",i,j);
12216: printf("%1d%1d",i,j);
12217: fprintf(ficlog,"%1d%1d",i,j);
12218: for(k=1; k<=ncovmodel;k++){
12219: printf(" %.5e",delti[jk]);
12220: fprintf(ficlog," %.5e",delti[jk]);
12221: fprintf(ficres," %.5e",delti[jk]);
12222: jk++;
12223: }
12224: printf("\n");
12225: fprintf(ficlog,"\n");
12226: fprintf(ficres,"\n");
12227: }
1.126 brouard 12228: }
12229: }
12230:
12231: 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 12232: if(mle >= 1) /* To big for the screen */
1.126 brouard 12233: 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");
12234: 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");
12235: /* # 121 Var(a12)\n\ */
12236: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12237: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12238: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12239: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12240: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12241: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12242: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12243:
12244:
12245: /* Just to have a covariance matrix which will be more understandable
12246: even is we still don't want to manage dictionary of variables
12247: */
12248: for(itimes=1;itimes<=2;itimes++){
12249: jj=0;
12250: for(i=1; i <=nlstate; i++){
1.225 brouard 12251: for(j=1; j <=nlstate+ndeath; j++){
12252: if(j==i) continue;
12253: for(k=1; k<=ncovmodel;k++){
12254: jj++;
12255: ca[0]= k+'a'-1;ca[1]='\0';
12256: if(itimes==1){
12257: if(mle>=1)
12258: printf("#%1d%1d%d",i,j,k);
12259: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12260: fprintf(ficres,"#%1d%1d%d",i,j,k);
12261: }else{
12262: if(mle>=1)
12263: printf("%1d%1d%d",i,j,k);
12264: fprintf(ficlog,"%1d%1d%d",i,j,k);
12265: fprintf(ficres,"%1d%1d%d",i,j,k);
12266: }
12267: ll=0;
12268: for(li=1;li <=nlstate; li++){
12269: for(lj=1;lj <=nlstate+ndeath; lj++){
12270: if(lj==li) continue;
12271: for(lk=1;lk<=ncovmodel;lk++){
12272: ll++;
12273: if(ll<=jj){
12274: cb[0]= lk +'a'-1;cb[1]='\0';
12275: if(ll<jj){
12276: if(itimes==1){
12277: if(mle>=1)
12278: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12279: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12280: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12281: }else{
12282: if(mle>=1)
12283: printf(" %.5e",matcov[jj][ll]);
12284: fprintf(ficlog," %.5e",matcov[jj][ll]);
12285: fprintf(ficres," %.5e",matcov[jj][ll]);
12286: }
12287: }else{
12288: if(itimes==1){
12289: if(mle>=1)
12290: printf(" Var(%s%1d%1d)",ca,i,j);
12291: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12292: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12293: }else{
12294: if(mle>=1)
12295: printf(" %.7e",matcov[jj][ll]);
12296: fprintf(ficlog," %.7e",matcov[jj][ll]);
12297: fprintf(ficres," %.7e",matcov[jj][ll]);
12298: }
12299: }
12300: }
12301: } /* end lk */
12302: } /* end lj */
12303: } /* end li */
12304: if(mle>=1)
12305: printf("\n");
12306: fprintf(ficlog,"\n");
12307: fprintf(ficres,"\n");
12308: numlinepar++;
12309: } /* end k*/
12310: } /*end j */
1.126 brouard 12311: } /* end i */
12312: } /* end itimes */
12313:
12314: fflush(ficlog);
12315: fflush(ficres);
1.225 brouard 12316: while(fgets(line, MAXLINE, ficpar)) {
12317: /* If line starts with a # it is a comment */
12318: if (line[0] == '#') {
12319: numlinepar++;
12320: fputs(line,stdout);
12321: fputs(line,ficparo);
12322: fputs(line,ficlog);
1.299 brouard 12323: fputs(line,ficres);
1.225 brouard 12324: continue;
12325: }else
12326: break;
12327: }
12328:
1.209 brouard 12329: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12330: /* ungetc(c,ficpar); */
12331: /* fgets(line, MAXLINE, ficpar); */
12332: /* fputs(line,stdout); */
12333: /* fputs(line,ficparo); */
12334: /* } */
12335: /* ungetc(c,ficpar); */
1.126 brouard 12336:
12337: estepm=0;
1.209 brouard 12338: 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 12339:
12340: if (num_filled != 6) {
12341: 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);
12342: 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);
12343: goto end;
12344: }
12345: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12346: }
12347: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12348: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12349:
1.209 brouard 12350: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12351: if (estepm==0 || estepm < stepm) estepm=stepm;
12352: if (fage <= 2) {
12353: bage = ageminpar;
12354: fage = agemaxpar;
12355: }
12356:
12357: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12358: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12359: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12360:
1.186 brouard 12361: /* Other stuffs, more or less useful */
1.254 brouard 12362: while(fgets(line, MAXLINE, ficpar)) {
12363: /* If line starts with a # it is a comment */
12364: if (line[0] == '#') {
12365: numlinepar++;
12366: fputs(line,stdout);
12367: fputs(line,ficparo);
12368: fputs(line,ficlog);
1.299 brouard 12369: fputs(line,ficres);
1.254 brouard 12370: continue;
12371: }else
12372: break;
12373: }
12374:
12375: 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){
12376:
12377: if (num_filled != 7) {
12378: 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);
12379: 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);
12380: goto end;
12381: }
12382: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12383: 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);
12384: 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);
12385: 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 12386: }
1.254 brouard 12387:
12388: while(fgets(line, MAXLINE, ficpar)) {
12389: /* If line starts with a # it is a comment */
12390: if (line[0] == '#') {
12391: numlinepar++;
12392: fputs(line,stdout);
12393: fputs(line,ficparo);
12394: fputs(line,ficlog);
1.299 brouard 12395: fputs(line,ficres);
1.254 brouard 12396: continue;
12397: }else
12398: break;
1.126 brouard 12399: }
12400:
12401:
12402: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12403: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12404:
1.254 brouard 12405: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12406: if (num_filled != 1) {
12407: 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);
12408: 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);
12409: goto end;
12410: }
12411: printf("pop_based=%d\n",popbased);
12412: fprintf(ficlog,"pop_based=%d\n",popbased);
12413: fprintf(ficparo,"pop_based=%d\n",popbased);
12414: fprintf(ficres,"pop_based=%d\n",popbased);
12415: }
12416:
1.258 brouard 12417: /* Results */
1.307 ! brouard 12418: endishere=0;
1.258 brouard 12419: nresult=0;
12420: do{
12421: if(!fgets(line, MAXLINE, ficpar)){
12422: endishere=1;
12423: }else if (line[0] == '#') {
12424: /* If line starts with a # it is a comment */
1.254 brouard 12425: numlinepar++;
12426: fputs(line,stdout);
12427: fputs(line,ficparo);
12428: fputs(line,ficlog);
1.299 brouard 12429: fputs(line,ficres);
1.254 brouard 12430: continue;
1.258 brouard 12431: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12432: parameterline=11;
1.296 brouard 12433: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12434: parameterline=12;
1.307 ! brouard 12435: else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258 brouard 12436: parameterline=13;
1.307 ! brouard 12437: }
1.258 brouard 12438: else{
12439: parameterline=14;
1.254 brouard 12440: }
1.258 brouard 12441: switch (parameterline){
12442: case 11:
1.296 brouard 12443: 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)){
12444: 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 12445: 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);
12446: 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);
12447: 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);
12448: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12449: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12450: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12451: prvforecast = 1;
12452: }
12453: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.302 brouard 12454: printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12455: fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12456: fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12457: prvforecast = 2;
12458: }
12459: else {
12460: 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);
12461: 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);
12462: goto end;
1.258 brouard 12463: }
1.254 brouard 12464: break;
1.258 brouard 12465: case 12:
1.296 brouard 12466: 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)){
12467: 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);
12468: 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);
12469: 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);
12470: 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);
12471: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12472: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12473: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12474: prvbackcast = 1;
12475: }
12476: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.302 brouard 12477: printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12478: fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12479: fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12480: prvbackcast = 2;
12481: }
12482: else {
12483: 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);
12484: 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);
12485: goto end;
1.258 brouard 12486: }
1.230 brouard 12487: break;
1.258 brouard 12488: case 13:
1.307 ! brouard 12489: num_filled=sscanf(line,"result:%[^\n]\n",resultline);
! 12490: nresult++; /* Sum of resultlines */
! 12491: printf("Result %d: result:%s\n",nresult, resultline);
! 12492: if(nresult > MAXRESULTLINES){
! 12493: 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);
! 12494: 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);
! 12495: goto end;
! 12496: }
! 12497: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
! 12498: fprintf(ficparo,"result: %s\n",resultline);
! 12499: fprintf(ficres,"result: %s\n",resultline);
! 12500: fprintf(ficlog,"result: %s\n",resultline);
! 12501: break;
! 12502: case 14:
! 12503: printf("Error: Unknown command '%s'\n",line);
! 12504: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
! 12505: if(ncovmodel >=2 && nresult==0 ){
! 12506: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
! 12507: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12508: }
1.307 ! brouard 12509: /* goto end; */
! 12510: break;
! 12511: default:
! 12512: nresult=1;
! 12513: decoderesult(".",nresult ); /* No covariate */
1.258 brouard 12514: } /* End switch parameterline */
1.307 ! brouard 12515: parameterline=0;
1.258 brouard 12516: }while(endishere==0); /* End do */
1.126 brouard 12517:
1.230 brouard 12518: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12519: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12520:
12521: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12522: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12523: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12524: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12525: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12526: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12527: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12528: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12529: }else{
1.270 brouard 12530: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12531: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12532: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12533: if(prvforecast==1){
12534: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12535: jprojd=jproj1;
12536: mprojd=mproj1;
12537: anprojd=anproj1;
12538: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12539: jprojf=jproj2;
12540: mprojf=mproj2;
12541: anprojf=anproj2;
12542: } else if(prvforecast == 2){
12543: dateprojd=dateintmean;
12544: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12545: dateprojf=dateintmean+yrfproj;
12546: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12547: }
12548: if(prvbackcast==1){
12549: datebackd=(jback1+12*mback1+365*anback1)/365;
12550: jbackd=jback1;
12551: mbackd=mback1;
12552: anbackd=anback1;
12553: datebackf=(jback2+12*mback2+365*anback2)/365;
12554: jbackf=jback2;
12555: mbackf=mback2;
12556: anbackf=anback2;
12557: } else if(prvbackcast == 2){
12558: datebackd=dateintmean;
12559: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12560: datebackf=dateintmean-yrbproj;
12561: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12562: }
12563:
12564: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12565: }
12566: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12567: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12568: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12569:
1.225 brouard 12570: /*------------ free_vector -------------*/
12571: /* chdir(path); */
1.220 brouard 12572:
1.215 brouard 12573: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12574: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12575: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12576: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12577: free_lvector(num,firstobs,lastobs);
12578: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12579: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12580: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12581: fclose(ficparo);
12582: fclose(ficres);
1.220 brouard 12583:
12584:
1.186 brouard 12585: /* Other results (useful)*/
1.220 brouard 12586:
12587:
1.126 brouard 12588: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12589: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12590: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12591: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12592: fclose(ficrespl);
12593:
12594: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12595: /*#include "hpijx.h"*/
12596: hPijx(p, bage, fage);
1.145 brouard 12597: fclose(ficrespij);
1.227 brouard 12598:
1.220 brouard 12599: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12600: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12601: k=1;
1.126 brouard 12602: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12603:
1.269 brouard 12604: /* Prevalence for each covariate combination in probs[age][status][cov] */
12605: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12606: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12607: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12608: for(k=1;k<=ncovcombmax;k++)
12609: probs[i][j][k]=0.;
1.269 brouard 12610: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12611: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12612: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12613: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12614: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12615: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12616: for(k=1;k<=ncovcombmax;k++)
12617: mobaverages[i][j][k]=0.;
1.219 brouard 12618: mobaverage=mobaverages;
12619: if (mobilav!=0) {
1.235 brouard 12620: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12621: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12622: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12623: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12624: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12625: }
1.269 brouard 12626: } else if (mobilavproj !=0) {
1.235 brouard 12627: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12628: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12629: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12630: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12631: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12632: }
1.269 brouard 12633: }else{
12634: printf("Internal error moving average\n");
12635: fflush(stdout);
12636: exit(1);
1.219 brouard 12637: }
12638: }/* end if moving average */
1.227 brouard 12639:
1.126 brouard 12640: /*---------- Forecasting ------------------*/
1.296 brouard 12641: if(prevfcast==1){
12642: /* /\* if(stepm ==1){*\/ */
12643: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12644: /*This done previously after freqsummary.*/
12645: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12646: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12647:
12648: /* } else if (prvforecast==2){ */
12649: /* /\* if(stepm ==1){*\/ */
12650: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12651: /* } */
12652: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12653: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12654: }
1.269 brouard 12655:
1.296 brouard 12656: /* Prevbcasting */
12657: if(prevbcast==1){
1.219 brouard 12658: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12659: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12660: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12661:
12662: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12663:
12664: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12665:
1.219 brouard 12666: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12667: fclose(ficresplb);
12668:
1.222 brouard 12669: hBijx(p, bage, fage, mobaverage);
12670: fclose(ficrespijb);
1.219 brouard 12671:
1.296 brouard 12672: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12673: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12674: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12675: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12676: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12677: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12678:
12679:
1.269 brouard 12680: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12681:
12682:
1.269 brouard 12683: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12684: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12685: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12686: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12687: } /* end Prevbcasting */
1.268 brouard 12688:
1.186 brouard 12689:
12690: /* ------ Other prevalence ratios------------ */
1.126 brouard 12691:
1.215 brouard 12692: free_ivector(wav,1,imx);
12693: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12694: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12695: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12696:
12697:
1.127 brouard 12698: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12699:
1.201 brouard 12700: strcpy(filerese,"E_");
12701: strcat(filerese,fileresu);
1.126 brouard 12702: if((ficreseij=fopen(filerese,"w"))==NULL) {
12703: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12704: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12705: }
1.208 brouard 12706: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12707: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12708:
12709: pstamp(ficreseij);
1.219 brouard 12710:
1.235 brouard 12711: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12712: if (cptcovn < 1){i1=1;}
12713:
12714: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12715: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12716: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12717: continue;
1.219 brouard 12718: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12719: printf("\n#****** ");
1.225 brouard 12720: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12721: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12722: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12723: }
12724: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12725: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12726: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12727: }
12728: fprintf(ficreseij,"******\n");
1.235 brouard 12729: printf("******\n");
1.219 brouard 12730:
12731: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12732: oldm=oldms;savm=savms;
1.235 brouard 12733: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12734:
1.219 brouard 12735: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12736: }
12737: fclose(ficreseij);
1.208 brouard 12738: printf("done evsij\n");fflush(stdout);
12739: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12740:
1.218 brouard 12741:
1.227 brouard 12742: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12743:
1.201 brouard 12744: strcpy(filerest,"T_");
12745: strcat(filerest,fileresu);
1.127 brouard 12746: if((ficrest=fopen(filerest,"w"))==NULL) {
12747: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12748: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12749: }
1.208 brouard 12750: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12751: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12752: strcpy(fileresstde,"STDE_");
12753: strcat(fileresstde,fileresu);
1.126 brouard 12754: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12755: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12756: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12757: }
1.227 brouard 12758: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12759: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12760:
1.201 brouard 12761: strcpy(filerescve,"CVE_");
12762: strcat(filerescve,fileresu);
1.126 brouard 12763: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12764: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12765: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12766: }
1.227 brouard 12767: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12768: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12769:
1.201 brouard 12770: strcpy(fileresv,"V_");
12771: strcat(fileresv,fileresu);
1.126 brouard 12772: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12773: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12774: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12775: }
1.227 brouard 12776: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12777: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12778:
1.235 brouard 12779: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12780: if (cptcovn < 1){i1=1;}
12781:
12782: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12783: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12784: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12785: continue;
1.242 brouard 12786: printf("\n#****** Result for:");
12787: fprintf(ficrest,"\n#****** Result for:");
12788: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12789: for(j=1;j<=cptcoveff;j++){
12790: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12791: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12792: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12793: }
1.235 brouard 12794: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12795: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12796: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12797: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12798: }
1.208 brouard 12799: fprintf(ficrest,"******\n");
1.227 brouard 12800: fprintf(ficlog,"******\n");
12801: printf("******\n");
1.208 brouard 12802:
12803: fprintf(ficresstdeij,"\n#****** ");
12804: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12805: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12806: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12807: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12808: }
1.235 brouard 12809: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12810: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12811: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12812: }
1.208 brouard 12813: fprintf(ficresstdeij,"******\n");
12814: fprintf(ficrescveij,"******\n");
12815:
12816: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12817: /* pstamp(ficresvij); */
1.225 brouard 12818: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12819: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12820: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12821: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12822: }
1.208 brouard 12823: fprintf(ficresvij,"******\n");
12824:
12825: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12826: oldm=oldms;savm=savms;
1.235 brouard 12827: printf(" cvevsij ");
12828: fprintf(ficlog, " cvevsij ");
12829: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12830: printf(" end cvevsij \n ");
12831: fprintf(ficlog, " end cvevsij \n ");
12832:
12833: /*
12834: */
12835: /* goto endfree; */
12836:
12837: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12838: pstamp(ficrest);
12839:
1.269 brouard 12840: epj=vector(1,nlstate+1);
1.208 brouard 12841: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12842: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12843: cptcod= 0; /* To be deleted */
12844: printf("varevsij vpopbased=%d \n",vpopbased);
12845: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12846: 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 12847: 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 ");
12848: if(vpopbased==1)
12849: 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);
12850: else
1.288 brouard 12851: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12852: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12853: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12854: fprintf(ficrest,"\n");
12855: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12856: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12857: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12858: for(age=bage; age <=fage ;age++){
1.235 brouard 12859: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12860: if (vpopbased==1) {
12861: if(mobilav ==0){
12862: for(i=1; i<=nlstate;i++)
12863: prlim[i][i]=probs[(int)age][i][k];
12864: }else{ /* mobilav */
12865: for(i=1; i<=nlstate;i++)
12866: prlim[i][i]=mobaverage[(int)age][i][k];
12867: }
12868: }
1.219 brouard 12869:
1.227 brouard 12870: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12871: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12872: /* printf(" age %4.0f ",age); */
12873: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12874: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12875: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12876: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12877: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12878: }
12879: epj[nlstate+1] +=epj[j];
12880: }
12881: /* printf(" age %4.0f \n",age); */
1.219 brouard 12882:
1.227 brouard 12883: for(i=1, vepp=0.;i <=nlstate;i++)
12884: for(j=1;j <=nlstate;j++)
12885: vepp += vareij[i][j][(int)age];
12886: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12887: for(j=1;j <=nlstate;j++){
12888: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12889: }
12890: fprintf(ficrest,"\n");
12891: }
1.208 brouard 12892: } /* End vpopbased */
1.269 brouard 12893: free_vector(epj,1,nlstate+1);
1.208 brouard 12894: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12895: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12896: printf("done selection\n");fflush(stdout);
12897: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12898:
1.235 brouard 12899: } /* End k selection */
1.227 brouard 12900:
12901: printf("done State-specific expectancies\n");fflush(stdout);
12902: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12903:
1.288 brouard 12904: /* variance-covariance of forward period prevalence*/
1.269 brouard 12905: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12906:
1.227 brouard 12907:
1.290 brouard 12908: free_vector(weight,firstobs,lastobs);
1.227 brouard 12909: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12910: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12911: free_matrix(anint,1,maxwav,firstobs,lastobs);
12912: free_matrix(mint,1,maxwav,firstobs,lastobs);
12913: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12914: free_ivector(tab,1,NCOVMAX);
12915: fclose(ficresstdeij);
12916: fclose(ficrescveij);
12917: fclose(ficresvij);
12918: fclose(ficrest);
12919: fclose(ficpar);
12920:
12921:
1.126 brouard 12922: /*---------- End : free ----------------*/
1.219 brouard 12923: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12924: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12925: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12926: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12927: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12928: } /* mle==-3 arrives here for freeing */
1.227 brouard 12929: /* endfree:*/
12930: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12931: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12932: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12933: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12934: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12935: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12936: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12937: free_matrix(matcov,1,npar,1,npar);
12938: free_matrix(hess,1,npar,1,npar);
12939: /*free_vector(delti,1,npar);*/
12940: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12941: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12942: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12943: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12944:
12945: free_ivector(ncodemax,1,NCOVMAX);
12946: free_ivector(ncodemaxwundef,1,NCOVMAX);
12947: free_ivector(Dummy,-1,NCOVMAX);
12948: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12949: free_ivector(DummyV,1,NCOVMAX);
12950: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12951: free_ivector(Typevar,-1,NCOVMAX);
12952: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12953: free_ivector(TvarsQ,1,NCOVMAX);
12954: free_ivector(TvarsQind,1,NCOVMAX);
12955: free_ivector(TvarsD,1,NCOVMAX);
12956: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12957: free_ivector(TvarFD,1,NCOVMAX);
12958: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12959: free_ivector(TvarF,1,NCOVMAX);
12960: free_ivector(TvarFind,1,NCOVMAX);
12961: free_ivector(TvarV,1,NCOVMAX);
12962: free_ivector(TvarVind,1,NCOVMAX);
12963: free_ivector(TvarA,1,NCOVMAX);
12964: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12965: free_ivector(TvarFQ,1,NCOVMAX);
12966: free_ivector(TvarFQind,1,NCOVMAX);
12967: free_ivector(TvarVD,1,NCOVMAX);
12968: free_ivector(TvarVDind,1,NCOVMAX);
12969: free_ivector(TvarVQ,1,NCOVMAX);
12970: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12971: free_ivector(Tvarsel,1,NCOVMAX);
12972: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12973: free_ivector(Tposprod,1,NCOVMAX);
12974: free_ivector(Tprod,1,NCOVMAX);
12975: free_ivector(Tvaraff,1,NCOVMAX);
12976: free_ivector(invalidvarcomb,1,ncovcombmax);
12977: free_ivector(Tage,1,NCOVMAX);
12978: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12979: free_ivector(TmodelInvind,1,NCOVMAX);
12980: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12981:
12982: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12983: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12984: fflush(fichtm);
12985: fflush(ficgp);
12986:
1.227 brouard 12987:
1.126 brouard 12988: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12989: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12990: 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 12991: }else{
12992: printf("End of Imach\n");
12993: fprintf(ficlog,"End of Imach\n");
12994: }
12995: printf("See log file on %s\n",filelog);
12996: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12997: /*(void) gettimeofday(&end_time,&tzp);*/
12998: rend_time = time(NULL);
12999: end_time = *localtime(&rend_time);
13000: /* tml = *localtime(&end_time.tm_sec); */
13001: strcpy(strtend,asctime(&end_time));
1.126 brouard 13002: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13003: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13004: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13005:
1.157 brouard 13006: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13007: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13008: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13009: /* printf("Total time was %d uSec.\n", total_usecs);*/
13010: /* if(fileappend(fichtm,optionfilehtm)){ */
13011: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13012: fclose(fichtm);
13013: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13014: fclose(fichtmcov);
13015: fclose(ficgp);
13016: fclose(ficlog);
13017: /*------ End -----------*/
1.227 brouard 13018:
1.281 brouard 13019:
13020: /* Executes gnuplot */
1.227 brouard 13021:
13022: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13023: #ifdef WIN32
1.227 brouard 13024: if (_chdir(pathcd) != 0)
13025: printf("Can't move to directory %s!\n",path);
13026: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13027: #else
1.227 brouard 13028: if(chdir(pathcd) != 0)
13029: printf("Can't move to directory %s!\n", path);
13030: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13031: #endif
1.126 brouard 13032: printf("Current directory %s!\n",pathcd);
13033: /*strcat(plotcmd,CHARSEPARATOR);*/
13034: sprintf(plotcmd,"gnuplot");
1.157 brouard 13035: #ifdef _WIN32
1.126 brouard 13036: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13037: #endif
13038: if(!stat(plotcmd,&info)){
1.158 brouard 13039: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13040: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13041: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13042: }else
13043: strcpy(pplotcmd,plotcmd);
1.157 brouard 13044: #ifdef __unix
1.126 brouard 13045: strcpy(plotcmd,GNUPLOTPROGRAM);
13046: if(!stat(plotcmd,&info)){
1.158 brouard 13047: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13048: }else
13049: strcpy(pplotcmd,plotcmd);
13050: #endif
13051: }else
13052: strcpy(pplotcmd,plotcmd);
13053:
13054: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13055: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13056: strcpy(pplotcmd,plotcmd);
1.227 brouard 13057:
1.126 brouard 13058: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13059: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13060: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13061: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13062: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13063: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13064: strcpy(plotcmd,pplotcmd);
13065: }
1.126 brouard 13066: }
1.158 brouard 13067: printf(" Successful, please wait...");
1.126 brouard 13068: while (z[0] != 'q') {
13069: /* chdir(path); */
1.154 brouard 13070: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13071: scanf("%s",z);
13072: /* if (z[0] == 'c') system("./imach"); */
13073: if (z[0] == 'e') {
1.158 brouard 13074: #ifdef __APPLE__
1.152 brouard 13075: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13076: #elif __linux
13077: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13078: #else
1.152 brouard 13079: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13080: #endif
13081: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13082: system(pplotcmd);
1.126 brouard 13083: }
13084: else if (z[0] == 'g') system(plotcmd);
13085: else if (z[0] == 'q') exit(0);
13086: }
1.227 brouard 13087: end:
1.126 brouard 13088: while (z[0] != 'q') {
1.195 brouard 13089: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13090: scanf("%s",z);
13091: }
1.283 brouard 13092: printf("End\n");
1.282 brouard 13093: exit(0);
1.126 brouard 13094: }
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