Annotation of imach/src/imach.c, revision 1.297
1.297 ! brouard 1: /* $Id: imach.c,v 1.296 2019/05/20 13:03:18 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.297 ! brouard 4: Revision 1.296 2019/05/20 13:03:18 brouard
! 5: Summary: Projection syntax simplified
! 6:
! 7:
! 8: We can now start projections, forward or backward, from the mean date
! 9: of inteviews up to or down to a number of years of projection:
! 10: prevforecast=1 yearsfproj=15.3 mobil_average=0
! 11: or
! 12: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
! 13: or
! 14: prevbackcast=1 yearsbproj=12.3 mobil_average=1
! 15: or
! 16: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
! 17:
1.296 brouard 18: Revision 1.295 2019/05/18 09:52:50 brouard
19: Summary: doxygen tex bug
20:
1.295 brouard 21: Revision 1.294 2019/05/16 14:54:33 brouard
22: Summary: There was some wrong lines added
23:
1.294 brouard 24: Revision 1.293 2019/05/09 15:17:34 brouard
25: *** empty log message ***
26:
1.293 brouard 27: Revision 1.292 2019/05/09 14:17:20 brouard
28: Summary: Some updates
29:
1.292 brouard 30: Revision 1.291 2019/05/09 13:44:18 brouard
31: Summary: Before ncovmax
32:
1.291 brouard 33: Revision 1.290 2019/05/09 13:39:37 brouard
34: Summary: 0.99r18 unlimited number of individuals
35:
36: 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.
37:
1.290 brouard 38: Revision 1.289 2018/12/13 09:16:26 brouard
39: Summary: Bug for young ages (<-30) will be in r17
40:
1.289 brouard 41: Revision 1.288 2018/05/02 20:58:27 brouard
42: Summary: Some bugs fixed
43:
1.288 brouard 44: Revision 1.287 2018/05/01 17:57:25 brouard
45: Summary: Bug fixed by providing frequencies only for non missing covariates
46:
1.287 brouard 47: Revision 1.286 2018/04/27 14:27:04 brouard
48: Summary: some minor bugs
49:
1.286 brouard 50: Revision 1.285 2018/04/21 21:02:16 brouard
51: Summary: Some bugs fixed, valgrind tested
52:
1.285 brouard 53: Revision 1.284 2018/04/20 05:22:13 brouard
54: Summary: Computing mean and stdeviation of fixed quantitative variables
55:
1.284 brouard 56: Revision 1.283 2018/04/19 14:49:16 brouard
57: Summary: Some minor bugs fixed
58:
1.283 brouard 59: Revision 1.282 2018/02/27 22:50:02 brouard
60: *** empty log message ***
61:
1.282 brouard 62: Revision 1.281 2018/02/27 19:25:23 brouard
63: Summary: Adding second argument for quitting
64:
1.281 brouard 65: Revision 1.280 2018/02/21 07:58:13 brouard
66: Summary: 0.99r15
67:
68: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
69:
1.280 brouard 70: Revision 1.279 2017/07/20 13:35:01 brouard
71: Summary: temporary working
72:
1.279 brouard 73: Revision 1.278 2017/07/19 14:09:02 brouard
74: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
75:
1.278 brouard 76: Revision 1.277 2017/07/17 08:53:49 brouard
77: Summary: BOM files can be read now
78:
1.277 brouard 79: Revision 1.276 2017/06/30 15:48:31 brouard
80: Summary: Graphs improvements
81:
1.276 brouard 82: Revision 1.275 2017/06/30 13:39:33 brouard
83: Summary: Saito's color
84:
1.275 brouard 85: Revision 1.274 2017/06/29 09:47:08 brouard
86: Summary: Version 0.99r14
87:
1.274 brouard 88: Revision 1.273 2017/06/27 11:06:02 brouard
89: Summary: More documentation on projections
90:
1.273 brouard 91: Revision 1.272 2017/06/27 10:22:40 brouard
92: Summary: Color of backprojection changed from 6 to 5(yellow)
93:
1.272 brouard 94: Revision 1.271 2017/06/27 10:17:50 brouard
95: Summary: Some bug with rint
96:
1.271 brouard 97: Revision 1.270 2017/05/24 05:45:29 brouard
98: *** empty log message ***
99:
1.270 brouard 100: Revision 1.269 2017/05/23 08:39:25 brouard
101: Summary: Code into subroutine, cleanings
102:
1.269 brouard 103: Revision 1.268 2017/05/18 20:09:32 brouard
104: Summary: backprojection and confidence intervals of backprevalence
105:
1.268 brouard 106: Revision 1.267 2017/05/13 10:25:05 brouard
107: Summary: temporary save for backprojection
108:
1.267 brouard 109: Revision 1.266 2017/05/13 07:26:12 brouard
110: Summary: Version 0.99r13 (improvements and bugs fixed)
111:
1.266 brouard 112: Revision 1.265 2017/04/26 16:22:11 brouard
113: Summary: imach 0.99r13 Some bugs fixed
114:
1.265 brouard 115: Revision 1.264 2017/04/26 06:01:29 brouard
116: Summary: Labels in graphs
117:
1.264 brouard 118: Revision 1.263 2017/04/24 15:23:15 brouard
119: Summary: to save
120:
1.263 brouard 121: Revision 1.262 2017/04/18 16:48:12 brouard
122: *** empty log message ***
123:
1.262 brouard 124: Revision 1.261 2017/04/05 10:14:09 brouard
125: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
126:
1.261 brouard 127: Revision 1.260 2017/04/04 17:46:59 brouard
128: Summary: Gnuplot indexations fixed (humm)
129:
1.260 brouard 130: Revision 1.259 2017/04/04 13:01:16 brouard
131: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
132:
1.259 brouard 133: Revision 1.258 2017/04/03 10:17:47 brouard
134: Summary: Version 0.99r12
135:
136: Some cleanings, conformed with updated documentation.
137:
1.258 brouard 138: Revision 1.257 2017/03/29 16:53:30 brouard
139: Summary: Temp
140:
1.257 brouard 141: Revision 1.256 2017/03/27 05:50:23 brouard
142: Summary: Temporary
143:
1.256 brouard 144: Revision 1.255 2017/03/08 16:02:28 brouard
145: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
146:
1.255 brouard 147: Revision 1.254 2017/03/08 07:13:00 brouard
148: Summary: Fixing data parameter line
149:
1.254 brouard 150: Revision 1.253 2016/12/15 11:59:41 brouard
151: Summary: 0.99 in progress
152:
1.253 brouard 153: Revision 1.252 2016/09/15 21:15:37 brouard
154: *** empty log message ***
155:
1.252 brouard 156: Revision 1.251 2016/09/15 15:01:13 brouard
157: Summary: not working
158:
1.251 brouard 159: Revision 1.250 2016/09/08 16:07:27 brouard
160: Summary: continue
161:
1.250 brouard 162: Revision 1.249 2016/09/07 17:14:18 brouard
163: Summary: Starting values from frequencies
164:
1.249 brouard 165: Revision 1.248 2016/09/07 14:10:18 brouard
166: *** empty log message ***
167:
1.248 brouard 168: Revision 1.247 2016/09/02 11:11:21 brouard
169: *** empty log message ***
170:
1.247 brouard 171: Revision 1.246 2016/09/02 08:49:22 brouard
172: *** empty log message ***
173:
1.246 brouard 174: Revision 1.245 2016/09/02 07:25:01 brouard
175: *** empty log message ***
176:
1.245 brouard 177: Revision 1.244 2016/09/02 07:17:34 brouard
178: *** empty log message ***
179:
1.244 brouard 180: Revision 1.243 2016/09/02 06:45:35 brouard
181: *** empty log message ***
182:
1.243 brouard 183: Revision 1.242 2016/08/30 15:01:20 brouard
184: Summary: Fixing a lots
185:
1.242 brouard 186: Revision 1.241 2016/08/29 17:17:25 brouard
187: Summary: gnuplot problem in Back projection to fix
188:
1.241 brouard 189: Revision 1.240 2016/08/29 07:53:18 brouard
190: Summary: Better
191:
1.240 brouard 192: Revision 1.239 2016/08/26 15:51:03 brouard
193: Summary: Improvement in Powell output in order to copy and paste
194:
195: Author:
196:
1.239 brouard 197: Revision 1.238 2016/08/26 14:23:35 brouard
198: Summary: Starting tests of 0.99
199:
1.238 brouard 200: Revision 1.237 2016/08/26 09:20:19 brouard
201: Summary: to valgrind
202:
1.237 brouard 203: Revision 1.236 2016/08/25 10:50:18 brouard
204: *** empty log message ***
205:
1.236 brouard 206: Revision 1.235 2016/08/25 06:59:23 brouard
207: *** empty log message ***
208:
1.235 brouard 209: Revision 1.234 2016/08/23 16:51:20 brouard
210: *** empty log message ***
211:
1.234 brouard 212: Revision 1.233 2016/08/23 07:40:50 brouard
213: Summary: not working
214:
1.233 brouard 215: Revision 1.232 2016/08/22 14:20:21 brouard
216: Summary: not working
217:
1.232 brouard 218: Revision 1.231 2016/08/22 07:17:15 brouard
219: Summary: not working
220:
1.231 brouard 221: Revision 1.230 2016/08/22 06:55:53 brouard
222: Summary: Not working
223:
1.230 brouard 224: Revision 1.229 2016/07/23 09:45:53 brouard
225: Summary: Completing for func too
226:
1.229 brouard 227: Revision 1.228 2016/07/22 17:45:30 brouard
228: Summary: Fixing some arrays, still debugging
229:
1.227 brouard 230: Revision 1.226 2016/07/12 18:42:34 brouard
231: Summary: temp
232:
1.226 brouard 233: Revision 1.225 2016/07/12 08:40:03 brouard
234: Summary: saving but not running
235:
1.225 brouard 236: Revision 1.224 2016/07/01 13:16:01 brouard
237: Summary: Fixes
238:
1.224 brouard 239: Revision 1.223 2016/02/19 09:23:35 brouard
240: Summary: temporary
241:
1.223 brouard 242: Revision 1.222 2016/02/17 08:14:50 brouard
243: Summary: Probably last 0.98 stable version 0.98r6
244:
1.222 brouard 245: Revision 1.221 2016/02/15 23:35:36 brouard
246: Summary: minor bug
247:
1.220 brouard 248: Revision 1.219 2016/02/15 00:48:12 brouard
249: *** empty log message ***
250:
1.219 brouard 251: Revision 1.218 2016/02/12 11:29:23 brouard
252: Summary: 0.99 Back projections
253:
1.218 brouard 254: Revision 1.217 2015/12/23 17:18:31 brouard
255: Summary: Experimental backcast
256:
1.217 brouard 257: Revision 1.216 2015/12/18 17:32:11 brouard
258: Summary: 0.98r4 Warning and status=-2
259:
260: Version 0.98r4 is now:
261: - displaying an error when status is -1, date of interview unknown and date of death known;
262: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
263: Older changes concerning s=-2, dating from 2005 have been supersed.
264:
1.216 brouard 265: Revision 1.215 2015/12/16 08:52:24 brouard
266: Summary: 0.98r4 working
267:
1.215 brouard 268: Revision 1.214 2015/12/16 06:57:54 brouard
269: Summary: temporary not working
270:
1.214 brouard 271: Revision 1.213 2015/12/11 18:22:17 brouard
272: Summary: 0.98r4
273:
1.213 brouard 274: Revision 1.212 2015/11/21 12:47:24 brouard
275: Summary: minor typo
276:
1.212 brouard 277: Revision 1.211 2015/11/21 12:41:11 brouard
278: Summary: 0.98r3 with some graph of projected cross-sectional
279:
280: Author: Nicolas Brouard
281:
1.211 brouard 282: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 283: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 284: Summary: Adding ftolpl parameter
285: Author: N Brouard
286:
287: We had difficulties to get smoothed confidence intervals. It was due
288: to the period prevalence which wasn't computed accurately. The inner
289: parameter ftolpl is now an outer parameter of the .imach parameter
290: file after estepm. If ftolpl is small 1.e-4 and estepm too,
291: computation are long.
292:
1.209 brouard 293: Revision 1.208 2015/11/17 14:31:57 brouard
294: Summary: temporary
295:
1.208 brouard 296: Revision 1.207 2015/10/27 17:36:57 brouard
297: *** empty log message ***
298:
1.207 brouard 299: Revision 1.206 2015/10/24 07:14:11 brouard
300: *** empty log message ***
301:
1.206 brouard 302: Revision 1.205 2015/10/23 15:50:53 brouard
303: Summary: 0.98r3 some clarification for graphs on likelihood contributions
304:
1.205 brouard 305: Revision 1.204 2015/10/01 16:20:26 brouard
306: Summary: Some new graphs of contribution to likelihood
307:
1.204 brouard 308: Revision 1.203 2015/09/30 17:45:14 brouard
309: Summary: looking at better estimation of the hessian
310:
311: Also a better criteria for convergence to the period prevalence And
312: therefore adding the number of years needed to converge. (The
313: prevalence in any alive state shold sum to one
314:
1.203 brouard 315: Revision 1.202 2015/09/22 19:45:16 brouard
316: Summary: Adding some overall graph on contribution to likelihood. Might change
317:
1.202 brouard 318: Revision 1.201 2015/09/15 17:34:58 brouard
319: Summary: 0.98r0
320:
321: - Some new graphs like suvival functions
322: - Some bugs fixed like model=1+age+V2.
323:
1.201 brouard 324: Revision 1.200 2015/09/09 16:53:55 brouard
325: Summary: Big bug thanks to Flavia
326:
327: Even model=1+age+V2. did not work anymore
328:
1.200 brouard 329: Revision 1.199 2015/09/07 14:09:23 brouard
330: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
331:
1.199 brouard 332: Revision 1.198 2015/09/03 07:14:39 brouard
333: Summary: 0.98q5 Flavia
334:
1.198 brouard 335: Revision 1.197 2015/09/01 18:24:39 brouard
336: *** empty log message ***
337:
1.197 brouard 338: Revision 1.196 2015/08/18 23:17:52 brouard
339: Summary: 0.98q5
340:
1.196 brouard 341: Revision 1.195 2015/08/18 16:28:39 brouard
342: Summary: Adding a hack for testing purpose
343:
344: After reading the title, ftol and model lines, if the comment line has
345: a q, starting with #q, the answer at the end of the run is quit. It
346: permits to run test files in batch with ctest. The former workaround was
347: $ echo q | imach foo.imach
348:
1.195 brouard 349: Revision 1.194 2015/08/18 13:32:00 brouard
350: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
351:
1.194 brouard 352: Revision 1.193 2015/08/04 07:17:42 brouard
353: Summary: 0.98q4
354:
1.193 brouard 355: Revision 1.192 2015/07/16 16:49:02 brouard
356: Summary: Fixing some outputs
357:
1.192 brouard 358: Revision 1.191 2015/07/14 10:00:33 brouard
359: Summary: Some fixes
360:
1.191 brouard 361: Revision 1.190 2015/05/05 08:51:13 brouard
362: Summary: Adding digits in output parameters (7 digits instead of 6)
363:
364: Fix 1+age+.
365:
1.190 brouard 366: Revision 1.189 2015/04/30 14:45:16 brouard
367: Summary: 0.98q2
368:
1.189 brouard 369: Revision 1.188 2015/04/30 08:27:53 brouard
370: *** empty log message ***
371:
1.188 brouard 372: Revision 1.187 2015/04/29 09:11:15 brouard
373: *** empty log message ***
374:
1.187 brouard 375: Revision 1.186 2015/04/23 12:01:52 brouard
376: Summary: V1*age is working now, version 0.98q1
377:
378: Some codes had been disabled in order to simplify and Vn*age was
379: working in the optimization phase, ie, giving correct MLE parameters,
380: but, as usual, outputs were not correct and program core dumped.
381:
1.186 brouard 382: Revision 1.185 2015/03/11 13:26:42 brouard
383: Summary: Inclusion of compile and links command line for Intel Compiler
384:
1.185 brouard 385: Revision 1.184 2015/03/11 11:52:39 brouard
386: Summary: Back from Windows 8. Intel Compiler
387:
1.184 brouard 388: Revision 1.183 2015/03/10 20:34:32 brouard
389: Summary: 0.98q0, trying with directest, mnbrak fixed
390:
391: We use directest instead of original Powell test; probably no
392: incidence on the results, but better justifications;
393: We fixed Numerical Recipes mnbrak routine which was wrong and gave
394: wrong results.
395:
1.183 brouard 396: Revision 1.182 2015/02/12 08:19:57 brouard
397: Summary: Trying to keep directest which seems simpler and more general
398: Author: Nicolas Brouard
399:
1.182 brouard 400: Revision 1.181 2015/02/11 23:22:24 brouard
401: Summary: Comments on Powell added
402:
403: Author:
404:
1.181 brouard 405: Revision 1.180 2015/02/11 17:33:45 brouard
406: Summary: Finishing move from main to function (hpijx and prevalence_limit)
407:
1.180 brouard 408: Revision 1.179 2015/01/04 09:57:06 brouard
409: Summary: back to OS/X
410:
1.179 brouard 411: Revision 1.178 2015/01/04 09:35:48 brouard
412: *** empty log message ***
413:
1.178 brouard 414: Revision 1.177 2015/01/03 18:40:56 brouard
415: Summary: Still testing ilc32 on OSX
416:
1.177 brouard 417: Revision 1.176 2015/01/03 16:45:04 brouard
418: *** empty log message ***
419:
1.176 brouard 420: Revision 1.175 2015/01/03 16:33:42 brouard
421: *** empty log message ***
422:
1.175 brouard 423: Revision 1.174 2015/01/03 16:15:49 brouard
424: Summary: Still in cross-compilation
425:
1.174 brouard 426: Revision 1.173 2015/01/03 12:06:26 brouard
427: Summary: trying to detect cross-compilation
428:
1.173 brouard 429: Revision 1.172 2014/12/27 12:07:47 brouard
430: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
431:
1.172 brouard 432: Revision 1.171 2014/12/23 13:26:59 brouard
433: Summary: Back from Visual C
434:
435: Still problem with utsname.h on Windows
436:
1.171 brouard 437: Revision 1.170 2014/12/23 11:17:12 brouard
438: Summary: Cleaning some \%% back to %%
439:
440: The escape was mandatory for a specific compiler (which one?), but too many warnings.
441:
1.170 brouard 442: Revision 1.169 2014/12/22 23:08:31 brouard
443: Summary: 0.98p
444:
445: Outputs some informations on compiler used, OS etc. Testing on different platforms.
446:
1.169 brouard 447: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 448: Summary: update
1.169 brouard 449:
1.168 brouard 450: Revision 1.167 2014/12/22 13:50:56 brouard
451: Summary: Testing uname and compiler version and if compiled 32 or 64
452:
453: Testing on Linux 64
454:
1.167 brouard 455: Revision 1.166 2014/12/22 11:40:47 brouard
456: *** empty log message ***
457:
1.166 brouard 458: Revision 1.165 2014/12/16 11:20:36 brouard
459: Summary: After compiling on Visual C
460:
461: * imach.c (Module): Merging 1.61 to 1.162
462:
1.165 brouard 463: Revision 1.164 2014/12/16 10:52:11 brouard
464: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
465:
466: * imach.c (Module): Merging 1.61 to 1.162
467:
1.164 brouard 468: Revision 1.163 2014/12/16 10:30:11 brouard
469: * imach.c (Module): Merging 1.61 to 1.162
470:
1.163 brouard 471: Revision 1.162 2014/09/25 11:43:39 brouard
472: Summary: temporary backup 0.99!
473:
1.162 brouard 474: Revision 1.1 2014/09/16 11:06:58 brouard
475: Summary: With some code (wrong) for nlopt
476:
477: Author:
478:
479: Revision 1.161 2014/09/15 20:41:41 brouard
480: Summary: Problem with macro SQR on Intel compiler
481:
1.161 brouard 482: Revision 1.160 2014/09/02 09:24:05 brouard
483: *** empty log message ***
484:
1.160 brouard 485: Revision 1.159 2014/09/01 10:34:10 brouard
486: Summary: WIN32
487: Author: Brouard
488:
1.159 brouard 489: Revision 1.158 2014/08/27 17:11:51 brouard
490: *** empty log message ***
491:
1.158 brouard 492: Revision 1.157 2014/08/27 16:26:55 brouard
493: Summary: Preparing windows Visual studio version
494: Author: Brouard
495:
496: In order to compile on Visual studio, time.h is now correct and time_t
497: and tm struct should be used. difftime should be used but sometimes I
498: just make the differences in raw time format (time(&now).
499: Trying to suppress #ifdef LINUX
500: Add xdg-open for __linux in order to open default browser.
501:
1.157 brouard 502: Revision 1.156 2014/08/25 20:10:10 brouard
503: *** empty log message ***
504:
1.156 brouard 505: Revision 1.155 2014/08/25 18:32:34 brouard
506: Summary: New compile, minor changes
507: Author: Brouard
508:
1.155 brouard 509: Revision 1.154 2014/06/20 17:32:08 brouard
510: Summary: Outputs now all graphs of convergence to period prevalence
511:
1.154 brouard 512: Revision 1.153 2014/06/20 16:45:46 brouard
513: Summary: If 3 live state, convergence to period prevalence on same graph
514: Author: Brouard
515:
1.153 brouard 516: Revision 1.152 2014/06/18 17:54:09 brouard
517: Summary: open browser, use gnuplot on same dir than imach if not found in the path
518:
1.152 brouard 519: Revision 1.151 2014/06/18 16:43:30 brouard
520: *** empty log message ***
521:
1.151 brouard 522: Revision 1.150 2014/06/18 16:42:35 brouard
523: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
524: Author: brouard
525:
1.150 brouard 526: Revision 1.149 2014/06/18 15:51:14 brouard
527: Summary: Some fixes in parameter files errors
528: Author: Nicolas Brouard
529:
1.149 brouard 530: Revision 1.148 2014/06/17 17:38:48 brouard
531: Summary: Nothing new
532: Author: Brouard
533:
534: Just a new packaging for OS/X version 0.98nS
535:
1.148 brouard 536: Revision 1.147 2014/06/16 10:33:11 brouard
537: *** empty log message ***
538:
1.147 brouard 539: Revision 1.146 2014/06/16 10:20:28 brouard
540: Summary: Merge
541: Author: Brouard
542:
543: Merge, before building revised version.
544:
1.146 brouard 545: Revision 1.145 2014/06/10 21:23:15 brouard
546: Summary: Debugging with valgrind
547: Author: Nicolas Brouard
548:
549: Lot of changes in order to output the results with some covariates
550: After the Edimburgh REVES conference 2014, it seems mandatory to
551: improve the code.
552: No more memory valgrind error but a lot has to be done in order to
553: continue the work of splitting the code into subroutines.
554: Also, decodemodel has been improved. Tricode is still not
555: optimal. nbcode should be improved. Documentation has been added in
556: the source code.
557:
1.144 brouard 558: Revision 1.143 2014/01/26 09:45:38 brouard
559: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
560:
561: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
562: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
563:
1.143 brouard 564: Revision 1.142 2014/01/26 03:57:36 brouard
565: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
566:
567: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
568:
1.142 brouard 569: Revision 1.141 2014/01/26 02:42:01 brouard
570: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
571:
1.141 brouard 572: Revision 1.140 2011/09/02 10:37:54 brouard
573: Summary: times.h is ok with mingw32 now.
574:
1.140 brouard 575: Revision 1.139 2010/06/14 07:50:17 brouard
576: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
577: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
578:
1.139 brouard 579: Revision 1.138 2010/04/30 18:19:40 brouard
580: *** empty log message ***
581:
1.138 brouard 582: Revision 1.137 2010/04/29 18:11:38 brouard
583: (Module): Checking covariates for more complex models
584: than V1+V2. A lot of change to be done. Unstable.
585:
1.137 brouard 586: Revision 1.136 2010/04/26 20:30:53 brouard
587: (Module): merging some libgsl code. Fixing computation
588: of likelione (using inter/intrapolation if mle = 0) in order to
589: get same likelihood as if mle=1.
590: Some cleaning of code and comments added.
591:
1.136 brouard 592: Revision 1.135 2009/10/29 15:33:14 brouard
593: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
594:
1.135 brouard 595: Revision 1.134 2009/10/29 13:18:53 brouard
596: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
597:
1.134 brouard 598: Revision 1.133 2009/07/06 10:21:25 brouard
599: just nforces
600:
1.133 brouard 601: Revision 1.132 2009/07/06 08:22:05 brouard
602: Many tings
603:
1.132 brouard 604: Revision 1.131 2009/06/20 16:22:47 brouard
605: Some dimensions resccaled
606:
1.131 brouard 607: Revision 1.130 2009/05/26 06:44:34 brouard
608: (Module): Max Covariate is now set to 20 instead of 8. A
609: lot of cleaning with variables initialized to 0. Trying to make
610: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
611:
1.130 brouard 612: Revision 1.129 2007/08/31 13:49:27 lievre
613: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
614:
1.129 lievre 615: Revision 1.128 2006/06/30 13:02:05 brouard
616: (Module): Clarifications on computing e.j
617:
1.128 brouard 618: Revision 1.127 2006/04/28 18:11:50 brouard
619: (Module): Yes the sum of survivors was wrong since
620: imach-114 because nhstepm was no more computed in the age
621: loop. Now we define nhstepma in the age loop.
622: (Module): In order to speed up (in case of numerous covariates) we
623: compute health expectancies (without variances) in a first step
624: and then all the health expectancies with variances or standard
625: deviation (needs data from the Hessian matrices) which slows the
626: computation.
627: In the future we should be able to stop the program is only health
628: expectancies and graph are needed without standard deviations.
629:
1.127 brouard 630: Revision 1.126 2006/04/28 17:23:28 brouard
631: (Module): Yes the sum of survivors was wrong since
632: imach-114 because nhstepm was no more computed in the age
633: loop. Now we define nhstepma in the age loop.
634: Version 0.98h
635:
1.126 brouard 636: Revision 1.125 2006/04/04 15:20:31 lievre
637: Errors in calculation of health expectancies. Age was not initialized.
638: Forecasting file added.
639:
640: Revision 1.124 2006/03/22 17:13:53 lievre
641: Parameters are printed with %lf instead of %f (more numbers after the comma).
642: The log-likelihood is printed in the log file
643:
644: Revision 1.123 2006/03/20 10:52:43 brouard
645: * imach.c (Module): <title> changed, corresponds to .htm file
646: name. <head> headers where missing.
647:
648: * imach.c (Module): Weights can have a decimal point as for
649: English (a comma might work with a correct LC_NUMERIC environment,
650: otherwise the weight is truncated).
651: Modification of warning when the covariates values are not 0 or
652: 1.
653: Version 0.98g
654:
655: Revision 1.122 2006/03/20 09:45:41 brouard
656: (Module): Weights can have a decimal point as for
657: English (a comma might work with a correct LC_NUMERIC environment,
658: otherwise the weight is truncated).
659: Modification of warning when the covariates values are not 0 or
660: 1.
661: Version 0.98g
662:
663: Revision 1.121 2006/03/16 17:45:01 lievre
664: * imach.c (Module): Comments concerning covariates added
665:
666: * imach.c (Module): refinements in the computation of lli if
667: status=-2 in order to have more reliable computation if stepm is
668: not 1 month. Version 0.98f
669:
670: Revision 1.120 2006/03/16 15:10:38 lievre
671: (Module): refinements in the computation of lli if
672: status=-2 in order to have more reliable computation if stepm is
673: not 1 month. Version 0.98f
674:
675: Revision 1.119 2006/03/15 17:42:26 brouard
676: (Module): Bug if status = -2, the loglikelihood was
677: computed as likelihood omitting the logarithm. Version O.98e
678:
679: Revision 1.118 2006/03/14 18:20:07 brouard
680: (Module): varevsij Comments added explaining the second
681: table of variances if popbased=1 .
682: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
683: (Module): Function pstamp added
684: (Module): Version 0.98d
685:
686: Revision 1.117 2006/03/14 17:16:22 brouard
687: (Module): varevsij Comments added explaining the second
688: table of variances if popbased=1 .
689: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
690: (Module): Function pstamp added
691: (Module): Version 0.98d
692:
693: Revision 1.116 2006/03/06 10:29:27 brouard
694: (Module): Variance-covariance wrong links and
695: varian-covariance of ej. is needed (Saito).
696:
697: Revision 1.115 2006/02/27 12:17:45 brouard
698: (Module): One freematrix added in mlikeli! 0.98c
699:
700: Revision 1.114 2006/02/26 12:57:58 brouard
701: (Module): Some improvements in processing parameter
702: filename with strsep.
703:
704: Revision 1.113 2006/02/24 14:20:24 brouard
705: (Module): Memory leaks checks with valgrind and:
706: datafile was not closed, some imatrix were not freed and on matrix
707: allocation too.
708:
709: Revision 1.112 2006/01/30 09:55:26 brouard
710: (Module): Back to gnuplot.exe instead of wgnuplot.exe
711:
712: Revision 1.111 2006/01/25 20:38:18 brouard
713: (Module): Lots of cleaning and bugs added (Gompertz)
714: (Module): Comments can be added in data file. Missing date values
715: can be a simple dot '.'.
716:
717: Revision 1.110 2006/01/25 00:51:50 brouard
718: (Module): Lots of cleaning and bugs added (Gompertz)
719:
720: Revision 1.109 2006/01/24 19:37:15 brouard
721: (Module): Comments (lines starting with a #) are allowed in data.
722:
723: Revision 1.108 2006/01/19 18:05:42 lievre
724: Gnuplot problem appeared...
725: To be fixed
726:
727: Revision 1.107 2006/01/19 16:20:37 brouard
728: Test existence of gnuplot in imach path
729:
730: Revision 1.106 2006/01/19 13:24:36 brouard
731: Some cleaning and links added in html output
732:
733: Revision 1.105 2006/01/05 20:23:19 lievre
734: *** empty log message ***
735:
736: Revision 1.104 2005/09/30 16:11:43 lievre
737: (Module): sump fixed, loop imx fixed, and simplifications.
738: (Module): If the status is missing at the last wave but we know
739: that the person is alive, then we can code his/her status as -2
740: (instead of missing=-1 in earlier versions) and his/her
741: contributions to the likelihood is 1 - Prob of dying from last
742: health status (= 1-p13= p11+p12 in the easiest case of somebody in
743: the healthy state at last known wave). Version is 0.98
744:
745: Revision 1.103 2005/09/30 15:54:49 lievre
746: (Module): sump fixed, loop imx fixed, and simplifications.
747:
748: Revision 1.102 2004/09/15 17:31:30 brouard
749: Add the possibility to read data file including tab characters.
750:
751: Revision 1.101 2004/09/15 10:38:38 brouard
752: Fix on curr_time
753:
754: Revision 1.100 2004/07/12 18:29:06 brouard
755: Add version for Mac OS X. Just define UNIX in Makefile
756:
757: Revision 1.99 2004/06/05 08:57:40 brouard
758: *** empty log message ***
759:
760: Revision 1.98 2004/05/16 15:05:56 brouard
761: New version 0.97 . First attempt to estimate force of mortality
762: directly from the data i.e. without the need of knowing the health
763: state at each age, but using a Gompertz model: log u =a + b*age .
764: This is the basic analysis of mortality and should be done before any
765: other analysis, in order to test if the mortality estimated from the
766: cross-longitudinal survey is different from the mortality estimated
767: from other sources like vital statistic data.
768:
769: The same imach parameter file can be used but the option for mle should be -3.
770:
1.133 brouard 771: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 772: former routines in order to include the new code within the former code.
773:
774: The output is very simple: only an estimate of the intercept and of
775: the slope with 95% confident intervals.
776:
777: Current limitations:
778: A) Even if you enter covariates, i.e. with the
779: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
780: B) There is no computation of Life Expectancy nor Life Table.
781:
782: Revision 1.97 2004/02/20 13:25:42 lievre
783: Version 0.96d. Population forecasting command line is (temporarily)
784: suppressed.
785:
786: Revision 1.96 2003/07/15 15:38:55 brouard
787: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
788: rewritten within the same printf. Workaround: many printfs.
789:
790: Revision 1.95 2003/07/08 07:54:34 brouard
791: * imach.c (Repository):
792: (Repository): Using imachwizard code to output a more meaningful covariance
793: matrix (cov(a12,c31) instead of numbers.
794:
795: Revision 1.94 2003/06/27 13:00:02 brouard
796: Just cleaning
797:
798: Revision 1.93 2003/06/25 16:33:55 brouard
799: (Module): On windows (cygwin) function asctime_r doesn't
800: exist so I changed back to asctime which exists.
801: (Module): Version 0.96b
802:
803: Revision 1.92 2003/06/25 16:30:45 brouard
804: (Module): On windows (cygwin) function asctime_r doesn't
805: exist so I changed back to asctime which exists.
806:
807: Revision 1.91 2003/06/25 15:30:29 brouard
808: * imach.c (Repository): Duplicated warning errors corrected.
809: (Repository): Elapsed time after each iteration is now output. It
810: helps to forecast when convergence will be reached. Elapsed time
811: is stamped in powell. We created a new html file for the graphs
812: concerning matrix of covariance. It has extension -cov.htm.
813:
814: Revision 1.90 2003/06/24 12:34:15 brouard
815: (Module): Some bugs corrected for windows. Also, when
816: mle=-1 a template is output in file "or"mypar.txt with the design
817: of the covariance matrix to be input.
818:
819: Revision 1.89 2003/06/24 12:30:52 brouard
820: (Module): Some bugs corrected for windows. Also, when
821: mle=-1 a template is output in file "or"mypar.txt with the design
822: of the covariance matrix to be input.
823:
824: Revision 1.88 2003/06/23 17:54:56 brouard
825: * 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.
826:
827: Revision 1.87 2003/06/18 12:26:01 brouard
828: Version 0.96
829:
830: Revision 1.86 2003/06/17 20:04:08 brouard
831: (Module): Change position of html and gnuplot routines and added
832: routine fileappend.
833:
834: Revision 1.85 2003/06/17 13:12:43 brouard
835: * imach.c (Repository): Check when date of death was earlier that
836: current date of interview. It may happen when the death was just
837: prior to the death. In this case, dh was negative and likelihood
838: was wrong (infinity). We still send an "Error" but patch by
839: assuming that the date of death was just one stepm after the
840: interview.
841: (Repository): Because some people have very long ID (first column)
842: we changed int to long in num[] and we added a new lvector for
843: memory allocation. But we also truncated to 8 characters (left
844: truncation)
845: (Repository): No more line truncation errors.
846:
847: Revision 1.84 2003/06/13 21:44:43 brouard
848: * imach.c (Repository): Replace "freqsummary" at a correct
849: place. It differs from routine "prevalence" which may be called
850: many times. Probs is memory consuming and must be used with
851: parcimony.
852: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
853:
854: Revision 1.83 2003/06/10 13:39:11 lievre
855: *** empty log message ***
856:
857: Revision 1.82 2003/06/05 15:57:20 brouard
858: Add log in imach.c and fullversion number is now printed.
859:
860: */
861: /*
862: Interpolated Markov Chain
863:
864: Short summary of the programme:
865:
1.227 brouard 866: This program computes Healthy Life Expectancies or State-specific
867: (if states aren't health statuses) Expectancies from
868: cross-longitudinal data. Cross-longitudinal data consist in:
869:
870: -1- a first survey ("cross") where individuals from different ages
871: are interviewed on their health status or degree of disability (in
872: the case of a health survey which is our main interest)
873:
874: -2- at least a second wave of interviews ("longitudinal") which
875: measure each change (if any) in individual health status. Health
876: expectancies are computed from the time spent in each health state
877: according to a model. More health states you consider, more time is
878: necessary to reach the Maximum Likelihood of the parameters involved
879: in the model. The simplest model is the multinomial logistic model
880: where pij is the probability to be observed in state j at the second
881: wave conditional to be observed in state i at the first
882: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
883: etc , where 'age' is age and 'sex' is a covariate. If you want to
884: have a more complex model than "constant and age", you should modify
885: the program where the markup *Covariates have to be included here
886: again* invites you to do it. More covariates you add, slower the
1.126 brouard 887: convergence.
888:
889: The advantage of this computer programme, compared to a simple
890: multinomial logistic model, is clear when the delay between waves is not
891: identical for each individual. Also, if a individual missed an
892: intermediate interview, the information is lost, but taken into
893: account using an interpolation or extrapolation.
894:
895: hPijx is the probability to be observed in state i at age x+h
896: conditional to the observed state i at age x. The delay 'h' can be
897: split into an exact number (nh*stepm) of unobserved intermediate
898: states. This elementary transition (by month, quarter,
899: semester or year) is modelled as a multinomial logistic. The hPx
900: matrix is simply the matrix product of nh*stepm elementary matrices
901: and the contribution of each individual to the likelihood is simply
902: hPijx.
903:
904: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 905: of the life expectancies. It also computes the period (stable) prevalence.
906:
907: Back prevalence and projections:
1.227 brouard 908:
909: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
910: double agemaxpar, double ftolpl, int *ncvyearp, double
911: dateprev1,double dateprev2, int firstpass, int lastpass, int
912: mobilavproj)
913:
914: Computes the back prevalence limit for any combination of
915: covariate values k at any age between ageminpar and agemaxpar and
916: returns it in **bprlim. In the loops,
917:
918: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
919: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
920:
921: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 922: Computes for any combination of covariates k and any age between bage and fage
923: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
924: oldm=oldms;savm=savms;
1.227 brouard 925:
1.267 brouard 926: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 927: Computes the transition matrix starting at age 'age' over
928: 'nhstepm*hstepm*stepm' months (i.e. until
929: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 930: nhstepm*hstepm matrices.
931:
932: Returns p3mat[i][j][h] after calling
933: p3mat[i][j][h]=matprod2(newm,
934: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
935: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
936: oldm);
1.226 brouard 937:
938: Important routines
939:
940: - func (or funcone), computes logit (pij) distinguishing
941: o fixed variables (single or product dummies or quantitative);
942: o varying variables by:
943: (1) wave (single, product dummies, quantitative),
944: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
945: % fixed dummy (treated) or quantitative (not done because time-consuming);
946: % varying dummy (not done) or quantitative (not done);
947: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
948: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
949: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
950: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
951: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 952:
1.226 brouard 953:
954:
1.133 brouard 955: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
956: Institut national d'études démographiques, Paris.
1.126 brouard 957: This software have been partly granted by Euro-REVES, a concerted action
958: from the European Union.
959: It is copyrighted identically to a GNU software product, ie programme and
960: software can be distributed freely for non commercial use. Latest version
961: can be accessed at http://euroreves.ined.fr/imach .
962:
963: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
964: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
965:
966: **********************************************************************/
967: /*
968: main
969: read parameterfile
970: read datafile
971: concatwav
972: freqsummary
973: if (mle >= 1)
974: mlikeli
975: print results files
976: if mle==1
977: computes hessian
978: read end of parameter file: agemin, agemax, bage, fage, estepm
979: begin-prev-date,...
980: open gnuplot file
981: open html file
1.145 brouard 982: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
983: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
984: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
985: freexexit2 possible for memory heap.
986:
987: h Pij x | pij_nom ficrestpij
988: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
989: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
990: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
991:
992: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
993: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
994: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
995: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
996: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
997:
1.126 brouard 998: forecasting if prevfcast==1 prevforecast call prevalence()
999: health expectancies
1000: Variance-covariance of DFLE
1001: prevalence()
1002: movingaverage()
1003: varevsij()
1004: if popbased==1 varevsij(,popbased)
1005: total life expectancies
1006: Variance of period (stable) prevalence
1007: end
1008: */
1009:
1.187 brouard 1010: /* #define DEBUG */
1011: /* #define DEBUGBRENT */
1.203 brouard 1012: /* #define DEBUGLINMIN */
1013: /* #define DEBUGHESS */
1014: #define DEBUGHESSIJ
1.224 brouard 1015: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1016: #define POWELL /* Instead of NLOPT */
1.224 brouard 1017: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1018: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1019: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1020:
1021: #include <math.h>
1022: #include <stdio.h>
1023: #include <stdlib.h>
1024: #include <string.h>
1.226 brouard 1025: #include <ctype.h>
1.159 brouard 1026:
1027: #ifdef _WIN32
1028: #include <io.h>
1.172 brouard 1029: #include <windows.h>
1030: #include <tchar.h>
1.159 brouard 1031: #else
1.126 brouard 1032: #include <unistd.h>
1.159 brouard 1033: #endif
1.126 brouard 1034:
1035: #include <limits.h>
1036: #include <sys/types.h>
1.171 brouard 1037:
1038: #if defined(__GNUC__)
1039: #include <sys/utsname.h> /* Doesn't work on Windows */
1040: #endif
1041:
1.126 brouard 1042: #include <sys/stat.h>
1043: #include <errno.h>
1.159 brouard 1044: /* extern int errno; */
1.126 brouard 1045:
1.157 brouard 1046: /* #ifdef LINUX */
1047: /* #include <time.h> */
1048: /* #include "timeval.h" */
1049: /* #else */
1050: /* #include <sys/time.h> */
1051: /* #endif */
1052:
1.126 brouard 1053: #include <time.h>
1054:
1.136 brouard 1055: #ifdef GSL
1056: #include <gsl/gsl_errno.h>
1057: #include <gsl/gsl_multimin.h>
1058: #endif
1059:
1.167 brouard 1060:
1.162 brouard 1061: #ifdef NLOPT
1062: #include <nlopt.h>
1063: typedef struct {
1064: double (* function)(double [] );
1065: } myfunc_data ;
1066: #endif
1067:
1.126 brouard 1068: /* #include <libintl.h> */
1069: /* #define _(String) gettext (String) */
1070:
1.251 brouard 1071: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1072:
1073: #define GNUPLOTPROGRAM "gnuplot"
1074: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1075: #define FILENAMELENGTH 132
1076:
1077: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1078: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1079:
1.144 brouard 1080: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1081: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1082:
1083: #define NINTERVMAX 8
1.144 brouard 1084: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1085: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1086: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1087: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1088: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1089: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1090: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1091: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1092: /* #define AGESUP 130 */
1.288 brouard 1093: /* #define AGESUP 150 */
1094: #define AGESUP 200
1.268 brouard 1095: #define AGEINF 0
1.218 brouard 1096: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1097: #define AGEBASE 40
1.194 brouard 1098: #define AGEOVERFLOW 1.e20
1.164 brouard 1099: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1100: #ifdef _WIN32
1101: #define DIRSEPARATOR '\\'
1102: #define CHARSEPARATOR "\\"
1103: #define ODIRSEPARATOR '/'
1104: #else
1.126 brouard 1105: #define DIRSEPARATOR '/'
1106: #define CHARSEPARATOR "/"
1107: #define ODIRSEPARATOR '\\'
1108: #endif
1109:
1.297 ! brouard 1110: /* $Id: imach.c,v 1.296 2019/05/20 13:03:18 brouard Exp $ */
1.126 brouard 1111: /* $State: Exp $ */
1.196 brouard 1112: #include "version.h"
1113: char version[]=__IMACH_VERSION__;
1.283 brouard 1114: char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.297 ! brouard 1115: char fullversion[]="$Revision: 1.296 $ $Date: 2019/05/20 13:03:18 $";
1.126 brouard 1116: char strstart[80];
1117: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1118: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1119: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1120: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1121: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1122: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1123: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1124: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1125: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1126: int cptcovprodnoage=0; /**< Number of covariate products without age */
1127: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1128: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1129: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1130: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1131: int nsd=0; /**< Total number of single dummy variables (output) */
1132: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1133: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1134: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1135: int ntveff=0; /**< ntveff number of effective time varying variables */
1136: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1137: int cptcov=0; /* Working variable */
1.290 brouard 1138: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1139: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 1140: int npar=NPARMAX;
1141: int nlstate=2; /* Number of live states */
1142: int ndeath=1; /* Number of dead states */
1.130 brouard 1143: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1144: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1145: int popbased=0;
1146:
1147: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1148: int maxwav=0; /* Maxim number of waves */
1149: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1150: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1151: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1152: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1153: int mle=1, weightopt=0;
1.126 brouard 1154: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1155: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1156: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1157: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1158: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1159: int selected(int kvar); /* Is covariate kvar selected for printing results */
1160:
1.130 brouard 1161: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1162: double **matprod2(); /* test */
1.126 brouard 1163: double **oldm, **newm, **savm; /* Working pointers to matrices */
1164: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1165: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1166:
1.136 brouard 1167: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1168: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1169: FILE *ficlog, *ficrespow;
1.130 brouard 1170: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1171: double fretone; /* Only one call to likelihood */
1.130 brouard 1172: long ipmx=0; /* Number of contributions */
1.126 brouard 1173: double sw; /* Sum of weights */
1174: char filerespow[FILENAMELENGTH];
1175: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1176: FILE *ficresilk;
1177: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1178: FILE *ficresprobmorprev;
1179: FILE *fichtm, *fichtmcov; /* Html File */
1180: FILE *ficreseij;
1181: char filerese[FILENAMELENGTH];
1182: FILE *ficresstdeij;
1183: char fileresstde[FILENAMELENGTH];
1184: FILE *ficrescveij;
1185: char filerescve[FILENAMELENGTH];
1186: FILE *ficresvij;
1187: char fileresv[FILENAMELENGTH];
1.269 brouard 1188:
1.126 brouard 1189: char title[MAXLINE];
1.234 brouard 1190: char model[MAXLINE]; /**< The model line */
1.217 brouard 1191: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1192: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1193: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1194: char command[FILENAMELENGTH];
1195: int outcmd=0;
1196:
1.217 brouard 1197: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1198: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1199: char filelog[FILENAMELENGTH]; /* Log file */
1200: char filerest[FILENAMELENGTH];
1201: char fileregp[FILENAMELENGTH];
1202: char popfile[FILENAMELENGTH];
1203:
1204: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1205:
1.157 brouard 1206: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1207: /* struct timezone tzp; */
1208: /* extern int gettimeofday(); */
1209: struct tm tml, *gmtime(), *localtime();
1210:
1211: extern time_t time();
1212:
1213: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1214: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1215: struct tm tm;
1216:
1.126 brouard 1217: char strcurr[80], strfor[80];
1218:
1219: char *endptr;
1220: long lval;
1221: double dval;
1222:
1223: #define NR_END 1
1224: #define FREE_ARG char*
1225: #define FTOL 1.0e-10
1226:
1227: #define NRANSI
1.240 brouard 1228: #define ITMAX 200
1229: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1230:
1231: #define TOL 2.0e-4
1232:
1233: #define CGOLD 0.3819660
1234: #define ZEPS 1.0e-10
1235: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1236:
1237: #define GOLD 1.618034
1238: #define GLIMIT 100.0
1239: #define TINY 1.0e-20
1240:
1241: static double maxarg1,maxarg2;
1242: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1243: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1244:
1245: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1246: #define rint(a) floor(a+0.5)
1.166 brouard 1247: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1248: #define mytinydouble 1.0e-16
1.166 brouard 1249: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1250: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1251: /* static double dsqrarg; */
1252: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1253: static double sqrarg;
1254: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1255: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1256: int agegomp= AGEGOMP;
1257:
1258: int imx;
1259: int stepm=1;
1260: /* Stepm, step in month: minimum step interpolation*/
1261:
1262: int estepm;
1263: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1264:
1265: int m,nb;
1266: long *num;
1.197 brouard 1267: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1268: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1269: covariate for which somebody answered excluding
1270: undefined. Usually 2: 0 and 1. */
1271: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1272: covariate for which somebody answered including
1273: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1274: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1275: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1276: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1277: double *ageexmed,*agecens;
1278: double dateintmean=0;
1.296 brouard 1279: double anprojd, mprojd, jprojd; /* For eventual projections */
1280: double anprojf, mprojf, jprojf;
1.126 brouard 1281:
1.296 brouard 1282: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1283: double anbackf, mbackf, jbackf;
1284: double jintmean,mintmean,aintmean;
1.126 brouard 1285: double *weight;
1286: int **s; /* Status */
1.141 brouard 1287: double *agedc;
1.145 brouard 1288: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1289: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1290: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1291: double **coqvar; /* Fixed quantitative covariate nqv */
1292: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1293: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1294: double idx;
1295: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1296: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1297: /*k 1 2 3 4 5 6 7 8 9 */
1298: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1299: /* Tndvar[k] 1 2 3 4 5 */
1300: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1301: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1302: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1303: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1304: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1305: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1306: /* Tprod[i]=k 4 7 */
1307: /* Tage[i]=k 5 8 */
1308: /* */
1309: /* Type */
1310: /* V 1 2 3 4 5 */
1311: /* F F V V V */
1312: /* D Q D D Q */
1313: /* */
1314: int *TvarsD;
1315: int *TvarsDind;
1316: int *TvarsQ;
1317: int *TvarsQind;
1318:
1.235 brouard 1319: #define MAXRESULTLINES 10
1320: int nresult=0;
1.258 brouard 1321: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1322: int TKresult[MAXRESULTLINES];
1.237 brouard 1323: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1324: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1325: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1326: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1327: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1328: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1329:
1.234 brouard 1330: /* 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 1331: 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 */
1332: 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 */
1333: 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 */
1334: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1335: 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 */
1336: 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 1337: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1338: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1339: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1340: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1341: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1342: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1343: 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 */
1344: 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 */
1345:
1.230 brouard 1346: int *Tvarsel; /**< Selected covariates for output */
1347: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1348: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1349: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1350: 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 1351: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1352: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1353: int *Tage;
1.227 brouard 1354: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1355: 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 1356: 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*/
1357: 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 1358: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1359: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1360: int **Tvard;
1361: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1362: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1363: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1364: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1365: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1366: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1367: double *lsurv, *lpop, *tpop;
1368:
1.231 brouard 1369: #define FD 1; /* Fixed dummy covariate */
1370: #define FQ 2; /* Fixed quantitative covariate */
1371: #define FP 3; /* Fixed product covariate */
1372: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1373: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1374: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1375: #define VD 10; /* Varying dummy covariate */
1376: #define VQ 11; /* Varying quantitative covariate */
1377: #define VP 12; /* Varying product covariate */
1378: #define VPDD 13; /* Varying product dummy*dummy covariate */
1379: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1380: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1381: #define APFD 16; /* Age product * fixed dummy covariate */
1382: #define APFQ 17; /* Age product * fixed quantitative covariate */
1383: #define APVD 18; /* Age product * varying dummy covariate */
1384: #define APVQ 19; /* Age product * varying quantitative covariate */
1385:
1386: #define FTYPE 1; /* Fixed covariate */
1387: #define VTYPE 2; /* Varying covariate (loop in wave) */
1388: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1389:
1390: struct kmodel{
1391: int maintype; /* main type */
1392: int subtype; /* subtype */
1393: };
1394: struct kmodel modell[NCOVMAX];
1395:
1.143 brouard 1396: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1397: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1398:
1399: /**************** split *************************/
1400: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1401: {
1402: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1403: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1404: */
1405: char *ss; /* pointer */
1.186 brouard 1406: int l1=0, l2=0; /* length counters */
1.126 brouard 1407:
1408: l1 = strlen(path ); /* length of path */
1409: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1410: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1411: if ( ss == NULL ) { /* no directory, so determine current directory */
1412: strcpy( name, path ); /* we got the fullname name because no directory */
1413: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1414: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1415: /* get current working directory */
1416: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1417: #ifdef WIN32
1418: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1419: #else
1420: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1421: #endif
1.126 brouard 1422: return( GLOCK_ERROR_GETCWD );
1423: }
1424: /* got dirc from getcwd*/
1425: printf(" DIRC = %s \n",dirc);
1.205 brouard 1426: } else { /* strip directory from path */
1.126 brouard 1427: ss++; /* after this, the filename */
1428: l2 = strlen( ss ); /* length of filename */
1429: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1430: strcpy( name, ss ); /* save file name */
1431: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1432: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1433: printf(" DIRC2 = %s \n",dirc);
1434: }
1435: /* We add a separator at the end of dirc if not exists */
1436: l1 = strlen( dirc ); /* length of directory */
1437: if( dirc[l1-1] != DIRSEPARATOR ){
1438: dirc[l1] = DIRSEPARATOR;
1439: dirc[l1+1] = 0;
1440: printf(" DIRC3 = %s \n",dirc);
1441: }
1442: ss = strrchr( name, '.' ); /* find last / */
1443: if (ss >0){
1444: ss++;
1445: strcpy(ext,ss); /* save extension */
1446: l1= strlen( name);
1447: l2= strlen(ss)+1;
1448: strncpy( finame, name, l1-l2);
1449: finame[l1-l2]= 0;
1450: }
1451:
1452: return( 0 ); /* we're done */
1453: }
1454:
1455:
1456: /******************************************/
1457:
1458: void replace_back_to_slash(char *s, char*t)
1459: {
1460: int i;
1461: int lg=0;
1462: i=0;
1463: lg=strlen(t);
1464: for(i=0; i<= lg; i++) {
1465: (s[i] = t[i]);
1466: if (t[i]== '\\') s[i]='/';
1467: }
1468: }
1469:
1.132 brouard 1470: char *trimbb(char *out, char *in)
1.137 brouard 1471: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1472: char *s;
1473: s=out;
1474: while (*in != '\0'){
1.137 brouard 1475: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1476: in++;
1477: }
1478: *out++ = *in++;
1479: }
1480: *out='\0';
1481: return s;
1482: }
1483:
1.187 brouard 1484: /* char *substrchaine(char *out, char *in, char *chain) */
1485: /* { */
1486: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1487: /* char *s, *t; */
1488: /* t=in;s=out; */
1489: /* while ((*in != *chain) && (*in != '\0')){ */
1490: /* *out++ = *in++; */
1491: /* } */
1492:
1493: /* /\* *in matches *chain *\/ */
1494: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1495: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1496: /* } */
1497: /* in--; chain--; */
1498: /* while ( (*in != '\0')){ */
1499: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1500: /* *out++ = *in++; */
1501: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1502: /* } */
1503: /* *out='\0'; */
1504: /* out=s; */
1505: /* return out; */
1506: /* } */
1507: char *substrchaine(char *out, char *in, char *chain)
1508: {
1509: /* Substract chain 'chain' from 'in', return and output 'out' */
1510: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1511:
1512: char *strloc;
1513:
1514: strcpy (out, in);
1515: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1516: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1517: if(strloc != NULL){
1518: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1519: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1520: /* strcpy (strloc, strloc +strlen(chain));*/
1521: }
1522: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1523: return out;
1524: }
1525:
1526:
1.145 brouard 1527: char *cutl(char *blocc, char *alocc, char *in, char occ)
1528: {
1.187 brouard 1529: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1530: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1531: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1532: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1533: */
1.160 brouard 1534: char *s, *t;
1.145 brouard 1535: t=in;s=in;
1536: while ((*in != occ) && (*in != '\0')){
1537: *alocc++ = *in++;
1538: }
1539: if( *in == occ){
1540: *(alocc)='\0';
1541: s=++in;
1542: }
1543:
1544: if (s == t) {/* occ not found */
1545: *(alocc-(in-s))='\0';
1546: in=s;
1547: }
1548: while ( *in != '\0'){
1549: *blocc++ = *in++;
1550: }
1551:
1552: *blocc='\0';
1553: return t;
1554: }
1.137 brouard 1555: char *cutv(char *blocc, char *alocc, char *in, char occ)
1556: {
1.187 brouard 1557: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1558: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1559: gives blocc="abcdef2ghi" and alocc="j".
1560: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1561: */
1562: char *s, *t;
1563: t=in;s=in;
1564: while (*in != '\0'){
1565: while( *in == occ){
1566: *blocc++ = *in++;
1567: s=in;
1568: }
1569: *blocc++ = *in++;
1570: }
1571: if (s == t) /* occ not found */
1572: *(blocc-(in-s))='\0';
1573: else
1574: *(blocc-(in-s)-1)='\0';
1575: in=s;
1576: while ( *in != '\0'){
1577: *alocc++ = *in++;
1578: }
1579:
1580: *alocc='\0';
1581: return s;
1582: }
1583:
1.126 brouard 1584: int nbocc(char *s, char occ)
1585: {
1586: int i,j=0;
1587: int lg=20;
1588: i=0;
1589: lg=strlen(s);
1590: for(i=0; i<= lg; i++) {
1.234 brouard 1591: if (s[i] == occ ) j++;
1.126 brouard 1592: }
1593: return j;
1594: }
1595:
1.137 brouard 1596: /* void cutv(char *u,char *v, char*t, char occ) */
1597: /* { */
1598: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1599: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1600: /* gives u="abcdef2ghi" and v="j" *\/ */
1601: /* int i,lg,j,p=0; */
1602: /* i=0; */
1603: /* lg=strlen(t); */
1604: /* for(j=0; j<=lg-1; j++) { */
1605: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1606: /* } */
1.126 brouard 1607:
1.137 brouard 1608: /* for(j=0; j<p; j++) { */
1609: /* (u[j] = t[j]); */
1610: /* } */
1611: /* u[p]='\0'; */
1.126 brouard 1612:
1.137 brouard 1613: /* for(j=0; j<= lg; j++) { */
1614: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1615: /* } */
1616: /* } */
1.126 brouard 1617:
1.160 brouard 1618: #ifdef _WIN32
1619: char * strsep(char **pp, const char *delim)
1620: {
1621: char *p, *q;
1622:
1623: if ((p = *pp) == NULL)
1624: return 0;
1625: if ((q = strpbrk (p, delim)) != NULL)
1626: {
1627: *pp = q + 1;
1628: *q = '\0';
1629: }
1630: else
1631: *pp = 0;
1632: return p;
1633: }
1634: #endif
1635:
1.126 brouard 1636: /********************** nrerror ********************/
1637:
1638: void nrerror(char error_text[])
1639: {
1640: fprintf(stderr,"ERREUR ...\n");
1641: fprintf(stderr,"%s\n",error_text);
1642: exit(EXIT_FAILURE);
1643: }
1644: /*********************** vector *******************/
1645: double *vector(int nl, int nh)
1646: {
1647: double *v;
1648: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1649: if (!v) nrerror("allocation failure in vector");
1650: return v-nl+NR_END;
1651: }
1652:
1653: /************************ free vector ******************/
1654: void free_vector(double*v, int nl, int nh)
1655: {
1656: free((FREE_ARG)(v+nl-NR_END));
1657: }
1658:
1659: /************************ivector *******************************/
1660: int *ivector(long nl,long nh)
1661: {
1662: int *v;
1663: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1664: if (!v) nrerror("allocation failure in ivector");
1665: return v-nl+NR_END;
1666: }
1667:
1668: /******************free ivector **************************/
1669: void free_ivector(int *v, long nl, long nh)
1670: {
1671: free((FREE_ARG)(v+nl-NR_END));
1672: }
1673:
1674: /************************lvector *******************************/
1675: long *lvector(long nl,long nh)
1676: {
1677: long *v;
1678: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1679: if (!v) nrerror("allocation failure in ivector");
1680: return v-nl+NR_END;
1681: }
1682:
1683: /******************free lvector **************************/
1684: void free_lvector(long *v, long nl, long nh)
1685: {
1686: free((FREE_ARG)(v+nl-NR_END));
1687: }
1688:
1689: /******************* imatrix *******************************/
1690: int **imatrix(long nrl, long nrh, long ncl, long nch)
1691: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1692: {
1693: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1694: int **m;
1695:
1696: /* allocate pointers to rows */
1697: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1698: if (!m) nrerror("allocation failure 1 in matrix()");
1699: m += NR_END;
1700: m -= nrl;
1701:
1702:
1703: /* allocate rows and set pointers to them */
1704: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1705: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1706: m[nrl] += NR_END;
1707: m[nrl] -= ncl;
1708:
1709: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1710:
1711: /* return pointer to array of pointers to rows */
1712: return m;
1713: }
1714:
1715: /****************** free_imatrix *************************/
1716: void free_imatrix(m,nrl,nrh,ncl,nch)
1717: int **m;
1718: long nch,ncl,nrh,nrl;
1719: /* free an int matrix allocated by imatrix() */
1720: {
1721: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1722: free((FREE_ARG) (m+nrl-NR_END));
1723: }
1724:
1725: /******************* matrix *******************************/
1726: double **matrix(long nrl, long nrh, long ncl, long nch)
1727: {
1728: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1729: double **m;
1730:
1731: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1732: if (!m) nrerror("allocation failure 1 in matrix()");
1733: m += NR_END;
1734: m -= nrl;
1735:
1736: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1737: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1738: m[nrl] += NR_END;
1739: m[nrl] -= ncl;
1740:
1741: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1742: return m;
1.145 brouard 1743: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1744: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1745: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1746: */
1747: }
1748:
1749: /*************************free matrix ************************/
1750: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1751: {
1752: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1753: free((FREE_ARG)(m+nrl-NR_END));
1754: }
1755:
1756: /******************* ma3x *******************************/
1757: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1758: {
1759: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1760: double ***m;
1761:
1762: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1763: if (!m) nrerror("allocation failure 1 in matrix()");
1764: m += NR_END;
1765: m -= nrl;
1766:
1767: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1768: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1769: m[nrl] += NR_END;
1770: m[nrl] -= ncl;
1771:
1772: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1773:
1774: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1775: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1776: m[nrl][ncl] += NR_END;
1777: m[nrl][ncl] -= nll;
1778: for (j=ncl+1; j<=nch; j++)
1779: m[nrl][j]=m[nrl][j-1]+nlay;
1780:
1781: for (i=nrl+1; i<=nrh; i++) {
1782: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1783: for (j=ncl+1; j<=nch; j++)
1784: m[i][j]=m[i][j-1]+nlay;
1785: }
1786: return m;
1787: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1788: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1789: */
1790: }
1791:
1792: /*************************free ma3x ************************/
1793: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1794: {
1795: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1796: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1797: free((FREE_ARG)(m+nrl-NR_END));
1798: }
1799:
1800: /*************** function subdirf ***********/
1801: char *subdirf(char fileres[])
1802: {
1803: /* Caution optionfilefiname is hidden */
1804: strcpy(tmpout,optionfilefiname);
1805: strcat(tmpout,"/"); /* Add to the right */
1806: strcat(tmpout,fileres);
1807: return tmpout;
1808: }
1809:
1810: /*************** function subdirf2 ***********/
1811: char *subdirf2(char fileres[], char *preop)
1812: {
1813:
1814: /* Caution optionfilefiname is hidden */
1815: strcpy(tmpout,optionfilefiname);
1816: strcat(tmpout,"/");
1817: strcat(tmpout,preop);
1818: strcat(tmpout,fileres);
1819: return tmpout;
1820: }
1821:
1822: /*************** function subdirf3 ***********/
1823: char *subdirf3(char fileres[], char *preop, char *preop2)
1824: {
1825:
1826: /* Caution optionfilefiname is hidden */
1827: strcpy(tmpout,optionfilefiname);
1828: strcat(tmpout,"/");
1829: strcat(tmpout,preop);
1830: strcat(tmpout,preop2);
1831: strcat(tmpout,fileres);
1832: return tmpout;
1833: }
1.213 brouard 1834:
1835: /*************** function subdirfext ***********/
1836: char *subdirfext(char fileres[], char *preop, char *postop)
1837: {
1838:
1839: strcpy(tmpout,preop);
1840: strcat(tmpout,fileres);
1841: strcat(tmpout,postop);
1842: return tmpout;
1843: }
1.126 brouard 1844:
1.213 brouard 1845: /*************** function subdirfext3 ***********/
1846: char *subdirfext3(char fileres[], char *preop, char *postop)
1847: {
1848:
1849: /* Caution optionfilefiname is hidden */
1850: strcpy(tmpout,optionfilefiname);
1851: strcat(tmpout,"/");
1852: strcat(tmpout,preop);
1853: strcat(tmpout,fileres);
1854: strcat(tmpout,postop);
1855: return tmpout;
1856: }
1857:
1.162 brouard 1858: char *asc_diff_time(long time_sec, char ascdiff[])
1859: {
1860: long sec_left, days, hours, minutes;
1861: days = (time_sec) / (60*60*24);
1862: sec_left = (time_sec) % (60*60*24);
1863: hours = (sec_left) / (60*60) ;
1864: sec_left = (sec_left) %(60*60);
1865: minutes = (sec_left) /60;
1866: sec_left = (sec_left) % (60);
1867: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1868: return ascdiff;
1869: }
1870:
1.126 brouard 1871: /***************** f1dim *************************/
1872: extern int ncom;
1873: extern double *pcom,*xicom;
1874: extern double (*nrfunc)(double []);
1875:
1876: double f1dim(double x)
1877: {
1878: int j;
1879: double f;
1880: double *xt;
1881:
1882: xt=vector(1,ncom);
1883: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1884: f=(*nrfunc)(xt);
1885: free_vector(xt,1,ncom);
1886: return f;
1887: }
1888:
1889: /*****************brent *************************/
1890: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1891: {
1892: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1893: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1894: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1895: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1896: * returned function value.
1897: */
1.126 brouard 1898: int iter;
1899: double a,b,d,etemp;
1.159 brouard 1900: double fu=0,fv,fw,fx;
1.164 brouard 1901: double ftemp=0.;
1.126 brouard 1902: double p,q,r,tol1,tol2,u,v,w,x,xm;
1903: double e=0.0;
1904:
1905: a=(ax < cx ? ax : cx);
1906: b=(ax > cx ? ax : cx);
1907: x=w=v=bx;
1908: fw=fv=fx=(*f)(x);
1909: for (iter=1;iter<=ITMAX;iter++) {
1910: xm=0.5*(a+b);
1911: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1912: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1913: printf(".");fflush(stdout);
1914: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1915: #ifdef DEBUGBRENT
1.126 brouard 1916: 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);
1917: 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);
1918: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1919: #endif
1920: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1921: *xmin=x;
1922: return fx;
1923: }
1924: ftemp=fu;
1925: if (fabs(e) > tol1) {
1926: r=(x-w)*(fx-fv);
1927: q=(x-v)*(fx-fw);
1928: p=(x-v)*q-(x-w)*r;
1929: q=2.0*(q-r);
1930: if (q > 0.0) p = -p;
1931: q=fabs(q);
1932: etemp=e;
1933: e=d;
1934: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1935: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1936: else {
1.224 brouard 1937: d=p/q;
1938: u=x+d;
1939: if (u-a < tol2 || b-u < tol2)
1940: d=SIGN(tol1,xm-x);
1.126 brouard 1941: }
1942: } else {
1943: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1944: }
1945: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1946: fu=(*f)(u);
1947: if (fu <= fx) {
1948: if (u >= x) a=x; else b=x;
1949: SHFT(v,w,x,u)
1.183 brouard 1950: SHFT(fv,fw,fx,fu)
1951: } else {
1952: if (u < x) a=u; else b=u;
1953: if (fu <= fw || w == x) {
1.224 brouard 1954: v=w;
1955: w=u;
1956: fv=fw;
1957: fw=fu;
1.183 brouard 1958: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1959: v=u;
1960: fv=fu;
1.183 brouard 1961: }
1962: }
1.126 brouard 1963: }
1964: nrerror("Too many iterations in brent");
1965: *xmin=x;
1966: return fx;
1967: }
1968:
1969: /****************** mnbrak ***********************/
1970:
1971: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1972: double (*func)(double))
1.183 brouard 1973: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1974: the downhill direction (defined by the function as evaluated at the initial points) and returns
1975: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1976: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1977: */
1.126 brouard 1978: double ulim,u,r,q, dum;
1979: double fu;
1.187 brouard 1980:
1981: double scale=10.;
1982: int iterscale=0;
1983:
1984: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1985: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1986:
1987:
1988: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1989: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1990: /* *bx = *ax - (*ax - *bx)/scale; */
1991: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1992: /* } */
1993:
1.126 brouard 1994: if (*fb > *fa) {
1995: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1996: SHFT(dum,*fb,*fa,dum)
1997: }
1.126 brouard 1998: *cx=(*bx)+GOLD*(*bx-*ax);
1999: *fc=(*func)(*cx);
1.183 brouard 2000: #ifdef DEBUG
1.224 brouard 2001: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2002: 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 2003: #endif
1.224 brouard 2004: 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 2005: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2006: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2007: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2008: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2009: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2010: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2011: fu=(*func)(u);
1.163 brouard 2012: #ifdef DEBUG
2013: /* f(x)=A(x-u)**2+f(u) */
2014: double A, fparabu;
2015: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2016: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2017: 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);
2018: 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 2019: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2020: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2021: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2022: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2023: #endif
1.184 brouard 2024: #ifdef MNBRAKORIGINAL
1.183 brouard 2025: #else
1.191 brouard 2026: /* if (fu > *fc) { */
2027: /* #ifdef DEBUG */
2028: /* printf("mnbrak4 fu > fc \n"); */
2029: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2030: /* #endif */
2031: /* /\* 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 *\\/ *\/ */
2032: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2033: /* dum=u; /\* Shifting c and u *\/ */
2034: /* u = *cx; */
2035: /* *cx = dum; */
2036: /* dum = fu; */
2037: /* fu = *fc; */
2038: /* *fc =dum; */
2039: /* } else { /\* end *\/ */
2040: /* #ifdef DEBUG */
2041: /* printf("mnbrak3 fu < fc \n"); */
2042: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2043: /* #endif */
2044: /* dum=u; /\* Shifting c and u *\/ */
2045: /* u = *cx; */
2046: /* *cx = dum; */
2047: /* dum = fu; */
2048: /* fu = *fc; */
2049: /* *fc =dum; */
2050: /* } */
1.224 brouard 2051: #ifdef DEBUGMNBRAK
2052: double A, fparabu;
2053: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2054: fparabu= *fa - A*(*ax-u)*(*ax-u);
2055: 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);
2056: 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 2057: #endif
1.191 brouard 2058: dum=u; /* Shifting c and u */
2059: u = *cx;
2060: *cx = dum;
2061: dum = fu;
2062: fu = *fc;
2063: *fc =dum;
1.183 brouard 2064: #endif
1.162 brouard 2065: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2066: #ifdef DEBUG
1.224 brouard 2067: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2068: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2069: #endif
1.126 brouard 2070: fu=(*func)(u);
2071: if (fu < *fc) {
1.183 brouard 2072: #ifdef DEBUG
1.224 brouard 2073: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2074: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2075: #endif
2076: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2077: SHFT(*fb,*fc,fu,(*func)(u))
2078: #ifdef DEBUG
2079: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2080: #endif
2081: }
1.162 brouard 2082: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2083: #ifdef DEBUG
1.224 brouard 2084: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2085: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2086: #endif
1.126 brouard 2087: u=ulim;
2088: fu=(*func)(u);
1.183 brouard 2089: } else { /* u could be left to b (if r > q parabola has a maximum) */
2090: #ifdef DEBUG
1.224 brouard 2091: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2092: 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 2093: #endif
1.126 brouard 2094: u=(*cx)+GOLD*(*cx-*bx);
2095: fu=(*func)(u);
1.224 brouard 2096: #ifdef DEBUG
2097: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2098: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2099: #endif
1.183 brouard 2100: } /* end tests */
1.126 brouard 2101: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2102: SHFT(*fa,*fb,*fc,fu)
2103: #ifdef DEBUG
1.224 brouard 2104: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2105: 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 2106: #endif
2107: } /* 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 2108: }
2109:
2110: /*************** linmin ************************/
1.162 brouard 2111: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2112: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2113: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2114: the value of func at the returned location p . This is actually all accomplished by calling the
2115: routines mnbrak and brent .*/
1.126 brouard 2116: int ncom;
2117: double *pcom,*xicom;
2118: double (*nrfunc)(double []);
2119:
1.224 brouard 2120: #ifdef LINMINORIGINAL
1.126 brouard 2121: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2122: #else
2123: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2124: #endif
1.126 brouard 2125: {
2126: double brent(double ax, double bx, double cx,
2127: double (*f)(double), double tol, double *xmin);
2128: double f1dim(double x);
2129: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2130: double *fc, double (*func)(double));
2131: int j;
2132: double xx,xmin,bx,ax;
2133: double fx,fb,fa;
1.187 brouard 2134:
1.203 brouard 2135: #ifdef LINMINORIGINAL
2136: #else
2137: double scale=10., axs, xxs; /* Scale added for infinity */
2138: #endif
2139:
1.126 brouard 2140: ncom=n;
2141: pcom=vector(1,n);
2142: xicom=vector(1,n);
2143: nrfunc=func;
2144: for (j=1;j<=n;j++) {
2145: pcom[j]=p[j];
1.202 brouard 2146: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2147: }
1.187 brouard 2148:
1.203 brouard 2149: #ifdef LINMINORIGINAL
2150: xx=1.;
2151: #else
2152: axs=0.0;
2153: xxs=1.;
2154: do{
2155: xx= xxs;
2156: #endif
1.187 brouard 2157: ax=0.;
2158: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2159: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2160: /* 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)) */
2161: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2162: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2163: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2164: /* 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 2165: #ifdef LINMINORIGINAL
2166: #else
2167: if (fx != fx){
1.224 brouard 2168: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2169: printf("|");
2170: fprintf(ficlog,"|");
1.203 brouard 2171: #ifdef DEBUGLINMIN
1.224 brouard 2172: 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 2173: #endif
2174: }
1.224 brouard 2175: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2176: #endif
2177:
1.191 brouard 2178: #ifdef DEBUGLINMIN
2179: 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 2180: 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 2181: #endif
1.224 brouard 2182: #ifdef LINMINORIGINAL
2183: #else
2184: if(fb == fx){ /* Flat function in the direction */
2185: xmin=xx;
2186: *flat=1;
2187: }else{
2188: *flat=0;
2189: #endif
2190: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2191: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2192: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2193: /* fmin = f(p[j] + xmin * xi[j]) */
2194: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2195: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2196: #ifdef DEBUG
1.224 brouard 2197: 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);
2198: 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);
2199: #endif
2200: #ifdef LINMINORIGINAL
2201: #else
2202: }
1.126 brouard 2203: #endif
1.191 brouard 2204: #ifdef DEBUGLINMIN
2205: printf("linmin end ");
1.202 brouard 2206: fprintf(ficlog,"linmin end ");
1.191 brouard 2207: #endif
1.126 brouard 2208: for (j=1;j<=n;j++) {
1.203 brouard 2209: #ifdef LINMINORIGINAL
2210: xi[j] *= xmin;
2211: #else
2212: #ifdef DEBUGLINMIN
2213: if(xxs <1.0)
2214: printf(" before xi[%d]=%12.8f", j,xi[j]);
2215: #endif
2216: 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) */
2217: #ifdef DEBUGLINMIN
2218: if(xxs <1.0)
2219: 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 );
2220: #endif
2221: #endif
1.187 brouard 2222: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2223: }
1.191 brouard 2224: #ifdef DEBUGLINMIN
1.203 brouard 2225: printf("\n");
1.191 brouard 2226: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2227: 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 2228: for (j=1;j<=n;j++) {
1.202 brouard 2229: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2230: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2231: if(j % ncovmodel == 0){
1.191 brouard 2232: printf("\n");
1.202 brouard 2233: fprintf(ficlog,"\n");
2234: }
1.191 brouard 2235: }
1.203 brouard 2236: #else
1.191 brouard 2237: #endif
1.126 brouard 2238: free_vector(xicom,1,n);
2239: free_vector(pcom,1,n);
2240: }
2241:
2242:
2243: /*************** powell ************************/
1.162 brouard 2244: /*
2245: Minimization of a function func of n variables. Input consists of an initial starting point
2246: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2247: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2248: such that failure to decrease by more than this amount on one iteration signals doneness. On
2249: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2250: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2251: */
1.224 brouard 2252: #ifdef LINMINORIGINAL
2253: #else
2254: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2255: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2256: #endif
1.126 brouard 2257: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2258: double (*func)(double []))
2259: {
1.224 brouard 2260: #ifdef LINMINORIGINAL
2261: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2262: double (*func)(double []));
1.224 brouard 2263: #else
1.241 brouard 2264: void linmin(double p[], double xi[], int n, double *fret,
2265: double (*func)(double []),int *flat);
1.224 brouard 2266: #endif
1.239 brouard 2267: int i,ibig,j,jk,k;
1.126 brouard 2268: double del,t,*pt,*ptt,*xit;
1.181 brouard 2269: double directest;
1.126 brouard 2270: double fp,fptt;
2271: double *xits;
2272: int niterf, itmp;
1.224 brouard 2273: #ifdef LINMINORIGINAL
2274: #else
2275:
2276: flatdir=ivector(1,n);
2277: for (j=1;j<=n;j++) flatdir[j]=0;
2278: #endif
1.126 brouard 2279:
2280: pt=vector(1,n);
2281: ptt=vector(1,n);
2282: xit=vector(1,n);
2283: xits=vector(1,n);
2284: *fret=(*func)(p);
2285: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2286: rcurr_time = time(NULL);
1.126 brouard 2287: for (*iter=1;;++(*iter)) {
1.187 brouard 2288: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2289: ibig=0;
2290: del=0.0;
1.157 brouard 2291: rlast_time=rcurr_time;
2292: /* (void) gettimeofday(&curr_time,&tzp); */
2293: rcurr_time = time(NULL);
2294: curr_time = *localtime(&rcurr_time);
2295: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2296: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2297: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2298: for (i=1;i<=n;i++) {
1.126 brouard 2299: fprintf(ficrespow," %.12lf", p[i]);
2300: }
1.239 brouard 2301: fprintf(ficrespow,"\n");fflush(ficrespow);
2302: printf("\n#model= 1 + age ");
2303: fprintf(ficlog,"\n#model= 1 + age ");
2304: if(nagesqr==1){
1.241 brouard 2305: printf(" + age*age ");
2306: fprintf(ficlog," + age*age ");
1.239 brouard 2307: }
2308: for(j=1;j <=ncovmodel-2;j++){
2309: if(Typevar[j]==0) {
2310: printf(" + V%d ",Tvar[j]);
2311: fprintf(ficlog," + V%d ",Tvar[j]);
2312: }else if(Typevar[j]==1) {
2313: printf(" + V%d*age ",Tvar[j]);
2314: fprintf(ficlog," + V%d*age ",Tvar[j]);
2315: }else if(Typevar[j]==2) {
2316: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2317: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2318: }
2319: }
1.126 brouard 2320: printf("\n");
1.239 brouard 2321: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2322: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2323: fprintf(ficlog,"\n");
1.239 brouard 2324: for(i=1,jk=1; i <=nlstate; i++){
2325: for(k=1; k <=(nlstate+ndeath); k++){
2326: if (k != i) {
2327: printf("%d%d ",i,k);
2328: fprintf(ficlog,"%d%d ",i,k);
2329: for(j=1; j <=ncovmodel; j++){
2330: printf("%12.7f ",p[jk]);
2331: fprintf(ficlog,"%12.7f ",p[jk]);
2332: jk++;
2333: }
2334: printf("\n");
2335: fprintf(ficlog,"\n");
2336: }
2337: }
2338: }
1.241 brouard 2339: if(*iter <=3 && *iter >1){
1.157 brouard 2340: tml = *localtime(&rcurr_time);
2341: strcpy(strcurr,asctime(&tml));
2342: rforecast_time=rcurr_time;
1.126 brouard 2343: itmp = strlen(strcurr);
2344: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2345: strcurr[itmp-1]='\0';
1.162 brouard 2346: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2347: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2348: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2349: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2350: forecast_time = *localtime(&rforecast_time);
2351: strcpy(strfor,asctime(&forecast_time));
2352: itmp = strlen(strfor);
2353: if(strfor[itmp-1]=='\n')
2354: strfor[itmp-1]='\0';
2355: 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);
2356: 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 2357: }
2358: }
1.187 brouard 2359: for (i=1;i<=n;i++) { /* For each direction i */
2360: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2361: fptt=(*fret);
2362: #ifdef DEBUG
1.203 brouard 2363: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2364: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2365: #endif
1.203 brouard 2366: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2367: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2368: #ifdef LINMINORIGINAL
1.188 brouard 2369: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2370: #else
2371: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2372: flatdir[i]=flat; /* Function is vanishing in that direction i */
2373: #endif
2374: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2375: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2376: /* because that direction will be replaced unless the gain del is small */
2377: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2378: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2379: /* with the new direction. */
2380: del=fabs(fptt-(*fret));
2381: ibig=i;
1.126 brouard 2382: }
2383: #ifdef DEBUG
2384: printf("%d %.12e",i,(*fret));
2385: fprintf(ficlog,"%d %.12e",i,(*fret));
2386: for (j=1;j<=n;j++) {
1.224 brouard 2387: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2388: printf(" x(%d)=%.12e",j,xit[j]);
2389: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2390: }
2391: for(j=1;j<=n;j++) {
1.225 brouard 2392: printf(" p(%d)=%.12e",j,p[j]);
2393: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2394: }
2395: printf("\n");
2396: fprintf(ficlog,"\n");
2397: #endif
1.187 brouard 2398: } /* end loop on each direction i */
2399: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2400: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2401: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2402: for(j=1;j<=n;j++) {
1.225 brouard 2403: if(flatdir[j] >0){
2404: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2405: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2406: }
2407: /* printf("\n"); */
2408: /* fprintf(ficlog,"\n"); */
2409: }
1.243 brouard 2410: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2411: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2412: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2413: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2414: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2415: /* decreased of more than 3.84 */
2416: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2417: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2418: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2419:
1.188 brouard 2420: /* Starting the program with initial values given by a former maximization will simply change */
2421: /* the scales of the directions and the directions, because the are reset to canonical directions */
2422: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2423: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2424: #ifdef DEBUG
2425: int k[2],l;
2426: k[0]=1;
2427: k[1]=-1;
2428: printf("Max: %.12e",(*func)(p));
2429: fprintf(ficlog,"Max: %.12e",(*func)(p));
2430: for (j=1;j<=n;j++) {
2431: printf(" %.12e",p[j]);
2432: fprintf(ficlog," %.12e",p[j]);
2433: }
2434: printf("\n");
2435: fprintf(ficlog,"\n");
2436: for(l=0;l<=1;l++) {
2437: for (j=1;j<=n;j++) {
2438: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2439: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2440: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2441: }
2442: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2443: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2444: }
2445: #endif
2446:
1.224 brouard 2447: #ifdef LINMINORIGINAL
2448: #else
2449: free_ivector(flatdir,1,n);
2450: #endif
1.126 brouard 2451: free_vector(xit,1,n);
2452: free_vector(xits,1,n);
2453: free_vector(ptt,1,n);
2454: free_vector(pt,1,n);
2455: return;
1.192 brouard 2456: } /* enough precision */
1.240 brouard 2457: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2458: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2459: ptt[j]=2.0*p[j]-pt[j];
2460: xit[j]=p[j]-pt[j];
2461: pt[j]=p[j];
2462: }
1.181 brouard 2463: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2464: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2465: if (*iter <=4) {
1.225 brouard 2466: #else
2467: #endif
1.224 brouard 2468: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2469: #else
1.161 brouard 2470: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2471: #endif
1.162 brouard 2472: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2473: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2474: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2475: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2476: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2477: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2478: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2479: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2480: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2481: /* Even if f3 <f1, directest can be negative and t >0 */
2482: /* mu² and del² are equal when f3=f1 */
2483: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2484: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2485: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2486: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2487: #ifdef NRCORIGINAL
2488: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2489: #else
2490: 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 2491: t= t- del*SQR(fp-fptt);
1.183 brouard 2492: #endif
1.202 brouard 2493: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2494: #ifdef DEBUG
1.181 brouard 2495: 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);
2496: 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 2497: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2498: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2499: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2500: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2501: 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);
2502: 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);
2503: #endif
1.183 brouard 2504: #ifdef POWELLORIGINAL
2505: if (t < 0.0) { /* Then we use it for new direction */
2506: #else
1.182 brouard 2507: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2508: 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 2509: 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 2510: 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 2511: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2512: }
1.181 brouard 2513: if (directest < 0.0) { /* Then we use it for new direction */
2514: #endif
1.191 brouard 2515: #ifdef DEBUGLINMIN
1.234 brouard 2516: printf("Before linmin in direction P%d-P0\n",n);
2517: for (j=1;j<=n;j++) {
2518: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2519: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2520: if(j % ncovmodel == 0){
2521: printf("\n");
2522: fprintf(ficlog,"\n");
2523: }
2524: }
1.224 brouard 2525: #endif
2526: #ifdef LINMINORIGINAL
1.234 brouard 2527: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2528: #else
1.234 brouard 2529: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2530: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2531: #endif
1.234 brouard 2532:
1.191 brouard 2533: #ifdef DEBUGLINMIN
1.234 brouard 2534: for (j=1;j<=n;j++) {
2535: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2536: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2537: if(j % ncovmodel == 0){
2538: printf("\n");
2539: fprintf(ficlog,"\n");
2540: }
2541: }
1.224 brouard 2542: #endif
1.234 brouard 2543: for (j=1;j<=n;j++) {
2544: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2545: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2546: }
1.224 brouard 2547: #ifdef LINMINORIGINAL
2548: #else
1.234 brouard 2549: for (j=1, flatd=0;j<=n;j++) {
2550: if(flatdir[j]>0)
2551: flatd++;
2552: }
2553: if(flatd >0){
1.255 brouard 2554: printf("%d flat directions: ",flatd);
2555: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2556: for (j=1;j<=n;j++) {
2557: if(flatdir[j]>0){
2558: printf("%d ",j);
2559: fprintf(ficlog,"%d ",j);
2560: }
2561: }
2562: printf("\n");
2563: fprintf(ficlog,"\n");
2564: }
1.191 brouard 2565: #endif
1.234 brouard 2566: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2567: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2568:
1.126 brouard 2569: #ifdef DEBUG
1.234 brouard 2570: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2571: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2572: for(j=1;j<=n;j++){
2573: printf(" %lf",xit[j]);
2574: fprintf(ficlog," %lf",xit[j]);
2575: }
2576: printf("\n");
2577: fprintf(ficlog,"\n");
1.126 brouard 2578: #endif
1.192 brouard 2579: } /* end of t or directest negative */
1.224 brouard 2580: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2581: #else
1.234 brouard 2582: } /* end if (fptt < fp) */
1.192 brouard 2583: #endif
1.225 brouard 2584: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2585: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2586: #else
1.224 brouard 2587: #endif
1.234 brouard 2588: } /* loop iteration */
1.126 brouard 2589: }
1.234 brouard 2590:
1.126 brouard 2591: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2592:
1.235 brouard 2593: 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 2594: {
1.279 brouard 2595: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2596: * (and selected quantitative values in nres)
2597: * by left multiplying the unit
2598: * matrix by transitions matrix until convergence is reached with precision ftolpl
2599: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2600: * Wx is row vector: population in state 1, population in state 2, population dead
2601: * or prevalence in state 1, prevalence in state 2, 0
2602: * newm is the matrix after multiplications, its rows are identical at a factor.
2603: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2604: * Output is prlim.
2605: * Initial matrix pimij
2606: */
1.206 brouard 2607: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2608: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2609: /* 0, 0 , 1} */
2610: /*
2611: * and after some iteration: */
2612: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2613: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2614: /* 0, 0 , 1} */
2615: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2616: /* {0.51571254859325999, 0.4842874514067399, */
2617: /* 0.51326036147820708, 0.48673963852179264} */
2618: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2619:
1.126 brouard 2620: int i, ii,j,k;
1.209 brouard 2621: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2622: /* double **matprod2(); */ /* test */
1.218 brouard 2623: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2624: double **newm;
1.209 brouard 2625: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2626: int ncvloop=0;
1.288 brouard 2627: int first=0;
1.169 brouard 2628:
1.209 brouard 2629: min=vector(1,nlstate);
2630: max=vector(1,nlstate);
2631: meandiff=vector(1,nlstate);
2632:
1.218 brouard 2633: /* Starting with matrix unity */
1.126 brouard 2634: for (ii=1;ii<=nlstate+ndeath;ii++)
2635: for (j=1;j<=nlstate+ndeath;j++){
2636: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2637: }
1.169 brouard 2638:
2639: cov[1]=1.;
2640:
2641: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2642: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2643: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2644: ncvloop++;
1.126 brouard 2645: newm=savm;
2646: /* Covariates have to be included here again */
1.138 brouard 2647: cov[2]=agefin;
1.187 brouard 2648: if(nagesqr==1)
2649: cov[3]= agefin*agefin;;
1.234 brouard 2650: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2651: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2652: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2653: /* 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 2654: }
2655: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2656: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2657: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2658: /* 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 2659: }
1.237 brouard 2660: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2661: if(Dummy[Tvar[Tage[k]]]){
2662: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2663: } else{
1.235 brouard 2664: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2665: }
1.235 brouard 2666: /* 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 2667: }
1.237 brouard 2668: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2669: /* 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 2670: if(Dummy[Tvard[k][1]==0]){
2671: if(Dummy[Tvard[k][2]==0]){
2672: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2673: }else{
2674: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2675: }
2676: }else{
2677: if(Dummy[Tvard[k][2]==0]){
2678: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2679: }else{
2680: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2681: }
2682: }
1.234 brouard 2683: }
1.138 brouard 2684: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2685: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2686: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2687: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2688: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2689: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2690: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2691:
1.126 brouard 2692: savm=oldm;
2693: oldm=newm;
1.209 brouard 2694:
2695: for(j=1; j<=nlstate; j++){
2696: max[j]=0.;
2697: min[j]=1.;
2698: }
2699: for(i=1;i<=nlstate;i++){
2700: sumnew=0;
2701: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2702: for(j=1; j<=nlstate; j++){
2703: prlim[i][j]= newm[i][j]/(1-sumnew);
2704: max[j]=FMAX(max[j],prlim[i][j]);
2705: min[j]=FMIN(min[j],prlim[i][j]);
2706: }
2707: }
2708:
1.126 brouard 2709: maxmax=0.;
1.209 brouard 2710: for(j=1; j<=nlstate; j++){
2711: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2712: maxmax=FMAX(maxmax,meandiff[j]);
2713: /* 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 2714: } /* j loop */
1.203 brouard 2715: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2716: /* 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 2717: if(maxmax < ftolpl){
1.209 brouard 2718: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2719: free_vector(min,1,nlstate);
2720: free_vector(max,1,nlstate);
2721: free_vector(meandiff,1,nlstate);
1.126 brouard 2722: return prlim;
2723: }
1.288 brouard 2724: } /* agefin loop */
1.208 brouard 2725: /* After some age loop it doesn't converge */
1.288 brouard 2726: if(!first){
2727: first=1;
2728: 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);
2729: }
2730: 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);
2731:
1.209 brouard 2732: /* 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); */
2733: free_vector(min,1,nlstate);
2734: free_vector(max,1,nlstate);
2735: free_vector(meandiff,1,nlstate);
1.208 brouard 2736:
1.169 brouard 2737: return prlim; /* should not reach here */
1.126 brouard 2738: }
2739:
1.217 brouard 2740:
2741: /**** Back Prevalence limit (stable or period prevalence) ****************/
2742:
1.218 brouard 2743: /* 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) */
2744: /* 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 2745: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2746: {
1.264 brouard 2747: /* 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 2748: matrix by transitions matrix until convergence is reached with precision ftolpl */
2749: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2750: /* Wx is row vector: population in state 1, population in state 2, population dead */
2751: /* or prevalence in state 1, prevalence in state 2, 0 */
2752: /* newm is the matrix after multiplications, its rows are identical at a factor */
2753: /* Initial matrix pimij */
2754: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2755: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2756: /* 0, 0 , 1} */
2757: /*
2758: * and after some iteration: */
2759: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2760: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2761: /* 0, 0 , 1} */
2762: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2763: /* {0.51571254859325999, 0.4842874514067399, */
2764: /* 0.51326036147820708, 0.48673963852179264} */
2765: /* If we start from prlim again, prlim tends to a constant matrix */
2766:
2767: int i, ii,j,k;
1.247 brouard 2768: int first=0;
1.217 brouard 2769: double *min, *max, *meandiff, maxmax,sumnew=0.;
2770: /* double **matprod2(); */ /* test */
2771: double **out, cov[NCOVMAX+1], **bmij();
2772: double **newm;
1.218 brouard 2773: double **dnewm, **doldm, **dsavm; /* for use */
2774: double **oldm, **savm; /* for use */
2775:
1.217 brouard 2776: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2777: int ncvloop=0;
2778:
2779: min=vector(1,nlstate);
2780: max=vector(1,nlstate);
2781: meandiff=vector(1,nlstate);
2782:
1.266 brouard 2783: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2784: oldm=oldms; savm=savms;
2785:
2786: /* Starting with matrix unity */
2787: for (ii=1;ii<=nlstate+ndeath;ii++)
2788: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2789: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2790: }
2791:
2792: cov[1]=1.;
2793:
2794: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2795: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2796: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2797: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2798: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2799: ncvloop++;
1.218 brouard 2800: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2801: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2802: /* Covariates have to be included here again */
2803: cov[2]=agefin;
2804: if(nagesqr==1)
2805: cov[3]= agefin*agefin;;
1.242 brouard 2806: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2807: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2808: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2809: /* 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 2810: }
2811: /* for (k=1; k<=cptcovn;k++) { */
2812: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2813: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2814: /* /\* 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])]); *\/ */
2815: /* } */
2816: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2817: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2818: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2819: /* 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]); */
2820: }
2821: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2822: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2823: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2824: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2825: for (k=1; k<=cptcovage;k++){ /* For product with age */
2826: if(Dummy[Tvar[Tage[k]]]){
2827: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2828: } else{
2829: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2830: }
2831: /* 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]); */
2832: }
2833: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2834: /* 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]); */
2835: if(Dummy[Tvard[k][1]==0]){
2836: if(Dummy[Tvard[k][2]==0]){
2837: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2838: }else{
2839: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2840: }
2841: }else{
2842: if(Dummy[Tvard[k][2]==0]){
2843: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2844: }else{
2845: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2846: }
2847: }
1.217 brouard 2848: }
2849:
2850: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2851: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2852: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2853: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2854: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2855: /* ij should be linked to the correct index of cov */
2856: /* age and covariate values ij are in 'cov', but we need to pass
2857: * ij for the observed prevalence at age and status and covariate
2858: * number: prevacurrent[(int)agefin][ii][ij]
2859: */
2860: /* 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 *\/ */
2861: /* 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 *\/ */
2862: 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 2863: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2864: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2865: /* for(i=1; i<=nlstate+ndeath; i++) { */
2866: /* printf("%d newm= ",i); */
2867: /* for(j=1;j<=nlstate+ndeath;j++) { */
2868: /* printf("%f ",newm[i][j]); */
2869: /* } */
2870: /* printf("oldm * "); */
2871: /* for(j=1;j<=nlstate+ndeath;j++) { */
2872: /* printf("%f ",oldm[i][j]); */
2873: /* } */
1.268 brouard 2874: /* printf(" bmmij "); */
1.266 brouard 2875: /* for(j=1;j<=nlstate+ndeath;j++) { */
2876: /* printf("%f ",pmmij[i][j]); */
2877: /* } */
2878: /* printf("\n"); */
2879: /* } */
2880: /* } */
1.217 brouard 2881: savm=oldm;
2882: oldm=newm;
1.266 brouard 2883:
1.217 brouard 2884: for(j=1; j<=nlstate; j++){
2885: max[j]=0.;
2886: min[j]=1.;
2887: }
2888: for(j=1; j<=nlstate; j++){
2889: for(i=1;i<=nlstate;i++){
1.234 brouard 2890: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2891: bprlim[i][j]= newm[i][j];
2892: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2893: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2894: }
2895: }
1.218 brouard 2896:
1.217 brouard 2897: maxmax=0.;
2898: for(i=1; i<=nlstate; i++){
2899: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2900: maxmax=FMAX(maxmax,meandiff[i]);
2901: /* 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 2902: } /* i loop */
1.217 brouard 2903: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2904: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2905: if(maxmax < ftolpl){
1.220 brouard 2906: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2907: free_vector(min,1,nlstate);
2908: free_vector(max,1,nlstate);
2909: free_vector(meandiff,1,nlstate);
2910: return bprlim;
2911: }
1.288 brouard 2912: } /* agefin loop */
1.217 brouard 2913: /* After some age loop it doesn't converge */
1.288 brouard 2914: if(!first){
1.247 brouard 2915: first=1;
2916: 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\
2917: 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);
2918: }
2919: 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 2920: 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);
2921: /* 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); */
2922: free_vector(min,1,nlstate);
2923: free_vector(max,1,nlstate);
2924: free_vector(meandiff,1,nlstate);
2925:
2926: return bprlim; /* should not reach here */
2927: }
2928:
1.126 brouard 2929: /*************** transition probabilities ***************/
2930:
2931: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2932: {
1.138 brouard 2933: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2934: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2935: model to the ncovmodel covariates (including constant and age).
2936: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2937: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2938: ncth covariate in the global vector x is given by the formula:
2939: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2940: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2941: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2942: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2943: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2944: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2945: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2946: */
2947: double s1, lnpijopii;
1.126 brouard 2948: /*double t34;*/
1.164 brouard 2949: int i,j, nc, ii, jj;
1.126 brouard 2950:
1.223 brouard 2951: for(i=1; i<= nlstate; i++){
2952: for(j=1; j<i;j++){
2953: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2954: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2955: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2956: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2957: }
2958: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2959: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2960: }
2961: for(j=i+1; j<=nlstate+ndeath;j++){
2962: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2963: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2964: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2965: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2966: }
2967: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2968: }
2969: }
1.218 brouard 2970:
1.223 brouard 2971: for(i=1; i<= nlstate; i++){
2972: s1=0;
2973: for(j=1; j<i; j++){
2974: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2975: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2976: }
2977: for(j=i+1; j<=nlstate+ndeath; j++){
2978: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2979: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2980: }
2981: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2982: ps[i][i]=1./(s1+1.);
2983: /* Computing other pijs */
2984: for(j=1; j<i; j++)
2985: ps[i][j]= exp(ps[i][j])*ps[i][i];
2986: for(j=i+1; j<=nlstate+ndeath; j++)
2987: ps[i][j]= exp(ps[i][j])*ps[i][i];
2988: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2989: } /* end i */
1.218 brouard 2990:
1.223 brouard 2991: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2992: for(jj=1; jj<= nlstate+ndeath; jj++){
2993: ps[ii][jj]=0;
2994: ps[ii][ii]=1;
2995: }
2996: }
1.294 brouard 2997:
2998:
1.223 brouard 2999: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3000: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3001: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3002: /* } */
3003: /* printf("\n "); */
3004: /* } */
3005: /* printf("\n ");printf("%lf ",cov[2]);*/
3006: /*
3007: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3008: goto end;*/
1.266 brouard 3009: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3010: }
3011:
1.218 brouard 3012: /*************** backward transition probabilities ***************/
3013:
3014: /* 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 ) */
3015: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3016: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3017: {
1.266 brouard 3018: /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
3019: * 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 3020: */
1.218 brouard 3021: int i, ii, j,k;
1.222 brouard 3022:
3023: double **out, **pmij();
3024: double sumnew=0.;
1.218 brouard 3025: double agefin;
1.292 brouard 3026: 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 3027: double **dnewm, **dsavm, **doldm;
3028: double **bbmij;
3029:
1.218 brouard 3030: doldm=ddoldms; /* global pointers */
1.222 brouard 3031: dnewm=ddnewms;
3032: dsavm=ddsavms;
3033:
3034: agefin=cov[2];
1.268 brouard 3035: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3036: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3037: the observed prevalence (with this covariate ij) at beginning of transition */
3038: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3039:
3040: /* P_x */
1.266 brouard 3041: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3042: /* outputs pmmij which is a stochastic matrix in row */
3043:
3044: /* Diag(w_x) */
1.292 brouard 3045: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3046: sumnew=0.;
1.269 brouard 3047: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3048: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 ! brouard 3049: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3050: sumnew+=prevacurrent[(int)agefin][ii][ij];
3051: }
3052: if(sumnew >0.01){ /* At least some value in the prevalence */
3053: for (ii=1;ii<=nlstate+ndeath;ii++){
3054: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3055: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3056: }
3057: }else{
3058: for (ii=1;ii<=nlstate+ndeath;ii++){
3059: for (j=1;j<=nlstate+ndeath;j++)
3060: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3061: }
3062: /* if(sumnew <0.9){ */
3063: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3064: /* } */
3065: }
3066: k3=0.0; /* We put the last diagonal to 0 */
3067: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3068: doldm[ii][ii]= k3;
3069: }
3070: /* End doldm, At the end doldm is diag[(w_i)] */
3071:
1.292 brouard 3072: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3073: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3074:
1.292 brouard 3075: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3076: /* 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 3077: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3078: sumnew=0.;
1.222 brouard 3079: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3080: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3081: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3082: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3083: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3084: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3085: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3086: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3087: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3088: /* }else */
1.268 brouard 3089: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3090: } /*End ii */
3091: } /* 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 */
3092:
1.292 brouard 3093: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3094: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3095: /* end bmij */
1.266 brouard 3096: return ps; /*pointer is unchanged */
1.218 brouard 3097: }
1.217 brouard 3098: /*************** transition probabilities ***************/
3099:
1.218 brouard 3100: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3101: {
3102: /* According to parameters values stored in x and the covariate's values stored in cov,
3103: computes the probability to be observed in state j being in state i by appying the
3104: model to the ncovmodel covariates (including constant and age).
3105: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3106: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3107: ncth covariate in the global vector x is given by the formula:
3108: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3109: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3110: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3111: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3112: Outputs ps[i][j] the probability to be observed in j being in j according to
3113: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3114: */
3115: double s1, lnpijopii;
3116: /*double t34;*/
3117: int i,j, nc, ii, jj;
3118:
1.234 brouard 3119: for(i=1; i<= nlstate; i++){
3120: for(j=1; j<i;j++){
3121: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3122: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3123: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3124: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3125: }
3126: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3127: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3128: }
3129: for(j=i+1; j<=nlstate+ndeath;j++){
3130: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3131: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3132: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3133: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3134: }
3135: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3136: }
3137: }
3138:
3139: for(i=1; i<= nlstate; i++){
3140: s1=0;
3141: for(j=1; j<i; j++){
3142: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3143: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3144: }
3145: for(j=i+1; j<=nlstate+ndeath; j++){
3146: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3147: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3148: }
3149: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3150: ps[i][i]=1./(s1+1.);
3151: /* Computing other pijs */
3152: for(j=1; j<i; j++)
3153: ps[i][j]= exp(ps[i][j])*ps[i][i];
3154: for(j=i+1; j<=nlstate+ndeath; j++)
3155: ps[i][j]= exp(ps[i][j])*ps[i][i];
3156: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3157: } /* end i */
3158:
3159: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3160: for(jj=1; jj<= nlstate+ndeath; jj++){
3161: ps[ii][jj]=0;
3162: ps[ii][ii]=1;
3163: }
3164: }
1.296 brouard 3165: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3166: for(jj=1; jj<= nlstate+ndeath; jj++){
3167: s1=0.;
3168: for(ii=1; ii<= nlstate+ndeath; ii++){
3169: s1+=ps[ii][jj];
3170: }
3171: for(ii=1; ii<= nlstate; ii++){
3172: ps[ii][jj]=ps[ii][jj]/s1;
3173: }
3174: }
3175: /* Transposition */
3176: for(jj=1; jj<= nlstate+ndeath; jj++){
3177: for(ii=jj; ii<= nlstate+ndeath; ii++){
3178: s1=ps[ii][jj];
3179: ps[ii][jj]=ps[jj][ii];
3180: ps[jj][ii]=s1;
3181: }
3182: }
3183: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3184: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3185: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3186: /* } */
3187: /* printf("\n "); */
3188: /* } */
3189: /* printf("\n ");printf("%lf ",cov[2]);*/
3190: /*
3191: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3192: goto end;*/
3193: return ps;
1.217 brouard 3194: }
3195:
3196:
1.126 brouard 3197: /**************** Product of 2 matrices ******************/
3198:
1.145 brouard 3199: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3200: {
3201: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3202: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3203: /* in, b, out are matrice of pointers which should have been initialized
3204: before: only the contents of out is modified. The function returns
3205: a pointer to pointers identical to out */
1.145 brouard 3206: int i, j, k;
1.126 brouard 3207: for(i=nrl; i<= nrh; i++)
1.145 brouard 3208: for(k=ncolol; k<=ncoloh; k++){
3209: out[i][k]=0.;
3210: for(j=ncl; j<=nch; j++)
3211: out[i][k] +=in[i][j]*b[j][k];
3212: }
1.126 brouard 3213: return out;
3214: }
3215:
3216:
3217: /************* Higher Matrix Product ***************/
3218:
1.235 brouard 3219: 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 3220: {
1.218 brouard 3221: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3222: 'nhstepm*hstepm*stepm' months (i.e. until
3223: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3224: nhstepm*hstepm matrices.
3225: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3226: (typically every 2 years instead of every month which is too big
3227: for the memory).
3228: Model is determined by parameters x and covariates have to be
3229: included manually here.
3230:
3231: */
3232:
3233: int i, j, d, h, k;
1.131 brouard 3234: double **out, cov[NCOVMAX+1];
1.126 brouard 3235: double **newm;
1.187 brouard 3236: double agexact;
1.214 brouard 3237: double agebegin, ageend;
1.126 brouard 3238:
3239: /* Hstepm could be zero and should return the unit matrix */
3240: for (i=1;i<=nlstate+ndeath;i++)
3241: for (j=1;j<=nlstate+ndeath;j++){
3242: oldm[i][j]=(i==j ? 1.0 : 0.0);
3243: po[i][j][0]=(i==j ? 1.0 : 0.0);
3244: }
3245: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3246: for(h=1; h <=nhstepm; h++){
3247: for(d=1; d <=hstepm; d++){
3248: newm=savm;
3249: /* Covariates have to be included here again */
3250: cov[1]=1.;
1.214 brouard 3251: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3252: cov[2]=agexact;
3253: if(nagesqr==1)
1.227 brouard 3254: cov[3]= agexact*agexact;
1.235 brouard 3255: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3256: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3257: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3258: /* 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)); */
3259: }
3260: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3261: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3262: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3263: /* 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]); */
3264: }
3265: for (k=1; k<=cptcovage;k++){
3266: if(Dummy[Tvar[Tage[k]]]){
3267: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3268: } else{
3269: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3270: }
3271: /* 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]); */
3272: }
3273: for (k=1; k<=cptcovprod;k++){ /* */
3274: /* 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]); */
3275: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3276: }
3277: /* for (k=1; k<=cptcovn;k++) */
3278: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3279: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3280: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3281: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3282: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3283:
3284:
1.126 brouard 3285: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3286: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3287: /* right multiplication of oldm by the current matrix */
1.126 brouard 3288: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3289: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3290: /* if((int)age == 70){ */
3291: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3292: /* for(i=1; i<=nlstate+ndeath; i++) { */
3293: /* printf("%d pmmij ",i); */
3294: /* for(j=1;j<=nlstate+ndeath;j++) { */
3295: /* printf("%f ",pmmij[i][j]); */
3296: /* } */
3297: /* printf(" oldm "); */
3298: /* for(j=1;j<=nlstate+ndeath;j++) { */
3299: /* printf("%f ",oldm[i][j]); */
3300: /* } */
3301: /* printf("\n"); */
3302: /* } */
3303: /* } */
1.126 brouard 3304: savm=oldm;
3305: oldm=newm;
3306: }
3307: for(i=1; i<=nlstate+ndeath; i++)
3308: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3309: po[i][j][h]=newm[i][j];
3310: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3311: }
1.128 brouard 3312: /*printf("h=%d ",h);*/
1.126 brouard 3313: } /* end h */
1.267 brouard 3314: /* printf("\n H=%d \n",h); */
1.126 brouard 3315: return po;
3316: }
3317:
1.217 brouard 3318: /************* Higher Back Matrix Product ***************/
1.218 brouard 3319: /* 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 3320: 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 3321: {
1.266 brouard 3322: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3323: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3324: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3325: nhstepm*hstepm matrices.
3326: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3327: (typically every 2 years instead of every month which is too big
1.217 brouard 3328: for the memory).
1.218 brouard 3329: Model is determined by parameters x and covariates have to be
1.266 brouard 3330: included manually here. Then we use a call to bmij(x and cov)
3331: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3332: */
1.217 brouard 3333:
3334: int i, j, d, h, k;
1.266 brouard 3335: double **out, cov[NCOVMAX+1], **bmij();
3336: double **newm, ***newmm;
1.217 brouard 3337: double agexact;
3338: double agebegin, ageend;
1.222 brouard 3339: double **oldm, **savm;
1.217 brouard 3340:
1.266 brouard 3341: newmm=po; /* To be saved */
3342: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3343: /* Hstepm could be zero and should return the unit matrix */
3344: for (i=1;i<=nlstate+ndeath;i++)
3345: for (j=1;j<=nlstate+ndeath;j++){
3346: oldm[i][j]=(i==j ? 1.0 : 0.0);
3347: po[i][j][0]=(i==j ? 1.0 : 0.0);
3348: }
3349: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3350: for(h=1; h <=nhstepm; h++){
3351: for(d=1; d <=hstepm; d++){
3352: newm=savm;
3353: /* Covariates have to be included here again */
3354: cov[1]=1.;
1.271 brouard 3355: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3356: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3357: cov[2]=agexact;
3358: if(nagesqr==1)
1.222 brouard 3359: cov[3]= agexact*agexact;
1.266 brouard 3360: for (k=1; k<=cptcovn;k++){
3361: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3362: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3363: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3364: /* 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)); */
3365: }
1.267 brouard 3366: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3367: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3368: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3369: /* 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]); */
3370: }
3371: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3372: if(Dummy[Tvar[Tage[k]]]){
3373: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3374: } else{
3375: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3376: }
3377: /* 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]); */
3378: }
3379: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3380: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3381: }
1.217 brouard 3382: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3383: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3384:
1.218 brouard 3385: /* Careful transposed matrix */
1.266 brouard 3386: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3387: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3388: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3389: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3390: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3391: /* if((int)age == 70){ */
3392: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3393: /* for(i=1; i<=nlstate+ndeath; i++) { */
3394: /* printf("%d pmmij ",i); */
3395: /* for(j=1;j<=nlstate+ndeath;j++) { */
3396: /* printf("%f ",pmmij[i][j]); */
3397: /* } */
3398: /* printf(" oldm "); */
3399: /* for(j=1;j<=nlstate+ndeath;j++) { */
3400: /* printf("%f ",oldm[i][j]); */
3401: /* } */
3402: /* printf("\n"); */
3403: /* } */
3404: /* } */
3405: savm=oldm;
3406: oldm=newm;
3407: }
3408: for(i=1; i<=nlstate+ndeath; i++)
3409: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3410: po[i][j][h]=newm[i][j];
1.268 brouard 3411: /* if(h==nhstepm) */
3412: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3413: }
1.268 brouard 3414: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3415: } /* end h */
1.268 brouard 3416: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3417: return po;
3418: }
3419:
3420:
1.162 brouard 3421: #ifdef NLOPT
3422: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3423: double fret;
3424: double *xt;
3425: int j;
3426: myfunc_data *d2 = (myfunc_data *) pd;
3427: /* xt = (p1-1); */
3428: xt=vector(1,n);
3429: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3430:
3431: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3432: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3433: printf("Function = %.12lf ",fret);
3434: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3435: printf("\n");
3436: free_vector(xt,1,n);
3437: return fret;
3438: }
3439: #endif
1.126 brouard 3440:
3441: /*************** log-likelihood *************/
3442: double func( double *x)
3443: {
1.226 brouard 3444: int i, ii, j, k, mi, d, kk;
3445: int ioffset=0;
3446: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3447: double **out;
3448: double lli; /* Individual log likelihood */
3449: int s1, s2;
1.228 brouard 3450: 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 3451: double bbh, survp;
3452: long ipmx;
3453: double agexact;
3454: /*extern weight */
3455: /* We are differentiating ll according to initial status */
3456: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3457: /*for(i=1;i<imx;i++)
3458: printf(" %d\n",s[4][i]);
3459: */
1.162 brouard 3460:
1.226 brouard 3461: ++countcallfunc;
1.162 brouard 3462:
1.226 brouard 3463: cov[1]=1.;
1.126 brouard 3464:
1.226 brouard 3465: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3466: ioffset=0;
1.226 brouard 3467: if(mle==1){
3468: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3469: /* Computes the values of the ncovmodel covariates of the model
3470: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3471: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3472: to be observed in j being in i according to the model.
3473: */
1.243 brouard 3474: ioffset=2+nagesqr ;
1.233 brouard 3475: /* Fixed */
1.234 brouard 3476: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3477: 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)*/
3478: }
1.226 brouard 3479: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3480: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3481: has been calculated etc */
3482: /* For an individual i, wav[i] gives the number of effective waves */
3483: /* We compute the contribution to Likelihood of each effective transition
3484: mw[mi][i] is real wave of the mi th effectve wave */
3485: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3486: s2=s[mw[mi+1][i]][i];
3487: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3488: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3489: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3490: */
3491: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3492: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3493: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3494: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3495: }
3496: for (ii=1;ii<=nlstate+ndeath;ii++)
3497: for (j=1;j<=nlstate+ndeath;j++){
3498: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3499: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3500: }
3501: for(d=0; d<dh[mi][i]; d++){
3502: newm=savm;
3503: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3504: cov[2]=agexact;
3505: if(nagesqr==1)
3506: cov[3]= agexact*agexact; /* Should be changed here */
3507: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3508: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3509: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3510: else
3511: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3512: }
3513: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3514: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3515: savm=oldm;
3516: oldm=newm;
3517: } /* end mult */
3518:
3519: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3520: /* But now since version 0.9 we anticipate for bias at large stepm.
3521: * If stepm is larger than one month (smallest stepm) and if the exact delay
3522: * (in months) between two waves is not a multiple of stepm, we rounded to
3523: * the nearest (and in case of equal distance, to the lowest) interval but now
3524: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3525: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3526: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3527: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3528: * -stepm/2 to stepm/2 .
3529: * For stepm=1 the results are the same as for previous versions of Imach.
3530: * For stepm > 1 the results are less biased than in previous versions.
3531: */
1.234 brouard 3532: s1=s[mw[mi][i]][i];
3533: s2=s[mw[mi+1][i]][i];
3534: bbh=(double)bh[mi][i]/(double)stepm;
3535: /* bias bh is positive if real duration
3536: * is higher than the multiple of stepm and negative otherwise.
3537: */
3538: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3539: if( s2 > nlstate){
3540: /* i.e. if s2 is a death state and if the date of death is known
3541: then the contribution to the likelihood is the probability to
3542: die between last step unit time and current step unit time,
3543: which is also equal to probability to die before dh
3544: minus probability to die before dh-stepm .
3545: In version up to 0.92 likelihood was computed
3546: as if date of death was unknown. Death was treated as any other
3547: health state: the date of the interview describes the actual state
3548: and not the date of a change in health state. The former idea was
3549: to consider that at each interview the state was recorded
3550: (healthy, disable or death) and IMaCh was corrected; but when we
3551: introduced the exact date of death then we should have modified
3552: the contribution of an exact death to the likelihood. This new
3553: contribution is smaller and very dependent of the step unit
3554: stepm. It is no more the probability to die between last interview
3555: and month of death but the probability to survive from last
3556: interview up to one month before death multiplied by the
3557: probability to die within a month. Thanks to Chris
3558: Jackson for correcting this bug. Former versions increased
3559: mortality artificially. The bad side is that we add another loop
3560: which slows down the processing. The difference can be up to 10%
3561: lower mortality.
3562: */
3563: /* If, at the beginning of the maximization mostly, the
3564: cumulative probability or probability to be dead is
3565: constant (ie = 1) over time d, the difference is equal to
3566: 0. out[s1][3] = savm[s1][3]: probability, being at state
3567: s1 at precedent wave, to be dead a month before current
3568: wave is equal to probability, being at state s1 at
3569: precedent wave, to be dead at mont of the current
3570: wave. Then the observed probability (that this person died)
3571: is null according to current estimated parameter. In fact,
3572: it should be very low but not zero otherwise the log go to
3573: infinity.
3574: */
1.183 brouard 3575: /* #ifdef INFINITYORIGINAL */
3576: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3577: /* #else */
3578: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3579: /* lli=log(mytinydouble); */
3580: /* else */
3581: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3582: /* #endif */
1.226 brouard 3583: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3584:
1.226 brouard 3585: } else if ( s2==-1 ) { /* alive */
3586: for (j=1,survp=0. ; j<=nlstate; j++)
3587: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3588: /*survp += out[s1][j]; */
3589: lli= log(survp);
3590: }
3591: else if (s2==-4) {
3592: for (j=3,survp=0. ; j<=nlstate; j++)
3593: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3594: lli= log(survp);
3595: }
3596: else if (s2==-5) {
3597: for (j=1,survp=0. ; j<=2; j++)
3598: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3599: lli= log(survp);
3600: }
3601: else{
3602: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3603: /* 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 */
3604: }
3605: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3606: /*if(lli ==000.0)*/
3607: /*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); */
3608: ipmx +=1;
3609: sw += weight[i];
3610: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3611: /* if (lli < log(mytinydouble)){ */
3612: /* 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); */
3613: /* 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]); */
3614: /* } */
3615: } /* end of wave */
3616: } /* end of individual */
3617: } else if(mle==2){
3618: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3619: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3620: for(mi=1; mi<= wav[i]-1; mi++){
3621: for (ii=1;ii<=nlstate+ndeath;ii++)
3622: for (j=1;j<=nlstate+ndeath;j++){
3623: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3624: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3625: }
3626: for(d=0; d<=dh[mi][i]; d++){
3627: newm=savm;
3628: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3629: cov[2]=agexact;
3630: if(nagesqr==1)
3631: cov[3]= agexact*agexact;
3632: for (kk=1; kk<=cptcovage;kk++) {
3633: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3634: }
3635: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3636: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3637: savm=oldm;
3638: oldm=newm;
3639: } /* end mult */
3640:
3641: s1=s[mw[mi][i]][i];
3642: s2=s[mw[mi+1][i]][i];
3643: bbh=(double)bh[mi][i]/(double)stepm;
3644: 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 */
3645: ipmx +=1;
3646: sw += weight[i];
3647: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3648: } /* end of wave */
3649: } /* end of individual */
3650: } else if(mle==3){ /* exponential inter-extrapolation */
3651: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3652: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3653: for(mi=1; mi<= wav[i]-1; mi++){
3654: for (ii=1;ii<=nlstate+ndeath;ii++)
3655: for (j=1;j<=nlstate+ndeath;j++){
3656: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3657: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3658: }
3659: for(d=0; d<dh[mi][i]; d++){
3660: newm=savm;
3661: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3662: cov[2]=agexact;
3663: if(nagesqr==1)
3664: cov[3]= agexact*agexact;
3665: for (kk=1; kk<=cptcovage;kk++) {
3666: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3667: }
3668: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3669: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3670: savm=oldm;
3671: oldm=newm;
3672: } /* end mult */
3673:
3674: s1=s[mw[mi][i]][i];
3675: s2=s[mw[mi+1][i]][i];
3676: bbh=(double)bh[mi][i]/(double)stepm;
3677: 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 */
3678: ipmx +=1;
3679: sw += weight[i];
3680: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3681: } /* end of wave */
3682: } /* end of individual */
3683: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3684: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3685: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3686: for(mi=1; mi<= wav[i]-1; mi++){
3687: for (ii=1;ii<=nlstate+ndeath;ii++)
3688: for (j=1;j<=nlstate+ndeath;j++){
3689: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3690: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3691: }
3692: for(d=0; d<dh[mi][i]; d++){
3693: newm=savm;
3694: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3695: cov[2]=agexact;
3696: if(nagesqr==1)
3697: cov[3]= agexact*agexact;
3698: for (kk=1; kk<=cptcovage;kk++) {
3699: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3700: }
1.126 brouard 3701:
1.226 brouard 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: if( s2 > nlstate){
3711: lli=log(out[s1][s2] - savm[s1][s2]);
3712: } else if ( s2==-1 ) { /* alive */
3713: for (j=1,survp=0. ; j<=nlstate; j++)
3714: survp += out[s1][j];
3715: lli= log(survp);
3716: }else{
3717: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3718: }
3719: ipmx +=1;
3720: sw += weight[i];
3721: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3722: /* 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 3723: } /* end of wave */
3724: } /* end of individual */
3725: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3726: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3727: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3728: for(mi=1; mi<= wav[i]-1; mi++){
3729: for (ii=1;ii<=nlstate+ndeath;ii++)
3730: for (j=1;j<=nlstate+ndeath;j++){
3731: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3732: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3733: }
3734: for(d=0; d<dh[mi][i]; d++){
3735: newm=savm;
3736: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3737: cov[2]=agexact;
3738: if(nagesqr==1)
3739: cov[3]= agexact*agexact;
3740: for (kk=1; kk<=cptcovage;kk++) {
3741: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3742: }
1.126 brouard 3743:
1.226 brouard 3744: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3745: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3746: savm=oldm;
3747: oldm=newm;
3748: } /* end mult */
3749:
3750: s1=s[mw[mi][i]][i];
3751: s2=s[mw[mi+1][i]][i];
3752: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3753: ipmx +=1;
3754: sw += weight[i];
3755: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
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]);*/
3757: } /* end of wave */
3758: } /* end of individual */
3759: } /* End of if */
3760: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3761: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3762: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3763: return -l;
1.126 brouard 3764: }
3765:
3766: /*************** log-likelihood *************/
3767: double funcone( double *x)
3768: {
1.228 brouard 3769: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3770: int i, ii, j, k, mi, d, kk;
1.228 brouard 3771: int ioffset=0;
1.131 brouard 3772: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3773: double **out;
3774: double lli; /* Individual log likelihood */
3775: double llt;
3776: int s1, s2;
1.228 brouard 3777: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3778:
1.126 brouard 3779: double bbh, survp;
1.187 brouard 3780: double agexact;
1.214 brouard 3781: double agebegin, ageend;
1.126 brouard 3782: /*extern weight */
3783: /* We are differentiating ll according to initial status */
3784: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3785: /*for(i=1;i<imx;i++)
3786: printf(" %d\n",s[4][i]);
3787: */
3788: cov[1]=1.;
3789:
3790: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3791: ioffset=0;
3792: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3793: /* ioffset=2+nagesqr+cptcovage; */
3794: ioffset=2+nagesqr;
1.232 brouard 3795: /* Fixed */
1.224 brouard 3796: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3797: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3798: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3799: 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)*/
3800: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3801: /* cov[2+6]=covar[Tvar[6]][i]; */
3802: /* cov[2+6]=covar[2][i]; V2 */
3803: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3804: /* cov[2+7]=covar[Tvar[7]][i]; */
3805: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3806: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3807: /* cov[2+9]=covar[Tvar[9]][i]; */
3808: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3809: }
1.232 brouard 3810: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3811: /* 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?)*\/ */
3812: /* } */
1.231 brouard 3813: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3814: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3815: /* } */
1.225 brouard 3816:
1.233 brouard 3817:
3818: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3819: /* Wave varying (but not age varying) */
3820: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3821: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3822: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3823: }
1.232 brouard 3824: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3825: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3826: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3827: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3828: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3829: /* 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 3830: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3831: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3832: /* /\* 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]); *\/ */
3833: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3834: /* } */
1.126 brouard 3835: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3836: for (j=1;j<=nlstate+ndeath;j++){
3837: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3838: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3839: }
1.214 brouard 3840:
3841: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3842: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3843: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3844: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3845: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3846: and mw[mi+1][i]. dh depends on stepm.*/
3847: newm=savm;
1.247 brouard 3848: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3849: cov[2]=agexact;
3850: if(nagesqr==1)
3851: cov[3]= agexact*agexact;
3852: for (kk=1; kk<=cptcovage;kk++) {
3853: if(!FixedV[Tvar[Tage[kk]]])
3854: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3855: else
3856: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3857: }
3858: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3859: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3860: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3861: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3862: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3863: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3864: savm=oldm;
3865: oldm=newm;
1.126 brouard 3866: } /* end mult */
3867:
3868: s1=s[mw[mi][i]][i];
3869: s2=s[mw[mi+1][i]][i];
1.217 brouard 3870: /* if(s2==-1){ */
1.268 brouard 3871: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3872: /* /\* exit(1); *\/ */
3873: /* } */
1.126 brouard 3874: bbh=(double)bh[mi][i]/(double)stepm;
3875: /* bias is positive if real duration
3876: * is higher than the multiple of stepm and negative otherwise.
3877: */
3878: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3879: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3880: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3881: for (j=1,survp=0. ; j<=nlstate; j++)
3882: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3883: lli= log(survp);
1.126 brouard 3884: }else if (mle==1){
1.242 brouard 3885: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3886: } else if(mle==2){
1.242 brouard 3887: 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 3888: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3889: 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 3890: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3891: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3892: } else{ /* mle=0 back to 1 */
1.242 brouard 3893: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3894: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3895: } /* End of if */
3896: ipmx +=1;
3897: sw += weight[i];
3898: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3899: /*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 3900: if(globpr){
1.246 brouard 3901: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3902: %11.6f %11.6f %11.6f ", \
1.242 brouard 3903: 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 3904: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3905: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3906: llt +=ll[k]*gipmx/gsw;
3907: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3908: }
3909: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3910: }
1.232 brouard 3911: } /* end of wave */
3912: } /* end of individual */
3913: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3914: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3915: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3916: if(globpr==0){ /* First time we count the contributions and weights */
3917: gipmx=ipmx;
3918: gsw=sw;
3919: }
3920: return -l;
1.126 brouard 3921: }
3922:
3923:
3924: /*************** function likelione ***********/
1.292 brouard 3925: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3926: {
3927: /* This routine should help understanding what is done with
3928: the selection of individuals/waves and
3929: to check the exact contribution to the likelihood.
3930: Plotting could be done.
3931: */
3932: int k;
3933:
3934: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3935: strcpy(fileresilk,"ILK_");
1.202 brouard 3936: strcat(fileresilk,fileresu);
1.126 brouard 3937: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3938: printf("Problem with resultfile: %s\n", fileresilk);
3939: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3940: }
1.214 brouard 3941: 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");
3942: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3943: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3944: for(k=1; k<=nlstate; k++)
3945: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3946: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3947: }
3948:
1.292 brouard 3949: *fretone=(*func)(p);
1.126 brouard 3950: if(*globpri !=0){
3951: fclose(ficresilk);
1.205 brouard 3952: if (mle ==0)
3953: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3954: else if(mle >=1)
3955: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3956: 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 3957: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3958:
3959: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3960: 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 3961: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3962: }
1.207 brouard 3963: 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 3964: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3965: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3966: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3967: fflush(fichtm);
1.205 brouard 3968: }
1.126 brouard 3969: return;
3970: }
3971:
3972:
3973: /*********** Maximum Likelihood Estimation ***************/
3974:
3975: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3976: {
1.165 brouard 3977: int i,j, iter=0;
1.126 brouard 3978: double **xi;
3979: double fret;
3980: double fretone; /* Only one call to likelihood */
3981: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3982:
3983: #ifdef NLOPT
3984: int creturn;
3985: nlopt_opt opt;
3986: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3987: double *lb;
3988: double minf; /* the minimum objective value, upon return */
3989: double * p1; /* Shifted parameters from 0 instead of 1 */
3990: myfunc_data dinst, *d = &dinst;
3991: #endif
3992:
3993:
1.126 brouard 3994: xi=matrix(1,npar,1,npar);
3995: for (i=1;i<=npar;i++)
3996: for (j=1;j<=npar;j++)
3997: xi[i][j]=(i==j ? 1.0 : 0.0);
3998: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3999: strcpy(filerespow,"POW_");
1.126 brouard 4000: strcat(filerespow,fileres);
4001: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4002: printf("Problem with resultfile: %s\n", filerespow);
4003: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4004: }
4005: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4006: for (i=1;i<=nlstate;i++)
4007: for(j=1;j<=nlstate+ndeath;j++)
4008: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4009: fprintf(ficrespow,"\n");
1.162 brouard 4010: #ifdef POWELL
1.126 brouard 4011: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4012: #endif
1.126 brouard 4013:
1.162 brouard 4014: #ifdef NLOPT
4015: #ifdef NEWUOA
4016: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4017: #else
4018: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4019: #endif
4020: lb=vector(0,npar-1);
4021: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4022: nlopt_set_lower_bounds(opt, lb);
4023: nlopt_set_initial_step1(opt, 0.1);
4024:
4025: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4026: d->function = func;
4027: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4028: nlopt_set_min_objective(opt, myfunc, d);
4029: nlopt_set_xtol_rel(opt, ftol);
4030: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4031: printf("nlopt failed! %d\n",creturn);
4032: }
4033: else {
4034: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4035: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4036: iter=1; /* not equal */
4037: }
4038: nlopt_destroy(opt);
4039: #endif
1.126 brouard 4040: free_matrix(xi,1,npar,1,npar);
4041: fclose(ficrespow);
1.203 brouard 4042: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4043: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4044: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4045:
4046: }
4047:
4048: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4049: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4050: {
4051: double **a,**y,*x,pd;
1.203 brouard 4052: /* double **hess; */
1.164 brouard 4053: int i, j;
1.126 brouard 4054: int *indx;
4055:
4056: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4057: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4058: void lubksb(double **a, int npar, int *indx, double b[]) ;
4059: void ludcmp(double **a, int npar, int *indx, double *d) ;
4060: double gompertz(double p[]);
1.203 brouard 4061: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4062:
4063: printf("\nCalculation of the hessian matrix. Wait...\n");
4064: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4065: for (i=1;i<=npar;i++){
1.203 brouard 4066: printf("%d-",i);fflush(stdout);
4067: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4068:
4069: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4070:
4071: /* printf(" %f ",p[i]);
4072: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4073: }
4074:
4075: for (i=1;i<=npar;i++) {
4076: for (j=1;j<=npar;j++) {
4077: if (j>i) {
1.203 brouard 4078: printf(".%d-%d",i,j);fflush(stdout);
4079: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4080: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4081:
4082: hess[j][i]=hess[i][j];
4083: /*printf(" %lf ",hess[i][j]);*/
4084: }
4085: }
4086: }
4087: printf("\n");
4088: fprintf(ficlog,"\n");
4089:
4090: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4091: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4092:
4093: a=matrix(1,npar,1,npar);
4094: y=matrix(1,npar,1,npar);
4095: x=vector(1,npar);
4096: indx=ivector(1,npar);
4097: for (i=1;i<=npar;i++)
4098: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4099: ludcmp(a,npar,indx,&pd);
4100:
4101: for (j=1;j<=npar;j++) {
4102: for (i=1;i<=npar;i++) x[i]=0;
4103: x[j]=1;
4104: lubksb(a,npar,indx,x);
4105: for (i=1;i<=npar;i++){
4106: matcov[i][j]=x[i];
4107: }
4108: }
4109:
4110: printf("\n#Hessian matrix#\n");
4111: fprintf(ficlog,"\n#Hessian matrix#\n");
4112: for (i=1;i<=npar;i++) {
4113: for (j=1;j<=npar;j++) {
1.203 brouard 4114: printf("%.6e ",hess[i][j]);
4115: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4116: }
4117: printf("\n");
4118: fprintf(ficlog,"\n");
4119: }
4120:
1.203 brouard 4121: /* printf("\n#Covariance matrix#\n"); */
4122: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4123: /* for (i=1;i<=npar;i++) { */
4124: /* for (j=1;j<=npar;j++) { */
4125: /* printf("%.6e ",matcov[i][j]); */
4126: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4127: /* } */
4128: /* printf("\n"); */
4129: /* fprintf(ficlog,"\n"); */
4130: /* } */
4131:
1.126 brouard 4132: /* Recompute Inverse */
1.203 brouard 4133: /* for (i=1;i<=npar;i++) */
4134: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4135: /* ludcmp(a,npar,indx,&pd); */
4136:
4137: /* printf("\n#Hessian matrix recomputed#\n"); */
4138:
4139: /* for (j=1;j<=npar;j++) { */
4140: /* for (i=1;i<=npar;i++) x[i]=0; */
4141: /* x[j]=1; */
4142: /* lubksb(a,npar,indx,x); */
4143: /* for (i=1;i<=npar;i++){ */
4144: /* y[i][j]=x[i]; */
4145: /* printf("%.3e ",y[i][j]); */
4146: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4147: /* } */
4148: /* printf("\n"); */
4149: /* fprintf(ficlog,"\n"); */
4150: /* } */
4151:
4152: /* Verifying the inverse matrix */
4153: #ifdef DEBUGHESS
4154: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4155:
1.203 brouard 4156: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4157: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4158:
4159: for (j=1;j<=npar;j++) {
4160: for (i=1;i<=npar;i++){
1.203 brouard 4161: printf("%.2f ",y[i][j]);
4162: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4163: }
4164: printf("\n");
4165: fprintf(ficlog,"\n");
4166: }
1.203 brouard 4167: #endif
1.126 brouard 4168:
4169: free_matrix(a,1,npar,1,npar);
4170: free_matrix(y,1,npar,1,npar);
4171: free_vector(x,1,npar);
4172: free_ivector(indx,1,npar);
1.203 brouard 4173: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4174:
4175:
4176: }
4177:
4178: /*************** hessian matrix ****************/
4179: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4180: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4181: int i;
4182: int l=1, lmax=20;
1.203 brouard 4183: double k1,k2, res, fx;
1.132 brouard 4184: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4185: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4186: int k=0,kmax=10;
4187: double l1;
4188:
4189: fx=func(x);
4190: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4191: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4192: l1=pow(10,l);
4193: delts=delt;
4194: for(k=1 ; k <kmax; k=k+1){
4195: delt = delta*(l1*k);
4196: p2[theta]=x[theta] +delt;
1.145 brouard 4197: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4198: p2[theta]=x[theta]-delt;
4199: k2=func(p2)-fx;
4200: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4201: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4202:
1.203 brouard 4203: #ifdef DEBUGHESSII
1.126 brouard 4204: 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);
4205: 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);
4206: #endif
4207: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4208: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4209: k=kmax;
4210: }
4211: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4212: k=kmax; l=lmax*10;
1.126 brouard 4213: }
4214: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4215: delts=delt;
4216: }
1.203 brouard 4217: } /* End loop k */
1.126 brouard 4218: }
4219: delti[theta]=delts;
4220: return res;
4221:
4222: }
4223:
1.203 brouard 4224: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4225: {
4226: int i;
1.164 brouard 4227: int l=1, lmax=20;
1.126 brouard 4228: double k1,k2,k3,k4,res,fx;
1.132 brouard 4229: double p2[MAXPARM+1];
1.203 brouard 4230: int k, kmax=1;
4231: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4232:
4233: int firstime=0;
1.203 brouard 4234:
1.126 brouard 4235: fx=func(x);
1.203 brouard 4236: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4237: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4238: p2[thetai]=x[thetai]+delti[thetai]*k;
4239: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4240: k1=func(p2)-fx;
4241:
1.203 brouard 4242: p2[thetai]=x[thetai]+delti[thetai]*k;
4243: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4244: k2=func(p2)-fx;
4245:
1.203 brouard 4246: p2[thetai]=x[thetai]-delti[thetai]*k;
4247: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4248: k3=func(p2)-fx;
4249:
1.203 brouard 4250: p2[thetai]=x[thetai]-delti[thetai]*k;
4251: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4252: k4=func(p2)-fx;
1.203 brouard 4253: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4254: if(k1*k2*k3*k4 <0.){
1.208 brouard 4255: firstime=1;
1.203 brouard 4256: kmax=kmax+10;
1.208 brouard 4257: }
4258: if(kmax >=10 || firstime ==1){
1.246 brouard 4259: 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);
4260: 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 4261: 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);
4262: 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);
4263: }
4264: #ifdef DEBUGHESSIJ
4265: v1=hess[thetai][thetai];
4266: v2=hess[thetaj][thetaj];
4267: cv12=res;
4268: /* Computing eigen value of Hessian matrix */
4269: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4270: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4271: if ((lc2 <0) || (lc1 <0) ){
4272: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4273: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4274: 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);
4275: 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);
4276: }
1.126 brouard 4277: #endif
4278: }
4279: return res;
4280: }
4281:
1.203 brouard 4282: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4283: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4284: /* { */
4285: /* int i; */
4286: /* int l=1, lmax=20; */
4287: /* double k1,k2,k3,k4,res,fx; */
4288: /* double p2[MAXPARM+1]; */
4289: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4290: /* int k=0,kmax=10; */
4291: /* double l1; */
4292:
4293: /* fx=func(x); */
4294: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4295: /* l1=pow(10,l); */
4296: /* delts=delt; */
4297: /* for(k=1 ; k <kmax; k=k+1){ */
4298: /* delt = delti*(l1*k); */
4299: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4300: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4301: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4302: /* k1=func(p2)-fx; */
4303:
4304: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4305: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4306: /* k2=func(p2)-fx; */
4307:
4308: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4309: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4310: /* k3=func(p2)-fx; */
4311:
4312: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4313: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4314: /* k4=func(p2)-fx; */
4315: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4316: /* #ifdef DEBUGHESSIJ */
4317: /* 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); */
4318: /* 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); */
4319: /* #endif */
4320: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4321: /* k=kmax; */
4322: /* } */
4323: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4324: /* k=kmax; l=lmax*10; */
4325: /* } */
4326: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4327: /* delts=delt; */
4328: /* } */
4329: /* } /\* End loop k *\/ */
4330: /* } */
4331: /* delti[theta]=delts; */
4332: /* return res; */
4333: /* } */
4334:
4335:
1.126 brouard 4336: /************** Inverse of matrix **************/
4337: void ludcmp(double **a, int n, int *indx, double *d)
4338: {
4339: int i,imax,j,k;
4340: double big,dum,sum,temp;
4341: double *vv;
4342:
4343: vv=vector(1,n);
4344: *d=1.0;
4345: for (i=1;i<=n;i++) {
4346: big=0.0;
4347: for (j=1;j<=n;j++)
4348: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4349: if (big == 0.0){
4350: printf(" Singular Hessian matrix at row %d:\n",i);
4351: for (j=1;j<=n;j++) {
4352: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4353: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4354: }
4355: fflush(ficlog);
4356: fclose(ficlog);
4357: nrerror("Singular matrix in routine ludcmp");
4358: }
1.126 brouard 4359: vv[i]=1.0/big;
4360: }
4361: for (j=1;j<=n;j++) {
4362: for (i=1;i<j;i++) {
4363: sum=a[i][j];
4364: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4365: a[i][j]=sum;
4366: }
4367: big=0.0;
4368: for (i=j;i<=n;i++) {
4369: sum=a[i][j];
4370: for (k=1;k<j;k++)
4371: sum -= a[i][k]*a[k][j];
4372: a[i][j]=sum;
4373: if ( (dum=vv[i]*fabs(sum)) >= big) {
4374: big=dum;
4375: imax=i;
4376: }
4377: }
4378: if (j != imax) {
4379: for (k=1;k<=n;k++) {
4380: dum=a[imax][k];
4381: a[imax][k]=a[j][k];
4382: a[j][k]=dum;
4383: }
4384: *d = -(*d);
4385: vv[imax]=vv[j];
4386: }
4387: indx[j]=imax;
4388: if (a[j][j] == 0.0) a[j][j]=TINY;
4389: if (j != n) {
4390: dum=1.0/(a[j][j]);
4391: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4392: }
4393: }
4394: free_vector(vv,1,n); /* Doesn't work */
4395: ;
4396: }
4397:
4398: void lubksb(double **a, int n, int *indx, double b[])
4399: {
4400: int i,ii=0,ip,j;
4401: double sum;
4402:
4403: for (i=1;i<=n;i++) {
4404: ip=indx[i];
4405: sum=b[ip];
4406: b[ip]=b[i];
4407: if (ii)
4408: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4409: else if (sum) ii=i;
4410: b[i]=sum;
4411: }
4412: for (i=n;i>=1;i--) {
4413: sum=b[i];
4414: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4415: b[i]=sum/a[i][i];
4416: }
4417: }
4418:
4419: void pstamp(FILE *fichier)
4420: {
1.196 brouard 4421: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4422: }
4423:
1.297 ! brouard 4424: void date2dmy(double date,double *day, double *month, double *year){
! 4425: double yp=0., yp1=0., yp2=0.;
! 4426:
! 4427: yp1=modf(date,&yp);/* extracts integral of date in yp and
! 4428: fractional in yp1 */
! 4429: *year=yp;
! 4430: yp2=modf((yp1*12),&yp);
! 4431: *month=yp;
! 4432: yp1=modf((yp2*30.5),&yp);
! 4433: *day=yp;
! 4434: if(*day==0) *day=1;
! 4435: if(*month==0) *month=1;
! 4436: }
! 4437:
1.253 brouard 4438:
4439:
1.126 brouard 4440: /************ Frequencies ********************/
1.251 brouard 4441: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4442: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4443: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4444: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4445:
1.265 brouard 4446: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4447: int iind=0, iage=0;
4448: int mi; /* Effective wave */
4449: int first;
4450: double ***freq; /* Frequencies */
1.268 brouard 4451: 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 */
4452: 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 4453: double *meanq, *stdq, *idq;
1.226 brouard 4454: double **meanqt;
4455: double *pp, **prop, *posprop, *pospropt;
4456: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4457: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4458: double agebegin, ageend;
4459:
4460: pp=vector(1,nlstate);
1.251 brouard 4461: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4462: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4463: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4464: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4465: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4466: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4467: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4468: meanqt=matrix(1,lastpass,1,nqtveff);
4469: strcpy(fileresp,"P_");
4470: strcat(fileresp,fileresu);
4471: /*strcat(fileresphtm,fileresu);*/
4472: if((ficresp=fopen(fileresp,"w"))==NULL) {
4473: printf("Problem with prevalence resultfile: %s\n", fileresp);
4474: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4475: exit(0);
4476: }
1.240 brouard 4477:
1.226 brouard 4478: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4479: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4480: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4481: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4482: fflush(ficlog);
4483: exit(70);
4484: }
4485: else{
4486: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4487: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4488: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4489: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4490: }
1.237 brouard 4491: 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 4492:
1.226 brouard 4493: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4494: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4495: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4496: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4497: fflush(ficlog);
4498: exit(70);
1.240 brouard 4499: } else{
1.226 brouard 4500: 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 4501: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4502: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4503: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4504: }
1.240 brouard 4505: 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);
4506:
1.253 brouard 4507: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4508: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4509: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4510: j1=0;
1.126 brouard 4511:
1.227 brouard 4512: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4513: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4514: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4515:
4516:
1.226 brouard 4517: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4518: reference=low_education V1=0,V2=0
4519: med_educ V1=1 V2=0,
4520: high_educ V1=0 V2=1
4521: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4522: */
1.249 brouard 4523: dateintsum=0;
4524: k2cpt=0;
4525:
1.253 brouard 4526: if(cptcoveff == 0 )
1.265 brouard 4527: nl=1; /* Constant and age model only */
1.253 brouard 4528: else
4529: nl=2;
1.265 brouard 4530:
4531: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4532: /* Loop on nj=1 or 2 if dummy covariates j!=0
4533: * Loop on j1(1 to 2**cptcoveff) covariate combination
4534: * freq[s1][s2][iage] =0.
4535: * Loop on iind
4536: * ++freq[s1][s2][iage] weighted
4537: * end iind
4538: * if covariate and j!0
4539: * headers Variable on one line
4540: * endif cov j!=0
4541: * header of frequency table by age
4542: * Loop on age
4543: * pp[s1]+=freq[s1][s2][iage] weighted
4544: * pos+=freq[s1][s2][iage] weighted
4545: * Loop on s1 initial state
4546: * fprintf(ficresp
4547: * end s1
4548: * end age
4549: * if j!=0 computes starting values
4550: * end compute starting values
4551: * end j1
4552: * end nl
4553: */
1.253 brouard 4554: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4555: if(nj==1)
4556: j=0; /* First pass for the constant */
1.265 brouard 4557: else{
1.253 brouard 4558: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4559: }
1.251 brouard 4560: first=1;
1.265 brouard 4561: 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 4562: posproptt=0.;
4563: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4564: scanf("%d", i);*/
4565: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4566: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4567: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4568: freq[i][s2][m]=0;
1.251 brouard 4569:
4570: for (i=1; i<=nlstate; i++) {
1.240 brouard 4571: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4572: prop[i][m]=0;
4573: posprop[i]=0;
4574: pospropt[i]=0;
4575: }
1.283 brouard 4576: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4577: idq[z1]=0.;
4578: meanq[z1]=0.;
4579: stdq[z1]=0.;
1.283 brouard 4580: }
4581: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4582: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4583: /* meanqt[m][z1]=0.; */
4584: /* } */
4585: /* } */
1.251 brouard 4586: /* dateintsum=0; */
4587: /* k2cpt=0; */
4588:
1.265 brouard 4589: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4590: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4591: bool=1;
4592: if(j !=0){
4593: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4594: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4595: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4596: /* if(Tvaraff[z1] ==-20){ */
4597: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4598: /* }else if(Tvaraff[z1] ==-10){ */
4599: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4600: /* }else */
4601: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4602: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4603: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4604: /* 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",
4605: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4606: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4607: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4608: } /* Onlyf fixed */
4609: } /* end z1 */
4610: } /* cptcovn > 0 */
4611: } /* end any */
4612: }/* end j==0 */
1.265 brouard 4613: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4614: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4615: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4616: m=mw[mi][iind];
4617: if(j!=0){
4618: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4619: for (z1=1; z1<=cptcoveff; z1++) {
4620: if( Fixed[Tmodelind[z1]]==1){
4621: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4622: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4623: value is -1, we don't select. It differs from the
4624: constant and age model which counts them. */
4625: bool=0; /* not selected */
4626: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4627: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4628: bool=0;
4629: }
4630: }
4631: }
4632: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4633: } /* end j==0 */
4634: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4635: if(bool==1){ /*Selected */
1.251 brouard 4636: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4637: and mw[mi+1][iind]. dh depends on stepm. */
4638: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4639: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4640: if(m >=firstpass && m <=lastpass){
4641: k2=anint[m][iind]+(mint[m][iind]/12.);
4642: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4643: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4644: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4645: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4646: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4647: if (m<lastpass) {
4648: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4649: /* 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]); */
4650: if(s[m][iind]==-1)
4651: 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.));
4652: 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 4653: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4654: idq[z1]=idq[z1]+weight[iind];
4655: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4656: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4657: }
1.251 brouard 4658: /* if((int)agev[m][iind] == 55) */
4659: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4660: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4661: 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 4662: }
1.251 brouard 4663: } /* end if between passes */
4664: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4665: dateintsum=dateintsum+k2; /* on all covariates ?*/
4666: k2cpt++;
4667: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4668: }
1.251 brouard 4669: }else{
4670: bool=1;
4671: }/* end bool 2 */
4672: } /* end m */
1.284 brouard 4673: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4674: /* idq[z1]=idq[z1]+weight[iind]; */
4675: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4676: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4677: /* } */
1.251 brouard 4678: } /* end bool */
4679: } /* end iind = 1 to imx */
4680: /* prop[s][age] is feeded for any initial and valid live state as well as
4681: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4682:
4683:
4684: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4685: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4686: pstamp(ficresp);
1.251 brouard 4687: if (cptcoveff>0 && j!=0){
1.265 brouard 4688: pstamp(ficresp);
1.251 brouard 4689: printf( "\n#********** Variable ");
4690: fprintf(ficresp, "\n#********** Variable ");
4691: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4692: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4693: fprintf(ficlog, "\n#********** Variable ");
4694: for (z1=1; z1<=cptcoveff; z1++){
4695: if(!FixedV[Tvaraff[z1]]){
4696: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4697: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4698: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4699: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4700: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4701: }else{
1.251 brouard 4702: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4703: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4704: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4705: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4706: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4707: }
4708: }
4709: printf( "**********\n#");
4710: fprintf(ficresp, "**********\n#");
4711: fprintf(ficresphtm, "**********</h3>\n");
4712: fprintf(ficresphtmfr, "**********</h3>\n");
4713: fprintf(ficlog, "**********\n");
4714: }
1.284 brouard 4715: /*
4716: Printing means of quantitative variables if any
4717: */
4718: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4719: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4720: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4721: if(weightopt==1){
4722: printf(" Weighted mean and standard deviation of");
4723: fprintf(ficlog," Weighted mean and standard deviation of");
4724: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4725: }
1.285 brouard 4726: 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]));
4727: 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]));
4728: 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 4729: }
4730: /* for (z1=1; z1<= nqtveff; z1++) { */
4731: /* for(m=1;m<=lastpass;m++){ */
4732: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4733: /* } */
4734: /* } */
1.283 brouard 4735:
1.251 brouard 4736: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4737: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4738: fprintf(ficresp, " Age");
4739: 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 4740: for(i=1; i<=nlstate;i++) {
1.265 brouard 4741: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4742: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4743: }
1.265 brouard 4744: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4745: fprintf(ficresphtm, "\n");
4746:
4747: /* Header of frequency table by age */
4748: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4749: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4750: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4751: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4752: if(s2!=0 && m!=0)
4753: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4754: }
1.226 brouard 4755: }
1.251 brouard 4756: fprintf(ficresphtmfr, "\n");
4757:
4758: /* For each age */
4759: for(iage=iagemin; iage <= iagemax+3; iage++){
4760: fprintf(ficresphtm,"<tr>");
4761: if(iage==iagemax+1){
4762: fprintf(ficlog,"1");
4763: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4764: }else if(iage==iagemax+2){
4765: fprintf(ficlog,"0");
4766: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4767: }else if(iage==iagemax+3){
4768: fprintf(ficlog,"Total");
4769: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4770: }else{
1.240 brouard 4771: if(first==1){
1.251 brouard 4772: first=0;
4773: printf("See log file for details...\n");
4774: }
4775: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4776: fprintf(ficlog,"Age %d", iage);
4777: }
1.265 brouard 4778: for(s1=1; s1 <=nlstate ; s1++){
4779: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4780: pp[s1] += freq[s1][m][iage];
1.251 brouard 4781: }
1.265 brouard 4782: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4783: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4784: pos += freq[s1][m][iage];
4785: if(pp[s1]>=1.e-10){
1.251 brouard 4786: if(first==1){
1.265 brouard 4787: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4788: }
1.265 brouard 4789: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4790: }else{
4791: if(first==1)
1.265 brouard 4792: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4793: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4794: }
4795: }
4796:
1.265 brouard 4797: for(s1=1; s1 <=nlstate ; s1++){
4798: /* posprop[s1]=0; */
4799: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4800: pp[s1] += freq[s1][m][iage];
4801: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4802:
4803: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4804: pos += pp[s1]; /* pos is the total number of transitions until this age */
4805: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4806: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4807: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4808: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4809: }
4810:
4811: /* Writing ficresp */
4812: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4813: if( iage <= iagemax){
4814: fprintf(ficresp," %d",iage);
4815: }
4816: }else if( nj==2){
4817: if( iage <= iagemax){
4818: fprintf(ficresp," %d",iage);
4819: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4820: }
1.240 brouard 4821: }
1.265 brouard 4822: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4823: if(pos>=1.e-5){
1.251 brouard 4824: if(first==1)
1.265 brouard 4825: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4826: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4827: }else{
4828: if(first==1)
1.265 brouard 4829: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4830: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4831: }
4832: if( iage <= iagemax){
4833: if(pos>=1.e-5){
1.265 brouard 4834: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4835: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4836: }else if( nj==2){
4837: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4838: }
4839: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4840: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4841: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4842: } else{
4843: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4844: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4845: }
1.240 brouard 4846: }
1.265 brouard 4847: pospropt[s1] +=posprop[s1];
4848: } /* end loop s1 */
1.251 brouard 4849: /* pospropt=0.; */
1.265 brouard 4850: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4851: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4852: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4853: if(first==1){
1.265 brouard 4854: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4855: }
1.265 brouard 4856: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4857: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4858: }
1.265 brouard 4859: if(s1!=0 && m!=0)
4860: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4861: }
1.265 brouard 4862: } /* end loop s1 */
1.251 brouard 4863: posproptt=0.;
1.265 brouard 4864: for(s1=1; s1 <=nlstate; s1++){
4865: posproptt += pospropt[s1];
1.251 brouard 4866: }
4867: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4868: fprintf(ficresphtm,"</tr>\n");
4869: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4870: if(iage <= iagemax)
4871: fprintf(ficresp,"\n");
1.240 brouard 4872: }
1.251 brouard 4873: if(first==1)
4874: printf("Others in log...\n");
4875: fprintf(ficlog,"\n");
4876: } /* end loop age iage */
1.265 brouard 4877:
1.251 brouard 4878: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4879: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4880: if(posproptt < 1.e-5){
1.265 brouard 4881: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4882: }else{
1.265 brouard 4883: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4884: }
1.226 brouard 4885: }
1.251 brouard 4886: fprintf(ficresphtm,"</tr>\n");
4887: fprintf(ficresphtm,"</table>\n");
4888: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4889: if(posproptt < 1.e-5){
1.251 brouard 4890: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4891: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4892: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4893: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4894: invalidvarcomb[j1]=1;
1.226 brouard 4895: }else{
1.251 brouard 4896: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4897: invalidvarcomb[j1]=0;
1.226 brouard 4898: }
1.251 brouard 4899: fprintf(ficresphtmfr,"</table>\n");
4900: fprintf(ficlog,"\n");
4901: if(j!=0){
4902: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4903: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4904: for(k=1; k <=(nlstate+ndeath); k++){
4905: if (k != i) {
1.265 brouard 4906: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4907: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4908: if(j1==1){ /* All dummy covariates to zero */
4909: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4910: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4911: printf("%d%d ",i,k);
4912: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4913: 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]));
4914: 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]));
4915: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4916: }
1.253 brouard 4917: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4918: for(iage=iagemin; iage <= iagemax+3; iage++){
4919: x[iage]= (double)iage;
4920: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4921: /* 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 4922: }
1.268 brouard 4923: /* Some are not finite, but linreg will ignore these ages */
4924: no=0;
1.253 brouard 4925: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4926: pstart[s1]=b;
4927: pstart[s1-1]=a;
1.252 brouard 4928: }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 */
4929: 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]);
4930: 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 4931: 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 4932: printf("%d%d ",i,k);
4933: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4934: 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 4935: }else{ /* Other cases, like quantitative fixed or varying covariates */
4936: ;
4937: }
4938: /* printf("%12.7f )", param[i][jj][k]); */
4939: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4940: s1++;
1.251 brouard 4941: } /* end jj */
4942: } /* end k!= i */
4943: } /* end k */
1.265 brouard 4944: } /* end i, s1 */
1.251 brouard 4945: } /* end j !=0 */
4946: } /* end selected combination of covariate j1 */
4947: if(j==0){ /* We can estimate starting values from the occurences in each case */
4948: printf("#Freqsummary: Starting values for the constants:\n");
4949: fprintf(ficlog,"\n");
1.265 brouard 4950: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4951: for(k=1; k <=(nlstate+ndeath); k++){
4952: if (k != i) {
4953: printf("%d%d ",i,k);
4954: fprintf(ficlog,"%d%d ",i,k);
4955: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4956: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4957: if(jj==1){ /* Age has to be done */
1.265 brouard 4958: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4959: 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]));
4960: 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 4961: }
4962: /* printf("%12.7f )", param[i][jj][k]); */
4963: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4964: s1++;
1.250 brouard 4965: }
1.251 brouard 4966: printf("\n");
4967: fprintf(ficlog,"\n");
1.250 brouard 4968: }
4969: }
1.284 brouard 4970: } /* end of state i */
1.251 brouard 4971: printf("#Freqsummary\n");
4972: fprintf(ficlog,"\n");
1.265 brouard 4973: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4974: for(s2=-1; s2 <=nlstate+ndeath; s2++){
4975: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
4976: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4977: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4978: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
4979: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
4980: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 4981: /* } */
4982: }
1.265 brouard 4983: } /* end loop s1 */
1.251 brouard 4984:
4985: printf("\n");
4986: fprintf(ficlog,"\n");
4987: } /* end j=0 */
1.249 brouard 4988: } /* end j */
1.252 brouard 4989:
1.253 brouard 4990: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4991: for(i=1, jk=1; i <=nlstate; i++){
4992: for(j=1; j <=nlstate+ndeath; j++){
4993: if(j!=i){
4994: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4995: printf("%1d%1d",i,j);
4996: fprintf(ficparo,"%1d%1d",i,j);
4997: for(k=1; k<=ncovmodel;k++){
4998: /* printf(" %lf",param[i][j][k]); */
4999: /* fprintf(ficparo," %lf",param[i][j][k]); */
5000: p[jk]=pstart[jk];
5001: printf(" %f ",pstart[jk]);
5002: fprintf(ficparo," %f ",pstart[jk]);
5003: jk++;
5004: }
5005: printf("\n");
5006: fprintf(ficparo,"\n");
5007: }
5008: }
5009: }
5010: } /* end mle=-2 */
1.226 brouard 5011: dateintmean=dateintsum/k2cpt;
1.296 brouard 5012: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5013:
1.226 brouard 5014: fclose(ficresp);
5015: fclose(ficresphtm);
5016: fclose(ficresphtmfr);
1.283 brouard 5017: free_vector(idq,1,nqfveff);
1.226 brouard 5018: free_vector(meanq,1,nqfveff);
1.284 brouard 5019: free_vector(stdq,1,nqfveff);
1.226 brouard 5020: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5021: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5022: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5023: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5024: free_vector(pospropt,1,nlstate);
5025: free_vector(posprop,1,nlstate);
1.251 brouard 5026: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5027: free_vector(pp,1,nlstate);
5028: /* End of freqsummary */
5029: }
1.126 brouard 5030:
1.268 brouard 5031: /* Simple linear regression */
5032: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5033:
5034: /* y=a+bx regression */
5035: double sumx = 0.0; /* sum of x */
5036: double sumx2 = 0.0; /* sum of x**2 */
5037: double sumxy = 0.0; /* sum of x * y */
5038: double sumy = 0.0; /* sum of y */
5039: double sumy2 = 0.0; /* sum of y**2 */
5040: double sume2 = 0.0; /* sum of square or residuals */
5041: double yhat;
5042:
5043: double denom=0;
5044: int i;
5045: int ne=*no;
5046:
5047: for ( i=ifi, ne=0;i<=ila;i++) {
5048: if(!isfinite(x[i]) || !isfinite(y[i])){
5049: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5050: continue;
5051: }
5052: ne=ne+1;
5053: sumx += x[i];
5054: sumx2 += x[i]*x[i];
5055: sumxy += x[i] * y[i];
5056: sumy += y[i];
5057: sumy2 += y[i]*y[i];
5058: denom = (ne * sumx2 - sumx*sumx);
5059: /* 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); */
5060: }
5061:
5062: denom = (ne * sumx2 - sumx*sumx);
5063: if (denom == 0) {
5064: // vertical, slope m is infinity
5065: *b = INFINITY;
5066: *a = 0;
5067: if (r) *r = 0;
5068: return 1;
5069: }
5070:
5071: *b = (ne * sumxy - sumx * sumy) / denom;
5072: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5073: if (r!=NULL) {
5074: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5075: sqrt((sumx2 - sumx*sumx/ne) *
5076: (sumy2 - sumy*sumy/ne));
5077: }
5078: *no=ne;
5079: for ( i=ifi, ne=0;i<=ila;i++) {
5080: if(!isfinite(x[i]) || !isfinite(y[i])){
5081: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5082: continue;
5083: }
5084: ne=ne+1;
5085: yhat = y[i] - *a -*b* x[i];
5086: sume2 += yhat * yhat ;
5087:
5088: denom = (ne * sumx2 - sumx*sumx);
5089: /* 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); */
5090: }
5091: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5092: *sa= *sb * sqrt(sumx2/ne);
5093:
5094: return 0;
5095: }
5096:
1.126 brouard 5097: /************ Prevalence ********************/
1.227 brouard 5098: 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)
5099: {
5100: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5101: in each health status at the date of interview (if between dateprev1 and dateprev2).
5102: We still use firstpass and lastpass as another selection.
5103: */
1.126 brouard 5104:
1.227 brouard 5105: int i, m, jk, j1, bool, z1,j, iv;
5106: int mi; /* Effective wave */
5107: int iage;
5108: double agebegin, ageend;
5109:
5110: double **prop;
5111: double posprop;
5112: double y2; /* in fractional years */
5113: int iagemin, iagemax;
5114: int first; /** to stop verbosity which is redirected to log file */
5115:
5116: iagemin= (int) agemin;
5117: iagemax= (int) agemax;
5118: /*pp=vector(1,nlstate);*/
1.251 brouard 5119: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5120: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5121: j1=0;
1.222 brouard 5122:
1.227 brouard 5123: /*j=cptcoveff;*/
5124: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5125:
1.288 brouard 5126: first=0;
1.227 brouard 5127: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5128: for (i=1; i<=nlstate; i++)
1.251 brouard 5129: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5130: prop[i][iage]=0.0;
5131: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5132: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5133: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5134:
5135: for (i=1; i<=imx; i++) { /* Each individual */
5136: bool=1;
5137: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5138: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5139: m=mw[mi][i];
5140: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5141: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5142: for (z1=1; z1<=cptcoveff; z1++){
5143: if( Fixed[Tmodelind[z1]]==1){
5144: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5145: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5146: bool=0;
5147: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5148: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5149: bool=0;
5150: }
5151: }
5152: if(bool==1){ /* Otherwise we skip that wave/person */
5153: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5154: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5155: if(m >=firstpass && m <=lastpass){
5156: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5157: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5158: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5159: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5160: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5161: 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);
5162: exit(1);
5163: }
5164: if (s[m][i]>0 && s[m][i]<=nlstate) {
5165: /*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]]);*/
5166: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5167: prop[s[m][i]][iagemax+3] += weight[i];
5168: } /* end valid statuses */
5169: } /* end selection of dates */
5170: } /* end selection of waves */
5171: } /* end bool */
5172: } /* end wave */
5173: } /* end individual */
5174: for(i=iagemin; i <= iagemax+3; i++){
5175: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5176: posprop += prop[jk][i];
5177: }
5178:
5179: for(jk=1; jk <=nlstate ; jk++){
5180: if( i <= iagemax){
5181: if(posprop>=1.e-5){
5182: probs[i][jk][j1]= prop[jk][i]/posprop;
5183: } else{
1.288 brouard 5184: if(!first){
5185: first=1;
1.266 brouard 5186: 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]);
5187: }else{
1.288 brouard 5188: 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 5189: }
5190: }
5191: }
5192: }/* end jk */
5193: }/* end i */
1.222 brouard 5194: /*} *//* end i1 */
1.227 brouard 5195: } /* end j1 */
1.222 brouard 5196:
1.227 brouard 5197: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5198: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5199: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5200: } /* End of prevalence */
1.126 brouard 5201:
5202: /************* Waves Concatenation ***************/
5203:
5204: 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)
5205: {
5206: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
5207: Death is a valid wave (if date is known).
5208: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5209: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
5210: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 5211: */
1.126 brouard 5212:
1.224 brouard 5213: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5214: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5215: double sum=0., jmean=0.;*/
1.224 brouard 5216: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5217: int j, k=0,jk, ju, jl;
5218: double sum=0.;
5219: first=0;
1.214 brouard 5220: firstwo=0;
1.217 brouard 5221: firsthree=0;
1.218 brouard 5222: firstfour=0;
1.164 brouard 5223: jmin=100000;
1.126 brouard 5224: jmax=-1;
5225: jmean=0.;
1.224 brouard 5226:
5227: /* Treating live states */
1.214 brouard 5228: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5229: mi=0; /* First valid wave */
1.227 brouard 5230: mli=0; /* Last valid wave */
1.126 brouard 5231: m=firstpass;
1.214 brouard 5232: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5233: 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 */
5234: mli=m-1;/* mw[++mi][i]=m-1; */
5235: }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 */
5236: mw[++mi][i]=m;
5237: mli=m;
1.224 brouard 5238: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5239: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5240: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5241: }
1.227 brouard 5242: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5243: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5244: break;
1.224 brouard 5245: #else
1.227 brouard 5246: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5247: if(firsthree == 0){
1.262 brouard 5248: 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 5249: firsthree=1;
5250: }
1.262 brouard 5251: 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 5252: mw[++mi][i]=m;
5253: mli=m;
5254: }
5255: if(s[m][i]==-2){ /* Vital status is really unknown */
5256: nbwarn++;
5257: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5258: 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);
5259: 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);
5260: }
5261: break;
5262: }
5263: break;
1.224 brouard 5264: #endif
1.227 brouard 5265: }/* End m >= lastpass */
1.126 brouard 5266: }/* end while */
1.224 brouard 5267:
1.227 brouard 5268: /* 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 5269: /* After last pass */
1.224 brouard 5270: /* Treating death states */
1.214 brouard 5271: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5272: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5273: /* } */
1.126 brouard 5274: mi++; /* Death is another wave */
5275: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5276: /* Only death is a correct wave */
1.126 brouard 5277: mw[mi][i]=m;
1.257 brouard 5278: } /* else not in a death state */
1.224 brouard 5279: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5280: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5281: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5282: 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 */
5283: nbwarn++;
5284: if(firstfiv==0){
5285: 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 );
5286: firstfiv=1;
5287: }else{
5288: 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 );
5289: }
5290: }else{ /* Death occured afer last wave potential bias */
5291: nberr++;
5292: if(firstwo==0){
1.257 brouard 5293: 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 5294: firstwo=1;
5295: }
1.257 brouard 5296: 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 5297: }
1.257 brouard 5298: }else{ /* if date of interview is unknown */
1.227 brouard 5299: /* death is known but not confirmed by death status at any wave */
5300: if(firstfour==0){
5301: 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 );
5302: firstfour=1;
5303: }
5304: 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 5305: }
1.224 brouard 5306: } /* end if date of death is known */
5307: #endif
5308: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5309: /* wav[i]=mw[mi][i]; */
1.126 brouard 5310: if(mi==0){
5311: nbwarn++;
5312: if(first==0){
1.227 brouard 5313: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5314: first=1;
1.126 brouard 5315: }
5316: if(first==1){
1.227 brouard 5317: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5318: }
5319: } /* end mi==0 */
5320: } /* End individuals */
1.214 brouard 5321: /* wav and mw are no more changed */
1.223 brouard 5322:
1.214 brouard 5323:
1.126 brouard 5324: for(i=1; i<=imx; i++){
5325: for(mi=1; mi<wav[i];mi++){
5326: if (stepm <=0)
1.227 brouard 5327: dh[mi][i]=1;
1.126 brouard 5328: else{
1.260 brouard 5329: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5330: if (agedc[i] < 2*AGESUP) {
5331: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5332: if(j==0) j=1; /* Survives at least one month after exam */
5333: else if(j<0){
5334: nberr++;
5335: 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]);
5336: j=1; /* Temporary Dangerous patch */
5337: 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);
5338: 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]);
5339: 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);
5340: }
5341: k=k+1;
5342: if (j >= jmax){
5343: jmax=j;
5344: ijmax=i;
5345: }
5346: if (j <= jmin){
5347: jmin=j;
5348: ijmin=i;
5349: }
5350: sum=sum+j;
5351: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5352: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5353: }
5354: }
5355: else{
5356: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5357: /* 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 5358:
1.227 brouard 5359: k=k+1;
5360: if (j >= jmax) {
5361: jmax=j;
5362: ijmax=i;
5363: }
5364: else if (j <= jmin){
5365: jmin=j;
5366: ijmin=i;
5367: }
5368: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5369: /*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]);*/
5370: if(j<0){
5371: nberr++;
5372: 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]);
5373: 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]);
5374: }
5375: sum=sum+j;
5376: }
5377: jk= j/stepm;
5378: jl= j -jk*stepm;
5379: ju= j -(jk+1)*stepm;
5380: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5381: if(jl==0){
5382: dh[mi][i]=jk;
5383: bh[mi][i]=0;
5384: }else{ /* We want a negative bias in order to only have interpolation ie
5385: * to avoid the price of an extra matrix product in likelihood */
5386: dh[mi][i]=jk+1;
5387: bh[mi][i]=ju;
5388: }
5389: }else{
5390: if(jl <= -ju){
5391: dh[mi][i]=jk;
5392: bh[mi][i]=jl; /* bias is positive if real duration
5393: * is higher than the multiple of stepm and negative otherwise.
5394: */
5395: }
5396: else{
5397: dh[mi][i]=jk+1;
5398: bh[mi][i]=ju;
5399: }
5400: if(dh[mi][i]==0){
5401: dh[mi][i]=1; /* At least one step */
5402: bh[mi][i]=ju; /* At least one step */
5403: /* 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);*/
5404: }
5405: } /* end if mle */
1.126 brouard 5406: }
5407: } /* end wave */
5408: }
5409: jmean=sum/k;
5410: 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 5411: 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 5412: }
1.126 brouard 5413:
5414: /*********** Tricode ****************************/
1.220 brouard 5415: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5416: {
5417: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5418: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5419: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5420: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5421: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5422: */
1.130 brouard 5423:
1.242 brouard 5424: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5425: int modmaxcovj=0; /* Modality max of covariates j */
5426: int cptcode=0; /* Modality max of covariates j */
5427: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5428:
5429:
1.242 brouard 5430: /* cptcoveff=0; */
5431: /* *cptcov=0; */
1.126 brouard 5432:
1.242 brouard 5433: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5434: for (k=1; k <= maxncov; k++)
5435: for(j=1; j<=2; j++)
5436: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5437:
1.242 brouard 5438: /* Loop on covariates without age and products and no quantitative variable */
5439: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5440: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5441: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5442: switch(Fixed[k]) {
5443: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5444: 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*/
5445: ij=(int)(covar[Tvar[k]][i]);
5446: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5447: * If product of Vn*Vm, still boolean *:
5448: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5449: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5450: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5451: modality of the nth covariate of individual i. */
5452: if (ij > modmaxcovj)
5453: modmaxcovj=ij;
5454: else if (ij < modmincovj)
5455: modmincovj=ij;
1.287 brouard 5456: if (ij <0 || ij >1 ){
5457: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5458: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5459: }
5460: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5461: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5462: exit(1);
5463: }else
5464: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5465: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5466: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5467: /* getting the maximum value of the modality of the covariate
5468: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5469: female ies 1, then modmaxcovj=1.
5470: */
5471: } /* end for loop on individuals i */
5472: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5473: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5474: cptcode=modmaxcovj;
5475: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5476: /*for (i=0; i<=cptcode; i++) {*/
5477: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5478: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5479: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5480: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5481: if( j != -1){
5482: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5483: covariate for which somebody answered excluding
5484: undefined. Usually 2: 0 and 1. */
5485: }
5486: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5487: covariate for which somebody answered including
5488: undefined. Usually 3: -1, 0 and 1. */
5489: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5490: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5491: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5492:
1.242 brouard 5493: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5494: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5495: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5496: /* modmincovj=3; modmaxcovj = 7; */
5497: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5498: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5499: /* defining two dummy variables: variables V1_1 and V1_2.*/
5500: /* nbcode[Tvar[j]][ij]=k; */
5501: /* nbcode[Tvar[j]][1]=0; */
5502: /* nbcode[Tvar[j]][2]=1; */
5503: /* nbcode[Tvar[j]][3]=2; */
5504: /* To be continued (not working yet). */
5505: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5506:
5507: /* 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*/
5508: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5509: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5510: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5511: /*, could be restored in the future */
5512: 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 5513: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5514: break;
5515: }
5516: ij++;
1.287 brouard 5517: 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 5518: cptcode = ij; /* New max modality for covar j */
5519: } /* end of loop on modality i=-1 to 1 or more */
5520: break;
5521: case 1: /* Testing on varying covariate, could be simple and
5522: * should look at waves or product of fixed *
5523: * varying. No time to test -1, assuming 0 and 1 only */
5524: ij=0;
5525: for(i=0; i<=1;i++){
5526: nbcode[Tvar[k]][++ij]=i;
5527: }
5528: break;
5529: default:
5530: break;
5531: } /* end switch */
5532: } /* end dummy test */
1.287 brouard 5533: } /* 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 5534:
5535: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5536: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5537: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5538: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5539: 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 */
5540: 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 */
5541: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5542: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5543:
5544: ij=0;
5545: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5546: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5547: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5548: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5549: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5550: /* If product not in single variable we don't print results */
5551: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5552: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5553: 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*/
5554: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5555: 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 */
5556: if(Fixed[k]!=0)
5557: anyvaryingduminmodel=1;
5558: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5559: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5560: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5561: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5562: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5563: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5564: }
5565: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5566: /* ij--; */
5567: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5568: *cptcov=ij; /*Number of total real effective covariates: effective
5569: * because they can be excluded from the model and real
5570: * if in the model but excluded because missing values, but how to get k from ij?*/
5571: for(j=ij+1; j<= cptcovt; j++){
5572: Tvaraff[j]=0;
5573: Tmodelind[j]=0;
5574: }
5575: for(j=ntveff+1; j<= cptcovt; j++){
5576: TmodelInvind[j]=0;
5577: }
5578: /* To be sorted */
5579: ;
5580: }
1.126 brouard 5581:
1.145 brouard 5582:
1.126 brouard 5583: /*********** Health Expectancies ****************/
5584:
1.235 brouard 5585: 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 5586:
5587: {
5588: /* Health expectancies, no variances */
1.164 brouard 5589: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5590: int nhstepma, nstepma; /* Decreasing with age */
5591: double age, agelim, hf;
5592: double ***p3mat;
5593: double eip;
5594:
1.238 brouard 5595: /* pstamp(ficreseij); */
1.126 brouard 5596: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5597: fprintf(ficreseij,"# Age");
5598: for(i=1; i<=nlstate;i++){
5599: for(j=1; j<=nlstate;j++){
5600: fprintf(ficreseij," e%1d%1d ",i,j);
5601: }
5602: fprintf(ficreseij," e%1d. ",i);
5603: }
5604: fprintf(ficreseij,"\n");
5605:
5606:
5607: if(estepm < stepm){
5608: printf ("Problem %d lower than %d\n",estepm, stepm);
5609: }
5610: else hstepm=estepm;
5611: /* We compute the life expectancy from trapezoids spaced every estepm months
5612: * This is mainly to measure the difference between two models: for example
5613: * if stepm=24 months pijx are given only every 2 years and by summing them
5614: * we are calculating an estimate of the Life Expectancy assuming a linear
5615: * progression in between and thus overestimating or underestimating according
5616: * to the curvature of the survival function. If, for the same date, we
5617: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5618: * to compare the new estimate of Life expectancy with the same linear
5619: * hypothesis. A more precise result, taking into account a more precise
5620: * curvature will be obtained if estepm is as small as stepm. */
5621:
5622: /* For example we decided to compute the life expectancy with the smallest unit */
5623: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5624: nhstepm is the number of hstepm from age to agelim
5625: nstepm is the number of stepm from age to agelin.
1.270 brouard 5626: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5627: and note for a fixed period like estepm months */
5628: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5629: survival function given by stepm (the optimization length). Unfortunately it
5630: means that if the survival funtion is printed only each two years of age and if
5631: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5632: results. So we changed our mind and took the option of the best precision.
5633: */
5634: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5635:
5636: agelim=AGESUP;
5637: /* If stepm=6 months */
5638: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5639: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5640:
5641: /* nhstepm age range expressed in number of stepm */
5642: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5643: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5644: /* if (stepm >= YEARM) hstepm=1;*/
5645: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5646: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5647:
5648: for (age=bage; age<=fage; age ++){
5649: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5650: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5651: /* if (stepm >= YEARM) hstepm=1;*/
5652: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5653:
5654: /* If stepm=6 months */
5655: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5656: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5657:
1.235 brouard 5658: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5659:
5660: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5661:
5662: printf("%d|",(int)age);fflush(stdout);
5663: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5664:
5665: /* Computing expectancies */
5666: for(i=1; i<=nlstate;i++)
5667: for(j=1; j<=nlstate;j++)
5668: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5669: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5670:
5671: /* 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]);*/
5672:
5673: }
5674:
5675: fprintf(ficreseij,"%3.0f",age );
5676: for(i=1; i<=nlstate;i++){
5677: eip=0;
5678: for(j=1; j<=nlstate;j++){
5679: eip +=eij[i][j][(int)age];
5680: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5681: }
5682: fprintf(ficreseij,"%9.4f", eip );
5683: }
5684: fprintf(ficreseij,"\n");
5685:
5686: }
5687: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5688: printf("\n");
5689: fprintf(ficlog,"\n");
5690:
5691: }
5692:
1.235 brouard 5693: 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 5694:
5695: {
5696: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5697: to initial status i, ei. .
1.126 brouard 5698: */
5699: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5700: int nhstepma, nstepma; /* Decreasing with age */
5701: double age, agelim, hf;
5702: double ***p3matp, ***p3matm, ***varhe;
5703: double **dnewm,**doldm;
5704: double *xp, *xm;
5705: double **gp, **gm;
5706: double ***gradg, ***trgradg;
5707: int theta;
5708:
5709: double eip, vip;
5710:
5711: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5712: xp=vector(1,npar);
5713: xm=vector(1,npar);
5714: dnewm=matrix(1,nlstate*nlstate,1,npar);
5715: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5716:
5717: pstamp(ficresstdeij);
5718: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5719: fprintf(ficresstdeij,"# Age");
5720: for(i=1; i<=nlstate;i++){
5721: for(j=1; j<=nlstate;j++)
5722: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5723: fprintf(ficresstdeij," e%1d. ",i);
5724: }
5725: fprintf(ficresstdeij,"\n");
5726:
5727: pstamp(ficrescveij);
5728: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5729: fprintf(ficrescveij,"# Age");
5730: for(i=1; i<=nlstate;i++)
5731: for(j=1; j<=nlstate;j++){
5732: cptj= (j-1)*nlstate+i;
5733: for(i2=1; i2<=nlstate;i2++)
5734: for(j2=1; j2<=nlstate;j2++){
5735: cptj2= (j2-1)*nlstate+i2;
5736: if(cptj2 <= cptj)
5737: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5738: }
5739: }
5740: fprintf(ficrescveij,"\n");
5741:
5742: if(estepm < stepm){
5743: printf ("Problem %d lower than %d\n",estepm, stepm);
5744: }
5745: else hstepm=estepm;
5746: /* We compute the life expectancy from trapezoids spaced every estepm months
5747: * This is mainly to measure the difference between two models: for example
5748: * if stepm=24 months pijx are given only every 2 years and by summing them
5749: * we are calculating an estimate of the Life Expectancy assuming a linear
5750: * progression in between and thus overestimating or underestimating according
5751: * to the curvature of the survival function. If, for the same date, we
5752: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5753: * to compare the new estimate of Life expectancy with the same linear
5754: * hypothesis. A more precise result, taking into account a more precise
5755: * curvature will be obtained if estepm is as small as stepm. */
5756:
5757: /* For example we decided to compute the life expectancy with the smallest unit */
5758: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5759: nhstepm is the number of hstepm from age to agelim
5760: nstepm is the number of stepm from age to agelin.
5761: Look at hpijx to understand the reason of that which relies in memory size
5762: and note for a fixed period like estepm months */
5763: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5764: survival function given by stepm (the optimization length). Unfortunately it
5765: means that if the survival funtion is printed only each two years of age and if
5766: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5767: results. So we changed our mind and took the option of the best precision.
5768: */
5769: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5770:
5771: /* If stepm=6 months */
5772: /* nhstepm age range expressed in number of stepm */
5773: agelim=AGESUP;
5774: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5775: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5776: /* if (stepm >= YEARM) hstepm=1;*/
5777: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5778:
5779: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5780: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5781: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5782: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5783: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5784: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5785:
5786: for (age=bage; age<=fage; age ++){
5787: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5788: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5789: /* if (stepm >= YEARM) hstepm=1;*/
5790: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5791:
1.126 brouard 5792: /* If stepm=6 months */
5793: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5794: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5795:
5796: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5797:
1.126 brouard 5798: /* Computing Variances of health expectancies */
5799: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5800: decrease memory allocation */
5801: for(theta=1; theta <=npar; theta++){
5802: for(i=1; i<=npar; i++){
1.222 brouard 5803: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5804: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5805: }
1.235 brouard 5806: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5807: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5808:
1.126 brouard 5809: for(j=1; j<= nlstate; j++){
1.222 brouard 5810: for(i=1; i<=nlstate; i++){
5811: for(h=0; h<=nhstepm-1; h++){
5812: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5813: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5814: }
5815: }
1.126 brouard 5816: }
1.218 brouard 5817:
1.126 brouard 5818: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5819: for(h=0; h<=nhstepm-1; h++){
5820: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5821: }
1.126 brouard 5822: }/* End theta */
5823:
5824:
5825: for(h=0; h<=nhstepm-1; h++)
5826: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5827: for(theta=1; theta <=npar; theta++)
5828: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5829:
1.218 brouard 5830:
1.222 brouard 5831: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5832: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5833: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5834:
1.222 brouard 5835: printf("%d|",(int)age);fflush(stdout);
5836: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5837: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5838: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5839: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5840: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5841: for(ij=1;ij<=nlstate*nlstate;ij++)
5842: for(ji=1;ji<=nlstate*nlstate;ji++)
5843: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5844: }
5845: }
1.218 brouard 5846:
1.126 brouard 5847: /* Computing expectancies */
1.235 brouard 5848: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5849: for(i=1; i<=nlstate;i++)
5850: for(j=1; j<=nlstate;j++)
1.222 brouard 5851: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5852: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5853:
1.222 brouard 5854: /* 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 5855:
1.222 brouard 5856: }
1.269 brouard 5857:
5858: /* Standard deviation of expectancies ij */
1.126 brouard 5859: fprintf(ficresstdeij,"%3.0f",age );
5860: for(i=1; i<=nlstate;i++){
5861: eip=0.;
5862: vip=0.;
5863: for(j=1; j<=nlstate;j++){
1.222 brouard 5864: eip += eij[i][j][(int)age];
5865: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5866: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5867: 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 5868: }
5869: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5870: }
5871: fprintf(ficresstdeij,"\n");
1.218 brouard 5872:
1.269 brouard 5873: /* Variance of expectancies ij */
1.126 brouard 5874: fprintf(ficrescveij,"%3.0f",age );
5875: for(i=1; i<=nlstate;i++)
5876: for(j=1; j<=nlstate;j++){
1.222 brouard 5877: cptj= (j-1)*nlstate+i;
5878: for(i2=1; i2<=nlstate;i2++)
5879: for(j2=1; j2<=nlstate;j2++){
5880: cptj2= (j2-1)*nlstate+i2;
5881: if(cptj2 <= cptj)
5882: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5883: }
1.126 brouard 5884: }
5885: fprintf(ficrescveij,"\n");
1.218 brouard 5886:
1.126 brouard 5887: }
5888: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5889: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5890: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5891: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5892: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5893: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5894: printf("\n");
5895: fprintf(ficlog,"\n");
1.218 brouard 5896:
1.126 brouard 5897: free_vector(xm,1,npar);
5898: free_vector(xp,1,npar);
5899: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5900: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5901: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5902: }
1.218 brouard 5903:
1.126 brouard 5904: /************ Variance ******************/
1.235 brouard 5905: 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 5906: {
1.279 brouard 5907: /** Variance of health expectancies
5908: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5909: * double **newm;
5910: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5911: */
1.218 brouard 5912:
5913: /* int movingaverage(); */
5914: double **dnewm,**doldm;
5915: double **dnewmp,**doldmp;
5916: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5917: int first=0;
1.218 brouard 5918: int k;
5919: double *xp;
1.279 brouard 5920: double **gp, **gm; /**< for var eij */
5921: double ***gradg, ***trgradg; /**< for var eij */
5922: double **gradgp, **trgradgp; /**< for var p point j */
5923: double *gpp, *gmp; /**< for var p point j */
5924: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5925: double ***p3mat;
5926: double age,agelim, hf;
5927: /* double ***mobaverage; */
5928: int theta;
5929: char digit[4];
5930: char digitp[25];
5931:
5932: char fileresprobmorprev[FILENAMELENGTH];
5933:
5934: if(popbased==1){
5935: if(mobilav!=0)
5936: strcpy(digitp,"-POPULBASED-MOBILAV_");
5937: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5938: }
5939: else
5940: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5941:
1.218 brouard 5942: /* if (mobilav!=0) { */
5943: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5944: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5945: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5946: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5947: /* } */
5948: /* } */
5949:
5950: strcpy(fileresprobmorprev,"PRMORPREV-");
5951: sprintf(digit,"%-d",ij);
5952: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5953: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5954: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5955: strcat(fileresprobmorprev,fileresu);
5956: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5957: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5958: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5959: }
5960: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5961: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5962: pstamp(ficresprobmorprev);
5963: 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 5964: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5965: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5966: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5967: }
5968: for(j=1;j<=cptcoveff;j++)
5969: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5970: fprintf(ficresprobmorprev,"\n");
5971:
1.218 brouard 5972: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5973: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5974: fprintf(ficresprobmorprev," p.%-d SE",j);
5975: for(i=1; i<=nlstate;i++)
5976: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5977: }
5978: fprintf(ficresprobmorprev,"\n");
5979:
5980: fprintf(ficgp,"\n# Routine varevsij");
5981: fprintf(ficgp,"\nunset title \n");
5982: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5983: 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");
5984: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 5985:
1.218 brouard 5986: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5987: pstamp(ficresvij);
5988: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5989: if(popbased==1)
5990: 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);
5991: else
5992: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5993: fprintf(ficresvij,"# Age");
5994: for(i=1; i<=nlstate;i++)
5995: for(j=1; j<=nlstate;j++)
5996: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5997: fprintf(ficresvij,"\n");
5998:
5999: xp=vector(1,npar);
6000: dnewm=matrix(1,nlstate,1,npar);
6001: doldm=matrix(1,nlstate,1,nlstate);
6002: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6003: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6004:
6005: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6006: gpp=vector(nlstate+1,nlstate+ndeath);
6007: gmp=vector(nlstate+1,nlstate+ndeath);
6008: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6009:
1.218 brouard 6010: if(estepm < stepm){
6011: printf ("Problem %d lower than %d\n",estepm, stepm);
6012: }
6013: else hstepm=estepm;
6014: /* For example we decided to compute the life expectancy with the smallest unit */
6015: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6016: nhstepm is the number of hstepm from age to agelim
6017: nstepm is the number of stepm from age to agelim.
6018: Look at function hpijx to understand why because of memory size limitations,
6019: we decided (b) to get a life expectancy respecting the most precise curvature of the
6020: survival function given by stepm (the optimization length). Unfortunately it
6021: means that if the survival funtion is printed every two years of age and if
6022: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6023: results. So we changed our mind and took the option of the best precision.
6024: */
6025: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6026: agelim = AGESUP;
6027: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6028: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6029: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6030: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6031: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6032: gp=matrix(0,nhstepm,1,nlstate);
6033: gm=matrix(0,nhstepm,1,nlstate);
6034:
6035:
6036: for(theta=1; theta <=npar; theta++){
6037: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6038: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6039: }
1.279 brouard 6040: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6041: * returns into prlim .
1.288 brouard 6042: */
1.242 brouard 6043: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6044:
6045: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6046: if (popbased==1) {
6047: if(mobilav ==0){
6048: for(i=1; i<=nlstate;i++)
6049: prlim[i][i]=probs[(int)age][i][ij];
6050: }else{ /* mobilav */
6051: for(i=1; i<=nlstate;i++)
6052: prlim[i][i]=mobaverage[(int)age][i][ij];
6053: }
6054: }
1.295 brouard 6055: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6056: */
6057: 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 6058: /**< 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 6059: * at horizon h in state j including mortality.
6060: */
1.218 brouard 6061: for(j=1; j<= nlstate; j++){
6062: for(h=0; h<=nhstepm; h++){
6063: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6064: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6065: }
6066: }
1.279 brouard 6067: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6068: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6069: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6070: */
6071: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6072: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6073: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6074: }
6075:
6076: /* Again with minus shift */
1.218 brouard 6077:
6078: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6079: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6080:
1.242 brouard 6081: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6082:
6083: if (popbased==1) {
6084: if(mobilav ==0){
6085: for(i=1; i<=nlstate;i++)
6086: prlim[i][i]=probs[(int)age][i][ij];
6087: }else{ /* mobilav */
6088: for(i=1; i<=nlstate;i++)
6089: prlim[i][i]=mobaverage[(int)age][i][ij];
6090: }
6091: }
6092:
1.235 brouard 6093: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6094:
6095: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6096: for(h=0; h<=nhstepm; h++){
6097: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6098: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6099: }
6100: }
6101: /* This for computing probability of death (h=1 means
6102: computed over hstepm matrices product = hstepm*stepm months)
6103: as a weighted average of prlim.
6104: */
6105: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6106: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6107: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6108: }
1.279 brouard 6109: /* end shifting computations */
6110:
6111: /**< Computing gradient matrix at horizon h
6112: */
1.218 brouard 6113: for(j=1; j<= nlstate; j++) /* vareij */
6114: for(h=0; h<=nhstepm; h++){
6115: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6116: }
1.279 brouard 6117: /**< Gradient of overall mortality p.3 (or p.j)
6118: */
6119: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6120: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6121: }
6122:
6123: } /* End theta */
1.279 brouard 6124:
6125: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6126: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6127:
6128: for(h=0; h<=nhstepm; h++) /* veij */
6129: for(j=1; j<=nlstate;j++)
6130: for(theta=1; theta <=npar; theta++)
6131: trgradg[h][j][theta]=gradg[h][theta][j];
6132:
6133: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6134: for(theta=1; theta <=npar; theta++)
6135: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6136: /**< as well as its transposed matrix
6137: */
1.218 brouard 6138:
6139: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6140: for(i=1;i<=nlstate;i++)
6141: for(j=1;j<=nlstate;j++)
6142: vareij[i][j][(int)age] =0.;
1.279 brouard 6143:
6144: /* Computing trgradg by matcov by gradg at age and summing over h
6145: * and k (nhstepm) formula 15 of article
6146: * Lievre-Brouard-Heathcote
6147: */
6148:
1.218 brouard 6149: for(h=0;h<=nhstepm;h++){
6150: for(k=0;k<=nhstepm;k++){
6151: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6152: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6153: for(i=1;i<=nlstate;i++)
6154: for(j=1;j<=nlstate;j++)
6155: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6156: }
6157: }
6158:
1.279 brouard 6159: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6160: * p.j overall mortality formula 49 but computed directly because
6161: * we compute the grad (wix pijx) instead of grad (pijx),even if
6162: * wix is independent of theta.
6163: */
1.218 brouard 6164: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6165: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6166: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6167: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6168: varppt[j][i]=doldmp[j][i];
6169: /* end ppptj */
6170: /* x centered again */
6171:
1.242 brouard 6172: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6173:
6174: if (popbased==1) {
6175: if(mobilav ==0){
6176: for(i=1; i<=nlstate;i++)
6177: prlim[i][i]=probs[(int)age][i][ij];
6178: }else{ /* mobilav */
6179: for(i=1; i<=nlstate;i++)
6180: prlim[i][i]=mobaverage[(int)age][i][ij];
6181: }
6182: }
6183:
6184: /* This for computing probability of death (h=1 means
6185: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6186: as a weighted average of prlim.
6187: */
1.235 brouard 6188: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6189: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6190: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6191: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6192: }
6193: /* end probability of death */
6194:
6195: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6196: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6197: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6198: for(i=1; i<=nlstate;i++){
6199: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6200: }
6201: }
6202: fprintf(ficresprobmorprev,"\n");
6203:
6204: fprintf(ficresvij,"%.0f ",age );
6205: for(i=1; i<=nlstate;i++)
6206: for(j=1; j<=nlstate;j++){
6207: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6208: }
6209: fprintf(ficresvij,"\n");
6210: free_matrix(gp,0,nhstepm,1,nlstate);
6211: free_matrix(gm,0,nhstepm,1,nlstate);
6212: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6213: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6214: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6215: } /* End age */
6216: free_vector(gpp,nlstate+1,nlstate+ndeath);
6217: free_vector(gmp,nlstate+1,nlstate+ndeath);
6218: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6219: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6220: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6221: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6222: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6223: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6224: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6225: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6226: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6227: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6228: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6229: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6230: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6231: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6232: 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);
6233: /* 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 6234: */
1.218 brouard 6235: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6236: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6237:
1.218 brouard 6238: free_vector(xp,1,npar);
6239: free_matrix(doldm,1,nlstate,1,nlstate);
6240: free_matrix(dnewm,1,nlstate,1,npar);
6241: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6242: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6243: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6244: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6245: fclose(ficresprobmorprev);
6246: fflush(ficgp);
6247: fflush(fichtm);
6248: } /* end varevsij */
1.126 brouard 6249:
6250: /************ Variance of prevlim ******************/
1.269 brouard 6251: 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 6252: {
1.205 brouard 6253: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6254: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6255:
1.268 brouard 6256: double **dnewmpar,**doldm;
1.126 brouard 6257: int i, j, nhstepm, hstepm;
6258: double *xp;
6259: double *gp, *gm;
6260: double **gradg, **trgradg;
1.208 brouard 6261: double **mgm, **mgp;
1.126 brouard 6262: double age,agelim;
6263: int theta;
6264:
6265: pstamp(ficresvpl);
1.288 brouard 6266: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6267: fprintf(ficresvpl,"# Age ");
6268: if(nresult >=1)
6269: fprintf(ficresvpl," Result# ");
1.126 brouard 6270: for(i=1; i<=nlstate;i++)
6271: fprintf(ficresvpl," %1d-%1d",i,i);
6272: fprintf(ficresvpl,"\n");
6273:
6274: xp=vector(1,npar);
1.268 brouard 6275: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6276: doldm=matrix(1,nlstate,1,nlstate);
6277:
6278: hstepm=1*YEARM; /* Every year of age */
6279: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6280: agelim = AGESUP;
6281: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6282: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6283: if (stepm >= YEARM) hstepm=1;
6284: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6285: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6286: mgp=matrix(1,npar,1,nlstate);
6287: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6288: gp=vector(1,nlstate);
6289: gm=vector(1,nlstate);
6290:
6291: for(theta=1; theta <=npar; theta++){
6292: for(i=1; i<=npar; i++){ /* Computes gradient */
6293: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6294: }
1.288 brouard 6295: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6296: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6297: /* else */
6298: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6299: for(i=1;i<=nlstate;i++){
1.126 brouard 6300: gp[i] = prlim[i][i];
1.208 brouard 6301: mgp[theta][i] = prlim[i][i];
6302: }
1.126 brouard 6303: for(i=1; i<=npar; i++) /* Computes gradient */
6304: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6305: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6306: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6307: /* else */
6308: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6309: for(i=1;i<=nlstate;i++){
1.126 brouard 6310: gm[i] = prlim[i][i];
1.208 brouard 6311: mgm[theta][i] = prlim[i][i];
6312: }
1.126 brouard 6313: for(i=1;i<=nlstate;i++)
6314: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6315: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6316: } /* End theta */
6317:
6318: trgradg =matrix(1,nlstate,1,npar);
6319:
6320: for(j=1; j<=nlstate;j++)
6321: for(theta=1; theta <=npar; theta++)
6322: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6323: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6324: /* printf("\nmgm mgp %d ",(int)age); */
6325: /* for(j=1; j<=nlstate;j++){ */
6326: /* printf(" %d ",j); */
6327: /* for(theta=1; theta <=npar; theta++) */
6328: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6329: /* printf("\n "); */
6330: /* } */
6331: /* } */
6332: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6333: /* printf("\n gradg %d ",(int)age); */
6334: /* for(j=1; j<=nlstate;j++){ */
6335: /* printf("%d ",j); */
6336: /* for(theta=1; theta <=npar; theta++) */
6337: /* printf("%d %lf ",theta,gradg[theta][j]); */
6338: /* printf("\n "); */
6339: /* } */
6340: /* } */
1.126 brouard 6341:
6342: for(i=1;i<=nlstate;i++)
6343: varpl[i][(int)age] =0.;
1.209 brouard 6344: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6345: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6346: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6347: }else{
1.268 brouard 6348: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6349: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6350: }
1.126 brouard 6351: for(i=1;i<=nlstate;i++)
6352: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6353:
6354: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6355: if(nresult >=1)
6356: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6357: for(i=1; i<=nlstate;i++){
1.126 brouard 6358: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6359: /* for(j=1;j<=nlstate;j++) */
6360: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6361: }
1.126 brouard 6362: fprintf(ficresvpl,"\n");
6363: free_vector(gp,1,nlstate);
6364: free_vector(gm,1,nlstate);
1.208 brouard 6365: free_matrix(mgm,1,npar,1,nlstate);
6366: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6367: free_matrix(gradg,1,npar,1,nlstate);
6368: free_matrix(trgradg,1,nlstate,1,npar);
6369: } /* End age */
6370:
6371: free_vector(xp,1,npar);
6372: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6373: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6374:
6375: }
6376:
6377:
6378: /************ Variance of backprevalence limit ******************/
1.269 brouard 6379: 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 6380: {
6381: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6382: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6383:
6384: double **dnewmpar,**doldm;
6385: int i, j, nhstepm, hstepm;
6386: double *xp;
6387: double *gp, *gm;
6388: double **gradg, **trgradg;
6389: double **mgm, **mgp;
6390: double age,agelim;
6391: int theta;
6392:
6393: pstamp(ficresvbl);
6394: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6395: fprintf(ficresvbl,"# Age ");
6396: if(nresult >=1)
6397: fprintf(ficresvbl," Result# ");
6398: for(i=1; i<=nlstate;i++)
6399: fprintf(ficresvbl," %1d-%1d",i,i);
6400: fprintf(ficresvbl,"\n");
6401:
6402: xp=vector(1,npar);
6403: dnewmpar=matrix(1,nlstate,1,npar);
6404: doldm=matrix(1,nlstate,1,nlstate);
6405:
6406: hstepm=1*YEARM; /* Every year of age */
6407: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6408: agelim = AGEINF;
6409: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6410: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6411: if (stepm >= YEARM) hstepm=1;
6412: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6413: gradg=matrix(1,npar,1,nlstate);
6414: mgp=matrix(1,npar,1,nlstate);
6415: mgm=matrix(1,npar,1,nlstate);
6416: gp=vector(1,nlstate);
6417: gm=vector(1,nlstate);
6418:
6419: for(theta=1; theta <=npar; theta++){
6420: for(i=1; i<=npar; i++){ /* Computes gradient */
6421: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6422: }
6423: if(mobilavproj > 0 )
6424: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6425: else
6426: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6427: for(i=1;i<=nlstate;i++){
6428: gp[i] = bprlim[i][i];
6429: mgp[theta][i] = bprlim[i][i];
6430: }
6431: for(i=1; i<=npar; i++) /* Computes gradient */
6432: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6433: if(mobilavproj > 0 )
6434: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6435: else
6436: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6437: for(i=1;i<=nlstate;i++){
6438: gm[i] = bprlim[i][i];
6439: mgm[theta][i] = bprlim[i][i];
6440: }
6441: for(i=1;i<=nlstate;i++)
6442: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6443: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6444: } /* End theta */
6445:
6446: trgradg =matrix(1,nlstate,1,npar);
6447:
6448: for(j=1; j<=nlstate;j++)
6449: for(theta=1; theta <=npar; theta++)
6450: trgradg[j][theta]=gradg[theta][j];
6451: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6452: /* printf("\nmgm mgp %d ",(int)age); */
6453: /* for(j=1; j<=nlstate;j++){ */
6454: /* printf(" %d ",j); */
6455: /* for(theta=1; theta <=npar; theta++) */
6456: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6457: /* printf("\n "); */
6458: /* } */
6459: /* } */
6460: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6461: /* printf("\n gradg %d ",(int)age); */
6462: /* for(j=1; j<=nlstate;j++){ */
6463: /* printf("%d ",j); */
6464: /* for(theta=1; theta <=npar; theta++) */
6465: /* printf("%d %lf ",theta,gradg[theta][j]); */
6466: /* printf("\n "); */
6467: /* } */
6468: /* } */
6469:
6470: for(i=1;i<=nlstate;i++)
6471: varbpl[i][(int)age] =0.;
6472: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6473: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6474: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6475: }else{
6476: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6477: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6478: }
6479: for(i=1;i<=nlstate;i++)
6480: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6481:
6482: fprintf(ficresvbl,"%.0f ",age );
6483: if(nresult >=1)
6484: fprintf(ficresvbl,"%d ",nres );
6485: for(i=1; i<=nlstate;i++)
6486: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6487: fprintf(ficresvbl,"\n");
6488: free_vector(gp,1,nlstate);
6489: free_vector(gm,1,nlstate);
6490: free_matrix(mgm,1,npar,1,nlstate);
6491: free_matrix(mgp,1,npar,1,nlstate);
6492: free_matrix(gradg,1,npar,1,nlstate);
6493: free_matrix(trgradg,1,nlstate,1,npar);
6494: } /* End age */
6495:
6496: free_vector(xp,1,npar);
6497: free_matrix(doldm,1,nlstate,1,npar);
6498: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6499:
6500: }
6501:
6502: /************ Variance of one-step probabilities ******************/
6503: 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 6504: {
6505: int i, j=0, k1, l1, tj;
6506: int k2, l2, j1, z1;
6507: int k=0, l;
6508: int first=1, first1, first2;
6509: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6510: double **dnewm,**doldm;
6511: double *xp;
6512: double *gp, *gm;
6513: double **gradg, **trgradg;
6514: double **mu;
6515: double age, cov[NCOVMAX+1];
6516: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6517: int theta;
6518: char fileresprob[FILENAMELENGTH];
6519: char fileresprobcov[FILENAMELENGTH];
6520: char fileresprobcor[FILENAMELENGTH];
6521: double ***varpij;
6522:
6523: strcpy(fileresprob,"PROB_");
6524: strcat(fileresprob,fileres);
6525: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6526: printf("Problem with resultfile: %s\n", fileresprob);
6527: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6528: }
6529: strcpy(fileresprobcov,"PROBCOV_");
6530: strcat(fileresprobcov,fileresu);
6531: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6532: printf("Problem with resultfile: %s\n", fileresprobcov);
6533: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6534: }
6535: strcpy(fileresprobcor,"PROBCOR_");
6536: strcat(fileresprobcor,fileresu);
6537: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6538: printf("Problem with resultfile: %s\n", fileresprobcor);
6539: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6540: }
6541: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6542: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6543: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6544: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6545: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6546: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6547: pstamp(ficresprob);
6548: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6549: fprintf(ficresprob,"# Age");
6550: pstamp(ficresprobcov);
6551: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6552: fprintf(ficresprobcov,"# Age");
6553: pstamp(ficresprobcor);
6554: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6555: fprintf(ficresprobcor,"# Age");
1.126 brouard 6556:
6557:
1.222 brouard 6558: for(i=1; i<=nlstate;i++)
6559: for(j=1; j<=(nlstate+ndeath);j++){
6560: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6561: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6562: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6563: }
6564: /* fprintf(ficresprob,"\n");
6565: fprintf(ficresprobcov,"\n");
6566: fprintf(ficresprobcor,"\n");
6567: */
6568: xp=vector(1,npar);
6569: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6570: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6571: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6572: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6573: first=1;
6574: fprintf(ficgp,"\n# Routine varprob");
6575: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6576: fprintf(fichtm,"\n");
6577:
1.288 brouard 6578: 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 6579: 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);
6580: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6581: and drawn. It helps understanding how is the covariance between two incidences.\
6582: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6583: 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 6584: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6585: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6586: standard deviations wide on each axis. <br>\
6587: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6588: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6589: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6590:
1.222 brouard 6591: cov[1]=1;
6592: /* tj=cptcoveff; */
1.225 brouard 6593: tj = (int) pow(2,cptcoveff);
1.222 brouard 6594: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6595: j1=0;
1.224 brouard 6596: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6597: if (cptcovn>0) {
6598: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6599: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6600: fprintf(ficresprob, "**********\n#\n");
6601: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6602: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6603: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6604:
1.222 brouard 6605: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6606: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6607: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6608:
6609:
1.222 brouard 6610: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6611: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6612: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6613:
1.222 brouard 6614: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6615: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6616: fprintf(ficresprobcor, "**********\n#");
6617: if(invalidvarcomb[j1]){
6618: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6619: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6620: continue;
6621: }
6622: }
6623: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6624: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6625: gp=vector(1,(nlstate)*(nlstate+ndeath));
6626: gm=vector(1,(nlstate)*(nlstate+ndeath));
6627: for (age=bage; age<=fage; age ++){
6628: cov[2]=age;
6629: if(nagesqr==1)
6630: cov[3]= age*age;
6631: for (k=1; k<=cptcovn;k++) {
6632: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6633: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6634: * 1 1 1 1 1
6635: * 2 2 1 1 1
6636: * 3 1 2 1 1
6637: */
6638: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6639: }
6640: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6641: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6642: for (k=1; k<=cptcovprod;k++)
6643: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6644:
6645:
1.222 brouard 6646: for(theta=1; theta <=npar; theta++){
6647: for(i=1; i<=npar; i++)
6648: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6649:
1.222 brouard 6650: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6651:
1.222 brouard 6652: k=0;
6653: for(i=1; i<= (nlstate); i++){
6654: for(j=1; j<=(nlstate+ndeath);j++){
6655: k=k+1;
6656: gp[k]=pmmij[i][j];
6657: }
6658: }
1.220 brouard 6659:
1.222 brouard 6660: for(i=1; i<=npar; i++)
6661: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6662:
1.222 brouard 6663: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6664: k=0;
6665: for(i=1; i<=(nlstate); i++){
6666: for(j=1; j<=(nlstate+ndeath);j++){
6667: k=k+1;
6668: gm[k]=pmmij[i][j];
6669: }
6670: }
1.220 brouard 6671:
1.222 brouard 6672: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6673: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6674: }
1.126 brouard 6675:
1.222 brouard 6676: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6677: for(theta=1; theta <=npar; theta++)
6678: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6679:
1.222 brouard 6680: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6681: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6682:
1.222 brouard 6683: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6684:
1.222 brouard 6685: k=0;
6686: for(i=1; i<=(nlstate); i++){
6687: for(j=1; j<=(nlstate+ndeath);j++){
6688: k=k+1;
6689: mu[k][(int) age]=pmmij[i][j];
6690: }
6691: }
6692: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6693: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6694: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6695:
1.222 brouard 6696: /*printf("\n%d ",(int)age);
6697: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6698: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6699: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6700: }*/
1.220 brouard 6701:
1.222 brouard 6702: fprintf(ficresprob,"\n%d ",(int)age);
6703: fprintf(ficresprobcov,"\n%d ",(int)age);
6704: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6705:
1.222 brouard 6706: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6707: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6708: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6709: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6710: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6711: }
6712: i=0;
6713: for (k=1; k<=(nlstate);k++){
6714: for (l=1; l<=(nlstate+ndeath);l++){
6715: i++;
6716: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6717: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6718: for (j=1; j<=i;j++){
6719: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6720: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6721: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6722: }
6723: }
6724: }/* end of loop for state */
6725: } /* end of loop for age */
6726: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6727: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6728: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6729: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6730:
6731: /* Confidence intervalle of pij */
6732: /*
6733: fprintf(ficgp,"\nunset parametric;unset label");
6734: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6735: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6736: 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);
6737: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6738: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6739: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6740: */
6741:
6742: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6743: first1=1;first2=2;
6744: for (k2=1; k2<=(nlstate);k2++){
6745: for (l2=1; l2<=(nlstate+ndeath);l2++){
6746: if(l2==k2) continue;
6747: j=(k2-1)*(nlstate+ndeath)+l2;
6748: for (k1=1; k1<=(nlstate);k1++){
6749: for (l1=1; l1<=(nlstate+ndeath);l1++){
6750: if(l1==k1) continue;
6751: i=(k1-1)*(nlstate+ndeath)+l1;
6752: if(i<=j) continue;
6753: for (age=bage; age<=fage; age ++){
6754: if ((int)age %5==0){
6755: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6756: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6757: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6758: mu1=mu[i][(int) age]/stepm*YEARM ;
6759: mu2=mu[j][(int) age]/stepm*YEARM;
6760: c12=cv12/sqrt(v1*v2);
6761: /* Computing eigen value of matrix of covariance */
6762: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6763: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6764: if ((lc2 <0) || (lc1 <0) ){
6765: if(first2==1){
6766: first1=0;
6767: 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);
6768: }
6769: 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);
6770: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6771: /* lc2=fabs(lc2); */
6772: }
1.220 brouard 6773:
1.222 brouard 6774: /* Eigen vectors */
1.280 brouard 6775: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6776: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6777: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6778: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6779: }else
6780: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6781: /*v21=sqrt(1.-v11*v11); *//* error */
6782: v21=(lc1-v1)/cv12*v11;
6783: v12=-v21;
6784: v22=v11;
6785: tnalp=v21/v11;
6786: if(first1==1){
6787: first1=0;
6788: 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);
6789: }
6790: 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);
6791: /*printf(fignu*/
6792: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6793: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6794: if(first==1){
6795: first=0;
6796: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6797: fprintf(ficgp,"\nset parametric;unset label");
6798: 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);
6799: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6800: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6801: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6802: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6803: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6804: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6805: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6806: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6807: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6808: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6809: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6810: 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 6811: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6812: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6813: }else{
6814: first=0;
6815: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6816: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6817: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6818: 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 6819: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6820: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6821: }/* if first */
6822: } /* age mod 5 */
6823: } /* end loop age */
6824: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6825: first=1;
6826: } /*l12 */
6827: } /* k12 */
6828: } /*l1 */
6829: }/* k1 */
6830: } /* loop on combination of covariates j1 */
6831: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6832: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6833: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6834: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6835: free_vector(xp,1,npar);
6836: fclose(ficresprob);
6837: fclose(ficresprobcov);
6838: fclose(ficresprobcor);
6839: fflush(ficgp);
6840: fflush(fichtmcov);
6841: }
1.126 brouard 6842:
6843:
6844: /******************* Printing html file ***********/
1.201 brouard 6845: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6846: int lastpass, int stepm, int weightopt, char model[],\
6847: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6848: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6849: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6850: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6851: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6852:
6853: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6854: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6855: </ul>");
1.237 brouard 6856: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6857: </ul>", model);
1.214 brouard 6858: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6859: 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",
6860: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6861: 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 6862: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6863: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6864: fprintf(fichtm,"\
6865: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6866: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6867: fprintf(fichtm,"\
1.217 brouard 6868: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6869: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6870: fprintf(fichtm,"\
1.288 brouard 6871: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6872: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6873: fprintf(fichtm,"\
1.288 brouard 6874: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6875: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6876: fprintf(fichtm,"\
1.211 brouard 6877: - (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 6878: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6879: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6880: if(prevfcast==1){
6881: fprintf(fichtm,"\
6882: - Prevalence projections by age and states: \
1.201 brouard 6883: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6884: }
1.126 brouard 6885:
6886:
1.225 brouard 6887: m=pow(2,cptcoveff);
1.222 brouard 6888: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6889:
1.264 brouard 6890: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6891:
6892: jj1=0;
6893:
6894: fprintf(fichtm," \n<ul>");
6895: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6896: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6897: if(m != 1 && TKresult[nres]!= k1)
6898: continue;
6899: jj1++;
6900: if (cptcovn > 0) {
6901: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6902: for (cpt=1; cpt<=cptcoveff;cpt++){
6903: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6904: }
6905: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6906: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6907: }
6908: fprintf(fichtm,"\">");
6909:
6910: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6911: fprintf(fichtm,"************ Results for covariates");
6912: for (cpt=1; cpt<=cptcoveff;cpt++){
6913: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6914: }
6915: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6916: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6917: }
6918: if(invalidvarcomb[k1]){
6919: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6920: continue;
6921: }
6922: fprintf(fichtm,"</a></li>");
6923: } /* cptcovn >0 */
6924: }
6925: fprintf(fichtm," \n</ul>");
6926:
1.222 brouard 6927: jj1=0;
1.237 brouard 6928:
6929: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6930: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6931: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6932: continue;
1.220 brouard 6933:
1.222 brouard 6934: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6935: jj1++;
6936: if (cptcovn > 0) {
1.264 brouard 6937: fprintf(fichtm,"\n<p><a name=\"rescov");
6938: for (cpt=1; cpt<=cptcoveff;cpt++){
6939: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6940: }
6941: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6942: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6943: }
6944: fprintf(fichtm,"\"</a>");
6945:
1.222 brouard 6946: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6947: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6948: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6949: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6950: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6951: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6952: }
1.237 brouard 6953: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6954: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6955: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6956: }
6957:
1.230 brouard 6958: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6959: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6960: if(invalidvarcomb[k1]){
6961: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6962: printf("\nCombination (%d) ignored because no cases \n",k1);
6963: continue;
6964: }
6965: }
6966: /* aij, bij */
1.259 brouard 6967: 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 6968: <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 6969: /* Pij */
1.241 brouard 6970: 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> \
6971: <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 6972: /* Quasi-incidences */
6973: 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 6974: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6975: 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 6976: 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> \
6977: <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 6978: /* Survival functions (period) in state j */
6979: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 6980: 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 6981: <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 6982: }
6983: /* State specific survival functions (period) */
6984: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 6985: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
6986: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 6987: <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 6988: }
1.288 brouard 6989: /* Period (forward stable) prevalence in each health state */
1.222 brouard 6990: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6991: 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> \
6992: <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 6993: }
1.296 brouard 6994: if(prevbcast==1){
1.288 brouard 6995: /* Backward prevalence in each health state */
1.222 brouard 6996: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6997: 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 6998: <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 6999: }
1.217 brouard 7000: }
1.222 brouard 7001: if(prevfcast==1){
1.288 brouard 7002: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7003: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7004: 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 7005: <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 7006: }
7007: }
1.296 brouard 7008: if(prevbcast==1){
1.268 brouard 7009: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7010: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7011: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7012: 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 \
7013: 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) \
7014: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7015: <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 7016: }
7017: }
1.220 brouard 7018:
1.222 brouard 7019: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7020: 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> \
7021: <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 7022: }
7023: /* } /\* end i1 *\/ */
7024: }/* End k1 */
7025: fprintf(fichtm,"</ul>");
1.126 brouard 7026:
1.222 brouard 7027: fprintf(fichtm,"\
1.126 brouard 7028: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7029: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7030: - 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 7031: But because parameters are usually highly correlated (a higher incidence of disability \
7032: and a higher incidence of recovery can give very close observed transition) it might \
7033: be very useful to look not only at linear confidence intervals estimated from the \
7034: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7035: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7036: covariance matrix of the one-step probabilities. \
7037: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7038:
1.222 brouard 7039: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7040: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7041: fprintf(fichtm,"\
1.126 brouard 7042: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7043: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7044:
1.222 brouard 7045: fprintf(fichtm,"\
1.126 brouard 7046: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7047: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7048: fprintf(fichtm,"\
1.126 brouard 7049: - 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): \
7050: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7051: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7052: fprintf(fichtm,"\
1.126 brouard 7053: - (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): \
7054: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7055: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7056: fprintf(fichtm,"\
1.288 brouard 7057: - 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 7058: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7059: fprintf(fichtm,"\
1.128 brouard 7060: - 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 7061: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7062: fprintf(fichtm,"\
1.288 brouard 7063: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7064: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7065:
7066: /* if(popforecast==1) fprintf(fichtm,"\n */
7067: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7068: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7069: /* <br>",fileres,fileres,fileres,fileres); */
7070: /* else */
7071: /* 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 7072: fflush(fichtm);
7073: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7074:
1.225 brouard 7075: m=pow(2,cptcoveff);
1.222 brouard 7076: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7077:
1.222 brouard 7078: jj1=0;
1.237 brouard 7079:
1.241 brouard 7080: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7081: for(k1=1; k1<=m;k1++){
1.253 brouard 7082: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7083: continue;
1.222 brouard 7084: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7085: jj1++;
1.126 brouard 7086: if (cptcovn > 0) {
7087: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7088: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7089: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7090: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7091: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7092: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7093: }
7094:
1.126 brouard 7095: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7096:
1.222 brouard 7097: if(invalidvarcomb[k1]){
7098: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7099: continue;
7100: }
1.126 brouard 7101: }
7102: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7103: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7104: 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 7105: <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 7106: }
7107: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7108: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7109: true period expectancies (those weighted with period prevalences are also\
7110: drawn in addition to the population based expectancies computed using\
1.241 brouard 7111: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7112: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7113: /* } /\* end i1 *\/ */
7114: }/* End k1 */
1.241 brouard 7115: }/* End nres */
1.222 brouard 7116: fprintf(fichtm,"</ul>");
7117: fflush(fichtm);
1.126 brouard 7118: }
7119:
7120: /******************* Gnuplot file **************/
1.296 brouard 7121: 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 7122:
7123: char dirfileres[132],optfileres[132];
1.264 brouard 7124: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7125: 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 7126: int lv=0, vlv=0, kl=0;
1.130 brouard 7127: int ng=0;
1.201 brouard 7128: int vpopbased;
1.223 brouard 7129: int ioffset; /* variable offset for columns */
1.270 brouard 7130: int iyearc=1; /* variable column for year of projection */
7131: int iagec=1; /* variable column for age of projection */
1.235 brouard 7132: int nres=0; /* Index of resultline */
1.266 brouard 7133: int istart=1; /* For starting graphs in projections */
1.219 brouard 7134:
1.126 brouard 7135: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7136: /* printf("Problem with file %s",optionfilegnuplot); */
7137: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7138: /* } */
7139:
7140: /*#ifdef windows */
7141: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7142: /*#endif */
1.225 brouard 7143: m=pow(2,cptcoveff);
1.126 brouard 7144:
1.274 brouard 7145: /* diagram of the model */
7146: fprintf(ficgp,"\n#Diagram of the model \n");
7147: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7148: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7149: 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);
7150:
7151: 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);
7152: fprintf(ficgp,"\n#show arrow\nunset label\n");
7153: 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);
7154: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7155: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7156: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7157: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7158:
1.202 brouard 7159: /* Contribution to likelihood */
7160: /* Plot the probability implied in the likelihood */
1.223 brouard 7161: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7162: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7163: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7164: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7165: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7166: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7167: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7168: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7169: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7170: 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));
7171: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7172: 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));
7173: for (i=1; i<= nlstate ; i ++) {
7174: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7175: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7176: 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);
7177: for (j=2; j<= nlstate+ndeath ; j ++) {
7178: 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);
7179: }
7180: fprintf(ficgp,";\nset out; unset ylabel;\n");
7181: }
7182: /* 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 */
7183: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7184: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7185: fprintf(ficgp,"\nset out;unset log\n");
7186: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7187:
1.126 brouard 7188: strcpy(dirfileres,optionfilefiname);
7189: strcpy(optfileres,"vpl");
1.223 brouard 7190: /* 1eme*/
1.238 brouard 7191: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7192: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7193: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7194: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7195: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7196: continue;
7197: /* We are interested in selected combination by the resultline */
1.246 brouard 7198: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7199: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7200: strcpy(gplotlabel,"(");
1.238 brouard 7201: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7202: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7203: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7204: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7205: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7206: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7207: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7208: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7209: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7210: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7211: }
7212: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7213: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7214: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7215: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7216: }
7217: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7218: /* printf("\n#\n"); */
1.238 brouard 7219: fprintf(ficgp,"\n#\n");
7220: if(invalidvarcomb[k1]){
1.260 brouard 7221: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7222: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7223: continue;
7224: }
1.235 brouard 7225:
1.241 brouard 7226: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7227: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7228: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7229: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7230: 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);
7231: /* 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); */
7232: /* k1-1 error should be nres-1*/
1.238 brouard 7233: for (i=1; i<= nlstate ; i ++) {
7234: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7235: else fprintf(ficgp," %%*lf (%%*lf)");
7236: }
1.288 brouard 7237: 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 7238: for (i=1; i<= nlstate ; i ++) {
7239: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7240: else fprintf(ficgp," %%*lf (%%*lf)");
7241: }
1.260 brouard 7242: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7243: for (i=1; i<= nlstate ; i ++) {
7244: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7245: else fprintf(ficgp," %%*lf (%%*lf)");
7246: }
1.265 brouard 7247: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7248:
7249: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7250: if(cptcoveff ==0){
1.271 brouard 7251: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7252: }else{
7253: kl=0;
7254: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7255: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7256: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7257: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7258: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7259: vlv= nbcode[Tvaraff[k]][lv];
7260: kl++;
7261: /* 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 *\/ */
7262: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7263: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7264: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7265: if(k==cptcoveff){
7266: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7267: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7268: }else{
7269: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7270: kl++;
7271: }
7272: } /* end covariate */
7273: } /* end if no covariate */
7274:
1.296 brouard 7275: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7276: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7277: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7278: if(cptcoveff ==0){
1.245 brouard 7279: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7280: }else{
7281: kl=0;
7282: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7283: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7284: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7285: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7286: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7287: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7288: kl++;
1.238 brouard 7289: /* 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 *\/ */
7290: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7291: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7292: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7293: if(k==cptcoveff){
1.245 brouard 7294: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7295: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7296: }else{
7297: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7298: kl++;
7299: }
7300: } /* end covariate */
7301: } /* end if no covariate */
1.296 brouard 7302: if(prevbcast == 1){
1.268 brouard 7303: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7304: /* k1-1 error should be nres-1*/
7305: for (i=1; i<= nlstate ; i ++) {
7306: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7307: else fprintf(ficgp," %%*lf (%%*lf)");
7308: }
1.271 brouard 7309: 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 7310: for (i=1; i<= nlstate ; i ++) {
7311: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7312: else fprintf(ficgp," %%*lf (%%*lf)");
7313: }
1.276 brouard 7314: 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 7315: for (i=1; i<= nlstate ; i ++) {
7316: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7317: else fprintf(ficgp," %%*lf (%%*lf)");
7318: }
1.274 brouard 7319: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7320: } /* end if backprojcast */
1.296 brouard 7321: } /* end if prevbcast */
1.276 brouard 7322: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7323: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7324: } /* nres */
1.201 brouard 7325: } /* k1 */
7326: } /* cpt */
1.235 brouard 7327:
7328:
1.126 brouard 7329: /*2 eme*/
1.238 brouard 7330: for (k1=1; k1<= m ; k1 ++){
7331: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7332: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7333: continue;
7334: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7335: strcpy(gplotlabel,"(");
1.238 brouard 7336: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7337: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7338: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7339: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7340: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7341: vlv= nbcode[Tvaraff[k]][lv];
7342: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7343: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7344: }
1.237 brouard 7345: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7346: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7347: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7348: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7349: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7350: }
1.264 brouard 7351: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7352: fprintf(ficgp,"\n#\n");
1.223 brouard 7353: if(invalidvarcomb[k1]){
7354: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7355: continue;
7356: }
1.219 brouard 7357:
1.241 brouard 7358: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7359: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7360: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7361: if(vpopbased==0){
1.238 brouard 7362: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7363: }else
1.238 brouard 7364: fprintf(ficgp,"\nreplot ");
7365: for (i=1; i<= nlstate+1 ; i ++) {
7366: k=2*i;
1.261 brouard 7367: 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 7368: for (j=1; j<= nlstate+1 ; j ++) {
7369: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7370: else fprintf(ficgp," %%*lf (%%*lf)");
7371: }
7372: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7373: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7374: 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 7375: for (j=1; j<= nlstate+1 ; j ++) {
7376: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7377: else fprintf(ficgp," %%*lf (%%*lf)");
7378: }
7379: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7380: 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 7381: for (j=1; j<= nlstate+1 ; j ++) {
7382: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7383: else fprintf(ficgp," %%*lf (%%*lf)");
7384: }
7385: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7386: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7387: } /* state */
7388: } /* vpopbased */
1.264 brouard 7389: 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 7390: } /* end nres */
7391: } /* k1 end 2 eme*/
7392:
7393:
7394: /*3eme*/
7395: for (k1=1; k1<= m ; k1 ++){
7396: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7397: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7398: continue;
7399:
7400: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7401: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7402: strcpy(gplotlabel,"(");
1.238 brouard 7403: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7404: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7405: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7406: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7407: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7408: vlv= nbcode[Tvaraff[k]][lv];
7409: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7410: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7411: }
7412: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7413: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7414: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7415: }
1.264 brouard 7416: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7417: fprintf(ficgp,"\n#\n");
7418: if(invalidvarcomb[k1]){
7419: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7420: continue;
7421: }
7422:
7423: /* k=2+nlstate*(2*cpt-2); */
7424: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7425: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7426: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7427: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7428: 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 7429: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7430: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7431: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7432: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7433: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7434: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7435:
1.238 brouard 7436: */
7437: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7438: 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 7439: /* 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 7440:
1.238 brouard 7441: }
1.261 brouard 7442: 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 7443: }
1.264 brouard 7444: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7445: } /* end nres */
7446: } /* end kl 3eme */
1.126 brouard 7447:
1.223 brouard 7448: /* 4eme */
1.201 brouard 7449: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7450: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7451: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7452: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7453: continue;
1.238 brouard 7454: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7455: strcpy(gplotlabel,"(");
1.238 brouard 7456: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7457: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7458: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7459: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7460: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7461: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7462: vlv= nbcode[Tvaraff[k]][lv];
7463: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7464: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7465: }
7466: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7467: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7468: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7469: }
1.264 brouard 7470: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7471: fprintf(ficgp,"\n#\n");
7472: if(invalidvarcomb[k1]){
7473: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7474: continue;
1.223 brouard 7475: }
1.238 brouard 7476:
1.241 brouard 7477: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7478: 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 7479: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7480: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7481: k=3;
7482: for (i=1; i<= nlstate ; i ++){
7483: if(i==1){
7484: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7485: }else{
7486: fprintf(ficgp,", '' ");
7487: }
7488: l=(nlstate+ndeath)*(i-1)+1;
7489: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7490: for (j=2; j<= nlstate+ndeath ; j ++)
7491: fprintf(ficgp,"+$%d",k+l+j-1);
7492: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7493: } /* nlstate */
1.264 brouard 7494: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7495: } /* end cpt state*/
7496: } /* end nres */
7497: } /* end covariate k1 */
7498:
1.220 brouard 7499: /* 5eme */
1.201 brouard 7500: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7501: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7502: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7503: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7504: continue;
1.238 brouard 7505: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7506: strcpy(gplotlabel,"(");
1.238 brouard 7507: 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);
7508: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7509: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7510: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7511: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7512: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7513: vlv= nbcode[Tvaraff[k]][lv];
7514: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7515: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7516: }
7517: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7518: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7519: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7520: }
1.264 brouard 7521: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7522: fprintf(ficgp,"\n#\n");
7523: if(invalidvarcomb[k1]){
7524: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7525: continue;
7526: }
1.227 brouard 7527:
1.241 brouard 7528: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7529: 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 7530: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7531: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7532: k=3;
7533: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7534: if(j==1)
7535: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7536: else
7537: fprintf(ficgp,", '' ");
7538: l=(nlstate+ndeath)*(cpt-1) +j;
7539: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7540: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7541: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7542: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7543: } /* nlstate */
7544: fprintf(ficgp,", '' ");
7545: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7546: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7547: l=(nlstate+ndeath)*(cpt-1) +j;
7548: if(j < nlstate)
7549: fprintf(ficgp,"$%d +",k+l);
7550: else
7551: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7552: }
1.264 brouard 7553: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7554: } /* end cpt state*/
7555: } /* end covariate */
7556: } /* end nres */
1.227 brouard 7557:
1.220 brouard 7558: /* 6eme */
1.202 brouard 7559: /* CV preval stable (period) for each covariate */
1.237 brouard 7560: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7561: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7562: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7563: continue;
1.255 brouard 7564: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7565: strcpy(gplotlabel,"(");
1.288 brouard 7566: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7567: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7568: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7569: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7570: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7571: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7572: vlv= nbcode[Tvaraff[k]][lv];
7573: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7574: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7575: }
1.237 brouard 7576: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7577: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7578: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7579: }
1.264 brouard 7580: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7581: fprintf(ficgp,"\n#\n");
1.223 brouard 7582: if(invalidvarcomb[k1]){
1.227 brouard 7583: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7584: continue;
1.223 brouard 7585: }
1.227 brouard 7586:
1.241 brouard 7587: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7588: 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 7589: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7590: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7591: k=3; /* Offset */
1.255 brouard 7592: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7593: if(i==1)
7594: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7595: else
7596: fprintf(ficgp,", '' ");
1.255 brouard 7597: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7598: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7599: for (j=2; j<= nlstate ; j ++)
7600: fprintf(ficgp,"+$%d",k+l+j-1);
7601: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7602: } /* nlstate */
1.264 brouard 7603: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7604: } /* end cpt state*/
7605: } /* end covariate */
1.227 brouard 7606:
7607:
1.220 brouard 7608: /* 7eme */
1.296 brouard 7609: if(prevbcast == 1){
1.288 brouard 7610: /* CV backward prevalence for each covariate */
1.237 brouard 7611: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7612: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7613: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7614: continue;
1.268 brouard 7615: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7616: strcpy(gplotlabel,"(");
1.288 brouard 7617: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7618: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7619: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7620: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7621: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7622: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7623: vlv= nbcode[Tvaraff[k]][lv];
7624: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7625: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7626: }
1.237 brouard 7627: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7628: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7629: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7630: }
1.264 brouard 7631: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7632: fprintf(ficgp,"\n#\n");
7633: if(invalidvarcomb[k1]){
7634: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7635: continue;
7636: }
7637:
1.241 brouard 7638: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7639: 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 7640: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7641: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7642: k=3; /* Offset */
1.268 brouard 7643: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7644: if(i==1)
7645: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7646: else
7647: fprintf(ficgp,", '' ");
7648: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7649: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7650: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7651: /* 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 7652: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7653: /* for (j=2; j<= nlstate ; j ++) */
7654: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7655: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7656: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7657: } /* nlstate */
1.264 brouard 7658: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7659: } /* end cpt state*/
7660: } /* end covariate */
1.296 brouard 7661: } /* End if prevbcast */
1.218 brouard 7662:
1.223 brouard 7663: /* 8eme */
1.218 brouard 7664: if(prevfcast==1){
1.288 brouard 7665: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7666:
1.237 brouard 7667: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7668: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7669: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7670: continue;
1.211 brouard 7671: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7672: strcpy(gplotlabel,"(");
1.288 brouard 7673: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7674: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7675: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7676: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7677: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7678: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7679: vlv= nbcode[Tvaraff[k]][lv];
7680: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7681: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7682: }
1.237 brouard 7683: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7684: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7685: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7686: }
1.264 brouard 7687: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7688: fprintf(ficgp,"\n#\n");
7689: if(invalidvarcomb[k1]){
7690: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7691: continue;
7692: }
7693:
7694: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7695: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7696: 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 7697: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7698: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7699:
7700: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7701: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7702: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7703: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7704: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7705: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7706: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7707: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7708: if(i==istart){
1.227 brouard 7709: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7710: }else{
7711: fprintf(ficgp,",\\\n '' ");
7712: }
7713: if(cptcoveff ==0){ /* No covariate */
7714: ioffset=2; /* Age is in 2 */
7715: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7716: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7717: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7718: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7719: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7720: if(i==nlstate+1){
1.270 brouard 7721: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7722: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7723: fprintf(ficgp,",\\\n '' ");
7724: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7725: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7726: offyear, \
1.268 brouard 7727: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7728: }else
1.227 brouard 7729: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7730: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7731: }else{ /* more than 2 covariates */
1.270 brouard 7732: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7733: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7734: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7735: iyearc=ioffset-1;
7736: iagec=ioffset;
1.227 brouard 7737: fprintf(ficgp," u %d:(",ioffset);
7738: kl=0;
7739: strcpy(gplotcondition,"(");
7740: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7741: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7742: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7743: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7744: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7745: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7746: kl++;
7747: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7748: kl++;
7749: if(k <cptcoveff && cptcoveff>1)
7750: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7751: }
7752: strcpy(gplotcondition+strlen(gplotcondition),")");
7753: /* 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 *\/ */
7754: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7755: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7756: /* '' 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*/
7757: if(i==nlstate+1){
1.270 brouard 7758: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7759: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7760: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7761: fprintf(ficgp," u %d:(",iagec);
7762: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7763: iyearc, iagec, offyear, \
7764: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7765: /* '' 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 7766: }else{
7767: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7768: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7769: }
7770: } /* end if covariate */
7771: } /* nlstate */
1.264 brouard 7772: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7773: } /* end cpt state*/
7774: } /* end covariate */
7775: } /* End if prevfcast */
1.227 brouard 7776:
1.296 brouard 7777: if(prevbcast==1){
1.268 brouard 7778: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7779:
7780: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7781: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7782: if(m != 1 && TKresult[nres]!= k1)
7783: continue;
7784: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7785: strcpy(gplotlabel,"(");
7786: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7787: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7788: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7789: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7790: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7791: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7792: vlv= nbcode[Tvaraff[k]][lv];
7793: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7794: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7795: }
7796: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7797: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7798: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7799: }
7800: strcpy(gplotlabel+strlen(gplotlabel),")");
7801: fprintf(ficgp,"\n#\n");
7802: if(invalidvarcomb[k1]){
7803: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7804: continue;
7805: }
7806:
7807: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7808: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7809: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7810: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7811: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7812:
7813: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7814: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7815: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7816: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7817: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7818: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7819: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7820: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7821: if(i==istart){
7822: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7823: }else{
7824: fprintf(ficgp,",\\\n '' ");
7825: }
7826: if(cptcoveff ==0){ /* No covariate */
7827: ioffset=2; /* Age is in 2 */
7828: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7829: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7830: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7831: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7832: fprintf(ficgp," u %d:(", ioffset);
7833: if(i==nlstate+1){
1.270 brouard 7834: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7835: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7836: fprintf(ficgp,",\\\n '' ");
7837: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7838: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7839: offbyear, \
7840: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7841: }else
7842: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7843: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7844: }else{ /* more than 2 covariates */
1.270 brouard 7845: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7846: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7847: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7848: iyearc=ioffset-1;
7849: iagec=ioffset;
1.268 brouard 7850: fprintf(ficgp," u %d:(",ioffset);
7851: kl=0;
7852: strcpy(gplotcondition,"(");
7853: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7854: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7855: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7856: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7857: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7858: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7859: kl++;
7860: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7861: kl++;
7862: if(k <cptcoveff && cptcoveff>1)
7863: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7864: }
7865: strcpy(gplotcondition+strlen(gplotcondition),")");
7866: /* 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 *\/ */
7867: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7868: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7869: /* '' 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*/
7870: if(i==nlstate+1){
1.270 brouard 7871: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7872: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7873: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7874: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7875: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7876: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7877: iyearc,iagec,offbyear, \
7878: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7879: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7880: }else{
7881: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7882: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7883: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7884: }
7885: } /* end if covariate */
7886: } /* nlstate */
7887: fprintf(ficgp,"\nset out; unset label;\n");
7888: } /* end cpt state*/
7889: } /* end covariate */
1.296 brouard 7890: } /* End if prevbcast */
1.268 brouard 7891:
1.227 brouard 7892:
1.238 brouard 7893: /* 9eme writing MLE parameters */
7894: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7895: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7896: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7897: for(k=1; k <=(nlstate+ndeath); k++){
7898: if (k != i) {
1.227 brouard 7899: fprintf(ficgp,"# current state %d\n",k);
7900: for(j=1; j <=ncovmodel; j++){
7901: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7902: jk++;
7903: }
7904: fprintf(ficgp,"\n");
1.126 brouard 7905: }
7906: }
1.223 brouard 7907: }
1.187 brouard 7908: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7909:
1.145 brouard 7910: /*goto avoid;*/
1.238 brouard 7911: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7912: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7913: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7914: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7915: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7916: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7917: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7918: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7919: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7920: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7921: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7922: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7923: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7924: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7925: fprintf(ficgp,"#\n");
1.223 brouard 7926: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7927: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7928: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7929: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7930: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7931: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7932: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7933: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7934: continue;
1.264 brouard 7935: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7936: strcpy(gplotlabel,"(");
1.276 brouard 7937: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7938: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7939: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7940: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7941: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7942: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7943: vlv= nbcode[Tvaraff[k]][lv];
7944: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7945: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7946: }
1.237 brouard 7947: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7948: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7949: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7950: }
1.264 brouard 7951: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7952: fprintf(ficgp,"\n#\n");
1.264 brouard 7953: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7954: fprintf(ficgp,"\nset key outside ");
7955: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7956: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7957: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7958: if (ng==1){
7959: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7960: fprintf(ficgp,"\nunset log y");
7961: }else if (ng==2){
7962: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7963: fprintf(ficgp,"\nset log y");
7964: }else if (ng==3){
7965: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7966: fprintf(ficgp,"\nset log y");
7967: }else
7968: fprintf(ficgp,"\nunset title ");
7969: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7970: i=1;
7971: for(k2=1; k2<=nlstate; k2++) {
7972: k3=i;
7973: for(k=1; k<=(nlstate+ndeath); k++) {
7974: if (k != k2){
7975: switch( ng) {
7976: case 1:
7977: if(nagesqr==0)
7978: fprintf(ficgp," p%d+p%d*x",i,i+1);
7979: else /* nagesqr =1 */
7980: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7981: break;
7982: case 2: /* ng=2 */
7983: if(nagesqr==0)
7984: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7985: else /* nagesqr =1 */
7986: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7987: break;
7988: case 3:
7989: if(nagesqr==0)
7990: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7991: else /* nagesqr =1 */
7992: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7993: break;
7994: }
7995: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7996: ijp=1; /* product no age */
7997: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7998: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7999: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8000: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8001: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8002: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8003: if(DummyV[j]==0){
8004: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8005: }else{ /* quantitative */
8006: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8007: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8008: }
8009: ij++;
1.237 brouard 8010: }
1.268 brouard 8011: }
8012: }else if(cptcovprod >0){
8013: if(j==Tprod[ijp]) { /* */
8014: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8015: if(ijp <=cptcovprod) { /* Product */
8016: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8017: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8018: /* 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)]); */
8019: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8020: }else{ /* Vn is dummy and Vm is quanti */
8021: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8022: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8023: }
8024: }else{ /* Vn*Vm Vn is quanti */
8025: if(DummyV[Tvard[ijp][2]]==0){
8026: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8027: }else{ /* Both quanti */
8028: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8029: }
1.237 brouard 8030: }
1.268 brouard 8031: ijp++;
1.237 brouard 8032: }
1.268 brouard 8033: } /* end Tprod */
1.237 brouard 8034: } else{ /* simple covariate */
1.264 brouard 8035: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8036: if(Dummy[j]==0){
8037: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8038: }else{ /* quantitative */
8039: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8040: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8041: }
1.237 brouard 8042: } /* end simple */
8043: } /* end j */
1.223 brouard 8044: }else{
8045: i=i-ncovmodel;
8046: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8047: fprintf(ficgp," (1.");
8048: }
1.227 brouard 8049:
1.223 brouard 8050: if(ng != 1){
8051: fprintf(ficgp,")/(1");
1.227 brouard 8052:
1.264 brouard 8053: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8054: if(nagesqr==0)
1.264 brouard 8055: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8056: else /* nagesqr =1 */
1.264 brouard 8057: 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 8058:
1.223 brouard 8059: ij=1;
8060: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8061: if(cptcovage >0){
8062: if((j-2)==Tage[ij]) { /* Bug valgrind */
8063: if(ij <=cptcovage) { /* Bug valgrind */
8064: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8065: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8066: ij++;
8067: }
8068: }
8069: }else
8070: 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 8071: }
8072: fprintf(ficgp,")");
8073: }
8074: fprintf(ficgp,")");
8075: if(ng ==2)
1.276 brouard 8076: 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 8077: else /* ng= 3 */
1.276 brouard 8078: 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 8079: }else{ /* end ng <> 1 */
8080: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8081: 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 8082: }
8083: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8084: fprintf(ficgp,",");
8085: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8086: fprintf(ficgp,",");
8087: i=i+ncovmodel;
8088: } /* end k */
8089: } /* end k2 */
1.276 brouard 8090: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8091: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8092: } /* end k1 */
1.223 brouard 8093: } /* end ng */
8094: /* avoid: */
8095: fflush(ficgp);
1.126 brouard 8096: } /* end gnuplot */
8097:
8098:
8099: /*************** Moving average **************/
1.219 brouard 8100: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8101: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8102:
1.222 brouard 8103: int i, cpt, cptcod;
8104: int modcovmax =1;
8105: int mobilavrange, mob;
8106: int iage=0;
1.288 brouard 8107: int firstA1=0, firstA2=0;
1.222 brouard 8108:
1.266 brouard 8109: double sum=0., sumr=0.;
1.222 brouard 8110: double age;
1.266 brouard 8111: double *sumnewp, *sumnewm, *sumnewmr;
8112: double *agemingood, *agemaxgood;
8113: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8114:
8115:
1.278 brouard 8116: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8117: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8118:
8119: sumnewp = vector(1,ncovcombmax);
8120: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8121: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8122: agemingood = vector(1,ncovcombmax);
1.266 brouard 8123: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8124: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8125: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8126:
8127: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8128: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8129: sumnewp[cptcod]=0.;
1.266 brouard 8130: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8131: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8132: }
8133: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8134:
1.266 brouard 8135: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8136: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8137: else mobilavrange=mobilav;
8138: for (age=bage; age<=fage; age++)
8139: for (i=1; i<=nlstate;i++)
8140: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8141: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8142: /* We keep the original values on the extreme ages bage, fage and for
8143: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8144: we use a 5 terms etc. until the borders are no more concerned.
8145: */
8146: for (mob=3;mob <=mobilavrange;mob=mob+2){
8147: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8148: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8149: sumnewm[cptcod]=0.;
8150: for (i=1; i<=nlstate;i++){
1.222 brouard 8151: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8152: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8153: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8154: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8155: }
8156: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8157: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8158: } /* end i */
8159: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8160: } /* end cptcod */
1.222 brouard 8161: }/* end age */
8162: }/* end mob */
1.266 brouard 8163: }else{
8164: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8165: return -1;
1.266 brouard 8166: }
8167:
8168: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8169: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8170: if(invalidvarcomb[cptcod]){
8171: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8172: continue;
8173: }
1.219 brouard 8174:
1.266 brouard 8175: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8176: sumnewm[cptcod]=0.;
8177: sumnewmr[cptcod]=0.;
8178: for (i=1; i<=nlstate;i++){
8179: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8180: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8181: }
8182: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8183: agemingoodr[cptcod]=age;
8184: }
8185: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8186: agemingood[cptcod]=age;
8187: }
8188: } /* age */
8189: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8190: sumnewm[cptcod]=0.;
1.266 brouard 8191: sumnewmr[cptcod]=0.;
1.222 brouard 8192: for (i=1; i<=nlstate;i++){
8193: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8194: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8195: }
8196: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8197: agemaxgoodr[cptcod]=age;
1.222 brouard 8198: }
8199: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8200: agemaxgood[cptcod]=age;
8201: }
8202: } /* age */
8203: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8204: /* but they will change */
1.288 brouard 8205: firstA1=0;firstA2=0;
1.266 brouard 8206: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8207: sumnewm[cptcod]=0.;
8208: sumnewmr[cptcod]=0.;
8209: for (i=1; i<=nlstate;i++){
8210: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8211: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8212: }
8213: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8214: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8215: agemaxgoodr[cptcod]=age; /* age min */
8216: for (i=1; i<=nlstate;i++)
8217: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8218: }else{ /* bad we change the value with the values of good ages */
8219: for (i=1; i<=nlstate;i++){
8220: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8221: } /* i */
8222: } /* end bad */
8223: }else{
8224: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8225: agemaxgood[cptcod]=age;
8226: }else{ /* bad we change the value with the values of good ages */
8227: for (i=1; i<=nlstate;i++){
8228: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8229: } /* i */
8230: } /* end bad */
8231: }/* end else */
8232: sum=0.;sumr=0.;
8233: for (i=1; i<=nlstate;i++){
8234: sum+=mobaverage[(int)age][i][cptcod];
8235: sumr+=probs[(int)age][i][cptcod];
8236: }
8237: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8238: if(!firstA1){
8239: firstA1=1;
8240: 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);
8241: }
8242: 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 8243: } /* end bad */
8244: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8245: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8246: if(!firstA2){
8247: firstA2=1;
8248: 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);
8249: }
8250: 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 8251: } /* end bad */
8252: }/* age */
1.266 brouard 8253:
8254: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8255: sumnewm[cptcod]=0.;
1.266 brouard 8256: sumnewmr[cptcod]=0.;
1.222 brouard 8257: for (i=1; i<=nlstate;i++){
8258: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8259: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8260: }
8261: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8262: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8263: agemingoodr[cptcod]=age;
8264: for (i=1; i<=nlstate;i++)
8265: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8266: }else{ /* bad we change the value with the values of good ages */
8267: for (i=1; i<=nlstate;i++){
8268: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8269: } /* i */
8270: } /* end bad */
8271: }else{
8272: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8273: agemingood[cptcod]=age;
8274: }else{ /* bad */
8275: for (i=1; i<=nlstate;i++){
8276: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8277: } /* i */
8278: } /* end bad */
8279: }/* end else */
8280: sum=0.;sumr=0.;
8281: for (i=1; i<=nlstate;i++){
8282: sum+=mobaverage[(int)age][i][cptcod];
8283: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8284: }
1.266 brouard 8285: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8286: 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 8287: } /* end bad */
8288: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8289: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8290: 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 8291: } /* end bad */
8292: }/* age */
1.266 brouard 8293:
1.222 brouard 8294:
8295: for (age=bage; age<=fage; age++){
1.235 brouard 8296: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8297: sumnewp[cptcod]=0.;
8298: sumnewm[cptcod]=0.;
8299: for (i=1; i<=nlstate;i++){
8300: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8301: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8302: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8303: }
8304: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8305: }
8306: /* printf("\n"); */
8307: /* } */
1.266 brouard 8308:
1.222 brouard 8309: /* brutal averaging */
1.266 brouard 8310: /* for (i=1; i<=nlstate;i++){ */
8311: /* for (age=1; age<=bage; age++){ */
8312: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8313: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8314: /* } */
8315: /* for (age=fage; age<=AGESUP; age++){ */
8316: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8317: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8318: /* } */
8319: /* } /\* end i status *\/ */
8320: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8321: /* for (age=1; age<=AGESUP; age++){ */
8322: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8323: /* mobaverage[(int)age][i][cptcod]=0.; */
8324: /* } */
8325: /* } */
1.222 brouard 8326: }/* end cptcod */
1.266 brouard 8327: free_vector(agemaxgoodr,1, ncovcombmax);
8328: free_vector(agemaxgood,1, ncovcombmax);
8329: free_vector(agemingood,1, ncovcombmax);
8330: free_vector(agemingoodr,1, ncovcombmax);
8331: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8332: free_vector(sumnewm,1, ncovcombmax);
8333: free_vector(sumnewp,1, ncovcombmax);
8334: return 0;
8335: }/* End movingaverage */
1.218 brouard 8336:
1.126 brouard 8337:
1.296 brouard 8338:
1.126 brouard 8339: /************** Forecasting ******************/
1.296 brouard 8340: /* 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)*/
8341: 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){
8342: /* dateintemean, mean date of interviews
8343: dateprojd, year, month, day of starting projection
8344: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8345: agemin, agemax range of age
8346: dateprev1 dateprev2 range of dates during which prevalence is computed
8347: */
1.296 brouard 8348: /* double anprojd, mprojd, jprojd; */
8349: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8350: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8351: double agec; /* generic age */
1.296 brouard 8352: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8353: double *popeffectif,*popcount;
8354: double ***p3mat;
1.218 brouard 8355: /* double ***mobaverage; */
1.126 brouard 8356: char fileresf[FILENAMELENGTH];
8357:
8358: agelim=AGESUP;
1.211 brouard 8359: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8360: in each health status at the date of interview (if between dateprev1 and dateprev2).
8361: We still use firstpass and lastpass as another selection.
8362: */
1.214 brouard 8363: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8364: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8365:
1.201 brouard 8366: strcpy(fileresf,"F_");
8367: strcat(fileresf,fileresu);
1.126 brouard 8368: if((ficresf=fopen(fileresf,"w"))==NULL) {
8369: printf("Problem with forecast resultfile: %s\n", fileresf);
8370: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8371: }
1.235 brouard 8372: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8373: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8374:
1.225 brouard 8375: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8376:
8377:
8378: stepsize=(int) (stepm+YEARM-1)/YEARM;
8379: if (stepm<=12) stepsize=1;
8380: if(estepm < stepm){
8381: printf ("Problem %d lower than %d\n",estepm, stepm);
8382: }
1.270 brouard 8383: else{
8384: hstepm=estepm;
8385: }
8386: if(estepm > stepm){ /* Yes every two year */
8387: stepsize=2;
8388: }
1.296 brouard 8389: hstepm=hstepm/stepm;
1.126 brouard 8390:
1.296 brouard 8391:
8392: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8393: /* fractional in yp1 *\/ */
8394: /* aintmean=yp; */
8395: /* yp2=modf((yp1*12),&yp); */
8396: /* mintmean=yp; */
8397: /* yp1=modf((yp2*30.5),&yp); */
8398: /* jintmean=yp; */
8399: /* if(jintmean==0) jintmean=1; */
8400: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8401:
1.296 brouard 8402:
8403: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8404: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8405: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8406: i1=pow(2,cptcoveff);
1.126 brouard 8407: if (cptcovn < 1){i1=1;}
8408:
1.296 brouard 8409: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8410:
8411: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8412:
1.126 brouard 8413: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8414: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8415: for(k=1; k<=i1;k++){
1.253 brouard 8416: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8417: continue;
1.227 brouard 8418: if(invalidvarcomb[k]){
8419: printf("\nCombination (%d) projection ignored because no cases \n",k);
8420: continue;
8421: }
8422: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8423: for(j=1;j<=cptcoveff;j++) {
8424: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8425: }
1.235 brouard 8426: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8427: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8428: }
1.227 brouard 8429: fprintf(ficresf," yearproj age");
8430: for(j=1; j<=nlstate+ndeath;j++){
8431: for(i=1; i<=nlstate;i++)
8432: fprintf(ficresf," p%d%d",i,j);
8433: fprintf(ficresf," wp.%d",j);
8434: }
1.296 brouard 8435: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8436: fprintf(ficresf,"\n");
1.296 brouard 8437: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8438: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8439: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8440: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8441: nhstepm = nhstepm/hstepm;
8442: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8443: oldm=oldms;savm=savms;
1.268 brouard 8444: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8445: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8446: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8447: for (h=0; h<=nhstepm; h++){
8448: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8449: break;
8450: }
8451: }
8452: fprintf(ficresf,"\n");
8453: for(j=1;j<=cptcoveff;j++)
8454: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8455: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8456:
8457: for(j=1; j<=nlstate+ndeath;j++) {
8458: ppij=0.;
8459: for(i=1; i<=nlstate;i++) {
1.278 brouard 8460: if (mobilav>=1)
8461: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8462: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8463: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8464: }
1.268 brouard 8465: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8466: } /* end i */
8467: fprintf(ficresf," %.3f", ppij);
8468: }/* end j */
1.227 brouard 8469: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8470: } /* end agec */
1.266 brouard 8471: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8472: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8473: } /* end yearp */
8474: } /* end k */
1.219 brouard 8475:
1.126 brouard 8476: fclose(ficresf);
1.215 brouard 8477: printf("End of Computing forecasting \n");
8478: fprintf(ficlog,"End of Computing forecasting\n");
8479:
1.126 brouard 8480: }
8481:
1.269 brouard 8482: /************** Back Forecasting ******************/
1.296 brouard 8483: /* 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){ */
8484: 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){
8485: /* back1, year, month, day of starting backprojection
1.267 brouard 8486: agemin, agemax range of age
8487: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8488: anback2 year of end of backprojection (same day and month as back1).
8489: prevacurrent and prev are prevalences.
1.267 brouard 8490: */
8491: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8492: double agec; /* generic age */
1.296 brouard 8493: double agelim, ppij, ppi, yp,yp1,yp2,jintmean,mintmean,aintmean;
1.267 brouard 8494: double *popeffectif,*popcount;
8495: double ***p3mat;
8496: /* double ***mobaverage; */
8497: char fileresfb[FILENAMELENGTH];
8498:
1.268 brouard 8499: agelim=AGEINF;
1.267 brouard 8500: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8501: in each health status at the date of interview (if between dateprev1 and dateprev2).
8502: We still use firstpass and lastpass as another selection.
8503: */
8504: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8505: /* firstpass, lastpass, stepm, weightopt, model); */
8506:
8507: /*Do we need to compute prevalence again?*/
8508:
8509: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8510:
8511: strcpy(fileresfb,"FB_");
8512: strcat(fileresfb,fileresu);
8513: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8514: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8515: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8516: }
8517: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8518: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8519:
8520: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8521:
8522:
8523: stepsize=(int) (stepm+YEARM-1)/YEARM;
8524: if (stepm<=12) stepsize=1;
8525: if(estepm < stepm){
8526: printf ("Problem %d lower than %d\n",estepm, stepm);
8527: }
1.270 brouard 8528: else{
8529: hstepm=estepm;
8530: }
8531: if(estepm >= stepm){ /* Yes every two year */
8532: stepsize=2;
8533: }
1.267 brouard 8534:
8535: hstepm=hstepm/stepm;
1.296 brouard 8536: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8537: /* fractional in yp1 *\/ */
8538: /* aintmean=yp; */
8539: /* yp2=modf((yp1*12),&yp); */
8540: /* mintmean=yp; */
8541: /* yp1=modf((yp2*30.5),&yp); */
8542: /* jintmean=yp; */
8543: /* if(jintmean==0) jintmean=1; */
8544: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8545:
8546: i1=pow(2,cptcoveff);
8547: if (cptcovn < 1){i1=1;}
8548:
1.296 brouard 8549: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8550: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8551:
8552: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8553:
8554: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8555: for(k=1; k<=i1;k++){
8556: if(i1 != 1 && TKresult[nres]!= k)
8557: continue;
8558: if(invalidvarcomb[k]){
8559: printf("\nCombination (%d) projection ignored because no cases \n",k);
8560: continue;
8561: }
1.268 brouard 8562: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8563: for(j=1;j<=cptcoveff;j++) {
8564: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8565: }
8566: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8567: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8568: }
8569: fprintf(ficresfb," yearbproj age");
8570: for(j=1; j<=nlstate+ndeath;j++){
8571: for(i=1; i<=nlstate;i++)
1.268 brouard 8572: fprintf(ficresfb," b%d%d",i,j);
8573: fprintf(ficresfb," b.%d",j);
1.267 brouard 8574: }
1.296 brouard 8575: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8576: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8577: fprintf(ficresfb,"\n");
1.296 brouard 8578: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8579: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8580: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8581: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8582: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8583: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8584: nhstepm = nhstepm/hstepm;
8585: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8586: oldm=oldms;savm=savms;
1.268 brouard 8587: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8588: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8589: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8590: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8591: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8592: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8593: for (h=0; h<=nhstepm; h++){
1.268 brouard 8594: if (h*hstepm/YEARM*stepm ==-yearp) {
8595: break;
8596: }
8597: }
8598: fprintf(ficresfb,"\n");
8599: for(j=1;j<=cptcoveff;j++)
8600: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8601: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8602: for(i=1; i<=nlstate+ndeath;i++) {
8603: ppij=0.;ppi=0.;
8604: for(j=1; j<=nlstate;j++) {
8605: /* if (mobilav==1) */
1.269 brouard 8606: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8607: ppi=ppi+prevacurrent[(int)agec][j][k];
8608: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8609: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8610: /* else { */
8611: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8612: /* } */
1.268 brouard 8613: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8614: } /* end j */
8615: if(ppi <0.99){
8616: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8617: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8618: }
8619: fprintf(ficresfb," %.3f", ppij);
8620: }/* end j */
1.267 brouard 8621: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8622: } /* end agec */
8623: } /* end yearp */
8624: } /* end k */
1.217 brouard 8625:
1.267 brouard 8626: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8627:
1.267 brouard 8628: fclose(ficresfb);
8629: printf("End of Computing Back forecasting \n");
8630: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8631:
1.267 brouard 8632: }
1.217 brouard 8633:
1.269 brouard 8634: /* Variance of prevalence limit: varprlim */
8635: 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 8636: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8637:
8638: char fileresvpl[FILENAMELENGTH];
8639: FILE *ficresvpl;
8640: double **oldm, **savm;
8641: double **varpl; /* Variances of prevalence limits by age */
8642: int i1, k, nres, j ;
8643:
8644: strcpy(fileresvpl,"VPL_");
8645: strcat(fileresvpl,fileresu);
8646: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8647: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8648: exit(0);
8649: }
1.288 brouard 8650: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8651: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8652:
8653: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8654: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8655:
8656: i1=pow(2,cptcoveff);
8657: if (cptcovn < 1){i1=1;}
8658:
8659: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8660: for(k=1; k<=i1;k++){
8661: if(i1 != 1 && TKresult[nres]!= k)
8662: continue;
8663: fprintf(ficresvpl,"\n#****** ");
8664: printf("\n#****** ");
8665: fprintf(ficlog,"\n#****** ");
8666: for(j=1;j<=cptcoveff;j++) {
8667: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8668: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8669: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8670: }
8671: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8672: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8673: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8674: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8675: }
8676: fprintf(ficresvpl,"******\n");
8677: printf("******\n");
8678: fprintf(ficlog,"******\n");
8679:
8680: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8681: oldm=oldms;savm=savms;
8682: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8683: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8684: /*}*/
8685: }
8686:
8687: fclose(ficresvpl);
1.288 brouard 8688: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8689: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8690:
8691: }
8692: /* Variance of back prevalence: varbprlim */
8693: 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){
8694: /*------- Variance of back (stable) prevalence------*/
8695:
8696: char fileresvbl[FILENAMELENGTH];
8697: FILE *ficresvbl;
8698:
8699: double **oldm, **savm;
8700: double **varbpl; /* Variances of back prevalence limits by age */
8701: int i1, k, nres, j ;
8702:
8703: strcpy(fileresvbl,"VBL_");
8704: strcat(fileresvbl,fileresu);
8705: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8706: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8707: exit(0);
8708: }
8709: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8710: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8711:
8712:
8713: i1=pow(2,cptcoveff);
8714: if (cptcovn < 1){i1=1;}
8715:
8716: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8717: for(k=1; k<=i1;k++){
8718: if(i1 != 1 && TKresult[nres]!= k)
8719: continue;
8720: fprintf(ficresvbl,"\n#****** ");
8721: printf("\n#****** ");
8722: fprintf(ficlog,"\n#****** ");
8723: for(j=1;j<=cptcoveff;j++) {
8724: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8725: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8726: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8727: }
8728: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8729: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8730: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8731: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8732: }
8733: fprintf(ficresvbl,"******\n");
8734: printf("******\n");
8735: fprintf(ficlog,"******\n");
8736:
8737: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8738: oldm=oldms;savm=savms;
8739:
8740: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8741: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8742: /*}*/
8743: }
8744:
8745: fclose(ficresvbl);
8746: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8747: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8748:
8749: } /* End of varbprlim */
8750:
1.126 brouard 8751: /************** Forecasting *****not tested NB*************/
1.227 brouard 8752: /* 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 8753:
1.227 brouard 8754: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8755: /* int *popage; */
8756: /* double calagedatem, agelim, kk1, kk2; */
8757: /* double *popeffectif,*popcount; */
8758: /* double ***p3mat,***tabpop,***tabpopprev; */
8759: /* /\* double ***mobaverage; *\/ */
8760: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8761:
1.227 brouard 8762: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8763: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8764: /* agelim=AGESUP; */
8765: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8766:
1.227 brouard 8767: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8768:
8769:
1.227 brouard 8770: /* strcpy(filerespop,"POP_"); */
8771: /* strcat(filerespop,fileresu); */
8772: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8773: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8774: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8775: /* } */
8776: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8777: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8778:
1.227 brouard 8779: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8780:
1.227 brouard 8781: /* /\* if (mobilav!=0) { *\/ */
8782: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8783: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8784: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8785: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8786: /* /\* } *\/ */
8787: /* /\* } *\/ */
1.126 brouard 8788:
1.227 brouard 8789: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8790: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8791:
1.227 brouard 8792: /* agelim=AGESUP; */
1.126 brouard 8793:
1.227 brouard 8794: /* hstepm=1; */
8795: /* hstepm=hstepm/stepm; */
1.218 brouard 8796:
1.227 brouard 8797: /* if (popforecast==1) { */
8798: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8799: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8800: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8801: /* } */
8802: /* popage=ivector(0,AGESUP); */
8803: /* popeffectif=vector(0,AGESUP); */
8804: /* popcount=vector(0,AGESUP); */
1.126 brouard 8805:
1.227 brouard 8806: /* i=1; */
8807: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8808:
1.227 brouard 8809: /* imx=i; */
8810: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8811: /* } */
1.218 brouard 8812:
1.227 brouard 8813: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8814: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8815: /* k=k+1; */
8816: /* fprintf(ficrespop,"\n#******"); */
8817: /* for(j=1;j<=cptcoveff;j++) { */
8818: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8819: /* } */
8820: /* fprintf(ficrespop,"******\n"); */
8821: /* fprintf(ficrespop,"# Age"); */
8822: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8823: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8824:
1.227 brouard 8825: /* for (cpt=0; cpt<=0;cpt++) { */
8826: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8827:
1.227 brouard 8828: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8829: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8830: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8831:
1.227 brouard 8832: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8833: /* oldm=oldms;savm=savms; */
8834: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8835:
1.227 brouard 8836: /* for (h=0; h<=nhstepm; h++){ */
8837: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8838: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8839: /* } */
8840: /* for(j=1; j<=nlstate+ndeath;j++) { */
8841: /* kk1=0.;kk2=0; */
8842: /* for(i=1; i<=nlstate;i++) { */
8843: /* if (mobilav==1) */
8844: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8845: /* else { */
8846: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8847: /* } */
8848: /* } */
8849: /* if (h==(int)(calagedatem+12*cpt)){ */
8850: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8851: /* /\*fprintf(ficrespop," %.3f", kk1); */
8852: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8853: /* } */
8854: /* } */
8855: /* for(i=1; i<=nlstate;i++){ */
8856: /* kk1=0.; */
8857: /* for(j=1; j<=nlstate;j++){ */
8858: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8859: /* } */
8860: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8861: /* } */
1.218 brouard 8862:
1.227 brouard 8863: /* if (h==(int)(calagedatem+12*cpt)) */
8864: /* for(j=1; j<=nlstate;j++) */
8865: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8866: /* } */
8867: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8868: /* } */
8869: /* } */
1.218 brouard 8870:
1.227 brouard 8871: /* /\******\/ */
1.218 brouard 8872:
1.227 brouard 8873: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8874: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8875: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8876: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8877: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8878:
1.227 brouard 8879: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8880: /* oldm=oldms;savm=savms; */
8881: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8882: /* for (h=0; h<=nhstepm; h++){ */
8883: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8884: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8885: /* } */
8886: /* for(j=1; j<=nlstate+ndeath;j++) { */
8887: /* kk1=0.;kk2=0; */
8888: /* for(i=1; i<=nlstate;i++) { */
8889: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8890: /* } */
8891: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8892: /* } */
8893: /* } */
8894: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8895: /* } */
8896: /* } */
8897: /* } */
8898: /* } */
1.218 brouard 8899:
1.227 brouard 8900: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8901:
1.227 brouard 8902: /* if (popforecast==1) { */
8903: /* free_ivector(popage,0,AGESUP); */
8904: /* free_vector(popeffectif,0,AGESUP); */
8905: /* free_vector(popcount,0,AGESUP); */
8906: /* } */
8907: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8908: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8909: /* fclose(ficrespop); */
8910: /* } /\* End of popforecast *\/ */
1.218 brouard 8911:
1.126 brouard 8912: int fileappend(FILE *fichier, char *optionfich)
8913: {
8914: if((fichier=fopen(optionfich,"a"))==NULL) {
8915: printf("Problem with file: %s\n", optionfich);
8916: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8917: return (0);
8918: }
8919: fflush(fichier);
8920: return (1);
8921: }
8922:
8923:
8924: /**************** function prwizard **********************/
8925: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8926: {
8927:
8928: /* Wizard to print covariance matrix template */
8929:
1.164 brouard 8930: char ca[32], cb[32];
8931: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8932: int numlinepar;
8933:
8934: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8935: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8936: for(i=1; i <=nlstate; i++){
8937: jj=0;
8938: for(j=1; j <=nlstate+ndeath; j++){
8939: if(j==i) continue;
8940: jj++;
8941: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8942: printf("%1d%1d",i,j);
8943: fprintf(ficparo,"%1d%1d",i,j);
8944: for(k=1; k<=ncovmodel;k++){
8945: /* printf(" %lf",param[i][j][k]); */
8946: /* fprintf(ficparo," %lf",param[i][j][k]); */
8947: printf(" 0.");
8948: fprintf(ficparo," 0.");
8949: }
8950: printf("\n");
8951: fprintf(ficparo,"\n");
8952: }
8953: }
8954: printf("# Scales (for hessian or gradient estimation)\n");
8955: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8956: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8957: for(i=1; i <=nlstate; i++){
8958: jj=0;
8959: for(j=1; j <=nlstate+ndeath; j++){
8960: if(j==i) continue;
8961: jj++;
8962: fprintf(ficparo,"%1d%1d",i,j);
8963: printf("%1d%1d",i,j);
8964: fflush(stdout);
8965: for(k=1; k<=ncovmodel;k++){
8966: /* printf(" %le",delti3[i][j][k]); */
8967: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8968: printf(" 0.");
8969: fprintf(ficparo," 0.");
8970: }
8971: numlinepar++;
8972: printf("\n");
8973: fprintf(ficparo,"\n");
8974: }
8975: }
8976: printf("# Covariance matrix\n");
8977: /* # 121 Var(a12)\n\ */
8978: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8979: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8980: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8981: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8982: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8983: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8984: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8985: fflush(stdout);
8986: fprintf(ficparo,"# Covariance matrix\n");
8987: /* # 121 Var(a12)\n\ */
8988: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8989: /* # ...\n\ */
8990: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8991:
8992: for(itimes=1;itimes<=2;itimes++){
8993: jj=0;
8994: for(i=1; i <=nlstate; i++){
8995: for(j=1; j <=nlstate+ndeath; j++){
8996: if(j==i) continue;
8997: for(k=1; k<=ncovmodel;k++){
8998: jj++;
8999: ca[0]= k+'a'-1;ca[1]='\0';
9000: if(itimes==1){
9001: printf("#%1d%1d%d",i,j,k);
9002: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9003: }else{
9004: printf("%1d%1d%d",i,j,k);
9005: fprintf(ficparo,"%1d%1d%d",i,j,k);
9006: /* printf(" %.5le",matcov[i][j]); */
9007: }
9008: ll=0;
9009: for(li=1;li <=nlstate; li++){
9010: for(lj=1;lj <=nlstate+ndeath; lj++){
9011: if(lj==li) continue;
9012: for(lk=1;lk<=ncovmodel;lk++){
9013: ll++;
9014: if(ll<=jj){
9015: cb[0]= lk +'a'-1;cb[1]='\0';
9016: if(ll<jj){
9017: if(itimes==1){
9018: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9019: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9020: }else{
9021: printf(" 0.");
9022: fprintf(ficparo," 0.");
9023: }
9024: }else{
9025: if(itimes==1){
9026: printf(" Var(%s%1d%1d)",ca,i,j);
9027: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9028: }else{
9029: printf(" 0.");
9030: fprintf(ficparo," 0.");
9031: }
9032: }
9033: }
9034: } /* end lk */
9035: } /* end lj */
9036: } /* end li */
9037: printf("\n");
9038: fprintf(ficparo,"\n");
9039: numlinepar++;
9040: } /* end k*/
9041: } /*end j */
9042: } /* end i */
9043: } /* end itimes */
9044:
9045: } /* end of prwizard */
9046: /******************* Gompertz Likelihood ******************************/
9047: double gompertz(double x[])
9048: {
9049: double A,B,L=0.0,sump=0.,num=0.;
9050: int i,n=0; /* n is the size of the sample */
9051:
1.220 brouard 9052: for (i=1;i<=imx ; i++) {
1.126 brouard 9053: sump=sump+weight[i];
9054: /* sump=sump+1;*/
9055: num=num+1;
9056: }
9057:
9058:
9059: /* for (i=0; i<=imx; i++)
9060: 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]);*/
9061:
9062: for (i=1;i<=imx ; i++)
9063: {
9064: if (cens[i] == 1 && wav[i]>1)
9065: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9066:
9067: if (cens[i] == 0 && wav[i]>1)
9068: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
9069: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
9070:
9071: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9072: if (wav[i] > 1 ) { /* ??? */
9073: L=L+A*weight[i];
9074: /* 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]);*/
9075: }
9076: }
9077:
9078: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9079:
9080: return -2*L*num/sump;
9081: }
9082:
1.136 brouard 9083: #ifdef GSL
9084: /******************* Gompertz_f Likelihood ******************************/
9085: double gompertz_f(const gsl_vector *v, void *params)
9086: {
9087: double A,B,LL=0.0,sump=0.,num=0.;
9088: double *x= (double *) v->data;
9089: int i,n=0; /* n is the size of the sample */
9090:
9091: for (i=0;i<=imx-1 ; i++) {
9092: sump=sump+weight[i];
9093: /* sump=sump+1;*/
9094: num=num+1;
9095: }
9096:
9097:
9098: /* for (i=0; i<=imx; i++)
9099: 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]);*/
9100: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9101: for (i=1;i<=imx ; i++)
9102: {
9103: if (cens[i] == 1 && wav[i]>1)
9104: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9105:
9106: if (cens[i] == 0 && wav[i]>1)
9107: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9108: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9109:
9110: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9111: if (wav[i] > 1 ) { /* ??? */
9112: LL=LL+A*weight[i];
9113: /* 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]);*/
9114: }
9115: }
9116:
9117: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9118: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9119:
9120: return -2*LL*num/sump;
9121: }
9122: #endif
9123:
1.126 brouard 9124: /******************* Printing html file ***********/
1.201 brouard 9125: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9126: int lastpass, int stepm, int weightopt, char model[],\
9127: int imx, double p[],double **matcov,double agemortsup){
9128: int i,k;
9129:
9130: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9131: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9132: for (i=1;i<=2;i++)
9133: 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 9134: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9135: fprintf(fichtm,"</ul>");
9136:
9137: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9138:
9139: 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>");
9140:
9141: for (k=agegomp;k<(agemortsup-2);k++)
9142: 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]);
9143:
9144:
9145: fflush(fichtm);
9146: }
9147:
9148: /******************* Gnuplot file **************/
1.201 brouard 9149: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9150:
9151: char dirfileres[132],optfileres[132];
1.164 brouard 9152:
1.126 brouard 9153: int ng;
9154:
9155:
9156: /*#ifdef windows */
9157: fprintf(ficgp,"cd \"%s\" \n",pathc);
9158: /*#endif */
9159:
9160:
9161: strcpy(dirfileres,optionfilefiname);
9162: strcpy(optfileres,"vpl");
1.199 brouard 9163: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9164: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9165: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9166: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9167: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9168:
9169: }
9170:
1.136 brouard 9171: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9172: {
1.126 brouard 9173:
1.136 brouard 9174: /*-------- data file ----------*/
9175: FILE *fic;
9176: char dummy[]=" ";
1.240 brouard 9177: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9178: int lstra;
1.136 brouard 9179: int linei, month, year,iout;
9180: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9181: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9182: char *stratrunc;
1.223 brouard 9183:
1.240 brouard 9184: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9185: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9186:
1.240 brouard 9187: for(v=1; v <=ncovcol;v++){
9188: DummyV[v]=0;
9189: FixedV[v]=0;
9190: }
9191: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9192: DummyV[v]=1;
9193: FixedV[v]=0;
9194: }
9195: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9196: DummyV[v]=0;
9197: FixedV[v]=1;
9198: }
9199: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9200: DummyV[v]=1;
9201: FixedV[v]=1;
9202: }
9203: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9204: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9205: 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]);
9206: }
1.126 brouard 9207:
1.136 brouard 9208: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9209: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9210: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9211: }
1.126 brouard 9212:
1.136 brouard 9213: i=1;
9214: linei=0;
9215: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9216: linei=linei+1;
9217: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9218: if(line[j] == '\t')
9219: line[j] = ' ';
9220: }
9221: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9222: ;
9223: };
9224: line[j+1]=0; /* Trims blanks at end of line */
9225: if(line[0]=='#'){
9226: fprintf(ficlog,"Comment line\n%s\n",line);
9227: printf("Comment line\n%s\n",line);
9228: continue;
9229: }
9230: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9231: strcpy(line, linetmp);
1.223 brouard 9232:
9233: /* Loops on waves */
9234: for (j=maxwav;j>=1;j--){
9235: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9236: cutv(stra, strb, line, ' ');
9237: if(strb[0]=='.') { /* Missing value */
9238: lval=-1;
9239: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9240: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9241: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9242: 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);
9243: 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);
9244: return 1;
9245: }
9246: }else{
9247: errno=0;
9248: /* what_kind_of_number(strb); */
9249: dval=strtod(strb,&endptr);
9250: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9251: /* if(strb != endptr && *endptr == '\0') */
9252: /* dval=dlval; */
9253: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9254: if( strb[0]=='\0' || (*endptr != '\0')){
9255: 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);
9256: 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);
9257: return 1;
9258: }
9259: cotqvar[j][iv][i]=dval;
9260: cotvar[j][ntv+iv][i]=dval;
9261: }
9262: strcpy(line,stra);
1.223 brouard 9263: }/* end loop ntqv */
1.225 brouard 9264:
1.223 brouard 9265: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9266: cutv(stra, strb, line, ' ');
9267: if(strb[0]=='.') { /* Missing value */
9268: lval=-1;
9269: }else{
9270: errno=0;
9271: lval=strtol(strb,&endptr,10);
9272: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9273: if( strb[0]=='\0' || (*endptr != '\0')){
9274: 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);
9275: 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);
9276: return 1;
9277: }
9278: }
9279: if(lval <-1 || lval >1){
9280: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9281: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9282: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9283: For example, for multinomial values like 1, 2 and 3,\n \
9284: build V1=0 V2=0 for the reference value (1),\n \
9285: V1=1 V2=0 for (2) \n \
1.223 brouard 9286: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9287: output of IMaCh is often meaningless.\n \
1.223 brouard 9288: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9289: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9290: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9291: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9292: For example, for multinomial values like 1, 2 and 3,\n \
9293: build V1=0 V2=0 for the reference value (1),\n \
9294: V1=1 V2=0 for (2) \n \
1.223 brouard 9295: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9296: output of IMaCh is often meaningless.\n \
1.223 brouard 9297: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9298: return 1;
9299: }
9300: cotvar[j][iv][i]=(double)(lval);
9301: strcpy(line,stra);
1.223 brouard 9302: }/* end loop ntv */
1.225 brouard 9303:
1.223 brouard 9304: /* Statuses at wave */
1.137 brouard 9305: cutv(stra, strb, line, ' ');
1.223 brouard 9306: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9307: lval=-1;
1.136 brouard 9308: }else{
1.238 brouard 9309: errno=0;
9310: lval=strtol(strb,&endptr,10);
9311: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9312: if( strb[0]=='\0' || (*endptr != '\0')){
9313: 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);
9314: 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);
9315: return 1;
9316: }
1.136 brouard 9317: }
1.225 brouard 9318:
1.136 brouard 9319: s[j][i]=lval;
1.225 brouard 9320:
1.223 brouard 9321: /* Date of Interview */
1.136 brouard 9322: strcpy(line,stra);
9323: cutv(stra, strb,line,' ');
1.169 brouard 9324: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9325: }
1.169 brouard 9326: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9327: month=99;
9328: year=9999;
1.136 brouard 9329: }else{
1.225 brouard 9330: 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);
9331: 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);
9332: return 1;
1.136 brouard 9333: }
9334: anint[j][i]= (double) year;
9335: mint[j][i]= (double)month;
9336: strcpy(line,stra);
1.223 brouard 9337: } /* End loop on waves */
1.225 brouard 9338:
1.223 brouard 9339: /* Date of death */
1.136 brouard 9340: cutv(stra, strb,line,' ');
1.169 brouard 9341: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9342: }
1.169 brouard 9343: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9344: month=99;
9345: year=9999;
9346: }else{
1.141 brouard 9347: 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 9348: 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);
9349: return 1;
1.136 brouard 9350: }
9351: andc[i]=(double) year;
9352: moisdc[i]=(double) month;
9353: strcpy(line,stra);
9354:
1.223 brouard 9355: /* Date of birth */
1.136 brouard 9356: cutv(stra, strb,line,' ');
1.169 brouard 9357: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9358: }
1.169 brouard 9359: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9360: month=99;
9361: year=9999;
9362: }else{
1.141 brouard 9363: 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);
9364: 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 9365: return 1;
1.136 brouard 9366: }
9367: if (year==9999) {
1.141 brouard 9368: 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);
9369: 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 9370: return 1;
9371:
1.136 brouard 9372: }
9373: annais[i]=(double)(year);
9374: moisnais[i]=(double)(month);
9375: strcpy(line,stra);
1.225 brouard 9376:
1.223 brouard 9377: /* Sample weight */
1.136 brouard 9378: cutv(stra, strb,line,' ');
9379: errno=0;
9380: dval=strtod(strb,&endptr);
9381: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9382: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9383: 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 9384: fflush(ficlog);
9385: return 1;
9386: }
9387: weight[i]=dval;
9388: strcpy(line,stra);
1.225 brouard 9389:
1.223 brouard 9390: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9391: cutv(stra, strb, line, ' ');
9392: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9393: lval=-1;
1.223 brouard 9394: }else{
1.225 brouard 9395: errno=0;
9396: /* what_kind_of_number(strb); */
9397: dval=strtod(strb,&endptr);
9398: /* if(strb != endptr && *endptr == '\0') */
9399: /* dval=dlval; */
9400: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9401: if( strb[0]=='\0' || (*endptr != '\0')){
9402: 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);
9403: 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);
9404: return 1;
9405: }
9406: coqvar[iv][i]=dval;
1.226 brouard 9407: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9408: }
9409: strcpy(line,stra);
9410: }/* end loop nqv */
1.136 brouard 9411:
1.223 brouard 9412: /* Covariate values */
1.136 brouard 9413: for (j=ncovcol;j>=1;j--){
9414: cutv(stra, strb,line,' ');
1.223 brouard 9415: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9416: lval=-1;
1.136 brouard 9417: }else{
1.225 brouard 9418: errno=0;
9419: lval=strtol(strb,&endptr,10);
9420: if( strb[0]=='\0' || (*endptr != '\0')){
9421: 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);
9422: 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);
9423: return 1;
9424: }
1.136 brouard 9425: }
9426: if(lval <-1 || lval >1){
1.225 brouard 9427: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9428: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9429: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9430: For example, for multinomial values like 1, 2 and 3,\n \
9431: build V1=0 V2=0 for the reference value (1),\n \
9432: V1=1 V2=0 for (2) \n \
1.136 brouard 9433: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9434: output of IMaCh is often meaningless.\n \
1.136 brouard 9435: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9436: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9437: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9438: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9439: For example, for multinomial values like 1, 2 and 3,\n \
9440: build V1=0 V2=0 for the reference value (1),\n \
9441: V1=1 V2=0 for (2) \n \
1.136 brouard 9442: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9443: output of IMaCh is often meaningless.\n \
1.136 brouard 9444: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9445: return 1;
1.136 brouard 9446: }
9447: covar[j][i]=(double)(lval);
9448: strcpy(line,stra);
9449: }
9450: lstra=strlen(stra);
1.225 brouard 9451:
1.136 brouard 9452: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9453: stratrunc = &(stra[lstra-9]);
9454: num[i]=atol(stratrunc);
9455: }
9456: else
9457: num[i]=atol(stra);
9458: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9459: 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;}*/
9460:
9461: i=i+1;
9462: } /* End loop reading data */
1.225 brouard 9463:
1.136 brouard 9464: *imax=i-1; /* Number of individuals */
9465: fclose(fic);
1.225 brouard 9466:
1.136 brouard 9467: return (0);
1.164 brouard 9468: /* endread: */
1.225 brouard 9469: printf("Exiting readdata: ");
9470: fclose(fic);
9471: return (1);
1.223 brouard 9472: }
1.126 brouard 9473:
1.234 brouard 9474: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9475: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9476: while (*p2 == ' ')
1.234 brouard 9477: p2++;
9478: /* while ((*p1++ = *p2++) !=0) */
9479: /* ; */
9480: /* do */
9481: /* while (*p2 == ' ') */
9482: /* p2++; */
9483: /* while (*p1++ == *p2++); */
9484: *stri=p2;
1.145 brouard 9485: }
9486:
1.235 brouard 9487: int decoderesult ( char resultline[], int nres)
1.230 brouard 9488: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9489: {
1.235 brouard 9490: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9491: char resultsav[MAXLINE];
1.234 brouard 9492: int resultmodel[MAXLINE];
9493: int modelresult[MAXLINE];
1.230 brouard 9494: char stra[80], strb[80], strc[80], strd[80],stre[80];
9495:
1.234 brouard 9496: removefirstspace(&resultline);
1.233 brouard 9497: printf("decoderesult:%s\n",resultline);
1.230 brouard 9498:
9499: if (strstr(resultline,"v") !=0){
9500: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9501: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9502: return 1;
9503: }
9504: trimbb(resultsav, resultline);
9505: if (strlen(resultsav) >1){
9506: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9507: }
1.253 brouard 9508: if(j == 0){ /* Resultline but no = */
9509: TKresult[nres]=0; /* Combination for the nresult and the model */
9510: return (0);
9511: }
9512:
1.234 brouard 9513: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9514: 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);
9515: 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);
9516: }
9517: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9518: if(nbocc(resultsav,'=') >1){
9519: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9520: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9521: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9522: }else
9523: cutl(strc,strd,resultsav,'=');
1.230 brouard 9524: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9525:
1.230 brouard 9526: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9527: Tvarsel[k]=atoi(strc);
9528: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9529: /* cptcovsel++; */
9530: if (nbocc(stra,'=') >0)
9531: strcpy(resultsav,stra); /* and analyzes it */
9532: }
1.235 brouard 9533: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9534: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9535: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9536: match=0;
1.236 brouard 9537: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9538: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9539: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9540: match=1;
9541: break;
9542: }
9543: }
9544: if(match == 0){
9545: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9546: }
9547: }
9548: }
1.235 brouard 9549: /* Checking for missing or useless values in comparison of current model needs */
9550: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9551: match=0;
1.235 brouard 9552: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9553: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9554: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9555: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9556: ++match;
9557: }
9558: }
9559: }
9560: if(match == 0){
9561: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9562: }else if(match > 1){
9563: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9564: }
9565: }
1.235 brouard 9566:
1.234 brouard 9567: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9568: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9569: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9570: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9571: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9572: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9573: /* 1 0 0 0 */
9574: /* 2 1 0 0 */
9575: /* 3 0 1 0 */
9576: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9577: /* 5 0 0 1 */
9578: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9579: /* 7 0 1 1 */
9580: /* 8 1 1 1 */
1.237 brouard 9581: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9582: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9583: /* V5*age V5 known which value for nres? */
9584: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9585: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9586: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9587: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9588: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9589: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9590: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9591: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9592: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9593: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9594: k4++;;
9595: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9596: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9597: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9598: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9599: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9600: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9601: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9602: k4q++;;
9603: }
9604: }
1.234 brouard 9605:
1.235 brouard 9606: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9607: return (0);
9608: }
1.235 brouard 9609:
1.230 brouard 9610: int decodemodel( char model[], int lastobs)
9611: /**< This routine decodes the model and returns:
1.224 brouard 9612: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9613: * - nagesqr = 1 if age*age in the model, otherwise 0.
9614: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9615: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9616: * - cptcovage number of covariates with age*products =2
9617: * - cptcovs number of simple covariates
9618: * - 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
9619: * which is a new column after the 9 (ncovcol) variables.
9620: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9621: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9622: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9623: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9624: */
1.136 brouard 9625: {
1.238 brouard 9626: int i, j, k, ks, v;
1.227 brouard 9627: int j1, k1, k2, k3, k4;
1.136 brouard 9628: char modelsav[80];
1.145 brouard 9629: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9630: char *strpt;
1.136 brouard 9631:
1.145 brouard 9632: /*removespace(model);*/
1.136 brouard 9633: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9634: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9635: if (strstr(model,"AGE") !=0){
1.192 brouard 9636: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9637: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9638: return 1;
9639: }
1.141 brouard 9640: if (strstr(model,"v") !=0){
9641: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9642: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9643: return 1;
9644: }
1.187 brouard 9645: strcpy(modelsav,model);
9646: if ((strpt=strstr(model,"age*age")) !=0){
9647: printf(" strpt=%s, model=%s\n",strpt, model);
9648: if(strpt != model){
1.234 brouard 9649: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9650: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9651: corresponding column of parameters.\n",model);
1.234 brouard 9652: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9653: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9654: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9655: return 1;
1.225 brouard 9656: }
1.187 brouard 9657: nagesqr=1;
9658: if (strstr(model,"+age*age") !=0)
1.234 brouard 9659: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9660: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9661: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9662: else
1.234 brouard 9663: substrchaine(modelsav, model, "age*age");
1.187 brouard 9664: }else
9665: nagesqr=0;
9666: if (strlen(modelsav) >1){
9667: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9668: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9669: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9670: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9671: * cst, age and age*age
9672: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9673: /* including age products which are counted in cptcovage.
9674: * but the covariates which are products must be treated
9675: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9676: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9677: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9678:
9679:
1.187 brouard 9680: /* Design
9681: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9682: * < ncovcol=8 >
9683: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9684: * k= 1 2 3 4 5 6 7 8
9685: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9686: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9687: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9688: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9689: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9690: * Tage[++cptcovage]=k
9691: * if products, new covar are created after ncovcol with k1
9692: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9693: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9694: * 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
9695: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9696: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9697: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9698: * < ncovcol=8 >
9699: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9700: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9701: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9702: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9703: * p Tprod[1]@2={ 6, 5}
9704: *p Tvard[1][1]@4= {7, 8, 5, 6}
9705: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9706: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9707: *How to reorganize?
9708: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9709: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9710: * {2, 1, 4, 8, 5, 6, 3, 7}
9711: * Struct []
9712: */
1.225 brouard 9713:
1.187 brouard 9714: /* This loop fills the array Tvar from the string 'model'.*/
9715: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9716: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9717: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9718: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9719: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9720: /* k=1 Tvar[1]=2 (from V2) */
9721: /* k=5 Tvar[5] */
9722: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9723: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9724: /* } */
1.198 brouard 9725: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9726: /*
9727: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9728: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9729: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9730: }
1.187 brouard 9731: cptcovage=0;
9732: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9733: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9734: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9735: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9736: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9737: /*scanf("%d",i);*/
9738: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9739: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9740: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9741: /* covar is not filled and then is empty */
9742: cptcovprod--;
9743: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9744: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9745: Typevar[k]=1; /* 1 for age product */
9746: cptcovage++; /* Sums the number of covariates which include age as a product */
9747: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9748: /*printf("stre=%s ", stre);*/
9749: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9750: cptcovprod--;
9751: cutl(stre,strb,strc,'V');
9752: Tvar[k]=atoi(stre);
9753: Typevar[k]=1; /* 1 for age product */
9754: cptcovage++;
9755: Tage[cptcovage]=k;
9756: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9757: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9758: cptcovn++;
9759: cptcovprodnoage++;k1++;
9760: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9761: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9762: because this model-covariate is a construction we invent a new column
9763: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9764: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9765: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9766: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9767: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9768: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9769: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9770: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9771: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9772: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9773: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9774: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9775: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9776: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9777: for (i=1; i<=lastobs;i++){
9778: /* Computes the new covariate which is a product of
9779: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9780: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9781: }
9782: } /* End age is not in the model */
9783: } /* End if model includes a product */
9784: else { /* no more sum */
9785: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9786: /* scanf("%d",i);*/
9787: cutl(strd,strc,strb,'V');
9788: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9789: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9790: Tvar[k]=atoi(strd);
9791: Typevar[k]=0; /* 0 for simple covariates */
9792: }
9793: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9794: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9795: scanf("%d",i);*/
1.187 brouard 9796: } /* end of loop + on total covariates */
9797: } /* end if strlen(modelsave == 0) age*age might exist */
9798: } /* end if strlen(model == 0) */
1.136 brouard 9799:
9800: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9801: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9802:
1.136 brouard 9803: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9804: printf("cptcovprod=%d ", cptcovprod);
9805: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9806: scanf("%d ",i);*/
9807:
9808:
1.230 brouard 9809: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9810: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9811: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9812: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9813: k = 1 2 3 4 5 6 7 8 9
9814: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9815: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9816: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9817: Dummy[k] 1 0 0 0 3 1 1 2 3
9818: Tmodelind[combination of covar]=k;
1.225 brouard 9819: */
9820: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9821: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9822: /* 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 9823: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9824: printf("Model=%s\n\
9825: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9826: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9827: 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);
9828: fprintf(ficlog,"Model=%s\n\
9829: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9830: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9831: 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 9832: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9833: 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 */
9834: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9835: Fixed[k]= 0;
9836: Dummy[k]= 0;
1.225 brouard 9837: ncoveff++;
1.232 brouard 9838: ncovf++;
1.234 brouard 9839: nsd++;
9840: modell[k].maintype= FTYPE;
9841: TvarsD[nsd]=Tvar[k];
9842: TvarsDind[nsd]=k;
9843: TvarF[ncovf]=Tvar[k];
9844: TvarFind[ncovf]=k;
9845: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9846: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9847: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9848: Fixed[k]= 0;
9849: Dummy[k]= 0;
9850: ncoveff++;
9851: ncovf++;
9852: modell[k].maintype= FTYPE;
9853: TvarF[ncovf]=Tvar[k];
9854: TvarFind[ncovf]=k;
1.230 brouard 9855: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9856: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9857: }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 9858: Fixed[k]= 0;
9859: Dummy[k]= 1;
1.230 brouard 9860: nqfveff++;
1.234 brouard 9861: modell[k].maintype= FTYPE;
9862: modell[k].subtype= FQ;
9863: nsq++;
9864: TvarsQ[nsq]=Tvar[k];
9865: TvarsQind[nsq]=k;
1.232 brouard 9866: ncovf++;
1.234 brouard 9867: TvarF[ncovf]=Tvar[k];
9868: TvarFind[ncovf]=k;
1.231 brouard 9869: 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 9870: 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 9871: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9872: Fixed[k]= 1;
9873: Dummy[k]= 0;
1.225 brouard 9874: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9875: modell[k].maintype= VTYPE;
9876: modell[k].subtype= VD;
9877: nsd++;
9878: TvarsD[nsd]=Tvar[k];
9879: TvarsDind[nsd]=k;
9880: ncovv++; /* Only simple time varying variables */
9881: TvarV[ncovv]=Tvar[k];
1.242 brouard 9882: 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 9883: 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 */
9884: 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 9885: 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);
9886: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9887: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9888: Fixed[k]= 1;
9889: Dummy[k]= 1;
9890: nqtveff++;
9891: modell[k].maintype= VTYPE;
9892: modell[k].subtype= VQ;
9893: ncovv++; /* Only simple time varying variables */
9894: nsq++;
9895: TvarsQ[nsq]=Tvar[k];
9896: TvarsQind[nsq]=k;
9897: TvarV[ncovv]=Tvar[k];
1.242 brouard 9898: 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 9899: 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 */
9900: 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 9901: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9902: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9903: 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 9904: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9905: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9906: ncova++;
9907: TvarA[ncova]=Tvar[k];
9908: TvarAind[ncova]=k;
1.231 brouard 9909: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9910: Fixed[k]= 2;
9911: Dummy[k]= 2;
9912: modell[k].maintype= ATYPE;
9913: modell[k].subtype= APFD;
9914: /* ncoveff++; */
1.227 brouard 9915: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 9916: Fixed[k]= 2;
9917: Dummy[k]= 3;
9918: modell[k].maintype= ATYPE;
9919: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
9920: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 9921: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 9922: Fixed[k]= 3;
9923: Dummy[k]= 2;
9924: modell[k].maintype= ATYPE;
9925: modell[k].subtype= APVD; /* Product age * varying dummy */
9926: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 9927: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9928: Fixed[k]= 3;
9929: Dummy[k]= 3;
9930: modell[k].maintype= ATYPE;
9931: modell[k].subtype= APVQ; /* Product age * varying quantitative */
9932: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 9933: }
9934: }else if (Typevar[k] == 2) { /* product without age */
9935: k1=Tposprod[k];
9936: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 9937: if(Tvard[k1][2] <=ncovcol){
9938: Fixed[k]= 1;
9939: Dummy[k]= 0;
9940: modell[k].maintype= FTYPE;
9941: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
9942: ncovf++; /* Fixed variables without age */
9943: TvarF[ncovf]=Tvar[k];
9944: TvarFind[ncovf]=k;
9945: }else if(Tvard[k1][2] <=ncovcol+nqv){
9946: Fixed[k]= 0; /* or 2 ?*/
9947: Dummy[k]= 1;
9948: modell[k].maintype= FTYPE;
9949: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
9950: ncovf++; /* Varying variables without age */
9951: TvarF[ncovf]=Tvar[k];
9952: TvarFind[ncovf]=k;
9953: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9954: Fixed[k]= 1;
9955: Dummy[k]= 0;
9956: modell[k].maintype= VTYPE;
9957: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
9958: ncovv++; /* Varying variables without age */
9959: TvarV[ncovv]=Tvar[k];
9960: TvarVind[ncovv]=k;
9961: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9962: Fixed[k]= 1;
9963: Dummy[k]= 1;
9964: modell[k].maintype= VTYPE;
9965: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
9966: ncovv++; /* Varying variables without age */
9967: TvarV[ncovv]=Tvar[k];
9968: TvarVind[ncovv]=k;
9969: }
1.227 brouard 9970: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 9971: if(Tvard[k1][2] <=ncovcol){
9972: Fixed[k]= 0; /* or 2 ?*/
9973: Dummy[k]= 1;
9974: modell[k].maintype= FTYPE;
9975: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
9976: ncovf++; /* Fixed variables without age */
9977: TvarF[ncovf]=Tvar[k];
9978: TvarFind[ncovf]=k;
9979: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9980: Fixed[k]= 1;
9981: Dummy[k]= 1;
9982: modell[k].maintype= VTYPE;
9983: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
9984: ncovv++; /* Varying variables without age */
9985: TvarV[ncovv]=Tvar[k];
9986: TvarVind[ncovv]=k;
9987: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9988: Fixed[k]= 1;
9989: Dummy[k]= 1;
9990: modell[k].maintype= VTYPE;
9991: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
9992: ncovv++; /* Varying variables without age */
9993: TvarV[ncovv]=Tvar[k];
9994: TvarVind[ncovv]=k;
9995: ncovv++; /* Varying variables without age */
9996: TvarV[ncovv]=Tvar[k];
9997: TvarVind[ncovv]=k;
9998: }
1.227 brouard 9999: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10000: if(Tvard[k1][2] <=ncovcol){
10001: Fixed[k]= 1;
10002: Dummy[k]= 1;
10003: modell[k].maintype= VTYPE;
10004: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10005: ncovv++; /* Varying variables without age */
10006: TvarV[ncovv]=Tvar[k];
10007: TvarVind[ncovv]=k;
10008: }else if(Tvard[k1][2] <=ncovcol+nqv){
10009: Fixed[k]= 1;
10010: Dummy[k]= 1;
10011: modell[k].maintype= VTYPE;
10012: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10013: ncovv++; /* Varying variables without age */
10014: TvarV[ncovv]=Tvar[k];
10015: TvarVind[ncovv]=k;
10016: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10017: Fixed[k]= 1;
10018: Dummy[k]= 0;
10019: modell[k].maintype= VTYPE;
10020: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10021: ncovv++; /* Varying variables without age */
10022: TvarV[ncovv]=Tvar[k];
10023: TvarVind[ncovv]=k;
10024: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10025: Fixed[k]= 1;
10026: Dummy[k]= 1;
10027: modell[k].maintype= VTYPE;
10028: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10029: ncovv++; /* Varying variables without age */
10030: TvarV[ncovv]=Tvar[k];
10031: TvarVind[ncovv]=k;
10032: }
1.227 brouard 10033: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10034: if(Tvard[k1][2] <=ncovcol){
10035: Fixed[k]= 1;
10036: Dummy[k]= 1;
10037: modell[k].maintype= VTYPE;
10038: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10039: ncovv++; /* Varying variables without age */
10040: TvarV[ncovv]=Tvar[k];
10041: TvarVind[ncovv]=k;
10042: }else if(Tvard[k1][2] <=ncovcol+nqv){
10043: Fixed[k]= 1;
10044: Dummy[k]= 1;
10045: modell[k].maintype= VTYPE;
10046: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10047: ncovv++; /* Varying variables without age */
10048: TvarV[ncovv]=Tvar[k];
10049: TvarVind[ncovv]=k;
10050: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10051: Fixed[k]= 1;
10052: Dummy[k]= 1;
10053: modell[k].maintype= VTYPE;
10054: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10055: ncovv++; /* Varying variables without age */
10056: TvarV[ncovv]=Tvar[k];
10057: TvarVind[ncovv]=k;
10058: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10059: Fixed[k]= 1;
10060: Dummy[k]= 1;
10061: modell[k].maintype= VTYPE;
10062: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10063: ncovv++; /* Varying variables without age */
10064: TvarV[ncovv]=Tvar[k];
10065: TvarVind[ncovv]=k;
10066: }
1.227 brouard 10067: }else{
1.240 brouard 10068: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10069: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10070: } /*end k1*/
1.225 brouard 10071: }else{
1.226 brouard 10072: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10073: 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 10074: }
1.227 brouard 10075: 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 10076: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10077: 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]);
10078: }
10079: /* Searching for doublons in the model */
10080: for(k1=1; k1<= cptcovt;k1++){
10081: for(k2=1; k2 <k1;k2++){
1.285 brouard 10082: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10083: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10084: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10085: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10086: 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]);
10087: 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 10088: return(1);
10089: }
10090: }else if (Typevar[k1] ==2){
10091: k3=Tposprod[k1];
10092: k4=Tposprod[k2];
10093: 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])) ){
10094: 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]]);
10095: 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);
10096: return(1);
10097: }
10098: }
1.227 brouard 10099: }
10100: }
1.225 brouard 10101: }
10102: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10103: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10104: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10105: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10106: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10107: /*endread:*/
1.225 brouard 10108: printf("Exiting decodemodel: ");
10109: return (1);
1.136 brouard 10110: }
10111:
1.169 brouard 10112: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10113: {/* Check ages at death */
1.136 brouard 10114: int i, m;
1.218 brouard 10115: int firstone=0;
10116:
1.136 brouard 10117: for (i=1; i<=imx; i++) {
10118: for(m=2; (m<= maxwav); m++) {
10119: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10120: anint[m][i]=9999;
1.216 brouard 10121: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10122: s[m][i]=-1;
1.136 brouard 10123: }
10124: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10125: *nberr = *nberr + 1;
1.218 brouard 10126: if(firstone == 0){
10127: firstone=1;
1.260 brouard 10128: 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 10129: }
1.262 brouard 10130: 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 10131: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10132: }
10133: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10134: (*nberr)++;
1.259 brouard 10135: 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 10136: 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 10137: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10138: }
10139: }
10140: }
10141:
10142: for (i=1; i<=imx; i++) {
10143: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10144: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10145: 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 10146: if (s[m][i] >= nlstate+1) {
1.169 brouard 10147: if(agedc[i]>0){
10148: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10149: agev[m][i]=agedc[i];
1.214 brouard 10150: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10151: }else {
1.136 brouard 10152: if ((int)andc[i]!=9999){
10153: nbwarn++;
10154: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10155: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10156: agev[m][i]=-1;
10157: }
10158: }
1.169 brouard 10159: } /* agedc > 0 */
1.214 brouard 10160: } /* end if */
1.136 brouard 10161: else if(s[m][i] !=9){ /* Standard case, age in fractional
10162: years but with the precision of a month */
10163: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10164: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10165: agev[m][i]=1;
10166: else if(agev[m][i] < *agemin){
10167: *agemin=agev[m][i];
10168: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10169: }
10170: else if(agev[m][i] >*agemax){
10171: *agemax=agev[m][i];
1.156 brouard 10172: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10173: }
10174: /*agev[m][i]=anint[m][i]-annais[i];*/
10175: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10176: } /* en if 9*/
1.136 brouard 10177: else { /* =9 */
1.214 brouard 10178: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10179: agev[m][i]=1;
10180: s[m][i]=-1;
10181: }
10182: }
1.214 brouard 10183: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10184: agev[m][i]=1;
1.214 brouard 10185: else{
10186: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10187: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10188: agev[m][i]=0;
10189: }
10190: } /* End for lastpass */
10191: }
1.136 brouard 10192:
10193: for (i=1; i<=imx; i++) {
10194: for(m=firstpass; (m<=lastpass); m++){
10195: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10196: (*nberr)++;
1.136 brouard 10197: 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);
10198: 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);
10199: return 1;
10200: }
10201: }
10202: }
10203:
10204: /*for (i=1; i<=imx; i++){
10205: for (m=firstpass; (m<lastpass); m++){
10206: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10207: }
10208:
10209: }*/
10210:
10211:
1.139 brouard 10212: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10213: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10214:
10215: return (0);
1.164 brouard 10216: /* endread:*/
1.136 brouard 10217: printf("Exiting calandcheckages: ");
10218: return (1);
10219: }
10220:
1.172 brouard 10221: #if defined(_MSC_VER)
10222: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10223: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10224: //#include "stdafx.h"
10225: //#include <stdio.h>
10226: //#include <tchar.h>
10227: //#include <windows.h>
10228: //#include <iostream>
10229: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10230:
10231: LPFN_ISWOW64PROCESS fnIsWow64Process;
10232:
10233: BOOL IsWow64()
10234: {
10235: BOOL bIsWow64 = FALSE;
10236:
10237: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10238: // (HANDLE, PBOOL);
10239:
10240: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10241:
10242: HMODULE module = GetModuleHandle(_T("kernel32"));
10243: const char funcName[] = "IsWow64Process";
10244: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10245: GetProcAddress(module, funcName);
10246:
10247: if (NULL != fnIsWow64Process)
10248: {
10249: if (!fnIsWow64Process(GetCurrentProcess(),
10250: &bIsWow64))
10251: //throw std::exception("Unknown error");
10252: printf("Unknown error\n");
10253: }
10254: return bIsWow64 != FALSE;
10255: }
10256: #endif
1.177 brouard 10257:
1.191 brouard 10258: void syscompilerinfo(int logged)
1.292 brouard 10259: {
10260: #include <stdint.h>
10261:
10262: /* #include "syscompilerinfo.h"*/
1.185 brouard 10263: /* command line Intel compiler 32bit windows, XP compatible:*/
10264: /* /GS /W3 /Gy
10265: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10266: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10267: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10268: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10269: */
10270: /* 64 bits */
1.185 brouard 10271: /*
10272: /GS /W3 /Gy
10273: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10274: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10275: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10276: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10277: /* Optimization are useless and O3 is slower than O2 */
10278: /*
10279: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10280: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10281: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10282: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10283: */
1.186 brouard 10284: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10285: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10286: /PDB:"visual studio
10287: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10288: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10289: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10290: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10291: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10292: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10293: uiAccess='false'"
10294: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10295: /NOLOGO /TLBID:1
10296: */
1.292 brouard 10297:
10298:
1.177 brouard 10299: #if defined __INTEL_COMPILER
1.178 brouard 10300: #if defined(__GNUC__)
10301: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10302: #endif
1.177 brouard 10303: #elif defined(__GNUC__)
1.179 brouard 10304: #ifndef __APPLE__
1.174 brouard 10305: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10306: #endif
1.177 brouard 10307: struct utsname sysInfo;
1.178 brouard 10308: int cross = CROSS;
10309: if (cross){
10310: printf("Cross-");
1.191 brouard 10311: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10312: }
1.174 brouard 10313: #endif
10314:
1.191 brouard 10315: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10316: #if defined(__clang__)
1.191 brouard 10317: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10318: #endif
10319: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10320: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10321: #endif
10322: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10323: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10324: #endif
10325: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10326: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10327: #endif
10328: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10329: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10330: #endif
10331: #if defined(_MSC_VER)
1.191 brouard 10332: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10333: #endif
10334: #if defined(__PGI)
1.191 brouard 10335: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10336: #endif
10337: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10338: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10339: #endif
1.191 brouard 10340: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10341:
1.167 brouard 10342: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10343: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10344: // Windows (x64 and x86)
1.191 brouard 10345: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10346: #elif __unix__ // all unices, not all compilers
10347: // Unix
1.191 brouard 10348: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10349: #elif __linux__
10350: // linux
1.191 brouard 10351: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10352: #elif __APPLE__
1.174 brouard 10353: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10354: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10355: #endif
10356:
10357: /* __MINGW32__ */
10358: /* __CYGWIN__ */
10359: /* __MINGW64__ */
10360: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10361: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10362: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10363: /* _WIN64 // Defined for applications for Win64. */
10364: /* _M_X64 // Defined for compilations that target x64 processors. */
10365: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10366:
1.167 brouard 10367: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10368: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10369: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10370: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10371: #else
1.191 brouard 10372: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10373: #endif
10374:
1.169 brouard 10375: #if defined(__GNUC__)
10376: # if defined(__GNUC_PATCHLEVEL__)
10377: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10378: + __GNUC_MINOR__ * 100 \
10379: + __GNUC_PATCHLEVEL__)
10380: # else
10381: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10382: + __GNUC_MINOR__ * 100)
10383: # endif
1.174 brouard 10384: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10385: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10386:
10387: if (uname(&sysInfo) != -1) {
10388: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10389: 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 10390: }
10391: else
10392: perror("uname() error");
1.179 brouard 10393: //#ifndef __INTEL_COMPILER
10394: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10395: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10396: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10397: #endif
1.169 brouard 10398: #endif
1.172 brouard 10399:
1.286 brouard 10400: // void main ()
1.172 brouard 10401: // {
1.169 brouard 10402: #if defined(_MSC_VER)
1.174 brouard 10403: if (IsWow64()){
1.191 brouard 10404: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10405: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10406: }
10407: else{
1.191 brouard 10408: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10409: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10410: }
1.172 brouard 10411: // printf("\nPress Enter to continue...");
10412: // getchar();
10413: // }
10414:
1.169 brouard 10415: #endif
10416:
1.167 brouard 10417:
1.219 brouard 10418: }
1.136 brouard 10419:
1.219 brouard 10420: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10421: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10422: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10423: /* double ftolpl = 1.e-10; */
1.180 brouard 10424: double age, agebase, agelim;
1.203 brouard 10425: double tot;
1.180 brouard 10426:
1.202 brouard 10427: strcpy(filerespl,"PL_");
10428: strcat(filerespl,fileresu);
10429: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10430: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10431: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10432: }
1.288 brouard 10433: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10434: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10435: pstamp(ficrespl);
1.288 brouard 10436: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10437: fprintf(ficrespl,"#Age ");
10438: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10439: fprintf(ficrespl,"\n");
1.180 brouard 10440:
1.219 brouard 10441: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10442:
1.219 brouard 10443: agebase=ageminpar;
10444: agelim=agemaxpar;
1.180 brouard 10445:
1.227 brouard 10446: /* i1=pow(2,ncoveff); */
1.234 brouard 10447: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10448: if (cptcovn < 1){i1=1;}
1.180 brouard 10449:
1.238 brouard 10450: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10451: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10452: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10453: continue;
1.235 brouard 10454:
1.238 brouard 10455: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10456: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10457: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10458: /* k=k+1; */
10459: /* to clean */
10460: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10461: fprintf(ficrespl,"#******");
10462: printf("#******");
10463: fprintf(ficlog,"#******");
10464: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10465: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10466: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10467: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10468: }
10469: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10470: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10471: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10472: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10473: }
10474: fprintf(ficrespl,"******\n");
10475: printf("******\n");
10476: fprintf(ficlog,"******\n");
10477: if(invalidvarcomb[k]){
10478: printf("\nCombination (%d) ignored because no case \n",k);
10479: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10480: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10481: continue;
10482: }
1.219 brouard 10483:
1.238 brouard 10484: fprintf(ficrespl,"#Age ");
10485: for(j=1;j<=cptcoveff;j++) {
10486: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10487: }
10488: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10489: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10490:
1.238 brouard 10491: for (age=agebase; age<=agelim; age++){
10492: /* for (age=agebase; age<=agebase; age++){ */
10493: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10494: fprintf(ficrespl,"%.0f ",age );
10495: for(j=1;j<=cptcoveff;j++)
10496: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10497: tot=0.;
10498: for(i=1; i<=nlstate;i++){
10499: tot += prlim[i][i];
10500: fprintf(ficrespl," %.5f", prlim[i][i]);
10501: }
10502: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10503: } /* Age */
10504: /* was end of cptcod */
10505: } /* cptcov */
10506: } /* nres */
1.219 brouard 10507: return 0;
1.180 brouard 10508: }
10509:
1.218 brouard 10510: 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 10511: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10512:
10513: /* Computes the back prevalence limit for any combination of covariate values
10514: * at any age between ageminpar and agemaxpar
10515: */
1.235 brouard 10516: int i, j, k, i1, nres=0 ;
1.217 brouard 10517: /* double ftolpl = 1.e-10; */
10518: double age, agebase, agelim;
10519: double tot;
1.218 brouard 10520: /* double ***mobaverage; */
10521: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10522:
10523: strcpy(fileresplb,"PLB_");
10524: strcat(fileresplb,fileresu);
10525: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10526: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10527: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10528: }
1.288 brouard 10529: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10530: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10531: pstamp(ficresplb);
1.288 brouard 10532: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10533: fprintf(ficresplb,"#Age ");
10534: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10535: fprintf(ficresplb,"\n");
10536:
1.218 brouard 10537:
10538: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10539:
10540: agebase=ageminpar;
10541: agelim=agemaxpar;
10542:
10543:
1.227 brouard 10544: i1=pow(2,cptcoveff);
1.218 brouard 10545: if (cptcovn < 1){i1=1;}
1.227 brouard 10546:
1.238 brouard 10547: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10548: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10549: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10550: continue;
10551: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10552: fprintf(ficresplb,"#******");
10553: printf("#******");
10554: fprintf(ficlog,"#******");
10555: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10556: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10557: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10558: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10559: }
10560: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10561: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10562: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10563: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10564: }
10565: fprintf(ficresplb,"******\n");
10566: printf("******\n");
10567: fprintf(ficlog,"******\n");
10568: if(invalidvarcomb[k]){
10569: printf("\nCombination (%d) ignored because no cases \n",k);
10570: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10571: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10572: continue;
10573: }
1.218 brouard 10574:
1.238 brouard 10575: fprintf(ficresplb,"#Age ");
10576: for(j=1;j<=cptcoveff;j++) {
10577: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10578: }
10579: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10580: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10581:
10582:
1.238 brouard 10583: for (age=agebase; age<=agelim; age++){
10584: /* for (age=agebase; age<=agebase; age++){ */
10585: if(mobilavproj > 0){
10586: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10587: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10588: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10589: }else if (mobilavproj == 0){
10590: 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);
10591: 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);
10592: exit(1);
10593: }else{
10594: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10595: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10596: /* printf("TOTOT\n"); */
10597: /* exit(1); */
1.238 brouard 10598: }
10599: fprintf(ficresplb,"%.0f ",age );
10600: for(j=1;j<=cptcoveff;j++)
10601: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10602: tot=0.;
10603: for(i=1; i<=nlstate;i++){
10604: tot += bprlim[i][i];
10605: fprintf(ficresplb," %.5f", bprlim[i][i]);
10606: }
10607: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10608: } /* Age */
10609: /* was end of cptcod */
1.255 brouard 10610: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10611: } /* end of any combination */
10612: } /* end of nres */
1.218 brouard 10613: /* hBijx(p, bage, fage); */
10614: /* fclose(ficrespijb); */
10615:
10616: return 0;
1.217 brouard 10617: }
1.218 brouard 10618:
1.180 brouard 10619: int hPijx(double *p, int bage, int fage){
10620: /*------------- h Pij x at various ages ------------*/
10621:
10622: int stepsize;
10623: int agelim;
10624: int hstepm;
10625: int nhstepm;
1.235 brouard 10626: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10627:
10628: double agedeb;
10629: double ***p3mat;
10630:
1.201 brouard 10631: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10632: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10633: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10634: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10635: }
10636: printf("Computing pij: result on file '%s' \n", filerespij);
10637: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10638:
10639: stepsize=(int) (stepm+YEARM-1)/YEARM;
10640: /*if (stepm<=24) stepsize=2;*/
10641:
10642: agelim=AGESUP;
10643: hstepm=stepsize*YEARM; /* Every year of age */
10644: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10645:
1.180 brouard 10646: /* hstepm=1; aff par mois*/
10647: pstamp(ficrespij);
10648: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10649: i1= pow(2,cptcoveff);
1.218 brouard 10650: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10651: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10652: /* k=k+1; */
1.235 brouard 10653: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10654: for(k=1; k<=i1;k++){
1.253 brouard 10655: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10656: continue;
1.183 brouard 10657: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10658: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10659: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10660: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10661: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10662: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10663: }
1.183 brouard 10664: fprintf(ficrespij,"******\n");
10665:
10666: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10667: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10668: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10669:
10670: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10671:
1.183 brouard 10672: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10673: oldm=oldms;savm=savms;
1.235 brouard 10674: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10675: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10676: for(i=1; i<=nlstate;i++)
10677: for(j=1; j<=nlstate+ndeath;j++)
10678: fprintf(ficrespij," %1d-%1d",i,j);
10679: fprintf(ficrespij,"\n");
10680: for (h=0; h<=nhstepm; h++){
10681: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10682: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10683: for(i=1; i<=nlstate;i++)
10684: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10685: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10686: fprintf(ficrespij,"\n");
10687: }
1.183 brouard 10688: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10689: fprintf(ficrespij,"\n");
10690: }
1.180 brouard 10691: /*}*/
10692: }
1.218 brouard 10693: return 0;
1.180 brouard 10694: }
1.218 brouard 10695:
10696: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10697: /*------------- h Bij x at various ages ------------*/
10698:
10699: int stepsize;
1.218 brouard 10700: /* int agelim; */
10701: int ageminl;
1.217 brouard 10702: int hstepm;
10703: int nhstepm;
1.238 brouard 10704: int h, i, i1, j, k, nres;
1.218 brouard 10705:
1.217 brouard 10706: double agedeb;
10707: double ***p3mat;
1.218 brouard 10708:
10709: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10710: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10711: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10712: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10713: }
10714: printf("Computing pij back: result on file '%s' \n", filerespijb);
10715: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10716:
10717: stepsize=(int) (stepm+YEARM-1)/YEARM;
10718: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10719:
1.218 brouard 10720: /* agelim=AGESUP; */
1.289 brouard 10721: ageminl=AGEINF; /* was 30 */
1.218 brouard 10722: hstepm=stepsize*YEARM; /* Every year of age */
10723: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10724:
10725: /* hstepm=1; aff par mois*/
10726: pstamp(ficrespijb);
1.255 brouard 10727: 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 10728: i1= pow(2,cptcoveff);
1.218 brouard 10729: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10730: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10731: /* k=k+1; */
1.238 brouard 10732: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10733: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10734: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10735: continue;
10736: fprintf(ficrespijb,"\n#****** ");
10737: for(j=1;j<=cptcoveff;j++)
10738: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10739: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10740: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10741: }
10742: fprintf(ficrespijb,"******\n");
1.264 brouard 10743: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10744: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10745: continue;
10746: }
10747:
10748: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10749: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10750: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 ! brouard 10751: 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 */
! 10752: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10753:
10754: /* nhstepm=nhstepm*YEARM; aff par mois*/
10755:
1.266 brouard 10756: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10757: /* and memory limitations if stepm is small */
10758:
1.238 brouard 10759: /* oldm=oldms;savm=savms; */
10760: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10761: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10762: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10763: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10764: for(i=1; i<=nlstate;i++)
10765: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10766: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10767: fprintf(ficrespijb,"\n");
1.238 brouard 10768: for (h=0; h<=nhstepm; h++){
10769: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10770: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10771: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10772: for(i=1; i<=nlstate;i++)
10773: for(j=1; j<=nlstate+ndeath;j++)
10774: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10775: fprintf(ficrespijb,"\n");
10776: }
10777: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10778: fprintf(ficrespijb,"\n");
10779: } /* end age deb */
10780: } /* end combination */
10781: } /* end nres */
1.218 brouard 10782: return 0;
10783: } /* hBijx */
1.217 brouard 10784:
1.180 brouard 10785:
1.136 brouard 10786: /***********************************************/
10787: /**************** Main Program *****************/
10788: /***********************************************/
10789:
10790: int main(int argc, char *argv[])
10791: {
10792: #ifdef GSL
10793: const gsl_multimin_fminimizer_type *T;
10794: size_t iteri = 0, it;
10795: int rval = GSL_CONTINUE;
10796: int status = GSL_SUCCESS;
10797: double ssval;
10798: #endif
10799: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10800: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10801: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10802: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10803: int jj, ll, li, lj, lk;
1.136 brouard 10804: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10805: int num_filled;
1.136 brouard 10806: int itimes;
10807: int NDIM=2;
10808: int vpopbased=0;
1.235 brouard 10809: int nres=0;
1.258 brouard 10810: int endishere=0;
1.277 brouard 10811: int noffset=0;
1.274 brouard 10812: int ncurrv=0; /* Temporary variable */
10813:
1.164 brouard 10814: char ca[32], cb[32];
1.136 brouard 10815: /* FILE *fichtm; *//* Html File */
10816: /* FILE *ficgp;*/ /*Gnuplot File */
10817: struct stat info;
1.191 brouard 10818: double agedeb=0.;
1.194 brouard 10819:
10820: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10821: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10822:
1.165 brouard 10823: double fret;
1.191 brouard 10824: double dum=0.; /* Dummy variable */
1.136 brouard 10825: double ***p3mat;
1.218 brouard 10826: /* double ***mobaverage; */
1.164 brouard 10827:
10828: char line[MAXLINE];
1.197 brouard 10829: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10830:
1.234 brouard 10831: char modeltemp[MAXLINE];
1.230 brouard 10832: char resultline[MAXLINE];
10833:
1.136 brouard 10834: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10835: char *tok, *val; /* pathtot */
1.290 brouard 10836: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10837: int c, h , cpt, c2;
1.191 brouard 10838: int jl=0;
10839: int i1, j1, jk, stepsize=0;
1.194 brouard 10840: int count=0;
10841:
1.164 brouard 10842: int *tab;
1.136 brouard 10843: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10844: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10845: /* double anprojf, mprojf, jprojf; */
10846: /* double jintmean,mintmean,aintmean; */
10847: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10848: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10849: double yrfproj= 10.0; /* Number of years of forward projections */
10850: double yrbproj= 10.0; /* Number of years of backward projections */
10851: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10852: int mobilav=0,popforecast=0;
1.191 brouard 10853: int hstepm=0, nhstepm=0;
1.136 brouard 10854: int agemortsup;
10855: float sumlpop=0.;
10856: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10857: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10858:
1.191 brouard 10859: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10860: double ftolpl=FTOL;
10861: double **prlim;
1.217 brouard 10862: double **bprlim;
1.136 brouard 10863: double ***param; /* Matrix of parameters */
1.251 brouard 10864: double ***paramstart; /* Matrix of starting parameter values */
10865: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10866: double **matcov; /* Matrix of covariance */
1.203 brouard 10867: double **hess; /* Hessian matrix */
1.136 brouard 10868: double ***delti3; /* Scale */
10869: double *delti; /* Scale */
10870: double ***eij, ***vareij;
10871: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10872:
1.136 brouard 10873: double *epj, vepp;
1.164 brouard 10874:
1.273 brouard 10875: double dateprev1, dateprev2;
1.296 brouard 10876: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10877: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10878:
1.217 brouard 10879:
1.136 brouard 10880: double **ximort;
1.145 brouard 10881: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10882: int *dcwave;
10883:
1.164 brouard 10884: char z[1]="c";
1.136 brouard 10885:
10886: /*char *strt;*/
10887: char strtend[80];
1.126 brouard 10888:
1.164 brouard 10889:
1.126 brouard 10890: /* setlocale (LC_ALL, ""); */
10891: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10892: /* textdomain (PACKAGE); */
10893: /* setlocale (LC_CTYPE, ""); */
10894: /* setlocale (LC_MESSAGES, ""); */
10895:
10896: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10897: rstart_time = time(NULL);
10898: /* (void) gettimeofday(&start_time,&tzp);*/
10899: start_time = *localtime(&rstart_time);
1.126 brouard 10900: curr_time=start_time;
1.157 brouard 10901: /*tml = *localtime(&start_time.tm_sec);*/
10902: /* strcpy(strstart,asctime(&tml)); */
10903: strcpy(strstart,asctime(&start_time));
1.126 brouard 10904:
10905: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10906: /* tp.tm_sec = tp.tm_sec +86400; */
10907: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10908: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10909: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10910: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10911: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 10912: /* strt=asctime(&tmg); */
10913: /* printf("Time(after) =%s",strstart); */
10914: /* (void) time (&time_value);
10915: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
10916: * tm = *localtime(&time_value);
10917: * strstart=asctime(&tm);
10918: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
10919: */
10920:
10921: nberr=0; /* Number of errors and warnings */
10922: nbwarn=0;
1.184 brouard 10923: #ifdef WIN32
10924: _getcwd(pathcd, size);
10925: #else
1.126 brouard 10926: getcwd(pathcd, size);
1.184 brouard 10927: #endif
1.191 brouard 10928: syscompilerinfo(0);
1.196 brouard 10929: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 10930: if(argc <=1){
10931: printf("\nEnter the parameter file name: ");
1.205 brouard 10932: if(!fgets(pathr,FILENAMELENGTH,stdin)){
10933: printf("ERROR Empty parameter file name\n");
10934: goto end;
10935: }
1.126 brouard 10936: i=strlen(pathr);
10937: if(pathr[i-1]=='\n')
10938: pathr[i-1]='\0';
1.156 brouard 10939: i=strlen(pathr);
1.205 brouard 10940: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 10941: pathr[i-1]='\0';
1.205 brouard 10942: }
10943: i=strlen(pathr);
10944: if( i==0 ){
10945: printf("ERROR Empty parameter file name\n");
10946: goto end;
10947: }
10948: for (tok = pathr; tok != NULL; ){
1.126 brouard 10949: printf("Pathr |%s|\n",pathr);
10950: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
10951: printf("val= |%s| pathr=%s\n",val,pathr);
10952: strcpy (pathtot, val);
10953: if(pathr[0] == '\0') break; /* Dirty */
10954: }
10955: }
1.281 brouard 10956: else if (argc<=2){
10957: strcpy(pathtot,argv[1]);
10958: }
1.126 brouard 10959: else{
10960: strcpy(pathtot,argv[1]);
1.281 brouard 10961: strcpy(z,argv[2]);
10962: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 10963: }
10964: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
10965: /*cygwin_split_path(pathtot,path,optionfile);
10966: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
10967: /* cutv(path,optionfile,pathtot,'\\');*/
10968:
10969: /* Split argv[0], imach program to get pathimach */
10970: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
10971: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10972: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10973: /* strcpy(pathimach,argv[0]); */
10974: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
10975: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
10976: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 10977: #ifdef WIN32
10978: _chdir(path); /* Can be a relative path */
10979: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
10980: #else
1.126 brouard 10981: chdir(path); /* Can be a relative path */
1.184 brouard 10982: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
10983: #endif
10984: printf("Current directory %s!\n",pathcd);
1.126 brouard 10985: strcpy(command,"mkdir ");
10986: strcat(command,optionfilefiname);
10987: if((outcmd=system(command)) != 0){
1.169 brouard 10988: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 10989: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
10990: /* fclose(ficlog); */
10991: /* exit(1); */
10992: }
10993: /* if((imk=mkdir(optionfilefiname))<0){ */
10994: /* perror("mkdir"); */
10995: /* } */
10996:
10997: /*-------- arguments in the command line --------*/
10998:
1.186 brouard 10999: /* Main Log file */
1.126 brouard 11000: strcat(filelog, optionfilefiname);
11001: strcat(filelog,".log"); /* */
11002: if((ficlog=fopen(filelog,"w"))==NULL) {
11003: printf("Problem with logfile %s\n",filelog);
11004: goto end;
11005: }
11006: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11007: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11008: fprintf(ficlog,"\nEnter the parameter file name: \n");
11009: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11010: path=%s \n\
11011: optionfile=%s\n\
11012: optionfilext=%s\n\
1.156 brouard 11013: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11014:
1.197 brouard 11015: syscompilerinfo(1);
1.167 brouard 11016:
1.126 brouard 11017: printf("Local time (at start):%s",strstart);
11018: fprintf(ficlog,"Local time (at start): %s",strstart);
11019: fflush(ficlog);
11020: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11021: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11022:
11023: /* */
11024: strcpy(fileres,"r");
11025: strcat(fileres, optionfilefiname);
1.201 brouard 11026: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11027: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11028: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11029:
1.186 brouard 11030: /* Main ---------arguments file --------*/
1.126 brouard 11031:
11032: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11033: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11034: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11035: fflush(ficlog);
1.149 brouard 11036: /* goto end; */
11037: exit(70);
1.126 brouard 11038: }
11039:
11040: strcpy(filereso,"o");
1.201 brouard 11041: strcat(filereso,fileresu);
1.126 brouard 11042: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11043: printf("Problem with Output resultfile: %s\n", filereso);
11044: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11045: fflush(ficlog);
11046: goto end;
11047: }
1.278 brouard 11048: /*-------- Rewriting parameter file ----------*/
11049: strcpy(rfileres,"r"); /* "Rparameterfile */
11050: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11051: strcat(rfileres,"."); /* */
11052: strcat(rfileres,optionfilext); /* Other files have txt extension */
11053: if((ficres =fopen(rfileres,"w"))==NULL) {
11054: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11055: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11056: fflush(ficlog);
11057: goto end;
11058: }
11059: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11060:
1.278 brouard 11061:
1.126 brouard 11062: /* Reads comments: lines beginning with '#' */
11063: numlinepar=0;
1.277 brouard 11064: /* Is it a BOM UTF-8 Windows file? */
11065: /* First parameter line */
1.197 brouard 11066: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11067: noffset=0;
11068: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11069: {
11070: noffset=noffset+3;
11071: printf("# File is an UTF8 Bom.\n"); // 0xBF
11072: }
11073: else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
11074: {
11075: noffset=noffset+2;
11076: printf("# File is an UTF16BE BOM file\n");
11077: }
11078: else if( line[0] == 0 && line[1] == 0)
11079: {
11080: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11081: noffset=noffset+4;
11082: printf("# File is an UTF16BE BOM file\n");
11083: }
11084: } else{
11085: ;/*printf(" Not a BOM file\n");*/
11086: }
11087:
1.197 brouard 11088: /* If line starts with a # it is a comment */
1.277 brouard 11089: if (line[noffset] == '#') {
1.197 brouard 11090: numlinepar++;
11091: fputs(line,stdout);
11092: fputs(line,ficparo);
1.278 brouard 11093: fputs(line,ficres);
1.197 brouard 11094: fputs(line,ficlog);
11095: continue;
11096: }else
11097: break;
11098: }
11099: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11100: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11101: if (num_filled != 5) {
11102: printf("Should be 5 parameters\n");
1.283 brouard 11103: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11104: }
1.126 brouard 11105: numlinepar++;
1.197 brouard 11106: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11107: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11108: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11109: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11110: }
11111: /* Second parameter line */
11112: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11113: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11114: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11115: if (line[0] == '#') {
11116: numlinepar++;
1.283 brouard 11117: printf("%s",line);
11118: fprintf(ficres,"%s",line);
11119: fprintf(ficparo,"%s",line);
11120: fprintf(ficlog,"%s",line);
1.197 brouard 11121: continue;
11122: }else
11123: break;
11124: }
1.223 brouard 11125: 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", \
11126: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11127: if (num_filled != 11) {
11128: 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 11129: printf("but line=%s\n",line);
1.283 brouard 11130: 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");
11131: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11132: }
1.286 brouard 11133: if( lastpass > maxwav){
11134: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11135: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11136: fflush(ficlog);
11137: goto end;
11138: }
11139: 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 11140: 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 11141: 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 11142: 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 11143: }
1.203 brouard 11144: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11145: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11146: /* Third parameter line */
11147: while(fgets(line, MAXLINE, ficpar)) {
11148: /* If line starts with a # it is a comment */
11149: if (line[0] == '#') {
11150: numlinepar++;
1.283 brouard 11151: printf("%s",line);
11152: fprintf(ficres,"%s",line);
11153: fprintf(ficparo,"%s",line);
11154: fprintf(ficlog,"%s",line);
1.197 brouard 11155: continue;
11156: }else
11157: break;
11158: }
1.201 brouard 11159: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11160: if (num_filled != 1){
11161: printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
11162: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
1.197 brouard 11163: model[0]='\0';
11164: goto end;
11165: }
11166: else{
11167: if (model[0]=='+'){
11168: for(i=1; i<=strlen(model);i++)
11169: modeltemp[i-1]=model[i];
1.201 brouard 11170: strcpy(model,modeltemp);
1.197 brouard 11171: }
11172: }
1.199 brouard 11173: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11174: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11175: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11176: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11177: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11178: }
11179: /* 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); */
11180: /* numlinepar=numlinepar+3; /\* In general *\/ */
11181: /* 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 11182: /* 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); */
11183: /* 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 11184: fflush(ficlog);
1.190 brouard 11185: /* if(model[0]=='#'|| model[0]== '\0'){ */
11186: if(model[0]=='#'){
1.279 brouard 11187: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11188: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11189: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11190: if(mle != -1){
1.279 brouard 11191: 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 11192: exit(1);
11193: }
11194: }
1.126 brouard 11195: while((c=getc(ficpar))=='#' && c!= EOF){
11196: ungetc(c,ficpar);
11197: fgets(line, MAXLINE, ficpar);
11198: numlinepar++;
1.195 brouard 11199: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11200: z[0]=line[1];
11201: }
11202: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11203: fputs(line, stdout);
11204: //puts(line);
1.126 brouard 11205: fputs(line,ficparo);
11206: fputs(line,ficlog);
11207: }
11208: ungetc(c,ficpar);
11209:
11210:
1.290 brouard 11211: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11212: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11213: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11214: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11215: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11216: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11217: v1+v2*age+v2*v3 makes cptcovn = 3
11218: */
11219: if (strlen(model)>1)
1.187 brouard 11220: 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 11221: else
1.187 brouard 11222: ncovmodel=2; /* Constant and age */
1.133 brouard 11223: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11224: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11225: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11226: 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);
11227: 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);
11228: fflush(stdout);
11229: fclose (ficlog);
11230: goto end;
11231: }
1.126 brouard 11232: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11233: delti=delti3[1][1];
11234: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11235: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11236: /* We could also provide initial parameters values giving by simple logistic regression
11237: * only one way, that is without matrix product. We will have nlstate maximizations */
11238: /* for(i=1;i<nlstate;i++){ */
11239: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11240: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11241: /* } */
1.126 brouard 11242: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11243: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11244: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11245: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11246: fclose (ficparo);
11247: fclose (ficlog);
11248: goto end;
11249: exit(0);
1.220 brouard 11250: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11251: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11252: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11253: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11254: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11255: matcov=matrix(1,npar,1,npar);
1.203 brouard 11256: hess=matrix(1,npar,1,npar);
1.220 brouard 11257: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11258: /* Read guessed parameters */
1.126 brouard 11259: /* Reads comments: lines beginning with '#' */
11260: while((c=getc(ficpar))=='#' && c!= EOF){
11261: ungetc(c,ficpar);
11262: fgets(line, MAXLINE, ficpar);
11263: numlinepar++;
1.141 brouard 11264: fputs(line,stdout);
1.126 brouard 11265: fputs(line,ficparo);
11266: fputs(line,ficlog);
11267: }
11268: ungetc(c,ficpar);
11269:
11270: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11271: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11272: for(i=1; i <=nlstate; i++){
1.234 brouard 11273: j=0;
1.126 brouard 11274: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11275: if(jj==i) continue;
11276: j++;
1.292 brouard 11277: while((c=getc(ficpar))=='#' && c!= EOF){
11278: ungetc(c,ficpar);
11279: fgets(line, MAXLINE, ficpar);
11280: numlinepar++;
11281: fputs(line,stdout);
11282: fputs(line,ficparo);
11283: fputs(line,ficlog);
11284: }
11285: ungetc(c,ficpar);
1.234 brouard 11286: fscanf(ficpar,"%1d%1d",&i1,&j1);
11287: if ((i1 != i) || (j1 != jj)){
11288: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11289: It might be a problem of design; if ncovcol and the model are correct\n \
11290: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11291: exit(1);
11292: }
11293: fprintf(ficparo,"%1d%1d",i1,j1);
11294: if(mle==1)
11295: printf("%1d%1d",i,jj);
11296: fprintf(ficlog,"%1d%1d",i,jj);
11297: for(k=1; k<=ncovmodel;k++){
11298: fscanf(ficpar," %lf",¶m[i][j][k]);
11299: if(mle==1){
11300: printf(" %lf",param[i][j][k]);
11301: fprintf(ficlog," %lf",param[i][j][k]);
11302: }
11303: else
11304: fprintf(ficlog," %lf",param[i][j][k]);
11305: fprintf(ficparo," %lf",param[i][j][k]);
11306: }
11307: fscanf(ficpar,"\n");
11308: numlinepar++;
11309: if(mle==1)
11310: printf("\n");
11311: fprintf(ficlog,"\n");
11312: fprintf(ficparo,"\n");
1.126 brouard 11313: }
11314: }
11315: fflush(ficlog);
1.234 brouard 11316:
1.251 brouard 11317: /* Reads parameters values */
1.126 brouard 11318: p=param[1][1];
1.251 brouard 11319: pstart=paramstart[1][1];
1.126 brouard 11320:
11321: /* Reads comments: lines beginning with '#' */
11322: while((c=getc(ficpar))=='#' && c!= EOF){
11323: ungetc(c,ficpar);
11324: fgets(line, MAXLINE, ficpar);
11325: numlinepar++;
1.141 brouard 11326: fputs(line,stdout);
1.126 brouard 11327: fputs(line,ficparo);
11328: fputs(line,ficlog);
11329: }
11330: ungetc(c,ficpar);
11331:
11332: for(i=1; i <=nlstate; i++){
11333: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11334: fscanf(ficpar,"%1d%1d",&i1,&j1);
11335: if ( (i1-i) * (j1-j) != 0){
11336: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11337: exit(1);
11338: }
11339: printf("%1d%1d",i,j);
11340: fprintf(ficparo,"%1d%1d",i1,j1);
11341: fprintf(ficlog,"%1d%1d",i1,j1);
11342: for(k=1; k<=ncovmodel;k++){
11343: fscanf(ficpar,"%le",&delti3[i][j][k]);
11344: printf(" %le",delti3[i][j][k]);
11345: fprintf(ficparo," %le",delti3[i][j][k]);
11346: fprintf(ficlog," %le",delti3[i][j][k]);
11347: }
11348: fscanf(ficpar,"\n");
11349: numlinepar++;
11350: printf("\n");
11351: fprintf(ficparo,"\n");
11352: fprintf(ficlog,"\n");
1.126 brouard 11353: }
11354: }
11355: fflush(ficlog);
1.234 brouard 11356:
1.145 brouard 11357: /* Reads covariance matrix */
1.126 brouard 11358: delti=delti3[1][1];
1.220 brouard 11359:
11360:
1.126 brouard 11361: /* 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 11362:
1.126 brouard 11363: /* Reads comments: lines beginning with '#' */
11364: while((c=getc(ficpar))=='#' && c!= EOF){
11365: ungetc(c,ficpar);
11366: fgets(line, MAXLINE, ficpar);
11367: numlinepar++;
1.141 brouard 11368: fputs(line,stdout);
1.126 brouard 11369: fputs(line,ficparo);
11370: fputs(line,ficlog);
11371: }
11372: ungetc(c,ficpar);
1.220 brouard 11373:
1.126 brouard 11374: matcov=matrix(1,npar,1,npar);
1.203 brouard 11375: hess=matrix(1,npar,1,npar);
1.131 brouard 11376: for(i=1; i <=npar; i++)
11377: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11378:
1.194 brouard 11379: /* Scans npar lines */
1.126 brouard 11380: for(i=1; i <=npar; i++){
1.226 brouard 11381: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11382: if(count != 3){
1.226 brouard 11383: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11384: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11385: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11386: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11387: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11388: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11389: exit(1);
1.220 brouard 11390: }else{
1.226 brouard 11391: if(mle==1)
11392: printf("%1d%1d%d",i1,j1,jk);
11393: }
11394: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11395: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11396: for(j=1; j <=i; j++){
1.226 brouard 11397: fscanf(ficpar," %le",&matcov[i][j]);
11398: if(mle==1){
11399: printf(" %.5le",matcov[i][j]);
11400: }
11401: fprintf(ficlog," %.5le",matcov[i][j]);
11402: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11403: }
11404: fscanf(ficpar,"\n");
11405: numlinepar++;
11406: if(mle==1)
1.220 brouard 11407: printf("\n");
1.126 brouard 11408: fprintf(ficlog,"\n");
11409: fprintf(ficparo,"\n");
11410: }
1.194 brouard 11411: /* End of read covariance matrix npar lines */
1.126 brouard 11412: for(i=1; i <=npar; i++)
11413: for(j=i+1;j<=npar;j++)
1.226 brouard 11414: matcov[i][j]=matcov[j][i];
1.126 brouard 11415:
11416: if(mle==1)
11417: printf("\n");
11418: fprintf(ficlog,"\n");
11419:
11420: fflush(ficlog);
11421:
11422: } /* End of mle != -3 */
1.218 brouard 11423:
1.186 brouard 11424: /* Main data
11425: */
1.290 brouard 11426: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11427: /* num=lvector(1,n); */
11428: /* moisnais=vector(1,n); */
11429: /* annais=vector(1,n); */
11430: /* moisdc=vector(1,n); */
11431: /* andc=vector(1,n); */
11432: /* weight=vector(1,n); */
11433: /* agedc=vector(1,n); */
11434: /* cod=ivector(1,n); */
11435: /* for(i=1;i<=n;i++){ */
11436: num=lvector(firstobs,lastobs);
11437: moisnais=vector(firstobs,lastobs);
11438: annais=vector(firstobs,lastobs);
11439: moisdc=vector(firstobs,lastobs);
11440: andc=vector(firstobs,lastobs);
11441: weight=vector(firstobs,lastobs);
11442: agedc=vector(firstobs,lastobs);
11443: cod=ivector(firstobs,lastobs);
11444: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11445: num[i]=0;
11446: moisnais[i]=0;
11447: annais[i]=0;
11448: moisdc[i]=0;
11449: andc[i]=0;
11450: agedc[i]=0;
11451: cod[i]=0;
11452: weight[i]=1.0; /* Equal weights, 1 by default */
11453: }
1.290 brouard 11454: mint=matrix(1,maxwav,firstobs,lastobs);
11455: anint=matrix(1,maxwav,firstobs,lastobs);
11456: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11457: tab=ivector(1,NCOVMAX);
1.144 brouard 11458: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11459: 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 11460:
1.136 brouard 11461: /* Reads data from file datafile */
11462: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11463: goto end;
11464:
11465: /* Calculation of the number of parameters from char model */
1.234 brouard 11466: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11467: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11468: k=3 V4 Tvar[k=3]= 4 (from V4)
11469: k=2 V1 Tvar[k=2]= 1 (from V1)
11470: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11471: */
11472:
11473: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11474: TvarsDind=ivector(1,NCOVMAX); /* */
11475: TvarsD=ivector(1,NCOVMAX); /* */
11476: TvarsQind=ivector(1,NCOVMAX); /* */
11477: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11478: TvarF=ivector(1,NCOVMAX); /* */
11479: TvarFind=ivector(1,NCOVMAX); /* */
11480: TvarV=ivector(1,NCOVMAX); /* */
11481: TvarVind=ivector(1,NCOVMAX); /* */
11482: TvarA=ivector(1,NCOVMAX); /* */
11483: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11484: TvarFD=ivector(1,NCOVMAX); /* */
11485: TvarFDind=ivector(1,NCOVMAX); /* */
11486: TvarFQ=ivector(1,NCOVMAX); /* */
11487: TvarFQind=ivector(1,NCOVMAX); /* */
11488: TvarVD=ivector(1,NCOVMAX); /* */
11489: TvarVDind=ivector(1,NCOVMAX); /* */
11490: TvarVQ=ivector(1,NCOVMAX); /* */
11491: TvarVQind=ivector(1,NCOVMAX); /* */
11492:
1.230 brouard 11493: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11494: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11495: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11496: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11497: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11498: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11499: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11500: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11501: */
11502: /* For model-covariate k tells which data-covariate to use but
11503: because this model-covariate is a construction we invent a new column
11504: ncovcol + k1
11505: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11506: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11507: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11508: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11509: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11510: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11511: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11512: */
1.145 brouard 11513: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11514: 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 11515: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11516: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11517: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11518: 4 covariates (3 plus signs)
11519: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11520: */
1.230 brouard 11521: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11522: * individual dummy, fixed or varying:
11523: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11524: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11525: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11526: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11527: * Tmodelind[1]@9={9,0,3,2,}*/
11528: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11529: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11530: * individual quantitative, fixed or varying:
11531: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11532: * 3, 1, 0, 0, 0, 0, 0, 0},
11533: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11534: /* Main decodemodel */
11535:
1.187 brouard 11536:
1.223 brouard 11537: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11538: goto end;
11539:
1.137 brouard 11540: if((double)(lastobs-imx)/(double)imx > 1.10){
11541: nbwarn++;
11542: 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);
11543: 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);
11544: }
1.136 brouard 11545: /* if(mle==1){*/
1.137 brouard 11546: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11547: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11548: }
11549:
11550: /*-calculation of age at interview from date of interview and age at death -*/
11551: agev=matrix(1,maxwav,1,imx);
11552:
11553: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11554: goto end;
11555:
1.126 brouard 11556:
1.136 brouard 11557: agegomp=(int)agemin;
1.290 brouard 11558: free_vector(moisnais,firstobs,lastobs);
11559: free_vector(annais,firstobs,lastobs);
1.126 brouard 11560: /* free_matrix(mint,1,maxwav,1,n);
11561: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11562: /* free_vector(moisdc,1,n); */
11563: /* free_vector(andc,1,n); */
1.145 brouard 11564: /* */
11565:
1.126 brouard 11566: wav=ivector(1,imx);
1.214 brouard 11567: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11568: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11569: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11570: 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.*/
11571: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11572: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11573:
11574: /* Concatenates waves */
1.214 brouard 11575: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11576: Death is a valid wave (if date is known).
11577: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11578: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11579: and mw[mi+1][i]. dh depends on stepm.
11580: */
11581:
1.126 brouard 11582: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11583: /* Concatenates waves */
1.145 brouard 11584:
1.290 brouard 11585: free_vector(moisdc,firstobs,lastobs);
11586: free_vector(andc,firstobs,lastobs);
1.215 brouard 11587:
1.126 brouard 11588: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11589: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11590: ncodemax[1]=1;
1.145 brouard 11591: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11592: cptcoveff=0;
1.220 brouard 11593: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11594: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11595: }
11596:
11597: ncovcombmax=pow(2,cptcoveff);
11598: invalidvarcomb=ivector(1, ncovcombmax);
11599: for(i=1;i<ncovcombmax;i++)
11600: invalidvarcomb[i]=0;
11601:
1.211 brouard 11602: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11603: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11604: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11605:
1.200 brouard 11606: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11607: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11608: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11609: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11610: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11611: * (currently 0 or 1) in the data.
11612: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11613: * corresponding modality (h,j).
11614: */
11615:
1.145 brouard 11616: h=0;
11617: /*if (cptcovn > 0) */
1.126 brouard 11618: m=pow(2,cptcoveff);
11619:
1.144 brouard 11620: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11621: * For k=4 covariates, h goes from 1 to m=2**k
11622: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11623: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11624: * h\k 1 2 3 4
1.143 brouard 11625: *______________________________
11626: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11627: * 2 2 1 1 1
11628: * 3 i=2 1 2 1 1
11629: * 4 2 2 1 1
11630: * 5 i=3 1 i=2 1 2 1
11631: * 6 2 1 2 1
11632: * 7 i=4 1 2 2 1
11633: * 8 2 2 2 1
1.197 brouard 11634: * 9 i=5 1 i=3 1 i=2 1 2
11635: * 10 2 1 1 2
11636: * 11 i=6 1 2 1 2
11637: * 12 2 2 1 2
11638: * 13 i=7 1 i=4 1 2 2
11639: * 14 2 1 2 2
11640: * 15 i=8 1 2 2 2
11641: * 16 2 2 2 2
1.143 brouard 11642: */
1.212 brouard 11643: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11644: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11645: * and the value of each covariate?
11646: * V1=1, V2=1, V3=2, V4=1 ?
11647: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11648: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11649: * In order to get the real value in the data, we use nbcode
11650: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11651: * We are keeping this crazy system in order to be able (in the future?)
11652: * to have more than 2 values (0 or 1) for a covariate.
11653: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11654: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11655: * bbbbbbbb
11656: * 76543210
11657: * h-1 00000101 (6-1=5)
1.219 brouard 11658: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11659: * &
11660: * 1 00000001 (1)
1.219 brouard 11661: * 00000000 = 1 & ((h-1) >> (k-1))
11662: * +1= 00000001 =1
1.211 brouard 11663: *
11664: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11665: * h' 1101 =2^3+2^2+0x2^1+2^0
11666: * >>k' 11
11667: * & 00000001
11668: * = 00000001
11669: * +1 = 00000010=2 = codtabm(14,3)
11670: * Reverse h=6 and m=16?
11671: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11672: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11673: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11674: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11675: * V3=decodtabm(14,3,2**4)=2
11676: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11677: *(h-1) >> (j-1) 0011 =13 >> 2
11678: * &1 000000001
11679: * = 000000001
11680: * +1= 000000010 =2
11681: * 2211
11682: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11683: * V3=2
1.220 brouard 11684: * codtabm and decodtabm are identical
1.211 brouard 11685: */
11686:
1.145 brouard 11687:
11688: free_ivector(Ndum,-1,NCOVMAX);
11689:
11690:
1.126 brouard 11691:
1.186 brouard 11692: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11693: strcpy(optionfilegnuplot,optionfilefiname);
11694: if(mle==-3)
1.201 brouard 11695: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11696: strcat(optionfilegnuplot,".gp");
11697:
11698: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11699: printf("Problem with file %s",optionfilegnuplot);
11700: }
11701: else{
1.204 brouard 11702: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11703: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11704: //fprintf(ficgp,"set missing 'NaNq'\n");
11705: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11706: }
11707: /* fclose(ficgp);*/
1.186 brouard 11708:
11709:
11710: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11711:
11712: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11713: if(mle==-3)
1.201 brouard 11714: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11715: strcat(optionfilehtm,".htm");
11716: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11717: printf("Problem with %s \n",optionfilehtm);
11718: exit(0);
1.126 brouard 11719: }
11720:
11721: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11722: strcat(optionfilehtmcov,"-cov.htm");
11723: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11724: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11725: }
11726: else{
11727: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11728: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11729: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11730: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11731: }
11732:
1.213 brouard 11733: 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 11734: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11735: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11736: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11737: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11738: \n\
11739: <hr size=\"2\" color=\"#EC5E5E\">\
11740: <ul><li><h4>Parameter files</h4>\n\
11741: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11742: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11743: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11744: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11745: - Date and time at start: %s</ul>\n",\
11746: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11747: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11748: fileres,fileres,\
11749: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11750: fflush(fichtm);
11751:
11752: strcpy(pathr,path);
11753: strcat(pathr,optionfilefiname);
1.184 brouard 11754: #ifdef WIN32
11755: _chdir(optionfilefiname); /* Move to directory named optionfile */
11756: #else
1.126 brouard 11757: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11758: #endif
11759:
1.126 brouard 11760:
1.220 brouard 11761: /* Calculates basic frequencies. Computes observed prevalence at single age
11762: and for any valid combination of covariates
1.126 brouard 11763: and prints on file fileres'p'. */
1.251 brouard 11764: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11765: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11766:
11767: fprintf(fichtm,"\n");
1.286 brouard 11768: 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 11769: ftol, stepm);
11770: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11771: ncurrv=1;
11772: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11773: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11774: ncurrv=i;
11775: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11776: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11777: ncurrv=i;
11778: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11779: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11780: ncurrv=i;
11781: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11782: 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", \
11783: nlstate, ndeath, maxwav, mle, weightopt);
11784:
11785: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11786: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11787:
11788:
11789: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11790: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11791: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11792: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11793: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11794: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11795: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11796: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11797: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11798:
1.126 brouard 11799: /* For Powell, parameters are in a vector p[] starting at p[1]
11800: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11801: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11802:
11803: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11804: /* For mortality only */
1.126 brouard 11805: if (mle==-3){
1.136 brouard 11806: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11807: for(i=1;i<=NDIM;i++)
11808: for(j=1;j<=NDIM;j++)
11809: ximort[i][j]=0.;
1.186 brouard 11810: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11811: cens=ivector(firstobs,lastobs);
11812: ageexmed=vector(firstobs,lastobs);
11813: agecens=vector(firstobs,lastobs);
11814: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11815:
1.126 brouard 11816: for (i=1; i<=imx; i++){
11817: dcwave[i]=-1;
11818: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11819: if (s[m][i]>nlstate) {
11820: dcwave[i]=m;
11821: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11822: break;
11823: }
1.126 brouard 11824: }
1.226 brouard 11825:
1.126 brouard 11826: for (i=1; i<=imx; i++) {
11827: if (wav[i]>0){
1.226 brouard 11828: ageexmed[i]=agev[mw[1][i]][i];
11829: j=wav[i];
11830: agecens[i]=1.;
11831:
11832: if (ageexmed[i]> 1 && wav[i] > 0){
11833: agecens[i]=agev[mw[j][i]][i];
11834: cens[i]= 1;
11835: }else if (ageexmed[i]< 1)
11836: cens[i]= -1;
11837: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11838: cens[i]=0 ;
1.126 brouard 11839: }
11840: else cens[i]=-1;
11841: }
11842:
11843: for (i=1;i<=NDIM;i++) {
11844: for (j=1;j<=NDIM;j++)
1.226 brouard 11845: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11846: }
11847:
1.145 brouard 11848: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 11849: /*printf("%lf %lf", p[1], p[2]);*/
11850:
11851:
1.136 brouard 11852: #ifdef GSL
11853: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11854: #else
1.126 brouard 11855: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11856: #endif
1.201 brouard 11857: strcpy(filerespow,"POW-MORT_");
11858: strcat(filerespow,fileresu);
1.126 brouard 11859: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11860: printf("Problem with resultfile: %s\n", filerespow);
11861: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11862: }
1.136 brouard 11863: #ifdef GSL
11864: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11865: #else
1.126 brouard 11866: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11867: #endif
1.126 brouard 11868: /* for (i=1;i<=nlstate;i++)
11869: for(j=1;j<=nlstate+ndeath;j++)
11870: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11871: */
11872: fprintf(ficrespow,"\n");
1.136 brouard 11873: #ifdef GSL
11874: /* gsl starts here */
11875: T = gsl_multimin_fminimizer_nmsimplex;
11876: gsl_multimin_fminimizer *sfm = NULL;
11877: gsl_vector *ss, *x;
11878: gsl_multimin_function minex_func;
11879:
11880: /* Initial vertex size vector */
11881: ss = gsl_vector_alloc (NDIM);
11882:
11883: if (ss == NULL){
11884: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11885: }
11886: /* Set all step sizes to 1 */
11887: gsl_vector_set_all (ss, 0.001);
11888:
11889: /* Starting point */
1.126 brouard 11890:
1.136 brouard 11891: x = gsl_vector_alloc (NDIM);
11892:
11893: if (x == NULL){
11894: gsl_vector_free(ss);
11895: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11896: }
11897:
11898: /* Initialize method and iterate */
11899: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11900: /* gsl_vector_set(x, 0, 0.0268); */
11901: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11902: gsl_vector_set(x, 0, p[1]);
11903: gsl_vector_set(x, 1, p[2]);
11904:
11905: minex_func.f = &gompertz_f;
11906: minex_func.n = NDIM;
11907: minex_func.params = (void *)&p; /* ??? */
11908:
11909: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11910: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
11911:
11912: printf("Iterations beginning .....\n\n");
11913: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
11914:
11915: iteri=0;
11916: while (rval == GSL_CONTINUE){
11917: iteri++;
11918: status = gsl_multimin_fminimizer_iterate(sfm);
11919:
11920: if (status) printf("error: %s\n", gsl_strerror (status));
11921: fflush(0);
11922:
11923: if (status)
11924: break;
11925:
11926: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
11927: ssval = gsl_multimin_fminimizer_size (sfm);
11928:
11929: if (rval == GSL_SUCCESS)
11930: printf ("converged to a local maximum at\n");
11931:
11932: printf("%5d ", iteri);
11933: for (it = 0; it < NDIM; it++){
11934: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
11935: }
11936: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
11937: }
11938:
11939: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
11940:
11941: gsl_vector_free(x); /* initial values */
11942: gsl_vector_free(ss); /* inital step size */
11943: for (it=0; it<NDIM; it++){
11944: p[it+1]=gsl_vector_get(sfm->x,it);
11945: fprintf(ficrespow," %.12lf", p[it]);
11946: }
11947: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
11948: #endif
11949: #ifdef POWELL
11950: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
11951: #endif
1.126 brouard 11952: fclose(ficrespow);
11953:
1.203 brouard 11954: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 11955:
11956: for(i=1; i <=NDIM; i++)
11957: for(j=i+1;j<=NDIM;j++)
1.220 brouard 11958: matcov[i][j]=matcov[j][i];
1.126 brouard 11959:
11960: printf("\nCovariance matrix\n ");
1.203 brouard 11961: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 11962: for(i=1; i <=NDIM; i++) {
11963: for(j=1;j<=NDIM;j++){
1.220 brouard 11964: printf("%f ",matcov[i][j]);
11965: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 11966: }
1.203 brouard 11967: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 11968: }
11969:
11970: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 11971: for (i=1;i<=NDIM;i++) {
1.126 brouard 11972: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 11973: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
11974: }
1.126 brouard 11975: lsurv=vector(1,AGESUP);
11976: lpop=vector(1,AGESUP);
11977: tpop=vector(1,AGESUP);
11978: lsurv[agegomp]=100000;
11979:
11980: for (k=agegomp;k<=AGESUP;k++) {
11981: agemortsup=k;
11982: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
11983: }
11984:
11985: for (k=agegomp;k<agemortsup;k++)
11986: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
11987:
11988: for (k=agegomp;k<agemortsup;k++){
11989: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
11990: sumlpop=sumlpop+lpop[k];
11991: }
11992:
11993: tpop[agegomp]=sumlpop;
11994: for (k=agegomp;k<(agemortsup-3);k++){
11995: /* tpop[k+1]=2;*/
11996: tpop[k+1]=tpop[k]-lpop[k];
11997: }
11998:
11999:
12000: printf("\nAge lx qx dx Lx Tx e(x)\n");
12001: for (k=agegomp;k<(agemortsup-2);k++)
12002: 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]);
12003:
12004:
12005: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12006: ageminpar=50;
12007: agemaxpar=100;
1.194 brouard 12008: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12009: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12010: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12011: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12012: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12013: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12014: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12015: }else{
12016: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12017: 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 12018: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12019: }
1.201 brouard 12020: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12021: stepm, weightopt,\
12022: model,imx,p,matcov,agemortsup);
12023:
12024: free_vector(lsurv,1,AGESUP);
12025: free_vector(lpop,1,AGESUP);
12026: free_vector(tpop,1,AGESUP);
1.220 brouard 12027: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12028: free_ivector(dcwave,firstobs,lastobs);
12029: free_vector(agecens,firstobs,lastobs);
12030: free_vector(ageexmed,firstobs,lastobs);
12031: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12032: #ifdef GSL
1.136 brouard 12033: #endif
1.186 brouard 12034: } /* Endof if mle==-3 mortality only */
1.205 brouard 12035: /* Standard */
12036: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12037: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12038: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12039: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12040: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12041: for (k=1; k<=npar;k++)
12042: printf(" %d %8.5f",k,p[k]);
12043: printf("\n");
1.205 brouard 12044: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12045: /* mlikeli uses func not funcone */
1.247 brouard 12046: /* for(i=1;i<nlstate;i++){ */
12047: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12048: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12049: /* } */
1.205 brouard 12050: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12051: }
12052: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12053: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12054: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12055: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12056: }
12057: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12058: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12059: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12060: for (k=1; k<=npar;k++)
12061: printf(" %d %8.5f",k,p[k]);
12062: printf("\n");
12063:
12064: /*--------- results files --------------*/
1.283 brouard 12065: /* 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 12066:
12067:
12068: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12069: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12070: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12071: for(i=1,jk=1; i <=nlstate; i++){
12072: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12073: if (k != i) {
12074: printf("%d%d ",i,k);
12075: fprintf(ficlog,"%d%d ",i,k);
12076: fprintf(ficres,"%1d%1d ",i,k);
12077: for(j=1; j <=ncovmodel; j++){
12078: printf("%12.7f ",p[jk]);
12079: fprintf(ficlog,"%12.7f ",p[jk]);
12080: fprintf(ficres,"%12.7f ",p[jk]);
12081: jk++;
12082: }
12083: printf("\n");
12084: fprintf(ficlog,"\n");
12085: fprintf(ficres,"\n");
12086: }
1.126 brouard 12087: }
12088: }
1.203 brouard 12089: if(mle != 0){
12090: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12091: ftolhess=ftol; /* Usually correct */
1.203 brouard 12092: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12093: 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");
12094: 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");
12095: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12096: for(k=1; k <=(nlstate+ndeath); k++){
12097: if (k != i) {
12098: printf("%d%d ",i,k);
12099: fprintf(ficlog,"%d%d ",i,k);
12100: for(j=1; j <=ncovmodel; j++){
12101: 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]));
12102: 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]));
12103: jk++;
12104: }
12105: printf("\n");
12106: fprintf(ficlog,"\n");
12107: }
12108: }
1.193 brouard 12109: }
1.203 brouard 12110: } /* end of hesscov and Wald tests */
1.225 brouard 12111:
1.203 brouard 12112: /* */
1.126 brouard 12113: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12114: printf("# Scales (for hessian or gradient estimation)\n");
12115: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12116: for(i=1,jk=1; i <=nlstate; i++){
12117: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12118: if (j!=i) {
12119: fprintf(ficres,"%1d%1d",i,j);
12120: printf("%1d%1d",i,j);
12121: fprintf(ficlog,"%1d%1d",i,j);
12122: for(k=1; k<=ncovmodel;k++){
12123: printf(" %.5e",delti[jk]);
12124: fprintf(ficlog," %.5e",delti[jk]);
12125: fprintf(ficres," %.5e",delti[jk]);
12126: jk++;
12127: }
12128: printf("\n");
12129: fprintf(ficlog,"\n");
12130: fprintf(ficres,"\n");
12131: }
1.126 brouard 12132: }
12133: }
12134:
12135: 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 12136: if(mle >= 1) /* To big for the screen */
1.126 brouard 12137: 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");
12138: 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");
12139: /* # 121 Var(a12)\n\ */
12140: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12141: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12142: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12143: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12144: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12145: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12146: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12147:
12148:
12149: /* Just to have a covariance matrix which will be more understandable
12150: even is we still don't want to manage dictionary of variables
12151: */
12152: for(itimes=1;itimes<=2;itimes++){
12153: jj=0;
12154: for(i=1; i <=nlstate; i++){
1.225 brouard 12155: for(j=1; j <=nlstate+ndeath; j++){
12156: if(j==i) continue;
12157: for(k=1; k<=ncovmodel;k++){
12158: jj++;
12159: ca[0]= k+'a'-1;ca[1]='\0';
12160: if(itimes==1){
12161: if(mle>=1)
12162: printf("#%1d%1d%d",i,j,k);
12163: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12164: fprintf(ficres,"#%1d%1d%d",i,j,k);
12165: }else{
12166: if(mle>=1)
12167: printf("%1d%1d%d",i,j,k);
12168: fprintf(ficlog,"%1d%1d%d",i,j,k);
12169: fprintf(ficres,"%1d%1d%d",i,j,k);
12170: }
12171: ll=0;
12172: for(li=1;li <=nlstate; li++){
12173: for(lj=1;lj <=nlstate+ndeath; lj++){
12174: if(lj==li) continue;
12175: for(lk=1;lk<=ncovmodel;lk++){
12176: ll++;
12177: if(ll<=jj){
12178: cb[0]= lk +'a'-1;cb[1]='\0';
12179: if(ll<jj){
12180: if(itimes==1){
12181: if(mle>=1)
12182: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12183: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12184: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12185: }else{
12186: if(mle>=1)
12187: printf(" %.5e",matcov[jj][ll]);
12188: fprintf(ficlog," %.5e",matcov[jj][ll]);
12189: fprintf(ficres," %.5e",matcov[jj][ll]);
12190: }
12191: }else{
12192: if(itimes==1){
12193: if(mle>=1)
12194: printf(" Var(%s%1d%1d)",ca,i,j);
12195: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12196: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12197: }else{
12198: if(mle>=1)
12199: printf(" %.7e",matcov[jj][ll]);
12200: fprintf(ficlog," %.7e",matcov[jj][ll]);
12201: fprintf(ficres," %.7e",matcov[jj][ll]);
12202: }
12203: }
12204: }
12205: } /* end lk */
12206: } /* end lj */
12207: } /* end li */
12208: if(mle>=1)
12209: printf("\n");
12210: fprintf(ficlog,"\n");
12211: fprintf(ficres,"\n");
12212: numlinepar++;
12213: } /* end k*/
12214: } /*end j */
1.126 brouard 12215: } /* end i */
12216: } /* end itimes */
12217:
12218: fflush(ficlog);
12219: fflush(ficres);
1.225 brouard 12220: while(fgets(line, MAXLINE, ficpar)) {
12221: /* If line starts with a # it is a comment */
12222: if (line[0] == '#') {
12223: numlinepar++;
12224: fputs(line,stdout);
12225: fputs(line,ficparo);
12226: fputs(line,ficlog);
12227: continue;
12228: }else
12229: break;
12230: }
12231:
1.209 brouard 12232: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12233: /* ungetc(c,ficpar); */
12234: /* fgets(line, MAXLINE, ficpar); */
12235: /* fputs(line,stdout); */
12236: /* fputs(line,ficparo); */
12237: /* } */
12238: /* ungetc(c,ficpar); */
1.126 brouard 12239:
12240: estepm=0;
1.209 brouard 12241: 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 12242:
12243: if (num_filled != 6) {
12244: 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);
12245: 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);
12246: goto end;
12247: }
12248: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12249: }
12250: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12251: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12252:
1.209 brouard 12253: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12254: if (estepm==0 || estepm < stepm) estepm=stepm;
12255: if (fage <= 2) {
12256: bage = ageminpar;
12257: fage = agemaxpar;
12258: }
12259:
12260: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12261: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12262: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12263:
1.186 brouard 12264: /* Other stuffs, more or less useful */
1.254 brouard 12265: while(fgets(line, MAXLINE, ficpar)) {
12266: /* If line starts with a # it is a comment */
12267: if (line[0] == '#') {
12268: numlinepar++;
12269: fputs(line,stdout);
12270: fputs(line,ficparo);
12271: fputs(line,ficlog);
12272: continue;
12273: }else
12274: break;
12275: }
12276:
12277: 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){
12278:
12279: if (num_filled != 7) {
12280: 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);
12281: 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);
12282: goto end;
12283: }
12284: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12285: 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);
12286: 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);
12287: 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 12288: }
1.254 brouard 12289:
12290: while(fgets(line, MAXLINE, ficpar)) {
12291: /* If line starts with a # it is a comment */
12292: if (line[0] == '#') {
12293: numlinepar++;
12294: fputs(line,stdout);
12295: fputs(line,ficparo);
12296: fputs(line,ficlog);
12297: continue;
12298: }else
12299: break;
1.126 brouard 12300: }
12301:
12302:
12303: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12304: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12305:
1.254 brouard 12306: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12307: if (num_filled != 1) {
12308: 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);
12309: 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);
12310: goto end;
12311: }
12312: printf("pop_based=%d\n",popbased);
12313: fprintf(ficlog,"pop_based=%d\n",popbased);
12314: fprintf(ficparo,"pop_based=%d\n",popbased);
12315: fprintf(ficres,"pop_based=%d\n",popbased);
12316: }
12317:
1.258 brouard 12318: /* Results */
12319: nresult=0;
12320: do{
12321: if(!fgets(line, MAXLINE, ficpar)){
12322: endishere=1;
12323: parameterline=14;
12324: }else if (line[0] == '#') {
12325: /* If line starts with a # it is a comment */
1.254 brouard 12326: numlinepar++;
12327: fputs(line,stdout);
12328: fputs(line,ficparo);
12329: fputs(line,ficlog);
12330: continue;
1.258 brouard 12331: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12332: parameterline=11;
1.296 brouard 12333: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12334: parameterline=12;
12335: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12336: parameterline=13;
12337: else{
12338: parameterline=14;
1.254 brouard 12339: }
1.258 brouard 12340: switch (parameterline){
12341: case 11:
1.296 brouard 12342: 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)){
12343: 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 12344: 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);
12345: 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);
12346: 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);
12347: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12348: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12349: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12350: prvforecast = 1;
12351: }
12352: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
12353: printf(" Num_filled=%d, yearsfproj=%lf, mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12354: prvforecast = 2;
12355: }
12356: else {
12357: 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);
12358: 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);
12359: goto end;
1.258 brouard 12360: }
1.254 brouard 12361: break;
1.258 brouard 12362: case 12:
1.296 brouard 12363: 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)){
12364: 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);
12365: 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);
12366: 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);
12367: 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);
12368: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12369: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12370: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12371: prvbackcast = 1;
12372: }
12373: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
12374: printf(" Num_filled=%d, yearsbproj=%lf, mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12375: prvbackcast = 2;
12376: }
12377: else {
12378: 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);
12379: 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);
12380: goto end;
1.258 brouard 12381: }
1.230 brouard 12382: break;
1.296 brouard 12383: /* /\*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*\/ */
12384: /* if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){ */
12385: /* if (num_filled != 8) { */
12386: /* printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); */
12387: /* fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line); */
12388: /* goto end; */
12389: /* } */
12390: /* printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); */
12391: /* fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); */
12392: /* fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); */
12393: /* fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj); */
12394: /* /\* day and month of proj2 are not used but only year anproj2.*\/ */
12395: /* dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.; */
12396: /* dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.; */
12397: /* } */
12398: /* break; */
1.258 brouard 12399: case 13:
12400: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12401: if (num_filled == 0){
12402: resultline[0]='\0';
12403: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12404: fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12405: break;
12406: } else if (num_filled != 1){
12407: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12408: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12409: }
12410: nresult++; /* Sum of resultlines */
12411: printf("Result %d: result=%s\n",nresult, resultline);
12412: if(nresult > MAXRESULTLINES){
12413: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12414: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12415: goto end;
12416: }
12417: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12418: fprintf(ficparo,"result: %s\n",resultline);
12419: fprintf(ficres,"result: %s\n",resultline);
12420: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12421: break;
1.258 brouard 12422: case 14:
1.259 brouard 12423: if(ncovmodel >2 && nresult==0 ){
12424: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12425: goto end;
12426: }
1.259 brouard 12427: break;
1.258 brouard 12428: default:
12429: nresult=1;
12430: decoderesult(".",nresult ); /* No covariate */
12431: }
12432: } /* End switch parameterline */
12433: }while(endishere==0); /* End do */
1.126 brouard 12434:
1.230 brouard 12435: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12436: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12437:
12438: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12439: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12440: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12441: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12442: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12443: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12444: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12445: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12446: }else{
1.270 brouard 12447: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12448: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12449: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12450: if(prvforecast==1){
12451: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12452: jprojd=jproj1;
12453: mprojd=mproj1;
12454: anprojd=anproj1;
12455: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12456: jprojf=jproj2;
12457: mprojf=mproj2;
12458: anprojf=anproj2;
12459: } else if(prvforecast == 2){
12460: dateprojd=dateintmean;
12461: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12462: dateprojf=dateintmean+yrfproj;
12463: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12464: }
12465: if(prvbackcast==1){
12466: datebackd=(jback1+12*mback1+365*anback1)/365;
12467: jbackd=jback1;
12468: mbackd=mback1;
12469: anbackd=anback1;
12470: datebackf=(jback2+12*mback2+365*anback2)/365;
12471: jbackf=jback2;
12472: mbackf=mback2;
12473: anbackf=anback2;
12474: } else if(prvbackcast == 2){
12475: datebackd=dateintmean;
12476: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12477: datebackf=dateintmean-yrbproj;
12478: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12479: }
12480:
12481: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12482: }
12483: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12484: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12485: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12486:
1.225 brouard 12487: /*------------ free_vector -------------*/
12488: /* chdir(path); */
1.220 brouard 12489:
1.215 brouard 12490: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12491: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12492: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12493: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12494: free_lvector(num,firstobs,lastobs);
12495: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12496: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12497: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12498: fclose(ficparo);
12499: fclose(ficres);
1.220 brouard 12500:
12501:
1.186 brouard 12502: /* Other results (useful)*/
1.220 brouard 12503:
12504:
1.126 brouard 12505: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12506: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12507: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12508: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12509: fclose(ficrespl);
12510:
12511: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12512: /*#include "hpijx.h"*/
12513: hPijx(p, bage, fage);
1.145 brouard 12514: fclose(ficrespij);
1.227 brouard 12515:
1.220 brouard 12516: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12517: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12518: k=1;
1.126 brouard 12519: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12520:
1.269 brouard 12521: /* Prevalence for each covariate combination in probs[age][status][cov] */
12522: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12523: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12524: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12525: for(k=1;k<=ncovcombmax;k++)
12526: probs[i][j][k]=0.;
1.269 brouard 12527: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12528: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12529: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12530: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12531: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12532: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12533: for(k=1;k<=ncovcombmax;k++)
12534: mobaverages[i][j][k]=0.;
1.219 brouard 12535: mobaverage=mobaverages;
12536: if (mobilav!=0) {
1.235 brouard 12537: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12538: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12539: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12540: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12541: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12542: }
1.269 brouard 12543: } else if (mobilavproj !=0) {
1.235 brouard 12544: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12545: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12546: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12547: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12548: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12549: }
1.269 brouard 12550: }else{
12551: printf("Internal error moving average\n");
12552: fflush(stdout);
12553: exit(1);
1.219 brouard 12554: }
12555: }/* end if moving average */
1.227 brouard 12556:
1.126 brouard 12557: /*---------- Forecasting ------------------*/
1.296 brouard 12558: if(prevfcast==1){
12559: /* /\* if(stepm ==1){*\/ */
12560: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12561: /*This done previously after freqsummary.*/
12562: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12563: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12564:
12565: /* } else if (prvforecast==2){ */
12566: /* /\* if(stepm ==1){*\/ */
12567: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12568: /* } */
12569: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12570: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12571: }
1.269 brouard 12572:
1.296 brouard 12573: /* Prevbcasting */
12574: if(prevbcast==1){
1.219 brouard 12575: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12576: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12577: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12578:
12579: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12580:
12581: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12582:
1.219 brouard 12583: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12584: fclose(ficresplb);
12585:
1.222 brouard 12586: hBijx(p, bage, fage, mobaverage);
12587: fclose(ficrespijb);
1.219 brouard 12588:
1.296 brouard 12589: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12590: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12591: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12592: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12593: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12594: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12595:
12596:
1.269 brouard 12597: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12598:
12599:
1.269 brouard 12600: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12601: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12602: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12603: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12604: } /* end Prevbcasting */
1.268 brouard 12605:
1.186 brouard 12606:
12607: /* ------ Other prevalence ratios------------ */
1.126 brouard 12608:
1.215 brouard 12609: free_ivector(wav,1,imx);
12610: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12611: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12612: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12613:
12614:
1.127 brouard 12615: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12616:
1.201 brouard 12617: strcpy(filerese,"E_");
12618: strcat(filerese,fileresu);
1.126 brouard 12619: if((ficreseij=fopen(filerese,"w"))==NULL) {
12620: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12621: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12622: }
1.208 brouard 12623: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12624: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12625:
12626: pstamp(ficreseij);
1.219 brouard 12627:
1.235 brouard 12628: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12629: if (cptcovn < 1){i1=1;}
12630:
12631: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12632: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12633: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12634: continue;
1.219 brouard 12635: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12636: printf("\n#****** ");
1.225 brouard 12637: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12638: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12639: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12640: }
12641: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12642: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12643: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12644: }
12645: fprintf(ficreseij,"******\n");
1.235 brouard 12646: printf("******\n");
1.219 brouard 12647:
12648: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12649: oldm=oldms;savm=savms;
1.235 brouard 12650: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12651:
1.219 brouard 12652: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12653: }
12654: fclose(ficreseij);
1.208 brouard 12655: printf("done evsij\n");fflush(stdout);
12656: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12657:
1.218 brouard 12658:
1.227 brouard 12659: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12660:
1.201 brouard 12661: strcpy(filerest,"T_");
12662: strcat(filerest,fileresu);
1.127 brouard 12663: if((ficrest=fopen(filerest,"w"))==NULL) {
12664: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12665: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12666: }
1.208 brouard 12667: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12668: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12669: strcpy(fileresstde,"STDE_");
12670: strcat(fileresstde,fileresu);
1.126 brouard 12671: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12672: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12673: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12674: }
1.227 brouard 12675: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12676: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12677:
1.201 brouard 12678: strcpy(filerescve,"CVE_");
12679: strcat(filerescve,fileresu);
1.126 brouard 12680: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12681: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12682: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12683: }
1.227 brouard 12684: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12685: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12686:
1.201 brouard 12687: strcpy(fileresv,"V_");
12688: strcat(fileresv,fileresu);
1.126 brouard 12689: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12690: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12691: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12692: }
1.227 brouard 12693: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12694: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12695:
1.235 brouard 12696: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12697: if (cptcovn < 1){i1=1;}
12698:
12699: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12700: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12701: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12702: continue;
1.242 brouard 12703: printf("\n#****** Result for:");
12704: fprintf(ficrest,"\n#****** Result for:");
12705: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12706: for(j=1;j<=cptcoveff;j++){
12707: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12708: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12709: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12710: }
1.235 brouard 12711: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12712: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12713: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12714: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12715: }
1.208 brouard 12716: fprintf(ficrest,"******\n");
1.227 brouard 12717: fprintf(ficlog,"******\n");
12718: printf("******\n");
1.208 brouard 12719:
12720: fprintf(ficresstdeij,"\n#****** ");
12721: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12722: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12723: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12724: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12725: }
1.235 brouard 12726: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12727: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12728: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12729: }
1.208 brouard 12730: fprintf(ficresstdeij,"******\n");
12731: fprintf(ficrescveij,"******\n");
12732:
12733: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12734: /* pstamp(ficresvij); */
1.225 brouard 12735: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12736: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12737: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12738: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12739: }
1.208 brouard 12740: fprintf(ficresvij,"******\n");
12741:
12742: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12743: oldm=oldms;savm=savms;
1.235 brouard 12744: printf(" cvevsij ");
12745: fprintf(ficlog, " cvevsij ");
12746: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12747: printf(" end cvevsij \n ");
12748: fprintf(ficlog, " end cvevsij \n ");
12749:
12750: /*
12751: */
12752: /* goto endfree; */
12753:
12754: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12755: pstamp(ficrest);
12756:
1.269 brouard 12757: epj=vector(1,nlstate+1);
1.208 brouard 12758: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12759: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12760: cptcod= 0; /* To be deleted */
12761: printf("varevsij vpopbased=%d \n",vpopbased);
12762: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12763: 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 12764: 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 ");
12765: if(vpopbased==1)
12766: 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);
12767: else
1.288 brouard 12768: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12769: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12770: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12771: fprintf(ficrest,"\n");
12772: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12773: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12774: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12775: for(age=bage; age <=fage ;age++){
1.235 brouard 12776: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12777: if (vpopbased==1) {
12778: if(mobilav ==0){
12779: for(i=1; i<=nlstate;i++)
12780: prlim[i][i]=probs[(int)age][i][k];
12781: }else{ /* mobilav */
12782: for(i=1; i<=nlstate;i++)
12783: prlim[i][i]=mobaverage[(int)age][i][k];
12784: }
12785: }
1.219 brouard 12786:
1.227 brouard 12787: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12788: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12789: /* printf(" age %4.0f ",age); */
12790: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12791: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12792: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12793: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12794: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12795: }
12796: epj[nlstate+1] +=epj[j];
12797: }
12798: /* printf(" age %4.0f \n",age); */
1.219 brouard 12799:
1.227 brouard 12800: for(i=1, vepp=0.;i <=nlstate;i++)
12801: for(j=1;j <=nlstate;j++)
12802: vepp += vareij[i][j][(int)age];
12803: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12804: for(j=1;j <=nlstate;j++){
12805: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12806: }
12807: fprintf(ficrest,"\n");
12808: }
1.208 brouard 12809: } /* End vpopbased */
1.269 brouard 12810: free_vector(epj,1,nlstate+1);
1.208 brouard 12811: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12812: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12813: printf("done selection\n");fflush(stdout);
12814: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12815:
1.235 brouard 12816: } /* End k selection */
1.227 brouard 12817:
12818: printf("done State-specific expectancies\n");fflush(stdout);
12819: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12820:
1.288 brouard 12821: /* variance-covariance of forward period prevalence*/
1.269 brouard 12822: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12823:
1.227 brouard 12824:
1.290 brouard 12825: free_vector(weight,firstobs,lastobs);
1.227 brouard 12826: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12827: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12828: free_matrix(anint,1,maxwav,firstobs,lastobs);
12829: free_matrix(mint,1,maxwav,firstobs,lastobs);
12830: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12831: free_ivector(tab,1,NCOVMAX);
12832: fclose(ficresstdeij);
12833: fclose(ficrescveij);
12834: fclose(ficresvij);
12835: fclose(ficrest);
12836: fclose(ficpar);
12837:
12838:
1.126 brouard 12839: /*---------- End : free ----------------*/
1.219 brouard 12840: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12841: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12842: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12843: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12844: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12845: } /* mle==-3 arrives here for freeing */
1.227 brouard 12846: /* endfree:*/
12847: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12848: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12849: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12850: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12851: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12852: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12853: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12854: free_matrix(matcov,1,npar,1,npar);
12855: free_matrix(hess,1,npar,1,npar);
12856: /*free_vector(delti,1,npar);*/
12857: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12858: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12859: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12860: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12861:
12862: free_ivector(ncodemax,1,NCOVMAX);
12863: free_ivector(ncodemaxwundef,1,NCOVMAX);
12864: free_ivector(Dummy,-1,NCOVMAX);
12865: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12866: free_ivector(DummyV,1,NCOVMAX);
12867: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12868: free_ivector(Typevar,-1,NCOVMAX);
12869: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12870: free_ivector(TvarsQ,1,NCOVMAX);
12871: free_ivector(TvarsQind,1,NCOVMAX);
12872: free_ivector(TvarsD,1,NCOVMAX);
12873: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12874: free_ivector(TvarFD,1,NCOVMAX);
12875: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12876: free_ivector(TvarF,1,NCOVMAX);
12877: free_ivector(TvarFind,1,NCOVMAX);
12878: free_ivector(TvarV,1,NCOVMAX);
12879: free_ivector(TvarVind,1,NCOVMAX);
12880: free_ivector(TvarA,1,NCOVMAX);
12881: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12882: free_ivector(TvarFQ,1,NCOVMAX);
12883: free_ivector(TvarFQind,1,NCOVMAX);
12884: free_ivector(TvarVD,1,NCOVMAX);
12885: free_ivector(TvarVDind,1,NCOVMAX);
12886: free_ivector(TvarVQ,1,NCOVMAX);
12887: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12888: free_ivector(Tvarsel,1,NCOVMAX);
12889: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12890: free_ivector(Tposprod,1,NCOVMAX);
12891: free_ivector(Tprod,1,NCOVMAX);
12892: free_ivector(Tvaraff,1,NCOVMAX);
12893: free_ivector(invalidvarcomb,1,ncovcombmax);
12894: free_ivector(Tage,1,NCOVMAX);
12895: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12896: free_ivector(TmodelInvind,1,NCOVMAX);
12897: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12898:
12899: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12900: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12901: fflush(fichtm);
12902: fflush(ficgp);
12903:
1.227 brouard 12904:
1.126 brouard 12905: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12906: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12907: 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 12908: }else{
12909: printf("End of Imach\n");
12910: fprintf(ficlog,"End of Imach\n");
12911: }
12912: printf("See log file on %s\n",filelog);
12913: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12914: /*(void) gettimeofday(&end_time,&tzp);*/
12915: rend_time = time(NULL);
12916: end_time = *localtime(&rend_time);
12917: /* tml = *localtime(&end_time.tm_sec); */
12918: strcpy(strtend,asctime(&end_time));
1.126 brouard 12919: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
12920: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 12921: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 12922:
1.157 brouard 12923: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
12924: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
12925: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 12926: /* printf("Total time was %d uSec.\n", total_usecs);*/
12927: /* if(fileappend(fichtm,optionfilehtm)){ */
12928: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12929: fclose(fichtm);
12930: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12931: fclose(fichtmcov);
12932: fclose(ficgp);
12933: fclose(ficlog);
12934: /*------ End -----------*/
1.227 brouard 12935:
1.281 brouard 12936:
12937: /* Executes gnuplot */
1.227 brouard 12938:
12939: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 12940: #ifdef WIN32
1.227 brouard 12941: if (_chdir(pathcd) != 0)
12942: printf("Can't move to directory %s!\n",path);
12943: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 12944: #else
1.227 brouard 12945: if(chdir(pathcd) != 0)
12946: printf("Can't move to directory %s!\n", path);
12947: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 12948: #endif
1.126 brouard 12949: printf("Current directory %s!\n",pathcd);
12950: /*strcat(plotcmd,CHARSEPARATOR);*/
12951: sprintf(plotcmd,"gnuplot");
1.157 brouard 12952: #ifdef _WIN32
1.126 brouard 12953: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
12954: #endif
12955: if(!stat(plotcmd,&info)){
1.158 brouard 12956: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12957: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 12958: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 12959: }else
12960: strcpy(pplotcmd,plotcmd);
1.157 brouard 12961: #ifdef __unix
1.126 brouard 12962: strcpy(plotcmd,GNUPLOTPROGRAM);
12963: if(!stat(plotcmd,&info)){
1.158 brouard 12964: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12965: }else
12966: strcpy(pplotcmd,plotcmd);
12967: #endif
12968: }else
12969: strcpy(pplotcmd,plotcmd);
12970:
12971: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 12972: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 12973: strcpy(pplotcmd,plotcmd);
1.227 brouard 12974:
1.126 brouard 12975: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 12976: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 12977: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 12978: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 12979: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 12980: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 12981: strcpy(plotcmd,pplotcmd);
12982: }
1.126 brouard 12983: }
1.158 brouard 12984: printf(" Successful, please wait...");
1.126 brouard 12985: while (z[0] != 'q') {
12986: /* chdir(path); */
1.154 brouard 12987: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 12988: scanf("%s",z);
12989: /* if (z[0] == 'c') system("./imach"); */
12990: if (z[0] == 'e') {
1.158 brouard 12991: #ifdef __APPLE__
1.152 brouard 12992: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 12993: #elif __linux
12994: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 12995: #else
1.152 brouard 12996: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 12997: #endif
12998: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
12999: system(pplotcmd);
1.126 brouard 13000: }
13001: else if (z[0] == 'g') system(plotcmd);
13002: else if (z[0] == 'q') exit(0);
13003: }
1.227 brouard 13004: end:
1.126 brouard 13005: while (z[0] != 'q') {
1.195 brouard 13006: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13007: scanf("%s",z);
13008: }
1.283 brouard 13009: printf("End\n");
1.282 brouard 13010: exit(0);
1.126 brouard 13011: }
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