Annotation of imach/src/imach.c, revision 1.291
1.291 ! brouard 1: /* $Id: imach.c,v 1.290 2019/05/09 13:39:37 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.291 ! brouard 4: Revision 1.290 2019/05/09 13:39:37 brouard
! 5: Summary: 0.99r18 unlimited number of individuals
! 6:
! 7: 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.
! 8:
1.290 brouard 9: Revision 1.289 2018/12/13 09:16:26 brouard
10: Summary: Bug for young ages (<-30) will be in r17
11:
1.289 brouard 12: Revision 1.288 2018/05/02 20:58:27 brouard
13: Summary: Some bugs fixed
14:
1.288 brouard 15: Revision 1.287 2018/05/01 17:57:25 brouard
16: Summary: Bug fixed by providing frequencies only for non missing covariates
17:
1.287 brouard 18: Revision 1.286 2018/04/27 14:27:04 brouard
19: Summary: some minor bugs
20:
1.286 brouard 21: Revision 1.285 2018/04/21 21:02:16 brouard
22: Summary: Some bugs fixed, valgrind tested
23:
1.285 brouard 24: Revision 1.284 2018/04/20 05:22:13 brouard
25: Summary: Computing mean and stdeviation of fixed quantitative variables
26:
1.284 brouard 27: Revision 1.283 2018/04/19 14:49:16 brouard
28: Summary: Some minor bugs fixed
29:
1.283 brouard 30: Revision 1.282 2018/02/27 22:50:02 brouard
31: *** empty log message ***
32:
1.282 brouard 33: Revision 1.281 2018/02/27 19:25:23 brouard
34: Summary: Adding second argument for quitting
35:
1.281 brouard 36: Revision 1.280 2018/02/21 07:58:13 brouard
37: Summary: 0.99r15
38:
39: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
40:
1.280 brouard 41: Revision 1.279 2017/07/20 13:35:01 brouard
42: Summary: temporary working
43:
1.279 brouard 44: Revision 1.278 2017/07/19 14:09:02 brouard
45: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
46:
1.278 brouard 47: Revision 1.277 2017/07/17 08:53:49 brouard
48: Summary: BOM files can be read now
49:
1.277 brouard 50: Revision 1.276 2017/06/30 15:48:31 brouard
51: Summary: Graphs improvements
52:
1.276 brouard 53: Revision 1.275 2017/06/30 13:39:33 brouard
54: Summary: Saito's color
55:
1.275 brouard 56: Revision 1.274 2017/06/29 09:47:08 brouard
57: Summary: Version 0.99r14
58:
1.274 brouard 59: Revision 1.273 2017/06/27 11:06:02 brouard
60: Summary: More documentation on projections
61:
1.273 brouard 62: Revision 1.272 2017/06/27 10:22:40 brouard
63: Summary: Color of backprojection changed from 6 to 5(yellow)
64:
1.272 brouard 65: Revision 1.271 2017/06/27 10:17:50 brouard
66: Summary: Some bug with rint
67:
1.271 brouard 68: Revision 1.270 2017/05/24 05:45:29 brouard
69: *** empty log message ***
70:
1.270 brouard 71: Revision 1.269 2017/05/23 08:39:25 brouard
72: Summary: Code into subroutine, cleanings
73:
1.269 brouard 74: Revision 1.268 2017/05/18 20:09:32 brouard
75: Summary: backprojection and confidence intervals of backprevalence
76:
1.268 brouard 77: Revision 1.267 2017/05/13 10:25:05 brouard
78: Summary: temporary save for backprojection
79:
1.267 brouard 80: Revision 1.266 2017/05/13 07:26:12 brouard
81: Summary: Version 0.99r13 (improvements and bugs fixed)
82:
1.266 brouard 83: Revision 1.265 2017/04/26 16:22:11 brouard
84: Summary: imach 0.99r13 Some bugs fixed
85:
1.265 brouard 86: Revision 1.264 2017/04/26 06:01:29 brouard
87: Summary: Labels in graphs
88:
1.264 brouard 89: Revision 1.263 2017/04/24 15:23:15 brouard
90: Summary: to save
91:
1.263 brouard 92: Revision 1.262 2017/04/18 16:48:12 brouard
93: *** empty log message ***
94:
1.262 brouard 95: Revision 1.261 2017/04/05 10:14:09 brouard
96: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
97:
1.261 brouard 98: Revision 1.260 2017/04/04 17:46:59 brouard
99: Summary: Gnuplot indexations fixed (humm)
100:
1.260 brouard 101: Revision 1.259 2017/04/04 13:01:16 brouard
102: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
103:
1.259 brouard 104: Revision 1.258 2017/04/03 10:17:47 brouard
105: Summary: Version 0.99r12
106:
107: Some cleanings, conformed with updated documentation.
108:
1.258 brouard 109: Revision 1.257 2017/03/29 16:53:30 brouard
110: Summary: Temp
111:
1.257 brouard 112: Revision 1.256 2017/03/27 05:50:23 brouard
113: Summary: Temporary
114:
1.256 brouard 115: Revision 1.255 2017/03/08 16:02:28 brouard
116: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
117:
1.255 brouard 118: Revision 1.254 2017/03/08 07:13:00 brouard
119: Summary: Fixing data parameter line
120:
1.254 brouard 121: Revision 1.253 2016/12/15 11:59:41 brouard
122: Summary: 0.99 in progress
123:
1.253 brouard 124: Revision 1.252 2016/09/15 21:15:37 brouard
125: *** empty log message ***
126:
1.252 brouard 127: Revision 1.251 2016/09/15 15:01:13 brouard
128: Summary: not working
129:
1.251 brouard 130: Revision 1.250 2016/09/08 16:07:27 brouard
131: Summary: continue
132:
1.250 brouard 133: Revision 1.249 2016/09/07 17:14:18 brouard
134: Summary: Starting values from frequencies
135:
1.249 brouard 136: Revision 1.248 2016/09/07 14:10:18 brouard
137: *** empty log message ***
138:
1.248 brouard 139: Revision 1.247 2016/09/02 11:11:21 brouard
140: *** empty log message ***
141:
1.247 brouard 142: Revision 1.246 2016/09/02 08:49:22 brouard
143: *** empty log message ***
144:
1.246 brouard 145: Revision 1.245 2016/09/02 07:25:01 brouard
146: *** empty log message ***
147:
1.245 brouard 148: Revision 1.244 2016/09/02 07:17:34 brouard
149: *** empty log message ***
150:
1.244 brouard 151: Revision 1.243 2016/09/02 06:45:35 brouard
152: *** empty log message ***
153:
1.243 brouard 154: Revision 1.242 2016/08/30 15:01:20 brouard
155: Summary: Fixing a lots
156:
1.242 brouard 157: Revision 1.241 2016/08/29 17:17:25 brouard
158: Summary: gnuplot problem in Back projection to fix
159:
1.241 brouard 160: Revision 1.240 2016/08/29 07:53:18 brouard
161: Summary: Better
162:
1.240 brouard 163: Revision 1.239 2016/08/26 15:51:03 brouard
164: Summary: Improvement in Powell output in order to copy and paste
165:
166: Author:
167:
1.239 brouard 168: Revision 1.238 2016/08/26 14:23:35 brouard
169: Summary: Starting tests of 0.99
170:
1.238 brouard 171: Revision 1.237 2016/08/26 09:20:19 brouard
172: Summary: to valgrind
173:
1.237 brouard 174: Revision 1.236 2016/08/25 10:50:18 brouard
175: *** empty log message ***
176:
1.236 brouard 177: Revision 1.235 2016/08/25 06:59:23 brouard
178: *** empty log message ***
179:
1.235 brouard 180: Revision 1.234 2016/08/23 16:51:20 brouard
181: *** empty log message ***
182:
1.234 brouard 183: Revision 1.233 2016/08/23 07:40:50 brouard
184: Summary: not working
185:
1.233 brouard 186: Revision 1.232 2016/08/22 14:20:21 brouard
187: Summary: not working
188:
1.232 brouard 189: Revision 1.231 2016/08/22 07:17:15 brouard
190: Summary: not working
191:
1.231 brouard 192: Revision 1.230 2016/08/22 06:55:53 brouard
193: Summary: Not working
194:
1.230 brouard 195: Revision 1.229 2016/07/23 09:45:53 brouard
196: Summary: Completing for func too
197:
1.229 brouard 198: Revision 1.228 2016/07/22 17:45:30 brouard
199: Summary: Fixing some arrays, still debugging
200:
1.227 brouard 201: Revision 1.226 2016/07/12 18:42:34 brouard
202: Summary: temp
203:
1.226 brouard 204: Revision 1.225 2016/07/12 08:40:03 brouard
205: Summary: saving but not running
206:
1.225 brouard 207: Revision 1.224 2016/07/01 13:16:01 brouard
208: Summary: Fixes
209:
1.224 brouard 210: Revision 1.223 2016/02/19 09:23:35 brouard
211: Summary: temporary
212:
1.223 brouard 213: Revision 1.222 2016/02/17 08:14:50 brouard
214: Summary: Probably last 0.98 stable version 0.98r6
215:
1.222 brouard 216: Revision 1.221 2016/02/15 23:35:36 brouard
217: Summary: minor bug
218:
1.220 brouard 219: Revision 1.219 2016/02/15 00:48:12 brouard
220: *** empty log message ***
221:
1.219 brouard 222: Revision 1.218 2016/02/12 11:29:23 brouard
223: Summary: 0.99 Back projections
224:
1.218 brouard 225: Revision 1.217 2015/12/23 17:18:31 brouard
226: Summary: Experimental backcast
227:
1.217 brouard 228: Revision 1.216 2015/12/18 17:32:11 brouard
229: Summary: 0.98r4 Warning and status=-2
230:
231: Version 0.98r4 is now:
232: - displaying an error when status is -1, date of interview unknown and date of death known;
233: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
234: Older changes concerning s=-2, dating from 2005 have been supersed.
235:
1.216 brouard 236: Revision 1.215 2015/12/16 08:52:24 brouard
237: Summary: 0.98r4 working
238:
1.215 brouard 239: Revision 1.214 2015/12/16 06:57:54 brouard
240: Summary: temporary not working
241:
1.214 brouard 242: Revision 1.213 2015/12/11 18:22:17 brouard
243: Summary: 0.98r4
244:
1.213 brouard 245: Revision 1.212 2015/11/21 12:47:24 brouard
246: Summary: minor typo
247:
1.212 brouard 248: Revision 1.211 2015/11/21 12:41:11 brouard
249: Summary: 0.98r3 with some graph of projected cross-sectional
250:
251: Author: Nicolas Brouard
252:
1.211 brouard 253: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 254: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 255: Summary: Adding ftolpl parameter
256: Author: N Brouard
257:
258: We had difficulties to get smoothed confidence intervals. It was due
259: to the period prevalence which wasn't computed accurately. The inner
260: parameter ftolpl is now an outer parameter of the .imach parameter
261: file after estepm. If ftolpl is small 1.e-4 and estepm too,
262: computation are long.
263:
1.209 brouard 264: Revision 1.208 2015/11/17 14:31:57 brouard
265: Summary: temporary
266:
1.208 brouard 267: Revision 1.207 2015/10/27 17:36:57 brouard
268: *** empty log message ***
269:
1.207 brouard 270: Revision 1.206 2015/10/24 07:14:11 brouard
271: *** empty log message ***
272:
1.206 brouard 273: Revision 1.205 2015/10/23 15:50:53 brouard
274: Summary: 0.98r3 some clarification for graphs on likelihood contributions
275:
1.205 brouard 276: Revision 1.204 2015/10/01 16:20:26 brouard
277: Summary: Some new graphs of contribution to likelihood
278:
1.204 brouard 279: Revision 1.203 2015/09/30 17:45:14 brouard
280: Summary: looking at better estimation of the hessian
281:
282: Also a better criteria for convergence to the period prevalence And
283: therefore adding the number of years needed to converge. (The
284: prevalence in any alive state shold sum to one
285:
1.203 brouard 286: Revision 1.202 2015/09/22 19:45:16 brouard
287: Summary: Adding some overall graph on contribution to likelihood. Might change
288:
1.202 brouard 289: Revision 1.201 2015/09/15 17:34:58 brouard
290: Summary: 0.98r0
291:
292: - Some new graphs like suvival functions
293: - Some bugs fixed like model=1+age+V2.
294:
1.201 brouard 295: Revision 1.200 2015/09/09 16:53:55 brouard
296: Summary: Big bug thanks to Flavia
297:
298: Even model=1+age+V2. did not work anymore
299:
1.200 brouard 300: Revision 1.199 2015/09/07 14:09:23 brouard
301: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
302:
1.199 brouard 303: Revision 1.198 2015/09/03 07:14:39 brouard
304: Summary: 0.98q5 Flavia
305:
1.198 brouard 306: Revision 1.197 2015/09/01 18:24:39 brouard
307: *** empty log message ***
308:
1.197 brouard 309: Revision 1.196 2015/08/18 23:17:52 brouard
310: Summary: 0.98q5
311:
1.196 brouard 312: Revision 1.195 2015/08/18 16:28:39 brouard
313: Summary: Adding a hack for testing purpose
314:
315: After reading the title, ftol and model lines, if the comment line has
316: a q, starting with #q, the answer at the end of the run is quit. It
317: permits to run test files in batch with ctest. The former workaround was
318: $ echo q | imach foo.imach
319:
1.195 brouard 320: Revision 1.194 2015/08/18 13:32:00 brouard
321: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
322:
1.194 brouard 323: Revision 1.193 2015/08/04 07:17:42 brouard
324: Summary: 0.98q4
325:
1.193 brouard 326: Revision 1.192 2015/07/16 16:49:02 brouard
327: Summary: Fixing some outputs
328:
1.192 brouard 329: Revision 1.191 2015/07/14 10:00:33 brouard
330: Summary: Some fixes
331:
1.191 brouard 332: Revision 1.190 2015/05/05 08:51:13 brouard
333: Summary: Adding digits in output parameters (7 digits instead of 6)
334:
335: Fix 1+age+.
336:
1.190 brouard 337: Revision 1.189 2015/04/30 14:45:16 brouard
338: Summary: 0.98q2
339:
1.189 brouard 340: Revision 1.188 2015/04/30 08:27:53 brouard
341: *** empty log message ***
342:
1.188 brouard 343: Revision 1.187 2015/04/29 09:11:15 brouard
344: *** empty log message ***
345:
1.187 brouard 346: Revision 1.186 2015/04/23 12:01:52 brouard
347: Summary: V1*age is working now, version 0.98q1
348:
349: Some codes had been disabled in order to simplify and Vn*age was
350: working in the optimization phase, ie, giving correct MLE parameters,
351: but, as usual, outputs were not correct and program core dumped.
352:
1.186 brouard 353: Revision 1.185 2015/03/11 13:26:42 brouard
354: Summary: Inclusion of compile and links command line for Intel Compiler
355:
1.185 brouard 356: Revision 1.184 2015/03/11 11:52:39 brouard
357: Summary: Back from Windows 8. Intel Compiler
358:
1.184 brouard 359: Revision 1.183 2015/03/10 20:34:32 brouard
360: Summary: 0.98q0, trying with directest, mnbrak fixed
361:
362: We use directest instead of original Powell test; probably no
363: incidence on the results, but better justifications;
364: We fixed Numerical Recipes mnbrak routine which was wrong and gave
365: wrong results.
366:
1.183 brouard 367: Revision 1.182 2015/02/12 08:19:57 brouard
368: Summary: Trying to keep directest which seems simpler and more general
369: Author: Nicolas Brouard
370:
1.182 brouard 371: Revision 1.181 2015/02/11 23:22:24 brouard
372: Summary: Comments on Powell added
373:
374: Author:
375:
1.181 brouard 376: Revision 1.180 2015/02/11 17:33:45 brouard
377: Summary: Finishing move from main to function (hpijx and prevalence_limit)
378:
1.180 brouard 379: Revision 1.179 2015/01/04 09:57:06 brouard
380: Summary: back to OS/X
381:
1.179 brouard 382: Revision 1.178 2015/01/04 09:35:48 brouard
383: *** empty log message ***
384:
1.178 brouard 385: Revision 1.177 2015/01/03 18:40:56 brouard
386: Summary: Still testing ilc32 on OSX
387:
1.177 brouard 388: Revision 1.176 2015/01/03 16:45:04 brouard
389: *** empty log message ***
390:
1.176 brouard 391: Revision 1.175 2015/01/03 16:33:42 brouard
392: *** empty log message ***
393:
1.175 brouard 394: Revision 1.174 2015/01/03 16:15:49 brouard
395: Summary: Still in cross-compilation
396:
1.174 brouard 397: Revision 1.173 2015/01/03 12:06:26 brouard
398: Summary: trying to detect cross-compilation
399:
1.173 brouard 400: Revision 1.172 2014/12/27 12:07:47 brouard
401: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
402:
1.172 brouard 403: Revision 1.171 2014/12/23 13:26:59 brouard
404: Summary: Back from Visual C
405:
406: Still problem with utsname.h on Windows
407:
1.171 brouard 408: Revision 1.170 2014/12/23 11:17:12 brouard
409: Summary: Cleaning some \%% back to %%
410:
411: The escape was mandatory for a specific compiler (which one?), but too many warnings.
412:
1.170 brouard 413: Revision 1.169 2014/12/22 23:08:31 brouard
414: Summary: 0.98p
415:
416: Outputs some informations on compiler used, OS etc. Testing on different platforms.
417:
1.169 brouard 418: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 419: Summary: update
1.169 brouard 420:
1.168 brouard 421: Revision 1.167 2014/12/22 13:50:56 brouard
422: Summary: Testing uname and compiler version and if compiled 32 or 64
423:
424: Testing on Linux 64
425:
1.167 brouard 426: Revision 1.166 2014/12/22 11:40:47 brouard
427: *** empty log message ***
428:
1.166 brouard 429: Revision 1.165 2014/12/16 11:20:36 brouard
430: Summary: After compiling on Visual C
431:
432: * imach.c (Module): Merging 1.61 to 1.162
433:
1.165 brouard 434: Revision 1.164 2014/12/16 10:52:11 brouard
435: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
436:
437: * imach.c (Module): Merging 1.61 to 1.162
438:
1.164 brouard 439: Revision 1.163 2014/12/16 10:30:11 brouard
440: * imach.c (Module): Merging 1.61 to 1.162
441:
1.163 brouard 442: Revision 1.162 2014/09/25 11:43:39 brouard
443: Summary: temporary backup 0.99!
444:
1.162 brouard 445: Revision 1.1 2014/09/16 11:06:58 brouard
446: Summary: With some code (wrong) for nlopt
447:
448: Author:
449:
450: Revision 1.161 2014/09/15 20:41:41 brouard
451: Summary: Problem with macro SQR on Intel compiler
452:
1.161 brouard 453: Revision 1.160 2014/09/02 09:24:05 brouard
454: *** empty log message ***
455:
1.160 brouard 456: Revision 1.159 2014/09/01 10:34:10 brouard
457: Summary: WIN32
458: Author: Brouard
459:
1.159 brouard 460: Revision 1.158 2014/08/27 17:11:51 brouard
461: *** empty log message ***
462:
1.158 brouard 463: Revision 1.157 2014/08/27 16:26:55 brouard
464: Summary: Preparing windows Visual studio version
465: Author: Brouard
466:
467: In order to compile on Visual studio, time.h is now correct and time_t
468: and tm struct should be used. difftime should be used but sometimes I
469: just make the differences in raw time format (time(&now).
470: Trying to suppress #ifdef LINUX
471: Add xdg-open for __linux in order to open default browser.
472:
1.157 brouard 473: Revision 1.156 2014/08/25 20:10:10 brouard
474: *** empty log message ***
475:
1.156 brouard 476: Revision 1.155 2014/08/25 18:32:34 brouard
477: Summary: New compile, minor changes
478: Author: Brouard
479:
1.155 brouard 480: Revision 1.154 2014/06/20 17:32:08 brouard
481: Summary: Outputs now all graphs of convergence to period prevalence
482:
1.154 brouard 483: Revision 1.153 2014/06/20 16:45:46 brouard
484: Summary: If 3 live state, convergence to period prevalence on same graph
485: Author: Brouard
486:
1.153 brouard 487: Revision 1.152 2014/06/18 17:54:09 brouard
488: Summary: open browser, use gnuplot on same dir than imach if not found in the path
489:
1.152 brouard 490: Revision 1.151 2014/06/18 16:43:30 brouard
491: *** empty log message ***
492:
1.151 brouard 493: Revision 1.150 2014/06/18 16:42:35 brouard
494: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
495: Author: brouard
496:
1.150 brouard 497: Revision 1.149 2014/06/18 15:51:14 brouard
498: Summary: Some fixes in parameter files errors
499: Author: Nicolas Brouard
500:
1.149 brouard 501: Revision 1.148 2014/06/17 17:38:48 brouard
502: Summary: Nothing new
503: Author: Brouard
504:
505: Just a new packaging for OS/X version 0.98nS
506:
1.148 brouard 507: Revision 1.147 2014/06/16 10:33:11 brouard
508: *** empty log message ***
509:
1.147 brouard 510: Revision 1.146 2014/06/16 10:20:28 brouard
511: Summary: Merge
512: Author: Brouard
513:
514: Merge, before building revised version.
515:
1.146 brouard 516: Revision 1.145 2014/06/10 21:23:15 brouard
517: Summary: Debugging with valgrind
518: Author: Nicolas Brouard
519:
520: Lot of changes in order to output the results with some covariates
521: After the Edimburgh REVES conference 2014, it seems mandatory to
522: improve the code.
523: No more memory valgrind error but a lot has to be done in order to
524: continue the work of splitting the code into subroutines.
525: Also, decodemodel has been improved. Tricode is still not
526: optimal. nbcode should be improved. Documentation has been added in
527: the source code.
528:
1.144 brouard 529: Revision 1.143 2014/01/26 09:45:38 brouard
530: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
531:
532: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
533: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
534:
1.143 brouard 535: Revision 1.142 2014/01/26 03:57:36 brouard
536: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
537:
538: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
539:
1.142 brouard 540: Revision 1.141 2014/01/26 02:42:01 brouard
541: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
542:
1.141 brouard 543: Revision 1.140 2011/09/02 10:37:54 brouard
544: Summary: times.h is ok with mingw32 now.
545:
1.140 brouard 546: Revision 1.139 2010/06/14 07:50:17 brouard
547: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
548: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
549:
1.139 brouard 550: Revision 1.138 2010/04/30 18:19:40 brouard
551: *** empty log message ***
552:
1.138 brouard 553: Revision 1.137 2010/04/29 18:11:38 brouard
554: (Module): Checking covariates for more complex models
555: than V1+V2. A lot of change to be done. Unstable.
556:
1.137 brouard 557: Revision 1.136 2010/04/26 20:30:53 brouard
558: (Module): merging some libgsl code. Fixing computation
559: of likelione (using inter/intrapolation if mle = 0) in order to
560: get same likelihood as if mle=1.
561: Some cleaning of code and comments added.
562:
1.136 brouard 563: Revision 1.135 2009/10/29 15:33:14 brouard
564: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
565:
1.135 brouard 566: Revision 1.134 2009/10/29 13:18:53 brouard
567: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
568:
1.134 brouard 569: Revision 1.133 2009/07/06 10:21:25 brouard
570: just nforces
571:
1.133 brouard 572: Revision 1.132 2009/07/06 08:22:05 brouard
573: Many tings
574:
1.132 brouard 575: Revision 1.131 2009/06/20 16:22:47 brouard
576: Some dimensions resccaled
577:
1.131 brouard 578: Revision 1.130 2009/05/26 06:44:34 brouard
579: (Module): Max Covariate is now set to 20 instead of 8. A
580: lot of cleaning with variables initialized to 0. Trying to make
581: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
582:
1.130 brouard 583: Revision 1.129 2007/08/31 13:49:27 lievre
584: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
585:
1.129 lievre 586: Revision 1.128 2006/06/30 13:02:05 brouard
587: (Module): Clarifications on computing e.j
588:
1.128 brouard 589: Revision 1.127 2006/04/28 18:11:50 brouard
590: (Module): Yes the sum of survivors was wrong since
591: imach-114 because nhstepm was no more computed in the age
592: loop. Now we define nhstepma in the age loop.
593: (Module): In order to speed up (in case of numerous covariates) we
594: compute health expectancies (without variances) in a first step
595: and then all the health expectancies with variances or standard
596: deviation (needs data from the Hessian matrices) which slows the
597: computation.
598: In the future we should be able to stop the program is only health
599: expectancies and graph are needed without standard deviations.
600:
1.127 brouard 601: Revision 1.126 2006/04/28 17:23:28 brouard
602: (Module): Yes the sum of survivors was wrong since
603: imach-114 because nhstepm was no more computed in the age
604: loop. Now we define nhstepma in the age loop.
605: Version 0.98h
606:
1.126 brouard 607: Revision 1.125 2006/04/04 15:20:31 lievre
608: Errors in calculation of health expectancies. Age was not initialized.
609: Forecasting file added.
610:
611: Revision 1.124 2006/03/22 17:13:53 lievre
612: Parameters are printed with %lf instead of %f (more numbers after the comma).
613: The log-likelihood is printed in the log file
614:
615: Revision 1.123 2006/03/20 10:52:43 brouard
616: * imach.c (Module): <title> changed, corresponds to .htm file
617: name. <head> headers where missing.
618:
619: * imach.c (Module): Weights can have a decimal point as for
620: English (a comma might work with a correct LC_NUMERIC environment,
621: otherwise the weight is truncated).
622: Modification of warning when the covariates values are not 0 or
623: 1.
624: Version 0.98g
625:
626: Revision 1.122 2006/03/20 09:45:41 brouard
627: (Module): Weights can have a decimal point as for
628: English (a comma might work with a correct LC_NUMERIC environment,
629: otherwise the weight is truncated).
630: Modification of warning when the covariates values are not 0 or
631: 1.
632: Version 0.98g
633:
634: Revision 1.121 2006/03/16 17:45:01 lievre
635: * imach.c (Module): Comments concerning covariates added
636:
637: * imach.c (Module): refinements in the computation of lli if
638: status=-2 in order to have more reliable computation if stepm is
639: not 1 month. Version 0.98f
640:
641: Revision 1.120 2006/03/16 15:10:38 lievre
642: (Module): refinements in the computation of lli if
643: status=-2 in order to have more reliable computation if stepm is
644: not 1 month. Version 0.98f
645:
646: Revision 1.119 2006/03/15 17:42:26 brouard
647: (Module): Bug if status = -2, the loglikelihood was
648: computed as likelihood omitting the logarithm. Version O.98e
649:
650: Revision 1.118 2006/03/14 18:20:07 brouard
651: (Module): varevsij Comments added explaining the second
652: table of variances if popbased=1 .
653: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
654: (Module): Function pstamp added
655: (Module): Version 0.98d
656:
657: Revision 1.117 2006/03/14 17:16:22 brouard
658: (Module): varevsij Comments added explaining the second
659: table of variances if popbased=1 .
660: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
661: (Module): Function pstamp added
662: (Module): Version 0.98d
663:
664: Revision 1.116 2006/03/06 10:29:27 brouard
665: (Module): Variance-covariance wrong links and
666: varian-covariance of ej. is needed (Saito).
667:
668: Revision 1.115 2006/02/27 12:17:45 brouard
669: (Module): One freematrix added in mlikeli! 0.98c
670:
671: Revision 1.114 2006/02/26 12:57:58 brouard
672: (Module): Some improvements in processing parameter
673: filename with strsep.
674:
675: Revision 1.113 2006/02/24 14:20:24 brouard
676: (Module): Memory leaks checks with valgrind and:
677: datafile was not closed, some imatrix were not freed and on matrix
678: allocation too.
679:
680: Revision 1.112 2006/01/30 09:55:26 brouard
681: (Module): Back to gnuplot.exe instead of wgnuplot.exe
682:
683: Revision 1.111 2006/01/25 20:38:18 brouard
684: (Module): Lots of cleaning and bugs added (Gompertz)
685: (Module): Comments can be added in data file. Missing date values
686: can be a simple dot '.'.
687:
688: Revision 1.110 2006/01/25 00:51:50 brouard
689: (Module): Lots of cleaning and bugs added (Gompertz)
690:
691: Revision 1.109 2006/01/24 19:37:15 brouard
692: (Module): Comments (lines starting with a #) are allowed in data.
693:
694: Revision 1.108 2006/01/19 18:05:42 lievre
695: Gnuplot problem appeared...
696: To be fixed
697:
698: Revision 1.107 2006/01/19 16:20:37 brouard
699: Test existence of gnuplot in imach path
700:
701: Revision 1.106 2006/01/19 13:24:36 brouard
702: Some cleaning and links added in html output
703:
704: Revision 1.105 2006/01/05 20:23:19 lievre
705: *** empty log message ***
706:
707: Revision 1.104 2005/09/30 16:11:43 lievre
708: (Module): sump fixed, loop imx fixed, and simplifications.
709: (Module): If the status is missing at the last wave but we know
710: that the person is alive, then we can code his/her status as -2
711: (instead of missing=-1 in earlier versions) and his/her
712: contributions to the likelihood is 1 - Prob of dying from last
713: health status (= 1-p13= p11+p12 in the easiest case of somebody in
714: the healthy state at last known wave). Version is 0.98
715:
716: Revision 1.103 2005/09/30 15:54:49 lievre
717: (Module): sump fixed, loop imx fixed, and simplifications.
718:
719: Revision 1.102 2004/09/15 17:31:30 brouard
720: Add the possibility to read data file including tab characters.
721:
722: Revision 1.101 2004/09/15 10:38:38 brouard
723: Fix on curr_time
724:
725: Revision 1.100 2004/07/12 18:29:06 brouard
726: Add version for Mac OS X. Just define UNIX in Makefile
727:
728: Revision 1.99 2004/06/05 08:57:40 brouard
729: *** empty log message ***
730:
731: Revision 1.98 2004/05/16 15:05:56 brouard
732: New version 0.97 . First attempt to estimate force of mortality
733: directly from the data i.e. without the need of knowing the health
734: state at each age, but using a Gompertz model: log u =a + b*age .
735: This is the basic analysis of mortality and should be done before any
736: other analysis, in order to test if the mortality estimated from the
737: cross-longitudinal survey is different from the mortality estimated
738: from other sources like vital statistic data.
739:
740: The same imach parameter file can be used but the option for mle should be -3.
741:
1.133 brouard 742: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 743: former routines in order to include the new code within the former code.
744:
745: The output is very simple: only an estimate of the intercept and of
746: the slope with 95% confident intervals.
747:
748: Current limitations:
749: A) Even if you enter covariates, i.e. with the
750: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
751: B) There is no computation of Life Expectancy nor Life Table.
752:
753: Revision 1.97 2004/02/20 13:25:42 lievre
754: Version 0.96d. Population forecasting command line is (temporarily)
755: suppressed.
756:
757: Revision 1.96 2003/07/15 15:38:55 brouard
758: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
759: rewritten within the same printf. Workaround: many printfs.
760:
761: Revision 1.95 2003/07/08 07:54:34 brouard
762: * imach.c (Repository):
763: (Repository): Using imachwizard code to output a more meaningful covariance
764: matrix (cov(a12,c31) instead of numbers.
765:
766: Revision 1.94 2003/06/27 13:00:02 brouard
767: Just cleaning
768:
769: Revision 1.93 2003/06/25 16:33:55 brouard
770: (Module): On windows (cygwin) function asctime_r doesn't
771: exist so I changed back to asctime which exists.
772: (Module): Version 0.96b
773:
774: Revision 1.92 2003/06/25 16:30:45 brouard
775: (Module): On windows (cygwin) function asctime_r doesn't
776: exist so I changed back to asctime which exists.
777:
778: Revision 1.91 2003/06/25 15:30:29 brouard
779: * imach.c (Repository): Duplicated warning errors corrected.
780: (Repository): Elapsed time after each iteration is now output. It
781: helps to forecast when convergence will be reached. Elapsed time
782: is stamped in powell. We created a new html file for the graphs
783: concerning matrix of covariance. It has extension -cov.htm.
784:
785: Revision 1.90 2003/06/24 12:34:15 brouard
786: (Module): Some bugs corrected for windows. Also, when
787: mle=-1 a template is output in file "or"mypar.txt with the design
788: of the covariance matrix to be input.
789:
790: Revision 1.89 2003/06/24 12:30:52 brouard
791: (Module): Some bugs corrected for windows. Also, when
792: mle=-1 a template is output in file "or"mypar.txt with the design
793: of the covariance matrix to be input.
794:
795: Revision 1.88 2003/06/23 17:54:56 brouard
796: * 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.
797:
798: Revision 1.87 2003/06/18 12:26:01 brouard
799: Version 0.96
800:
801: Revision 1.86 2003/06/17 20:04:08 brouard
802: (Module): Change position of html and gnuplot routines and added
803: routine fileappend.
804:
805: Revision 1.85 2003/06/17 13:12:43 brouard
806: * imach.c (Repository): Check when date of death was earlier that
807: current date of interview. It may happen when the death was just
808: prior to the death. In this case, dh was negative and likelihood
809: was wrong (infinity). We still send an "Error" but patch by
810: assuming that the date of death was just one stepm after the
811: interview.
812: (Repository): Because some people have very long ID (first column)
813: we changed int to long in num[] and we added a new lvector for
814: memory allocation. But we also truncated to 8 characters (left
815: truncation)
816: (Repository): No more line truncation errors.
817:
818: Revision 1.84 2003/06/13 21:44:43 brouard
819: * imach.c (Repository): Replace "freqsummary" at a correct
820: place. It differs from routine "prevalence" which may be called
821: many times. Probs is memory consuming and must be used with
822: parcimony.
823: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
824:
825: Revision 1.83 2003/06/10 13:39:11 lievre
826: *** empty log message ***
827:
828: Revision 1.82 2003/06/05 15:57:20 brouard
829: Add log in imach.c and fullversion number is now printed.
830:
831: */
832: /*
833: Interpolated Markov Chain
834:
835: Short summary of the programme:
836:
1.227 brouard 837: This program computes Healthy Life Expectancies or State-specific
838: (if states aren't health statuses) Expectancies from
839: cross-longitudinal data. Cross-longitudinal data consist in:
840:
841: -1- a first survey ("cross") where individuals from different ages
842: are interviewed on their health status or degree of disability (in
843: the case of a health survey which is our main interest)
844:
845: -2- at least a second wave of interviews ("longitudinal") which
846: measure each change (if any) in individual health status. Health
847: expectancies are computed from the time spent in each health state
848: according to a model. More health states you consider, more time is
849: necessary to reach the Maximum Likelihood of the parameters involved
850: in the model. The simplest model is the multinomial logistic model
851: where pij is the probability to be observed in state j at the second
852: wave conditional to be observed in state i at the first
853: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
854: etc , where 'age' is age and 'sex' is a covariate. If you want to
855: have a more complex model than "constant and age", you should modify
856: the program where the markup *Covariates have to be included here
857: again* invites you to do it. More covariates you add, slower the
1.126 brouard 858: convergence.
859:
860: The advantage of this computer programme, compared to a simple
861: multinomial logistic model, is clear when the delay between waves is not
862: identical for each individual. Also, if a individual missed an
863: intermediate interview, the information is lost, but taken into
864: account using an interpolation or extrapolation.
865:
866: hPijx is the probability to be observed in state i at age x+h
867: conditional to the observed state i at age x. The delay 'h' can be
868: split into an exact number (nh*stepm) of unobserved intermediate
869: states. This elementary transition (by month, quarter,
870: semester or year) is modelled as a multinomial logistic. The hPx
871: matrix is simply the matrix product of nh*stepm elementary matrices
872: and the contribution of each individual to the likelihood is simply
873: hPijx.
874:
875: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 876: of the life expectancies. It also computes the period (stable) prevalence.
877:
878: Back prevalence and projections:
1.227 brouard 879:
880: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
881: double agemaxpar, double ftolpl, int *ncvyearp, double
882: dateprev1,double dateprev2, int firstpass, int lastpass, int
883: mobilavproj)
884:
885: Computes the back prevalence limit for any combination of
886: covariate values k at any age between ageminpar and agemaxpar and
887: returns it in **bprlim. In the loops,
888:
889: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
890: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
891:
892: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 893: Computes for any combination of covariates k and any age between bage and fage
894: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
895: oldm=oldms;savm=savms;
1.227 brouard 896:
1.267 brouard 897: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 898: Computes the transition matrix starting at age 'age' over
899: 'nhstepm*hstepm*stepm' months (i.e. until
900: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 901: nhstepm*hstepm matrices.
902:
903: Returns p3mat[i][j][h] after calling
904: p3mat[i][j][h]=matprod2(newm,
905: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
906: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
907: oldm);
1.226 brouard 908:
909: Important routines
910:
911: - func (or funcone), computes logit (pij) distinguishing
912: o fixed variables (single or product dummies or quantitative);
913: o varying variables by:
914: (1) wave (single, product dummies, quantitative),
915: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
916: % fixed dummy (treated) or quantitative (not done because time-consuming);
917: % varying dummy (not done) or quantitative (not done);
918: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
919: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
920: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
921: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
922: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 923:
1.226 brouard 924:
925:
1.133 brouard 926: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
927: Institut national d'études démographiques, Paris.
1.126 brouard 928: This software have been partly granted by Euro-REVES, a concerted action
929: from the European Union.
930: It is copyrighted identically to a GNU software product, ie programme and
931: software can be distributed freely for non commercial use. Latest version
932: can be accessed at http://euroreves.ined.fr/imach .
933:
934: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
935: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
936:
937: **********************************************************************/
938: /*
939: main
940: read parameterfile
941: read datafile
942: concatwav
943: freqsummary
944: if (mle >= 1)
945: mlikeli
946: print results files
947: if mle==1
948: computes hessian
949: read end of parameter file: agemin, agemax, bage, fage, estepm
950: begin-prev-date,...
951: open gnuplot file
952: open html file
1.145 brouard 953: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
954: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
955: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
956: freexexit2 possible for memory heap.
957:
958: h Pij x | pij_nom ficrestpij
959: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
960: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
961: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
962:
963: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
964: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
965: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
966: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
967: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
968:
1.126 brouard 969: forecasting if prevfcast==1 prevforecast call prevalence()
970: health expectancies
971: Variance-covariance of DFLE
972: prevalence()
973: movingaverage()
974: varevsij()
975: if popbased==1 varevsij(,popbased)
976: total life expectancies
977: Variance of period (stable) prevalence
978: end
979: */
980:
1.187 brouard 981: /* #define DEBUG */
982: /* #define DEBUGBRENT */
1.203 brouard 983: /* #define DEBUGLINMIN */
984: /* #define DEBUGHESS */
985: #define DEBUGHESSIJ
1.224 brouard 986: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 987: #define POWELL /* Instead of NLOPT */
1.224 brouard 988: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 989: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
990: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 991:
992: #include <math.h>
993: #include <stdio.h>
994: #include <stdlib.h>
995: #include <string.h>
1.226 brouard 996: #include <ctype.h>
1.159 brouard 997:
998: #ifdef _WIN32
999: #include <io.h>
1.172 brouard 1000: #include <windows.h>
1001: #include <tchar.h>
1.159 brouard 1002: #else
1.126 brouard 1003: #include <unistd.h>
1.159 brouard 1004: #endif
1.126 brouard 1005:
1006: #include <limits.h>
1007: #include <sys/types.h>
1.171 brouard 1008:
1009: #if defined(__GNUC__)
1010: #include <sys/utsname.h> /* Doesn't work on Windows */
1011: #endif
1012:
1.126 brouard 1013: #include <sys/stat.h>
1014: #include <errno.h>
1.159 brouard 1015: /* extern int errno; */
1.126 brouard 1016:
1.157 brouard 1017: /* #ifdef LINUX */
1018: /* #include <time.h> */
1019: /* #include "timeval.h" */
1020: /* #else */
1021: /* #include <sys/time.h> */
1022: /* #endif */
1023:
1.126 brouard 1024: #include <time.h>
1025:
1.136 brouard 1026: #ifdef GSL
1027: #include <gsl/gsl_errno.h>
1028: #include <gsl/gsl_multimin.h>
1029: #endif
1030:
1.167 brouard 1031:
1.162 brouard 1032: #ifdef NLOPT
1033: #include <nlopt.h>
1034: typedef struct {
1035: double (* function)(double [] );
1036: } myfunc_data ;
1037: #endif
1038:
1.126 brouard 1039: /* #include <libintl.h> */
1040: /* #define _(String) gettext (String) */
1041:
1.251 brouard 1042: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1043:
1044: #define GNUPLOTPROGRAM "gnuplot"
1045: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1046: #define FILENAMELENGTH 132
1047:
1048: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1049: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1050:
1.144 brouard 1051: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1052: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1053:
1054: #define NINTERVMAX 8
1.144 brouard 1055: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1056: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 ! brouard 1057: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1058: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1059: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1060: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1061: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1062: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1063: /* #define AGESUP 130 */
1.288 brouard 1064: /* #define AGESUP 150 */
1065: #define AGESUP 200
1.268 brouard 1066: #define AGEINF 0
1.218 brouard 1067: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1068: #define AGEBASE 40
1.194 brouard 1069: #define AGEOVERFLOW 1.e20
1.164 brouard 1070: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1071: #ifdef _WIN32
1072: #define DIRSEPARATOR '\\'
1073: #define CHARSEPARATOR "\\"
1074: #define ODIRSEPARATOR '/'
1075: #else
1.126 brouard 1076: #define DIRSEPARATOR '/'
1077: #define CHARSEPARATOR "/"
1078: #define ODIRSEPARATOR '\\'
1079: #endif
1080:
1.291 ! brouard 1081: /* $Id: imach.c,v 1.290 2019/05/09 13:39:37 brouard Exp $ */
1.126 brouard 1082: /* $State: Exp $ */
1.196 brouard 1083: #include "version.h"
1084: char version[]=__IMACH_VERSION__;
1.283 brouard 1085: 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";
1.291 ! brouard 1086: char fullversion[]="$Revision: 1.290 $ $Date: 2019/05/09 13:39:37 $";
1.126 brouard 1087: char strstart[80];
1088: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1089: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1090: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1091: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1092: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1093: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1094: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1095: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1096: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1097: int cptcovprodnoage=0; /**< Number of covariate products without age */
1098: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1099: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1100: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1101: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1102: int nsd=0; /**< Total number of single dummy variables (output) */
1103: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1104: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1105: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1106: int ntveff=0; /**< ntveff number of effective time varying variables */
1107: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1108: int cptcov=0; /* Working variable */
1.290 brouard 1109: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1110: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 1111: int npar=NPARMAX;
1112: int nlstate=2; /* Number of live states */
1113: int ndeath=1; /* Number of dead states */
1.130 brouard 1114: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1115: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1116: int popbased=0;
1117:
1118: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1119: int maxwav=0; /* Maxim number of waves */
1120: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1121: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1122: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1123: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1124: int mle=1, weightopt=0;
1.126 brouard 1125: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1126: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1127: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1128: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1129: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1130: int selected(int kvar); /* Is covariate kvar selected for printing results */
1131:
1.130 brouard 1132: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1133: double **matprod2(); /* test */
1.126 brouard 1134: double **oldm, **newm, **savm; /* Working pointers to matrices */
1135: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1136: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1137:
1.136 brouard 1138: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1139: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1140: FILE *ficlog, *ficrespow;
1.130 brouard 1141: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1142: double fretone; /* Only one call to likelihood */
1.130 brouard 1143: long ipmx=0; /* Number of contributions */
1.126 brouard 1144: double sw; /* Sum of weights */
1145: char filerespow[FILENAMELENGTH];
1146: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1147: FILE *ficresilk;
1148: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1149: FILE *ficresprobmorprev;
1150: FILE *fichtm, *fichtmcov; /* Html File */
1151: FILE *ficreseij;
1152: char filerese[FILENAMELENGTH];
1153: FILE *ficresstdeij;
1154: char fileresstde[FILENAMELENGTH];
1155: FILE *ficrescveij;
1156: char filerescve[FILENAMELENGTH];
1157: FILE *ficresvij;
1158: char fileresv[FILENAMELENGTH];
1.269 brouard 1159:
1.126 brouard 1160: char title[MAXLINE];
1.234 brouard 1161: char model[MAXLINE]; /**< The model line */
1.217 brouard 1162: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1163: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1164: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1165: char command[FILENAMELENGTH];
1166: int outcmd=0;
1167:
1.217 brouard 1168: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1169: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1170: char filelog[FILENAMELENGTH]; /* Log file */
1171: char filerest[FILENAMELENGTH];
1172: char fileregp[FILENAMELENGTH];
1173: char popfile[FILENAMELENGTH];
1174:
1175: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1176:
1.157 brouard 1177: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1178: /* struct timezone tzp; */
1179: /* extern int gettimeofday(); */
1180: struct tm tml, *gmtime(), *localtime();
1181:
1182: extern time_t time();
1183:
1184: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1185: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1186: struct tm tm;
1187:
1.126 brouard 1188: char strcurr[80], strfor[80];
1189:
1190: char *endptr;
1191: long lval;
1192: double dval;
1193:
1194: #define NR_END 1
1195: #define FREE_ARG char*
1196: #define FTOL 1.0e-10
1197:
1198: #define NRANSI
1.240 brouard 1199: #define ITMAX 200
1200: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1201:
1202: #define TOL 2.0e-4
1203:
1204: #define CGOLD 0.3819660
1205: #define ZEPS 1.0e-10
1206: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1207:
1208: #define GOLD 1.618034
1209: #define GLIMIT 100.0
1210: #define TINY 1.0e-20
1211:
1212: static double maxarg1,maxarg2;
1213: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1214: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1215:
1216: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1217: #define rint(a) floor(a+0.5)
1.166 brouard 1218: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1219: #define mytinydouble 1.0e-16
1.166 brouard 1220: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1221: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1222: /* static double dsqrarg; */
1223: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1224: static double sqrarg;
1225: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1226: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1227: int agegomp= AGEGOMP;
1228:
1229: int imx;
1230: int stepm=1;
1231: /* Stepm, step in month: minimum step interpolation*/
1232:
1233: int estepm;
1234: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1235:
1236: int m,nb;
1237: long *num;
1.197 brouard 1238: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1239: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1240: covariate for which somebody answered excluding
1241: undefined. Usually 2: 0 and 1. */
1242: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1243: covariate for which somebody answered including
1244: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1245: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1246: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1247: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1248: double *ageexmed,*agecens;
1249: double dateintmean=0;
1250:
1251: double *weight;
1252: int **s; /* Status */
1.141 brouard 1253: double *agedc;
1.145 brouard 1254: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1255: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1256: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1257: double **coqvar; /* Fixed quantitative covariate nqv */
1258: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1259: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1260: double idx;
1261: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1262: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1263: /*k 1 2 3 4 5 6 7 8 9 */
1264: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1265: /* Tndvar[k] 1 2 3 4 5 */
1266: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1267: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1268: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1269: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1270: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1271: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1272: /* Tprod[i]=k 4 7 */
1273: /* Tage[i]=k 5 8 */
1274: /* */
1275: /* Type */
1276: /* V 1 2 3 4 5 */
1277: /* F F V V V */
1278: /* D Q D D Q */
1279: /* */
1280: int *TvarsD;
1281: int *TvarsDind;
1282: int *TvarsQ;
1283: int *TvarsQind;
1284:
1.235 brouard 1285: #define MAXRESULTLINES 10
1286: int nresult=0;
1.258 brouard 1287: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1288: int TKresult[MAXRESULTLINES];
1.237 brouard 1289: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1290: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1291: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1292: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1293: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1294: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1295:
1.234 brouard 1296: /* 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 1297: 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 */
1298: 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 */
1299: 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 */
1300: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1301: 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 */
1302: 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 1303: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1304: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1305: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1306: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1307: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1308: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1309: 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 */
1310: 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 */
1311:
1.230 brouard 1312: int *Tvarsel; /**< Selected covariates for output */
1313: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1314: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1315: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1316: 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 1317: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1318: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1319: int *Tage;
1.227 brouard 1320: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1321: 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 1322: 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*/
1323: 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 1324: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1325: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1326: int **Tvard;
1327: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1328: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1329: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1330: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1331: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1332: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1333: double *lsurv, *lpop, *tpop;
1334:
1.231 brouard 1335: #define FD 1; /* Fixed dummy covariate */
1336: #define FQ 2; /* Fixed quantitative covariate */
1337: #define FP 3; /* Fixed product covariate */
1338: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1339: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1340: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1341: #define VD 10; /* Varying dummy covariate */
1342: #define VQ 11; /* Varying quantitative covariate */
1343: #define VP 12; /* Varying product covariate */
1344: #define VPDD 13; /* Varying product dummy*dummy covariate */
1345: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1346: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1347: #define APFD 16; /* Age product * fixed dummy covariate */
1348: #define APFQ 17; /* Age product * fixed quantitative covariate */
1349: #define APVD 18; /* Age product * varying dummy covariate */
1350: #define APVQ 19; /* Age product * varying quantitative covariate */
1351:
1352: #define FTYPE 1; /* Fixed covariate */
1353: #define VTYPE 2; /* Varying covariate (loop in wave) */
1354: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1355:
1356: struct kmodel{
1357: int maintype; /* main type */
1358: int subtype; /* subtype */
1359: };
1360: struct kmodel modell[NCOVMAX];
1361:
1.143 brouard 1362: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1363: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1364:
1365: /**************** split *************************/
1366: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1367: {
1368: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1369: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1370: */
1371: char *ss; /* pointer */
1.186 brouard 1372: int l1=0, l2=0; /* length counters */
1.126 brouard 1373:
1374: l1 = strlen(path ); /* length of path */
1375: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1376: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1377: if ( ss == NULL ) { /* no directory, so determine current directory */
1378: strcpy( name, path ); /* we got the fullname name because no directory */
1379: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1380: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1381: /* get current working directory */
1382: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1383: #ifdef WIN32
1384: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1385: #else
1386: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1387: #endif
1.126 brouard 1388: return( GLOCK_ERROR_GETCWD );
1389: }
1390: /* got dirc from getcwd*/
1391: printf(" DIRC = %s \n",dirc);
1.205 brouard 1392: } else { /* strip directory from path */
1.126 brouard 1393: ss++; /* after this, the filename */
1394: l2 = strlen( ss ); /* length of filename */
1395: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1396: strcpy( name, ss ); /* save file name */
1397: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1398: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1399: printf(" DIRC2 = %s \n",dirc);
1400: }
1401: /* We add a separator at the end of dirc if not exists */
1402: l1 = strlen( dirc ); /* length of directory */
1403: if( dirc[l1-1] != DIRSEPARATOR ){
1404: dirc[l1] = DIRSEPARATOR;
1405: dirc[l1+1] = 0;
1406: printf(" DIRC3 = %s \n",dirc);
1407: }
1408: ss = strrchr( name, '.' ); /* find last / */
1409: if (ss >0){
1410: ss++;
1411: strcpy(ext,ss); /* save extension */
1412: l1= strlen( name);
1413: l2= strlen(ss)+1;
1414: strncpy( finame, name, l1-l2);
1415: finame[l1-l2]= 0;
1416: }
1417:
1418: return( 0 ); /* we're done */
1419: }
1420:
1421:
1422: /******************************************/
1423:
1424: void replace_back_to_slash(char *s, char*t)
1425: {
1426: int i;
1427: int lg=0;
1428: i=0;
1429: lg=strlen(t);
1430: for(i=0; i<= lg; i++) {
1431: (s[i] = t[i]);
1432: if (t[i]== '\\') s[i]='/';
1433: }
1434: }
1435:
1.132 brouard 1436: char *trimbb(char *out, char *in)
1.137 brouard 1437: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1438: char *s;
1439: s=out;
1440: while (*in != '\0'){
1.137 brouard 1441: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1442: in++;
1443: }
1444: *out++ = *in++;
1445: }
1446: *out='\0';
1447: return s;
1448: }
1449:
1.187 brouard 1450: /* char *substrchaine(char *out, char *in, char *chain) */
1451: /* { */
1452: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1453: /* char *s, *t; */
1454: /* t=in;s=out; */
1455: /* while ((*in != *chain) && (*in != '\0')){ */
1456: /* *out++ = *in++; */
1457: /* } */
1458:
1459: /* /\* *in matches *chain *\/ */
1460: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1461: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1462: /* } */
1463: /* in--; chain--; */
1464: /* while ( (*in != '\0')){ */
1465: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1466: /* *out++ = *in++; */
1467: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1468: /* } */
1469: /* *out='\0'; */
1470: /* out=s; */
1471: /* return out; */
1472: /* } */
1473: char *substrchaine(char *out, char *in, char *chain)
1474: {
1475: /* Substract chain 'chain' from 'in', return and output 'out' */
1476: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1477:
1478: char *strloc;
1479:
1480: strcpy (out, in);
1481: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1482: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1483: if(strloc != NULL){
1484: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1485: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1486: /* strcpy (strloc, strloc +strlen(chain));*/
1487: }
1488: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1489: return out;
1490: }
1491:
1492:
1.145 brouard 1493: char *cutl(char *blocc, char *alocc, char *in, char occ)
1494: {
1.187 brouard 1495: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1496: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1497: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1498: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1499: */
1.160 brouard 1500: char *s, *t;
1.145 brouard 1501: t=in;s=in;
1502: while ((*in != occ) && (*in != '\0')){
1503: *alocc++ = *in++;
1504: }
1505: if( *in == occ){
1506: *(alocc)='\0';
1507: s=++in;
1508: }
1509:
1510: if (s == t) {/* occ not found */
1511: *(alocc-(in-s))='\0';
1512: in=s;
1513: }
1514: while ( *in != '\0'){
1515: *blocc++ = *in++;
1516: }
1517:
1518: *blocc='\0';
1519: return t;
1520: }
1.137 brouard 1521: char *cutv(char *blocc, char *alocc, char *in, char occ)
1522: {
1.187 brouard 1523: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1524: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1525: gives blocc="abcdef2ghi" and alocc="j".
1526: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1527: */
1528: char *s, *t;
1529: t=in;s=in;
1530: while (*in != '\0'){
1531: while( *in == occ){
1532: *blocc++ = *in++;
1533: s=in;
1534: }
1535: *blocc++ = *in++;
1536: }
1537: if (s == t) /* occ not found */
1538: *(blocc-(in-s))='\0';
1539: else
1540: *(blocc-(in-s)-1)='\0';
1541: in=s;
1542: while ( *in != '\0'){
1543: *alocc++ = *in++;
1544: }
1545:
1546: *alocc='\0';
1547: return s;
1548: }
1549:
1.126 brouard 1550: int nbocc(char *s, char occ)
1551: {
1552: int i,j=0;
1553: int lg=20;
1554: i=0;
1555: lg=strlen(s);
1556: for(i=0; i<= lg; i++) {
1.234 brouard 1557: if (s[i] == occ ) j++;
1.126 brouard 1558: }
1559: return j;
1560: }
1561:
1.137 brouard 1562: /* void cutv(char *u,char *v, char*t, char occ) */
1563: /* { */
1564: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1565: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1566: /* gives u="abcdef2ghi" and v="j" *\/ */
1567: /* int i,lg,j,p=0; */
1568: /* i=0; */
1569: /* lg=strlen(t); */
1570: /* for(j=0; j<=lg-1; j++) { */
1571: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1572: /* } */
1.126 brouard 1573:
1.137 brouard 1574: /* for(j=0; j<p; j++) { */
1575: /* (u[j] = t[j]); */
1576: /* } */
1577: /* u[p]='\0'; */
1.126 brouard 1578:
1.137 brouard 1579: /* for(j=0; j<= lg; j++) { */
1580: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1581: /* } */
1582: /* } */
1.126 brouard 1583:
1.160 brouard 1584: #ifdef _WIN32
1585: char * strsep(char **pp, const char *delim)
1586: {
1587: char *p, *q;
1588:
1589: if ((p = *pp) == NULL)
1590: return 0;
1591: if ((q = strpbrk (p, delim)) != NULL)
1592: {
1593: *pp = q + 1;
1594: *q = '\0';
1595: }
1596: else
1597: *pp = 0;
1598: return p;
1599: }
1600: #endif
1601:
1.126 brouard 1602: /********************** nrerror ********************/
1603:
1604: void nrerror(char error_text[])
1605: {
1606: fprintf(stderr,"ERREUR ...\n");
1607: fprintf(stderr,"%s\n",error_text);
1608: exit(EXIT_FAILURE);
1609: }
1610: /*********************** vector *******************/
1611: double *vector(int nl, int nh)
1612: {
1613: double *v;
1614: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1615: if (!v) nrerror("allocation failure in vector");
1616: return v-nl+NR_END;
1617: }
1618:
1619: /************************ free vector ******************/
1620: void free_vector(double*v, int nl, int nh)
1621: {
1622: free((FREE_ARG)(v+nl-NR_END));
1623: }
1624:
1625: /************************ivector *******************************/
1626: int *ivector(long nl,long nh)
1627: {
1628: int *v;
1629: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1630: if (!v) nrerror("allocation failure in ivector");
1631: return v-nl+NR_END;
1632: }
1633:
1634: /******************free ivector **************************/
1635: void free_ivector(int *v, long nl, long nh)
1636: {
1637: free((FREE_ARG)(v+nl-NR_END));
1638: }
1639:
1640: /************************lvector *******************************/
1641: long *lvector(long nl,long nh)
1642: {
1643: long *v;
1644: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1645: if (!v) nrerror("allocation failure in ivector");
1646: return v-nl+NR_END;
1647: }
1648:
1649: /******************free lvector **************************/
1650: void free_lvector(long *v, long nl, long nh)
1651: {
1652: free((FREE_ARG)(v+nl-NR_END));
1653: }
1654:
1655: /******************* imatrix *******************************/
1656: int **imatrix(long nrl, long nrh, long ncl, long nch)
1657: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1658: {
1659: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1660: int **m;
1661:
1662: /* allocate pointers to rows */
1663: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1664: if (!m) nrerror("allocation failure 1 in matrix()");
1665: m += NR_END;
1666: m -= nrl;
1667:
1668:
1669: /* allocate rows and set pointers to them */
1670: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1671: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1672: m[nrl] += NR_END;
1673: m[nrl] -= ncl;
1674:
1675: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1676:
1677: /* return pointer to array of pointers to rows */
1678: return m;
1679: }
1680:
1681: /****************** free_imatrix *************************/
1682: void free_imatrix(m,nrl,nrh,ncl,nch)
1683: int **m;
1684: long nch,ncl,nrh,nrl;
1685: /* free an int matrix allocated by imatrix() */
1686: {
1687: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1688: free((FREE_ARG) (m+nrl-NR_END));
1689: }
1690:
1691: /******************* matrix *******************************/
1692: double **matrix(long nrl, long nrh, long ncl, long nch)
1693: {
1694: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1695: double **m;
1696:
1697: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1698: if (!m) nrerror("allocation failure 1 in matrix()");
1699: m += NR_END;
1700: m -= nrl;
1701:
1702: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1703: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1704: m[nrl] += NR_END;
1705: m[nrl] -= ncl;
1706:
1707: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1708: return m;
1.145 brouard 1709: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1710: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1711: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1712: */
1713: }
1714:
1715: /*************************free matrix ************************/
1716: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1717: {
1718: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1719: free((FREE_ARG)(m+nrl-NR_END));
1720: }
1721:
1722: /******************* ma3x *******************************/
1723: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1724: {
1725: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1726: double ***m;
1727:
1728: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1729: if (!m) nrerror("allocation failure 1 in matrix()");
1730: m += NR_END;
1731: m -= nrl;
1732:
1733: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1734: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1735: m[nrl] += NR_END;
1736: m[nrl] -= ncl;
1737:
1738: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1739:
1740: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1741: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1742: m[nrl][ncl] += NR_END;
1743: m[nrl][ncl] -= nll;
1744: for (j=ncl+1; j<=nch; j++)
1745: m[nrl][j]=m[nrl][j-1]+nlay;
1746:
1747: for (i=nrl+1; i<=nrh; i++) {
1748: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1749: for (j=ncl+1; j<=nch; j++)
1750: m[i][j]=m[i][j-1]+nlay;
1751: }
1752: return m;
1753: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1754: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1755: */
1756: }
1757:
1758: /*************************free ma3x ************************/
1759: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1760: {
1761: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1762: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1763: free((FREE_ARG)(m+nrl-NR_END));
1764: }
1765:
1766: /*************** function subdirf ***********/
1767: char *subdirf(char fileres[])
1768: {
1769: /* Caution optionfilefiname is hidden */
1770: strcpy(tmpout,optionfilefiname);
1771: strcat(tmpout,"/"); /* Add to the right */
1772: strcat(tmpout,fileres);
1773: return tmpout;
1774: }
1775:
1776: /*************** function subdirf2 ***********/
1777: char *subdirf2(char fileres[], char *preop)
1778: {
1779:
1780: /* Caution optionfilefiname is hidden */
1781: strcpy(tmpout,optionfilefiname);
1782: strcat(tmpout,"/");
1783: strcat(tmpout,preop);
1784: strcat(tmpout,fileres);
1785: return tmpout;
1786: }
1787:
1788: /*************** function subdirf3 ***********/
1789: char *subdirf3(char fileres[], char *preop, char *preop2)
1790: {
1791:
1792: /* Caution optionfilefiname is hidden */
1793: strcpy(tmpout,optionfilefiname);
1794: strcat(tmpout,"/");
1795: strcat(tmpout,preop);
1796: strcat(tmpout,preop2);
1797: strcat(tmpout,fileres);
1798: return tmpout;
1799: }
1.213 brouard 1800:
1801: /*************** function subdirfext ***********/
1802: char *subdirfext(char fileres[], char *preop, char *postop)
1803: {
1804:
1805: strcpy(tmpout,preop);
1806: strcat(tmpout,fileres);
1807: strcat(tmpout,postop);
1808: return tmpout;
1809: }
1.126 brouard 1810:
1.213 brouard 1811: /*************** function subdirfext3 ***********/
1812: char *subdirfext3(char fileres[], char *preop, char *postop)
1813: {
1814:
1815: /* Caution optionfilefiname is hidden */
1816: strcpy(tmpout,optionfilefiname);
1817: strcat(tmpout,"/");
1818: strcat(tmpout,preop);
1819: strcat(tmpout,fileres);
1820: strcat(tmpout,postop);
1821: return tmpout;
1822: }
1823:
1.162 brouard 1824: char *asc_diff_time(long time_sec, char ascdiff[])
1825: {
1826: long sec_left, days, hours, minutes;
1827: days = (time_sec) / (60*60*24);
1828: sec_left = (time_sec) % (60*60*24);
1829: hours = (sec_left) / (60*60) ;
1830: sec_left = (sec_left) %(60*60);
1831: minutes = (sec_left) /60;
1832: sec_left = (sec_left) % (60);
1833: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1834: return ascdiff;
1835: }
1836:
1.126 brouard 1837: /***************** f1dim *************************/
1838: extern int ncom;
1839: extern double *pcom,*xicom;
1840: extern double (*nrfunc)(double []);
1841:
1842: double f1dim(double x)
1843: {
1844: int j;
1845: double f;
1846: double *xt;
1847:
1848: xt=vector(1,ncom);
1849: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1850: f=(*nrfunc)(xt);
1851: free_vector(xt,1,ncom);
1852: return f;
1853: }
1854:
1855: /*****************brent *************************/
1856: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1857: {
1858: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1859: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1860: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1861: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1862: * returned function value.
1863: */
1.126 brouard 1864: int iter;
1865: double a,b,d,etemp;
1.159 brouard 1866: double fu=0,fv,fw,fx;
1.164 brouard 1867: double ftemp=0.;
1.126 brouard 1868: double p,q,r,tol1,tol2,u,v,w,x,xm;
1869: double e=0.0;
1870:
1871: a=(ax < cx ? ax : cx);
1872: b=(ax > cx ? ax : cx);
1873: x=w=v=bx;
1874: fw=fv=fx=(*f)(x);
1875: for (iter=1;iter<=ITMAX;iter++) {
1876: xm=0.5*(a+b);
1877: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1878: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1879: printf(".");fflush(stdout);
1880: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1881: #ifdef DEBUGBRENT
1.126 brouard 1882: 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);
1883: 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);
1884: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1885: #endif
1886: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1887: *xmin=x;
1888: return fx;
1889: }
1890: ftemp=fu;
1891: if (fabs(e) > tol1) {
1892: r=(x-w)*(fx-fv);
1893: q=(x-v)*(fx-fw);
1894: p=(x-v)*q-(x-w)*r;
1895: q=2.0*(q-r);
1896: if (q > 0.0) p = -p;
1897: q=fabs(q);
1898: etemp=e;
1899: e=d;
1900: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1901: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1902: else {
1.224 brouard 1903: d=p/q;
1904: u=x+d;
1905: if (u-a < tol2 || b-u < tol2)
1906: d=SIGN(tol1,xm-x);
1.126 brouard 1907: }
1908: } else {
1909: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1910: }
1911: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1912: fu=(*f)(u);
1913: if (fu <= fx) {
1914: if (u >= x) a=x; else b=x;
1915: SHFT(v,w,x,u)
1.183 brouard 1916: SHFT(fv,fw,fx,fu)
1917: } else {
1918: if (u < x) a=u; else b=u;
1919: if (fu <= fw || w == x) {
1.224 brouard 1920: v=w;
1921: w=u;
1922: fv=fw;
1923: fw=fu;
1.183 brouard 1924: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1925: v=u;
1926: fv=fu;
1.183 brouard 1927: }
1928: }
1.126 brouard 1929: }
1930: nrerror("Too many iterations in brent");
1931: *xmin=x;
1932: return fx;
1933: }
1934:
1935: /****************** mnbrak ***********************/
1936:
1937: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1938: double (*func)(double))
1.183 brouard 1939: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1940: the downhill direction (defined by the function as evaluated at the initial points) and returns
1941: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1942: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1943: */
1.126 brouard 1944: double ulim,u,r,q, dum;
1945: double fu;
1.187 brouard 1946:
1947: double scale=10.;
1948: int iterscale=0;
1949:
1950: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1951: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1952:
1953:
1954: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1955: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1956: /* *bx = *ax - (*ax - *bx)/scale; */
1957: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1958: /* } */
1959:
1.126 brouard 1960: if (*fb > *fa) {
1961: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1962: SHFT(dum,*fb,*fa,dum)
1963: }
1.126 brouard 1964: *cx=(*bx)+GOLD*(*bx-*ax);
1965: *fc=(*func)(*cx);
1.183 brouard 1966: #ifdef DEBUG
1.224 brouard 1967: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1968: 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 1969: #endif
1.224 brouard 1970: 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 1971: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1972: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1973: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1974: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1975: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1976: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1977: fu=(*func)(u);
1.163 brouard 1978: #ifdef DEBUG
1979: /* f(x)=A(x-u)**2+f(u) */
1980: double A, fparabu;
1981: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1982: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1983: 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);
1984: 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 1985: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1986: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1987: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1988: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1989: #endif
1.184 brouard 1990: #ifdef MNBRAKORIGINAL
1.183 brouard 1991: #else
1.191 brouard 1992: /* if (fu > *fc) { */
1993: /* #ifdef DEBUG */
1994: /* printf("mnbrak4 fu > fc \n"); */
1995: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1996: /* #endif */
1997: /* /\* 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 *\\/ *\/ */
1998: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1999: /* dum=u; /\* Shifting c and u *\/ */
2000: /* u = *cx; */
2001: /* *cx = dum; */
2002: /* dum = fu; */
2003: /* fu = *fc; */
2004: /* *fc =dum; */
2005: /* } else { /\* end *\/ */
2006: /* #ifdef DEBUG */
2007: /* printf("mnbrak3 fu < fc \n"); */
2008: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2009: /* #endif */
2010: /* dum=u; /\* Shifting c and u *\/ */
2011: /* u = *cx; */
2012: /* *cx = dum; */
2013: /* dum = fu; */
2014: /* fu = *fc; */
2015: /* *fc =dum; */
2016: /* } */
1.224 brouard 2017: #ifdef DEBUGMNBRAK
2018: double A, fparabu;
2019: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2020: fparabu= *fa - A*(*ax-u)*(*ax-u);
2021: 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);
2022: 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 2023: #endif
1.191 brouard 2024: dum=u; /* Shifting c and u */
2025: u = *cx;
2026: *cx = dum;
2027: dum = fu;
2028: fu = *fc;
2029: *fc =dum;
1.183 brouard 2030: #endif
1.162 brouard 2031: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2032: #ifdef DEBUG
1.224 brouard 2033: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2034: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2035: #endif
1.126 brouard 2036: fu=(*func)(u);
2037: if (fu < *fc) {
1.183 brouard 2038: #ifdef DEBUG
1.224 brouard 2039: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2040: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2041: #endif
2042: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2043: SHFT(*fb,*fc,fu,(*func)(u))
2044: #ifdef DEBUG
2045: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2046: #endif
2047: }
1.162 brouard 2048: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2049: #ifdef DEBUG
1.224 brouard 2050: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2051: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2052: #endif
1.126 brouard 2053: u=ulim;
2054: fu=(*func)(u);
1.183 brouard 2055: } else { /* u could be left to b (if r > q parabola has a maximum) */
2056: #ifdef DEBUG
1.224 brouard 2057: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2058: 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 2059: #endif
1.126 brouard 2060: u=(*cx)+GOLD*(*cx-*bx);
2061: fu=(*func)(u);
1.224 brouard 2062: #ifdef DEBUG
2063: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2064: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2065: #endif
1.183 brouard 2066: } /* end tests */
1.126 brouard 2067: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2068: SHFT(*fa,*fb,*fc,fu)
2069: #ifdef DEBUG
1.224 brouard 2070: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2071: 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 2072: #endif
2073: } /* 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 2074: }
2075:
2076: /*************** linmin ************************/
1.162 brouard 2077: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2078: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2079: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2080: the value of func at the returned location p . This is actually all accomplished by calling the
2081: routines mnbrak and brent .*/
1.126 brouard 2082: int ncom;
2083: double *pcom,*xicom;
2084: double (*nrfunc)(double []);
2085:
1.224 brouard 2086: #ifdef LINMINORIGINAL
1.126 brouard 2087: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2088: #else
2089: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2090: #endif
1.126 brouard 2091: {
2092: double brent(double ax, double bx, double cx,
2093: double (*f)(double), double tol, double *xmin);
2094: double f1dim(double x);
2095: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2096: double *fc, double (*func)(double));
2097: int j;
2098: double xx,xmin,bx,ax;
2099: double fx,fb,fa;
1.187 brouard 2100:
1.203 brouard 2101: #ifdef LINMINORIGINAL
2102: #else
2103: double scale=10., axs, xxs; /* Scale added for infinity */
2104: #endif
2105:
1.126 brouard 2106: ncom=n;
2107: pcom=vector(1,n);
2108: xicom=vector(1,n);
2109: nrfunc=func;
2110: for (j=1;j<=n;j++) {
2111: pcom[j]=p[j];
1.202 brouard 2112: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2113: }
1.187 brouard 2114:
1.203 brouard 2115: #ifdef LINMINORIGINAL
2116: xx=1.;
2117: #else
2118: axs=0.0;
2119: xxs=1.;
2120: do{
2121: xx= xxs;
2122: #endif
1.187 brouard 2123: ax=0.;
2124: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2125: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2126: /* 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)) */
2127: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2128: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2129: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2130: /* 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 2131: #ifdef LINMINORIGINAL
2132: #else
2133: if (fx != fx){
1.224 brouard 2134: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2135: printf("|");
2136: fprintf(ficlog,"|");
1.203 brouard 2137: #ifdef DEBUGLINMIN
1.224 brouard 2138: 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 2139: #endif
2140: }
1.224 brouard 2141: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2142: #endif
2143:
1.191 brouard 2144: #ifdef DEBUGLINMIN
2145: 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 2146: 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 2147: #endif
1.224 brouard 2148: #ifdef LINMINORIGINAL
2149: #else
2150: if(fb == fx){ /* Flat function in the direction */
2151: xmin=xx;
2152: *flat=1;
2153: }else{
2154: *flat=0;
2155: #endif
2156: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2157: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2158: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2159: /* fmin = f(p[j] + xmin * xi[j]) */
2160: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2161: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2162: #ifdef DEBUG
1.224 brouard 2163: 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);
2164: 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);
2165: #endif
2166: #ifdef LINMINORIGINAL
2167: #else
2168: }
1.126 brouard 2169: #endif
1.191 brouard 2170: #ifdef DEBUGLINMIN
2171: printf("linmin end ");
1.202 brouard 2172: fprintf(ficlog,"linmin end ");
1.191 brouard 2173: #endif
1.126 brouard 2174: for (j=1;j<=n;j++) {
1.203 brouard 2175: #ifdef LINMINORIGINAL
2176: xi[j] *= xmin;
2177: #else
2178: #ifdef DEBUGLINMIN
2179: if(xxs <1.0)
2180: printf(" before xi[%d]=%12.8f", j,xi[j]);
2181: #endif
2182: 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) */
2183: #ifdef DEBUGLINMIN
2184: if(xxs <1.0)
2185: 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 );
2186: #endif
2187: #endif
1.187 brouard 2188: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2189: }
1.191 brouard 2190: #ifdef DEBUGLINMIN
1.203 brouard 2191: printf("\n");
1.191 brouard 2192: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2193: 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 2194: for (j=1;j<=n;j++) {
1.202 brouard 2195: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2196: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2197: if(j % ncovmodel == 0){
1.191 brouard 2198: printf("\n");
1.202 brouard 2199: fprintf(ficlog,"\n");
2200: }
1.191 brouard 2201: }
1.203 brouard 2202: #else
1.191 brouard 2203: #endif
1.126 brouard 2204: free_vector(xicom,1,n);
2205: free_vector(pcom,1,n);
2206: }
2207:
2208:
2209: /*************** powell ************************/
1.162 brouard 2210: /*
2211: Minimization of a function func of n variables. Input consists of an initial starting point
2212: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2213: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2214: such that failure to decrease by more than this amount on one iteration signals doneness. On
2215: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2216: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2217: */
1.224 brouard 2218: #ifdef LINMINORIGINAL
2219: #else
2220: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2221: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2222: #endif
1.126 brouard 2223: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2224: double (*func)(double []))
2225: {
1.224 brouard 2226: #ifdef LINMINORIGINAL
2227: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2228: double (*func)(double []));
1.224 brouard 2229: #else
1.241 brouard 2230: void linmin(double p[], double xi[], int n, double *fret,
2231: double (*func)(double []),int *flat);
1.224 brouard 2232: #endif
1.239 brouard 2233: int i,ibig,j,jk,k;
1.126 brouard 2234: double del,t,*pt,*ptt,*xit;
1.181 brouard 2235: double directest;
1.126 brouard 2236: double fp,fptt;
2237: double *xits;
2238: int niterf, itmp;
1.224 brouard 2239: #ifdef LINMINORIGINAL
2240: #else
2241:
2242: flatdir=ivector(1,n);
2243: for (j=1;j<=n;j++) flatdir[j]=0;
2244: #endif
1.126 brouard 2245:
2246: pt=vector(1,n);
2247: ptt=vector(1,n);
2248: xit=vector(1,n);
2249: xits=vector(1,n);
2250: *fret=(*func)(p);
2251: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2252: rcurr_time = time(NULL);
1.126 brouard 2253: for (*iter=1;;++(*iter)) {
1.187 brouard 2254: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2255: ibig=0;
2256: del=0.0;
1.157 brouard 2257: rlast_time=rcurr_time;
2258: /* (void) gettimeofday(&curr_time,&tzp); */
2259: rcurr_time = time(NULL);
2260: curr_time = *localtime(&rcurr_time);
2261: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2262: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2263: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2264: for (i=1;i<=n;i++) {
1.126 brouard 2265: fprintf(ficrespow," %.12lf", p[i]);
2266: }
1.239 brouard 2267: fprintf(ficrespow,"\n");fflush(ficrespow);
2268: printf("\n#model= 1 + age ");
2269: fprintf(ficlog,"\n#model= 1 + age ");
2270: if(nagesqr==1){
1.241 brouard 2271: printf(" + age*age ");
2272: fprintf(ficlog," + age*age ");
1.239 brouard 2273: }
2274: for(j=1;j <=ncovmodel-2;j++){
2275: if(Typevar[j]==0) {
2276: printf(" + V%d ",Tvar[j]);
2277: fprintf(ficlog," + V%d ",Tvar[j]);
2278: }else if(Typevar[j]==1) {
2279: printf(" + V%d*age ",Tvar[j]);
2280: fprintf(ficlog," + V%d*age ",Tvar[j]);
2281: }else if(Typevar[j]==2) {
2282: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2283: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2284: }
2285: }
1.126 brouard 2286: printf("\n");
1.239 brouard 2287: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2288: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2289: fprintf(ficlog,"\n");
1.239 brouard 2290: for(i=1,jk=1; i <=nlstate; i++){
2291: for(k=1; k <=(nlstate+ndeath); k++){
2292: if (k != i) {
2293: printf("%d%d ",i,k);
2294: fprintf(ficlog,"%d%d ",i,k);
2295: for(j=1; j <=ncovmodel; j++){
2296: printf("%12.7f ",p[jk]);
2297: fprintf(ficlog,"%12.7f ",p[jk]);
2298: jk++;
2299: }
2300: printf("\n");
2301: fprintf(ficlog,"\n");
2302: }
2303: }
2304: }
1.241 brouard 2305: if(*iter <=3 && *iter >1){
1.157 brouard 2306: tml = *localtime(&rcurr_time);
2307: strcpy(strcurr,asctime(&tml));
2308: rforecast_time=rcurr_time;
1.126 brouard 2309: itmp = strlen(strcurr);
2310: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2311: strcurr[itmp-1]='\0';
1.162 brouard 2312: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2313: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2314: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2315: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2316: forecast_time = *localtime(&rforecast_time);
2317: strcpy(strfor,asctime(&forecast_time));
2318: itmp = strlen(strfor);
2319: if(strfor[itmp-1]=='\n')
2320: strfor[itmp-1]='\0';
2321: 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);
2322: 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 2323: }
2324: }
1.187 brouard 2325: for (i=1;i<=n;i++) { /* For each direction i */
2326: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2327: fptt=(*fret);
2328: #ifdef DEBUG
1.203 brouard 2329: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2330: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2331: #endif
1.203 brouard 2332: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2333: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2334: #ifdef LINMINORIGINAL
1.188 brouard 2335: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2336: #else
2337: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2338: flatdir[i]=flat; /* Function is vanishing in that direction i */
2339: #endif
2340: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2341: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2342: /* because that direction will be replaced unless the gain del is small */
2343: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2344: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2345: /* with the new direction. */
2346: del=fabs(fptt-(*fret));
2347: ibig=i;
1.126 brouard 2348: }
2349: #ifdef DEBUG
2350: printf("%d %.12e",i,(*fret));
2351: fprintf(ficlog,"%d %.12e",i,(*fret));
2352: for (j=1;j<=n;j++) {
1.224 brouard 2353: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2354: printf(" x(%d)=%.12e",j,xit[j]);
2355: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2356: }
2357: for(j=1;j<=n;j++) {
1.225 brouard 2358: printf(" p(%d)=%.12e",j,p[j]);
2359: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2360: }
2361: printf("\n");
2362: fprintf(ficlog,"\n");
2363: #endif
1.187 brouard 2364: } /* end loop on each direction i */
2365: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2366: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2367: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2368: for(j=1;j<=n;j++) {
1.225 brouard 2369: if(flatdir[j] >0){
2370: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2371: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2372: }
2373: /* printf("\n"); */
2374: /* fprintf(ficlog,"\n"); */
2375: }
1.243 brouard 2376: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2377: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2378: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2379: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2380: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2381: /* decreased of more than 3.84 */
2382: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2383: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2384: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2385:
1.188 brouard 2386: /* Starting the program with initial values given by a former maximization will simply change */
2387: /* the scales of the directions and the directions, because the are reset to canonical directions */
2388: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2389: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2390: #ifdef DEBUG
2391: int k[2],l;
2392: k[0]=1;
2393: k[1]=-1;
2394: printf("Max: %.12e",(*func)(p));
2395: fprintf(ficlog,"Max: %.12e",(*func)(p));
2396: for (j=1;j<=n;j++) {
2397: printf(" %.12e",p[j]);
2398: fprintf(ficlog," %.12e",p[j]);
2399: }
2400: printf("\n");
2401: fprintf(ficlog,"\n");
2402: for(l=0;l<=1;l++) {
2403: for (j=1;j<=n;j++) {
2404: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2405: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2406: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2407: }
2408: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2409: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2410: }
2411: #endif
2412:
1.224 brouard 2413: #ifdef LINMINORIGINAL
2414: #else
2415: free_ivector(flatdir,1,n);
2416: #endif
1.126 brouard 2417: free_vector(xit,1,n);
2418: free_vector(xits,1,n);
2419: free_vector(ptt,1,n);
2420: free_vector(pt,1,n);
2421: return;
1.192 brouard 2422: } /* enough precision */
1.240 brouard 2423: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2424: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2425: ptt[j]=2.0*p[j]-pt[j];
2426: xit[j]=p[j]-pt[j];
2427: pt[j]=p[j];
2428: }
1.181 brouard 2429: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2430: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2431: if (*iter <=4) {
1.225 brouard 2432: #else
2433: #endif
1.224 brouard 2434: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2435: #else
1.161 brouard 2436: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2437: #endif
1.162 brouard 2438: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2439: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2440: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2441: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2442: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2443: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2444: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2445: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2446: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2447: /* Even if f3 <f1, directest can be negative and t >0 */
2448: /* mu² and del² are equal when f3=f1 */
2449: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2450: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2451: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2452: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2453: #ifdef NRCORIGINAL
2454: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2455: #else
2456: 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 2457: t= t- del*SQR(fp-fptt);
1.183 brouard 2458: #endif
1.202 brouard 2459: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2460: #ifdef DEBUG
1.181 brouard 2461: 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);
2462: 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 2463: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2464: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2465: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2466: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2467: 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);
2468: 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);
2469: #endif
1.183 brouard 2470: #ifdef POWELLORIGINAL
2471: if (t < 0.0) { /* Then we use it for new direction */
2472: #else
1.182 brouard 2473: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2474: 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 2475: 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 2476: 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 2477: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2478: }
1.181 brouard 2479: if (directest < 0.0) { /* Then we use it for new direction */
2480: #endif
1.191 brouard 2481: #ifdef DEBUGLINMIN
1.234 brouard 2482: printf("Before linmin in direction P%d-P0\n",n);
2483: for (j=1;j<=n;j++) {
2484: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2485: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2486: if(j % ncovmodel == 0){
2487: printf("\n");
2488: fprintf(ficlog,"\n");
2489: }
2490: }
1.224 brouard 2491: #endif
2492: #ifdef LINMINORIGINAL
1.234 brouard 2493: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2494: #else
1.234 brouard 2495: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2496: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2497: #endif
1.234 brouard 2498:
1.191 brouard 2499: #ifdef DEBUGLINMIN
1.234 brouard 2500: for (j=1;j<=n;j++) {
2501: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2502: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2503: if(j % ncovmodel == 0){
2504: printf("\n");
2505: fprintf(ficlog,"\n");
2506: }
2507: }
1.224 brouard 2508: #endif
1.234 brouard 2509: for (j=1;j<=n;j++) {
2510: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2511: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2512: }
1.224 brouard 2513: #ifdef LINMINORIGINAL
2514: #else
1.234 brouard 2515: for (j=1, flatd=0;j<=n;j++) {
2516: if(flatdir[j]>0)
2517: flatd++;
2518: }
2519: if(flatd >0){
1.255 brouard 2520: printf("%d flat directions: ",flatd);
2521: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2522: for (j=1;j<=n;j++) {
2523: if(flatdir[j]>0){
2524: printf("%d ",j);
2525: fprintf(ficlog,"%d ",j);
2526: }
2527: }
2528: printf("\n");
2529: fprintf(ficlog,"\n");
2530: }
1.191 brouard 2531: #endif
1.234 brouard 2532: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2533: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2534:
1.126 brouard 2535: #ifdef DEBUG
1.234 brouard 2536: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2537: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2538: for(j=1;j<=n;j++){
2539: printf(" %lf",xit[j]);
2540: fprintf(ficlog," %lf",xit[j]);
2541: }
2542: printf("\n");
2543: fprintf(ficlog,"\n");
1.126 brouard 2544: #endif
1.192 brouard 2545: } /* end of t or directest negative */
1.224 brouard 2546: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2547: #else
1.234 brouard 2548: } /* end if (fptt < fp) */
1.192 brouard 2549: #endif
1.225 brouard 2550: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2551: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2552: #else
1.224 brouard 2553: #endif
1.234 brouard 2554: } /* loop iteration */
1.126 brouard 2555: }
1.234 brouard 2556:
1.126 brouard 2557: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2558:
1.235 brouard 2559: 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 2560: {
1.279 brouard 2561: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2562: * (and selected quantitative values in nres)
2563: * by left multiplying the unit
2564: * matrix by transitions matrix until convergence is reached with precision ftolpl
2565: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2566: * Wx is row vector: population in state 1, population in state 2, population dead
2567: * or prevalence in state 1, prevalence in state 2, 0
2568: * newm is the matrix after multiplications, its rows are identical at a factor.
2569: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2570: * Output is prlim.
2571: * Initial matrix pimij
2572: */
1.206 brouard 2573: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2574: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2575: /* 0, 0 , 1} */
2576: /*
2577: * and after some iteration: */
2578: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2579: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2580: /* 0, 0 , 1} */
2581: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2582: /* {0.51571254859325999, 0.4842874514067399, */
2583: /* 0.51326036147820708, 0.48673963852179264} */
2584: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2585:
1.126 brouard 2586: int i, ii,j,k;
1.209 brouard 2587: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2588: /* double **matprod2(); */ /* test */
1.218 brouard 2589: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2590: double **newm;
1.209 brouard 2591: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2592: int ncvloop=0;
1.288 brouard 2593: int first=0;
1.169 brouard 2594:
1.209 brouard 2595: min=vector(1,nlstate);
2596: max=vector(1,nlstate);
2597: meandiff=vector(1,nlstate);
2598:
1.218 brouard 2599: /* Starting with matrix unity */
1.126 brouard 2600: for (ii=1;ii<=nlstate+ndeath;ii++)
2601: for (j=1;j<=nlstate+ndeath;j++){
2602: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2603: }
1.169 brouard 2604:
2605: cov[1]=1.;
2606:
2607: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2608: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2609: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2610: ncvloop++;
1.126 brouard 2611: newm=savm;
2612: /* Covariates have to be included here again */
1.138 brouard 2613: cov[2]=agefin;
1.187 brouard 2614: if(nagesqr==1)
2615: cov[3]= agefin*agefin;;
1.234 brouard 2616: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2617: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2618: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2619: /* 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 2620: }
2621: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2622: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2623: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2624: /* 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 2625: }
1.237 brouard 2626: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2627: if(Dummy[Tvar[Tage[k]]]){
2628: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2629: } else{
1.235 brouard 2630: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2631: }
1.235 brouard 2632: /* 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 2633: }
1.237 brouard 2634: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2635: /* 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 2636: if(Dummy[Tvard[k][1]==0]){
2637: if(Dummy[Tvard[k][2]==0]){
2638: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2639: }else{
2640: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2641: }
2642: }else{
2643: if(Dummy[Tvard[k][2]==0]){
2644: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2645: }else{
2646: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2647: }
2648: }
1.234 brouard 2649: }
1.138 brouard 2650: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2651: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2652: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2653: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2654: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2655: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2656: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2657:
1.126 brouard 2658: savm=oldm;
2659: oldm=newm;
1.209 brouard 2660:
2661: for(j=1; j<=nlstate; j++){
2662: max[j]=0.;
2663: min[j]=1.;
2664: }
2665: for(i=1;i<=nlstate;i++){
2666: sumnew=0;
2667: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2668: for(j=1; j<=nlstate; j++){
2669: prlim[i][j]= newm[i][j]/(1-sumnew);
2670: max[j]=FMAX(max[j],prlim[i][j]);
2671: min[j]=FMIN(min[j],prlim[i][j]);
2672: }
2673: }
2674:
1.126 brouard 2675: maxmax=0.;
1.209 brouard 2676: for(j=1; j<=nlstate; j++){
2677: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2678: maxmax=FMAX(maxmax,meandiff[j]);
2679: /* 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 2680: } /* j loop */
1.203 brouard 2681: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2682: /* 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 2683: if(maxmax < ftolpl){
1.209 brouard 2684: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2685: free_vector(min,1,nlstate);
2686: free_vector(max,1,nlstate);
2687: free_vector(meandiff,1,nlstate);
1.126 brouard 2688: return prlim;
2689: }
1.288 brouard 2690: } /* agefin loop */
1.208 brouard 2691: /* After some age loop it doesn't converge */
1.288 brouard 2692: if(!first){
2693: first=1;
2694: 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);
2695: }
2696: 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);
2697:
1.209 brouard 2698: /* 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); */
2699: free_vector(min,1,nlstate);
2700: free_vector(max,1,nlstate);
2701: free_vector(meandiff,1,nlstate);
1.208 brouard 2702:
1.169 brouard 2703: return prlim; /* should not reach here */
1.126 brouard 2704: }
2705:
1.217 brouard 2706:
2707: /**** Back Prevalence limit (stable or period prevalence) ****************/
2708:
1.218 brouard 2709: /* 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) */
2710: /* 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 2711: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2712: {
1.264 brouard 2713: /* 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 2714: matrix by transitions matrix until convergence is reached with precision ftolpl */
2715: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2716: /* Wx is row vector: population in state 1, population in state 2, population dead */
2717: /* or prevalence in state 1, prevalence in state 2, 0 */
2718: /* newm is the matrix after multiplications, its rows are identical at a factor */
2719: /* Initial matrix pimij */
2720: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2721: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2722: /* 0, 0 , 1} */
2723: /*
2724: * and after some iteration: */
2725: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2726: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2727: /* 0, 0 , 1} */
2728: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2729: /* {0.51571254859325999, 0.4842874514067399, */
2730: /* 0.51326036147820708, 0.48673963852179264} */
2731: /* If we start from prlim again, prlim tends to a constant matrix */
2732:
2733: int i, ii,j,k;
1.247 brouard 2734: int first=0;
1.217 brouard 2735: double *min, *max, *meandiff, maxmax,sumnew=0.;
2736: /* double **matprod2(); */ /* test */
2737: double **out, cov[NCOVMAX+1], **bmij();
2738: double **newm;
1.218 brouard 2739: double **dnewm, **doldm, **dsavm; /* for use */
2740: double **oldm, **savm; /* for use */
2741:
1.217 brouard 2742: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2743: int ncvloop=0;
2744:
2745: min=vector(1,nlstate);
2746: max=vector(1,nlstate);
2747: meandiff=vector(1,nlstate);
2748:
1.266 brouard 2749: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2750: oldm=oldms; savm=savms;
2751:
2752: /* Starting with matrix unity */
2753: for (ii=1;ii<=nlstate+ndeath;ii++)
2754: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2755: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2756: }
2757:
2758: cov[1]=1.;
2759:
2760: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2761: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2762: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2763: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2764: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2765: ncvloop++;
1.218 brouard 2766: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2767: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2768: /* Covariates have to be included here again */
2769: cov[2]=agefin;
2770: if(nagesqr==1)
2771: cov[3]= agefin*agefin;;
1.242 brouard 2772: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2773: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2774: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2775: /* 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 2776: }
2777: /* for (k=1; k<=cptcovn;k++) { */
2778: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2779: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2780: /* /\* 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])]); *\/ */
2781: /* } */
2782: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2783: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2784: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2785: /* 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]); */
2786: }
2787: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2788: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2789: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2790: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2791: for (k=1; k<=cptcovage;k++){ /* For product with age */
2792: if(Dummy[Tvar[Tage[k]]]){
2793: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2794: } else{
2795: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2796: }
2797: /* 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]); */
2798: }
2799: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2800: /* 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]); */
2801: if(Dummy[Tvard[k][1]==0]){
2802: if(Dummy[Tvard[k][2]==0]){
2803: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2804: }else{
2805: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2806: }
2807: }else{
2808: if(Dummy[Tvard[k][2]==0]){
2809: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2810: }else{
2811: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2812: }
2813: }
1.217 brouard 2814: }
2815:
2816: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2817: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2818: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2819: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2820: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2821: /* ij should be linked to the correct index of cov */
2822: /* age and covariate values ij are in 'cov', but we need to pass
2823: * ij for the observed prevalence at age and status and covariate
2824: * number: prevacurrent[(int)agefin][ii][ij]
2825: */
2826: /* 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 *\/ */
2827: /* 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 *\/ */
2828: 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 2829: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2830: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2831: /* for(i=1; i<=nlstate+ndeath; i++) { */
2832: /* printf("%d newm= ",i); */
2833: /* for(j=1;j<=nlstate+ndeath;j++) { */
2834: /* printf("%f ",newm[i][j]); */
2835: /* } */
2836: /* printf("oldm * "); */
2837: /* for(j=1;j<=nlstate+ndeath;j++) { */
2838: /* printf("%f ",oldm[i][j]); */
2839: /* } */
1.268 brouard 2840: /* printf(" bmmij "); */
1.266 brouard 2841: /* for(j=1;j<=nlstate+ndeath;j++) { */
2842: /* printf("%f ",pmmij[i][j]); */
2843: /* } */
2844: /* printf("\n"); */
2845: /* } */
2846: /* } */
1.217 brouard 2847: savm=oldm;
2848: oldm=newm;
1.266 brouard 2849:
1.217 brouard 2850: for(j=1; j<=nlstate; j++){
2851: max[j]=0.;
2852: min[j]=1.;
2853: }
2854: for(j=1; j<=nlstate; j++){
2855: for(i=1;i<=nlstate;i++){
1.234 brouard 2856: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2857: bprlim[i][j]= newm[i][j];
2858: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2859: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2860: }
2861: }
1.218 brouard 2862:
1.217 brouard 2863: maxmax=0.;
2864: for(i=1; i<=nlstate; i++){
2865: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2866: maxmax=FMAX(maxmax,meandiff[i]);
2867: /* 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 2868: } /* i loop */
1.217 brouard 2869: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2870: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2871: if(maxmax < ftolpl){
1.220 brouard 2872: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2873: free_vector(min,1,nlstate);
2874: free_vector(max,1,nlstate);
2875: free_vector(meandiff,1,nlstate);
2876: return bprlim;
2877: }
1.288 brouard 2878: } /* agefin loop */
1.217 brouard 2879: /* After some age loop it doesn't converge */
1.288 brouard 2880: if(!first){
1.247 brouard 2881: first=1;
2882: 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\
2883: 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);
2884: }
2885: 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 2886: 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);
2887: /* 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); */
2888: free_vector(min,1,nlstate);
2889: free_vector(max,1,nlstate);
2890: free_vector(meandiff,1,nlstate);
2891:
2892: return bprlim; /* should not reach here */
2893: }
2894:
1.126 brouard 2895: /*************** transition probabilities ***************/
2896:
2897: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2898: {
1.138 brouard 2899: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2900: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2901: model to the ncovmodel covariates (including constant and age).
2902: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2903: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2904: ncth covariate in the global vector x is given by the formula:
2905: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2906: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2907: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2908: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2909: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2910: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2911: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2912: */
2913: double s1, lnpijopii;
1.126 brouard 2914: /*double t34;*/
1.164 brouard 2915: int i,j, nc, ii, jj;
1.126 brouard 2916:
1.223 brouard 2917: for(i=1; i<= nlstate; i++){
2918: for(j=1; j<i;j++){
2919: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2920: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2921: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2922: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2923: }
2924: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2925: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2926: }
2927: for(j=i+1; j<=nlstate+ndeath;j++){
2928: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2929: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2930: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2931: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2932: }
2933: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2934: }
2935: }
1.218 brouard 2936:
1.223 brouard 2937: for(i=1; i<= nlstate; i++){
2938: s1=0;
2939: for(j=1; j<i; j++){
2940: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2941: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2942: }
2943: for(j=i+1; j<=nlstate+ndeath; j++){
2944: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2945: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2946: }
2947: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2948: ps[i][i]=1./(s1+1.);
2949: /* Computing other pijs */
2950: for(j=1; j<i; j++)
2951: ps[i][j]= exp(ps[i][j])*ps[i][i];
2952: for(j=i+1; j<=nlstate+ndeath; j++)
2953: ps[i][j]= exp(ps[i][j])*ps[i][i];
2954: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2955: } /* end i */
1.218 brouard 2956:
1.223 brouard 2957: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2958: for(jj=1; jj<= nlstate+ndeath; jj++){
2959: ps[ii][jj]=0;
2960: ps[ii][ii]=1;
2961: }
2962: }
1.218 brouard 2963:
2964:
1.223 brouard 2965: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2966: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2967: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2968: /* } */
2969: /* printf("\n "); */
2970: /* } */
2971: /* printf("\n ");printf("%lf ",cov[2]);*/
2972: /*
2973: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2974: goto end;*/
1.266 brouard 2975: return ps; /* Pointer is unchanged since its call */
1.126 brouard 2976: }
2977:
1.218 brouard 2978: /*************** backward transition probabilities ***************/
2979:
2980: /* 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 ) */
2981: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2982: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2983: {
1.266 brouard 2984: /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
2985: * 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 2986: */
1.218 brouard 2987: int i, ii, j,k;
1.222 brouard 2988:
2989: double **out, **pmij();
2990: double sumnew=0.;
1.218 brouard 2991: double agefin;
1.268 brouard 2992: double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
1.222 brouard 2993: double **dnewm, **dsavm, **doldm;
2994: double **bbmij;
2995:
1.218 brouard 2996: doldm=ddoldms; /* global pointers */
1.222 brouard 2997: dnewm=ddnewms;
2998: dsavm=ddsavms;
2999:
3000: agefin=cov[2];
1.268 brouard 3001: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3002: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3003: the observed prevalence (with this covariate ij) at beginning of transition */
3004: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3005:
3006: /* P_x */
1.266 brouard 3007: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3008: /* outputs pmmij which is a stochastic matrix in row */
3009:
3010: /* Diag(w_x) */
3011: /* Problem with prevacurrent which can be zero */
3012: sumnew=0.;
1.269 brouard 3013: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3014: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.269 brouard 3015: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3016: sumnew+=prevacurrent[(int)agefin][ii][ij];
3017: }
3018: if(sumnew >0.01){ /* At least some value in the prevalence */
3019: for (ii=1;ii<=nlstate+ndeath;ii++){
3020: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3021: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3022: }
3023: }else{
3024: for (ii=1;ii<=nlstate+ndeath;ii++){
3025: for (j=1;j<=nlstate+ndeath;j++)
3026: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3027: }
3028: /* if(sumnew <0.9){ */
3029: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3030: /* } */
3031: }
3032: k3=0.0; /* We put the last diagonal to 0 */
3033: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3034: doldm[ii][ii]= k3;
3035: }
3036: /* End doldm, At the end doldm is diag[(w_i)] */
3037:
3038: /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
3039: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
3040:
3041: /* Diag(Sum_i w^i_x p^ij_x */
3042: /* 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 3043: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3044: sumnew=0.;
1.222 brouard 3045: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3046: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3047: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3048: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3049: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3050: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3051: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3052: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3053: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3054: /* }else */
1.268 brouard 3055: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3056: } /*End ii */
3057: } /* 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 */
3058:
3059: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
3060: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3061: /* end bmij */
1.266 brouard 3062: return ps; /*pointer is unchanged */
1.218 brouard 3063: }
1.217 brouard 3064: /*************** transition probabilities ***************/
3065:
1.218 brouard 3066: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3067: {
3068: /* According to parameters values stored in x and the covariate's values stored in cov,
3069: computes the probability to be observed in state j being in state i by appying the
3070: model to the ncovmodel covariates (including constant and age).
3071: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3072: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3073: ncth covariate in the global vector x is given by the formula:
3074: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3075: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3076: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3077: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3078: Outputs ps[i][j] the probability to be observed in j being in j according to
3079: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3080: */
3081: double s1, lnpijopii;
3082: /*double t34;*/
3083: int i,j, nc, ii, jj;
3084:
1.234 brouard 3085: for(i=1; i<= nlstate; i++){
3086: for(j=1; j<i;j++){
3087: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3088: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3089: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3090: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3091: }
3092: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3093: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3094: }
3095: for(j=i+1; j<=nlstate+ndeath;j++){
3096: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3097: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3098: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3099: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3100: }
3101: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3102: }
3103: }
3104:
3105: for(i=1; i<= nlstate; i++){
3106: s1=0;
3107: for(j=1; j<i; j++){
3108: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3109: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3110: }
3111: for(j=i+1; j<=nlstate+ndeath; j++){
3112: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3113: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3114: }
3115: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3116: ps[i][i]=1./(s1+1.);
3117: /* Computing other pijs */
3118: for(j=1; j<i; j++)
3119: ps[i][j]= exp(ps[i][j])*ps[i][i];
3120: for(j=i+1; j<=nlstate+ndeath; j++)
3121: ps[i][j]= exp(ps[i][j])*ps[i][i];
3122: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3123: } /* end i */
3124:
3125: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3126: for(jj=1; jj<= nlstate+ndeath; jj++){
3127: ps[ii][jj]=0;
3128: ps[ii][ii]=1;
3129: }
3130: }
3131: /* Added for backcast */ /* Transposed matrix too */
3132: for(jj=1; jj<= nlstate+ndeath; jj++){
3133: s1=0.;
3134: for(ii=1; ii<= nlstate+ndeath; ii++){
3135: s1+=ps[ii][jj];
3136: }
3137: for(ii=1; ii<= nlstate; ii++){
3138: ps[ii][jj]=ps[ii][jj]/s1;
3139: }
3140: }
3141: /* Transposition */
3142: for(jj=1; jj<= nlstate+ndeath; jj++){
3143: for(ii=jj; ii<= nlstate+ndeath; ii++){
3144: s1=ps[ii][jj];
3145: ps[ii][jj]=ps[jj][ii];
3146: ps[jj][ii]=s1;
3147: }
3148: }
3149: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3150: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3151: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3152: /* } */
3153: /* printf("\n "); */
3154: /* } */
3155: /* printf("\n ");printf("%lf ",cov[2]);*/
3156: /*
3157: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3158: goto end;*/
3159: return ps;
1.217 brouard 3160: }
3161:
3162:
1.126 brouard 3163: /**************** Product of 2 matrices ******************/
3164:
1.145 brouard 3165: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3166: {
3167: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3168: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3169: /* in, b, out are matrice of pointers which should have been initialized
3170: before: only the contents of out is modified. The function returns
3171: a pointer to pointers identical to out */
1.145 brouard 3172: int i, j, k;
1.126 brouard 3173: for(i=nrl; i<= nrh; i++)
1.145 brouard 3174: for(k=ncolol; k<=ncoloh; k++){
3175: out[i][k]=0.;
3176: for(j=ncl; j<=nch; j++)
3177: out[i][k] +=in[i][j]*b[j][k];
3178: }
1.126 brouard 3179: return out;
3180: }
3181:
3182:
3183: /************* Higher Matrix Product ***************/
3184:
1.235 brouard 3185: 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 3186: {
1.218 brouard 3187: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3188: 'nhstepm*hstepm*stepm' months (i.e. until
3189: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3190: nhstepm*hstepm matrices.
3191: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3192: (typically every 2 years instead of every month which is too big
3193: for the memory).
3194: Model is determined by parameters x and covariates have to be
3195: included manually here.
3196:
3197: */
3198:
3199: int i, j, d, h, k;
1.131 brouard 3200: double **out, cov[NCOVMAX+1];
1.126 brouard 3201: double **newm;
1.187 brouard 3202: double agexact;
1.214 brouard 3203: double agebegin, ageend;
1.126 brouard 3204:
3205: /* Hstepm could be zero and should return the unit matrix */
3206: for (i=1;i<=nlstate+ndeath;i++)
3207: for (j=1;j<=nlstate+ndeath;j++){
3208: oldm[i][j]=(i==j ? 1.0 : 0.0);
3209: po[i][j][0]=(i==j ? 1.0 : 0.0);
3210: }
3211: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3212: for(h=1; h <=nhstepm; h++){
3213: for(d=1; d <=hstepm; d++){
3214: newm=savm;
3215: /* Covariates have to be included here again */
3216: cov[1]=1.;
1.214 brouard 3217: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3218: cov[2]=agexact;
3219: if(nagesqr==1)
1.227 brouard 3220: cov[3]= agexact*agexact;
1.235 brouard 3221: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3222: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3223: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3224: /* 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)); */
3225: }
3226: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3227: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3228: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3229: /* 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]); */
3230: }
3231: for (k=1; k<=cptcovage;k++){
3232: if(Dummy[Tvar[Tage[k]]]){
3233: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3234: } else{
3235: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3236: }
3237: /* 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]); */
3238: }
3239: for (k=1; k<=cptcovprod;k++){ /* */
3240: /* 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]); */
3241: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3242: }
3243: /* for (k=1; k<=cptcovn;k++) */
3244: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3245: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3246: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3247: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3248: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3249:
3250:
1.126 brouard 3251: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3252: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3253: /* right multiplication of oldm by the current matrix */
1.126 brouard 3254: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3255: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3256: /* if((int)age == 70){ */
3257: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3258: /* for(i=1; i<=nlstate+ndeath; i++) { */
3259: /* printf("%d pmmij ",i); */
3260: /* for(j=1;j<=nlstate+ndeath;j++) { */
3261: /* printf("%f ",pmmij[i][j]); */
3262: /* } */
3263: /* printf(" oldm "); */
3264: /* for(j=1;j<=nlstate+ndeath;j++) { */
3265: /* printf("%f ",oldm[i][j]); */
3266: /* } */
3267: /* printf("\n"); */
3268: /* } */
3269: /* } */
1.126 brouard 3270: savm=oldm;
3271: oldm=newm;
3272: }
3273: for(i=1; i<=nlstate+ndeath; i++)
3274: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3275: po[i][j][h]=newm[i][j];
3276: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3277: }
1.128 brouard 3278: /*printf("h=%d ",h);*/
1.126 brouard 3279: } /* end h */
1.267 brouard 3280: /* printf("\n H=%d \n",h); */
1.126 brouard 3281: return po;
3282: }
3283:
1.217 brouard 3284: /************* Higher Back Matrix Product ***************/
1.218 brouard 3285: /* 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 3286: 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 3287: {
1.266 brouard 3288: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3289: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3290: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3291: nhstepm*hstepm matrices.
3292: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3293: (typically every 2 years instead of every month which is too big
1.217 brouard 3294: for the memory).
1.218 brouard 3295: Model is determined by parameters x and covariates have to be
1.266 brouard 3296: included manually here. Then we use a call to bmij(x and cov)
3297: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3298: */
1.217 brouard 3299:
3300: int i, j, d, h, k;
1.266 brouard 3301: double **out, cov[NCOVMAX+1], **bmij();
3302: double **newm, ***newmm;
1.217 brouard 3303: double agexact;
3304: double agebegin, ageend;
1.222 brouard 3305: double **oldm, **savm;
1.217 brouard 3306:
1.266 brouard 3307: newmm=po; /* To be saved */
3308: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3309: /* Hstepm could be zero and should return the unit matrix */
3310: for (i=1;i<=nlstate+ndeath;i++)
3311: for (j=1;j<=nlstate+ndeath;j++){
3312: oldm[i][j]=(i==j ? 1.0 : 0.0);
3313: po[i][j][0]=(i==j ? 1.0 : 0.0);
3314: }
3315: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3316: for(h=1; h <=nhstepm; h++){
3317: for(d=1; d <=hstepm; d++){
3318: newm=savm;
3319: /* Covariates have to be included here again */
3320: cov[1]=1.;
1.271 brouard 3321: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3322: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3323: cov[2]=agexact;
3324: if(nagesqr==1)
1.222 brouard 3325: cov[3]= agexact*agexact;
1.266 brouard 3326: for (k=1; k<=cptcovn;k++){
3327: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3328: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3329: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3330: /* 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)); */
3331: }
1.267 brouard 3332: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3333: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3334: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3335: /* 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]); */
3336: }
3337: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3338: if(Dummy[Tvar[Tage[k]]]){
3339: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3340: } else{
3341: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3342: }
3343: /* 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]); */
3344: }
3345: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3346: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3347: }
1.217 brouard 3348: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3349: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3350:
1.218 brouard 3351: /* Careful transposed matrix */
1.266 brouard 3352: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3353: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3354: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3355: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3356: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3357: /* if((int)age == 70){ */
3358: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3359: /* for(i=1; i<=nlstate+ndeath; i++) { */
3360: /* printf("%d pmmij ",i); */
3361: /* for(j=1;j<=nlstate+ndeath;j++) { */
3362: /* printf("%f ",pmmij[i][j]); */
3363: /* } */
3364: /* printf(" oldm "); */
3365: /* for(j=1;j<=nlstate+ndeath;j++) { */
3366: /* printf("%f ",oldm[i][j]); */
3367: /* } */
3368: /* printf("\n"); */
3369: /* } */
3370: /* } */
3371: savm=oldm;
3372: oldm=newm;
3373: }
3374: for(i=1; i<=nlstate+ndeath; i++)
3375: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3376: po[i][j][h]=newm[i][j];
1.268 brouard 3377: /* if(h==nhstepm) */
3378: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3379: }
1.268 brouard 3380: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3381: } /* end h */
1.268 brouard 3382: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3383: return po;
3384: }
3385:
3386:
1.162 brouard 3387: #ifdef NLOPT
3388: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3389: double fret;
3390: double *xt;
3391: int j;
3392: myfunc_data *d2 = (myfunc_data *) pd;
3393: /* xt = (p1-1); */
3394: xt=vector(1,n);
3395: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3396:
3397: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3398: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3399: printf("Function = %.12lf ",fret);
3400: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3401: printf("\n");
3402: free_vector(xt,1,n);
3403: return fret;
3404: }
3405: #endif
1.126 brouard 3406:
3407: /*************** log-likelihood *************/
3408: double func( double *x)
3409: {
1.226 brouard 3410: int i, ii, j, k, mi, d, kk;
3411: int ioffset=0;
3412: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3413: double **out;
3414: double lli; /* Individual log likelihood */
3415: int s1, s2;
1.228 brouard 3416: 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 3417: double bbh, survp;
3418: long ipmx;
3419: double agexact;
3420: /*extern weight */
3421: /* We are differentiating ll according to initial status */
3422: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3423: /*for(i=1;i<imx;i++)
3424: printf(" %d\n",s[4][i]);
3425: */
1.162 brouard 3426:
1.226 brouard 3427: ++countcallfunc;
1.162 brouard 3428:
1.226 brouard 3429: cov[1]=1.;
1.126 brouard 3430:
1.226 brouard 3431: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3432: ioffset=0;
1.226 brouard 3433: if(mle==1){
3434: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3435: /* Computes the values of the ncovmodel covariates of the model
3436: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3437: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3438: to be observed in j being in i according to the model.
3439: */
1.243 brouard 3440: ioffset=2+nagesqr ;
1.233 brouard 3441: /* Fixed */
1.234 brouard 3442: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3443: 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)*/
3444: }
1.226 brouard 3445: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3446: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3447: has been calculated etc */
3448: /* For an individual i, wav[i] gives the number of effective waves */
3449: /* We compute the contribution to Likelihood of each effective transition
3450: mw[mi][i] is real wave of the mi th effectve wave */
3451: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3452: s2=s[mw[mi+1][i]][i];
3453: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3454: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3455: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3456: */
3457: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3458: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3459: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3460: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3461: }
3462: for (ii=1;ii<=nlstate+ndeath;ii++)
3463: for (j=1;j<=nlstate+ndeath;j++){
3464: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3465: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3466: }
3467: for(d=0; d<dh[mi][i]; d++){
3468: newm=savm;
3469: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3470: cov[2]=agexact;
3471: if(nagesqr==1)
3472: cov[3]= agexact*agexact; /* Should be changed here */
3473: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3474: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3475: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3476: else
3477: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3478: }
3479: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3480: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3481: savm=oldm;
3482: oldm=newm;
3483: } /* end mult */
3484:
3485: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3486: /* But now since version 0.9 we anticipate for bias at large stepm.
3487: * If stepm is larger than one month (smallest stepm) and if the exact delay
3488: * (in months) between two waves is not a multiple of stepm, we rounded to
3489: * the nearest (and in case of equal distance, to the lowest) interval but now
3490: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3491: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3492: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3493: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3494: * -stepm/2 to stepm/2 .
3495: * For stepm=1 the results are the same as for previous versions of Imach.
3496: * For stepm > 1 the results are less biased than in previous versions.
3497: */
1.234 brouard 3498: s1=s[mw[mi][i]][i];
3499: s2=s[mw[mi+1][i]][i];
3500: bbh=(double)bh[mi][i]/(double)stepm;
3501: /* bias bh is positive if real duration
3502: * is higher than the multiple of stepm and negative otherwise.
3503: */
3504: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3505: if( s2 > nlstate){
3506: /* i.e. if s2 is a death state and if the date of death is known
3507: then the contribution to the likelihood is the probability to
3508: die between last step unit time and current step unit time,
3509: which is also equal to probability to die before dh
3510: minus probability to die before dh-stepm .
3511: In version up to 0.92 likelihood was computed
3512: as if date of death was unknown. Death was treated as any other
3513: health state: the date of the interview describes the actual state
3514: and not the date of a change in health state. The former idea was
3515: to consider that at each interview the state was recorded
3516: (healthy, disable or death) and IMaCh was corrected; but when we
3517: introduced the exact date of death then we should have modified
3518: the contribution of an exact death to the likelihood. This new
3519: contribution is smaller and very dependent of the step unit
3520: stepm. It is no more the probability to die between last interview
3521: and month of death but the probability to survive from last
3522: interview up to one month before death multiplied by the
3523: probability to die within a month. Thanks to Chris
3524: Jackson for correcting this bug. Former versions increased
3525: mortality artificially. The bad side is that we add another loop
3526: which slows down the processing. The difference can be up to 10%
3527: lower mortality.
3528: */
3529: /* If, at the beginning of the maximization mostly, the
3530: cumulative probability or probability to be dead is
3531: constant (ie = 1) over time d, the difference is equal to
3532: 0. out[s1][3] = savm[s1][3]: probability, being at state
3533: s1 at precedent wave, to be dead a month before current
3534: wave is equal to probability, being at state s1 at
3535: precedent wave, to be dead at mont of the current
3536: wave. Then the observed probability (that this person died)
3537: is null according to current estimated parameter. In fact,
3538: it should be very low but not zero otherwise the log go to
3539: infinity.
3540: */
1.183 brouard 3541: /* #ifdef INFINITYORIGINAL */
3542: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3543: /* #else */
3544: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3545: /* lli=log(mytinydouble); */
3546: /* else */
3547: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3548: /* #endif */
1.226 brouard 3549: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3550:
1.226 brouard 3551: } else if ( s2==-1 ) { /* alive */
3552: for (j=1,survp=0. ; j<=nlstate; j++)
3553: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3554: /*survp += out[s1][j]; */
3555: lli= log(survp);
3556: }
3557: else if (s2==-4) {
3558: for (j=3,survp=0. ; j<=nlstate; j++)
3559: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3560: lli= log(survp);
3561: }
3562: else if (s2==-5) {
3563: for (j=1,survp=0. ; j<=2; j++)
3564: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3565: lli= log(survp);
3566: }
3567: else{
3568: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3569: /* 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 */
3570: }
3571: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3572: /*if(lli ==000.0)*/
3573: /*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); */
3574: ipmx +=1;
3575: sw += weight[i];
3576: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3577: /* if (lli < log(mytinydouble)){ */
3578: /* 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); */
3579: /* 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]); */
3580: /* } */
3581: } /* end of wave */
3582: } /* end of individual */
3583: } else if(mle==2){
3584: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3585: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3586: for(mi=1; mi<= wav[i]-1; mi++){
3587: for (ii=1;ii<=nlstate+ndeath;ii++)
3588: for (j=1;j<=nlstate+ndeath;j++){
3589: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3590: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3591: }
3592: for(d=0; d<=dh[mi][i]; d++){
3593: newm=savm;
3594: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3595: cov[2]=agexact;
3596: if(nagesqr==1)
3597: cov[3]= agexact*agexact;
3598: for (kk=1; kk<=cptcovage;kk++) {
3599: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3600: }
3601: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3602: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3603: savm=oldm;
3604: oldm=newm;
3605: } /* end mult */
3606:
3607: s1=s[mw[mi][i]][i];
3608: s2=s[mw[mi+1][i]][i];
3609: bbh=(double)bh[mi][i]/(double)stepm;
3610: 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 */
3611: ipmx +=1;
3612: sw += weight[i];
3613: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3614: } /* end of wave */
3615: } /* end of individual */
3616: } else if(mle==3){ /* exponential inter-extrapolation */
3617: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3618: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3619: for(mi=1; mi<= wav[i]-1; mi++){
3620: for (ii=1;ii<=nlstate+ndeath;ii++)
3621: for (j=1;j<=nlstate+ndeath;j++){
3622: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3623: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3624: }
3625: for(d=0; d<dh[mi][i]; d++){
3626: newm=savm;
3627: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3628: cov[2]=agexact;
3629: if(nagesqr==1)
3630: cov[3]= agexact*agexact;
3631: for (kk=1; kk<=cptcovage;kk++) {
3632: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3633: }
3634: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3635: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3636: savm=oldm;
3637: oldm=newm;
3638: } /* end mult */
3639:
3640: s1=s[mw[mi][i]][i];
3641: s2=s[mw[mi+1][i]][i];
3642: bbh=(double)bh[mi][i]/(double)stepm;
3643: 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 */
3644: ipmx +=1;
3645: sw += weight[i];
3646: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3647: } /* end of wave */
3648: } /* end of individual */
3649: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3650: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3651: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3652: for(mi=1; mi<= wav[i]-1; mi++){
3653: for (ii=1;ii<=nlstate+ndeath;ii++)
3654: for (j=1;j<=nlstate+ndeath;j++){
3655: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3656: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3657: }
3658: for(d=0; d<dh[mi][i]; d++){
3659: newm=savm;
3660: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3661: cov[2]=agexact;
3662: if(nagesqr==1)
3663: cov[3]= agexact*agexact;
3664: for (kk=1; kk<=cptcovage;kk++) {
3665: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3666: }
1.126 brouard 3667:
1.226 brouard 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: if( s2 > nlstate){
3677: lli=log(out[s1][s2] - savm[s1][s2]);
3678: } else if ( s2==-1 ) { /* alive */
3679: for (j=1,survp=0. ; j<=nlstate; j++)
3680: survp += out[s1][j];
3681: lli= log(survp);
3682: }else{
3683: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3684: }
3685: ipmx +=1;
3686: sw += weight[i];
3687: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3688: /* 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 3689: } /* end of wave */
3690: } /* end of individual */
3691: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3692: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3693: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3694: for(mi=1; mi<= wav[i]-1; mi++){
3695: for (ii=1;ii<=nlstate+ndeath;ii++)
3696: for (j=1;j<=nlstate+ndeath;j++){
3697: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3698: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3699: }
3700: for(d=0; d<dh[mi][i]; d++){
3701: newm=savm;
3702: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3703: cov[2]=agexact;
3704: if(nagesqr==1)
3705: cov[3]= agexact*agexact;
3706: for (kk=1; kk<=cptcovage;kk++) {
3707: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3708: }
1.126 brouard 3709:
1.226 brouard 3710: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3711: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3712: savm=oldm;
3713: oldm=newm;
3714: } /* end mult */
3715:
3716: s1=s[mw[mi][i]][i];
3717: s2=s[mw[mi+1][i]][i];
3718: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3719: ipmx +=1;
3720: sw += weight[i];
3721: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
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]);*/
3723: } /* end of wave */
3724: } /* end of individual */
3725: } /* End of if */
3726: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3727: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3728: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3729: return -l;
1.126 brouard 3730: }
3731:
3732: /*************** log-likelihood *************/
3733: double funcone( double *x)
3734: {
1.228 brouard 3735: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3736: int i, ii, j, k, mi, d, kk;
1.228 brouard 3737: int ioffset=0;
1.131 brouard 3738: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3739: double **out;
3740: double lli; /* Individual log likelihood */
3741: double llt;
3742: int s1, s2;
1.228 brouard 3743: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3744:
1.126 brouard 3745: double bbh, survp;
1.187 brouard 3746: double agexact;
1.214 brouard 3747: double agebegin, ageend;
1.126 brouard 3748: /*extern weight */
3749: /* We are differentiating ll according to initial status */
3750: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3751: /*for(i=1;i<imx;i++)
3752: printf(" %d\n",s[4][i]);
3753: */
3754: cov[1]=1.;
3755:
3756: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3757: ioffset=0;
3758: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3759: /* ioffset=2+nagesqr+cptcovage; */
3760: ioffset=2+nagesqr;
1.232 brouard 3761: /* Fixed */
1.224 brouard 3762: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3763: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3764: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3765: 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)*/
3766: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3767: /* cov[2+6]=covar[Tvar[6]][i]; */
3768: /* cov[2+6]=covar[2][i]; V2 */
3769: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3770: /* cov[2+7]=covar[Tvar[7]][i]; */
3771: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3772: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3773: /* cov[2+9]=covar[Tvar[9]][i]; */
3774: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3775: }
1.232 brouard 3776: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3777: /* 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?)*\/ */
3778: /* } */
1.231 brouard 3779: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3780: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3781: /* } */
1.225 brouard 3782:
1.233 brouard 3783:
3784: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3785: /* Wave varying (but not age varying) */
3786: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3787: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3788: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3789: }
1.232 brouard 3790: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3791: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3792: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3793: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3794: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3795: /* 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 3796: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3797: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3798: /* /\* 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]); *\/ */
3799: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3800: /* } */
1.126 brouard 3801: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3802: for (j=1;j<=nlstate+ndeath;j++){
3803: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3804: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3805: }
1.214 brouard 3806:
3807: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3808: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3809: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3810: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3811: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3812: and mw[mi+1][i]. dh depends on stepm.*/
3813: newm=savm;
1.247 brouard 3814: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3815: cov[2]=agexact;
3816: if(nagesqr==1)
3817: cov[3]= agexact*agexact;
3818: for (kk=1; kk<=cptcovage;kk++) {
3819: if(!FixedV[Tvar[Tage[kk]]])
3820: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3821: else
3822: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3823: }
3824: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3825: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3826: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3827: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3828: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3829: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3830: savm=oldm;
3831: oldm=newm;
1.126 brouard 3832: } /* end mult */
3833:
3834: s1=s[mw[mi][i]][i];
3835: s2=s[mw[mi+1][i]][i];
1.217 brouard 3836: /* if(s2==-1){ */
1.268 brouard 3837: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3838: /* /\* exit(1); *\/ */
3839: /* } */
1.126 brouard 3840: bbh=(double)bh[mi][i]/(double)stepm;
3841: /* bias is positive if real duration
3842: * is higher than the multiple of stepm and negative otherwise.
3843: */
3844: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3845: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3846: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3847: for (j=1,survp=0. ; j<=nlstate; j++)
3848: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3849: lli= log(survp);
1.126 brouard 3850: }else if (mle==1){
1.242 brouard 3851: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3852: } else if(mle==2){
1.242 brouard 3853: 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 3854: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3855: 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 3856: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3857: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3858: } else{ /* mle=0 back to 1 */
1.242 brouard 3859: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3860: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3861: } /* End of if */
3862: ipmx +=1;
3863: sw += weight[i];
3864: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3865: /*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 3866: if(globpr){
1.246 brouard 3867: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3868: %11.6f %11.6f %11.6f ", \
1.242 brouard 3869: 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 3870: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3871: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3872: llt +=ll[k]*gipmx/gsw;
3873: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3874: }
3875: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3876: }
1.232 brouard 3877: } /* end of wave */
3878: } /* end of individual */
3879: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3880: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3881: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3882: if(globpr==0){ /* First time we count the contributions and weights */
3883: gipmx=ipmx;
3884: gsw=sw;
3885: }
3886: return -l;
1.126 brouard 3887: }
3888:
3889:
3890: /*************** function likelione ***********/
3891: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3892: {
3893: /* This routine should help understanding what is done with
3894: the selection of individuals/waves and
3895: to check the exact contribution to the likelihood.
3896: Plotting could be done.
3897: */
3898: int k;
3899:
3900: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3901: strcpy(fileresilk,"ILK_");
1.202 brouard 3902: strcat(fileresilk,fileresu);
1.126 brouard 3903: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3904: printf("Problem with resultfile: %s\n", fileresilk);
3905: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3906: }
1.214 brouard 3907: 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");
3908: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3909: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3910: for(k=1; k<=nlstate; k++)
3911: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3912: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3913: }
3914:
3915: *fretone=(*funcone)(p);
3916: if(*globpri !=0){
3917: fclose(ficresilk);
1.205 brouard 3918: if (mle ==0)
3919: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3920: else if(mle >=1)
3921: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3922: 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 3923: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3924:
3925: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3926: 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 3927: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3928: }
1.207 brouard 3929: 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 3930: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3931: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3932: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3933: fflush(fichtm);
1.205 brouard 3934: }
1.126 brouard 3935: return;
3936: }
3937:
3938:
3939: /*********** Maximum Likelihood Estimation ***************/
3940:
3941: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3942: {
1.165 brouard 3943: int i,j, iter=0;
1.126 brouard 3944: double **xi;
3945: double fret;
3946: double fretone; /* Only one call to likelihood */
3947: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3948:
3949: #ifdef NLOPT
3950: int creturn;
3951: nlopt_opt opt;
3952: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3953: double *lb;
3954: double minf; /* the minimum objective value, upon return */
3955: double * p1; /* Shifted parameters from 0 instead of 1 */
3956: myfunc_data dinst, *d = &dinst;
3957: #endif
3958:
3959:
1.126 brouard 3960: xi=matrix(1,npar,1,npar);
3961: for (i=1;i<=npar;i++)
3962: for (j=1;j<=npar;j++)
3963: xi[i][j]=(i==j ? 1.0 : 0.0);
3964: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3965: strcpy(filerespow,"POW_");
1.126 brouard 3966: strcat(filerespow,fileres);
3967: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3968: printf("Problem with resultfile: %s\n", filerespow);
3969: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3970: }
3971: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3972: for (i=1;i<=nlstate;i++)
3973: for(j=1;j<=nlstate+ndeath;j++)
3974: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3975: fprintf(ficrespow,"\n");
1.162 brouard 3976: #ifdef POWELL
1.126 brouard 3977: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3978: #endif
1.126 brouard 3979:
1.162 brouard 3980: #ifdef NLOPT
3981: #ifdef NEWUOA
3982: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3983: #else
3984: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3985: #endif
3986: lb=vector(0,npar-1);
3987: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3988: nlopt_set_lower_bounds(opt, lb);
3989: nlopt_set_initial_step1(opt, 0.1);
3990:
3991: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3992: d->function = func;
3993: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3994: nlopt_set_min_objective(opt, myfunc, d);
3995: nlopt_set_xtol_rel(opt, ftol);
3996: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3997: printf("nlopt failed! %d\n",creturn);
3998: }
3999: else {
4000: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4001: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4002: iter=1; /* not equal */
4003: }
4004: nlopt_destroy(opt);
4005: #endif
1.126 brouard 4006: free_matrix(xi,1,npar,1,npar);
4007: fclose(ficrespow);
1.203 brouard 4008: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4009: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4010: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4011:
4012: }
4013:
4014: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4015: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4016: {
4017: double **a,**y,*x,pd;
1.203 brouard 4018: /* double **hess; */
1.164 brouard 4019: int i, j;
1.126 brouard 4020: int *indx;
4021:
4022: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4023: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4024: void lubksb(double **a, int npar, int *indx, double b[]) ;
4025: void ludcmp(double **a, int npar, int *indx, double *d) ;
4026: double gompertz(double p[]);
1.203 brouard 4027: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4028:
4029: printf("\nCalculation of the hessian matrix. Wait...\n");
4030: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4031: for (i=1;i<=npar;i++){
1.203 brouard 4032: printf("%d-",i);fflush(stdout);
4033: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4034:
4035: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4036:
4037: /* printf(" %f ",p[i]);
4038: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4039: }
4040:
4041: for (i=1;i<=npar;i++) {
4042: for (j=1;j<=npar;j++) {
4043: if (j>i) {
1.203 brouard 4044: printf(".%d-%d",i,j);fflush(stdout);
4045: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4046: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4047:
4048: hess[j][i]=hess[i][j];
4049: /*printf(" %lf ",hess[i][j]);*/
4050: }
4051: }
4052: }
4053: printf("\n");
4054: fprintf(ficlog,"\n");
4055:
4056: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4057: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4058:
4059: a=matrix(1,npar,1,npar);
4060: y=matrix(1,npar,1,npar);
4061: x=vector(1,npar);
4062: indx=ivector(1,npar);
4063: for (i=1;i<=npar;i++)
4064: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4065: ludcmp(a,npar,indx,&pd);
4066:
4067: for (j=1;j<=npar;j++) {
4068: for (i=1;i<=npar;i++) x[i]=0;
4069: x[j]=1;
4070: lubksb(a,npar,indx,x);
4071: for (i=1;i<=npar;i++){
4072: matcov[i][j]=x[i];
4073: }
4074: }
4075:
4076: printf("\n#Hessian matrix#\n");
4077: fprintf(ficlog,"\n#Hessian matrix#\n");
4078: for (i=1;i<=npar;i++) {
4079: for (j=1;j<=npar;j++) {
1.203 brouard 4080: printf("%.6e ",hess[i][j]);
4081: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4082: }
4083: printf("\n");
4084: fprintf(ficlog,"\n");
4085: }
4086:
1.203 brouard 4087: /* printf("\n#Covariance matrix#\n"); */
4088: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4089: /* for (i=1;i<=npar;i++) { */
4090: /* for (j=1;j<=npar;j++) { */
4091: /* printf("%.6e ",matcov[i][j]); */
4092: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4093: /* } */
4094: /* printf("\n"); */
4095: /* fprintf(ficlog,"\n"); */
4096: /* } */
4097:
1.126 brouard 4098: /* Recompute Inverse */
1.203 brouard 4099: /* for (i=1;i<=npar;i++) */
4100: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4101: /* ludcmp(a,npar,indx,&pd); */
4102:
4103: /* printf("\n#Hessian matrix recomputed#\n"); */
4104:
4105: /* for (j=1;j<=npar;j++) { */
4106: /* for (i=1;i<=npar;i++) x[i]=0; */
4107: /* x[j]=1; */
4108: /* lubksb(a,npar,indx,x); */
4109: /* for (i=1;i<=npar;i++){ */
4110: /* y[i][j]=x[i]; */
4111: /* printf("%.3e ",y[i][j]); */
4112: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4113: /* } */
4114: /* printf("\n"); */
4115: /* fprintf(ficlog,"\n"); */
4116: /* } */
4117:
4118: /* Verifying the inverse matrix */
4119: #ifdef DEBUGHESS
4120: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4121:
1.203 brouard 4122: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4123: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4124:
4125: for (j=1;j<=npar;j++) {
4126: for (i=1;i<=npar;i++){
1.203 brouard 4127: printf("%.2f ",y[i][j]);
4128: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4129: }
4130: printf("\n");
4131: fprintf(ficlog,"\n");
4132: }
1.203 brouard 4133: #endif
1.126 brouard 4134:
4135: free_matrix(a,1,npar,1,npar);
4136: free_matrix(y,1,npar,1,npar);
4137: free_vector(x,1,npar);
4138: free_ivector(indx,1,npar);
1.203 brouard 4139: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4140:
4141:
4142: }
4143:
4144: /*************** hessian matrix ****************/
4145: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4146: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4147: int i;
4148: int l=1, lmax=20;
1.203 brouard 4149: double k1,k2, res, fx;
1.132 brouard 4150: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4151: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4152: int k=0,kmax=10;
4153: double l1;
4154:
4155: fx=func(x);
4156: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4157: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4158: l1=pow(10,l);
4159: delts=delt;
4160: for(k=1 ; k <kmax; k=k+1){
4161: delt = delta*(l1*k);
4162: p2[theta]=x[theta] +delt;
1.145 brouard 4163: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4164: p2[theta]=x[theta]-delt;
4165: k2=func(p2)-fx;
4166: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4167: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4168:
1.203 brouard 4169: #ifdef DEBUGHESSII
1.126 brouard 4170: 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);
4171: 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);
4172: #endif
4173: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4174: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4175: k=kmax;
4176: }
4177: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4178: k=kmax; l=lmax*10;
1.126 brouard 4179: }
4180: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4181: delts=delt;
4182: }
1.203 brouard 4183: } /* End loop k */
1.126 brouard 4184: }
4185: delti[theta]=delts;
4186: return res;
4187:
4188: }
4189:
1.203 brouard 4190: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4191: {
4192: int i;
1.164 brouard 4193: int l=1, lmax=20;
1.126 brouard 4194: double k1,k2,k3,k4,res,fx;
1.132 brouard 4195: double p2[MAXPARM+1];
1.203 brouard 4196: int k, kmax=1;
4197: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4198:
4199: int firstime=0;
1.203 brouard 4200:
1.126 brouard 4201: fx=func(x);
1.203 brouard 4202: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4203: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4204: p2[thetai]=x[thetai]+delti[thetai]*k;
4205: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4206: k1=func(p2)-fx;
4207:
1.203 brouard 4208: p2[thetai]=x[thetai]+delti[thetai]*k;
4209: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4210: k2=func(p2)-fx;
4211:
1.203 brouard 4212: p2[thetai]=x[thetai]-delti[thetai]*k;
4213: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4214: k3=func(p2)-fx;
4215:
1.203 brouard 4216: p2[thetai]=x[thetai]-delti[thetai]*k;
4217: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4218: k4=func(p2)-fx;
1.203 brouard 4219: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4220: if(k1*k2*k3*k4 <0.){
1.208 brouard 4221: firstime=1;
1.203 brouard 4222: kmax=kmax+10;
1.208 brouard 4223: }
4224: if(kmax >=10 || firstime ==1){
1.246 brouard 4225: 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);
4226: 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 4227: 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);
4228: 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);
4229: }
4230: #ifdef DEBUGHESSIJ
4231: v1=hess[thetai][thetai];
4232: v2=hess[thetaj][thetaj];
4233: cv12=res;
4234: /* Computing eigen value of Hessian matrix */
4235: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4236: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4237: if ((lc2 <0) || (lc1 <0) ){
4238: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4239: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4240: 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);
4241: 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);
4242: }
1.126 brouard 4243: #endif
4244: }
4245: return res;
4246: }
4247:
1.203 brouard 4248: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4249: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4250: /* { */
4251: /* int i; */
4252: /* int l=1, lmax=20; */
4253: /* double k1,k2,k3,k4,res,fx; */
4254: /* double p2[MAXPARM+1]; */
4255: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4256: /* int k=0,kmax=10; */
4257: /* double l1; */
4258:
4259: /* fx=func(x); */
4260: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4261: /* l1=pow(10,l); */
4262: /* delts=delt; */
4263: /* for(k=1 ; k <kmax; k=k+1){ */
4264: /* delt = delti*(l1*k); */
4265: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4266: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4267: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4268: /* k1=func(p2)-fx; */
4269:
4270: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4271: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4272: /* k2=func(p2)-fx; */
4273:
4274: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4275: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4276: /* k3=func(p2)-fx; */
4277:
4278: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4279: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4280: /* k4=func(p2)-fx; */
4281: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4282: /* #ifdef DEBUGHESSIJ */
4283: /* 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); */
4284: /* 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); */
4285: /* #endif */
4286: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4287: /* k=kmax; */
4288: /* } */
4289: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4290: /* k=kmax; l=lmax*10; */
4291: /* } */
4292: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4293: /* delts=delt; */
4294: /* } */
4295: /* } /\* End loop k *\/ */
4296: /* } */
4297: /* delti[theta]=delts; */
4298: /* return res; */
4299: /* } */
4300:
4301:
1.126 brouard 4302: /************** Inverse of matrix **************/
4303: void ludcmp(double **a, int n, int *indx, double *d)
4304: {
4305: int i,imax,j,k;
4306: double big,dum,sum,temp;
4307: double *vv;
4308:
4309: vv=vector(1,n);
4310: *d=1.0;
4311: for (i=1;i<=n;i++) {
4312: big=0.0;
4313: for (j=1;j<=n;j++)
4314: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4315: if (big == 0.0){
4316: printf(" Singular Hessian matrix at row %d:\n",i);
4317: for (j=1;j<=n;j++) {
4318: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4319: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4320: }
4321: fflush(ficlog);
4322: fclose(ficlog);
4323: nrerror("Singular matrix in routine ludcmp");
4324: }
1.126 brouard 4325: vv[i]=1.0/big;
4326: }
4327: for (j=1;j<=n;j++) {
4328: for (i=1;i<j;i++) {
4329: sum=a[i][j];
4330: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4331: a[i][j]=sum;
4332: }
4333: big=0.0;
4334: for (i=j;i<=n;i++) {
4335: sum=a[i][j];
4336: for (k=1;k<j;k++)
4337: sum -= a[i][k]*a[k][j];
4338: a[i][j]=sum;
4339: if ( (dum=vv[i]*fabs(sum)) >= big) {
4340: big=dum;
4341: imax=i;
4342: }
4343: }
4344: if (j != imax) {
4345: for (k=1;k<=n;k++) {
4346: dum=a[imax][k];
4347: a[imax][k]=a[j][k];
4348: a[j][k]=dum;
4349: }
4350: *d = -(*d);
4351: vv[imax]=vv[j];
4352: }
4353: indx[j]=imax;
4354: if (a[j][j] == 0.0) a[j][j]=TINY;
4355: if (j != n) {
4356: dum=1.0/(a[j][j]);
4357: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4358: }
4359: }
4360: free_vector(vv,1,n); /* Doesn't work */
4361: ;
4362: }
4363:
4364: void lubksb(double **a, int n, int *indx, double b[])
4365: {
4366: int i,ii=0,ip,j;
4367: double sum;
4368:
4369: for (i=1;i<=n;i++) {
4370: ip=indx[i];
4371: sum=b[ip];
4372: b[ip]=b[i];
4373: if (ii)
4374: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4375: else if (sum) ii=i;
4376: b[i]=sum;
4377: }
4378: for (i=n;i>=1;i--) {
4379: sum=b[i];
4380: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4381: b[i]=sum/a[i][i];
4382: }
4383: }
4384:
4385: void pstamp(FILE *fichier)
4386: {
1.196 brouard 4387: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4388: }
4389:
1.253 brouard 4390:
4391:
1.126 brouard 4392: /************ Frequencies ********************/
1.251 brouard 4393: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4394: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4395: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4396: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4397:
1.265 brouard 4398: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4399: int iind=0, iage=0;
4400: int mi; /* Effective wave */
4401: int first;
4402: double ***freq; /* Frequencies */
1.268 brouard 4403: 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 */
4404: 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 4405: double *meanq, *stdq, *idq;
1.226 brouard 4406: double **meanqt;
4407: double *pp, **prop, *posprop, *pospropt;
4408: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4409: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4410: double agebegin, ageend;
4411:
4412: pp=vector(1,nlstate);
1.251 brouard 4413: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4414: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4415: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4416: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4417: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4418: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4419: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4420: meanqt=matrix(1,lastpass,1,nqtveff);
4421: strcpy(fileresp,"P_");
4422: strcat(fileresp,fileresu);
4423: /*strcat(fileresphtm,fileresu);*/
4424: if((ficresp=fopen(fileresp,"w"))==NULL) {
4425: printf("Problem with prevalence resultfile: %s\n", fileresp);
4426: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4427: exit(0);
4428: }
1.240 brouard 4429:
1.226 brouard 4430: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4431: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4432: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4433: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4434: fflush(ficlog);
4435: exit(70);
4436: }
4437: else{
4438: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4439: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4440: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4441: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4442: }
1.237 brouard 4443: 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 4444:
1.226 brouard 4445: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4446: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4447: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4448: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4449: fflush(ficlog);
4450: exit(70);
1.240 brouard 4451: } else{
1.226 brouard 4452: 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 4453: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4454: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4455: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4456: }
1.240 brouard 4457: 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);
4458:
1.253 brouard 4459: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4460: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4461: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4462: j1=0;
1.126 brouard 4463:
1.227 brouard 4464: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4465: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4466: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4467:
4468:
1.226 brouard 4469: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4470: reference=low_education V1=0,V2=0
4471: med_educ V1=1 V2=0,
4472: high_educ V1=0 V2=1
4473: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4474: */
1.249 brouard 4475: dateintsum=0;
4476: k2cpt=0;
4477:
1.253 brouard 4478: if(cptcoveff == 0 )
1.265 brouard 4479: nl=1; /* Constant and age model only */
1.253 brouard 4480: else
4481: nl=2;
1.265 brouard 4482:
4483: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4484: /* Loop on nj=1 or 2 if dummy covariates j!=0
4485: * Loop on j1(1 to 2**cptcoveff) covariate combination
4486: * freq[s1][s2][iage] =0.
4487: * Loop on iind
4488: * ++freq[s1][s2][iage] weighted
4489: * end iind
4490: * if covariate and j!0
4491: * headers Variable on one line
4492: * endif cov j!=0
4493: * header of frequency table by age
4494: * Loop on age
4495: * pp[s1]+=freq[s1][s2][iage] weighted
4496: * pos+=freq[s1][s2][iage] weighted
4497: * Loop on s1 initial state
4498: * fprintf(ficresp
4499: * end s1
4500: * end age
4501: * if j!=0 computes starting values
4502: * end compute starting values
4503: * end j1
4504: * end nl
4505: */
1.253 brouard 4506: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4507: if(nj==1)
4508: j=0; /* First pass for the constant */
1.265 brouard 4509: else{
1.253 brouard 4510: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4511: }
1.251 brouard 4512: first=1;
1.265 brouard 4513: 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 4514: posproptt=0.;
4515: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4516: scanf("%d", i);*/
4517: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4518: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4519: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4520: freq[i][s2][m]=0;
1.251 brouard 4521:
4522: for (i=1; i<=nlstate; i++) {
1.240 brouard 4523: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4524: prop[i][m]=0;
4525: posprop[i]=0;
4526: pospropt[i]=0;
4527: }
1.283 brouard 4528: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4529: idq[z1]=0.;
4530: meanq[z1]=0.;
4531: stdq[z1]=0.;
1.283 brouard 4532: }
4533: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4534: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4535: /* meanqt[m][z1]=0.; */
4536: /* } */
4537: /* } */
1.251 brouard 4538: /* dateintsum=0; */
4539: /* k2cpt=0; */
4540:
1.265 brouard 4541: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4542: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4543: bool=1;
4544: if(j !=0){
4545: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4546: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4547: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4548: /* if(Tvaraff[z1] ==-20){ */
4549: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4550: /* }else if(Tvaraff[z1] ==-10){ */
4551: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4552: /* }else */
4553: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4554: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4555: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4556: /* 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",
4557: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4558: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4559: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4560: } /* Onlyf fixed */
4561: } /* end z1 */
4562: } /* cptcovn > 0 */
4563: } /* end any */
4564: }/* end j==0 */
1.265 brouard 4565: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4566: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4567: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4568: m=mw[mi][iind];
4569: if(j!=0){
4570: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4571: for (z1=1; z1<=cptcoveff; z1++) {
4572: if( Fixed[Tmodelind[z1]]==1){
4573: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4574: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4575: value is -1, we don't select. It differs from the
4576: constant and age model which counts them. */
4577: bool=0; /* not selected */
4578: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4579: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4580: bool=0;
4581: }
4582: }
4583: }
4584: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4585: } /* end j==0 */
4586: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4587: if(bool==1){ /*Selected */
1.251 brouard 4588: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4589: and mw[mi+1][iind]. dh depends on stepm. */
4590: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4591: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4592: if(m >=firstpass && m <=lastpass){
4593: k2=anint[m][iind]+(mint[m][iind]/12.);
4594: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4595: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4596: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4597: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4598: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4599: if (m<lastpass) {
4600: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4601: /* 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]); */
4602: if(s[m][iind]==-1)
4603: 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.));
4604: 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 4605: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4606: idq[z1]=idq[z1]+weight[iind];
4607: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4608: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4609: }
1.251 brouard 4610: /* if((int)agev[m][iind] == 55) */
4611: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4612: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4613: 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 4614: }
1.251 brouard 4615: } /* end if between passes */
4616: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4617: dateintsum=dateintsum+k2; /* on all covariates ?*/
4618: k2cpt++;
4619: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4620: }
1.251 brouard 4621: }else{
4622: bool=1;
4623: }/* end bool 2 */
4624: } /* end m */
1.284 brouard 4625: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4626: /* idq[z1]=idq[z1]+weight[iind]; */
4627: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4628: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4629: /* } */
1.251 brouard 4630: } /* end bool */
4631: } /* end iind = 1 to imx */
4632: /* prop[s][age] is feeded for any initial and valid live state as well as
4633: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4634:
4635:
4636: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4637: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4638: pstamp(ficresp);
1.251 brouard 4639: if (cptcoveff>0 && j!=0){
1.265 brouard 4640: pstamp(ficresp);
1.251 brouard 4641: printf( "\n#********** Variable ");
4642: fprintf(ficresp, "\n#********** Variable ");
4643: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4644: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4645: fprintf(ficlog, "\n#********** Variable ");
4646: for (z1=1; z1<=cptcoveff; z1++){
4647: if(!FixedV[Tvaraff[z1]]){
4648: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4649: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4650: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4651: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4652: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4653: }else{
1.251 brouard 4654: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4655: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4656: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4657: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4658: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4659: }
4660: }
4661: printf( "**********\n#");
4662: fprintf(ficresp, "**********\n#");
4663: fprintf(ficresphtm, "**********</h3>\n");
4664: fprintf(ficresphtmfr, "**********</h3>\n");
4665: fprintf(ficlog, "**********\n");
4666: }
1.284 brouard 4667: /*
4668: Printing means of quantitative variables if any
4669: */
4670: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4671: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4672: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4673: if(weightopt==1){
4674: printf(" Weighted mean and standard deviation of");
4675: fprintf(ficlog," Weighted mean and standard deviation of");
4676: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4677: }
1.285 brouard 4678: 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]));
4679: 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]));
4680: 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 4681: }
4682: /* for (z1=1; z1<= nqtveff; z1++) { */
4683: /* for(m=1;m<=lastpass;m++){ */
4684: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4685: /* } */
4686: /* } */
1.283 brouard 4687:
1.251 brouard 4688: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4689: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4690: fprintf(ficresp, " Age");
4691: 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 4692: for(i=1; i<=nlstate;i++) {
1.265 brouard 4693: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4694: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4695: }
1.265 brouard 4696: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4697: fprintf(ficresphtm, "\n");
4698:
4699: /* Header of frequency table by age */
4700: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4701: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4702: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4703: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4704: if(s2!=0 && m!=0)
4705: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4706: }
1.226 brouard 4707: }
1.251 brouard 4708: fprintf(ficresphtmfr, "\n");
4709:
4710: /* For each age */
4711: for(iage=iagemin; iage <= iagemax+3; iage++){
4712: fprintf(ficresphtm,"<tr>");
4713: if(iage==iagemax+1){
4714: fprintf(ficlog,"1");
4715: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4716: }else if(iage==iagemax+2){
4717: fprintf(ficlog,"0");
4718: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4719: }else if(iage==iagemax+3){
4720: fprintf(ficlog,"Total");
4721: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4722: }else{
1.240 brouard 4723: if(first==1){
1.251 brouard 4724: first=0;
4725: printf("See log file for details...\n");
4726: }
4727: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4728: fprintf(ficlog,"Age %d", iage);
4729: }
1.265 brouard 4730: for(s1=1; s1 <=nlstate ; s1++){
4731: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4732: pp[s1] += freq[s1][m][iage];
1.251 brouard 4733: }
1.265 brouard 4734: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4735: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4736: pos += freq[s1][m][iage];
4737: if(pp[s1]>=1.e-10){
1.251 brouard 4738: if(first==1){
1.265 brouard 4739: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4740: }
1.265 brouard 4741: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4742: }else{
4743: if(first==1)
1.265 brouard 4744: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4745: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4746: }
4747: }
4748:
1.265 brouard 4749: for(s1=1; s1 <=nlstate ; s1++){
4750: /* posprop[s1]=0; */
4751: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4752: pp[s1] += freq[s1][m][iage];
4753: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4754:
4755: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4756: pos += pp[s1]; /* pos is the total number of transitions until this age */
4757: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4758: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4759: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4760: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4761: }
4762:
4763: /* Writing ficresp */
4764: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4765: if( iage <= iagemax){
4766: fprintf(ficresp," %d",iage);
4767: }
4768: }else if( nj==2){
4769: if( iage <= iagemax){
4770: fprintf(ficresp," %d",iage);
4771: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4772: }
1.240 brouard 4773: }
1.265 brouard 4774: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4775: if(pos>=1.e-5){
1.251 brouard 4776: if(first==1)
1.265 brouard 4777: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4778: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4779: }else{
4780: if(first==1)
1.265 brouard 4781: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4782: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4783: }
4784: if( iage <= iagemax){
4785: if(pos>=1.e-5){
1.265 brouard 4786: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4787: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4788: }else if( nj==2){
4789: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4790: }
4791: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4792: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4793: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4794: } else{
4795: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4796: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4797: }
1.240 brouard 4798: }
1.265 brouard 4799: pospropt[s1] +=posprop[s1];
4800: } /* end loop s1 */
1.251 brouard 4801: /* pospropt=0.; */
1.265 brouard 4802: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4803: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4804: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4805: if(first==1){
1.265 brouard 4806: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4807: }
1.265 brouard 4808: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4809: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4810: }
1.265 brouard 4811: if(s1!=0 && m!=0)
4812: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4813: }
1.265 brouard 4814: } /* end loop s1 */
1.251 brouard 4815: posproptt=0.;
1.265 brouard 4816: for(s1=1; s1 <=nlstate; s1++){
4817: posproptt += pospropt[s1];
1.251 brouard 4818: }
4819: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4820: fprintf(ficresphtm,"</tr>\n");
4821: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4822: if(iage <= iagemax)
4823: fprintf(ficresp,"\n");
1.240 brouard 4824: }
1.251 brouard 4825: if(first==1)
4826: printf("Others in log...\n");
4827: fprintf(ficlog,"\n");
4828: } /* end loop age iage */
1.265 brouard 4829:
1.251 brouard 4830: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4831: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4832: if(posproptt < 1.e-5){
1.265 brouard 4833: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4834: }else{
1.265 brouard 4835: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4836: }
1.226 brouard 4837: }
1.251 brouard 4838: fprintf(ficresphtm,"</tr>\n");
4839: fprintf(ficresphtm,"</table>\n");
4840: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4841: if(posproptt < 1.e-5){
1.251 brouard 4842: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4843: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4844: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4845: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4846: invalidvarcomb[j1]=1;
1.226 brouard 4847: }else{
1.251 brouard 4848: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4849: invalidvarcomb[j1]=0;
1.226 brouard 4850: }
1.251 brouard 4851: fprintf(ficresphtmfr,"</table>\n");
4852: fprintf(ficlog,"\n");
4853: if(j!=0){
4854: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4855: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4856: for(k=1; k <=(nlstate+ndeath); k++){
4857: if (k != i) {
1.265 brouard 4858: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4859: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4860: if(j1==1){ /* All dummy covariates to zero */
4861: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4862: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4863: printf("%d%d ",i,k);
4864: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4865: 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]));
4866: 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]));
4867: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4868: }
1.253 brouard 4869: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4870: for(iage=iagemin; iage <= iagemax+3; iage++){
4871: x[iage]= (double)iage;
4872: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4873: /* 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 4874: }
1.268 brouard 4875: /* Some are not finite, but linreg will ignore these ages */
4876: no=0;
1.253 brouard 4877: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4878: pstart[s1]=b;
4879: pstart[s1-1]=a;
1.252 brouard 4880: }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 */
4881: 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]);
4882: 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 4883: 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 4884: printf("%d%d ",i,k);
4885: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4886: 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 4887: }else{ /* Other cases, like quantitative fixed or varying covariates */
4888: ;
4889: }
4890: /* printf("%12.7f )", param[i][jj][k]); */
4891: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4892: s1++;
1.251 brouard 4893: } /* end jj */
4894: } /* end k!= i */
4895: } /* end k */
1.265 brouard 4896: } /* end i, s1 */
1.251 brouard 4897: } /* end j !=0 */
4898: } /* end selected combination of covariate j1 */
4899: if(j==0){ /* We can estimate starting values from the occurences in each case */
4900: printf("#Freqsummary: Starting values for the constants:\n");
4901: fprintf(ficlog,"\n");
1.265 brouard 4902: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4903: for(k=1; k <=(nlstate+ndeath); k++){
4904: if (k != i) {
4905: printf("%d%d ",i,k);
4906: fprintf(ficlog,"%d%d ",i,k);
4907: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4908: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4909: if(jj==1){ /* Age has to be done */
1.265 brouard 4910: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4911: 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]));
4912: 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 4913: }
4914: /* printf("%12.7f )", param[i][jj][k]); */
4915: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4916: s1++;
1.250 brouard 4917: }
1.251 brouard 4918: printf("\n");
4919: fprintf(ficlog,"\n");
1.250 brouard 4920: }
4921: }
1.284 brouard 4922: } /* end of state i */
1.251 brouard 4923: printf("#Freqsummary\n");
4924: fprintf(ficlog,"\n");
1.265 brouard 4925: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4926: for(s2=-1; s2 <=nlstate+ndeath; s2++){
4927: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
4928: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4929: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4930: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
4931: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
4932: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 4933: /* } */
4934: }
1.265 brouard 4935: } /* end loop s1 */
1.251 brouard 4936:
4937: printf("\n");
4938: fprintf(ficlog,"\n");
4939: } /* end j=0 */
1.249 brouard 4940: } /* end j */
1.252 brouard 4941:
1.253 brouard 4942: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4943: for(i=1, jk=1; i <=nlstate; i++){
4944: for(j=1; j <=nlstate+ndeath; j++){
4945: if(j!=i){
4946: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4947: printf("%1d%1d",i,j);
4948: fprintf(ficparo,"%1d%1d",i,j);
4949: for(k=1; k<=ncovmodel;k++){
4950: /* printf(" %lf",param[i][j][k]); */
4951: /* fprintf(ficparo," %lf",param[i][j][k]); */
4952: p[jk]=pstart[jk];
4953: printf(" %f ",pstart[jk]);
4954: fprintf(ficparo," %f ",pstart[jk]);
4955: jk++;
4956: }
4957: printf("\n");
4958: fprintf(ficparo,"\n");
4959: }
4960: }
4961: }
4962: } /* end mle=-2 */
1.226 brouard 4963: dateintmean=dateintsum/k2cpt;
1.240 brouard 4964:
1.226 brouard 4965: fclose(ficresp);
4966: fclose(ficresphtm);
4967: fclose(ficresphtmfr);
1.283 brouard 4968: free_vector(idq,1,nqfveff);
1.226 brouard 4969: free_vector(meanq,1,nqfveff);
1.284 brouard 4970: free_vector(stdq,1,nqfveff);
1.226 brouard 4971: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 4972: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
4973: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 4974: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4975: free_vector(pospropt,1,nlstate);
4976: free_vector(posprop,1,nlstate);
1.251 brouard 4977: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4978: free_vector(pp,1,nlstate);
4979: /* End of freqsummary */
4980: }
1.126 brouard 4981:
1.268 brouard 4982: /* Simple linear regression */
4983: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
4984:
4985: /* y=a+bx regression */
4986: double sumx = 0.0; /* sum of x */
4987: double sumx2 = 0.0; /* sum of x**2 */
4988: double sumxy = 0.0; /* sum of x * y */
4989: double sumy = 0.0; /* sum of y */
4990: double sumy2 = 0.0; /* sum of y**2 */
4991: double sume2 = 0.0; /* sum of square or residuals */
4992: double yhat;
4993:
4994: double denom=0;
4995: int i;
4996: int ne=*no;
4997:
4998: for ( i=ifi, ne=0;i<=ila;i++) {
4999: if(!isfinite(x[i]) || !isfinite(y[i])){
5000: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5001: continue;
5002: }
5003: ne=ne+1;
5004: sumx += x[i];
5005: sumx2 += x[i]*x[i];
5006: sumxy += x[i] * y[i];
5007: sumy += y[i];
5008: sumy2 += y[i]*y[i];
5009: denom = (ne * sumx2 - sumx*sumx);
5010: /* 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); */
5011: }
5012:
5013: denom = (ne * sumx2 - sumx*sumx);
5014: if (denom == 0) {
5015: // vertical, slope m is infinity
5016: *b = INFINITY;
5017: *a = 0;
5018: if (r) *r = 0;
5019: return 1;
5020: }
5021:
5022: *b = (ne * sumxy - sumx * sumy) / denom;
5023: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5024: if (r!=NULL) {
5025: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5026: sqrt((sumx2 - sumx*sumx/ne) *
5027: (sumy2 - sumy*sumy/ne));
5028: }
5029: *no=ne;
5030: for ( i=ifi, ne=0;i<=ila;i++) {
5031: if(!isfinite(x[i]) || !isfinite(y[i])){
5032: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5033: continue;
5034: }
5035: ne=ne+1;
5036: yhat = y[i] - *a -*b* x[i];
5037: sume2 += yhat * yhat ;
5038:
5039: denom = (ne * sumx2 - sumx*sumx);
5040: /* 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); */
5041: }
5042: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5043: *sa= *sb * sqrt(sumx2/ne);
5044:
5045: return 0;
5046: }
5047:
1.126 brouard 5048: /************ Prevalence ********************/
1.227 brouard 5049: 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)
5050: {
5051: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5052: in each health status at the date of interview (if between dateprev1 and dateprev2).
5053: We still use firstpass and lastpass as another selection.
5054: */
1.126 brouard 5055:
1.227 brouard 5056: int i, m, jk, j1, bool, z1,j, iv;
5057: int mi; /* Effective wave */
5058: int iage;
5059: double agebegin, ageend;
5060:
5061: double **prop;
5062: double posprop;
5063: double y2; /* in fractional years */
5064: int iagemin, iagemax;
5065: int first; /** to stop verbosity which is redirected to log file */
5066:
5067: iagemin= (int) agemin;
5068: iagemax= (int) agemax;
5069: /*pp=vector(1,nlstate);*/
1.251 brouard 5070: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5071: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5072: j1=0;
1.222 brouard 5073:
1.227 brouard 5074: /*j=cptcoveff;*/
5075: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5076:
1.288 brouard 5077: first=0;
1.227 brouard 5078: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5079: for (i=1; i<=nlstate; i++)
1.251 brouard 5080: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5081: prop[i][iage]=0.0;
5082: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5083: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5084: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5085:
5086: for (i=1; i<=imx; i++) { /* Each individual */
5087: bool=1;
5088: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5089: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5090: m=mw[mi][i];
5091: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5092: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5093: for (z1=1; z1<=cptcoveff; z1++){
5094: if( Fixed[Tmodelind[z1]]==1){
5095: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5096: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5097: bool=0;
5098: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5099: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5100: bool=0;
5101: }
5102: }
5103: if(bool==1){ /* Otherwise we skip that wave/person */
5104: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5105: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5106: if(m >=firstpass && m <=lastpass){
5107: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5108: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5109: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5110: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5111: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5112: 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);
5113: exit(1);
5114: }
5115: if (s[m][i]>0 && s[m][i]<=nlstate) {
5116: /*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]]);*/
5117: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5118: prop[s[m][i]][iagemax+3] += weight[i];
5119: } /* end valid statuses */
5120: } /* end selection of dates */
5121: } /* end selection of waves */
5122: } /* end bool */
5123: } /* end wave */
5124: } /* end individual */
5125: for(i=iagemin; i <= iagemax+3; i++){
5126: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5127: posprop += prop[jk][i];
5128: }
5129:
5130: for(jk=1; jk <=nlstate ; jk++){
5131: if( i <= iagemax){
5132: if(posprop>=1.e-5){
5133: probs[i][jk][j1]= prop[jk][i]/posprop;
5134: } else{
1.288 brouard 5135: if(!first){
5136: first=1;
1.266 brouard 5137: 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]);
5138: }else{
1.288 brouard 5139: 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 5140: }
5141: }
5142: }
5143: }/* end jk */
5144: }/* end i */
1.222 brouard 5145: /*} *//* end i1 */
1.227 brouard 5146: } /* end j1 */
1.222 brouard 5147:
1.227 brouard 5148: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5149: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5150: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5151: } /* End of prevalence */
1.126 brouard 5152:
5153: /************* Waves Concatenation ***************/
5154:
5155: 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)
5156: {
5157: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
5158: Death is a valid wave (if date is known).
5159: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5160: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
5161: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 5162: */
1.126 brouard 5163:
1.224 brouard 5164: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5165: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5166: double sum=0., jmean=0.;*/
1.224 brouard 5167: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5168: int j, k=0,jk, ju, jl;
5169: double sum=0.;
5170: first=0;
1.214 brouard 5171: firstwo=0;
1.217 brouard 5172: firsthree=0;
1.218 brouard 5173: firstfour=0;
1.164 brouard 5174: jmin=100000;
1.126 brouard 5175: jmax=-1;
5176: jmean=0.;
1.224 brouard 5177:
5178: /* Treating live states */
1.214 brouard 5179: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5180: mi=0; /* First valid wave */
1.227 brouard 5181: mli=0; /* Last valid wave */
1.126 brouard 5182: m=firstpass;
1.214 brouard 5183: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5184: 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 */
5185: mli=m-1;/* mw[++mi][i]=m-1; */
5186: }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 */
5187: mw[++mi][i]=m;
5188: mli=m;
1.224 brouard 5189: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5190: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5191: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5192: }
1.227 brouard 5193: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5194: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5195: break;
1.224 brouard 5196: #else
1.227 brouard 5197: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5198: if(firsthree == 0){
1.262 brouard 5199: 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 5200: firsthree=1;
5201: }
1.262 brouard 5202: 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 5203: mw[++mi][i]=m;
5204: mli=m;
5205: }
5206: if(s[m][i]==-2){ /* Vital status is really unknown */
5207: nbwarn++;
5208: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5209: 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);
5210: 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);
5211: }
5212: break;
5213: }
5214: break;
1.224 brouard 5215: #endif
1.227 brouard 5216: }/* End m >= lastpass */
1.126 brouard 5217: }/* end while */
1.224 brouard 5218:
1.227 brouard 5219: /* 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 5220: /* After last pass */
1.224 brouard 5221: /* Treating death states */
1.214 brouard 5222: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5223: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5224: /* } */
1.126 brouard 5225: mi++; /* Death is another wave */
5226: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5227: /* Only death is a correct wave */
1.126 brouard 5228: mw[mi][i]=m;
1.257 brouard 5229: } /* else not in a death state */
1.224 brouard 5230: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5231: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5232: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5233: 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 */
5234: nbwarn++;
5235: if(firstfiv==0){
5236: 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 );
5237: firstfiv=1;
5238: }else{
5239: 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 );
5240: }
5241: }else{ /* Death occured afer last wave potential bias */
5242: nberr++;
5243: if(firstwo==0){
1.257 brouard 5244: 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 5245: firstwo=1;
5246: }
1.257 brouard 5247: 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 5248: }
1.257 brouard 5249: }else{ /* if date of interview is unknown */
1.227 brouard 5250: /* death is known but not confirmed by death status at any wave */
5251: if(firstfour==0){
5252: 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 );
5253: firstfour=1;
5254: }
5255: 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 5256: }
1.224 brouard 5257: } /* end if date of death is known */
5258: #endif
5259: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5260: /* wav[i]=mw[mi][i]; */
1.126 brouard 5261: if(mi==0){
5262: nbwarn++;
5263: if(first==0){
1.227 brouard 5264: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5265: first=1;
1.126 brouard 5266: }
5267: if(first==1){
1.227 brouard 5268: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5269: }
5270: } /* end mi==0 */
5271: } /* End individuals */
1.214 brouard 5272: /* wav and mw are no more changed */
1.223 brouard 5273:
1.214 brouard 5274:
1.126 brouard 5275: for(i=1; i<=imx; i++){
5276: for(mi=1; mi<wav[i];mi++){
5277: if (stepm <=0)
1.227 brouard 5278: dh[mi][i]=1;
1.126 brouard 5279: else{
1.260 brouard 5280: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5281: if (agedc[i] < 2*AGESUP) {
5282: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5283: if(j==0) j=1; /* Survives at least one month after exam */
5284: else if(j<0){
5285: nberr++;
5286: 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]);
5287: j=1; /* Temporary Dangerous patch */
5288: 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);
5289: 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]);
5290: 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);
5291: }
5292: k=k+1;
5293: if (j >= jmax){
5294: jmax=j;
5295: ijmax=i;
5296: }
5297: if (j <= jmin){
5298: jmin=j;
5299: ijmin=i;
5300: }
5301: sum=sum+j;
5302: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5303: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5304: }
5305: }
5306: else{
5307: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5308: /* 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 5309:
1.227 brouard 5310: k=k+1;
5311: if (j >= jmax) {
5312: jmax=j;
5313: ijmax=i;
5314: }
5315: else if (j <= jmin){
5316: jmin=j;
5317: ijmin=i;
5318: }
5319: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5320: /*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]);*/
5321: if(j<0){
5322: nberr++;
5323: 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]);
5324: 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]);
5325: }
5326: sum=sum+j;
5327: }
5328: jk= j/stepm;
5329: jl= j -jk*stepm;
5330: ju= j -(jk+1)*stepm;
5331: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5332: if(jl==0){
5333: dh[mi][i]=jk;
5334: bh[mi][i]=0;
5335: }else{ /* We want a negative bias in order to only have interpolation ie
5336: * to avoid the price of an extra matrix product in likelihood */
5337: dh[mi][i]=jk+1;
5338: bh[mi][i]=ju;
5339: }
5340: }else{
5341: if(jl <= -ju){
5342: dh[mi][i]=jk;
5343: bh[mi][i]=jl; /* bias is positive if real duration
5344: * is higher than the multiple of stepm and negative otherwise.
5345: */
5346: }
5347: else{
5348: dh[mi][i]=jk+1;
5349: bh[mi][i]=ju;
5350: }
5351: if(dh[mi][i]==0){
5352: dh[mi][i]=1; /* At least one step */
5353: bh[mi][i]=ju; /* At least one step */
5354: /* 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);*/
5355: }
5356: } /* end if mle */
1.126 brouard 5357: }
5358: } /* end wave */
5359: }
5360: jmean=sum/k;
5361: 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 5362: 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 5363: }
1.126 brouard 5364:
5365: /*********** Tricode ****************************/
1.220 brouard 5366: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5367: {
5368: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5369: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5370: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5371: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5372: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5373: */
1.130 brouard 5374:
1.242 brouard 5375: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5376: int modmaxcovj=0; /* Modality max of covariates j */
5377: int cptcode=0; /* Modality max of covariates j */
5378: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5379:
5380:
1.242 brouard 5381: /* cptcoveff=0; */
5382: /* *cptcov=0; */
1.126 brouard 5383:
1.242 brouard 5384: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5385: for (k=1; k <= maxncov; k++)
5386: for(j=1; j<=2; j++)
5387: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5388:
1.242 brouard 5389: /* Loop on covariates without age and products and no quantitative variable */
5390: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5391: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5392: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5393: switch(Fixed[k]) {
5394: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5395: 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*/
5396: ij=(int)(covar[Tvar[k]][i]);
5397: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5398: * If product of Vn*Vm, still boolean *:
5399: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5400: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5401: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5402: modality of the nth covariate of individual i. */
5403: if (ij > modmaxcovj)
5404: modmaxcovj=ij;
5405: else if (ij < modmincovj)
5406: modmincovj=ij;
1.287 brouard 5407: if (ij <0 || ij >1 ){
5408: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5409: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5410: }
5411: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5412: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5413: exit(1);
5414: }else
5415: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5416: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5417: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5418: /* getting the maximum value of the modality of the covariate
5419: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5420: female ies 1, then modmaxcovj=1.
5421: */
5422: } /* end for loop on individuals i */
5423: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5424: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5425: cptcode=modmaxcovj;
5426: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5427: /*for (i=0; i<=cptcode; i++) {*/
5428: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5429: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5430: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5431: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5432: if( j != -1){
5433: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5434: covariate for which somebody answered excluding
5435: undefined. Usually 2: 0 and 1. */
5436: }
5437: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5438: covariate for which somebody answered including
5439: undefined. Usually 3: -1, 0 and 1. */
5440: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5441: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5442: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5443:
1.242 brouard 5444: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5445: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5446: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5447: /* modmincovj=3; modmaxcovj = 7; */
5448: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5449: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5450: /* defining two dummy variables: variables V1_1 and V1_2.*/
5451: /* nbcode[Tvar[j]][ij]=k; */
5452: /* nbcode[Tvar[j]][1]=0; */
5453: /* nbcode[Tvar[j]][2]=1; */
5454: /* nbcode[Tvar[j]][3]=2; */
5455: /* To be continued (not working yet). */
5456: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5457:
5458: /* 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*/
5459: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5460: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5461: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5462: /*, could be restored in the future */
5463: 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 5464: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5465: break;
5466: }
5467: ij++;
1.287 brouard 5468: 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 5469: cptcode = ij; /* New max modality for covar j */
5470: } /* end of loop on modality i=-1 to 1 or more */
5471: break;
5472: case 1: /* Testing on varying covariate, could be simple and
5473: * should look at waves or product of fixed *
5474: * varying. No time to test -1, assuming 0 and 1 only */
5475: ij=0;
5476: for(i=0; i<=1;i++){
5477: nbcode[Tvar[k]][++ij]=i;
5478: }
5479: break;
5480: default:
5481: break;
5482: } /* end switch */
5483: } /* end dummy test */
1.287 brouard 5484: } /* 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 5485:
5486: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5487: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5488: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5489: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5490: 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 */
5491: 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 */
5492: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5493: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5494:
5495: ij=0;
5496: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5497: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5498: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5499: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5500: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5501: /* If product not in single variable we don't print results */
5502: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5503: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5504: 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*/
5505: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5506: 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 */
5507: if(Fixed[k]!=0)
5508: anyvaryingduminmodel=1;
5509: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5510: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5511: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5512: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5513: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5514: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5515: }
5516: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5517: /* ij--; */
5518: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5519: *cptcov=ij; /*Number of total real effective covariates: effective
5520: * because they can be excluded from the model and real
5521: * if in the model but excluded because missing values, but how to get k from ij?*/
5522: for(j=ij+1; j<= cptcovt; j++){
5523: Tvaraff[j]=0;
5524: Tmodelind[j]=0;
5525: }
5526: for(j=ntveff+1; j<= cptcovt; j++){
5527: TmodelInvind[j]=0;
5528: }
5529: /* To be sorted */
5530: ;
5531: }
1.126 brouard 5532:
1.145 brouard 5533:
1.126 brouard 5534: /*********** Health Expectancies ****************/
5535:
1.235 brouard 5536: 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 5537:
5538: {
5539: /* Health expectancies, no variances */
1.164 brouard 5540: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5541: int nhstepma, nstepma; /* Decreasing with age */
5542: double age, agelim, hf;
5543: double ***p3mat;
5544: double eip;
5545:
1.238 brouard 5546: /* pstamp(ficreseij); */
1.126 brouard 5547: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5548: fprintf(ficreseij,"# Age");
5549: for(i=1; i<=nlstate;i++){
5550: for(j=1; j<=nlstate;j++){
5551: fprintf(ficreseij," e%1d%1d ",i,j);
5552: }
5553: fprintf(ficreseij," e%1d. ",i);
5554: }
5555: fprintf(ficreseij,"\n");
5556:
5557:
5558: if(estepm < stepm){
5559: printf ("Problem %d lower than %d\n",estepm, stepm);
5560: }
5561: else hstepm=estepm;
5562: /* We compute the life expectancy from trapezoids spaced every estepm months
5563: * This is mainly to measure the difference between two models: for example
5564: * if stepm=24 months pijx are given only every 2 years and by summing them
5565: * we are calculating an estimate of the Life Expectancy assuming a linear
5566: * progression in between and thus overestimating or underestimating according
5567: * to the curvature of the survival function. If, for the same date, we
5568: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5569: * to compare the new estimate of Life expectancy with the same linear
5570: * hypothesis. A more precise result, taking into account a more precise
5571: * curvature will be obtained if estepm is as small as stepm. */
5572:
5573: /* For example we decided to compute the life expectancy with the smallest unit */
5574: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5575: nhstepm is the number of hstepm from age to agelim
5576: nstepm is the number of stepm from age to agelin.
1.270 brouard 5577: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5578: and note for a fixed period like estepm months */
5579: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5580: survival function given by stepm (the optimization length). Unfortunately it
5581: means that if the survival funtion is printed only each two years of age and if
5582: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5583: results. So we changed our mind and took the option of the best precision.
5584: */
5585: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5586:
5587: agelim=AGESUP;
5588: /* If stepm=6 months */
5589: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5590: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5591:
5592: /* nhstepm age range expressed in number of stepm */
5593: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5594: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5595: /* if (stepm >= YEARM) hstepm=1;*/
5596: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5597: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5598:
5599: for (age=bage; age<=fage; age ++){
5600: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5601: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5602: /* if (stepm >= YEARM) hstepm=1;*/
5603: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5604:
5605: /* If stepm=6 months */
5606: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5607: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5608:
1.235 brouard 5609: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5610:
5611: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5612:
5613: printf("%d|",(int)age);fflush(stdout);
5614: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5615:
5616: /* Computing expectancies */
5617: for(i=1; i<=nlstate;i++)
5618: for(j=1; j<=nlstate;j++)
5619: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5620: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5621:
5622: /* 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]);*/
5623:
5624: }
5625:
5626: fprintf(ficreseij,"%3.0f",age );
5627: for(i=1; i<=nlstate;i++){
5628: eip=0;
5629: for(j=1; j<=nlstate;j++){
5630: eip +=eij[i][j][(int)age];
5631: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5632: }
5633: fprintf(ficreseij,"%9.4f", eip );
5634: }
5635: fprintf(ficreseij,"\n");
5636:
5637: }
5638: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5639: printf("\n");
5640: fprintf(ficlog,"\n");
5641:
5642: }
5643:
1.235 brouard 5644: 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 5645:
5646: {
5647: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5648: to initial status i, ei. .
1.126 brouard 5649: */
5650: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5651: int nhstepma, nstepma; /* Decreasing with age */
5652: double age, agelim, hf;
5653: double ***p3matp, ***p3matm, ***varhe;
5654: double **dnewm,**doldm;
5655: double *xp, *xm;
5656: double **gp, **gm;
5657: double ***gradg, ***trgradg;
5658: int theta;
5659:
5660: double eip, vip;
5661:
5662: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5663: xp=vector(1,npar);
5664: xm=vector(1,npar);
5665: dnewm=matrix(1,nlstate*nlstate,1,npar);
5666: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5667:
5668: pstamp(ficresstdeij);
5669: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5670: fprintf(ficresstdeij,"# Age");
5671: for(i=1; i<=nlstate;i++){
5672: for(j=1; j<=nlstate;j++)
5673: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5674: fprintf(ficresstdeij," e%1d. ",i);
5675: }
5676: fprintf(ficresstdeij,"\n");
5677:
5678: pstamp(ficrescveij);
5679: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5680: fprintf(ficrescveij,"# Age");
5681: for(i=1; i<=nlstate;i++)
5682: for(j=1; j<=nlstate;j++){
5683: cptj= (j-1)*nlstate+i;
5684: for(i2=1; i2<=nlstate;i2++)
5685: for(j2=1; j2<=nlstate;j2++){
5686: cptj2= (j2-1)*nlstate+i2;
5687: if(cptj2 <= cptj)
5688: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5689: }
5690: }
5691: fprintf(ficrescveij,"\n");
5692:
5693: if(estepm < stepm){
5694: printf ("Problem %d lower than %d\n",estepm, stepm);
5695: }
5696: else hstepm=estepm;
5697: /* We compute the life expectancy from trapezoids spaced every estepm months
5698: * This is mainly to measure the difference between two models: for example
5699: * if stepm=24 months pijx are given only every 2 years and by summing them
5700: * we are calculating an estimate of the Life Expectancy assuming a linear
5701: * progression in between and thus overestimating or underestimating according
5702: * to the curvature of the survival function. If, for the same date, we
5703: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5704: * to compare the new estimate of Life expectancy with the same linear
5705: * hypothesis. A more precise result, taking into account a more precise
5706: * curvature will be obtained if estepm is as small as stepm. */
5707:
5708: /* For example we decided to compute the life expectancy with the smallest unit */
5709: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5710: nhstepm is the number of hstepm from age to agelim
5711: nstepm is the number of stepm from age to agelin.
5712: Look at hpijx to understand the reason of that which relies in memory size
5713: and note for a fixed period like estepm months */
5714: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5715: survival function given by stepm (the optimization length). Unfortunately it
5716: means that if the survival funtion is printed only each two years of age and if
5717: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5718: results. So we changed our mind and took the option of the best precision.
5719: */
5720: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5721:
5722: /* If stepm=6 months */
5723: /* nhstepm age range expressed in number of stepm */
5724: agelim=AGESUP;
5725: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5726: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5727: /* if (stepm >= YEARM) hstepm=1;*/
5728: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5729:
5730: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5731: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5732: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5733: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5734: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5735: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5736:
5737: for (age=bage; age<=fage; age ++){
5738: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5739: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5740: /* if (stepm >= YEARM) hstepm=1;*/
5741: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5742:
1.126 brouard 5743: /* If stepm=6 months */
5744: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5745: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5746:
5747: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5748:
1.126 brouard 5749: /* Computing Variances of health expectancies */
5750: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5751: decrease memory allocation */
5752: for(theta=1; theta <=npar; theta++){
5753: for(i=1; i<=npar; i++){
1.222 brouard 5754: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5755: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5756: }
1.235 brouard 5757: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5758: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5759:
1.126 brouard 5760: for(j=1; j<= nlstate; j++){
1.222 brouard 5761: for(i=1; i<=nlstate; i++){
5762: for(h=0; h<=nhstepm-1; h++){
5763: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5764: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5765: }
5766: }
1.126 brouard 5767: }
1.218 brouard 5768:
1.126 brouard 5769: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5770: for(h=0; h<=nhstepm-1; h++){
5771: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5772: }
1.126 brouard 5773: }/* End theta */
5774:
5775:
5776: for(h=0; h<=nhstepm-1; h++)
5777: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5778: for(theta=1; theta <=npar; theta++)
5779: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5780:
1.218 brouard 5781:
1.222 brouard 5782: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5783: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5784: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5785:
1.222 brouard 5786: printf("%d|",(int)age);fflush(stdout);
5787: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5788: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5789: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5790: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5791: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5792: for(ij=1;ij<=nlstate*nlstate;ij++)
5793: for(ji=1;ji<=nlstate*nlstate;ji++)
5794: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5795: }
5796: }
1.218 brouard 5797:
1.126 brouard 5798: /* Computing expectancies */
1.235 brouard 5799: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5800: for(i=1; i<=nlstate;i++)
5801: for(j=1; j<=nlstate;j++)
1.222 brouard 5802: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5803: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5804:
1.222 brouard 5805: /* 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 5806:
1.222 brouard 5807: }
1.269 brouard 5808:
5809: /* Standard deviation of expectancies ij */
1.126 brouard 5810: fprintf(ficresstdeij,"%3.0f",age );
5811: for(i=1; i<=nlstate;i++){
5812: eip=0.;
5813: vip=0.;
5814: for(j=1; j<=nlstate;j++){
1.222 brouard 5815: eip += eij[i][j][(int)age];
5816: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5817: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5818: 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 5819: }
5820: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5821: }
5822: fprintf(ficresstdeij,"\n");
1.218 brouard 5823:
1.269 brouard 5824: /* Variance of expectancies ij */
1.126 brouard 5825: fprintf(ficrescveij,"%3.0f",age );
5826: for(i=1; i<=nlstate;i++)
5827: for(j=1; j<=nlstate;j++){
1.222 brouard 5828: cptj= (j-1)*nlstate+i;
5829: for(i2=1; i2<=nlstate;i2++)
5830: for(j2=1; j2<=nlstate;j2++){
5831: cptj2= (j2-1)*nlstate+i2;
5832: if(cptj2 <= cptj)
5833: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5834: }
1.126 brouard 5835: }
5836: fprintf(ficrescveij,"\n");
1.218 brouard 5837:
1.126 brouard 5838: }
5839: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5840: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5841: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5842: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5843: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5844: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5845: printf("\n");
5846: fprintf(ficlog,"\n");
1.218 brouard 5847:
1.126 brouard 5848: free_vector(xm,1,npar);
5849: free_vector(xp,1,npar);
5850: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5851: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5852: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5853: }
1.218 brouard 5854:
1.126 brouard 5855: /************ Variance ******************/
1.235 brouard 5856: 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 5857: {
1.279 brouard 5858: /** Variance of health expectancies
5859: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5860: * double **newm;
5861: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5862: */
1.218 brouard 5863:
5864: /* int movingaverage(); */
5865: double **dnewm,**doldm;
5866: double **dnewmp,**doldmp;
5867: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5868: int first=0;
1.218 brouard 5869: int k;
5870: double *xp;
1.279 brouard 5871: double **gp, **gm; /**< for var eij */
5872: double ***gradg, ***trgradg; /**< for var eij */
5873: double **gradgp, **trgradgp; /**< for var p point j */
5874: double *gpp, *gmp; /**< for var p point j */
5875: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5876: double ***p3mat;
5877: double age,agelim, hf;
5878: /* double ***mobaverage; */
5879: int theta;
5880: char digit[4];
5881: char digitp[25];
5882:
5883: char fileresprobmorprev[FILENAMELENGTH];
5884:
5885: if(popbased==1){
5886: if(mobilav!=0)
5887: strcpy(digitp,"-POPULBASED-MOBILAV_");
5888: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5889: }
5890: else
5891: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5892:
1.218 brouard 5893: /* if (mobilav!=0) { */
5894: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5895: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5896: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5897: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5898: /* } */
5899: /* } */
5900:
5901: strcpy(fileresprobmorprev,"PRMORPREV-");
5902: sprintf(digit,"%-d",ij);
5903: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5904: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5905: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5906: strcat(fileresprobmorprev,fileresu);
5907: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5908: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5909: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5910: }
5911: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5912: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5913: pstamp(ficresprobmorprev);
5914: 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 5915: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5916: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5917: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5918: }
5919: for(j=1;j<=cptcoveff;j++)
5920: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5921: fprintf(ficresprobmorprev,"\n");
5922:
1.218 brouard 5923: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5924: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5925: fprintf(ficresprobmorprev," p.%-d SE",j);
5926: for(i=1; i<=nlstate;i++)
5927: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5928: }
5929: fprintf(ficresprobmorprev,"\n");
5930:
5931: fprintf(ficgp,"\n# Routine varevsij");
5932: fprintf(ficgp,"\nunset title \n");
5933: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5934: 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");
5935: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 5936:
1.218 brouard 5937: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5938: pstamp(ficresvij);
5939: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5940: if(popbased==1)
5941: 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);
5942: else
5943: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5944: fprintf(ficresvij,"# Age");
5945: for(i=1; i<=nlstate;i++)
5946: for(j=1; j<=nlstate;j++)
5947: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5948: fprintf(ficresvij,"\n");
5949:
5950: xp=vector(1,npar);
5951: dnewm=matrix(1,nlstate,1,npar);
5952: doldm=matrix(1,nlstate,1,nlstate);
5953: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5954: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5955:
5956: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5957: gpp=vector(nlstate+1,nlstate+ndeath);
5958: gmp=vector(nlstate+1,nlstate+ndeath);
5959: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5960:
1.218 brouard 5961: if(estepm < stepm){
5962: printf ("Problem %d lower than %d\n",estepm, stepm);
5963: }
5964: else hstepm=estepm;
5965: /* For example we decided to compute the life expectancy with the smallest unit */
5966: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5967: nhstepm is the number of hstepm from age to agelim
5968: nstepm is the number of stepm from age to agelim.
5969: Look at function hpijx to understand why because of memory size limitations,
5970: we decided (b) to get a life expectancy respecting the most precise curvature of the
5971: survival function given by stepm (the optimization length). Unfortunately it
5972: means that if the survival funtion is printed every two years of age and if
5973: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5974: results. So we changed our mind and took the option of the best precision.
5975: */
5976: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5977: agelim = AGESUP;
5978: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5979: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5980: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5981: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5982: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5983: gp=matrix(0,nhstepm,1,nlstate);
5984: gm=matrix(0,nhstepm,1,nlstate);
5985:
5986:
5987: for(theta=1; theta <=npar; theta++){
5988: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5989: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5990: }
1.279 brouard 5991: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
5992: * returns into prlim .
1.288 brouard 5993: */
1.242 brouard 5994: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 5995:
5996: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 5997: if (popbased==1) {
5998: if(mobilav ==0){
5999: for(i=1; i<=nlstate;i++)
6000: prlim[i][i]=probs[(int)age][i][ij];
6001: }else{ /* mobilav */
6002: for(i=1; i<=nlstate;i++)
6003: prlim[i][i]=mobaverage[(int)age][i][ij];
6004: }
6005: }
1.279 brouard 6006: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
6007: */
6008: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
6009: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
6010: * at horizon h in state j including mortality.
6011: */
1.218 brouard 6012: for(j=1; j<= nlstate; j++){
6013: for(h=0; h<=nhstepm; h++){
6014: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6015: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6016: }
6017: }
1.279 brouard 6018: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6019: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6020: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6021: */
6022: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6023: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6024: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6025: }
6026:
6027: /* Again with minus shift */
1.218 brouard 6028:
6029: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6030: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6031:
1.242 brouard 6032: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6033:
6034: if (popbased==1) {
6035: if(mobilav ==0){
6036: for(i=1; i<=nlstate;i++)
6037: prlim[i][i]=probs[(int)age][i][ij];
6038: }else{ /* mobilav */
6039: for(i=1; i<=nlstate;i++)
6040: prlim[i][i]=mobaverage[(int)age][i][ij];
6041: }
6042: }
6043:
1.235 brouard 6044: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6045:
6046: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6047: for(h=0; h<=nhstepm; h++){
6048: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6049: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6050: }
6051: }
6052: /* This for computing probability of death (h=1 means
6053: computed over hstepm matrices product = hstepm*stepm months)
6054: as a weighted average of prlim.
6055: */
6056: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6057: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6058: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6059: }
1.279 brouard 6060: /* end shifting computations */
6061:
6062: /**< Computing gradient matrix at horizon h
6063: */
1.218 brouard 6064: for(j=1; j<= nlstate; j++) /* vareij */
6065: for(h=0; h<=nhstepm; h++){
6066: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6067: }
1.279 brouard 6068: /**< Gradient of overall mortality p.3 (or p.j)
6069: */
6070: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6071: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6072: }
6073:
6074: } /* End theta */
1.279 brouard 6075:
6076: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6077: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6078:
6079: for(h=0; h<=nhstepm; h++) /* veij */
6080: for(j=1; j<=nlstate;j++)
6081: for(theta=1; theta <=npar; theta++)
6082: trgradg[h][j][theta]=gradg[h][theta][j];
6083:
6084: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6085: for(theta=1; theta <=npar; theta++)
6086: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6087: /**< as well as its transposed matrix
6088: */
1.218 brouard 6089:
6090: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6091: for(i=1;i<=nlstate;i++)
6092: for(j=1;j<=nlstate;j++)
6093: vareij[i][j][(int)age] =0.;
1.279 brouard 6094:
6095: /* Computing trgradg by matcov by gradg at age and summing over h
6096: * and k (nhstepm) formula 15 of article
6097: * Lievre-Brouard-Heathcote
6098: */
6099:
1.218 brouard 6100: for(h=0;h<=nhstepm;h++){
6101: for(k=0;k<=nhstepm;k++){
6102: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6103: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6104: for(i=1;i<=nlstate;i++)
6105: for(j=1;j<=nlstate;j++)
6106: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6107: }
6108: }
6109:
1.279 brouard 6110: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6111: * p.j overall mortality formula 49 but computed directly because
6112: * we compute the grad (wix pijx) instead of grad (pijx),even if
6113: * wix is independent of theta.
6114: */
1.218 brouard 6115: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6116: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6117: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6118: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6119: varppt[j][i]=doldmp[j][i];
6120: /* end ppptj */
6121: /* x centered again */
6122:
1.242 brouard 6123: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6124:
6125: if (popbased==1) {
6126: if(mobilav ==0){
6127: for(i=1; i<=nlstate;i++)
6128: prlim[i][i]=probs[(int)age][i][ij];
6129: }else{ /* mobilav */
6130: for(i=1; i<=nlstate;i++)
6131: prlim[i][i]=mobaverage[(int)age][i][ij];
6132: }
6133: }
6134:
6135: /* This for computing probability of death (h=1 means
6136: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6137: as a weighted average of prlim.
6138: */
1.235 brouard 6139: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6140: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6141: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6142: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6143: }
6144: /* end probability of death */
6145:
6146: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6147: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6148: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6149: for(i=1; i<=nlstate;i++){
6150: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6151: }
6152: }
6153: fprintf(ficresprobmorprev,"\n");
6154:
6155: fprintf(ficresvij,"%.0f ",age );
6156: for(i=1; i<=nlstate;i++)
6157: for(j=1; j<=nlstate;j++){
6158: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6159: }
6160: fprintf(ficresvij,"\n");
6161: free_matrix(gp,0,nhstepm,1,nlstate);
6162: free_matrix(gm,0,nhstepm,1,nlstate);
6163: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6164: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6165: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6166: } /* End age */
6167: free_vector(gpp,nlstate+1,nlstate+ndeath);
6168: free_vector(gmp,nlstate+1,nlstate+ndeath);
6169: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6170: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6171: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6172: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6173: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6174: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6175: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6176: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6177: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6178: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6179: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6180: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6181: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6182: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6183: 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);
6184: /* 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 6185: */
1.218 brouard 6186: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6187: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6188:
1.218 brouard 6189: free_vector(xp,1,npar);
6190: free_matrix(doldm,1,nlstate,1,nlstate);
6191: free_matrix(dnewm,1,nlstate,1,npar);
6192: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6193: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6194: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6195: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6196: fclose(ficresprobmorprev);
6197: fflush(ficgp);
6198: fflush(fichtm);
6199: } /* end varevsij */
1.126 brouard 6200:
6201: /************ Variance of prevlim ******************/
1.269 brouard 6202: 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 6203: {
1.205 brouard 6204: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6205: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6206:
1.268 brouard 6207: double **dnewmpar,**doldm;
1.126 brouard 6208: int i, j, nhstepm, hstepm;
6209: double *xp;
6210: double *gp, *gm;
6211: double **gradg, **trgradg;
1.208 brouard 6212: double **mgm, **mgp;
1.126 brouard 6213: double age,agelim;
6214: int theta;
6215:
6216: pstamp(ficresvpl);
1.288 brouard 6217: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6218: fprintf(ficresvpl,"# Age ");
6219: if(nresult >=1)
6220: fprintf(ficresvpl," Result# ");
1.126 brouard 6221: for(i=1; i<=nlstate;i++)
6222: fprintf(ficresvpl," %1d-%1d",i,i);
6223: fprintf(ficresvpl,"\n");
6224:
6225: xp=vector(1,npar);
1.268 brouard 6226: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6227: doldm=matrix(1,nlstate,1,nlstate);
6228:
6229: hstepm=1*YEARM; /* Every year of age */
6230: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6231: agelim = AGESUP;
6232: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6233: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6234: if (stepm >= YEARM) hstepm=1;
6235: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6236: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6237: mgp=matrix(1,npar,1,nlstate);
6238: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6239: gp=vector(1,nlstate);
6240: gm=vector(1,nlstate);
6241:
6242: for(theta=1; theta <=npar; theta++){
6243: for(i=1; i<=npar; i++){ /* Computes gradient */
6244: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6245: }
1.288 brouard 6246: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6247: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6248: /* else */
6249: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6250: for(i=1;i<=nlstate;i++){
1.126 brouard 6251: gp[i] = prlim[i][i];
1.208 brouard 6252: mgp[theta][i] = prlim[i][i];
6253: }
1.126 brouard 6254: for(i=1; i<=npar; i++) /* Computes gradient */
6255: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6256: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6257: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6258: /* else */
6259: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6260: for(i=1;i<=nlstate;i++){
1.126 brouard 6261: gm[i] = prlim[i][i];
1.208 brouard 6262: mgm[theta][i] = prlim[i][i];
6263: }
1.126 brouard 6264: for(i=1;i<=nlstate;i++)
6265: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6266: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6267: } /* End theta */
6268:
6269: trgradg =matrix(1,nlstate,1,npar);
6270:
6271: for(j=1; j<=nlstate;j++)
6272: for(theta=1; theta <=npar; theta++)
6273: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6274: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6275: /* printf("\nmgm mgp %d ",(int)age); */
6276: /* for(j=1; j<=nlstate;j++){ */
6277: /* printf(" %d ",j); */
6278: /* for(theta=1; theta <=npar; theta++) */
6279: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6280: /* printf("\n "); */
6281: /* } */
6282: /* } */
6283: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6284: /* printf("\n gradg %d ",(int)age); */
6285: /* for(j=1; j<=nlstate;j++){ */
6286: /* printf("%d ",j); */
6287: /* for(theta=1; theta <=npar; theta++) */
6288: /* printf("%d %lf ",theta,gradg[theta][j]); */
6289: /* printf("\n "); */
6290: /* } */
6291: /* } */
1.126 brouard 6292:
6293: for(i=1;i<=nlstate;i++)
6294: varpl[i][(int)age] =0.;
1.209 brouard 6295: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6296: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6297: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6298: }else{
1.268 brouard 6299: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6300: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6301: }
1.126 brouard 6302: for(i=1;i<=nlstate;i++)
6303: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6304:
6305: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6306: if(nresult >=1)
6307: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6308: for(i=1; i<=nlstate;i++){
1.126 brouard 6309: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6310: /* for(j=1;j<=nlstate;j++) */
6311: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6312: }
1.126 brouard 6313: fprintf(ficresvpl,"\n");
6314: free_vector(gp,1,nlstate);
6315: free_vector(gm,1,nlstate);
1.208 brouard 6316: free_matrix(mgm,1,npar,1,nlstate);
6317: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6318: free_matrix(gradg,1,npar,1,nlstate);
6319: free_matrix(trgradg,1,nlstate,1,npar);
6320: } /* End age */
6321:
6322: free_vector(xp,1,npar);
6323: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6324: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6325:
6326: }
6327:
6328:
6329: /************ Variance of backprevalence limit ******************/
1.269 brouard 6330: 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 6331: {
6332: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6333: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6334:
6335: double **dnewmpar,**doldm;
6336: int i, j, nhstepm, hstepm;
6337: double *xp;
6338: double *gp, *gm;
6339: double **gradg, **trgradg;
6340: double **mgm, **mgp;
6341: double age,agelim;
6342: int theta;
6343:
6344: pstamp(ficresvbl);
6345: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6346: fprintf(ficresvbl,"# Age ");
6347: if(nresult >=1)
6348: fprintf(ficresvbl," Result# ");
6349: for(i=1; i<=nlstate;i++)
6350: fprintf(ficresvbl," %1d-%1d",i,i);
6351: fprintf(ficresvbl,"\n");
6352:
6353: xp=vector(1,npar);
6354: dnewmpar=matrix(1,nlstate,1,npar);
6355: doldm=matrix(1,nlstate,1,nlstate);
6356:
6357: hstepm=1*YEARM; /* Every year of age */
6358: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6359: agelim = AGEINF;
6360: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6361: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6362: if (stepm >= YEARM) hstepm=1;
6363: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6364: gradg=matrix(1,npar,1,nlstate);
6365: mgp=matrix(1,npar,1,nlstate);
6366: mgm=matrix(1,npar,1,nlstate);
6367: gp=vector(1,nlstate);
6368: gm=vector(1,nlstate);
6369:
6370: for(theta=1; theta <=npar; theta++){
6371: for(i=1; i<=npar; i++){ /* Computes gradient */
6372: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6373: }
6374: if(mobilavproj > 0 )
6375: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6376: else
6377: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6378: for(i=1;i<=nlstate;i++){
6379: gp[i] = bprlim[i][i];
6380: mgp[theta][i] = bprlim[i][i];
6381: }
6382: for(i=1; i<=npar; i++) /* Computes gradient */
6383: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6384: if(mobilavproj > 0 )
6385: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6386: else
6387: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6388: for(i=1;i<=nlstate;i++){
6389: gm[i] = bprlim[i][i];
6390: mgm[theta][i] = bprlim[i][i];
6391: }
6392: for(i=1;i<=nlstate;i++)
6393: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6394: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6395: } /* End theta */
6396:
6397: trgradg =matrix(1,nlstate,1,npar);
6398:
6399: for(j=1; j<=nlstate;j++)
6400: for(theta=1; theta <=npar; theta++)
6401: trgradg[j][theta]=gradg[theta][j];
6402: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6403: /* printf("\nmgm mgp %d ",(int)age); */
6404: /* for(j=1; j<=nlstate;j++){ */
6405: /* printf(" %d ",j); */
6406: /* for(theta=1; theta <=npar; theta++) */
6407: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6408: /* printf("\n "); */
6409: /* } */
6410: /* } */
6411: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6412: /* printf("\n gradg %d ",(int)age); */
6413: /* for(j=1; j<=nlstate;j++){ */
6414: /* printf("%d ",j); */
6415: /* for(theta=1; theta <=npar; theta++) */
6416: /* printf("%d %lf ",theta,gradg[theta][j]); */
6417: /* printf("\n "); */
6418: /* } */
6419: /* } */
6420:
6421: for(i=1;i<=nlstate;i++)
6422: varbpl[i][(int)age] =0.;
6423: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6424: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6425: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6426: }else{
6427: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6428: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6429: }
6430: for(i=1;i<=nlstate;i++)
6431: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6432:
6433: fprintf(ficresvbl,"%.0f ",age );
6434: if(nresult >=1)
6435: fprintf(ficresvbl,"%d ",nres );
6436: for(i=1; i<=nlstate;i++)
6437: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6438: fprintf(ficresvbl,"\n");
6439: free_vector(gp,1,nlstate);
6440: free_vector(gm,1,nlstate);
6441: free_matrix(mgm,1,npar,1,nlstate);
6442: free_matrix(mgp,1,npar,1,nlstate);
6443: free_matrix(gradg,1,npar,1,nlstate);
6444: free_matrix(trgradg,1,nlstate,1,npar);
6445: } /* End age */
6446:
6447: free_vector(xp,1,npar);
6448: free_matrix(doldm,1,nlstate,1,npar);
6449: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6450:
6451: }
6452:
6453: /************ Variance of one-step probabilities ******************/
6454: 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 6455: {
6456: int i, j=0, k1, l1, tj;
6457: int k2, l2, j1, z1;
6458: int k=0, l;
6459: int first=1, first1, first2;
6460: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6461: double **dnewm,**doldm;
6462: double *xp;
6463: double *gp, *gm;
6464: double **gradg, **trgradg;
6465: double **mu;
6466: double age, cov[NCOVMAX+1];
6467: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6468: int theta;
6469: char fileresprob[FILENAMELENGTH];
6470: char fileresprobcov[FILENAMELENGTH];
6471: char fileresprobcor[FILENAMELENGTH];
6472: double ***varpij;
6473:
6474: strcpy(fileresprob,"PROB_");
6475: strcat(fileresprob,fileres);
6476: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6477: printf("Problem with resultfile: %s\n", fileresprob);
6478: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6479: }
6480: strcpy(fileresprobcov,"PROBCOV_");
6481: strcat(fileresprobcov,fileresu);
6482: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6483: printf("Problem with resultfile: %s\n", fileresprobcov);
6484: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6485: }
6486: strcpy(fileresprobcor,"PROBCOR_");
6487: strcat(fileresprobcor,fileresu);
6488: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6489: printf("Problem with resultfile: %s\n", fileresprobcor);
6490: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6491: }
6492: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6493: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6494: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6495: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6496: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6497: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6498: pstamp(ficresprob);
6499: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6500: fprintf(ficresprob,"# Age");
6501: pstamp(ficresprobcov);
6502: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6503: fprintf(ficresprobcov,"# Age");
6504: pstamp(ficresprobcor);
6505: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6506: fprintf(ficresprobcor,"# Age");
1.126 brouard 6507:
6508:
1.222 brouard 6509: for(i=1; i<=nlstate;i++)
6510: for(j=1; j<=(nlstate+ndeath);j++){
6511: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6512: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6513: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6514: }
6515: /* fprintf(ficresprob,"\n");
6516: fprintf(ficresprobcov,"\n");
6517: fprintf(ficresprobcor,"\n");
6518: */
6519: xp=vector(1,npar);
6520: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6521: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6522: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6523: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6524: first=1;
6525: fprintf(ficgp,"\n# Routine varprob");
6526: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6527: fprintf(fichtm,"\n");
6528:
1.288 brouard 6529: 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 6530: 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);
6531: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6532: and drawn. It helps understanding how is the covariance between two incidences.\
6533: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6534: 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 6535: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6536: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6537: standard deviations wide on each axis. <br>\
6538: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6539: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6540: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6541:
1.222 brouard 6542: cov[1]=1;
6543: /* tj=cptcoveff; */
1.225 brouard 6544: tj = (int) pow(2,cptcoveff);
1.222 brouard 6545: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6546: j1=0;
1.224 brouard 6547: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6548: if (cptcovn>0) {
6549: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6550: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6551: fprintf(ficresprob, "**********\n#\n");
6552: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6553: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6554: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6555:
1.222 brouard 6556: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6557: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6558: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6559:
6560:
1.222 brouard 6561: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6562: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6563: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6564:
1.222 brouard 6565: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6566: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6567: fprintf(ficresprobcor, "**********\n#");
6568: if(invalidvarcomb[j1]){
6569: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6570: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6571: continue;
6572: }
6573: }
6574: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6575: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6576: gp=vector(1,(nlstate)*(nlstate+ndeath));
6577: gm=vector(1,(nlstate)*(nlstate+ndeath));
6578: for (age=bage; age<=fage; age ++){
6579: cov[2]=age;
6580: if(nagesqr==1)
6581: cov[3]= age*age;
6582: for (k=1; k<=cptcovn;k++) {
6583: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6584: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6585: * 1 1 1 1 1
6586: * 2 2 1 1 1
6587: * 3 1 2 1 1
6588: */
6589: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6590: }
6591: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6592: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6593: for (k=1; k<=cptcovprod;k++)
6594: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6595:
6596:
1.222 brouard 6597: for(theta=1; theta <=npar; theta++){
6598: for(i=1; i<=npar; i++)
6599: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6600:
1.222 brouard 6601: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6602:
1.222 brouard 6603: k=0;
6604: for(i=1; i<= (nlstate); i++){
6605: for(j=1; j<=(nlstate+ndeath);j++){
6606: k=k+1;
6607: gp[k]=pmmij[i][j];
6608: }
6609: }
1.220 brouard 6610:
1.222 brouard 6611: for(i=1; i<=npar; i++)
6612: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6613:
1.222 brouard 6614: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6615: k=0;
6616: for(i=1; i<=(nlstate); i++){
6617: for(j=1; j<=(nlstate+ndeath);j++){
6618: k=k+1;
6619: gm[k]=pmmij[i][j];
6620: }
6621: }
1.220 brouard 6622:
1.222 brouard 6623: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6624: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6625: }
1.126 brouard 6626:
1.222 brouard 6627: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6628: for(theta=1; theta <=npar; theta++)
6629: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6630:
1.222 brouard 6631: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6632: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6633:
1.222 brouard 6634: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6635:
1.222 brouard 6636: k=0;
6637: for(i=1; i<=(nlstate); i++){
6638: for(j=1; j<=(nlstate+ndeath);j++){
6639: k=k+1;
6640: mu[k][(int) age]=pmmij[i][j];
6641: }
6642: }
6643: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6644: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6645: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6646:
1.222 brouard 6647: /*printf("\n%d ",(int)age);
6648: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6649: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6650: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6651: }*/
1.220 brouard 6652:
1.222 brouard 6653: fprintf(ficresprob,"\n%d ",(int)age);
6654: fprintf(ficresprobcov,"\n%d ",(int)age);
6655: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6656:
1.222 brouard 6657: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6658: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6659: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6660: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6661: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6662: }
6663: i=0;
6664: for (k=1; k<=(nlstate);k++){
6665: for (l=1; l<=(nlstate+ndeath);l++){
6666: i++;
6667: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6668: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6669: for (j=1; j<=i;j++){
6670: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6671: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6672: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6673: }
6674: }
6675: }/* end of loop for state */
6676: } /* end of loop for age */
6677: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6678: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6679: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6680: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6681:
6682: /* Confidence intervalle of pij */
6683: /*
6684: fprintf(ficgp,"\nunset parametric;unset label");
6685: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6686: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6687: 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);
6688: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6689: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6690: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6691: */
6692:
6693: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6694: first1=1;first2=2;
6695: for (k2=1; k2<=(nlstate);k2++){
6696: for (l2=1; l2<=(nlstate+ndeath);l2++){
6697: if(l2==k2) continue;
6698: j=(k2-1)*(nlstate+ndeath)+l2;
6699: for (k1=1; k1<=(nlstate);k1++){
6700: for (l1=1; l1<=(nlstate+ndeath);l1++){
6701: if(l1==k1) continue;
6702: i=(k1-1)*(nlstate+ndeath)+l1;
6703: if(i<=j) continue;
6704: for (age=bage; age<=fage; age ++){
6705: if ((int)age %5==0){
6706: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6707: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6708: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6709: mu1=mu[i][(int) age]/stepm*YEARM ;
6710: mu2=mu[j][(int) age]/stepm*YEARM;
6711: c12=cv12/sqrt(v1*v2);
6712: /* Computing eigen value of matrix of covariance */
6713: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6714: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6715: if ((lc2 <0) || (lc1 <0) ){
6716: if(first2==1){
6717: first1=0;
6718: 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);
6719: }
6720: 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);
6721: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6722: /* lc2=fabs(lc2); */
6723: }
1.220 brouard 6724:
1.222 brouard 6725: /* Eigen vectors */
1.280 brouard 6726: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6727: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6728: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6729: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6730: }else
6731: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6732: /*v21=sqrt(1.-v11*v11); *//* error */
6733: v21=(lc1-v1)/cv12*v11;
6734: v12=-v21;
6735: v22=v11;
6736: tnalp=v21/v11;
6737: if(first1==1){
6738: first1=0;
6739: 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);
6740: }
6741: 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);
6742: /*printf(fignu*/
6743: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6744: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6745: if(first==1){
6746: first=0;
6747: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6748: fprintf(ficgp,"\nset parametric;unset label");
6749: 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);
6750: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6751: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6752: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6753: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6754: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6755: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6756: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6757: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6758: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6759: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6760: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6761: 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 6762: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6763: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6764: }else{
6765: first=0;
6766: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6767: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6768: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6769: 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 6770: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6771: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6772: }/* if first */
6773: } /* age mod 5 */
6774: } /* end loop age */
6775: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6776: first=1;
6777: } /*l12 */
6778: } /* k12 */
6779: } /*l1 */
6780: }/* k1 */
6781: } /* loop on combination of covariates j1 */
6782: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6783: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6784: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6785: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6786: free_vector(xp,1,npar);
6787: fclose(ficresprob);
6788: fclose(ficresprobcov);
6789: fclose(ficresprobcor);
6790: fflush(ficgp);
6791: fflush(fichtmcov);
6792: }
1.126 brouard 6793:
6794:
6795: /******************* Printing html file ***********/
1.201 brouard 6796: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6797: int lastpass, int stepm, int weightopt, char model[],\
6798: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.258 brouard 6799: int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
1.273 brouard 6800: double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
6801: double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
1.237 brouard 6802: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6803:
6804: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6805: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6806: </ul>");
1.237 brouard 6807: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6808: </ul>", model);
1.214 brouard 6809: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6810: 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",
6811: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6812: 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 6813: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6814: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6815: fprintf(fichtm,"\
6816: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6817: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6818: fprintf(fichtm,"\
1.217 brouard 6819: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6820: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6821: fprintf(fichtm,"\
1.288 brouard 6822: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6823: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6824: fprintf(fichtm,"\
1.288 brouard 6825: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6826: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6827: fprintf(fichtm,"\
1.211 brouard 6828: - (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 6829: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6830: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6831: if(prevfcast==1){
6832: fprintf(fichtm,"\
6833: - Prevalence projections by age and states: \
1.201 brouard 6834: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6835: }
1.126 brouard 6836:
6837:
1.225 brouard 6838: m=pow(2,cptcoveff);
1.222 brouard 6839: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6840:
1.264 brouard 6841: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6842:
6843: jj1=0;
6844:
6845: fprintf(fichtm," \n<ul>");
6846: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6847: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6848: if(m != 1 && TKresult[nres]!= k1)
6849: continue;
6850: jj1++;
6851: if (cptcovn > 0) {
6852: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6853: for (cpt=1; cpt<=cptcoveff;cpt++){
6854: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6855: }
6856: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6857: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6858: }
6859: fprintf(fichtm,"\">");
6860:
6861: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6862: fprintf(fichtm,"************ Results for covariates");
6863: for (cpt=1; cpt<=cptcoveff;cpt++){
6864: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6865: }
6866: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6867: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6868: }
6869: if(invalidvarcomb[k1]){
6870: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6871: continue;
6872: }
6873: fprintf(fichtm,"</a></li>");
6874: } /* cptcovn >0 */
6875: }
6876: fprintf(fichtm," \n</ul>");
6877:
1.222 brouard 6878: jj1=0;
1.237 brouard 6879:
6880: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6881: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6882: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6883: continue;
1.220 brouard 6884:
1.222 brouard 6885: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6886: jj1++;
6887: if (cptcovn > 0) {
1.264 brouard 6888: fprintf(fichtm,"\n<p><a name=\"rescov");
6889: for (cpt=1; cpt<=cptcoveff;cpt++){
6890: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6891: }
6892: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6893: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6894: }
6895: fprintf(fichtm,"\"</a>");
6896:
1.222 brouard 6897: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6898: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6899: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6900: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6901: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6902: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6903: }
1.237 brouard 6904: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6905: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6906: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6907: }
6908:
1.230 brouard 6909: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6910: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6911: if(invalidvarcomb[k1]){
6912: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6913: printf("\nCombination (%d) ignored because no cases \n",k1);
6914: continue;
6915: }
6916: }
6917: /* aij, bij */
1.259 brouard 6918: 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 6919: <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 6920: /* Pij */
1.241 brouard 6921: 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> \
6922: <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 6923: /* Quasi-incidences */
6924: 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 6925: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6926: 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 6927: 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> \
6928: <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 6929: /* Survival functions (period) in state j */
6930: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6931: fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive 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> \
6932: <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 6933: }
6934: /* State specific survival functions (period) */
6935: for(cpt=1; cpt<=nlstate;cpt++){
6936: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6937: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.283 brouard 6938: <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 6939: }
1.288 brouard 6940: /* Period (forward stable) prevalence in each health state */
1.222 brouard 6941: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6942: 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> \
6943: <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 6944: }
6945: if(backcast==1){
1.288 brouard 6946: /* Backward prevalence in each health state */
1.222 brouard 6947: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6948: 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 6949: <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 6950: }
1.217 brouard 6951: }
1.222 brouard 6952: if(prevfcast==1){
1.288 brouard 6953: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 6954: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 6955: 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> \
1.273 brouard 6956: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 6957: }
6958: }
1.268 brouard 6959: if(backcast==1){
6960: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
6961: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6962: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
6963: 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 \
6964: 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) \
6965: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
6966: <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 6967: }
6968: }
1.220 brouard 6969:
1.222 brouard 6970: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 6971: 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> \
6972: <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 6973: }
6974: /* } /\* end i1 *\/ */
6975: }/* End k1 */
6976: fprintf(fichtm,"</ul>");
1.126 brouard 6977:
1.222 brouard 6978: fprintf(fichtm,"\
1.126 brouard 6979: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6980: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6981: - 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 6982: But because parameters are usually highly correlated (a higher incidence of disability \
6983: and a higher incidence of recovery can give very close observed transition) it might \
6984: be very useful to look not only at linear confidence intervals estimated from the \
6985: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6986: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6987: covariance matrix of the one-step probabilities. \
6988: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6989:
1.222 brouard 6990: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6991: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6992: fprintf(fichtm,"\
1.126 brouard 6993: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6994: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6995:
1.222 brouard 6996: fprintf(fichtm,"\
1.126 brouard 6997: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6998: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6999: fprintf(fichtm,"\
1.126 brouard 7000: - 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): \
7001: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7002: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7003: fprintf(fichtm,"\
1.126 brouard 7004: - (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): \
7005: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7006: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7007: fprintf(fichtm,"\
1.288 brouard 7008: - 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 7009: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7010: fprintf(fichtm,"\
1.128 brouard 7011: - 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 7012: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7013: fprintf(fichtm,"\
1.288 brouard 7014: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7015: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7016:
7017: /* if(popforecast==1) fprintf(fichtm,"\n */
7018: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7019: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7020: /* <br>",fileres,fileres,fileres,fileres); */
7021: /* else */
7022: /* 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 7023: fflush(fichtm);
7024: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7025:
1.225 brouard 7026: m=pow(2,cptcoveff);
1.222 brouard 7027: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7028:
1.222 brouard 7029: jj1=0;
1.237 brouard 7030:
1.241 brouard 7031: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7032: for(k1=1; k1<=m;k1++){
1.253 brouard 7033: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7034: continue;
1.222 brouard 7035: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7036: jj1++;
1.126 brouard 7037: if (cptcovn > 0) {
7038: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7039: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7040: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7041: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7042: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7043: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7044: }
7045:
1.126 brouard 7046: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7047:
1.222 brouard 7048: if(invalidvarcomb[k1]){
7049: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7050: continue;
7051: }
1.126 brouard 7052: }
7053: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7054: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7055: 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 7056: <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 7057: }
7058: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7059: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7060: true period expectancies (those weighted with period prevalences are also\
7061: drawn in addition to the population based expectancies computed using\
1.241 brouard 7062: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7063: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7064: /* } /\* end i1 *\/ */
7065: }/* End k1 */
1.241 brouard 7066: }/* End nres */
1.222 brouard 7067: fprintf(fichtm,"</ul>");
7068: fflush(fichtm);
1.126 brouard 7069: }
7070:
7071: /******************* Gnuplot file **************/
1.270 brouard 7072: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
1.126 brouard 7073:
7074: char dirfileres[132],optfileres[132];
1.264 brouard 7075: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7076: 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 7077: int lv=0, vlv=0, kl=0;
1.130 brouard 7078: int ng=0;
1.201 brouard 7079: int vpopbased;
1.223 brouard 7080: int ioffset; /* variable offset for columns */
1.270 brouard 7081: int iyearc=1; /* variable column for year of projection */
7082: int iagec=1; /* variable column for age of projection */
1.235 brouard 7083: int nres=0; /* Index of resultline */
1.266 brouard 7084: int istart=1; /* For starting graphs in projections */
1.219 brouard 7085:
1.126 brouard 7086: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7087: /* printf("Problem with file %s",optionfilegnuplot); */
7088: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7089: /* } */
7090:
7091: /*#ifdef windows */
7092: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7093: /*#endif */
1.225 brouard 7094: m=pow(2,cptcoveff);
1.126 brouard 7095:
1.274 brouard 7096: /* diagram of the model */
7097: fprintf(ficgp,"\n#Diagram of the model \n");
7098: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7099: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7100: 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);
7101:
7102: 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);
7103: fprintf(ficgp,"\n#show arrow\nunset label\n");
7104: 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);
7105: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7106: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7107: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7108: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7109:
1.202 brouard 7110: /* Contribution to likelihood */
7111: /* Plot the probability implied in the likelihood */
1.223 brouard 7112: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7113: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7114: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7115: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7116: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7117: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7118: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7119: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7120: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7121: 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));
7122: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7123: 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));
7124: for (i=1; i<= nlstate ; i ++) {
7125: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7126: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7127: 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);
7128: for (j=2; j<= nlstate+ndeath ; j ++) {
7129: 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);
7130: }
7131: fprintf(ficgp,";\nset out; unset ylabel;\n");
7132: }
7133: /* 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 */
7134: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7135: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7136: fprintf(ficgp,"\nset out;unset log\n");
7137: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7138:
1.126 brouard 7139: strcpy(dirfileres,optionfilefiname);
7140: strcpy(optfileres,"vpl");
1.223 brouard 7141: /* 1eme*/
1.238 brouard 7142: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7143: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7144: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7145: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7146: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7147: continue;
7148: /* We are interested in selected combination by the resultline */
1.246 brouard 7149: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7150: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7151: strcpy(gplotlabel,"(");
1.238 brouard 7152: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7153: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7154: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7155: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7156: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7157: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7158: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7159: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7160: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7161: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7162: }
7163: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7164: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7165: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7166: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7167: }
7168: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7169: /* printf("\n#\n"); */
1.238 brouard 7170: fprintf(ficgp,"\n#\n");
7171: if(invalidvarcomb[k1]){
1.260 brouard 7172: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7173: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7174: continue;
7175: }
1.235 brouard 7176:
1.241 brouard 7177: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7178: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7179: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7180: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7181: 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);
7182: /* 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); */
7183: /* k1-1 error should be nres-1*/
1.238 brouard 7184: for (i=1; i<= nlstate ; i ++) {
7185: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7186: else fprintf(ficgp," %%*lf (%%*lf)");
7187: }
1.288 brouard 7188: 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 7189: for (i=1; i<= nlstate ; i ++) {
7190: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7191: else fprintf(ficgp," %%*lf (%%*lf)");
7192: }
1.260 brouard 7193: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7194: for (i=1; i<= nlstate ; i ++) {
7195: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7196: else fprintf(ficgp," %%*lf (%%*lf)");
7197: }
1.265 brouard 7198: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7199:
7200: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7201: if(cptcoveff ==0){
1.271 brouard 7202: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7203: }else{
7204: kl=0;
7205: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7206: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7207: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7208: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7209: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7210: vlv= nbcode[Tvaraff[k]][lv];
7211: kl++;
7212: /* 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 *\/ */
7213: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7214: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7215: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7216: if(k==cptcoveff){
7217: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7218: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7219: }else{
7220: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7221: kl++;
7222: }
7223: } /* end covariate */
7224: } /* end if no covariate */
7225:
1.238 brouard 7226: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
7227: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7228: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7229: if(cptcoveff ==0){
1.245 brouard 7230: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7231: }else{
7232: kl=0;
7233: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7234: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7235: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7236: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7237: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7238: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7239: kl++;
1.238 brouard 7240: /* 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 *\/ */
7241: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7242: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7243: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7244: if(k==cptcoveff){
1.245 brouard 7245: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7246: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7247: }else{
7248: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7249: kl++;
7250: }
7251: } /* end covariate */
7252: } /* end if no covariate */
1.268 brouard 7253: if(backcast == 1){
7254: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7255: /* k1-1 error should be nres-1*/
7256: for (i=1; i<= nlstate ; i ++) {
7257: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7258: else fprintf(ficgp," %%*lf (%%*lf)");
7259: }
1.271 brouard 7260: 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 7261: for (i=1; i<= nlstate ; i ++) {
7262: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7263: else fprintf(ficgp," %%*lf (%%*lf)");
7264: }
1.276 brouard 7265: 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 7266: for (i=1; i<= nlstate ; i ++) {
7267: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7268: else fprintf(ficgp," %%*lf (%%*lf)");
7269: }
1.274 brouard 7270: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7271: } /* end if backprojcast */
1.238 brouard 7272: } /* end if backcast */
1.276 brouard 7273: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7274: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7275: } /* nres */
1.201 brouard 7276: } /* k1 */
7277: } /* cpt */
1.235 brouard 7278:
7279:
1.126 brouard 7280: /*2 eme*/
1.238 brouard 7281: for (k1=1; k1<= m ; k1 ++){
7282: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7283: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7284: continue;
7285: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7286: strcpy(gplotlabel,"(");
1.238 brouard 7287: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7288: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7289: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7290: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7291: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7292: vlv= nbcode[Tvaraff[k]][lv];
7293: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7294: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7295: }
1.237 brouard 7296: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7297: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7298: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7299: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7300: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7301: }
1.264 brouard 7302: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7303: fprintf(ficgp,"\n#\n");
1.223 brouard 7304: if(invalidvarcomb[k1]){
7305: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7306: continue;
7307: }
1.219 brouard 7308:
1.241 brouard 7309: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7310: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7311: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7312: if(vpopbased==0){
1.238 brouard 7313: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7314: }else
1.238 brouard 7315: fprintf(ficgp,"\nreplot ");
7316: for (i=1; i<= nlstate+1 ; i ++) {
7317: k=2*i;
1.261 brouard 7318: 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 7319: for (j=1; j<= nlstate+1 ; j ++) {
7320: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7321: else fprintf(ficgp," %%*lf (%%*lf)");
7322: }
7323: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7324: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7325: 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 7326: for (j=1; j<= nlstate+1 ; j ++) {
7327: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7328: else fprintf(ficgp," %%*lf (%%*lf)");
7329: }
7330: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7331: 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 7332: for (j=1; j<= nlstate+1 ; j ++) {
7333: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7334: else fprintf(ficgp," %%*lf (%%*lf)");
7335: }
7336: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7337: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7338: } /* state */
7339: } /* vpopbased */
1.264 brouard 7340: 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 7341: } /* end nres */
7342: } /* k1 end 2 eme*/
7343:
7344:
7345: /*3eme*/
7346: for (k1=1; k1<= m ; k1 ++){
7347: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7348: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7349: continue;
7350:
7351: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7352: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7353: strcpy(gplotlabel,"(");
1.238 brouard 7354: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7355: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7356: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7357: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7358: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7359: vlv= nbcode[Tvaraff[k]][lv];
7360: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7361: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7362: }
7363: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7364: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7365: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7366: }
1.264 brouard 7367: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7368: fprintf(ficgp,"\n#\n");
7369: if(invalidvarcomb[k1]){
7370: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7371: continue;
7372: }
7373:
7374: /* k=2+nlstate*(2*cpt-2); */
7375: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7376: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7377: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7378: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7379: 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 7380: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7381: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7382: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7383: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7384: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7385: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7386:
1.238 brouard 7387: */
7388: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7389: 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 7390: /* 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 7391:
1.238 brouard 7392: }
1.261 brouard 7393: 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 7394: }
1.264 brouard 7395: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7396: } /* end nres */
7397: } /* end kl 3eme */
1.126 brouard 7398:
1.223 brouard 7399: /* 4eme */
1.201 brouard 7400: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7401: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7402: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7403: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7404: continue;
1.238 brouard 7405: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7406: strcpy(gplotlabel,"(");
1.238 brouard 7407: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7408: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7409: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7410: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7411: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7412: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7413: vlv= nbcode[Tvaraff[k]][lv];
7414: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7415: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7416: }
7417: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7418: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7419: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7420: }
1.264 brouard 7421: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7422: fprintf(ficgp,"\n#\n");
7423: if(invalidvarcomb[k1]){
7424: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7425: continue;
1.223 brouard 7426: }
1.238 brouard 7427:
1.241 brouard 7428: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7429: 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 7430: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7431: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7432: k=3;
7433: for (i=1; i<= nlstate ; i ++){
7434: if(i==1){
7435: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7436: }else{
7437: fprintf(ficgp,", '' ");
7438: }
7439: l=(nlstate+ndeath)*(i-1)+1;
7440: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7441: for (j=2; j<= nlstate+ndeath ; j ++)
7442: fprintf(ficgp,"+$%d",k+l+j-1);
7443: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7444: } /* nlstate */
1.264 brouard 7445: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7446: } /* end cpt state*/
7447: } /* end nres */
7448: } /* end covariate k1 */
7449:
1.220 brouard 7450: /* 5eme */
1.201 brouard 7451: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7452: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7453: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7454: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7455: continue;
1.238 brouard 7456: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7457: strcpy(gplotlabel,"(");
1.238 brouard 7458: 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);
7459: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7460: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7461: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7462: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7463: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7464: vlv= nbcode[Tvaraff[k]][lv];
7465: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7466: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7467: }
7468: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7469: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7470: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7471: }
1.264 brouard 7472: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7473: fprintf(ficgp,"\n#\n");
7474: if(invalidvarcomb[k1]){
7475: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7476: continue;
7477: }
1.227 brouard 7478:
1.241 brouard 7479: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7480: 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 7481: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7482: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7483: k=3;
7484: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7485: if(j==1)
7486: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7487: else
7488: fprintf(ficgp,", '' ");
7489: l=(nlstate+ndeath)*(cpt-1) +j;
7490: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7491: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7492: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7493: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7494: } /* nlstate */
7495: fprintf(ficgp,", '' ");
7496: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7497: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7498: l=(nlstate+ndeath)*(cpt-1) +j;
7499: if(j < nlstate)
7500: fprintf(ficgp,"$%d +",k+l);
7501: else
7502: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7503: }
1.264 brouard 7504: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7505: } /* end cpt state*/
7506: } /* end covariate */
7507: } /* end nres */
1.227 brouard 7508:
1.220 brouard 7509: /* 6eme */
1.202 brouard 7510: /* CV preval stable (period) for each covariate */
1.237 brouard 7511: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7512: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7513: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7514: continue;
1.255 brouard 7515: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7516: strcpy(gplotlabel,"(");
1.288 brouard 7517: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7518: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7519: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7520: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7521: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7522: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7523: vlv= nbcode[Tvaraff[k]][lv];
7524: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7525: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7526: }
1.237 brouard 7527: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7528: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7529: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7530: }
1.264 brouard 7531: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7532: fprintf(ficgp,"\n#\n");
1.223 brouard 7533: if(invalidvarcomb[k1]){
1.227 brouard 7534: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7535: continue;
1.223 brouard 7536: }
1.227 brouard 7537:
1.241 brouard 7538: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7539: 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 7540: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7541: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7542: k=3; /* Offset */
1.255 brouard 7543: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7544: if(i==1)
7545: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7546: else
7547: fprintf(ficgp,", '' ");
1.255 brouard 7548: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7549: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7550: for (j=2; j<= nlstate ; j ++)
7551: fprintf(ficgp,"+$%d",k+l+j-1);
7552: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7553: } /* nlstate */
1.264 brouard 7554: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7555: } /* end cpt state*/
7556: } /* end covariate */
1.227 brouard 7557:
7558:
1.220 brouard 7559: /* 7eme */
1.218 brouard 7560: if(backcast == 1){
1.288 brouard 7561: /* CV backward prevalence for each covariate */
1.237 brouard 7562: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7563: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7564: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7565: continue;
1.268 brouard 7566: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7567: strcpy(gplotlabel,"(");
1.288 brouard 7568: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7569: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7570: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7571: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7572: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7573: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7574: vlv= nbcode[Tvaraff[k]][lv];
7575: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7576: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7577: }
1.237 brouard 7578: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7579: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7580: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7581: }
1.264 brouard 7582: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7583: fprintf(ficgp,"\n#\n");
7584: if(invalidvarcomb[k1]){
7585: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7586: continue;
7587: }
7588:
1.241 brouard 7589: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7590: 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 7591: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7592: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7593: k=3; /* Offset */
1.268 brouard 7594: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7595: if(i==1)
7596: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7597: else
7598: fprintf(ficgp,", '' ");
7599: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7600: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7601: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7602: /* 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 7603: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7604: /* for (j=2; j<= nlstate ; j ++) */
7605: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7606: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7607: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7608: } /* nlstate */
1.264 brouard 7609: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7610: } /* end cpt state*/
7611: } /* end covariate */
7612: } /* End if backcast */
7613:
1.223 brouard 7614: /* 8eme */
1.218 brouard 7615: if(prevfcast==1){
1.288 brouard 7616: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7617:
1.237 brouard 7618: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7619: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7620: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7621: continue;
1.211 brouard 7622: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7623: strcpy(gplotlabel,"(");
1.288 brouard 7624: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7625: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7626: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7627: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7628: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7629: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7630: vlv= nbcode[Tvaraff[k]][lv];
7631: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7632: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7633: }
1.237 brouard 7634: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7635: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7636: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7637: }
1.264 brouard 7638: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7639: fprintf(ficgp,"\n#\n");
7640: if(invalidvarcomb[k1]){
7641: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7642: continue;
7643: }
7644:
7645: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7646: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7647: 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 7648: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7649: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7650:
7651: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7652: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7653: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7654: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7655: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7656: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7657: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7658: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7659: if(i==istart){
1.227 brouard 7660: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7661: }else{
7662: fprintf(ficgp,",\\\n '' ");
7663: }
7664: if(cptcoveff ==0){ /* No covariate */
7665: ioffset=2; /* Age is in 2 */
7666: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7667: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7668: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7669: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7670: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7671: if(i==nlstate+1){
1.270 brouard 7672: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7673: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7674: fprintf(ficgp,",\\\n '' ");
7675: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7676: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7677: offyear, \
1.268 brouard 7678: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7679: }else
1.227 brouard 7680: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7681: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7682: }else{ /* more than 2 covariates */
1.270 brouard 7683: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7684: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7685: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7686: iyearc=ioffset-1;
7687: iagec=ioffset;
1.227 brouard 7688: fprintf(ficgp," u %d:(",ioffset);
7689: kl=0;
7690: strcpy(gplotcondition,"(");
7691: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7692: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7693: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7694: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7695: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7696: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7697: kl++;
7698: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7699: kl++;
7700: if(k <cptcoveff && cptcoveff>1)
7701: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7702: }
7703: strcpy(gplotcondition+strlen(gplotcondition),")");
7704: /* 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 *\/ */
7705: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7706: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7707: /* '' 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*/
7708: if(i==nlstate+1){
1.270 brouard 7709: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7710: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7711: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7712: fprintf(ficgp," u %d:(",iagec);
7713: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7714: iyearc, iagec, offyear, \
7715: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7716: /* '' 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 7717: }else{
7718: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7719: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7720: }
7721: } /* end if covariate */
7722: } /* nlstate */
1.264 brouard 7723: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7724: } /* end cpt state*/
7725: } /* end covariate */
7726: } /* End if prevfcast */
1.227 brouard 7727:
1.268 brouard 7728: if(backcast==1){
7729: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7730:
7731: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7732: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7733: if(m != 1 && TKresult[nres]!= k1)
7734: continue;
7735: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7736: strcpy(gplotlabel,"(");
7737: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7738: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7739: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7740: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7741: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7742: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7743: vlv= nbcode[Tvaraff[k]][lv];
7744: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7745: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7746: }
7747: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7748: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7749: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7750: }
7751: strcpy(gplotlabel+strlen(gplotlabel),")");
7752: fprintf(ficgp,"\n#\n");
7753: if(invalidvarcomb[k1]){
7754: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7755: continue;
7756: }
7757:
7758: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7759: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7760: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7761: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7762: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7763:
7764: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7765: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7766: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7767: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7768: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7769: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7770: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7771: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7772: if(i==istart){
7773: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7774: }else{
7775: fprintf(ficgp,",\\\n '' ");
7776: }
7777: if(cptcoveff ==0){ /* No covariate */
7778: ioffset=2; /* Age is in 2 */
7779: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7780: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7781: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7782: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7783: fprintf(ficgp," u %d:(", ioffset);
7784: if(i==nlstate+1){
1.270 brouard 7785: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7786: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7787: fprintf(ficgp,",\\\n '' ");
7788: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7789: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7790: offbyear, \
7791: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7792: }else
7793: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7794: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7795: }else{ /* more than 2 covariates */
1.270 brouard 7796: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7797: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7798: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7799: iyearc=ioffset-1;
7800: iagec=ioffset;
1.268 brouard 7801: fprintf(ficgp," u %d:(",ioffset);
7802: kl=0;
7803: strcpy(gplotcondition,"(");
7804: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7805: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7806: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7807: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7808: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7809: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7810: kl++;
7811: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7812: kl++;
7813: if(k <cptcoveff && cptcoveff>1)
7814: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7815: }
7816: strcpy(gplotcondition+strlen(gplotcondition),")");
7817: /* 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 *\/ */
7818: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7819: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7820: /* '' 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*/
7821: if(i==nlstate+1){
1.270 brouard 7822: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7823: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7824: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7825: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7826: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7827: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7828: iyearc,iagec,offbyear, \
7829: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7830: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7831: }else{
7832: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7833: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7834: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7835: }
7836: } /* end if covariate */
7837: } /* nlstate */
7838: fprintf(ficgp,"\nset out; unset label;\n");
7839: } /* end cpt state*/
7840: } /* end covariate */
7841: } /* End if backcast */
7842:
1.227 brouard 7843:
1.238 brouard 7844: /* 9eme writing MLE parameters */
7845: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7846: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7847: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7848: for(k=1; k <=(nlstate+ndeath); k++){
7849: if (k != i) {
1.227 brouard 7850: fprintf(ficgp,"# current state %d\n",k);
7851: for(j=1; j <=ncovmodel; j++){
7852: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7853: jk++;
7854: }
7855: fprintf(ficgp,"\n");
1.126 brouard 7856: }
7857: }
1.223 brouard 7858: }
1.187 brouard 7859: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7860:
1.145 brouard 7861: /*goto avoid;*/
1.238 brouard 7862: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7863: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7864: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7865: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7866: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7867: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7868: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7869: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7870: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7871: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7872: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7873: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7874: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7875: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7876: fprintf(ficgp,"#\n");
1.223 brouard 7877: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7878: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7879: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7880: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7881: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7882: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7883: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7884: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7885: continue;
1.264 brouard 7886: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7887: strcpy(gplotlabel,"(");
1.276 brouard 7888: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7889: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7890: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7891: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7892: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7893: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7894: vlv= nbcode[Tvaraff[k]][lv];
7895: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7896: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7897: }
1.237 brouard 7898: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7899: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7900: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7901: }
1.264 brouard 7902: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7903: fprintf(ficgp,"\n#\n");
1.264 brouard 7904: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7905: fprintf(ficgp,"\nset key outside ");
7906: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7907: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7908: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7909: if (ng==1){
7910: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7911: fprintf(ficgp,"\nunset log y");
7912: }else if (ng==2){
7913: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7914: fprintf(ficgp,"\nset log y");
7915: }else if (ng==3){
7916: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7917: fprintf(ficgp,"\nset log y");
7918: }else
7919: fprintf(ficgp,"\nunset title ");
7920: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7921: i=1;
7922: for(k2=1; k2<=nlstate; k2++) {
7923: k3=i;
7924: for(k=1; k<=(nlstate+ndeath); k++) {
7925: if (k != k2){
7926: switch( ng) {
7927: case 1:
7928: if(nagesqr==0)
7929: fprintf(ficgp," p%d+p%d*x",i,i+1);
7930: else /* nagesqr =1 */
7931: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7932: break;
7933: case 2: /* ng=2 */
7934: if(nagesqr==0)
7935: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7936: else /* nagesqr =1 */
7937: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7938: break;
7939: case 3:
7940: if(nagesqr==0)
7941: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7942: else /* nagesqr =1 */
7943: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7944: break;
7945: }
7946: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7947: ijp=1; /* product no age */
7948: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7949: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7950: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 7951: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7952: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
7953: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7954: if(DummyV[j]==0){
7955: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
7956: }else{ /* quantitative */
7957: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
7958: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7959: }
7960: ij++;
1.237 brouard 7961: }
1.268 brouard 7962: }
7963: }else if(cptcovprod >0){
7964: if(j==Tprod[ijp]) { /* */
7965: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
7966: if(ijp <=cptcovprod) { /* Product */
7967: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
7968: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
7969: /* 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)]); */
7970: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
7971: }else{ /* Vn is dummy and Vm is quanti */
7972: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
7973: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7974: }
7975: }else{ /* Vn*Vm Vn is quanti */
7976: if(DummyV[Tvard[ijp][2]]==0){
7977: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
7978: }else{ /* Both quanti */
7979: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7980: }
1.237 brouard 7981: }
1.268 brouard 7982: ijp++;
1.237 brouard 7983: }
1.268 brouard 7984: } /* end Tprod */
1.237 brouard 7985: } else{ /* simple covariate */
1.264 brouard 7986: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 7987: if(Dummy[j]==0){
7988: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
7989: }else{ /* quantitative */
7990: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 7991: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 7992: }
1.237 brouard 7993: } /* end simple */
7994: } /* end j */
1.223 brouard 7995: }else{
7996: i=i-ncovmodel;
7997: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
7998: fprintf(ficgp," (1.");
7999: }
1.227 brouard 8000:
1.223 brouard 8001: if(ng != 1){
8002: fprintf(ficgp,")/(1");
1.227 brouard 8003:
1.264 brouard 8004: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8005: if(nagesqr==0)
1.264 brouard 8006: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8007: else /* nagesqr =1 */
1.264 brouard 8008: 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 8009:
1.223 brouard 8010: ij=1;
8011: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8012: if(cptcovage >0){
8013: if((j-2)==Tage[ij]) { /* Bug valgrind */
8014: if(ij <=cptcovage) { /* Bug valgrind */
8015: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8016: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8017: ij++;
8018: }
8019: }
8020: }else
8021: 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 8022: }
8023: fprintf(ficgp,")");
8024: }
8025: fprintf(ficgp,")");
8026: if(ng ==2)
1.276 brouard 8027: 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 8028: else /* ng= 3 */
1.276 brouard 8029: 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 8030: }else{ /* end ng <> 1 */
8031: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8032: 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 8033: }
8034: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8035: fprintf(ficgp,",");
8036: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8037: fprintf(ficgp,",");
8038: i=i+ncovmodel;
8039: } /* end k */
8040: } /* end k2 */
1.276 brouard 8041: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8042: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8043: } /* end k1 */
1.223 brouard 8044: } /* end ng */
8045: /* avoid: */
8046: fflush(ficgp);
1.126 brouard 8047: } /* end gnuplot */
8048:
8049:
8050: /*************** Moving average **************/
1.219 brouard 8051: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8052: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8053:
1.222 brouard 8054: int i, cpt, cptcod;
8055: int modcovmax =1;
8056: int mobilavrange, mob;
8057: int iage=0;
1.288 brouard 8058: int firstA1=0, firstA2=0;
1.222 brouard 8059:
1.266 brouard 8060: double sum=0., sumr=0.;
1.222 brouard 8061: double age;
1.266 brouard 8062: double *sumnewp, *sumnewm, *sumnewmr;
8063: double *agemingood, *agemaxgood;
8064: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8065:
8066:
1.278 brouard 8067: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8068: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8069:
8070: sumnewp = vector(1,ncovcombmax);
8071: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8072: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8073: agemingood = vector(1,ncovcombmax);
1.266 brouard 8074: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8075: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8076: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8077:
8078: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8079: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8080: sumnewp[cptcod]=0.;
1.266 brouard 8081: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8082: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8083: }
8084: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8085:
1.266 brouard 8086: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8087: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8088: else mobilavrange=mobilav;
8089: for (age=bage; age<=fage; age++)
8090: for (i=1; i<=nlstate;i++)
8091: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8092: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8093: /* We keep the original values on the extreme ages bage, fage and for
8094: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8095: we use a 5 terms etc. until the borders are no more concerned.
8096: */
8097: for (mob=3;mob <=mobilavrange;mob=mob+2){
8098: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8099: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8100: sumnewm[cptcod]=0.;
8101: for (i=1; i<=nlstate;i++){
1.222 brouard 8102: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8103: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8104: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8105: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8106: }
8107: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8108: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8109: } /* end i */
8110: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8111: } /* end cptcod */
1.222 brouard 8112: }/* end age */
8113: }/* end mob */
1.266 brouard 8114: }else{
8115: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8116: return -1;
1.266 brouard 8117: }
8118:
8119: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8120: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8121: if(invalidvarcomb[cptcod]){
8122: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8123: continue;
8124: }
1.219 brouard 8125:
1.266 brouard 8126: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8127: sumnewm[cptcod]=0.;
8128: sumnewmr[cptcod]=0.;
8129: for (i=1; i<=nlstate;i++){
8130: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8131: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8132: }
8133: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8134: agemingoodr[cptcod]=age;
8135: }
8136: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8137: agemingood[cptcod]=age;
8138: }
8139: } /* age */
8140: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8141: sumnewm[cptcod]=0.;
1.266 brouard 8142: sumnewmr[cptcod]=0.;
1.222 brouard 8143: for (i=1; i<=nlstate;i++){
8144: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8145: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8146: }
8147: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8148: agemaxgoodr[cptcod]=age;
1.222 brouard 8149: }
8150: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8151: agemaxgood[cptcod]=age;
8152: }
8153: } /* age */
8154: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8155: /* but they will change */
1.288 brouard 8156: firstA1=0;firstA2=0;
1.266 brouard 8157: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8158: sumnewm[cptcod]=0.;
8159: sumnewmr[cptcod]=0.;
8160: for (i=1; i<=nlstate;i++){
8161: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8162: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8163: }
8164: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8165: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8166: agemaxgoodr[cptcod]=age; /* age min */
8167: for (i=1; i<=nlstate;i++)
8168: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8169: }else{ /* bad we change the value with the values of good ages */
8170: for (i=1; i<=nlstate;i++){
8171: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8172: } /* i */
8173: } /* end bad */
8174: }else{
8175: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8176: agemaxgood[cptcod]=age;
8177: }else{ /* bad we change the value with the values of good ages */
8178: for (i=1; i<=nlstate;i++){
8179: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8180: } /* i */
8181: } /* end bad */
8182: }/* end else */
8183: sum=0.;sumr=0.;
8184: for (i=1; i<=nlstate;i++){
8185: sum+=mobaverage[(int)age][i][cptcod];
8186: sumr+=probs[(int)age][i][cptcod];
8187: }
8188: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8189: if(!firstA1){
8190: firstA1=1;
8191: 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);
8192: }
8193: 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 8194: } /* end bad */
8195: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8196: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8197: if(!firstA2){
8198: firstA2=1;
8199: 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);
8200: }
8201: 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 8202: } /* end bad */
8203: }/* age */
1.266 brouard 8204:
8205: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8206: sumnewm[cptcod]=0.;
1.266 brouard 8207: sumnewmr[cptcod]=0.;
1.222 brouard 8208: for (i=1; i<=nlstate;i++){
8209: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8210: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8211: }
8212: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8213: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8214: agemingoodr[cptcod]=age;
8215: for (i=1; i<=nlstate;i++)
8216: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8217: }else{ /* bad we change the value with the values of good ages */
8218: for (i=1; i<=nlstate;i++){
8219: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8220: } /* i */
8221: } /* end bad */
8222: }else{
8223: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8224: agemingood[cptcod]=age;
8225: }else{ /* bad */
8226: for (i=1; i<=nlstate;i++){
8227: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8228: } /* i */
8229: } /* end bad */
8230: }/* end else */
8231: sum=0.;sumr=0.;
8232: for (i=1; i<=nlstate;i++){
8233: sum+=mobaverage[(int)age][i][cptcod];
8234: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8235: }
1.266 brouard 8236: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8237: 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 8238: } /* end bad */
8239: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8240: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8241: 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 8242: } /* end bad */
8243: }/* age */
1.266 brouard 8244:
1.222 brouard 8245:
8246: for (age=bage; age<=fage; age++){
1.235 brouard 8247: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8248: sumnewp[cptcod]=0.;
8249: sumnewm[cptcod]=0.;
8250: for (i=1; i<=nlstate;i++){
8251: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8252: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8253: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8254: }
8255: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8256: }
8257: /* printf("\n"); */
8258: /* } */
1.266 brouard 8259:
1.222 brouard 8260: /* brutal averaging */
1.266 brouard 8261: /* for (i=1; i<=nlstate;i++){ */
8262: /* for (age=1; age<=bage; age++){ */
8263: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8264: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8265: /* } */
8266: /* for (age=fage; age<=AGESUP; age++){ */
8267: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8268: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8269: /* } */
8270: /* } /\* end i status *\/ */
8271: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8272: /* for (age=1; age<=AGESUP; age++){ */
8273: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8274: /* mobaverage[(int)age][i][cptcod]=0.; */
8275: /* } */
8276: /* } */
1.222 brouard 8277: }/* end cptcod */
1.266 brouard 8278: free_vector(agemaxgoodr,1, ncovcombmax);
8279: free_vector(agemaxgood,1, ncovcombmax);
8280: free_vector(agemingood,1, ncovcombmax);
8281: free_vector(agemingoodr,1, ncovcombmax);
8282: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8283: free_vector(sumnewm,1, ncovcombmax);
8284: free_vector(sumnewp,1, ncovcombmax);
8285: return 0;
8286: }/* End movingaverage */
1.218 brouard 8287:
1.126 brouard 8288:
8289: /************** Forecasting ******************/
1.269 brouard 8290: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 8291: /* proj1, year, month, day of starting projection
8292: agemin, agemax range of age
8293: dateprev1 dateprev2 range of dates during which prevalence is computed
8294: anproj2 year of en of projection (same day and month as proj1).
8295: */
1.267 brouard 8296: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8297: double agec; /* generic age */
8298: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
8299: double *popeffectif,*popcount;
8300: double ***p3mat;
1.218 brouard 8301: /* double ***mobaverage; */
1.126 brouard 8302: char fileresf[FILENAMELENGTH];
8303:
8304: agelim=AGESUP;
1.211 brouard 8305: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8306: in each health status at the date of interview (if between dateprev1 and dateprev2).
8307: We still use firstpass and lastpass as another selection.
8308: */
1.214 brouard 8309: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8310: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8311:
1.201 brouard 8312: strcpy(fileresf,"F_");
8313: strcat(fileresf,fileresu);
1.126 brouard 8314: if((ficresf=fopen(fileresf,"w"))==NULL) {
8315: printf("Problem with forecast resultfile: %s\n", fileresf);
8316: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8317: }
1.235 brouard 8318: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8319: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8320:
1.225 brouard 8321: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8322:
8323:
8324: stepsize=(int) (stepm+YEARM-1)/YEARM;
8325: if (stepm<=12) stepsize=1;
8326: if(estepm < stepm){
8327: printf ("Problem %d lower than %d\n",estepm, stepm);
8328: }
1.270 brouard 8329: else{
8330: hstepm=estepm;
8331: }
8332: if(estepm > stepm){ /* Yes every two year */
8333: stepsize=2;
8334: }
1.126 brouard 8335:
8336: hstepm=hstepm/stepm;
8337: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8338: fractional in yp1 */
8339: anprojmean=yp;
8340: yp2=modf((yp1*12),&yp);
8341: mprojmean=yp;
8342: yp1=modf((yp2*30.5),&yp);
8343: jprojmean=yp;
8344: if(jprojmean==0) jprojmean=1;
8345: if(mprojmean==0) jprojmean=1;
8346:
1.227 brouard 8347: i1=pow(2,cptcoveff);
1.126 brouard 8348: if (cptcovn < 1){i1=1;}
8349:
8350: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
8351:
8352: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8353:
1.126 brouard 8354: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8355: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8356: for(k=1; k<=i1;k++){
1.253 brouard 8357: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8358: continue;
1.227 brouard 8359: if(invalidvarcomb[k]){
8360: printf("\nCombination (%d) projection ignored because no cases \n",k);
8361: continue;
8362: }
8363: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8364: for(j=1;j<=cptcoveff;j++) {
8365: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8366: }
1.235 brouard 8367: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8368: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8369: }
1.227 brouard 8370: fprintf(ficresf," yearproj age");
8371: for(j=1; j<=nlstate+ndeath;j++){
8372: for(i=1; i<=nlstate;i++)
8373: fprintf(ficresf," p%d%d",i,j);
8374: fprintf(ficresf," wp.%d",j);
8375: }
8376: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
8377: fprintf(ficresf,"\n");
8378: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.270 brouard 8379: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8380: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8381: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8382: nhstepm = nhstepm/hstepm;
8383: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8384: oldm=oldms;savm=savms;
1.268 brouard 8385: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8386: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8387: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8388: for (h=0; h<=nhstepm; h++){
8389: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8390: break;
8391: }
8392: }
8393: fprintf(ficresf,"\n");
8394: for(j=1;j<=cptcoveff;j++)
8395: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8396: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
8397:
8398: for(j=1; j<=nlstate+ndeath;j++) {
8399: ppij=0.;
8400: for(i=1; i<=nlstate;i++) {
1.278 brouard 8401: if (mobilav>=1)
8402: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8403: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8404: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8405: }
1.268 brouard 8406: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8407: } /* end i */
8408: fprintf(ficresf," %.3f", ppij);
8409: }/* end j */
1.227 brouard 8410: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8411: } /* end agec */
1.266 brouard 8412: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8413: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8414: } /* end yearp */
8415: } /* end k */
1.219 brouard 8416:
1.126 brouard 8417: fclose(ficresf);
1.215 brouard 8418: printf("End of Computing forecasting \n");
8419: fprintf(ficlog,"End of Computing forecasting\n");
8420:
1.126 brouard 8421: }
8422:
1.269 brouard 8423: /************** Back Forecasting ******************/
8424: 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){
1.267 brouard 8425: /* back1, year, month, day of starting backection
8426: agemin, agemax range of age
8427: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8428: anback2 year of end of backprojection (same day and month as back1).
8429: prevacurrent and prev are prevalences.
1.267 brouard 8430: */
8431: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8432: double agec; /* generic age */
1.268 brouard 8433: double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.267 brouard 8434: double *popeffectif,*popcount;
8435: double ***p3mat;
8436: /* double ***mobaverage; */
8437: char fileresfb[FILENAMELENGTH];
8438:
1.268 brouard 8439: agelim=AGEINF;
1.267 brouard 8440: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8441: in each health status at the date of interview (if between dateprev1 and dateprev2).
8442: We still use firstpass and lastpass as another selection.
8443: */
8444: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8445: /* firstpass, lastpass, stepm, weightopt, model); */
8446:
8447: /*Do we need to compute prevalence again?*/
8448:
8449: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8450:
8451: strcpy(fileresfb,"FB_");
8452: strcat(fileresfb,fileresu);
8453: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8454: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8455: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8456: }
8457: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8458: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8459:
8460: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8461:
8462:
8463: stepsize=(int) (stepm+YEARM-1)/YEARM;
8464: if (stepm<=12) stepsize=1;
8465: if(estepm < stepm){
8466: printf ("Problem %d lower than %d\n",estepm, stepm);
8467: }
1.270 brouard 8468: else{
8469: hstepm=estepm;
8470: }
8471: if(estepm >= stepm){ /* Yes every two year */
8472: stepsize=2;
8473: }
1.267 brouard 8474:
8475: hstepm=hstepm/stepm;
8476: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8477: fractional in yp1 */
8478: anprojmean=yp;
8479: yp2=modf((yp1*12),&yp);
8480: mprojmean=yp;
8481: yp1=modf((yp2*30.5),&yp);
8482: jprojmean=yp;
8483: if(jprojmean==0) jprojmean=1;
8484: if(mprojmean==0) jprojmean=1;
8485:
8486: i1=pow(2,cptcoveff);
8487: if (cptcovn < 1){i1=1;}
8488:
8489: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.268 brouard 8490: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8491:
8492: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8493:
8494: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8495: for(k=1; k<=i1;k++){
8496: if(i1 != 1 && TKresult[nres]!= k)
8497: continue;
8498: if(invalidvarcomb[k]){
8499: printf("\nCombination (%d) projection ignored because no cases \n",k);
8500: continue;
8501: }
1.268 brouard 8502: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8503: for(j=1;j<=cptcoveff;j++) {
8504: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8505: }
8506: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8507: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8508: }
8509: fprintf(ficresfb," yearbproj age");
8510: for(j=1; j<=nlstate+ndeath;j++){
8511: for(i=1; i<=nlstate;i++)
1.268 brouard 8512: fprintf(ficresfb," b%d%d",i,j);
8513: fprintf(ficresfb," b.%d",j);
1.267 brouard 8514: }
8515: for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
8516: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8517: fprintf(ficresfb,"\n");
8518: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
1.273 brouard 8519: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8520: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8521: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8522: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8523: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8524: nhstepm = nhstepm/hstepm;
8525: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8526: oldm=oldms;savm=savms;
1.268 brouard 8527: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8528: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8529: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8530: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8531: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8532: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8533: for (h=0; h<=nhstepm; h++){
1.268 brouard 8534: if (h*hstepm/YEARM*stepm ==-yearp) {
8535: break;
8536: }
8537: }
8538: fprintf(ficresfb,"\n");
8539: for(j=1;j<=cptcoveff;j++)
8540: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8541: fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
8542: for(i=1; i<=nlstate+ndeath;i++) {
8543: ppij=0.;ppi=0.;
8544: for(j=1; j<=nlstate;j++) {
8545: /* if (mobilav==1) */
1.269 brouard 8546: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8547: ppi=ppi+prevacurrent[(int)agec][j][k];
8548: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8549: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8550: /* else { */
8551: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8552: /* } */
1.268 brouard 8553: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8554: } /* end j */
8555: if(ppi <0.99){
8556: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8557: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8558: }
8559: fprintf(ficresfb," %.3f", ppij);
8560: }/* end j */
1.267 brouard 8561: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8562: } /* end agec */
8563: } /* end yearp */
8564: } /* end k */
1.217 brouard 8565:
1.267 brouard 8566: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8567:
1.267 brouard 8568: fclose(ficresfb);
8569: printf("End of Computing Back forecasting \n");
8570: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8571:
1.267 brouard 8572: }
1.217 brouard 8573:
1.269 brouard 8574: /* Variance of prevalence limit: varprlim */
8575: 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 8576: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8577:
8578: char fileresvpl[FILENAMELENGTH];
8579: FILE *ficresvpl;
8580: double **oldm, **savm;
8581: double **varpl; /* Variances of prevalence limits by age */
8582: int i1, k, nres, j ;
8583:
8584: strcpy(fileresvpl,"VPL_");
8585: strcat(fileresvpl,fileresu);
8586: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8587: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8588: exit(0);
8589: }
1.288 brouard 8590: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8591: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8592:
8593: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8594: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8595:
8596: i1=pow(2,cptcoveff);
8597: if (cptcovn < 1){i1=1;}
8598:
8599: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8600: for(k=1; k<=i1;k++){
8601: if(i1 != 1 && TKresult[nres]!= k)
8602: continue;
8603: fprintf(ficresvpl,"\n#****** ");
8604: printf("\n#****** ");
8605: fprintf(ficlog,"\n#****** ");
8606: for(j=1;j<=cptcoveff;j++) {
8607: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8608: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8609: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8610: }
8611: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8612: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8613: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8614: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8615: }
8616: fprintf(ficresvpl,"******\n");
8617: printf("******\n");
8618: fprintf(ficlog,"******\n");
8619:
8620: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8621: oldm=oldms;savm=savms;
8622: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8623: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8624: /*}*/
8625: }
8626:
8627: fclose(ficresvpl);
1.288 brouard 8628: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8629: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8630:
8631: }
8632: /* Variance of back prevalence: varbprlim */
8633: 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){
8634: /*------- Variance of back (stable) prevalence------*/
8635:
8636: char fileresvbl[FILENAMELENGTH];
8637: FILE *ficresvbl;
8638:
8639: double **oldm, **savm;
8640: double **varbpl; /* Variances of back prevalence limits by age */
8641: int i1, k, nres, j ;
8642:
8643: strcpy(fileresvbl,"VBL_");
8644: strcat(fileresvbl,fileresu);
8645: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8646: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8647: exit(0);
8648: }
8649: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8650: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8651:
8652:
8653: i1=pow(2,cptcoveff);
8654: if (cptcovn < 1){i1=1;}
8655:
8656: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8657: for(k=1; k<=i1;k++){
8658: if(i1 != 1 && TKresult[nres]!= k)
8659: continue;
8660: fprintf(ficresvbl,"\n#****** ");
8661: printf("\n#****** ");
8662: fprintf(ficlog,"\n#****** ");
8663: for(j=1;j<=cptcoveff;j++) {
8664: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8665: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8666: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8667: }
8668: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8669: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8670: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8671: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8672: }
8673: fprintf(ficresvbl,"******\n");
8674: printf("******\n");
8675: fprintf(ficlog,"******\n");
8676:
8677: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8678: oldm=oldms;savm=savms;
8679:
8680: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8681: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8682: /*}*/
8683: }
8684:
8685: fclose(ficresvbl);
8686: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8687: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8688:
8689: } /* End of varbprlim */
8690:
1.126 brouard 8691: /************** Forecasting *****not tested NB*************/
1.227 brouard 8692: /* 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 8693:
1.227 brouard 8694: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8695: /* int *popage; */
8696: /* double calagedatem, agelim, kk1, kk2; */
8697: /* double *popeffectif,*popcount; */
8698: /* double ***p3mat,***tabpop,***tabpopprev; */
8699: /* /\* double ***mobaverage; *\/ */
8700: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8701:
1.227 brouard 8702: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8703: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8704: /* agelim=AGESUP; */
8705: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8706:
1.227 brouard 8707: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8708:
8709:
1.227 brouard 8710: /* strcpy(filerespop,"POP_"); */
8711: /* strcat(filerespop,fileresu); */
8712: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8713: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8714: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8715: /* } */
8716: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8717: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8718:
1.227 brouard 8719: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8720:
1.227 brouard 8721: /* /\* if (mobilav!=0) { *\/ */
8722: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8723: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8724: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8725: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8726: /* /\* } *\/ */
8727: /* /\* } *\/ */
1.126 brouard 8728:
1.227 brouard 8729: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8730: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8731:
1.227 brouard 8732: /* agelim=AGESUP; */
1.126 brouard 8733:
1.227 brouard 8734: /* hstepm=1; */
8735: /* hstepm=hstepm/stepm; */
1.218 brouard 8736:
1.227 brouard 8737: /* if (popforecast==1) { */
8738: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8739: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8740: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8741: /* } */
8742: /* popage=ivector(0,AGESUP); */
8743: /* popeffectif=vector(0,AGESUP); */
8744: /* popcount=vector(0,AGESUP); */
1.126 brouard 8745:
1.227 brouard 8746: /* i=1; */
8747: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8748:
1.227 brouard 8749: /* imx=i; */
8750: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8751: /* } */
1.218 brouard 8752:
1.227 brouard 8753: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8754: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8755: /* k=k+1; */
8756: /* fprintf(ficrespop,"\n#******"); */
8757: /* for(j=1;j<=cptcoveff;j++) { */
8758: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8759: /* } */
8760: /* fprintf(ficrespop,"******\n"); */
8761: /* fprintf(ficrespop,"# Age"); */
8762: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8763: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8764:
1.227 brouard 8765: /* for (cpt=0; cpt<=0;cpt++) { */
8766: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8767:
1.227 brouard 8768: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8769: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8770: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8771:
1.227 brouard 8772: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8773: /* oldm=oldms;savm=savms; */
8774: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8775:
1.227 brouard 8776: /* for (h=0; h<=nhstepm; h++){ */
8777: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8778: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8779: /* } */
8780: /* for(j=1; j<=nlstate+ndeath;j++) { */
8781: /* kk1=0.;kk2=0; */
8782: /* for(i=1; i<=nlstate;i++) { */
8783: /* if (mobilav==1) */
8784: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8785: /* else { */
8786: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8787: /* } */
8788: /* } */
8789: /* if (h==(int)(calagedatem+12*cpt)){ */
8790: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8791: /* /\*fprintf(ficrespop," %.3f", kk1); */
8792: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8793: /* } */
8794: /* } */
8795: /* for(i=1; i<=nlstate;i++){ */
8796: /* kk1=0.; */
8797: /* for(j=1; j<=nlstate;j++){ */
8798: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8799: /* } */
8800: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8801: /* } */
1.218 brouard 8802:
1.227 brouard 8803: /* if (h==(int)(calagedatem+12*cpt)) */
8804: /* for(j=1; j<=nlstate;j++) */
8805: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8806: /* } */
8807: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8808: /* } */
8809: /* } */
1.218 brouard 8810:
1.227 brouard 8811: /* /\******\/ */
1.218 brouard 8812:
1.227 brouard 8813: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8814: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8815: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8816: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8817: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8818:
1.227 brouard 8819: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8820: /* oldm=oldms;savm=savms; */
8821: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8822: /* for (h=0; h<=nhstepm; h++){ */
8823: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8824: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8825: /* } */
8826: /* for(j=1; j<=nlstate+ndeath;j++) { */
8827: /* kk1=0.;kk2=0; */
8828: /* for(i=1; i<=nlstate;i++) { */
8829: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8830: /* } */
8831: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8832: /* } */
8833: /* } */
8834: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8835: /* } */
8836: /* } */
8837: /* } */
8838: /* } */
1.218 brouard 8839:
1.227 brouard 8840: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8841:
1.227 brouard 8842: /* if (popforecast==1) { */
8843: /* free_ivector(popage,0,AGESUP); */
8844: /* free_vector(popeffectif,0,AGESUP); */
8845: /* free_vector(popcount,0,AGESUP); */
8846: /* } */
8847: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8848: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8849: /* fclose(ficrespop); */
8850: /* } /\* End of popforecast *\/ */
1.218 brouard 8851:
1.126 brouard 8852: int fileappend(FILE *fichier, char *optionfich)
8853: {
8854: if((fichier=fopen(optionfich,"a"))==NULL) {
8855: printf("Problem with file: %s\n", optionfich);
8856: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8857: return (0);
8858: }
8859: fflush(fichier);
8860: return (1);
8861: }
8862:
8863:
8864: /**************** function prwizard **********************/
8865: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8866: {
8867:
8868: /* Wizard to print covariance matrix template */
8869:
1.164 brouard 8870: char ca[32], cb[32];
8871: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8872: int numlinepar;
8873:
8874: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8875: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8876: for(i=1; i <=nlstate; i++){
8877: jj=0;
8878: for(j=1; j <=nlstate+ndeath; j++){
8879: if(j==i) continue;
8880: jj++;
8881: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8882: printf("%1d%1d",i,j);
8883: fprintf(ficparo,"%1d%1d",i,j);
8884: for(k=1; k<=ncovmodel;k++){
8885: /* printf(" %lf",param[i][j][k]); */
8886: /* fprintf(ficparo," %lf",param[i][j][k]); */
8887: printf(" 0.");
8888: fprintf(ficparo," 0.");
8889: }
8890: printf("\n");
8891: fprintf(ficparo,"\n");
8892: }
8893: }
8894: printf("# Scales (for hessian or gradient estimation)\n");
8895: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8896: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8897: for(i=1; i <=nlstate; i++){
8898: jj=0;
8899: for(j=1; j <=nlstate+ndeath; j++){
8900: if(j==i) continue;
8901: jj++;
8902: fprintf(ficparo,"%1d%1d",i,j);
8903: printf("%1d%1d",i,j);
8904: fflush(stdout);
8905: for(k=1; k<=ncovmodel;k++){
8906: /* printf(" %le",delti3[i][j][k]); */
8907: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8908: printf(" 0.");
8909: fprintf(ficparo," 0.");
8910: }
8911: numlinepar++;
8912: printf("\n");
8913: fprintf(ficparo,"\n");
8914: }
8915: }
8916: printf("# Covariance matrix\n");
8917: /* # 121 Var(a12)\n\ */
8918: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8919: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8920: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8921: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8922: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8923: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8924: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8925: fflush(stdout);
8926: fprintf(ficparo,"# Covariance matrix\n");
8927: /* # 121 Var(a12)\n\ */
8928: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8929: /* # ...\n\ */
8930: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8931:
8932: for(itimes=1;itimes<=2;itimes++){
8933: jj=0;
8934: for(i=1; i <=nlstate; i++){
8935: for(j=1; j <=nlstate+ndeath; j++){
8936: if(j==i) continue;
8937: for(k=1; k<=ncovmodel;k++){
8938: jj++;
8939: ca[0]= k+'a'-1;ca[1]='\0';
8940: if(itimes==1){
8941: printf("#%1d%1d%d",i,j,k);
8942: fprintf(ficparo,"#%1d%1d%d",i,j,k);
8943: }else{
8944: printf("%1d%1d%d",i,j,k);
8945: fprintf(ficparo,"%1d%1d%d",i,j,k);
8946: /* printf(" %.5le",matcov[i][j]); */
8947: }
8948: ll=0;
8949: for(li=1;li <=nlstate; li++){
8950: for(lj=1;lj <=nlstate+ndeath; lj++){
8951: if(lj==li) continue;
8952: for(lk=1;lk<=ncovmodel;lk++){
8953: ll++;
8954: if(ll<=jj){
8955: cb[0]= lk +'a'-1;cb[1]='\0';
8956: if(ll<jj){
8957: if(itimes==1){
8958: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8959: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8960: }else{
8961: printf(" 0.");
8962: fprintf(ficparo," 0.");
8963: }
8964: }else{
8965: if(itimes==1){
8966: printf(" Var(%s%1d%1d)",ca,i,j);
8967: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
8968: }else{
8969: printf(" 0.");
8970: fprintf(ficparo," 0.");
8971: }
8972: }
8973: }
8974: } /* end lk */
8975: } /* end lj */
8976: } /* end li */
8977: printf("\n");
8978: fprintf(ficparo,"\n");
8979: numlinepar++;
8980: } /* end k*/
8981: } /*end j */
8982: } /* end i */
8983: } /* end itimes */
8984:
8985: } /* end of prwizard */
8986: /******************* Gompertz Likelihood ******************************/
8987: double gompertz(double x[])
8988: {
8989: double A,B,L=0.0,sump=0.,num=0.;
8990: int i,n=0; /* n is the size of the sample */
8991:
1.220 brouard 8992: for (i=1;i<=imx ; i++) {
1.126 brouard 8993: sump=sump+weight[i];
8994: /* sump=sump+1;*/
8995: num=num+1;
8996: }
8997:
8998:
8999: /* for (i=0; i<=imx; i++)
9000: 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]);*/
9001:
9002: for (i=1;i<=imx ; i++)
9003: {
9004: if (cens[i] == 1 && wav[i]>1)
9005: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9006:
9007: if (cens[i] == 0 && wav[i]>1)
9008: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
9009: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
9010:
9011: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9012: if (wav[i] > 1 ) { /* ??? */
9013: L=L+A*weight[i];
9014: /* 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]);*/
9015: }
9016: }
9017:
9018: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9019:
9020: return -2*L*num/sump;
9021: }
9022:
1.136 brouard 9023: #ifdef GSL
9024: /******************* Gompertz_f Likelihood ******************************/
9025: double gompertz_f(const gsl_vector *v, void *params)
9026: {
9027: double A,B,LL=0.0,sump=0.,num=0.;
9028: double *x= (double *) v->data;
9029: int i,n=0; /* n is the size of the sample */
9030:
9031: for (i=0;i<=imx-1 ; i++) {
9032: sump=sump+weight[i];
9033: /* sump=sump+1;*/
9034: num=num+1;
9035: }
9036:
9037:
9038: /* for (i=0; i<=imx; i++)
9039: 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]);*/
9040: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9041: for (i=1;i<=imx ; i++)
9042: {
9043: if (cens[i] == 1 && wav[i]>1)
9044: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9045:
9046: if (cens[i] == 0 && wav[i]>1)
9047: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9048: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9049:
9050: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9051: if (wav[i] > 1 ) { /* ??? */
9052: LL=LL+A*weight[i];
9053: /* 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]);*/
9054: }
9055: }
9056:
9057: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9058: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9059:
9060: return -2*LL*num/sump;
9061: }
9062: #endif
9063:
1.126 brouard 9064: /******************* Printing html file ***********/
1.201 brouard 9065: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9066: int lastpass, int stepm, int weightopt, char model[],\
9067: int imx, double p[],double **matcov,double agemortsup){
9068: int i,k;
9069:
9070: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9071: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9072: for (i=1;i<=2;i++)
9073: 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 9074: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9075: fprintf(fichtm,"</ul>");
9076:
9077: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9078:
9079: 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>");
9080:
9081: for (k=agegomp;k<(agemortsup-2);k++)
9082: 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]);
9083:
9084:
9085: fflush(fichtm);
9086: }
9087:
9088: /******************* Gnuplot file **************/
1.201 brouard 9089: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9090:
9091: char dirfileres[132],optfileres[132];
1.164 brouard 9092:
1.126 brouard 9093: int ng;
9094:
9095:
9096: /*#ifdef windows */
9097: fprintf(ficgp,"cd \"%s\" \n",pathc);
9098: /*#endif */
9099:
9100:
9101: strcpy(dirfileres,optionfilefiname);
9102: strcpy(optfileres,"vpl");
1.199 brouard 9103: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9104: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9105: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9106: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9107: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9108:
9109: }
9110:
1.136 brouard 9111: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9112: {
1.126 brouard 9113:
1.136 brouard 9114: /*-------- data file ----------*/
9115: FILE *fic;
9116: char dummy[]=" ";
1.240 brouard 9117: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9118: int lstra;
1.136 brouard 9119: int linei, month, year,iout;
9120: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9121: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9122: char *stratrunc;
1.223 brouard 9123:
1.240 brouard 9124: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9125: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9126:
1.240 brouard 9127: for(v=1; v <=ncovcol;v++){
9128: DummyV[v]=0;
9129: FixedV[v]=0;
9130: }
9131: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9132: DummyV[v]=1;
9133: FixedV[v]=0;
9134: }
9135: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9136: DummyV[v]=0;
9137: FixedV[v]=1;
9138: }
9139: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9140: DummyV[v]=1;
9141: FixedV[v]=1;
9142: }
9143: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9144: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9145: 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]);
9146: }
1.126 brouard 9147:
1.136 brouard 9148: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9149: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9150: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9151: }
1.126 brouard 9152:
1.136 brouard 9153: i=1;
9154: linei=0;
9155: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9156: linei=linei+1;
9157: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9158: if(line[j] == '\t')
9159: line[j] = ' ';
9160: }
9161: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9162: ;
9163: };
9164: line[j+1]=0; /* Trims blanks at end of line */
9165: if(line[0]=='#'){
9166: fprintf(ficlog,"Comment line\n%s\n",line);
9167: printf("Comment line\n%s\n",line);
9168: continue;
9169: }
9170: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9171: strcpy(line, linetmp);
1.223 brouard 9172:
9173: /* Loops on waves */
9174: for (j=maxwav;j>=1;j--){
9175: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9176: cutv(stra, strb, line, ' ');
9177: if(strb[0]=='.') { /* Missing value */
9178: lval=-1;
9179: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9180: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9181: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9182: 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);
9183: 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);
9184: return 1;
9185: }
9186: }else{
9187: errno=0;
9188: /* what_kind_of_number(strb); */
9189: dval=strtod(strb,&endptr);
9190: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9191: /* if(strb != endptr && *endptr == '\0') */
9192: /* dval=dlval; */
9193: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9194: if( strb[0]=='\0' || (*endptr != '\0')){
9195: 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);
9196: 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);
9197: return 1;
9198: }
9199: cotqvar[j][iv][i]=dval;
9200: cotvar[j][ntv+iv][i]=dval;
9201: }
9202: strcpy(line,stra);
1.223 brouard 9203: }/* end loop ntqv */
1.225 brouard 9204:
1.223 brouard 9205: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9206: cutv(stra, strb, line, ' ');
9207: if(strb[0]=='.') { /* Missing value */
9208: lval=-1;
9209: }else{
9210: errno=0;
9211: lval=strtol(strb,&endptr,10);
9212: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9213: if( strb[0]=='\0' || (*endptr != '\0')){
9214: 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);
9215: 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);
9216: return 1;
9217: }
9218: }
9219: if(lval <-1 || lval >1){
9220: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9221: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9222: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9223: For example, for multinomial values like 1, 2 and 3,\n \
9224: build V1=0 V2=0 for the reference value (1),\n \
9225: V1=1 V2=0 for (2) \n \
1.223 brouard 9226: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9227: output of IMaCh is often meaningless.\n \
1.223 brouard 9228: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9229: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9230: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9231: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9232: For example, for multinomial values like 1, 2 and 3,\n \
9233: build V1=0 V2=0 for the reference value (1),\n \
9234: V1=1 V2=0 for (2) \n \
1.223 brouard 9235: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9236: output of IMaCh is often meaningless.\n \
1.223 brouard 9237: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9238: return 1;
9239: }
9240: cotvar[j][iv][i]=(double)(lval);
9241: strcpy(line,stra);
1.223 brouard 9242: }/* end loop ntv */
1.225 brouard 9243:
1.223 brouard 9244: /* Statuses at wave */
1.137 brouard 9245: cutv(stra, strb, line, ' ');
1.223 brouard 9246: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9247: lval=-1;
1.136 brouard 9248: }else{
1.238 brouard 9249: errno=0;
9250: lval=strtol(strb,&endptr,10);
9251: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9252: if( strb[0]=='\0' || (*endptr != '\0')){
9253: 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);
9254: 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);
9255: return 1;
9256: }
1.136 brouard 9257: }
1.225 brouard 9258:
1.136 brouard 9259: s[j][i]=lval;
1.225 brouard 9260:
1.223 brouard 9261: /* Date of Interview */
1.136 brouard 9262: strcpy(line,stra);
9263: cutv(stra, strb,line,' ');
1.169 brouard 9264: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9265: }
1.169 brouard 9266: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9267: month=99;
9268: year=9999;
1.136 brouard 9269: }else{
1.225 brouard 9270: 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);
9271: 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);
9272: return 1;
1.136 brouard 9273: }
9274: anint[j][i]= (double) year;
9275: mint[j][i]= (double)month;
9276: strcpy(line,stra);
1.223 brouard 9277: } /* End loop on waves */
1.225 brouard 9278:
1.223 brouard 9279: /* Date of death */
1.136 brouard 9280: cutv(stra, strb,line,' ');
1.169 brouard 9281: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9282: }
1.169 brouard 9283: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9284: month=99;
9285: year=9999;
9286: }else{
1.141 brouard 9287: 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 9288: 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);
9289: return 1;
1.136 brouard 9290: }
9291: andc[i]=(double) year;
9292: moisdc[i]=(double) month;
9293: strcpy(line,stra);
9294:
1.223 brouard 9295: /* Date of birth */
1.136 brouard 9296: cutv(stra, strb,line,' ');
1.169 brouard 9297: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9298: }
1.169 brouard 9299: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9300: month=99;
9301: year=9999;
9302: }else{
1.141 brouard 9303: 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);
9304: 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 9305: return 1;
1.136 brouard 9306: }
9307: if (year==9999) {
1.141 brouard 9308: 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);
9309: 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 9310: return 1;
9311:
1.136 brouard 9312: }
9313: annais[i]=(double)(year);
9314: moisnais[i]=(double)(month);
9315: strcpy(line,stra);
1.225 brouard 9316:
1.223 brouard 9317: /* Sample weight */
1.136 brouard 9318: cutv(stra, strb,line,' ');
9319: errno=0;
9320: dval=strtod(strb,&endptr);
9321: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9322: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9323: 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 9324: fflush(ficlog);
9325: return 1;
9326: }
9327: weight[i]=dval;
9328: strcpy(line,stra);
1.225 brouard 9329:
1.223 brouard 9330: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9331: cutv(stra, strb, line, ' ');
9332: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9333: lval=-1;
1.223 brouard 9334: }else{
1.225 brouard 9335: errno=0;
9336: /* what_kind_of_number(strb); */
9337: dval=strtod(strb,&endptr);
9338: /* if(strb != endptr && *endptr == '\0') */
9339: /* dval=dlval; */
9340: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9341: if( strb[0]=='\0' || (*endptr != '\0')){
9342: 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);
9343: 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);
9344: return 1;
9345: }
9346: coqvar[iv][i]=dval;
1.226 brouard 9347: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9348: }
9349: strcpy(line,stra);
9350: }/* end loop nqv */
1.136 brouard 9351:
1.223 brouard 9352: /* Covariate values */
1.136 brouard 9353: for (j=ncovcol;j>=1;j--){
9354: cutv(stra, strb,line,' ');
1.223 brouard 9355: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9356: lval=-1;
1.136 brouard 9357: }else{
1.225 brouard 9358: errno=0;
9359: lval=strtol(strb,&endptr,10);
9360: if( strb[0]=='\0' || (*endptr != '\0')){
9361: 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);
9362: 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);
9363: return 1;
9364: }
1.136 brouard 9365: }
9366: if(lval <-1 || lval >1){
1.225 brouard 9367: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9368: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9369: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9370: For example, for multinomial values like 1, 2 and 3,\n \
9371: build V1=0 V2=0 for the reference value (1),\n \
9372: V1=1 V2=0 for (2) \n \
1.136 brouard 9373: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9374: output of IMaCh is often meaningless.\n \
1.136 brouard 9375: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9376: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9377: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9378: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9379: For example, for multinomial values like 1, 2 and 3,\n \
9380: build V1=0 V2=0 for the reference value (1),\n \
9381: V1=1 V2=0 for (2) \n \
1.136 brouard 9382: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9383: output of IMaCh is often meaningless.\n \
1.136 brouard 9384: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9385: return 1;
1.136 brouard 9386: }
9387: covar[j][i]=(double)(lval);
9388: strcpy(line,stra);
9389: }
9390: lstra=strlen(stra);
1.225 brouard 9391:
1.136 brouard 9392: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9393: stratrunc = &(stra[lstra-9]);
9394: num[i]=atol(stratrunc);
9395: }
9396: else
9397: num[i]=atol(stra);
9398: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9399: 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;}*/
9400:
9401: i=i+1;
9402: } /* End loop reading data */
1.225 brouard 9403:
1.136 brouard 9404: *imax=i-1; /* Number of individuals */
9405: fclose(fic);
1.225 brouard 9406:
1.136 brouard 9407: return (0);
1.164 brouard 9408: /* endread: */
1.225 brouard 9409: printf("Exiting readdata: ");
9410: fclose(fic);
9411: return (1);
1.223 brouard 9412: }
1.126 brouard 9413:
1.234 brouard 9414: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9415: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9416: while (*p2 == ' ')
1.234 brouard 9417: p2++;
9418: /* while ((*p1++ = *p2++) !=0) */
9419: /* ; */
9420: /* do */
9421: /* while (*p2 == ' ') */
9422: /* p2++; */
9423: /* while (*p1++ == *p2++); */
9424: *stri=p2;
1.145 brouard 9425: }
9426:
1.235 brouard 9427: int decoderesult ( char resultline[], int nres)
1.230 brouard 9428: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9429: {
1.235 brouard 9430: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9431: char resultsav[MAXLINE];
1.234 brouard 9432: int resultmodel[MAXLINE];
9433: int modelresult[MAXLINE];
1.230 brouard 9434: char stra[80], strb[80], strc[80], strd[80],stre[80];
9435:
1.234 brouard 9436: removefirstspace(&resultline);
1.233 brouard 9437: printf("decoderesult:%s\n",resultline);
1.230 brouard 9438:
9439: if (strstr(resultline,"v") !=0){
9440: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9441: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9442: return 1;
9443: }
9444: trimbb(resultsav, resultline);
9445: if (strlen(resultsav) >1){
9446: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9447: }
1.253 brouard 9448: if(j == 0){ /* Resultline but no = */
9449: TKresult[nres]=0; /* Combination for the nresult and the model */
9450: return (0);
9451: }
9452:
1.234 brouard 9453: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9454: 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);
9455: 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);
9456: }
9457: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9458: if(nbocc(resultsav,'=') >1){
9459: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9460: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9461: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9462: }else
9463: cutl(strc,strd,resultsav,'=');
1.230 brouard 9464: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9465:
1.230 brouard 9466: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9467: Tvarsel[k]=atoi(strc);
9468: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9469: /* cptcovsel++; */
9470: if (nbocc(stra,'=') >0)
9471: strcpy(resultsav,stra); /* and analyzes it */
9472: }
1.235 brouard 9473: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9474: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9475: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9476: match=0;
1.236 brouard 9477: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9478: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9479: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9480: match=1;
9481: break;
9482: }
9483: }
9484: if(match == 0){
9485: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9486: }
9487: }
9488: }
1.235 brouard 9489: /* Checking for missing or useless values in comparison of current model needs */
9490: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9491: match=0;
1.235 brouard 9492: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9493: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9494: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9495: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9496: ++match;
9497: }
9498: }
9499: }
9500: if(match == 0){
9501: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9502: }else if(match > 1){
9503: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9504: }
9505: }
1.235 brouard 9506:
1.234 brouard 9507: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9508: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9509: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9510: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9511: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9512: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9513: /* 1 0 0 0 */
9514: /* 2 1 0 0 */
9515: /* 3 0 1 0 */
9516: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9517: /* 5 0 0 1 */
9518: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9519: /* 7 0 1 1 */
9520: /* 8 1 1 1 */
1.237 brouard 9521: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9522: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9523: /* V5*age V5 known which value for nres? */
9524: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9525: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9526: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9527: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9528: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9529: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9530: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9531: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9532: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9533: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9534: k4++;;
9535: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9536: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9537: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9538: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9539: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9540: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9541: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9542: k4q++;;
9543: }
9544: }
1.234 brouard 9545:
1.235 brouard 9546: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9547: return (0);
9548: }
1.235 brouard 9549:
1.230 brouard 9550: int decodemodel( char model[], int lastobs)
9551: /**< This routine decodes the model and returns:
1.224 brouard 9552: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9553: * - nagesqr = 1 if age*age in the model, otherwise 0.
9554: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9555: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9556: * - cptcovage number of covariates with age*products =2
9557: * - cptcovs number of simple covariates
9558: * - 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
9559: * which is a new column after the 9 (ncovcol) variables.
9560: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9561: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9562: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9563: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9564: */
1.136 brouard 9565: {
1.238 brouard 9566: int i, j, k, ks, v;
1.227 brouard 9567: int j1, k1, k2, k3, k4;
1.136 brouard 9568: char modelsav[80];
1.145 brouard 9569: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9570: char *strpt;
1.136 brouard 9571:
1.145 brouard 9572: /*removespace(model);*/
1.136 brouard 9573: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9574: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9575: if (strstr(model,"AGE") !=0){
1.192 brouard 9576: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9577: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9578: return 1;
9579: }
1.141 brouard 9580: if (strstr(model,"v") !=0){
9581: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9582: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9583: return 1;
9584: }
1.187 brouard 9585: strcpy(modelsav,model);
9586: if ((strpt=strstr(model,"age*age")) !=0){
9587: printf(" strpt=%s, model=%s\n",strpt, model);
9588: if(strpt != model){
1.234 brouard 9589: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9590: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9591: corresponding column of parameters.\n",model);
1.234 brouard 9592: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9593: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9594: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9595: return 1;
1.225 brouard 9596: }
1.187 brouard 9597: nagesqr=1;
9598: if (strstr(model,"+age*age") !=0)
1.234 brouard 9599: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9600: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9601: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9602: else
1.234 brouard 9603: substrchaine(modelsav, model, "age*age");
1.187 brouard 9604: }else
9605: nagesqr=0;
9606: if (strlen(modelsav) >1){
9607: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9608: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9609: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9610: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9611: * cst, age and age*age
9612: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9613: /* including age products which are counted in cptcovage.
9614: * but the covariates which are products must be treated
9615: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9616: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9617: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9618:
9619:
1.187 brouard 9620: /* Design
9621: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9622: * < ncovcol=8 >
9623: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9624: * k= 1 2 3 4 5 6 7 8
9625: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9626: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9627: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9628: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9629: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9630: * Tage[++cptcovage]=k
9631: * if products, new covar are created after ncovcol with k1
9632: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9633: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9634: * 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
9635: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9636: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9637: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9638: * < ncovcol=8 >
9639: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9640: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9641: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9642: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9643: * p Tprod[1]@2={ 6, 5}
9644: *p Tvard[1][1]@4= {7, 8, 5, 6}
9645: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9646: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9647: *How to reorganize?
9648: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9649: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9650: * {2, 1, 4, 8, 5, 6, 3, 7}
9651: * Struct []
9652: */
1.225 brouard 9653:
1.187 brouard 9654: /* This loop fills the array Tvar from the string 'model'.*/
9655: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9656: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9657: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9658: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9659: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9660: /* k=1 Tvar[1]=2 (from V2) */
9661: /* k=5 Tvar[5] */
9662: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9663: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9664: /* } */
1.198 brouard 9665: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9666: /*
9667: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9668: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9669: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9670: }
1.187 brouard 9671: cptcovage=0;
9672: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9673: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9674: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9675: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9676: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9677: /*scanf("%d",i);*/
9678: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9679: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9680: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9681: /* covar is not filled and then is empty */
9682: cptcovprod--;
9683: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9684: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9685: Typevar[k]=1; /* 1 for age product */
9686: cptcovage++; /* Sums the number of covariates which include age as a product */
9687: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9688: /*printf("stre=%s ", stre);*/
9689: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9690: cptcovprod--;
9691: cutl(stre,strb,strc,'V');
9692: Tvar[k]=atoi(stre);
9693: Typevar[k]=1; /* 1 for age product */
9694: cptcovage++;
9695: Tage[cptcovage]=k;
9696: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9697: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9698: cptcovn++;
9699: cptcovprodnoage++;k1++;
9700: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9701: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9702: because this model-covariate is a construction we invent a new column
9703: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9704: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9705: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9706: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9707: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9708: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9709: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9710: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9711: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9712: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9713: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9714: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9715: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9716: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9717: for (i=1; i<=lastobs;i++){
9718: /* Computes the new covariate which is a product of
9719: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9720: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9721: }
9722: } /* End age is not in the model */
9723: } /* End if model includes a product */
9724: else { /* no more sum */
9725: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9726: /* scanf("%d",i);*/
9727: cutl(strd,strc,strb,'V');
9728: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9729: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9730: Tvar[k]=atoi(strd);
9731: Typevar[k]=0; /* 0 for simple covariates */
9732: }
9733: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9734: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9735: scanf("%d",i);*/
1.187 brouard 9736: } /* end of loop + on total covariates */
9737: } /* end if strlen(modelsave == 0) age*age might exist */
9738: } /* end if strlen(model == 0) */
1.136 brouard 9739:
9740: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9741: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9742:
1.136 brouard 9743: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9744: printf("cptcovprod=%d ", cptcovprod);
9745: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9746: scanf("%d ",i);*/
9747:
9748:
1.230 brouard 9749: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9750: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9751: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9752: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9753: k = 1 2 3 4 5 6 7 8 9
9754: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9755: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9756: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9757: Dummy[k] 1 0 0 0 3 1 1 2 3
9758: Tmodelind[combination of covar]=k;
1.225 brouard 9759: */
9760: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9761: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9762: /* 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 9763: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9764: printf("Model=%s\n\
9765: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9766: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9767: 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);
9768: fprintf(ficlog,"Model=%s\n\
9769: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9770: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9771: 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 9772: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9773: 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 */
9774: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9775: Fixed[k]= 0;
9776: Dummy[k]= 0;
1.225 brouard 9777: ncoveff++;
1.232 brouard 9778: ncovf++;
1.234 brouard 9779: nsd++;
9780: modell[k].maintype= FTYPE;
9781: TvarsD[nsd]=Tvar[k];
9782: TvarsDind[nsd]=k;
9783: TvarF[ncovf]=Tvar[k];
9784: TvarFind[ncovf]=k;
9785: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9786: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9787: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9788: Fixed[k]= 0;
9789: Dummy[k]= 0;
9790: ncoveff++;
9791: ncovf++;
9792: modell[k].maintype= FTYPE;
9793: TvarF[ncovf]=Tvar[k];
9794: TvarFind[ncovf]=k;
1.230 brouard 9795: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9796: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9797: }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 9798: Fixed[k]= 0;
9799: Dummy[k]= 1;
1.230 brouard 9800: nqfveff++;
1.234 brouard 9801: modell[k].maintype= FTYPE;
9802: modell[k].subtype= FQ;
9803: nsq++;
9804: TvarsQ[nsq]=Tvar[k];
9805: TvarsQind[nsq]=k;
1.232 brouard 9806: ncovf++;
1.234 brouard 9807: TvarF[ncovf]=Tvar[k];
9808: TvarFind[ncovf]=k;
1.231 brouard 9809: 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 9810: 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 9811: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9812: Fixed[k]= 1;
9813: Dummy[k]= 0;
1.225 brouard 9814: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9815: modell[k].maintype= VTYPE;
9816: modell[k].subtype= VD;
9817: nsd++;
9818: TvarsD[nsd]=Tvar[k];
9819: TvarsDind[nsd]=k;
9820: ncovv++; /* Only simple time varying variables */
9821: TvarV[ncovv]=Tvar[k];
1.242 brouard 9822: 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 9823: 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 */
9824: 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 9825: 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);
9826: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9827: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9828: Fixed[k]= 1;
9829: Dummy[k]= 1;
9830: nqtveff++;
9831: modell[k].maintype= VTYPE;
9832: modell[k].subtype= VQ;
9833: ncovv++; /* Only simple time varying variables */
9834: nsq++;
9835: TvarsQ[nsq]=Tvar[k];
9836: TvarsQind[nsq]=k;
9837: TvarV[ncovv]=Tvar[k];
1.242 brouard 9838: 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 9839: 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 */
9840: 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 9841: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9842: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9843: 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 9844: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9845: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9846: ncova++;
9847: TvarA[ncova]=Tvar[k];
9848: TvarAind[ncova]=k;
1.231 brouard 9849: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9850: Fixed[k]= 2;
9851: Dummy[k]= 2;
9852: modell[k].maintype= ATYPE;
9853: modell[k].subtype= APFD;
9854: /* ncoveff++; */
1.227 brouard 9855: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 9856: Fixed[k]= 2;
9857: Dummy[k]= 3;
9858: modell[k].maintype= ATYPE;
9859: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
9860: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 9861: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 9862: Fixed[k]= 3;
9863: Dummy[k]= 2;
9864: modell[k].maintype= ATYPE;
9865: modell[k].subtype= APVD; /* Product age * varying dummy */
9866: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 9867: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9868: Fixed[k]= 3;
9869: Dummy[k]= 3;
9870: modell[k].maintype= ATYPE;
9871: modell[k].subtype= APVQ; /* Product age * varying quantitative */
9872: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 9873: }
9874: }else if (Typevar[k] == 2) { /* product without age */
9875: k1=Tposprod[k];
9876: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 9877: if(Tvard[k1][2] <=ncovcol){
9878: Fixed[k]= 1;
9879: Dummy[k]= 0;
9880: modell[k].maintype= FTYPE;
9881: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
9882: ncovf++; /* Fixed variables without age */
9883: TvarF[ncovf]=Tvar[k];
9884: TvarFind[ncovf]=k;
9885: }else if(Tvard[k1][2] <=ncovcol+nqv){
9886: Fixed[k]= 0; /* or 2 ?*/
9887: Dummy[k]= 1;
9888: modell[k].maintype= FTYPE;
9889: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
9890: ncovf++; /* Varying variables without age */
9891: TvarF[ncovf]=Tvar[k];
9892: TvarFind[ncovf]=k;
9893: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9894: Fixed[k]= 1;
9895: Dummy[k]= 0;
9896: modell[k].maintype= VTYPE;
9897: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
9898: ncovv++; /* Varying variables without age */
9899: TvarV[ncovv]=Tvar[k];
9900: TvarVind[ncovv]=k;
9901: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9902: Fixed[k]= 1;
9903: Dummy[k]= 1;
9904: modell[k].maintype= VTYPE;
9905: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
9906: ncovv++; /* Varying variables without age */
9907: TvarV[ncovv]=Tvar[k];
9908: TvarVind[ncovv]=k;
9909: }
1.227 brouard 9910: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 9911: if(Tvard[k1][2] <=ncovcol){
9912: Fixed[k]= 0; /* or 2 ?*/
9913: Dummy[k]= 1;
9914: modell[k].maintype= FTYPE;
9915: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
9916: ncovf++; /* Fixed variables without age */
9917: TvarF[ncovf]=Tvar[k];
9918: TvarFind[ncovf]=k;
9919: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9920: Fixed[k]= 1;
9921: Dummy[k]= 1;
9922: modell[k].maintype= VTYPE;
9923: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
9924: ncovv++; /* Varying variables without age */
9925: TvarV[ncovv]=Tvar[k];
9926: TvarVind[ncovv]=k;
9927: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9928: Fixed[k]= 1;
9929: Dummy[k]= 1;
9930: modell[k].maintype= VTYPE;
9931: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
9932: ncovv++; /* Varying variables without age */
9933: TvarV[ncovv]=Tvar[k];
9934: TvarVind[ncovv]=k;
9935: ncovv++; /* Varying variables without age */
9936: TvarV[ncovv]=Tvar[k];
9937: TvarVind[ncovv]=k;
9938: }
1.227 brouard 9939: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 9940: if(Tvard[k1][2] <=ncovcol){
9941: Fixed[k]= 1;
9942: Dummy[k]= 1;
9943: modell[k].maintype= VTYPE;
9944: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
9945: ncovv++; /* Varying variables without age */
9946: TvarV[ncovv]=Tvar[k];
9947: TvarVind[ncovv]=k;
9948: }else if(Tvard[k1][2] <=ncovcol+nqv){
9949: Fixed[k]= 1;
9950: Dummy[k]= 1;
9951: modell[k].maintype= VTYPE;
9952: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
9953: ncovv++; /* Varying variables without age */
9954: TvarV[ncovv]=Tvar[k];
9955: TvarVind[ncovv]=k;
9956: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9957: Fixed[k]= 1;
9958: Dummy[k]= 0;
9959: modell[k].maintype= VTYPE;
9960: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
9961: ncovv++; /* Varying variables without age */
9962: TvarV[ncovv]=Tvar[k];
9963: TvarVind[ncovv]=k;
9964: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9965: Fixed[k]= 1;
9966: Dummy[k]= 1;
9967: modell[k].maintype= VTYPE;
9968: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
9969: ncovv++; /* Varying variables without age */
9970: TvarV[ncovv]=Tvar[k];
9971: TvarVind[ncovv]=k;
9972: }
1.227 brouard 9973: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9974: if(Tvard[k1][2] <=ncovcol){
9975: Fixed[k]= 1;
9976: Dummy[k]= 1;
9977: modell[k].maintype= VTYPE;
9978: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
9979: ncovv++; /* Varying variables without age */
9980: TvarV[ncovv]=Tvar[k];
9981: TvarVind[ncovv]=k;
9982: }else if(Tvard[k1][2] <=ncovcol+nqv){
9983: Fixed[k]= 1;
9984: Dummy[k]= 1;
9985: modell[k].maintype= VTYPE;
9986: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
9987: ncovv++; /* Varying variables without age */
9988: TvarV[ncovv]=Tvar[k];
9989: TvarVind[ncovv]=k;
9990: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9991: Fixed[k]= 1;
9992: Dummy[k]= 1;
9993: modell[k].maintype= VTYPE;
9994: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
9995: ncovv++; /* Varying variables without age */
9996: TvarV[ncovv]=Tvar[k];
9997: TvarVind[ncovv]=k;
9998: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9999: Fixed[k]= 1;
10000: Dummy[k]= 1;
10001: modell[k].maintype= VTYPE;
10002: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10003: ncovv++; /* Varying variables without age */
10004: TvarV[ncovv]=Tvar[k];
10005: TvarVind[ncovv]=k;
10006: }
1.227 brouard 10007: }else{
1.240 brouard 10008: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10009: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10010: } /*end k1*/
1.225 brouard 10011: }else{
1.226 brouard 10012: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10013: 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 10014: }
1.227 brouard 10015: 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 10016: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10017: 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]);
10018: }
10019: /* Searching for doublons in the model */
10020: for(k1=1; k1<= cptcovt;k1++){
10021: for(k2=1; k2 <k1;k2++){
1.285 brouard 10022: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10023: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10024: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10025: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10026: 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]);
10027: 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 10028: return(1);
10029: }
10030: }else if (Typevar[k1] ==2){
10031: k3=Tposprod[k1];
10032: k4=Tposprod[k2];
10033: 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])) ){
10034: 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]]);
10035: 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);
10036: return(1);
10037: }
10038: }
1.227 brouard 10039: }
10040: }
1.225 brouard 10041: }
10042: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10043: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10044: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10045: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10046: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10047: /*endread:*/
1.225 brouard 10048: printf("Exiting decodemodel: ");
10049: return (1);
1.136 brouard 10050: }
10051:
1.169 brouard 10052: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10053: {/* Check ages at death */
1.136 brouard 10054: int i, m;
1.218 brouard 10055: int firstone=0;
10056:
1.136 brouard 10057: for (i=1; i<=imx; i++) {
10058: for(m=2; (m<= maxwav); m++) {
10059: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10060: anint[m][i]=9999;
1.216 brouard 10061: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10062: s[m][i]=-1;
1.136 brouard 10063: }
10064: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10065: *nberr = *nberr + 1;
1.218 brouard 10066: if(firstone == 0){
10067: firstone=1;
1.260 brouard 10068: 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 10069: }
1.262 brouard 10070: 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 10071: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10072: }
10073: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10074: (*nberr)++;
1.259 brouard 10075: 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 10076: 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 10077: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10078: }
10079: }
10080: }
10081:
10082: for (i=1; i<=imx; i++) {
10083: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10084: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10085: 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 10086: if (s[m][i] >= nlstate+1) {
1.169 brouard 10087: if(agedc[i]>0){
10088: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10089: agev[m][i]=agedc[i];
1.214 brouard 10090: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10091: }else {
1.136 brouard 10092: if ((int)andc[i]!=9999){
10093: nbwarn++;
10094: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10095: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10096: agev[m][i]=-1;
10097: }
10098: }
1.169 brouard 10099: } /* agedc > 0 */
1.214 brouard 10100: } /* end if */
1.136 brouard 10101: else if(s[m][i] !=9){ /* Standard case, age in fractional
10102: years but with the precision of a month */
10103: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10104: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10105: agev[m][i]=1;
10106: else if(agev[m][i] < *agemin){
10107: *agemin=agev[m][i];
10108: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10109: }
10110: else if(agev[m][i] >*agemax){
10111: *agemax=agev[m][i];
1.156 brouard 10112: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10113: }
10114: /*agev[m][i]=anint[m][i]-annais[i];*/
10115: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10116: } /* en if 9*/
1.136 brouard 10117: else { /* =9 */
1.214 brouard 10118: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10119: agev[m][i]=1;
10120: s[m][i]=-1;
10121: }
10122: }
1.214 brouard 10123: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10124: agev[m][i]=1;
1.214 brouard 10125: else{
10126: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10127: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10128: agev[m][i]=0;
10129: }
10130: } /* End for lastpass */
10131: }
1.136 brouard 10132:
10133: for (i=1; i<=imx; i++) {
10134: for(m=firstpass; (m<=lastpass); m++){
10135: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10136: (*nberr)++;
1.136 brouard 10137: 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);
10138: 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);
10139: return 1;
10140: }
10141: }
10142: }
10143:
10144: /*for (i=1; i<=imx; i++){
10145: for (m=firstpass; (m<lastpass); m++){
10146: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10147: }
10148:
10149: }*/
10150:
10151:
1.139 brouard 10152: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10153: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10154:
10155: return (0);
1.164 brouard 10156: /* endread:*/
1.136 brouard 10157: printf("Exiting calandcheckages: ");
10158: return (1);
10159: }
10160:
1.172 brouard 10161: #if defined(_MSC_VER)
10162: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10163: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10164: //#include "stdafx.h"
10165: //#include <stdio.h>
10166: //#include <tchar.h>
10167: //#include <windows.h>
10168: //#include <iostream>
10169: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10170:
10171: LPFN_ISWOW64PROCESS fnIsWow64Process;
10172:
10173: BOOL IsWow64()
10174: {
10175: BOOL bIsWow64 = FALSE;
10176:
10177: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10178: // (HANDLE, PBOOL);
10179:
10180: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10181:
10182: HMODULE module = GetModuleHandle(_T("kernel32"));
10183: const char funcName[] = "IsWow64Process";
10184: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10185: GetProcAddress(module, funcName);
10186:
10187: if (NULL != fnIsWow64Process)
10188: {
10189: if (!fnIsWow64Process(GetCurrentProcess(),
10190: &bIsWow64))
10191: //throw std::exception("Unknown error");
10192: printf("Unknown error\n");
10193: }
10194: return bIsWow64 != FALSE;
10195: }
10196: #endif
1.177 brouard 10197:
1.191 brouard 10198: void syscompilerinfo(int logged)
1.167 brouard 10199: {
10200: /* #include "syscompilerinfo.h"*/
1.185 brouard 10201: /* command line Intel compiler 32bit windows, XP compatible:*/
10202: /* /GS /W3 /Gy
10203: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10204: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10205: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10206: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10207: */
10208: /* 64 bits */
1.185 brouard 10209: /*
10210: /GS /W3 /Gy
10211: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10212: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10213: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10214: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10215: /* Optimization are useless and O3 is slower than O2 */
10216: /*
10217: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10218: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10219: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10220: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10221: */
1.186 brouard 10222: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10223: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10224: /PDB:"visual studio
10225: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10226: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10227: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10228: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10229: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10230: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10231: uiAccess='false'"
10232: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10233: /NOLOGO /TLBID:1
10234: */
1.177 brouard 10235: #if defined __INTEL_COMPILER
1.178 brouard 10236: #if defined(__GNUC__)
10237: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10238: #endif
1.177 brouard 10239: #elif defined(__GNUC__)
1.179 brouard 10240: #ifndef __APPLE__
1.174 brouard 10241: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10242: #endif
1.177 brouard 10243: struct utsname sysInfo;
1.178 brouard 10244: int cross = CROSS;
10245: if (cross){
10246: printf("Cross-");
1.191 brouard 10247: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10248: }
1.174 brouard 10249: #endif
10250:
1.171 brouard 10251: #include <stdint.h>
1.178 brouard 10252:
1.191 brouard 10253: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10254: #if defined(__clang__)
1.191 brouard 10255: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10256: #endif
10257: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10258: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10259: #endif
10260: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10261: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10262: #endif
10263: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10264: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10265: #endif
10266: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10267: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10268: #endif
10269: #if defined(_MSC_VER)
1.191 brouard 10270: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10271: #endif
10272: #if defined(__PGI)
1.191 brouard 10273: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10274: #endif
10275: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10276: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10277: #endif
1.191 brouard 10278: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10279:
1.167 brouard 10280: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10281: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10282: // Windows (x64 and x86)
1.191 brouard 10283: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10284: #elif __unix__ // all unices, not all compilers
10285: // Unix
1.191 brouard 10286: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10287: #elif __linux__
10288: // linux
1.191 brouard 10289: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10290: #elif __APPLE__
1.174 brouard 10291: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10292: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10293: #endif
10294:
10295: /* __MINGW32__ */
10296: /* __CYGWIN__ */
10297: /* __MINGW64__ */
10298: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10299: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10300: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10301: /* _WIN64 // Defined for applications for Win64. */
10302: /* _M_X64 // Defined for compilations that target x64 processors. */
10303: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10304:
1.167 brouard 10305: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10306: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10307: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10308: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10309: #else
1.191 brouard 10310: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10311: #endif
10312:
1.169 brouard 10313: #if defined(__GNUC__)
10314: # if defined(__GNUC_PATCHLEVEL__)
10315: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10316: + __GNUC_MINOR__ * 100 \
10317: + __GNUC_PATCHLEVEL__)
10318: # else
10319: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10320: + __GNUC_MINOR__ * 100)
10321: # endif
1.174 brouard 10322: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10323: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10324:
10325: if (uname(&sysInfo) != -1) {
10326: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10327: 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 10328: }
10329: else
10330: perror("uname() error");
1.179 brouard 10331: //#ifndef __INTEL_COMPILER
10332: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10333: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10334: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10335: #endif
1.169 brouard 10336: #endif
1.172 brouard 10337:
1.286 brouard 10338: // void main ()
1.172 brouard 10339: // {
1.169 brouard 10340: #if defined(_MSC_VER)
1.174 brouard 10341: if (IsWow64()){
1.191 brouard 10342: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10343: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10344: }
10345: else{
1.191 brouard 10346: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10347: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10348: }
1.172 brouard 10349: // printf("\nPress Enter to continue...");
10350: // getchar();
10351: // }
10352:
1.169 brouard 10353: #endif
10354:
1.167 brouard 10355:
1.219 brouard 10356: }
1.136 brouard 10357:
1.219 brouard 10358: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10359: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10360: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10361: /* double ftolpl = 1.e-10; */
1.180 brouard 10362: double age, agebase, agelim;
1.203 brouard 10363: double tot;
1.180 brouard 10364:
1.202 brouard 10365: strcpy(filerespl,"PL_");
10366: strcat(filerespl,fileresu);
10367: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10368: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10369: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10370: }
1.288 brouard 10371: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10372: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10373: pstamp(ficrespl);
1.288 brouard 10374: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10375: fprintf(ficrespl,"#Age ");
10376: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10377: fprintf(ficrespl,"\n");
1.180 brouard 10378:
1.219 brouard 10379: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10380:
1.219 brouard 10381: agebase=ageminpar;
10382: agelim=agemaxpar;
1.180 brouard 10383:
1.227 brouard 10384: /* i1=pow(2,ncoveff); */
1.234 brouard 10385: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10386: if (cptcovn < 1){i1=1;}
1.180 brouard 10387:
1.238 brouard 10388: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10389: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10390: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10391: continue;
1.235 brouard 10392:
1.238 brouard 10393: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10394: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10395: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10396: /* k=k+1; */
10397: /* to clean */
10398: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10399: fprintf(ficrespl,"#******");
10400: printf("#******");
10401: fprintf(ficlog,"#******");
10402: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10403: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10404: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10405: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10406: }
10407: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10408: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10409: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10410: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10411: }
10412: fprintf(ficrespl,"******\n");
10413: printf("******\n");
10414: fprintf(ficlog,"******\n");
10415: if(invalidvarcomb[k]){
10416: printf("\nCombination (%d) ignored because no case \n",k);
10417: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10418: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10419: continue;
10420: }
1.219 brouard 10421:
1.238 brouard 10422: fprintf(ficrespl,"#Age ");
10423: for(j=1;j<=cptcoveff;j++) {
10424: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10425: }
10426: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10427: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10428:
1.238 brouard 10429: for (age=agebase; age<=agelim; age++){
10430: /* for (age=agebase; age<=agebase; age++){ */
10431: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10432: fprintf(ficrespl,"%.0f ",age );
10433: for(j=1;j<=cptcoveff;j++)
10434: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10435: tot=0.;
10436: for(i=1; i<=nlstate;i++){
10437: tot += prlim[i][i];
10438: fprintf(ficrespl," %.5f", prlim[i][i]);
10439: }
10440: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10441: } /* Age */
10442: /* was end of cptcod */
10443: } /* cptcov */
10444: } /* nres */
1.219 brouard 10445: return 0;
1.180 brouard 10446: }
10447:
1.218 brouard 10448: 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 10449: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10450:
10451: /* Computes the back prevalence limit for any combination of covariate values
10452: * at any age between ageminpar and agemaxpar
10453: */
1.235 brouard 10454: int i, j, k, i1, nres=0 ;
1.217 brouard 10455: /* double ftolpl = 1.e-10; */
10456: double age, agebase, agelim;
10457: double tot;
1.218 brouard 10458: /* double ***mobaverage; */
10459: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10460:
10461: strcpy(fileresplb,"PLB_");
10462: strcat(fileresplb,fileresu);
10463: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10464: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10465: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10466: }
1.288 brouard 10467: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10468: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10469: pstamp(ficresplb);
1.288 brouard 10470: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10471: fprintf(ficresplb,"#Age ");
10472: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10473: fprintf(ficresplb,"\n");
10474:
1.218 brouard 10475:
10476: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10477:
10478: agebase=ageminpar;
10479: agelim=agemaxpar;
10480:
10481:
1.227 brouard 10482: i1=pow(2,cptcoveff);
1.218 brouard 10483: if (cptcovn < 1){i1=1;}
1.227 brouard 10484:
1.238 brouard 10485: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10486: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10487: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10488: continue;
10489: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10490: fprintf(ficresplb,"#******");
10491: printf("#******");
10492: fprintf(ficlog,"#******");
10493: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10494: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10495: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10496: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10497: }
10498: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10499: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10500: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10501: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10502: }
10503: fprintf(ficresplb,"******\n");
10504: printf("******\n");
10505: fprintf(ficlog,"******\n");
10506: if(invalidvarcomb[k]){
10507: printf("\nCombination (%d) ignored because no cases \n",k);
10508: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10509: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10510: continue;
10511: }
1.218 brouard 10512:
1.238 brouard 10513: fprintf(ficresplb,"#Age ");
10514: for(j=1;j<=cptcoveff;j++) {
10515: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10516: }
10517: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10518: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10519:
10520:
1.238 brouard 10521: for (age=agebase; age<=agelim; age++){
10522: /* for (age=agebase; age<=agebase; age++){ */
10523: if(mobilavproj > 0){
10524: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10525: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10526: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10527: }else if (mobilavproj == 0){
10528: 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);
10529: 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);
10530: exit(1);
10531: }else{
10532: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10533: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10534: /* printf("TOTOT\n"); */
10535: /* exit(1); */
1.238 brouard 10536: }
10537: fprintf(ficresplb,"%.0f ",age );
10538: for(j=1;j<=cptcoveff;j++)
10539: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10540: tot=0.;
10541: for(i=1; i<=nlstate;i++){
10542: tot += bprlim[i][i];
10543: fprintf(ficresplb," %.5f", bprlim[i][i]);
10544: }
10545: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10546: } /* Age */
10547: /* was end of cptcod */
1.255 brouard 10548: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10549: } /* end of any combination */
10550: } /* end of nres */
1.218 brouard 10551: /* hBijx(p, bage, fage); */
10552: /* fclose(ficrespijb); */
10553:
10554: return 0;
1.217 brouard 10555: }
1.218 brouard 10556:
1.180 brouard 10557: int hPijx(double *p, int bage, int fage){
10558: /*------------- h Pij x at various ages ------------*/
10559:
10560: int stepsize;
10561: int agelim;
10562: int hstepm;
10563: int nhstepm;
1.235 brouard 10564: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10565:
10566: double agedeb;
10567: double ***p3mat;
10568:
1.201 brouard 10569: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10570: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10571: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10572: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10573: }
10574: printf("Computing pij: result on file '%s' \n", filerespij);
10575: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10576:
10577: stepsize=(int) (stepm+YEARM-1)/YEARM;
10578: /*if (stepm<=24) stepsize=2;*/
10579:
10580: agelim=AGESUP;
10581: hstepm=stepsize*YEARM; /* Every year of age */
10582: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10583:
1.180 brouard 10584: /* hstepm=1; aff par mois*/
10585: pstamp(ficrespij);
10586: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10587: i1= pow(2,cptcoveff);
1.218 brouard 10588: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10589: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10590: /* k=k+1; */
1.235 brouard 10591: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10592: for(k=1; k<=i1;k++){
1.253 brouard 10593: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10594: continue;
1.183 brouard 10595: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10596: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10597: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10598: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10599: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10600: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10601: }
1.183 brouard 10602: fprintf(ficrespij,"******\n");
10603:
10604: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10605: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10606: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10607:
10608: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10609:
1.183 brouard 10610: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10611: oldm=oldms;savm=savms;
1.235 brouard 10612: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10613: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10614: for(i=1; i<=nlstate;i++)
10615: for(j=1; j<=nlstate+ndeath;j++)
10616: fprintf(ficrespij," %1d-%1d",i,j);
10617: fprintf(ficrespij,"\n");
10618: for (h=0; h<=nhstepm; h++){
10619: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10620: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10621: for(i=1; i<=nlstate;i++)
10622: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10623: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10624: fprintf(ficrespij,"\n");
10625: }
1.183 brouard 10626: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10627: fprintf(ficrespij,"\n");
10628: }
1.180 brouard 10629: /*}*/
10630: }
1.218 brouard 10631: return 0;
1.180 brouard 10632: }
1.218 brouard 10633:
10634: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10635: /*------------- h Bij x at various ages ------------*/
10636:
10637: int stepsize;
1.218 brouard 10638: /* int agelim; */
10639: int ageminl;
1.217 brouard 10640: int hstepm;
10641: int nhstepm;
1.238 brouard 10642: int h, i, i1, j, k, nres;
1.218 brouard 10643:
1.217 brouard 10644: double agedeb;
10645: double ***p3mat;
1.218 brouard 10646:
10647: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10648: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10649: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10650: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10651: }
10652: printf("Computing pij back: result on file '%s' \n", filerespijb);
10653: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10654:
10655: stepsize=(int) (stepm+YEARM-1)/YEARM;
10656: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10657:
1.218 brouard 10658: /* agelim=AGESUP; */
1.289 brouard 10659: ageminl=AGEINF; /* was 30 */
1.218 brouard 10660: hstepm=stepsize*YEARM; /* Every year of age */
10661: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10662:
10663: /* hstepm=1; aff par mois*/
10664: pstamp(ficrespijb);
1.255 brouard 10665: 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 10666: i1= pow(2,cptcoveff);
1.218 brouard 10667: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10668: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10669: /* k=k+1; */
1.238 brouard 10670: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10671: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10672: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10673: continue;
10674: fprintf(ficrespijb,"\n#****** ");
10675: for(j=1;j<=cptcoveff;j++)
10676: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10677: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10678: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10679: }
10680: fprintf(ficrespijb,"******\n");
1.264 brouard 10681: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10682: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10683: continue;
10684: }
10685:
10686: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10687: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10688: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
10689: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10690: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
10691:
10692: /* nhstepm=nhstepm*YEARM; aff par mois*/
10693:
1.266 brouard 10694: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10695: /* and memory limitations if stepm is small */
10696:
1.238 brouard 10697: /* oldm=oldms;savm=savms; */
10698: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10699: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10700: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10701: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10702: for(i=1; i<=nlstate;i++)
10703: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10704: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10705: fprintf(ficrespijb,"\n");
1.238 brouard 10706: for (h=0; h<=nhstepm; h++){
10707: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10708: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10709: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10710: for(i=1; i<=nlstate;i++)
10711: for(j=1; j<=nlstate+ndeath;j++)
10712: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10713: fprintf(ficrespijb,"\n");
10714: }
10715: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10716: fprintf(ficrespijb,"\n");
10717: } /* end age deb */
10718: } /* end combination */
10719: } /* end nres */
1.218 brouard 10720: return 0;
10721: } /* hBijx */
1.217 brouard 10722:
1.180 brouard 10723:
1.136 brouard 10724: /***********************************************/
10725: /**************** Main Program *****************/
10726: /***********************************************/
10727:
10728: int main(int argc, char *argv[])
10729: {
10730: #ifdef GSL
10731: const gsl_multimin_fminimizer_type *T;
10732: size_t iteri = 0, it;
10733: int rval = GSL_CONTINUE;
10734: int status = GSL_SUCCESS;
10735: double ssval;
10736: #endif
10737: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10738: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10739: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10740: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10741: int jj, ll, li, lj, lk;
1.136 brouard 10742: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10743: int num_filled;
1.136 brouard 10744: int itimes;
10745: int NDIM=2;
10746: int vpopbased=0;
1.235 brouard 10747: int nres=0;
1.258 brouard 10748: int endishere=0;
1.277 brouard 10749: int noffset=0;
1.274 brouard 10750: int ncurrv=0; /* Temporary variable */
10751:
1.164 brouard 10752: char ca[32], cb[32];
1.136 brouard 10753: /* FILE *fichtm; *//* Html File */
10754: /* FILE *ficgp;*/ /*Gnuplot File */
10755: struct stat info;
1.191 brouard 10756: double agedeb=0.;
1.194 brouard 10757:
10758: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10759: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10760:
1.165 brouard 10761: double fret;
1.191 brouard 10762: double dum=0.; /* Dummy variable */
1.136 brouard 10763: double ***p3mat;
1.218 brouard 10764: /* double ***mobaverage; */
1.164 brouard 10765:
10766: char line[MAXLINE];
1.197 brouard 10767: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10768:
1.234 brouard 10769: char modeltemp[MAXLINE];
1.230 brouard 10770: char resultline[MAXLINE];
10771:
1.136 brouard 10772: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10773: char *tok, *val; /* pathtot */
1.290 brouard 10774: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10775: int c, h , cpt, c2;
1.191 brouard 10776: int jl=0;
10777: int i1, j1, jk, stepsize=0;
1.194 brouard 10778: int count=0;
10779:
1.164 brouard 10780: int *tab;
1.136 brouard 10781: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 10782: int backcast=0;
1.136 brouard 10783: int mobilav=0,popforecast=0;
1.191 brouard 10784: int hstepm=0, nhstepm=0;
1.136 brouard 10785: int agemortsup;
10786: float sumlpop=0.;
10787: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10788: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10789:
1.191 brouard 10790: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10791: double ftolpl=FTOL;
10792: double **prlim;
1.217 brouard 10793: double **bprlim;
1.136 brouard 10794: double ***param; /* Matrix of parameters */
1.251 brouard 10795: double ***paramstart; /* Matrix of starting parameter values */
10796: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10797: double **matcov; /* Matrix of covariance */
1.203 brouard 10798: double **hess; /* Hessian matrix */
1.136 brouard 10799: double ***delti3; /* Scale */
10800: double *delti; /* Scale */
10801: double ***eij, ***vareij;
10802: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10803:
1.136 brouard 10804: double *epj, vepp;
1.164 brouard 10805:
1.273 brouard 10806: double dateprev1, dateprev2;
10807: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
10808: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
1.217 brouard 10809:
1.136 brouard 10810: double **ximort;
1.145 brouard 10811: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10812: int *dcwave;
10813:
1.164 brouard 10814: char z[1]="c";
1.136 brouard 10815:
10816: /*char *strt;*/
10817: char strtend[80];
1.126 brouard 10818:
1.164 brouard 10819:
1.126 brouard 10820: /* setlocale (LC_ALL, ""); */
10821: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10822: /* textdomain (PACKAGE); */
10823: /* setlocale (LC_CTYPE, ""); */
10824: /* setlocale (LC_MESSAGES, ""); */
10825:
10826: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10827: rstart_time = time(NULL);
10828: /* (void) gettimeofday(&start_time,&tzp);*/
10829: start_time = *localtime(&rstart_time);
1.126 brouard 10830: curr_time=start_time;
1.157 brouard 10831: /*tml = *localtime(&start_time.tm_sec);*/
10832: /* strcpy(strstart,asctime(&tml)); */
10833: strcpy(strstart,asctime(&start_time));
1.126 brouard 10834:
10835: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10836: /* tp.tm_sec = tp.tm_sec +86400; */
10837: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10838: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10839: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10840: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10841: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 10842: /* strt=asctime(&tmg); */
10843: /* printf("Time(after) =%s",strstart); */
10844: /* (void) time (&time_value);
10845: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
10846: * tm = *localtime(&time_value);
10847: * strstart=asctime(&tm);
10848: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
10849: */
10850:
10851: nberr=0; /* Number of errors and warnings */
10852: nbwarn=0;
1.184 brouard 10853: #ifdef WIN32
10854: _getcwd(pathcd, size);
10855: #else
1.126 brouard 10856: getcwd(pathcd, size);
1.184 brouard 10857: #endif
1.191 brouard 10858: syscompilerinfo(0);
1.196 brouard 10859: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 10860: if(argc <=1){
10861: printf("\nEnter the parameter file name: ");
1.205 brouard 10862: if(!fgets(pathr,FILENAMELENGTH,stdin)){
10863: printf("ERROR Empty parameter file name\n");
10864: goto end;
10865: }
1.126 brouard 10866: i=strlen(pathr);
10867: if(pathr[i-1]=='\n')
10868: pathr[i-1]='\0';
1.156 brouard 10869: i=strlen(pathr);
1.205 brouard 10870: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 10871: pathr[i-1]='\0';
1.205 brouard 10872: }
10873: i=strlen(pathr);
10874: if( i==0 ){
10875: printf("ERROR Empty parameter file name\n");
10876: goto end;
10877: }
10878: for (tok = pathr; tok != NULL; ){
1.126 brouard 10879: printf("Pathr |%s|\n",pathr);
10880: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
10881: printf("val= |%s| pathr=%s\n",val,pathr);
10882: strcpy (pathtot, val);
10883: if(pathr[0] == '\0') break; /* Dirty */
10884: }
10885: }
1.281 brouard 10886: else if (argc<=2){
10887: strcpy(pathtot,argv[1]);
10888: }
1.126 brouard 10889: else{
10890: strcpy(pathtot,argv[1]);
1.281 brouard 10891: strcpy(z,argv[2]);
10892: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 10893: }
10894: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
10895: /*cygwin_split_path(pathtot,path,optionfile);
10896: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
10897: /* cutv(path,optionfile,pathtot,'\\');*/
10898:
10899: /* Split argv[0], imach program to get pathimach */
10900: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
10901: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10902: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10903: /* strcpy(pathimach,argv[0]); */
10904: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
10905: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
10906: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 10907: #ifdef WIN32
10908: _chdir(path); /* Can be a relative path */
10909: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
10910: #else
1.126 brouard 10911: chdir(path); /* Can be a relative path */
1.184 brouard 10912: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
10913: #endif
10914: printf("Current directory %s!\n",pathcd);
1.126 brouard 10915: strcpy(command,"mkdir ");
10916: strcat(command,optionfilefiname);
10917: if((outcmd=system(command)) != 0){
1.169 brouard 10918: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 10919: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
10920: /* fclose(ficlog); */
10921: /* exit(1); */
10922: }
10923: /* if((imk=mkdir(optionfilefiname))<0){ */
10924: /* perror("mkdir"); */
10925: /* } */
10926:
10927: /*-------- arguments in the command line --------*/
10928:
1.186 brouard 10929: /* Main Log file */
1.126 brouard 10930: strcat(filelog, optionfilefiname);
10931: strcat(filelog,".log"); /* */
10932: if((ficlog=fopen(filelog,"w"))==NULL) {
10933: printf("Problem with logfile %s\n",filelog);
10934: goto end;
10935: }
10936: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 10937: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 10938: fprintf(ficlog,"\nEnter the parameter file name: \n");
10939: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
10940: path=%s \n\
10941: optionfile=%s\n\
10942: optionfilext=%s\n\
1.156 brouard 10943: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 10944:
1.197 brouard 10945: syscompilerinfo(1);
1.167 brouard 10946:
1.126 brouard 10947: printf("Local time (at start):%s",strstart);
10948: fprintf(ficlog,"Local time (at start): %s",strstart);
10949: fflush(ficlog);
10950: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 10951: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 10952:
10953: /* */
10954: strcpy(fileres,"r");
10955: strcat(fileres, optionfilefiname);
1.201 brouard 10956: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 10957: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 10958: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 10959:
1.186 brouard 10960: /* Main ---------arguments file --------*/
1.126 brouard 10961:
10962: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 10963: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
10964: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 10965: fflush(ficlog);
1.149 brouard 10966: /* goto end; */
10967: exit(70);
1.126 brouard 10968: }
10969:
10970: strcpy(filereso,"o");
1.201 brouard 10971: strcat(filereso,fileresu);
1.126 brouard 10972: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
10973: printf("Problem with Output resultfile: %s\n", filereso);
10974: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
10975: fflush(ficlog);
10976: goto end;
10977: }
1.278 brouard 10978: /*-------- Rewriting parameter file ----------*/
10979: strcpy(rfileres,"r"); /* "Rparameterfile */
10980: strcat(rfileres,optionfilefiname); /* Parameter file first name */
10981: strcat(rfileres,"."); /* */
10982: strcat(rfileres,optionfilext); /* Other files have txt extension */
10983: if((ficres =fopen(rfileres,"w"))==NULL) {
10984: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
10985: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
10986: fflush(ficlog);
10987: goto end;
10988: }
10989: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 10990:
1.278 brouard 10991:
1.126 brouard 10992: /* Reads comments: lines beginning with '#' */
10993: numlinepar=0;
1.277 brouard 10994: /* Is it a BOM UTF-8 Windows file? */
10995: /* First parameter line */
1.197 brouard 10996: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 10997: noffset=0;
10998: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
10999: {
11000: noffset=noffset+3;
11001: printf("# File is an UTF8 Bom.\n"); // 0xBF
11002: }
11003: else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
11004: {
11005: noffset=noffset+2;
11006: printf("# File is an UTF16BE BOM file\n");
11007: }
11008: else if( line[0] == 0 && line[1] == 0)
11009: {
11010: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11011: noffset=noffset+4;
11012: printf("# File is an UTF16BE BOM file\n");
11013: }
11014: } else{
11015: ;/*printf(" Not a BOM file\n");*/
11016: }
11017:
1.197 brouard 11018: /* If line starts with a # it is a comment */
1.277 brouard 11019: if (line[noffset] == '#') {
1.197 brouard 11020: numlinepar++;
11021: fputs(line,stdout);
11022: fputs(line,ficparo);
1.278 brouard 11023: fputs(line,ficres);
1.197 brouard 11024: fputs(line,ficlog);
11025: continue;
11026: }else
11027: break;
11028: }
11029: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11030: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11031: if (num_filled != 5) {
11032: printf("Should be 5 parameters\n");
1.283 brouard 11033: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11034: }
1.126 brouard 11035: numlinepar++;
1.197 brouard 11036: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11037: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11038: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11039: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11040: }
11041: /* Second parameter line */
11042: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11043: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11044: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11045: if (line[0] == '#') {
11046: numlinepar++;
1.283 brouard 11047: printf("%s",line);
11048: fprintf(ficres,"%s",line);
11049: fprintf(ficparo,"%s",line);
11050: fprintf(ficlog,"%s",line);
1.197 brouard 11051: continue;
11052: }else
11053: break;
11054: }
1.223 brouard 11055: 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", \
11056: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11057: if (num_filled != 11) {
11058: 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 11059: printf("but line=%s\n",line);
1.283 brouard 11060: 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");
11061: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11062: }
1.286 brouard 11063: if( lastpass > maxwav){
11064: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11065: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11066: fflush(ficlog);
11067: goto end;
11068: }
11069: 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 11070: 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 11071: 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 11072: 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 11073: }
1.203 brouard 11074: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11075: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11076: /* Third parameter line */
11077: while(fgets(line, MAXLINE, ficpar)) {
11078: /* If line starts with a # it is a comment */
11079: if (line[0] == '#') {
11080: numlinepar++;
1.283 brouard 11081: printf("%s",line);
11082: fprintf(ficres,"%s",line);
11083: fprintf(ficparo,"%s",line);
11084: fprintf(ficlog,"%s",line);
1.197 brouard 11085: continue;
11086: }else
11087: break;
11088: }
1.201 brouard 11089: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11090: if (num_filled != 1){
11091: printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
11092: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
1.197 brouard 11093: model[0]='\0';
11094: goto end;
11095: }
11096: else{
11097: if (model[0]=='+'){
11098: for(i=1; i<=strlen(model);i++)
11099: modeltemp[i-1]=model[i];
1.201 brouard 11100: strcpy(model,modeltemp);
1.197 brouard 11101: }
11102: }
1.199 brouard 11103: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11104: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11105: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11106: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11107: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11108: }
11109: /* 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); */
11110: /* numlinepar=numlinepar+3; /\* In general *\/ */
11111: /* 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 11112: /* 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); */
11113: /* 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 11114: fflush(ficlog);
1.190 brouard 11115: /* if(model[0]=='#'|| model[0]== '\0'){ */
11116: if(model[0]=='#'){
1.279 brouard 11117: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11118: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11119: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11120: if(mle != -1){
1.279 brouard 11121: 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 11122: exit(1);
11123: }
11124: }
1.126 brouard 11125: while((c=getc(ficpar))=='#' && c!= EOF){
11126: ungetc(c,ficpar);
11127: fgets(line, MAXLINE, ficpar);
11128: numlinepar++;
1.195 brouard 11129: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11130: z[0]=line[1];
11131: }
11132: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11133: fputs(line, stdout);
11134: //puts(line);
1.126 brouard 11135: fputs(line,ficparo);
11136: fputs(line,ficlog);
11137: }
11138: ungetc(c,ficpar);
11139:
11140:
1.290 brouard 11141: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11142: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11143: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11144: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11145: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11146: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11147: v1+v2*age+v2*v3 makes cptcovn = 3
11148: */
11149: if (strlen(model)>1)
1.187 brouard 11150: 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 11151: else
1.187 brouard 11152: ncovmodel=2; /* Constant and age */
1.133 brouard 11153: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11154: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11155: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11156: 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);
11157: 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);
11158: fflush(stdout);
11159: fclose (ficlog);
11160: goto end;
11161: }
1.126 brouard 11162: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11163: delti=delti3[1][1];
11164: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11165: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11166: /* We could also provide initial parameters values giving by simple logistic regression
11167: * only one way, that is without matrix product. We will have nlstate maximizations */
11168: /* for(i=1;i<nlstate;i++){ */
11169: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11170: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11171: /* } */
1.126 brouard 11172: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11173: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11174: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11175: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11176: fclose (ficparo);
11177: fclose (ficlog);
11178: goto end;
11179: exit(0);
1.220 brouard 11180: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11181: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11182: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11183: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11184: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11185: matcov=matrix(1,npar,1,npar);
1.203 brouard 11186: hess=matrix(1,npar,1,npar);
1.220 brouard 11187: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11188: /* Read guessed parameters */
1.126 brouard 11189: /* Reads comments: lines beginning with '#' */
11190: while((c=getc(ficpar))=='#' && c!= EOF){
11191: ungetc(c,ficpar);
11192: fgets(line, MAXLINE, ficpar);
11193: numlinepar++;
1.141 brouard 11194: fputs(line,stdout);
1.126 brouard 11195: fputs(line,ficparo);
11196: fputs(line,ficlog);
11197: }
11198: ungetc(c,ficpar);
11199:
11200: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11201: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11202: for(i=1; i <=nlstate; i++){
1.234 brouard 11203: j=0;
1.126 brouard 11204: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11205: if(jj==i) continue;
11206: j++;
11207: fscanf(ficpar,"%1d%1d",&i1,&j1);
11208: if ((i1 != i) || (j1 != jj)){
11209: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11210: It might be a problem of design; if ncovcol and the model are correct\n \
11211: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11212: exit(1);
11213: }
11214: fprintf(ficparo,"%1d%1d",i1,j1);
11215: if(mle==1)
11216: printf("%1d%1d",i,jj);
11217: fprintf(ficlog,"%1d%1d",i,jj);
11218: for(k=1; k<=ncovmodel;k++){
11219: fscanf(ficpar," %lf",¶m[i][j][k]);
11220: if(mle==1){
11221: printf(" %lf",param[i][j][k]);
11222: fprintf(ficlog," %lf",param[i][j][k]);
11223: }
11224: else
11225: fprintf(ficlog," %lf",param[i][j][k]);
11226: fprintf(ficparo," %lf",param[i][j][k]);
11227: }
11228: fscanf(ficpar,"\n");
11229: numlinepar++;
11230: if(mle==1)
11231: printf("\n");
11232: fprintf(ficlog,"\n");
11233: fprintf(ficparo,"\n");
1.126 brouard 11234: }
11235: }
11236: fflush(ficlog);
1.234 brouard 11237:
1.251 brouard 11238: /* Reads parameters values */
1.126 brouard 11239: p=param[1][1];
1.251 brouard 11240: pstart=paramstart[1][1];
1.126 brouard 11241:
11242: /* Reads comments: lines beginning with '#' */
11243: while((c=getc(ficpar))=='#' && c!= EOF){
11244: ungetc(c,ficpar);
11245: fgets(line, MAXLINE, ficpar);
11246: numlinepar++;
1.141 brouard 11247: fputs(line,stdout);
1.126 brouard 11248: fputs(line,ficparo);
11249: fputs(line,ficlog);
11250: }
11251: ungetc(c,ficpar);
11252:
11253: for(i=1; i <=nlstate; i++){
11254: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11255: fscanf(ficpar,"%1d%1d",&i1,&j1);
11256: if ( (i1-i) * (j1-j) != 0){
11257: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11258: exit(1);
11259: }
11260: printf("%1d%1d",i,j);
11261: fprintf(ficparo,"%1d%1d",i1,j1);
11262: fprintf(ficlog,"%1d%1d",i1,j1);
11263: for(k=1; k<=ncovmodel;k++){
11264: fscanf(ficpar,"%le",&delti3[i][j][k]);
11265: printf(" %le",delti3[i][j][k]);
11266: fprintf(ficparo," %le",delti3[i][j][k]);
11267: fprintf(ficlog," %le",delti3[i][j][k]);
11268: }
11269: fscanf(ficpar,"\n");
11270: numlinepar++;
11271: printf("\n");
11272: fprintf(ficparo,"\n");
11273: fprintf(ficlog,"\n");
1.126 brouard 11274: }
11275: }
11276: fflush(ficlog);
1.234 brouard 11277:
1.145 brouard 11278: /* Reads covariance matrix */
1.126 brouard 11279: delti=delti3[1][1];
1.220 brouard 11280:
11281:
1.126 brouard 11282: /* 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 11283:
1.126 brouard 11284: /* Reads comments: lines beginning with '#' */
11285: while((c=getc(ficpar))=='#' && c!= EOF){
11286: ungetc(c,ficpar);
11287: fgets(line, MAXLINE, ficpar);
11288: numlinepar++;
1.141 brouard 11289: fputs(line,stdout);
1.126 brouard 11290: fputs(line,ficparo);
11291: fputs(line,ficlog);
11292: }
11293: ungetc(c,ficpar);
1.220 brouard 11294:
1.126 brouard 11295: matcov=matrix(1,npar,1,npar);
1.203 brouard 11296: hess=matrix(1,npar,1,npar);
1.131 brouard 11297: for(i=1; i <=npar; i++)
11298: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11299:
1.194 brouard 11300: /* Scans npar lines */
1.126 brouard 11301: for(i=1; i <=npar; i++){
1.226 brouard 11302: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11303: if(count != 3){
1.226 brouard 11304: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11305: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11306: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11307: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11308: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11309: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11310: exit(1);
1.220 brouard 11311: }else{
1.226 brouard 11312: if(mle==1)
11313: printf("%1d%1d%d",i1,j1,jk);
11314: }
11315: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11316: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11317: for(j=1; j <=i; j++){
1.226 brouard 11318: fscanf(ficpar," %le",&matcov[i][j]);
11319: if(mle==1){
11320: printf(" %.5le",matcov[i][j]);
11321: }
11322: fprintf(ficlog," %.5le",matcov[i][j]);
11323: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11324: }
11325: fscanf(ficpar,"\n");
11326: numlinepar++;
11327: if(mle==1)
1.220 brouard 11328: printf("\n");
1.126 brouard 11329: fprintf(ficlog,"\n");
11330: fprintf(ficparo,"\n");
11331: }
1.194 brouard 11332: /* End of read covariance matrix npar lines */
1.126 brouard 11333: for(i=1; i <=npar; i++)
11334: for(j=i+1;j<=npar;j++)
1.226 brouard 11335: matcov[i][j]=matcov[j][i];
1.126 brouard 11336:
11337: if(mle==1)
11338: printf("\n");
11339: fprintf(ficlog,"\n");
11340:
11341: fflush(ficlog);
11342:
11343: } /* End of mle != -3 */
1.218 brouard 11344:
1.186 brouard 11345: /* Main data
11346: */
1.290 brouard 11347: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11348: /* num=lvector(1,n); */
11349: /* moisnais=vector(1,n); */
11350: /* annais=vector(1,n); */
11351: /* moisdc=vector(1,n); */
11352: /* andc=vector(1,n); */
11353: /* weight=vector(1,n); */
11354: /* agedc=vector(1,n); */
11355: /* cod=ivector(1,n); */
11356: /* for(i=1;i<=n;i++){ */
11357: num=lvector(firstobs,lastobs);
11358: moisnais=vector(firstobs,lastobs);
11359: annais=vector(firstobs,lastobs);
11360: moisdc=vector(firstobs,lastobs);
11361: andc=vector(firstobs,lastobs);
11362: weight=vector(firstobs,lastobs);
11363: agedc=vector(firstobs,lastobs);
11364: cod=ivector(firstobs,lastobs);
11365: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11366: num[i]=0;
11367: moisnais[i]=0;
11368: annais[i]=0;
11369: moisdc[i]=0;
11370: andc[i]=0;
11371: agedc[i]=0;
11372: cod[i]=0;
11373: weight[i]=1.0; /* Equal weights, 1 by default */
11374: }
1.290 brouard 11375: mint=matrix(1,maxwav,firstobs,lastobs);
11376: anint=matrix(1,maxwav,firstobs,lastobs);
11377: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11378: tab=ivector(1,NCOVMAX);
1.144 brouard 11379: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11380: 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 11381:
1.136 brouard 11382: /* Reads data from file datafile */
11383: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11384: goto end;
11385:
11386: /* Calculation of the number of parameters from char model */
1.234 brouard 11387: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11388: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11389: k=3 V4 Tvar[k=3]= 4 (from V4)
11390: k=2 V1 Tvar[k=2]= 1 (from V1)
11391: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11392: */
11393:
11394: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11395: TvarsDind=ivector(1,NCOVMAX); /* */
11396: TvarsD=ivector(1,NCOVMAX); /* */
11397: TvarsQind=ivector(1,NCOVMAX); /* */
11398: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11399: TvarF=ivector(1,NCOVMAX); /* */
11400: TvarFind=ivector(1,NCOVMAX); /* */
11401: TvarV=ivector(1,NCOVMAX); /* */
11402: TvarVind=ivector(1,NCOVMAX); /* */
11403: TvarA=ivector(1,NCOVMAX); /* */
11404: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11405: TvarFD=ivector(1,NCOVMAX); /* */
11406: TvarFDind=ivector(1,NCOVMAX); /* */
11407: TvarFQ=ivector(1,NCOVMAX); /* */
11408: TvarFQind=ivector(1,NCOVMAX); /* */
11409: TvarVD=ivector(1,NCOVMAX); /* */
11410: TvarVDind=ivector(1,NCOVMAX); /* */
11411: TvarVQ=ivector(1,NCOVMAX); /* */
11412: TvarVQind=ivector(1,NCOVMAX); /* */
11413:
1.230 brouard 11414: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11415: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11416: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11417: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11418: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11419: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11420: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11421: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11422: */
11423: /* For model-covariate k tells which data-covariate to use but
11424: because this model-covariate is a construction we invent a new column
11425: ncovcol + k1
11426: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11427: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11428: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11429: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11430: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11431: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11432: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11433: */
1.145 brouard 11434: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11435: 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 11436: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11437: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11438: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11439: 4 covariates (3 plus signs)
11440: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11441: */
1.230 brouard 11442: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11443: * individual dummy, fixed or varying:
11444: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11445: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11446: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11447: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11448: * Tmodelind[1]@9={9,0,3,2,}*/
11449: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11450: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11451: * individual quantitative, fixed or varying:
11452: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11453: * 3, 1, 0, 0, 0, 0, 0, 0},
11454: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11455: /* Main decodemodel */
11456:
1.187 brouard 11457:
1.223 brouard 11458: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11459: goto end;
11460:
1.137 brouard 11461: if((double)(lastobs-imx)/(double)imx > 1.10){
11462: nbwarn++;
11463: 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);
11464: 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);
11465: }
1.136 brouard 11466: /* if(mle==1){*/
1.137 brouard 11467: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11468: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11469: }
11470:
11471: /*-calculation of age at interview from date of interview and age at death -*/
11472: agev=matrix(1,maxwav,1,imx);
11473:
11474: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11475: goto end;
11476:
1.126 brouard 11477:
1.136 brouard 11478: agegomp=(int)agemin;
1.290 brouard 11479: free_vector(moisnais,firstobs,lastobs);
11480: free_vector(annais,firstobs,lastobs);
1.126 brouard 11481: /* free_matrix(mint,1,maxwav,1,n);
11482: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11483: /* free_vector(moisdc,1,n); */
11484: /* free_vector(andc,1,n); */
1.145 brouard 11485: /* */
11486:
1.126 brouard 11487: wav=ivector(1,imx);
1.214 brouard 11488: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11489: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11490: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11491: 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.*/
11492: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11493: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11494:
11495: /* Concatenates waves */
1.214 brouard 11496: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11497: Death is a valid wave (if date is known).
11498: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11499: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11500: and mw[mi+1][i]. dh depends on stepm.
11501: */
11502:
1.126 brouard 11503: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11504: /* Concatenates waves */
1.145 brouard 11505:
1.290 brouard 11506: free_vector(moisdc,firstobs,lastobs);
11507: free_vector(andc,firstobs,lastobs);
1.215 brouard 11508:
1.126 brouard 11509: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11510: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11511: ncodemax[1]=1;
1.145 brouard 11512: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11513: cptcoveff=0;
1.220 brouard 11514: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11515: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11516: }
11517:
11518: ncovcombmax=pow(2,cptcoveff);
11519: invalidvarcomb=ivector(1, ncovcombmax);
11520: for(i=1;i<ncovcombmax;i++)
11521: invalidvarcomb[i]=0;
11522:
1.211 brouard 11523: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11524: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11525: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11526:
1.200 brouard 11527: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11528: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11529: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11530: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11531: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11532: * (currently 0 or 1) in the data.
11533: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11534: * corresponding modality (h,j).
11535: */
11536:
1.145 brouard 11537: h=0;
11538: /*if (cptcovn > 0) */
1.126 brouard 11539: m=pow(2,cptcoveff);
11540:
1.144 brouard 11541: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11542: * For k=4 covariates, h goes from 1 to m=2**k
11543: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11544: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11545: * h\k 1 2 3 4
1.143 brouard 11546: *______________________________
11547: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11548: * 2 2 1 1 1
11549: * 3 i=2 1 2 1 1
11550: * 4 2 2 1 1
11551: * 5 i=3 1 i=2 1 2 1
11552: * 6 2 1 2 1
11553: * 7 i=4 1 2 2 1
11554: * 8 2 2 2 1
1.197 brouard 11555: * 9 i=5 1 i=3 1 i=2 1 2
11556: * 10 2 1 1 2
11557: * 11 i=6 1 2 1 2
11558: * 12 2 2 1 2
11559: * 13 i=7 1 i=4 1 2 2
11560: * 14 2 1 2 2
11561: * 15 i=8 1 2 2 2
11562: * 16 2 2 2 2
1.143 brouard 11563: */
1.212 brouard 11564: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11565: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11566: * and the value of each covariate?
11567: * V1=1, V2=1, V3=2, V4=1 ?
11568: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11569: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11570: * In order to get the real value in the data, we use nbcode
11571: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11572: * We are keeping this crazy system in order to be able (in the future?)
11573: * to have more than 2 values (0 or 1) for a covariate.
11574: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11575: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11576: * bbbbbbbb
11577: * 76543210
11578: * h-1 00000101 (6-1=5)
1.219 brouard 11579: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11580: * &
11581: * 1 00000001 (1)
1.219 brouard 11582: * 00000000 = 1 & ((h-1) >> (k-1))
11583: * +1= 00000001 =1
1.211 brouard 11584: *
11585: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11586: * h' 1101 =2^3+2^2+0x2^1+2^0
11587: * >>k' 11
11588: * & 00000001
11589: * = 00000001
11590: * +1 = 00000010=2 = codtabm(14,3)
11591: * Reverse h=6 and m=16?
11592: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11593: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11594: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11595: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11596: * V3=decodtabm(14,3,2**4)=2
11597: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11598: *(h-1) >> (j-1) 0011 =13 >> 2
11599: * &1 000000001
11600: * = 000000001
11601: * +1= 000000010 =2
11602: * 2211
11603: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11604: * V3=2
1.220 brouard 11605: * codtabm and decodtabm are identical
1.211 brouard 11606: */
11607:
1.145 brouard 11608:
11609: free_ivector(Ndum,-1,NCOVMAX);
11610:
11611:
1.126 brouard 11612:
1.186 brouard 11613: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11614: strcpy(optionfilegnuplot,optionfilefiname);
11615: if(mle==-3)
1.201 brouard 11616: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11617: strcat(optionfilegnuplot,".gp");
11618:
11619: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11620: printf("Problem with file %s",optionfilegnuplot);
11621: }
11622: else{
1.204 brouard 11623: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11624: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11625: //fprintf(ficgp,"set missing 'NaNq'\n");
11626: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11627: }
11628: /* fclose(ficgp);*/
1.186 brouard 11629:
11630:
11631: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11632:
11633: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11634: if(mle==-3)
1.201 brouard 11635: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11636: strcat(optionfilehtm,".htm");
11637: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11638: printf("Problem with %s \n",optionfilehtm);
11639: exit(0);
1.126 brouard 11640: }
11641:
11642: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11643: strcat(optionfilehtmcov,"-cov.htm");
11644: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11645: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11646: }
11647: else{
11648: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11649: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11650: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11651: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11652: }
11653:
1.213 brouard 11654: 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 11655: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11656: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11657: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11658: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11659: \n\
11660: <hr size=\"2\" color=\"#EC5E5E\">\
11661: <ul><li><h4>Parameter files</h4>\n\
11662: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11663: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11664: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11665: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11666: - Date and time at start: %s</ul>\n",\
11667: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11668: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11669: fileres,fileres,\
11670: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11671: fflush(fichtm);
11672:
11673: strcpy(pathr,path);
11674: strcat(pathr,optionfilefiname);
1.184 brouard 11675: #ifdef WIN32
11676: _chdir(optionfilefiname); /* Move to directory named optionfile */
11677: #else
1.126 brouard 11678: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11679: #endif
11680:
1.126 brouard 11681:
1.220 brouard 11682: /* Calculates basic frequencies. Computes observed prevalence at single age
11683: and for any valid combination of covariates
1.126 brouard 11684: and prints on file fileres'p'. */
1.251 brouard 11685: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11686: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11687:
11688: fprintf(fichtm,"\n");
1.286 brouard 11689: 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 11690: ftol, stepm);
11691: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11692: ncurrv=1;
11693: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11694: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11695: ncurrv=i;
11696: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11697: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11698: ncurrv=i;
11699: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11700: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11701: ncurrv=i;
11702: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11703: 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", \
11704: nlstate, ndeath, maxwav, mle, weightopt);
11705:
11706: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11707: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11708:
11709:
11710: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11711: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11712: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11713: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11714: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11715: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11716: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11717: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11718: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11719:
1.126 brouard 11720: /* For Powell, parameters are in a vector p[] starting at p[1]
11721: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11722: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11723:
11724: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11725: /* For mortality only */
1.126 brouard 11726: if (mle==-3){
1.136 brouard 11727: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11728: for(i=1;i<=NDIM;i++)
11729: for(j=1;j<=NDIM;j++)
11730: ximort[i][j]=0.;
1.186 brouard 11731: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11732: cens=ivector(firstobs,lastobs);
11733: ageexmed=vector(firstobs,lastobs);
11734: agecens=vector(firstobs,lastobs);
11735: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11736:
1.126 brouard 11737: for (i=1; i<=imx; i++){
11738: dcwave[i]=-1;
11739: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11740: if (s[m][i]>nlstate) {
11741: dcwave[i]=m;
11742: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11743: break;
11744: }
1.126 brouard 11745: }
1.226 brouard 11746:
1.126 brouard 11747: for (i=1; i<=imx; i++) {
11748: if (wav[i]>0){
1.226 brouard 11749: ageexmed[i]=agev[mw[1][i]][i];
11750: j=wav[i];
11751: agecens[i]=1.;
11752:
11753: if (ageexmed[i]> 1 && wav[i] > 0){
11754: agecens[i]=agev[mw[j][i]][i];
11755: cens[i]= 1;
11756: }else if (ageexmed[i]< 1)
11757: cens[i]= -1;
11758: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11759: cens[i]=0 ;
1.126 brouard 11760: }
11761: else cens[i]=-1;
11762: }
11763:
11764: for (i=1;i<=NDIM;i++) {
11765: for (j=1;j<=NDIM;j++)
1.226 brouard 11766: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11767: }
11768:
1.145 brouard 11769: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 11770: /*printf("%lf %lf", p[1], p[2]);*/
11771:
11772:
1.136 brouard 11773: #ifdef GSL
11774: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11775: #else
1.126 brouard 11776: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11777: #endif
1.201 brouard 11778: strcpy(filerespow,"POW-MORT_");
11779: strcat(filerespow,fileresu);
1.126 brouard 11780: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11781: printf("Problem with resultfile: %s\n", filerespow);
11782: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11783: }
1.136 brouard 11784: #ifdef GSL
11785: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11786: #else
1.126 brouard 11787: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11788: #endif
1.126 brouard 11789: /* for (i=1;i<=nlstate;i++)
11790: for(j=1;j<=nlstate+ndeath;j++)
11791: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11792: */
11793: fprintf(ficrespow,"\n");
1.136 brouard 11794: #ifdef GSL
11795: /* gsl starts here */
11796: T = gsl_multimin_fminimizer_nmsimplex;
11797: gsl_multimin_fminimizer *sfm = NULL;
11798: gsl_vector *ss, *x;
11799: gsl_multimin_function minex_func;
11800:
11801: /* Initial vertex size vector */
11802: ss = gsl_vector_alloc (NDIM);
11803:
11804: if (ss == NULL){
11805: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11806: }
11807: /* Set all step sizes to 1 */
11808: gsl_vector_set_all (ss, 0.001);
11809:
11810: /* Starting point */
1.126 brouard 11811:
1.136 brouard 11812: x = gsl_vector_alloc (NDIM);
11813:
11814: if (x == NULL){
11815: gsl_vector_free(ss);
11816: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11817: }
11818:
11819: /* Initialize method and iterate */
11820: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11821: /* gsl_vector_set(x, 0, 0.0268); */
11822: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11823: gsl_vector_set(x, 0, p[1]);
11824: gsl_vector_set(x, 1, p[2]);
11825:
11826: minex_func.f = &gompertz_f;
11827: minex_func.n = NDIM;
11828: minex_func.params = (void *)&p; /* ??? */
11829:
11830: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11831: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
11832:
11833: printf("Iterations beginning .....\n\n");
11834: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
11835:
11836: iteri=0;
11837: while (rval == GSL_CONTINUE){
11838: iteri++;
11839: status = gsl_multimin_fminimizer_iterate(sfm);
11840:
11841: if (status) printf("error: %s\n", gsl_strerror (status));
11842: fflush(0);
11843:
11844: if (status)
11845: break;
11846:
11847: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
11848: ssval = gsl_multimin_fminimizer_size (sfm);
11849:
11850: if (rval == GSL_SUCCESS)
11851: printf ("converged to a local maximum at\n");
11852:
11853: printf("%5d ", iteri);
11854: for (it = 0; it < NDIM; it++){
11855: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
11856: }
11857: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
11858: }
11859:
11860: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
11861:
11862: gsl_vector_free(x); /* initial values */
11863: gsl_vector_free(ss); /* inital step size */
11864: for (it=0; it<NDIM; it++){
11865: p[it+1]=gsl_vector_get(sfm->x,it);
11866: fprintf(ficrespow," %.12lf", p[it]);
11867: }
11868: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
11869: #endif
11870: #ifdef POWELL
11871: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
11872: #endif
1.126 brouard 11873: fclose(ficrespow);
11874:
1.203 brouard 11875: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 11876:
11877: for(i=1; i <=NDIM; i++)
11878: for(j=i+1;j<=NDIM;j++)
1.220 brouard 11879: matcov[i][j]=matcov[j][i];
1.126 brouard 11880:
11881: printf("\nCovariance matrix\n ");
1.203 brouard 11882: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 11883: for(i=1; i <=NDIM; i++) {
11884: for(j=1;j<=NDIM;j++){
1.220 brouard 11885: printf("%f ",matcov[i][j]);
11886: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 11887: }
1.203 brouard 11888: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 11889: }
11890:
11891: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 11892: for (i=1;i<=NDIM;i++) {
1.126 brouard 11893: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 11894: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
11895: }
1.126 brouard 11896: lsurv=vector(1,AGESUP);
11897: lpop=vector(1,AGESUP);
11898: tpop=vector(1,AGESUP);
11899: lsurv[agegomp]=100000;
11900:
11901: for (k=agegomp;k<=AGESUP;k++) {
11902: agemortsup=k;
11903: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
11904: }
11905:
11906: for (k=agegomp;k<agemortsup;k++)
11907: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
11908:
11909: for (k=agegomp;k<agemortsup;k++){
11910: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
11911: sumlpop=sumlpop+lpop[k];
11912: }
11913:
11914: tpop[agegomp]=sumlpop;
11915: for (k=agegomp;k<(agemortsup-3);k++){
11916: /* tpop[k+1]=2;*/
11917: tpop[k+1]=tpop[k]-lpop[k];
11918: }
11919:
11920:
11921: printf("\nAge lx qx dx Lx Tx e(x)\n");
11922: for (k=agegomp;k<(agemortsup-2);k++)
11923: 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]);
11924:
11925:
11926: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 11927: ageminpar=50;
11928: agemaxpar=100;
1.194 brouard 11929: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
11930: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11931: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11932: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
11933: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11934: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11935: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 11936: }else{
11937: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
11938: 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 11939: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 11940: }
1.201 brouard 11941: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 11942: stepm, weightopt,\
11943: model,imx,p,matcov,agemortsup);
11944:
11945: free_vector(lsurv,1,AGESUP);
11946: free_vector(lpop,1,AGESUP);
11947: free_vector(tpop,1,AGESUP);
1.220 brouard 11948: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 11949: free_ivector(dcwave,firstobs,lastobs);
11950: free_vector(agecens,firstobs,lastobs);
11951: free_vector(ageexmed,firstobs,lastobs);
11952: free_ivector(cens,firstobs,lastobs);
1.220 brouard 11953: #ifdef GSL
1.136 brouard 11954: #endif
1.186 brouard 11955: } /* Endof if mle==-3 mortality only */
1.205 brouard 11956: /* Standard */
11957: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
11958: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11959: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 11960: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 11961: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11962: for (k=1; k<=npar;k++)
11963: printf(" %d %8.5f",k,p[k]);
11964: printf("\n");
1.205 brouard 11965: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
11966: /* mlikeli uses func not funcone */
1.247 brouard 11967: /* for(i=1;i<nlstate;i++){ */
11968: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11969: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11970: /* } */
1.205 brouard 11971: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
11972: }
11973: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
11974: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11975: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
11976: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11977: }
11978: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 11979: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11980: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11981: for (k=1; k<=npar;k++)
11982: printf(" %d %8.5f",k,p[k]);
11983: printf("\n");
11984:
11985: /*--------- results files --------------*/
1.283 brouard 11986: /* 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 11987:
11988:
11989: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11990: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11991: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11992: for(i=1,jk=1; i <=nlstate; i++){
11993: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 11994: if (k != i) {
11995: printf("%d%d ",i,k);
11996: fprintf(ficlog,"%d%d ",i,k);
11997: fprintf(ficres,"%1d%1d ",i,k);
11998: for(j=1; j <=ncovmodel; j++){
11999: printf("%12.7f ",p[jk]);
12000: fprintf(ficlog,"%12.7f ",p[jk]);
12001: fprintf(ficres,"%12.7f ",p[jk]);
12002: jk++;
12003: }
12004: printf("\n");
12005: fprintf(ficlog,"\n");
12006: fprintf(ficres,"\n");
12007: }
1.126 brouard 12008: }
12009: }
1.203 brouard 12010: if(mle != 0){
12011: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12012: ftolhess=ftol; /* Usually correct */
1.203 brouard 12013: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12014: 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");
12015: 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");
12016: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12017: for(k=1; k <=(nlstate+ndeath); k++){
12018: if (k != i) {
12019: printf("%d%d ",i,k);
12020: fprintf(ficlog,"%d%d ",i,k);
12021: for(j=1; j <=ncovmodel; j++){
12022: 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]));
12023: 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]));
12024: jk++;
12025: }
12026: printf("\n");
12027: fprintf(ficlog,"\n");
12028: }
12029: }
1.193 brouard 12030: }
1.203 brouard 12031: } /* end of hesscov and Wald tests */
1.225 brouard 12032:
1.203 brouard 12033: /* */
1.126 brouard 12034: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12035: printf("# Scales (for hessian or gradient estimation)\n");
12036: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12037: for(i=1,jk=1; i <=nlstate; i++){
12038: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12039: if (j!=i) {
12040: fprintf(ficres,"%1d%1d",i,j);
12041: printf("%1d%1d",i,j);
12042: fprintf(ficlog,"%1d%1d",i,j);
12043: for(k=1; k<=ncovmodel;k++){
12044: printf(" %.5e",delti[jk]);
12045: fprintf(ficlog," %.5e",delti[jk]);
12046: fprintf(ficres," %.5e",delti[jk]);
12047: jk++;
12048: }
12049: printf("\n");
12050: fprintf(ficlog,"\n");
12051: fprintf(ficres,"\n");
12052: }
1.126 brouard 12053: }
12054: }
12055:
12056: 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 12057: if(mle >= 1) /* To big for the screen */
1.126 brouard 12058: 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");
12059: 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");
12060: /* # 121 Var(a12)\n\ */
12061: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12062: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12063: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12064: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12065: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12066: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12067: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12068:
12069:
12070: /* Just to have a covariance matrix which will be more understandable
12071: even is we still don't want to manage dictionary of variables
12072: */
12073: for(itimes=1;itimes<=2;itimes++){
12074: jj=0;
12075: for(i=1; i <=nlstate; i++){
1.225 brouard 12076: for(j=1; j <=nlstate+ndeath; j++){
12077: if(j==i) continue;
12078: for(k=1; k<=ncovmodel;k++){
12079: jj++;
12080: ca[0]= k+'a'-1;ca[1]='\0';
12081: if(itimes==1){
12082: if(mle>=1)
12083: printf("#%1d%1d%d",i,j,k);
12084: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12085: fprintf(ficres,"#%1d%1d%d",i,j,k);
12086: }else{
12087: if(mle>=1)
12088: printf("%1d%1d%d",i,j,k);
12089: fprintf(ficlog,"%1d%1d%d",i,j,k);
12090: fprintf(ficres,"%1d%1d%d",i,j,k);
12091: }
12092: ll=0;
12093: for(li=1;li <=nlstate; li++){
12094: for(lj=1;lj <=nlstate+ndeath; lj++){
12095: if(lj==li) continue;
12096: for(lk=1;lk<=ncovmodel;lk++){
12097: ll++;
12098: if(ll<=jj){
12099: cb[0]= lk +'a'-1;cb[1]='\0';
12100: if(ll<jj){
12101: if(itimes==1){
12102: if(mle>=1)
12103: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12104: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12105: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12106: }else{
12107: if(mle>=1)
12108: printf(" %.5e",matcov[jj][ll]);
12109: fprintf(ficlog," %.5e",matcov[jj][ll]);
12110: fprintf(ficres," %.5e",matcov[jj][ll]);
12111: }
12112: }else{
12113: if(itimes==1){
12114: if(mle>=1)
12115: printf(" Var(%s%1d%1d)",ca,i,j);
12116: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12117: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12118: }else{
12119: if(mle>=1)
12120: printf(" %.7e",matcov[jj][ll]);
12121: fprintf(ficlog," %.7e",matcov[jj][ll]);
12122: fprintf(ficres," %.7e",matcov[jj][ll]);
12123: }
12124: }
12125: }
12126: } /* end lk */
12127: } /* end lj */
12128: } /* end li */
12129: if(mle>=1)
12130: printf("\n");
12131: fprintf(ficlog,"\n");
12132: fprintf(ficres,"\n");
12133: numlinepar++;
12134: } /* end k*/
12135: } /*end j */
1.126 brouard 12136: } /* end i */
12137: } /* end itimes */
12138:
12139: fflush(ficlog);
12140: fflush(ficres);
1.225 brouard 12141: while(fgets(line, MAXLINE, ficpar)) {
12142: /* If line starts with a # it is a comment */
12143: if (line[0] == '#') {
12144: numlinepar++;
12145: fputs(line,stdout);
12146: fputs(line,ficparo);
12147: fputs(line,ficlog);
12148: continue;
12149: }else
12150: break;
12151: }
12152:
1.209 brouard 12153: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12154: /* ungetc(c,ficpar); */
12155: /* fgets(line, MAXLINE, ficpar); */
12156: /* fputs(line,stdout); */
12157: /* fputs(line,ficparo); */
12158: /* } */
12159: /* ungetc(c,ficpar); */
1.126 brouard 12160:
12161: estepm=0;
1.209 brouard 12162: 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 12163:
12164: if (num_filled != 6) {
12165: 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);
12166: 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);
12167: goto end;
12168: }
12169: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12170: }
12171: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12172: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12173:
1.209 brouard 12174: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12175: if (estepm==0 || estepm < stepm) estepm=stepm;
12176: if (fage <= 2) {
12177: bage = ageminpar;
12178: fage = agemaxpar;
12179: }
12180:
12181: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12182: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12183: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12184:
1.186 brouard 12185: /* Other stuffs, more or less useful */
1.254 brouard 12186: while(fgets(line, MAXLINE, ficpar)) {
12187: /* If line starts with a # it is a comment */
12188: if (line[0] == '#') {
12189: numlinepar++;
12190: fputs(line,stdout);
12191: fputs(line,ficparo);
12192: fputs(line,ficlog);
12193: continue;
12194: }else
12195: break;
12196: }
12197:
12198: 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){
12199:
12200: if (num_filled != 7) {
12201: 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);
12202: 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);
12203: goto end;
12204: }
12205: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12206: 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);
12207: 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);
12208: 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 12209: }
1.254 brouard 12210:
12211: while(fgets(line, MAXLINE, ficpar)) {
12212: /* If line starts with a # it is a comment */
12213: if (line[0] == '#') {
12214: numlinepar++;
12215: fputs(line,stdout);
12216: fputs(line,ficparo);
12217: fputs(line,ficlog);
12218: continue;
12219: }else
12220: break;
1.126 brouard 12221: }
12222:
12223:
12224: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12225: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12226:
1.254 brouard 12227: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12228: if (num_filled != 1) {
12229: 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);
12230: 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);
12231: goto end;
12232: }
12233: printf("pop_based=%d\n",popbased);
12234: fprintf(ficlog,"pop_based=%d\n",popbased);
12235: fprintf(ficparo,"pop_based=%d\n",popbased);
12236: fprintf(ficres,"pop_based=%d\n",popbased);
12237: }
12238:
1.258 brouard 12239: /* Results */
12240: nresult=0;
12241: do{
12242: if(!fgets(line, MAXLINE, ficpar)){
12243: endishere=1;
12244: parameterline=14;
12245: }else if (line[0] == '#') {
12246: /* If line starts with a # it is a comment */
1.254 brouard 12247: numlinepar++;
12248: fputs(line,stdout);
12249: fputs(line,ficparo);
12250: fputs(line,ficlog);
12251: continue;
1.258 brouard 12252: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12253: parameterline=11;
12254: else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
12255: parameterline=12;
12256: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12257: parameterline=13;
12258: else{
12259: parameterline=14;
1.254 brouard 12260: }
1.258 brouard 12261: switch (parameterline){
12262: case 11:
12263: 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){
12264: if (num_filled != 8) {
12265: 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\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12266: 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 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12267: goto end;
12268: }
12269: 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);
12270: 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);
12271: 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);
12272: 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);
12273: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12274: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12275: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
12276:
1.258 brouard 12277: }
1.254 brouard 12278: break;
1.258 brouard 12279: case 12:
12280: /*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);*/
12281: 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){
12282: if (num_filled != 8) {
1.262 brouard 12283: 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);
12284: 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);
1.258 brouard 12285: goto end;
12286: }
12287: 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);
12288: 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);
12289: 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);
12290: 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);
12291: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12292: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12293: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.258 brouard 12294: }
1.230 brouard 12295: break;
1.258 brouard 12296: case 13:
12297: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12298: if (num_filled == 0){
12299: resultline[0]='\0';
12300: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12301: 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);
12302: break;
12303: } else if (num_filled != 1){
12304: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12305: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12306: }
12307: nresult++; /* Sum of resultlines */
12308: printf("Result %d: result=%s\n",nresult, resultline);
12309: if(nresult > MAXRESULTLINES){
12310: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12311: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12312: goto end;
12313: }
12314: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12315: fprintf(ficparo,"result: %s\n",resultline);
12316: fprintf(ficres,"result: %s\n",resultline);
12317: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12318: break;
1.258 brouard 12319: case 14:
1.259 brouard 12320: if(ncovmodel >2 && nresult==0 ){
12321: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12322: goto end;
12323: }
1.259 brouard 12324: break;
1.258 brouard 12325: default:
12326: nresult=1;
12327: decoderesult(".",nresult ); /* No covariate */
12328: }
12329: } /* End switch parameterline */
12330: }while(endishere==0); /* End do */
1.126 brouard 12331:
1.230 brouard 12332: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12333: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12334:
12335: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12336: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12337: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12338: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12339: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12340: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12341: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12342: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12343: }else{
1.270 brouard 12344: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
12345: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
1.220 brouard 12346: }
12347: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.258 brouard 12348: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
1.273 brouard 12349: jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
1.220 brouard 12350:
1.225 brouard 12351: /*------------ free_vector -------------*/
12352: /* chdir(path); */
1.220 brouard 12353:
1.215 brouard 12354: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12355: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12356: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12357: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12358: free_lvector(num,firstobs,lastobs);
12359: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12360: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12361: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12362: fclose(ficparo);
12363: fclose(ficres);
1.220 brouard 12364:
12365:
1.186 brouard 12366: /* Other results (useful)*/
1.220 brouard 12367:
12368:
1.126 brouard 12369: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12370: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12371: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12372: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12373: fclose(ficrespl);
12374:
12375: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12376: /*#include "hpijx.h"*/
12377: hPijx(p, bage, fage);
1.145 brouard 12378: fclose(ficrespij);
1.227 brouard 12379:
1.220 brouard 12380: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12381: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12382: k=1;
1.126 brouard 12383: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12384:
1.269 brouard 12385: /* Prevalence for each covariate combination in probs[age][status][cov] */
12386: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12387: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12388: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12389: for(k=1;k<=ncovcombmax;k++)
12390: probs[i][j][k]=0.;
1.269 brouard 12391: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12392: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12393: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12394: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12395: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12396: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12397: for(k=1;k<=ncovcombmax;k++)
12398: mobaverages[i][j][k]=0.;
1.219 brouard 12399: mobaverage=mobaverages;
12400: if (mobilav!=0) {
1.235 brouard 12401: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12402: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12403: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12404: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12405: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12406: }
1.269 brouard 12407: } else if (mobilavproj !=0) {
1.235 brouard 12408: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12409: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12410: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12411: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12412: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12413: }
1.269 brouard 12414: }else{
12415: printf("Internal error moving average\n");
12416: fflush(stdout);
12417: exit(1);
1.219 brouard 12418: }
12419: }/* end if moving average */
1.227 brouard 12420:
1.126 brouard 12421: /*---------- Forecasting ------------------*/
12422: if(prevfcast==1){
12423: /* if(stepm ==1){*/
1.269 brouard 12424: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 12425: }
1.269 brouard 12426:
12427: /* Backcasting */
1.217 brouard 12428: if(backcast==1){
1.219 brouard 12429: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12430: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12431: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12432:
12433: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12434:
12435: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12436:
1.219 brouard 12437: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12438: fclose(ficresplb);
12439:
1.222 brouard 12440: hBijx(p, bage, fage, mobaverage);
12441: fclose(ficrespijb);
1.219 brouard 12442:
1.269 brouard 12443: prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
12444: mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
12445: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12446:
12447:
1.269 brouard 12448: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12449: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12450: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12451: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.269 brouard 12452: } /* end Backcasting */
1.268 brouard 12453:
1.186 brouard 12454:
12455: /* ------ Other prevalence ratios------------ */
1.126 brouard 12456:
1.215 brouard 12457: free_ivector(wav,1,imx);
12458: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12459: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12460: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12461:
12462:
1.127 brouard 12463: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12464:
1.201 brouard 12465: strcpy(filerese,"E_");
12466: strcat(filerese,fileresu);
1.126 brouard 12467: if((ficreseij=fopen(filerese,"w"))==NULL) {
12468: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12469: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12470: }
1.208 brouard 12471: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12472: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12473:
12474: pstamp(ficreseij);
1.219 brouard 12475:
1.235 brouard 12476: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12477: if (cptcovn < 1){i1=1;}
12478:
12479: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12480: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12481: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12482: continue;
1.219 brouard 12483: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12484: printf("\n#****** ");
1.225 brouard 12485: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12486: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12487: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12488: }
12489: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12490: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12491: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12492: }
12493: fprintf(ficreseij,"******\n");
1.235 brouard 12494: printf("******\n");
1.219 brouard 12495:
12496: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12497: oldm=oldms;savm=savms;
1.235 brouard 12498: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12499:
1.219 brouard 12500: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12501: }
12502: fclose(ficreseij);
1.208 brouard 12503: printf("done evsij\n");fflush(stdout);
12504: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12505:
1.218 brouard 12506:
1.227 brouard 12507: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12508:
1.201 brouard 12509: strcpy(filerest,"T_");
12510: strcat(filerest,fileresu);
1.127 brouard 12511: if((ficrest=fopen(filerest,"w"))==NULL) {
12512: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12513: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12514: }
1.208 brouard 12515: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12516: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12517: strcpy(fileresstde,"STDE_");
12518: strcat(fileresstde,fileresu);
1.126 brouard 12519: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12520: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12521: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12522: }
1.227 brouard 12523: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12524: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12525:
1.201 brouard 12526: strcpy(filerescve,"CVE_");
12527: strcat(filerescve,fileresu);
1.126 brouard 12528: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12529: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12530: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12531: }
1.227 brouard 12532: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12533: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12534:
1.201 brouard 12535: strcpy(fileresv,"V_");
12536: strcat(fileresv,fileresu);
1.126 brouard 12537: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12538: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12539: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12540: }
1.227 brouard 12541: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12542: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12543:
1.235 brouard 12544: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12545: if (cptcovn < 1){i1=1;}
12546:
12547: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12548: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12549: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12550: continue;
1.242 brouard 12551: printf("\n#****** Result for:");
12552: fprintf(ficrest,"\n#****** Result for:");
12553: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12554: for(j=1;j<=cptcoveff;j++){
12555: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12556: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12557: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12558: }
1.235 brouard 12559: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12560: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12561: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12562: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12563: }
1.208 brouard 12564: fprintf(ficrest,"******\n");
1.227 brouard 12565: fprintf(ficlog,"******\n");
12566: printf("******\n");
1.208 brouard 12567:
12568: fprintf(ficresstdeij,"\n#****** ");
12569: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12570: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12571: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12572: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12573: }
1.235 brouard 12574: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12575: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12576: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12577: }
1.208 brouard 12578: fprintf(ficresstdeij,"******\n");
12579: fprintf(ficrescveij,"******\n");
12580:
12581: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12582: /* pstamp(ficresvij); */
1.225 brouard 12583: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12584: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12585: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12586: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12587: }
1.208 brouard 12588: fprintf(ficresvij,"******\n");
12589:
12590: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12591: oldm=oldms;savm=savms;
1.235 brouard 12592: printf(" cvevsij ");
12593: fprintf(ficlog, " cvevsij ");
12594: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12595: printf(" end cvevsij \n ");
12596: fprintf(ficlog, " end cvevsij \n ");
12597:
12598: /*
12599: */
12600: /* goto endfree; */
12601:
12602: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12603: pstamp(ficrest);
12604:
1.269 brouard 12605: epj=vector(1,nlstate+1);
1.208 brouard 12606: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12607: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12608: cptcod= 0; /* To be deleted */
12609: printf("varevsij vpopbased=%d \n",vpopbased);
12610: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12611: 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 12612: 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 ");
12613: if(vpopbased==1)
12614: 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);
12615: else
1.288 brouard 12616: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12617: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12618: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12619: fprintf(ficrest,"\n");
12620: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12621: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12622: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12623: for(age=bage; age <=fage ;age++){
1.235 brouard 12624: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12625: if (vpopbased==1) {
12626: if(mobilav ==0){
12627: for(i=1; i<=nlstate;i++)
12628: prlim[i][i]=probs[(int)age][i][k];
12629: }else{ /* mobilav */
12630: for(i=1; i<=nlstate;i++)
12631: prlim[i][i]=mobaverage[(int)age][i][k];
12632: }
12633: }
1.219 brouard 12634:
1.227 brouard 12635: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12636: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12637: /* printf(" age %4.0f ",age); */
12638: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12639: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12640: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12641: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12642: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12643: }
12644: epj[nlstate+1] +=epj[j];
12645: }
12646: /* printf(" age %4.0f \n",age); */
1.219 brouard 12647:
1.227 brouard 12648: for(i=1, vepp=0.;i <=nlstate;i++)
12649: for(j=1;j <=nlstate;j++)
12650: vepp += vareij[i][j][(int)age];
12651: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12652: for(j=1;j <=nlstate;j++){
12653: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12654: }
12655: fprintf(ficrest,"\n");
12656: }
1.208 brouard 12657: } /* End vpopbased */
1.269 brouard 12658: free_vector(epj,1,nlstate+1);
1.208 brouard 12659: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12660: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12661: printf("done selection\n");fflush(stdout);
12662: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12663:
1.235 brouard 12664: } /* End k selection */
1.227 brouard 12665:
12666: printf("done State-specific expectancies\n");fflush(stdout);
12667: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12668:
1.288 brouard 12669: /* variance-covariance of forward period prevalence*/
1.269 brouard 12670: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12671:
1.227 brouard 12672:
1.290 brouard 12673: free_vector(weight,firstobs,lastobs);
1.227 brouard 12674: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12675: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12676: free_matrix(anint,1,maxwav,firstobs,lastobs);
12677: free_matrix(mint,1,maxwav,firstobs,lastobs);
12678: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12679: free_ivector(tab,1,NCOVMAX);
12680: fclose(ficresstdeij);
12681: fclose(ficrescveij);
12682: fclose(ficresvij);
12683: fclose(ficrest);
12684: fclose(ficpar);
12685:
12686:
1.126 brouard 12687: /*---------- End : free ----------------*/
1.219 brouard 12688: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12689: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12690: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12691: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12692: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12693: } /* mle==-3 arrives here for freeing */
1.227 brouard 12694: /* endfree:*/
12695: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12696: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12697: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12698: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12699: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12700: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12701: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12702: free_matrix(matcov,1,npar,1,npar);
12703: free_matrix(hess,1,npar,1,npar);
12704: /*free_vector(delti,1,npar);*/
12705: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12706: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12707: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12708: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12709:
12710: free_ivector(ncodemax,1,NCOVMAX);
12711: free_ivector(ncodemaxwundef,1,NCOVMAX);
12712: free_ivector(Dummy,-1,NCOVMAX);
12713: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12714: free_ivector(DummyV,1,NCOVMAX);
12715: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12716: free_ivector(Typevar,-1,NCOVMAX);
12717: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12718: free_ivector(TvarsQ,1,NCOVMAX);
12719: free_ivector(TvarsQind,1,NCOVMAX);
12720: free_ivector(TvarsD,1,NCOVMAX);
12721: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12722: free_ivector(TvarFD,1,NCOVMAX);
12723: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12724: free_ivector(TvarF,1,NCOVMAX);
12725: free_ivector(TvarFind,1,NCOVMAX);
12726: free_ivector(TvarV,1,NCOVMAX);
12727: free_ivector(TvarVind,1,NCOVMAX);
12728: free_ivector(TvarA,1,NCOVMAX);
12729: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12730: free_ivector(TvarFQ,1,NCOVMAX);
12731: free_ivector(TvarFQind,1,NCOVMAX);
12732: free_ivector(TvarVD,1,NCOVMAX);
12733: free_ivector(TvarVDind,1,NCOVMAX);
12734: free_ivector(TvarVQ,1,NCOVMAX);
12735: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12736: free_ivector(Tvarsel,1,NCOVMAX);
12737: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12738: free_ivector(Tposprod,1,NCOVMAX);
12739: free_ivector(Tprod,1,NCOVMAX);
12740: free_ivector(Tvaraff,1,NCOVMAX);
12741: free_ivector(invalidvarcomb,1,ncovcombmax);
12742: free_ivector(Tage,1,NCOVMAX);
12743: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12744: free_ivector(TmodelInvind,1,NCOVMAX);
12745: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12746:
12747: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12748: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12749: fflush(fichtm);
12750: fflush(ficgp);
12751:
1.227 brouard 12752:
1.126 brouard 12753: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12754: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12755: 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 12756: }else{
12757: printf("End of Imach\n");
12758: fprintf(ficlog,"End of Imach\n");
12759: }
12760: printf("See log file on %s\n",filelog);
12761: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12762: /*(void) gettimeofday(&end_time,&tzp);*/
12763: rend_time = time(NULL);
12764: end_time = *localtime(&rend_time);
12765: /* tml = *localtime(&end_time.tm_sec); */
12766: strcpy(strtend,asctime(&end_time));
1.126 brouard 12767: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
12768: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 12769: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 12770:
1.157 brouard 12771: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
12772: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
12773: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 12774: /* printf("Total time was %d uSec.\n", total_usecs);*/
12775: /* if(fileappend(fichtm,optionfilehtm)){ */
12776: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12777: fclose(fichtm);
12778: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12779: fclose(fichtmcov);
12780: fclose(ficgp);
12781: fclose(ficlog);
12782: /*------ End -----------*/
1.227 brouard 12783:
1.281 brouard 12784:
12785: /* Executes gnuplot */
1.227 brouard 12786:
12787: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 12788: #ifdef WIN32
1.227 brouard 12789: if (_chdir(pathcd) != 0)
12790: printf("Can't move to directory %s!\n",path);
12791: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 12792: #else
1.227 brouard 12793: if(chdir(pathcd) != 0)
12794: printf("Can't move to directory %s!\n", path);
12795: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 12796: #endif
1.126 brouard 12797: printf("Current directory %s!\n",pathcd);
12798: /*strcat(plotcmd,CHARSEPARATOR);*/
12799: sprintf(plotcmd,"gnuplot");
1.157 brouard 12800: #ifdef _WIN32
1.126 brouard 12801: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
12802: #endif
12803: if(!stat(plotcmd,&info)){
1.158 brouard 12804: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12805: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 12806: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 12807: }else
12808: strcpy(pplotcmd,plotcmd);
1.157 brouard 12809: #ifdef __unix
1.126 brouard 12810: strcpy(plotcmd,GNUPLOTPROGRAM);
12811: if(!stat(plotcmd,&info)){
1.158 brouard 12812: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12813: }else
12814: strcpy(pplotcmd,plotcmd);
12815: #endif
12816: }else
12817: strcpy(pplotcmd,plotcmd);
12818:
12819: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 12820: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 12821:
1.126 brouard 12822: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 12823: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 12824: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 12825: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 12826: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 12827: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 12828: }
1.158 brouard 12829: printf(" Successful, please wait...");
1.126 brouard 12830: while (z[0] != 'q') {
12831: /* chdir(path); */
1.154 brouard 12832: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 12833: scanf("%s",z);
12834: /* if (z[0] == 'c') system("./imach"); */
12835: if (z[0] == 'e') {
1.158 brouard 12836: #ifdef __APPLE__
1.152 brouard 12837: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 12838: #elif __linux
12839: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 12840: #else
1.152 brouard 12841: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 12842: #endif
12843: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
12844: system(pplotcmd);
1.126 brouard 12845: }
12846: else if (z[0] == 'g') system(plotcmd);
12847: else if (z[0] == 'q') exit(0);
12848: }
1.227 brouard 12849: end:
1.126 brouard 12850: while (z[0] != 'q') {
1.195 brouard 12851: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 12852: scanf("%s",z);
12853: }
1.283 brouard 12854: printf("End\n");
1.282 brouard 12855: exit(0);
1.126 brouard 12856: }
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