Annotation of imach/src/imach.c, revision 1.305
1.305 ! brouard 1: /* $Id: imach.c,v 1.304 2021/02/12 11:34:20 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.305 ! brouard 4: Revision 1.304 2021/02/12 11:34:20 brouard
! 5: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
! 6:
1.304 brouard 7: Revision 1.303 2021/02/11 19:50:15 brouard
8: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
9:
1.303 brouard 10: Revision 1.302 2020/02/22 21:00:05 brouard
11: * (Module): imach.c Update mle=-3 (for computing Life expectancy
12: and life table from the data without any state)
13:
1.302 brouard 14: Revision 1.301 2019/06/04 13:51:20 brouard
15: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
16:
1.301 brouard 17: Revision 1.300 2019/05/22 19:09:45 brouard
18: Summary: version 0.99r19 of May 2019
19:
1.300 brouard 20: Revision 1.299 2019/05/22 18:37:08 brouard
21: Summary: Cleaned 0.99r19
22:
1.299 brouard 23: Revision 1.298 2019/05/22 18:19:56 brouard
24: *** empty log message ***
25:
1.298 brouard 26: Revision 1.297 2019/05/22 17:56:10 brouard
27: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
28:
1.297 brouard 29: Revision 1.296 2019/05/20 13:03:18 brouard
30: Summary: Projection syntax simplified
31:
32:
33: We can now start projections, forward or backward, from the mean date
34: of inteviews up to or down to a number of years of projection:
35: prevforecast=1 yearsfproj=15.3 mobil_average=0
36: or
37: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
38: or
39: prevbackcast=1 yearsbproj=12.3 mobil_average=1
40: or
41: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
42:
1.296 brouard 43: Revision 1.295 2019/05/18 09:52:50 brouard
44: Summary: doxygen tex bug
45:
1.295 brouard 46: Revision 1.294 2019/05/16 14:54:33 brouard
47: Summary: There was some wrong lines added
48:
1.294 brouard 49: Revision 1.293 2019/05/09 15:17:34 brouard
50: *** empty log message ***
51:
1.293 brouard 52: Revision 1.292 2019/05/09 14:17:20 brouard
53: Summary: Some updates
54:
1.292 brouard 55: Revision 1.291 2019/05/09 13:44:18 brouard
56: Summary: Before ncovmax
57:
1.291 brouard 58: Revision 1.290 2019/05/09 13:39:37 brouard
59: Summary: 0.99r18 unlimited number of individuals
60:
61: 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.
62:
1.290 brouard 63: Revision 1.289 2018/12/13 09:16:26 brouard
64: Summary: Bug for young ages (<-30) will be in r17
65:
1.289 brouard 66: Revision 1.288 2018/05/02 20:58:27 brouard
67: Summary: Some bugs fixed
68:
1.288 brouard 69: Revision 1.287 2018/05/01 17:57:25 brouard
70: Summary: Bug fixed by providing frequencies only for non missing covariates
71:
1.287 brouard 72: Revision 1.286 2018/04/27 14:27:04 brouard
73: Summary: some minor bugs
74:
1.286 brouard 75: Revision 1.285 2018/04/21 21:02:16 brouard
76: Summary: Some bugs fixed, valgrind tested
77:
1.285 brouard 78: Revision 1.284 2018/04/20 05:22:13 brouard
79: Summary: Computing mean and stdeviation of fixed quantitative variables
80:
1.284 brouard 81: Revision 1.283 2018/04/19 14:49:16 brouard
82: Summary: Some minor bugs fixed
83:
1.283 brouard 84: Revision 1.282 2018/02/27 22:50:02 brouard
85: *** empty log message ***
86:
1.282 brouard 87: Revision 1.281 2018/02/27 19:25:23 brouard
88: Summary: Adding second argument for quitting
89:
1.281 brouard 90: Revision 1.280 2018/02/21 07:58:13 brouard
91: Summary: 0.99r15
92:
93: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
94:
1.280 brouard 95: Revision 1.279 2017/07/20 13:35:01 brouard
96: Summary: temporary working
97:
1.279 brouard 98: Revision 1.278 2017/07/19 14:09:02 brouard
99: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
100:
1.278 brouard 101: Revision 1.277 2017/07/17 08:53:49 brouard
102: Summary: BOM files can be read now
103:
1.277 brouard 104: Revision 1.276 2017/06/30 15:48:31 brouard
105: Summary: Graphs improvements
106:
1.276 brouard 107: Revision 1.275 2017/06/30 13:39:33 brouard
108: Summary: Saito's color
109:
1.275 brouard 110: Revision 1.274 2017/06/29 09:47:08 brouard
111: Summary: Version 0.99r14
112:
1.274 brouard 113: Revision 1.273 2017/06/27 11:06:02 brouard
114: Summary: More documentation on projections
115:
1.273 brouard 116: Revision 1.272 2017/06/27 10:22:40 brouard
117: Summary: Color of backprojection changed from 6 to 5(yellow)
118:
1.272 brouard 119: Revision 1.271 2017/06/27 10:17:50 brouard
120: Summary: Some bug with rint
121:
1.271 brouard 122: Revision 1.270 2017/05/24 05:45:29 brouard
123: *** empty log message ***
124:
1.270 brouard 125: Revision 1.269 2017/05/23 08:39:25 brouard
126: Summary: Code into subroutine, cleanings
127:
1.269 brouard 128: Revision 1.268 2017/05/18 20:09:32 brouard
129: Summary: backprojection and confidence intervals of backprevalence
130:
1.268 brouard 131: Revision 1.267 2017/05/13 10:25:05 brouard
132: Summary: temporary save for backprojection
133:
1.267 brouard 134: Revision 1.266 2017/05/13 07:26:12 brouard
135: Summary: Version 0.99r13 (improvements and bugs fixed)
136:
1.266 brouard 137: Revision 1.265 2017/04/26 16:22:11 brouard
138: Summary: imach 0.99r13 Some bugs fixed
139:
1.265 brouard 140: Revision 1.264 2017/04/26 06:01:29 brouard
141: Summary: Labels in graphs
142:
1.264 brouard 143: Revision 1.263 2017/04/24 15:23:15 brouard
144: Summary: to save
145:
1.263 brouard 146: Revision 1.262 2017/04/18 16:48:12 brouard
147: *** empty log message ***
148:
1.262 brouard 149: Revision 1.261 2017/04/05 10:14:09 brouard
150: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
151:
1.261 brouard 152: Revision 1.260 2017/04/04 17:46:59 brouard
153: Summary: Gnuplot indexations fixed (humm)
154:
1.260 brouard 155: Revision 1.259 2017/04/04 13:01:16 brouard
156: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
157:
1.259 brouard 158: Revision 1.258 2017/04/03 10:17:47 brouard
159: Summary: Version 0.99r12
160:
161: Some cleanings, conformed with updated documentation.
162:
1.258 brouard 163: Revision 1.257 2017/03/29 16:53:30 brouard
164: Summary: Temp
165:
1.257 brouard 166: Revision 1.256 2017/03/27 05:50:23 brouard
167: Summary: Temporary
168:
1.256 brouard 169: Revision 1.255 2017/03/08 16:02:28 brouard
170: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
171:
1.255 brouard 172: Revision 1.254 2017/03/08 07:13:00 brouard
173: Summary: Fixing data parameter line
174:
1.254 brouard 175: Revision 1.253 2016/12/15 11:59:41 brouard
176: Summary: 0.99 in progress
177:
1.253 brouard 178: Revision 1.252 2016/09/15 21:15:37 brouard
179: *** empty log message ***
180:
1.252 brouard 181: Revision 1.251 2016/09/15 15:01:13 brouard
182: Summary: not working
183:
1.251 brouard 184: Revision 1.250 2016/09/08 16:07:27 brouard
185: Summary: continue
186:
1.250 brouard 187: Revision 1.249 2016/09/07 17:14:18 brouard
188: Summary: Starting values from frequencies
189:
1.249 brouard 190: Revision 1.248 2016/09/07 14:10:18 brouard
191: *** empty log message ***
192:
1.248 brouard 193: Revision 1.247 2016/09/02 11:11:21 brouard
194: *** empty log message ***
195:
1.247 brouard 196: Revision 1.246 2016/09/02 08:49:22 brouard
197: *** empty log message ***
198:
1.246 brouard 199: Revision 1.245 2016/09/02 07:25:01 brouard
200: *** empty log message ***
201:
1.245 brouard 202: Revision 1.244 2016/09/02 07:17:34 brouard
203: *** empty log message ***
204:
1.244 brouard 205: Revision 1.243 2016/09/02 06:45:35 brouard
206: *** empty log message ***
207:
1.243 brouard 208: Revision 1.242 2016/08/30 15:01:20 brouard
209: Summary: Fixing a lots
210:
1.242 brouard 211: Revision 1.241 2016/08/29 17:17:25 brouard
212: Summary: gnuplot problem in Back projection to fix
213:
1.241 brouard 214: Revision 1.240 2016/08/29 07:53:18 brouard
215: Summary: Better
216:
1.240 brouard 217: Revision 1.239 2016/08/26 15:51:03 brouard
218: Summary: Improvement in Powell output in order to copy and paste
219:
220: Author:
221:
1.239 brouard 222: Revision 1.238 2016/08/26 14:23:35 brouard
223: Summary: Starting tests of 0.99
224:
1.238 brouard 225: Revision 1.237 2016/08/26 09:20:19 brouard
226: Summary: to valgrind
227:
1.237 brouard 228: Revision 1.236 2016/08/25 10:50:18 brouard
229: *** empty log message ***
230:
1.236 brouard 231: Revision 1.235 2016/08/25 06:59:23 brouard
232: *** empty log message ***
233:
1.235 brouard 234: Revision 1.234 2016/08/23 16:51:20 brouard
235: *** empty log message ***
236:
1.234 brouard 237: Revision 1.233 2016/08/23 07:40:50 brouard
238: Summary: not working
239:
1.233 brouard 240: Revision 1.232 2016/08/22 14:20:21 brouard
241: Summary: not working
242:
1.232 brouard 243: Revision 1.231 2016/08/22 07:17:15 brouard
244: Summary: not working
245:
1.231 brouard 246: Revision 1.230 2016/08/22 06:55:53 brouard
247: Summary: Not working
248:
1.230 brouard 249: Revision 1.229 2016/07/23 09:45:53 brouard
250: Summary: Completing for func too
251:
1.229 brouard 252: Revision 1.228 2016/07/22 17:45:30 brouard
253: Summary: Fixing some arrays, still debugging
254:
1.227 brouard 255: Revision 1.226 2016/07/12 18:42:34 brouard
256: Summary: temp
257:
1.226 brouard 258: Revision 1.225 2016/07/12 08:40:03 brouard
259: Summary: saving but not running
260:
1.225 brouard 261: Revision 1.224 2016/07/01 13:16:01 brouard
262: Summary: Fixes
263:
1.224 brouard 264: Revision 1.223 2016/02/19 09:23:35 brouard
265: Summary: temporary
266:
1.223 brouard 267: Revision 1.222 2016/02/17 08:14:50 brouard
268: Summary: Probably last 0.98 stable version 0.98r6
269:
1.222 brouard 270: Revision 1.221 2016/02/15 23:35:36 brouard
271: Summary: minor bug
272:
1.220 brouard 273: Revision 1.219 2016/02/15 00:48:12 brouard
274: *** empty log message ***
275:
1.219 brouard 276: Revision 1.218 2016/02/12 11:29:23 brouard
277: Summary: 0.99 Back projections
278:
1.218 brouard 279: Revision 1.217 2015/12/23 17:18:31 brouard
280: Summary: Experimental backcast
281:
1.217 brouard 282: Revision 1.216 2015/12/18 17:32:11 brouard
283: Summary: 0.98r4 Warning and status=-2
284:
285: Version 0.98r4 is now:
286: - displaying an error when status is -1, date of interview unknown and date of death known;
287: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
288: Older changes concerning s=-2, dating from 2005 have been supersed.
289:
1.216 brouard 290: Revision 1.215 2015/12/16 08:52:24 brouard
291: Summary: 0.98r4 working
292:
1.215 brouard 293: Revision 1.214 2015/12/16 06:57:54 brouard
294: Summary: temporary not working
295:
1.214 brouard 296: Revision 1.213 2015/12/11 18:22:17 brouard
297: Summary: 0.98r4
298:
1.213 brouard 299: Revision 1.212 2015/11/21 12:47:24 brouard
300: Summary: minor typo
301:
1.212 brouard 302: Revision 1.211 2015/11/21 12:41:11 brouard
303: Summary: 0.98r3 with some graph of projected cross-sectional
304:
305: Author: Nicolas Brouard
306:
1.211 brouard 307: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 308: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 309: Summary: Adding ftolpl parameter
310: Author: N Brouard
311:
312: We had difficulties to get smoothed confidence intervals. It was due
313: to the period prevalence which wasn't computed accurately. The inner
314: parameter ftolpl is now an outer parameter of the .imach parameter
315: file after estepm. If ftolpl is small 1.e-4 and estepm too,
316: computation are long.
317:
1.209 brouard 318: Revision 1.208 2015/11/17 14:31:57 brouard
319: Summary: temporary
320:
1.208 brouard 321: Revision 1.207 2015/10/27 17:36:57 brouard
322: *** empty log message ***
323:
1.207 brouard 324: Revision 1.206 2015/10/24 07:14:11 brouard
325: *** empty log message ***
326:
1.206 brouard 327: Revision 1.205 2015/10/23 15:50:53 brouard
328: Summary: 0.98r3 some clarification for graphs on likelihood contributions
329:
1.205 brouard 330: Revision 1.204 2015/10/01 16:20:26 brouard
331: Summary: Some new graphs of contribution to likelihood
332:
1.204 brouard 333: Revision 1.203 2015/09/30 17:45:14 brouard
334: Summary: looking at better estimation of the hessian
335:
336: Also a better criteria for convergence to the period prevalence And
337: therefore adding the number of years needed to converge. (The
338: prevalence in any alive state shold sum to one
339:
1.203 brouard 340: Revision 1.202 2015/09/22 19:45:16 brouard
341: Summary: Adding some overall graph on contribution to likelihood. Might change
342:
1.202 brouard 343: Revision 1.201 2015/09/15 17:34:58 brouard
344: Summary: 0.98r0
345:
346: - Some new graphs like suvival functions
347: - Some bugs fixed like model=1+age+V2.
348:
1.201 brouard 349: Revision 1.200 2015/09/09 16:53:55 brouard
350: Summary: Big bug thanks to Flavia
351:
352: Even model=1+age+V2. did not work anymore
353:
1.200 brouard 354: Revision 1.199 2015/09/07 14:09:23 brouard
355: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
356:
1.199 brouard 357: Revision 1.198 2015/09/03 07:14:39 brouard
358: Summary: 0.98q5 Flavia
359:
1.198 brouard 360: Revision 1.197 2015/09/01 18:24:39 brouard
361: *** empty log message ***
362:
1.197 brouard 363: Revision 1.196 2015/08/18 23:17:52 brouard
364: Summary: 0.98q5
365:
1.196 brouard 366: Revision 1.195 2015/08/18 16:28:39 brouard
367: Summary: Adding a hack for testing purpose
368:
369: After reading the title, ftol and model lines, if the comment line has
370: a q, starting with #q, the answer at the end of the run is quit. It
371: permits to run test files in batch with ctest. The former workaround was
372: $ echo q | imach foo.imach
373:
1.195 brouard 374: Revision 1.194 2015/08/18 13:32:00 brouard
375: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
376:
1.194 brouard 377: Revision 1.193 2015/08/04 07:17:42 brouard
378: Summary: 0.98q4
379:
1.193 brouard 380: Revision 1.192 2015/07/16 16:49:02 brouard
381: Summary: Fixing some outputs
382:
1.192 brouard 383: Revision 1.191 2015/07/14 10:00:33 brouard
384: Summary: Some fixes
385:
1.191 brouard 386: Revision 1.190 2015/05/05 08:51:13 brouard
387: Summary: Adding digits in output parameters (7 digits instead of 6)
388:
389: Fix 1+age+.
390:
1.190 brouard 391: Revision 1.189 2015/04/30 14:45:16 brouard
392: Summary: 0.98q2
393:
1.189 brouard 394: Revision 1.188 2015/04/30 08:27:53 brouard
395: *** empty log message ***
396:
1.188 brouard 397: Revision 1.187 2015/04/29 09:11:15 brouard
398: *** empty log message ***
399:
1.187 brouard 400: Revision 1.186 2015/04/23 12:01:52 brouard
401: Summary: V1*age is working now, version 0.98q1
402:
403: Some codes had been disabled in order to simplify and Vn*age was
404: working in the optimization phase, ie, giving correct MLE parameters,
405: but, as usual, outputs were not correct and program core dumped.
406:
1.186 brouard 407: Revision 1.185 2015/03/11 13:26:42 brouard
408: Summary: Inclusion of compile and links command line for Intel Compiler
409:
1.185 brouard 410: Revision 1.184 2015/03/11 11:52:39 brouard
411: Summary: Back from Windows 8. Intel Compiler
412:
1.184 brouard 413: Revision 1.183 2015/03/10 20:34:32 brouard
414: Summary: 0.98q0, trying with directest, mnbrak fixed
415:
416: We use directest instead of original Powell test; probably no
417: incidence on the results, but better justifications;
418: We fixed Numerical Recipes mnbrak routine which was wrong and gave
419: wrong results.
420:
1.183 brouard 421: Revision 1.182 2015/02/12 08:19:57 brouard
422: Summary: Trying to keep directest which seems simpler and more general
423: Author: Nicolas Brouard
424:
1.182 brouard 425: Revision 1.181 2015/02/11 23:22:24 brouard
426: Summary: Comments on Powell added
427:
428: Author:
429:
1.181 brouard 430: Revision 1.180 2015/02/11 17:33:45 brouard
431: Summary: Finishing move from main to function (hpijx and prevalence_limit)
432:
1.180 brouard 433: Revision 1.179 2015/01/04 09:57:06 brouard
434: Summary: back to OS/X
435:
1.179 brouard 436: Revision 1.178 2015/01/04 09:35:48 brouard
437: *** empty log message ***
438:
1.178 brouard 439: Revision 1.177 2015/01/03 18:40:56 brouard
440: Summary: Still testing ilc32 on OSX
441:
1.177 brouard 442: Revision 1.176 2015/01/03 16:45:04 brouard
443: *** empty log message ***
444:
1.176 brouard 445: Revision 1.175 2015/01/03 16:33:42 brouard
446: *** empty log message ***
447:
1.175 brouard 448: Revision 1.174 2015/01/03 16:15:49 brouard
449: Summary: Still in cross-compilation
450:
1.174 brouard 451: Revision 1.173 2015/01/03 12:06:26 brouard
452: Summary: trying to detect cross-compilation
453:
1.173 brouard 454: Revision 1.172 2014/12/27 12:07:47 brouard
455: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
456:
1.172 brouard 457: Revision 1.171 2014/12/23 13:26:59 brouard
458: Summary: Back from Visual C
459:
460: Still problem with utsname.h on Windows
461:
1.171 brouard 462: Revision 1.170 2014/12/23 11:17:12 brouard
463: Summary: Cleaning some \%% back to %%
464:
465: The escape was mandatory for a specific compiler (which one?), but too many warnings.
466:
1.170 brouard 467: Revision 1.169 2014/12/22 23:08:31 brouard
468: Summary: 0.98p
469:
470: Outputs some informations on compiler used, OS etc. Testing on different platforms.
471:
1.169 brouard 472: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 473: Summary: update
1.169 brouard 474:
1.168 brouard 475: Revision 1.167 2014/12/22 13:50:56 brouard
476: Summary: Testing uname and compiler version and if compiled 32 or 64
477:
478: Testing on Linux 64
479:
1.167 brouard 480: Revision 1.166 2014/12/22 11:40:47 brouard
481: *** empty log message ***
482:
1.166 brouard 483: Revision 1.165 2014/12/16 11:20:36 brouard
484: Summary: After compiling on Visual C
485:
486: * imach.c (Module): Merging 1.61 to 1.162
487:
1.165 brouard 488: Revision 1.164 2014/12/16 10:52:11 brouard
489: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
490:
491: * imach.c (Module): Merging 1.61 to 1.162
492:
1.164 brouard 493: Revision 1.163 2014/12/16 10:30:11 brouard
494: * imach.c (Module): Merging 1.61 to 1.162
495:
1.163 brouard 496: Revision 1.162 2014/09/25 11:43:39 brouard
497: Summary: temporary backup 0.99!
498:
1.162 brouard 499: Revision 1.1 2014/09/16 11:06:58 brouard
500: Summary: With some code (wrong) for nlopt
501:
502: Author:
503:
504: Revision 1.161 2014/09/15 20:41:41 brouard
505: Summary: Problem with macro SQR on Intel compiler
506:
1.161 brouard 507: Revision 1.160 2014/09/02 09:24:05 brouard
508: *** empty log message ***
509:
1.160 brouard 510: Revision 1.159 2014/09/01 10:34:10 brouard
511: Summary: WIN32
512: Author: Brouard
513:
1.159 brouard 514: Revision 1.158 2014/08/27 17:11:51 brouard
515: *** empty log message ***
516:
1.158 brouard 517: Revision 1.157 2014/08/27 16:26:55 brouard
518: Summary: Preparing windows Visual studio version
519: Author: Brouard
520:
521: In order to compile on Visual studio, time.h is now correct and time_t
522: and tm struct should be used. difftime should be used but sometimes I
523: just make the differences in raw time format (time(&now).
524: Trying to suppress #ifdef LINUX
525: Add xdg-open for __linux in order to open default browser.
526:
1.157 brouard 527: Revision 1.156 2014/08/25 20:10:10 brouard
528: *** empty log message ***
529:
1.156 brouard 530: Revision 1.155 2014/08/25 18:32:34 brouard
531: Summary: New compile, minor changes
532: Author: Brouard
533:
1.155 brouard 534: Revision 1.154 2014/06/20 17:32:08 brouard
535: Summary: Outputs now all graphs of convergence to period prevalence
536:
1.154 brouard 537: Revision 1.153 2014/06/20 16:45:46 brouard
538: Summary: If 3 live state, convergence to period prevalence on same graph
539: Author: Brouard
540:
1.153 brouard 541: Revision 1.152 2014/06/18 17:54:09 brouard
542: Summary: open browser, use gnuplot on same dir than imach if not found in the path
543:
1.152 brouard 544: Revision 1.151 2014/06/18 16:43:30 brouard
545: *** empty log message ***
546:
1.151 brouard 547: Revision 1.150 2014/06/18 16:42:35 brouard
548: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
549: Author: brouard
550:
1.150 brouard 551: Revision 1.149 2014/06/18 15:51:14 brouard
552: Summary: Some fixes in parameter files errors
553: Author: Nicolas Brouard
554:
1.149 brouard 555: Revision 1.148 2014/06/17 17:38:48 brouard
556: Summary: Nothing new
557: Author: Brouard
558:
559: Just a new packaging for OS/X version 0.98nS
560:
1.148 brouard 561: Revision 1.147 2014/06/16 10:33:11 brouard
562: *** empty log message ***
563:
1.147 brouard 564: Revision 1.146 2014/06/16 10:20:28 brouard
565: Summary: Merge
566: Author: Brouard
567:
568: Merge, before building revised version.
569:
1.146 brouard 570: Revision 1.145 2014/06/10 21:23:15 brouard
571: Summary: Debugging with valgrind
572: Author: Nicolas Brouard
573:
574: Lot of changes in order to output the results with some covariates
575: After the Edimburgh REVES conference 2014, it seems mandatory to
576: improve the code.
577: No more memory valgrind error but a lot has to be done in order to
578: continue the work of splitting the code into subroutines.
579: Also, decodemodel has been improved. Tricode is still not
580: optimal. nbcode should be improved. Documentation has been added in
581: the source code.
582:
1.144 brouard 583: Revision 1.143 2014/01/26 09:45:38 brouard
584: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
585:
586: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
587: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
588:
1.143 brouard 589: Revision 1.142 2014/01/26 03:57:36 brouard
590: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
591:
592: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
593:
1.142 brouard 594: Revision 1.141 2014/01/26 02:42:01 brouard
595: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
596:
1.141 brouard 597: Revision 1.140 2011/09/02 10:37:54 brouard
598: Summary: times.h is ok with mingw32 now.
599:
1.140 brouard 600: Revision 1.139 2010/06/14 07:50:17 brouard
601: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
602: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
603:
1.139 brouard 604: Revision 1.138 2010/04/30 18:19:40 brouard
605: *** empty log message ***
606:
1.138 brouard 607: Revision 1.137 2010/04/29 18:11:38 brouard
608: (Module): Checking covariates for more complex models
609: than V1+V2. A lot of change to be done. Unstable.
610:
1.137 brouard 611: Revision 1.136 2010/04/26 20:30:53 brouard
612: (Module): merging some libgsl code. Fixing computation
613: of likelione (using inter/intrapolation if mle = 0) in order to
614: get same likelihood as if mle=1.
615: Some cleaning of code and comments added.
616:
1.136 brouard 617: Revision 1.135 2009/10/29 15:33:14 brouard
618: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
619:
1.135 brouard 620: Revision 1.134 2009/10/29 13:18:53 brouard
621: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
622:
1.134 brouard 623: Revision 1.133 2009/07/06 10:21:25 brouard
624: just nforces
625:
1.133 brouard 626: Revision 1.132 2009/07/06 08:22:05 brouard
627: Many tings
628:
1.132 brouard 629: Revision 1.131 2009/06/20 16:22:47 brouard
630: Some dimensions resccaled
631:
1.131 brouard 632: Revision 1.130 2009/05/26 06:44:34 brouard
633: (Module): Max Covariate is now set to 20 instead of 8. A
634: lot of cleaning with variables initialized to 0. Trying to make
635: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
636:
1.130 brouard 637: Revision 1.129 2007/08/31 13:49:27 lievre
638: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
639:
1.129 lievre 640: Revision 1.128 2006/06/30 13:02:05 brouard
641: (Module): Clarifications on computing e.j
642:
1.128 brouard 643: Revision 1.127 2006/04/28 18:11:50 brouard
644: (Module): Yes the sum of survivors was wrong since
645: imach-114 because nhstepm was no more computed in the age
646: loop. Now we define nhstepma in the age loop.
647: (Module): In order to speed up (in case of numerous covariates) we
648: compute health expectancies (without variances) in a first step
649: and then all the health expectancies with variances or standard
650: deviation (needs data from the Hessian matrices) which slows the
651: computation.
652: In the future we should be able to stop the program is only health
653: expectancies and graph are needed without standard deviations.
654:
1.127 brouard 655: Revision 1.126 2006/04/28 17:23:28 brouard
656: (Module): Yes the sum of survivors was wrong since
657: imach-114 because nhstepm was no more computed in the age
658: loop. Now we define nhstepma in the age loop.
659: Version 0.98h
660:
1.126 brouard 661: Revision 1.125 2006/04/04 15:20:31 lievre
662: Errors in calculation of health expectancies. Age was not initialized.
663: Forecasting file added.
664:
665: Revision 1.124 2006/03/22 17:13:53 lievre
666: Parameters are printed with %lf instead of %f (more numbers after the comma).
667: The log-likelihood is printed in the log file
668:
669: Revision 1.123 2006/03/20 10:52:43 brouard
670: * imach.c (Module): <title> changed, corresponds to .htm file
671: name. <head> headers where missing.
672:
673: * imach.c (Module): Weights can have a decimal point as for
674: English (a comma might work with a correct LC_NUMERIC environment,
675: otherwise the weight is truncated).
676: Modification of warning when the covariates values are not 0 or
677: 1.
678: Version 0.98g
679:
680: Revision 1.122 2006/03/20 09:45:41 brouard
681: (Module): Weights can have a decimal point as for
682: English (a comma might work with a correct LC_NUMERIC environment,
683: otherwise the weight is truncated).
684: Modification of warning when the covariates values are not 0 or
685: 1.
686: Version 0.98g
687:
688: Revision 1.121 2006/03/16 17:45:01 lievre
689: * imach.c (Module): Comments concerning covariates added
690:
691: * imach.c (Module): refinements in the computation of lli if
692: status=-2 in order to have more reliable computation if stepm is
693: not 1 month. Version 0.98f
694:
695: Revision 1.120 2006/03/16 15:10:38 lievre
696: (Module): refinements in the computation of lli if
697: status=-2 in order to have more reliable computation if stepm is
698: not 1 month. Version 0.98f
699:
700: Revision 1.119 2006/03/15 17:42:26 brouard
701: (Module): Bug if status = -2, the loglikelihood was
702: computed as likelihood omitting the logarithm. Version O.98e
703:
704: Revision 1.118 2006/03/14 18:20:07 brouard
705: (Module): varevsij Comments added explaining the second
706: table of variances if popbased=1 .
707: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
708: (Module): Function pstamp added
709: (Module): Version 0.98d
710:
711: Revision 1.117 2006/03/14 17:16:22 brouard
712: (Module): varevsij Comments added explaining the second
713: table of variances if popbased=1 .
714: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
715: (Module): Function pstamp added
716: (Module): Version 0.98d
717:
718: Revision 1.116 2006/03/06 10:29:27 brouard
719: (Module): Variance-covariance wrong links and
720: varian-covariance of ej. is needed (Saito).
721:
722: Revision 1.115 2006/02/27 12:17:45 brouard
723: (Module): One freematrix added in mlikeli! 0.98c
724:
725: Revision 1.114 2006/02/26 12:57:58 brouard
726: (Module): Some improvements in processing parameter
727: filename with strsep.
728:
729: Revision 1.113 2006/02/24 14:20:24 brouard
730: (Module): Memory leaks checks with valgrind and:
731: datafile was not closed, some imatrix were not freed and on matrix
732: allocation too.
733:
734: Revision 1.112 2006/01/30 09:55:26 brouard
735: (Module): Back to gnuplot.exe instead of wgnuplot.exe
736:
737: Revision 1.111 2006/01/25 20:38:18 brouard
738: (Module): Lots of cleaning and bugs added (Gompertz)
739: (Module): Comments can be added in data file. Missing date values
740: can be a simple dot '.'.
741:
742: Revision 1.110 2006/01/25 00:51:50 brouard
743: (Module): Lots of cleaning and bugs added (Gompertz)
744:
745: Revision 1.109 2006/01/24 19:37:15 brouard
746: (Module): Comments (lines starting with a #) are allowed in data.
747:
748: Revision 1.108 2006/01/19 18:05:42 lievre
749: Gnuplot problem appeared...
750: To be fixed
751:
752: Revision 1.107 2006/01/19 16:20:37 brouard
753: Test existence of gnuplot in imach path
754:
755: Revision 1.106 2006/01/19 13:24:36 brouard
756: Some cleaning and links added in html output
757:
758: Revision 1.105 2006/01/05 20:23:19 lievre
759: *** empty log message ***
760:
761: Revision 1.104 2005/09/30 16:11:43 lievre
762: (Module): sump fixed, loop imx fixed, and simplifications.
763: (Module): If the status is missing at the last wave but we know
764: that the person is alive, then we can code his/her status as -2
765: (instead of missing=-1 in earlier versions) and his/her
766: contributions to the likelihood is 1 - Prob of dying from last
767: health status (= 1-p13= p11+p12 in the easiest case of somebody in
768: the healthy state at last known wave). Version is 0.98
769:
770: Revision 1.103 2005/09/30 15:54:49 lievre
771: (Module): sump fixed, loop imx fixed, and simplifications.
772:
773: Revision 1.102 2004/09/15 17:31:30 brouard
774: Add the possibility to read data file including tab characters.
775:
776: Revision 1.101 2004/09/15 10:38:38 brouard
777: Fix on curr_time
778:
779: Revision 1.100 2004/07/12 18:29:06 brouard
780: Add version for Mac OS X. Just define UNIX in Makefile
781:
782: Revision 1.99 2004/06/05 08:57:40 brouard
783: *** empty log message ***
784:
785: Revision 1.98 2004/05/16 15:05:56 brouard
786: New version 0.97 . First attempt to estimate force of mortality
787: directly from the data i.e. without the need of knowing the health
788: state at each age, but using a Gompertz model: log u =a + b*age .
789: This is the basic analysis of mortality and should be done before any
790: other analysis, in order to test if the mortality estimated from the
791: cross-longitudinal survey is different from the mortality estimated
792: from other sources like vital statistic data.
793:
794: The same imach parameter file can be used but the option for mle should be -3.
795:
1.133 brouard 796: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 797: former routines in order to include the new code within the former code.
798:
799: The output is very simple: only an estimate of the intercept and of
800: the slope with 95% confident intervals.
801:
802: Current limitations:
803: A) Even if you enter covariates, i.e. with the
804: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
805: B) There is no computation of Life Expectancy nor Life Table.
806:
807: Revision 1.97 2004/02/20 13:25:42 lievre
808: Version 0.96d. Population forecasting command line is (temporarily)
809: suppressed.
810:
811: Revision 1.96 2003/07/15 15:38:55 brouard
812: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
813: rewritten within the same printf. Workaround: many printfs.
814:
815: Revision 1.95 2003/07/08 07:54:34 brouard
816: * imach.c (Repository):
817: (Repository): Using imachwizard code to output a more meaningful covariance
818: matrix (cov(a12,c31) instead of numbers.
819:
820: Revision 1.94 2003/06/27 13:00:02 brouard
821: Just cleaning
822:
823: Revision 1.93 2003/06/25 16:33:55 brouard
824: (Module): On windows (cygwin) function asctime_r doesn't
825: exist so I changed back to asctime which exists.
826: (Module): Version 0.96b
827:
828: Revision 1.92 2003/06/25 16:30:45 brouard
829: (Module): On windows (cygwin) function asctime_r doesn't
830: exist so I changed back to asctime which exists.
831:
832: Revision 1.91 2003/06/25 15:30:29 brouard
833: * imach.c (Repository): Duplicated warning errors corrected.
834: (Repository): Elapsed time after each iteration is now output. It
835: helps to forecast when convergence will be reached. Elapsed time
836: is stamped in powell. We created a new html file for the graphs
837: concerning matrix of covariance. It has extension -cov.htm.
838:
839: Revision 1.90 2003/06/24 12:34:15 brouard
840: (Module): Some bugs corrected for windows. Also, when
841: mle=-1 a template is output in file "or"mypar.txt with the design
842: of the covariance matrix to be input.
843:
844: Revision 1.89 2003/06/24 12:30:52 brouard
845: (Module): Some bugs corrected for windows. Also, when
846: mle=-1 a template is output in file "or"mypar.txt with the design
847: of the covariance matrix to be input.
848:
849: Revision 1.88 2003/06/23 17:54:56 brouard
850: * 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.
851:
852: Revision 1.87 2003/06/18 12:26:01 brouard
853: Version 0.96
854:
855: Revision 1.86 2003/06/17 20:04:08 brouard
856: (Module): Change position of html and gnuplot routines and added
857: routine fileappend.
858:
859: Revision 1.85 2003/06/17 13:12:43 brouard
860: * imach.c (Repository): Check when date of death was earlier that
861: current date of interview. It may happen when the death was just
862: prior to the death. In this case, dh was negative and likelihood
863: was wrong (infinity). We still send an "Error" but patch by
864: assuming that the date of death was just one stepm after the
865: interview.
866: (Repository): Because some people have very long ID (first column)
867: we changed int to long in num[] and we added a new lvector for
868: memory allocation. But we also truncated to 8 characters (left
869: truncation)
870: (Repository): No more line truncation errors.
871:
872: Revision 1.84 2003/06/13 21:44:43 brouard
873: * imach.c (Repository): Replace "freqsummary" at a correct
874: place. It differs from routine "prevalence" which may be called
875: many times. Probs is memory consuming and must be used with
876: parcimony.
877: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
878:
879: Revision 1.83 2003/06/10 13:39:11 lievre
880: *** empty log message ***
881:
882: Revision 1.82 2003/06/05 15:57:20 brouard
883: Add log in imach.c and fullversion number is now printed.
884:
885: */
886: /*
887: Interpolated Markov Chain
888:
889: Short summary of the programme:
890:
1.227 brouard 891: This program computes Healthy Life Expectancies or State-specific
892: (if states aren't health statuses) Expectancies from
893: cross-longitudinal data. Cross-longitudinal data consist in:
894:
895: -1- a first survey ("cross") where individuals from different ages
896: are interviewed on their health status or degree of disability (in
897: the case of a health survey which is our main interest)
898:
899: -2- at least a second wave of interviews ("longitudinal") which
900: measure each change (if any) in individual health status. Health
901: expectancies are computed from the time spent in each health state
902: according to a model. More health states you consider, more time is
903: necessary to reach the Maximum Likelihood of the parameters involved
904: in the model. The simplest model is the multinomial logistic model
905: where pij is the probability to be observed in state j at the second
906: wave conditional to be observed in state i at the first
907: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
908: etc , where 'age' is age and 'sex' is a covariate. If you want to
909: have a more complex model than "constant and age", you should modify
910: the program where the markup *Covariates have to be included here
911: again* invites you to do it. More covariates you add, slower the
1.126 brouard 912: convergence.
913:
914: The advantage of this computer programme, compared to a simple
915: multinomial logistic model, is clear when the delay between waves is not
916: identical for each individual. Also, if a individual missed an
917: intermediate interview, the information is lost, but taken into
918: account using an interpolation or extrapolation.
919:
920: hPijx is the probability to be observed in state i at age x+h
921: conditional to the observed state i at age x. The delay 'h' can be
922: split into an exact number (nh*stepm) of unobserved intermediate
923: states. This elementary transition (by month, quarter,
924: semester or year) is modelled as a multinomial logistic. The hPx
925: matrix is simply the matrix product of nh*stepm elementary matrices
926: and the contribution of each individual to the likelihood is simply
927: hPijx.
928:
929: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 930: of the life expectancies. It also computes the period (stable) prevalence.
931:
932: Back prevalence and projections:
1.227 brouard 933:
934: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
935: double agemaxpar, double ftolpl, int *ncvyearp, double
936: dateprev1,double dateprev2, int firstpass, int lastpass, int
937: mobilavproj)
938:
939: Computes the back prevalence limit for any combination of
940: covariate values k at any age between ageminpar and agemaxpar and
941: returns it in **bprlim. In the loops,
942:
943: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
944: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
945:
946: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 947: Computes for any combination of covariates k and any age between bage and fage
948: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
949: oldm=oldms;savm=savms;
1.227 brouard 950:
1.267 brouard 951: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 952: Computes the transition matrix starting at age 'age' over
953: 'nhstepm*hstepm*stepm' months (i.e. until
954: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 955: nhstepm*hstepm matrices.
956:
957: Returns p3mat[i][j][h] after calling
958: p3mat[i][j][h]=matprod2(newm,
959: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
960: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
961: oldm);
1.226 brouard 962:
963: Important routines
964:
965: - func (or funcone), computes logit (pij) distinguishing
966: o fixed variables (single or product dummies or quantitative);
967: o varying variables by:
968: (1) wave (single, product dummies, quantitative),
969: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
970: % fixed dummy (treated) or quantitative (not done because time-consuming);
971: % varying dummy (not done) or quantitative (not done);
972: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
973: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
974: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
975: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
976: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 977:
1.226 brouard 978:
979:
1.133 brouard 980: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
981: Institut national d'études démographiques, Paris.
1.126 brouard 982: This software have been partly granted by Euro-REVES, a concerted action
983: from the European Union.
984: It is copyrighted identically to a GNU software product, ie programme and
985: software can be distributed freely for non commercial use. Latest version
986: can be accessed at http://euroreves.ined.fr/imach .
987:
988: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
989: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
990:
991: **********************************************************************/
992: /*
993: main
994: read parameterfile
995: read datafile
996: concatwav
997: freqsummary
998: if (mle >= 1)
999: mlikeli
1000: print results files
1001: if mle==1
1002: computes hessian
1003: read end of parameter file: agemin, agemax, bage, fage, estepm
1004: begin-prev-date,...
1005: open gnuplot file
1006: open html file
1.145 brouard 1007: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1008: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1009: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1010: freexexit2 possible for memory heap.
1011:
1012: h Pij x | pij_nom ficrestpij
1013: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1014: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1015: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1016:
1017: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1018: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1019: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1020: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1021: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1022:
1.126 brouard 1023: forecasting if prevfcast==1 prevforecast call prevalence()
1024: health expectancies
1025: Variance-covariance of DFLE
1026: prevalence()
1027: movingaverage()
1028: varevsij()
1029: if popbased==1 varevsij(,popbased)
1030: total life expectancies
1031: Variance of period (stable) prevalence
1032: end
1033: */
1034:
1.187 brouard 1035: /* #define DEBUG */
1036: /* #define DEBUGBRENT */
1.203 brouard 1037: /* #define DEBUGLINMIN */
1038: /* #define DEBUGHESS */
1039: #define DEBUGHESSIJ
1.224 brouard 1040: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1041: #define POWELL /* Instead of NLOPT */
1.224 brouard 1042: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1043: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1044: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1045:
1046: #include <math.h>
1047: #include <stdio.h>
1048: #include <stdlib.h>
1049: #include <string.h>
1.226 brouard 1050: #include <ctype.h>
1.159 brouard 1051:
1052: #ifdef _WIN32
1053: #include <io.h>
1.172 brouard 1054: #include <windows.h>
1055: #include <tchar.h>
1.159 brouard 1056: #else
1.126 brouard 1057: #include <unistd.h>
1.159 brouard 1058: #endif
1.126 brouard 1059:
1060: #include <limits.h>
1061: #include <sys/types.h>
1.171 brouard 1062:
1063: #if defined(__GNUC__)
1064: #include <sys/utsname.h> /* Doesn't work on Windows */
1065: #endif
1066:
1.126 brouard 1067: #include <sys/stat.h>
1068: #include <errno.h>
1.159 brouard 1069: /* extern int errno; */
1.126 brouard 1070:
1.157 brouard 1071: /* #ifdef LINUX */
1072: /* #include <time.h> */
1073: /* #include "timeval.h" */
1074: /* #else */
1075: /* #include <sys/time.h> */
1076: /* #endif */
1077:
1.126 brouard 1078: #include <time.h>
1079:
1.136 brouard 1080: #ifdef GSL
1081: #include <gsl/gsl_errno.h>
1082: #include <gsl/gsl_multimin.h>
1083: #endif
1084:
1.167 brouard 1085:
1.162 brouard 1086: #ifdef NLOPT
1087: #include <nlopt.h>
1088: typedef struct {
1089: double (* function)(double [] );
1090: } myfunc_data ;
1091: #endif
1092:
1.126 brouard 1093: /* #include <libintl.h> */
1094: /* #define _(String) gettext (String) */
1095:
1.251 brouard 1096: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1097:
1098: #define GNUPLOTPROGRAM "gnuplot"
1099: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1100: #define FILENAMELENGTH 132
1101:
1102: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1103: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1104:
1.144 brouard 1105: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1106: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1107:
1108: #define NINTERVMAX 8
1.144 brouard 1109: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1110: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1111: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1112: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1113: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1114: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1115: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1116: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1117: /* #define AGESUP 130 */
1.288 brouard 1118: /* #define AGESUP 150 */
1119: #define AGESUP 200
1.268 brouard 1120: #define AGEINF 0
1.218 brouard 1121: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1122: #define AGEBASE 40
1.194 brouard 1123: #define AGEOVERFLOW 1.e20
1.164 brouard 1124: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1125: #ifdef _WIN32
1126: #define DIRSEPARATOR '\\'
1127: #define CHARSEPARATOR "\\"
1128: #define ODIRSEPARATOR '/'
1129: #else
1.126 brouard 1130: #define DIRSEPARATOR '/'
1131: #define CHARSEPARATOR "/"
1132: #define ODIRSEPARATOR '\\'
1133: #endif
1134:
1.305 ! brouard 1135: /* $Id: imach.c,v 1.304 2021/02/12 11:34:20 brouard Exp $ */
1.126 brouard 1136: /* $State: Exp $ */
1.196 brouard 1137: #include "version.h"
1138: char version[]=__IMACH_VERSION__;
1.300 brouard 1139: char copyright[]="May 2019,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020";
1.305 ! brouard 1140: char fullversion[]="$Revision: 1.304 $ $Date: 2021/02/12 11:34:20 $";
1.126 brouard 1141: char strstart[80];
1142: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1143: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1144: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1145: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1146: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1147: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1148: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1149: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1150: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1151: int cptcovprodnoage=0; /**< Number of covariate products without age */
1152: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1153: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1154: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1155: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1156: int nsd=0; /**< Total number of single dummy variables (output) */
1157: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1158: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1159: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1160: int ntveff=0; /**< ntveff number of effective time varying variables */
1161: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1162: int cptcov=0; /* Working variable */
1.290 brouard 1163: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1164: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1165: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1166: int nlstate=2; /* Number of live states */
1167: int ndeath=1; /* Number of dead states */
1.130 brouard 1168: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1169: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1170: int popbased=0;
1171:
1172: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1173: int maxwav=0; /* Maxim number of waves */
1174: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1175: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1176: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1177: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1178: int mle=1, weightopt=0;
1.126 brouard 1179: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1180: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1181: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1182: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1183: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1184: int selected(int kvar); /* Is covariate kvar selected for printing results */
1185:
1.130 brouard 1186: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1187: double **matprod2(); /* test */
1.126 brouard 1188: double **oldm, **newm, **savm; /* Working pointers to matrices */
1189: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1190: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1191:
1.136 brouard 1192: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1193: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1194: FILE *ficlog, *ficrespow;
1.130 brouard 1195: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1196: double fretone; /* Only one call to likelihood */
1.130 brouard 1197: long ipmx=0; /* Number of contributions */
1.126 brouard 1198: double sw; /* Sum of weights */
1199: char filerespow[FILENAMELENGTH];
1200: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1201: FILE *ficresilk;
1202: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1203: FILE *ficresprobmorprev;
1204: FILE *fichtm, *fichtmcov; /* Html File */
1205: FILE *ficreseij;
1206: char filerese[FILENAMELENGTH];
1207: FILE *ficresstdeij;
1208: char fileresstde[FILENAMELENGTH];
1209: FILE *ficrescveij;
1210: char filerescve[FILENAMELENGTH];
1211: FILE *ficresvij;
1212: char fileresv[FILENAMELENGTH];
1.269 brouard 1213:
1.126 brouard 1214: char title[MAXLINE];
1.234 brouard 1215: char model[MAXLINE]; /**< The model line */
1.217 brouard 1216: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1217: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1218: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1219: char command[FILENAMELENGTH];
1220: int outcmd=0;
1221:
1.217 brouard 1222: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1223: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1224: char filelog[FILENAMELENGTH]; /* Log file */
1225: char filerest[FILENAMELENGTH];
1226: char fileregp[FILENAMELENGTH];
1227: char popfile[FILENAMELENGTH];
1228:
1229: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1230:
1.157 brouard 1231: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1232: /* struct timezone tzp; */
1233: /* extern int gettimeofday(); */
1234: struct tm tml, *gmtime(), *localtime();
1235:
1236: extern time_t time();
1237:
1238: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1239: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1240: struct tm tm;
1241:
1.126 brouard 1242: char strcurr[80], strfor[80];
1243:
1244: char *endptr;
1245: long lval;
1246: double dval;
1247:
1248: #define NR_END 1
1249: #define FREE_ARG char*
1250: #define FTOL 1.0e-10
1251:
1252: #define NRANSI
1.240 brouard 1253: #define ITMAX 200
1254: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1255:
1256: #define TOL 2.0e-4
1257:
1258: #define CGOLD 0.3819660
1259: #define ZEPS 1.0e-10
1260: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1261:
1262: #define GOLD 1.618034
1263: #define GLIMIT 100.0
1264: #define TINY 1.0e-20
1265:
1266: static double maxarg1,maxarg2;
1267: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1268: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1269:
1270: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1271: #define rint(a) floor(a+0.5)
1.166 brouard 1272: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1273: #define mytinydouble 1.0e-16
1.166 brouard 1274: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1275: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1276: /* static double dsqrarg; */
1277: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1278: static double sqrarg;
1279: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1280: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1281: int agegomp= AGEGOMP;
1282:
1283: int imx;
1284: int stepm=1;
1285: /* Stepm, step in month: minimum step interpolation*/
1286:
1287: int estepm;
1288: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1289:
1290: int m,nb;
1291: long *num;
1.197 brouard 1292: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1293: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1294: covariate for which somebody answered excluding
1295: undefined. Usually 2: 0 and 1. */
1296: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1297: covariate for which somebody answered including
1298: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1299: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1300: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1301: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1302: double *ageexmed,*agecens;
1303: double dateintmean=0;
1.296 brouard 1304: double anprojd, mprojd, jprojd; /* For eventual projections */
1305: double anprojf, mprojf, jprojf;
1.126 brouard 1306:
1.296 brouard 1307: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1308: double anbackf, mbackf, jbackf;
1309: double jintmean,mintmean,aintmean;
1.126 brouard 1310: double *weight;
1311: int **s; /* Status */
1.141 brouard 1312: double *agedc;
1.145 brouard 1313: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1314: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1315: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1316: double **coqvar; /* Fixed quantitative covariate nqv */
1317: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1318: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1319: double idx;
1320: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1321: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1322: /*k 1 2 3 4 5 6 7 8 9 */
1323: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1324: /* Tndvar[k] 1 2 3 4 5 */
1325: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1326: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1327: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1328: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1329: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1330: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1331: /* Tprod[i]=k 4 7 */
1332: /* Tage[i]=k 5 8 */
1333: /* */
1334: /* Type */
1335: /* V 1 2 3 4 5 */
1336: /* F F V V V */
1337: /* D Q D D Q */
1338: /* */
1339: int *TvarsD;
1340: int *TvarsDind;
1341: int *TvarsQ;
1342: int *TvarsQind;
1343:
1.235 brouard 1344: #define MAXRESULTLINES 10
1345: int nresult=0;
1.258 brouard 1346: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1347: int TKresult[MAXRESULTLINES];
1.237 brouard 1348: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1349: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1350: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1351: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1352: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1353: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1354:
1.234 brouard 1355: /* 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 1356: 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 */
1357: 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 */
1358: 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 */
1359: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1360: 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 */
1361: 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 1362: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1363: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1364: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1365: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1366: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1367: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1368: 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 */
1369: 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 */
1370:
1.230 brouard 1371: int *Tvarsel; /**< Selected covariates for output */
1372: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1373: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1374: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1375: 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 1376: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1377: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1378: int *Tage;
1.227 brouard 1379: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1380: 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 1381: 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*/
1382: 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 1383: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1384: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1385: int **Tvard;
1386: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1387: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1388: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1389: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1390: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1391: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1392: double *lsurv, *lpop, *tpop;
1393:
1.231 brouard 1394: #define FD 1; /* Fixed dummy covariate */
1395: #define FQ 2; /* Fixed quantitative covariate */
1396: #define FP 3; /* Fixed product covariate */
1397: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1398: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1399: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1400: #define VD 10; /* Varying dummy covariate */
1401: #define VQ 11; /* Varying quantitative covariate */
1402: #define VP 12; /* Varying product covariate */
1403: #define VPDD 13; /* Varying product dummy*dummy covariate */
1404: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1405: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1406: #define APFD 16; /* Age product * fixed dummy covariate */
1407: #define APFQ 17; /* Age product * fixed quantitative covariate */
1408: #define APVD 18; /* Age product * varying dummy covariate */
1409: #define APVQ 19; /* Age product * varying quantitative covariate */
1410:
1411: #define FTYPE 1; /* Fixed covariate */
1412: #define VTYPE 2; /* Varying covariate (loop in wave) */
1413: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1414:
1415: struct kmodel{
1416: int maintype; /* main type */
1417: int subtype; /* subtype */
1418: };
1419: struct kmodel modell[NCOVMAX];
1420:
1.143 brouard 1421: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1422: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1423:
1424: /**************** split *************************/
1425: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1426: {
1427: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1428: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1429: */
1430: char *ss; /* pointer */
1.186 brouard 1431: int l1=0, l2=0; /* length counters */
1.126 brouard 1432:
1433: l1 = strlen(path ); /* length of path */
1434: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1435: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1436: if ( ss == NULL ) { /* no directory, so determine current directory */
1437: strcpy( name, path ); /* we got the fullname name because no directory */
1438: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1439: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1440: /* get current working directory */
1441: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1442: #ifdef WIN32
1443: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1444: #else
1445: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1446: #endif
1.126 brouard 1447: return( GLOCK_ERROR_GETCWD );
1448: }
1449: /* got dirc from getcwd*/
1450: printf(" DIRC = %s \n",dirc);
1.205 brouard 1451: } else { /* strip directory from path */
1.126 brouard 1452: ss++; /* after this, the filename */
1453: l2 = strlen( ss ); /* length of filename */
1454: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1455: strcpy( name, ss ); /* save file name */
1456: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1457: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1458: printf(" DIRC2 = %s \n",dirc);
1459: }
1460: /* We add a separator at the end of dirc if not exists */
1461: l1 = strlen( dirc ); /* length of directory */
1462: if( dirc[l1-1] != DIRSEPARATOR ){
1463: dirc[l1] = DIRSEPARATOR;
1464: dirc[l1+1] = 0;
1465: printf(" DIRC3 = %s \n",dirc);
1466: }
1467: ss = strrchr( name, '.' ); /* find last / */
1468: if (ss >0){
1469: ss++;
1470: strcpy(ext,ss); /* save extension */
1471: l1= strlen( name);
1472: l2= strlen(ss)+1;
1473: strncpy( finame, name, l1-l2);
1474: finame[l1-l2]= 0;
1475: }
1476:
1477: return( 0 ); /* we're done */
1478: }
1479:
1480:
1481: /******************************************/
1482:
1483: void replace_back_to_slash(char *s, char*t)
1484: {
1485: int i;
1486: int lg=0;
1487: i=0;
1488: lg=strlen(t);
1489: for(i=0; i<= lg; i++) {
1490: (s[i] = t[i]);
1491: if (t[i]== '\\') s[i]='/';
1492: }
1493: }
1494:
1.132 brouard 1495: char *trimbb(char *out, char *in)
1.137 brouard 1496: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1497: char *s;
1498: s=out;
1499: while (*in != '\0'){
1.137 brouard 1500: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1501: in++;
1502: }
1503: *out++ = *in++;
1504: }
1505: *out='\0';
1506: return s;
1507: }
1508:
1.187 brouard 1509: /* char *substrchaine(char *out, char *in, char *chain) */
1510: /* { */
1511: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1512: /* char *s, *t; */
1513: /* t=in;s=out; */
1514: /* while ((*in != *chain) && (*in != '\0')){ */
1515: /* *out++ = *in++; */
1516: /* } */
1517:
1518: /* /\* *in matches *chain *\/ */
1519: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1520: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1521: /* } */
1522: /* in--; chain--; */
1523: /* while ( (*in != '\0')){ */
1524: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1525: /* *out++ = *in++; */
1526: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1527: /* } */
1528: /* *out='\0'; */
1529: /* out=s; */
1530: /* return out; */
1531: /* } */
1532: char *substrchaine(char *out, char *in, char *chain)
1533: {
1534: /* Substract chain 'chain' from 'in', return and output 'out' */
1535: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1536:
1537: char *strloc;
1538:
1539: strcpy (out, in);
1540: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1541: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1542: if(strloc != NULL){
1543: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1544: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1545: /* strcpy (strloc, strloc +strlen(chain));*/
1546: }
1547: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1548: return out;
1549: }
1550:
1551:
1.145 brouard 1552: char *cutl(char *blocc, char *alocc, char *in, char occ)
1553: {
1.187 brouard 1554: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1555: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1556: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1557: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1558: */
1.160 brouard 1559: char *s, *t;
1.145 brouard 1560: t=in;s=in;
1561: while ((*in != occ) && (*in != '\0')){
1562: *alocc++ = *in++;
1563: }
1564: if( *in == occ){
1565: *(alocc)='\0';
1566: s=++in;
1567: }
1568:
1569: if (s == t) {/* occ not found */
1570: *(alocc-(in-s))='\0';
1571: in=s;
1572: }
1573: while ( *in != '\0'){
1574: *blocc++ = *in++;
1575: }
1576:
1577: *blocc='\0';
1578: return t;
1579: }
1.137 brouard 1580: char *cutv(char *blocc, char *alocc, char *in, char occ)
1581: {
1.187 brouard 1582: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1583: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1584: gives blocc="abcdef2ghi" and alocc="j".
1585: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1586: */
1587: char *s, *t;
1588: t=in;s=in;
1589: while (*in != '\0'){
1590: while( *in == occ){
1591: *blocc++ = *in++;
1592: s=in;
1593: }
1594: *blocc++ = *in++;
1595: }
1596: if (s == t) /* occ not found */
1597: *(blocc-(in-s))='\0';
1598: else
1599: *(blocc-(in-s)-1)='\0';
1600: in=s;
1601: while ( *in != '\0'){
1602: *alocc++ = *in++;
1603: }
1604:
1605: *alocc='\0';
1606: return s;
1607: }
1608:
1.126 brouard 1609: int nbocc(char *s, char occ)
1610: {
1611: int i,j=0;
1612: int lg=20;
1613: i=0;
1614: lg=strlen(s);
1615: for(i=0; i<= lg; i++) {
1.234 brouard 1616: if (s[i] == occ ) j++;
1.126 brouard 1617: }
1618: return j;
1619: }
1620:
1.137 brouard 1621: /* void cutv(char *u,char *v, char*t, char occ) */
1622: /* { */
1623: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1624: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1625: /* gives u="abcdef2ghi" and v="j" *\/ */
1626: /* int i,lg,j,p=0; */
1627: /* i=0; */
1628: /* lg=strlen(t); */
1629: /* for(j=0; j<=lg-1; j++) { */
1630: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1631: /* } */
1.126 brouard 1632:
1.137 brouard 1633: /* for(j=0; j<p; j++) { */
1634: /* (u[j] = t[j]); */
1635: /* } */
1636: /* u[p]='\0'; */
1.126 brouard 1637:
1.137 brouard 1638: /* for(j=0; j<= lg; j++) { */
1639: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1640: /* } */
1641: /* } */
1.126 brouard 1642:
1.160 brouard 1643: #ifdef _WIN32
1644: char * strsep(char **pp, const char *delim)
1645: {
1646: char *p, *q;
1647:
1648: if ((p = *pp) == NULL)
1649: return 0;
1650: if ((q = strpbrk (p, delim)) != NULL)
1651: {
1652: *pp = q + 1;
1653: *q = '\0';
1654: }
1655: else
1656: *pp = 0;
1657: return p;
1658: }
1659: #endif
1660:
1.126 brouard 1661: /********************** nrerror ********************/
1662:
1663: void nrerror(char error_text[])
1664: {
1665: fprintf(stderr,"ERREUR ...\n");
1666: fprintf(stderr,"%s\n",error_text);
1667: exit(EXIT_FAILURE);
1668: }
1669: /*********************** vector *******************/
1670: double *vector(int nl, int nh)
1671: {
1672: double *v;
1673: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1674: if (!v) nrerror("allocation failure in vector");
1675: return v-nl+NR_END;
1676: }
1677:
1678: /************************ free vector ******************/
1679: void free_vector(double*v, int nl, int nh)
1680: {
1681: free((FREE_ARG)(v+nl-NR_END));
1682: }
1683:
1684: /************************ivector *******************************/
1685: int *ivector(long nl,long nh)
1686: {
1687: int *v;
1688: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1689: if (!v) nrerror("allocation failure in ivector");
1690: return v-nl+NR_END;
1691: }
1692:
1693: /******************free ivector **************************/
1694: void free_ivector(int *v, long nl, long nh)
1695: {
1696: free((FREE_ARG)(v+nl-NR_END));
1697: }
1698:
1699: /************************lvector *******************************/
1700: long *lvector(long nl,long nh)
1701: {
1702: long *v;
1703: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1704: if (!v) nrerror("allocation failure in ivector");
1705: return v-nl+NR_END;
1706: }
1707:
1708: /******************free lvector **************************/
1709: void free_lvector(long *v, long nl, long nh)
1710: {
1711: free((FREE_ARG)(v+nl-NR_END));
1712: }
1713:
1714: /******************* imatrix *******************************/
1715: int **imatrix(long nrl, long nrh, long ncl, long nch)
1716: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1717: {
1718: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1719: int **m;
1720:
1721: /* allocate pointers to rows */
1722: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1723: if (!m) nrerror("allocation failure 1 in matrix()");
1724: m += NR_END;
1725: m -= nrl;
1726:
1727:
1728: /* allocate rows and set pointers to them */
1729: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1730: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1731: m[nrl] += NR_END;
1732: m[nrl] -= ncl;
1733:
1734: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1735:
1736: /* return pointer to array of pointers to rows */
1737: return m;
1738: }
1739:
1740: /****************** free_imatrix *************************/
1741: void free_imatrix(m,nrl,nrh,ncl,nch)
1742: int **m;
1743: long nch,ncl,nrh,nrl;
1744: /* free an int matrix allocated by imatrix() */
1745: {
1746: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1747: free((FREE_ARG) (m+nrl-NR_END));
1748: }
1749:
1750: /******************* matrix *******************************/
1751: double **matrix(long nrl, long nrh, long ncl, long nch)
1752: {
1753: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1754: double **m;
1755:
1756: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1757: if (!m) nrerror("allocation failure 1 in matrix()");
1758: m += NR_END;
1759: m -= nrl;
1760:
1761: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1762: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1763: m[nrl] += NR_END;
1764: m[nrl] -= ncl;
1765:
1766: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1767: return m;
1.145 brouard 1768: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1769: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1770: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1771: */
1772: }
1773:
1774: /*************************free matrix ************************/
1775: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1776: {
1777: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1778: free((FREE_ARG)(m+nrl-NR_END));
1779: }
1780:
1781: /******************* ma3x *******************************/
1782: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1783: {
1784: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1785: double ***m;
1786:
1787: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1788: if (!m) nrerror("allocation failure 1 in matrix()");
1789: m += NR_END;
1790: m -= nrl;
1791:
1792: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1793: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1794: m[nrl] += NR_END;
1795: m[nrl] -= ncl;
1796:
1797: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1798:
1799: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1800: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1801: m[nrl][ncl] += NR_END;
1802: m[nrl][ncl] -= nll;
1803: for (j=ncl+1; j<=nch; j++)
1804: m[nrl][j]=m[nrl][j-1]+nlay;
1805:
1806: for (i=nrl+1; i<=nrh; i++) {
1807: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1808: for (j=ncl+1; j<=nch; j++)
1809: m[i][j]=m[i][j-1]+nlay;
1810: }
1811: return m;
1812: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1813: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1814: */
1815: }
1816:
1817: /*************************free ma3x ************************/
1818: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1819: {
1820: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1821: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1822: free((FREE_ARG)(m+nrl-NR_END));
1823: }
1824:
1825: /*************** function subdirf ***********/
1826: char *subdirf(char fileres[])
1827: {
1828: /* Caution optionfilefiname is hidden */
1829: strcpy(tmpout,optionfilefiname);
1830: strcat(tmpout,"/"); /* Add to the right */
1831: strcat(tmpout,fileres);
1832: return tmpout;
1833: }
1834:
1835: /*************** function subdirf2 ***********/
1836: char *subdirf2(char fileres[], char *preop)
1837: {
1838:
1839: /* Caution optionfilefiname is hidden */
1840: strcpy(tmpout,optionfilefiname);
1841: strcat(tmpout,"/");
1842: strcat(tmpout,preop);
1843: strcat(tmpout,fileres);
1844: return tmpout;
1845: }
1846:
1847: /*************** function subdirf3 ***********/
1848: char *subdirf3(char fileres[], char *preop, char *preop2)
1849: {
1850:
1851: /* Caution optionfilefiname is hidden */
1852: strcpy(tmpout,optionfilefiname);
1853: strcat(tmpout,"/");
1854: strcat(tmpout,preop);
1855: strcat(tmpout,preop2);
1856: strcat(tmpout,fileres);
1857: return tmpout;
1858: }
1.213 brouard 1859:
1860: /*************** function subdirfext ***********/
1861: char *subdirfext(char fileres[], char *preop, char *postop)
1862: {
1863:
1864: strcpy(tmpout,preop);
1865: strcat(tmpout,fileres);
1866: strcat(tmpout,postop);
1867: return tmpout;
1868: }
1.126 brouard 1869:
1.213 brouard 1870: /*************** function subdirfext3 ***********/
1871: char *subdirfext3(char fileres[], char *preop, char *postop)
1872: {
1873:
1874: /* Caution optionfilefiname is hidden */
1875: strcpy(tmpout,optionfilefiname);
1876: strcat(tmpout,"/");
1877: strcat(tmpout,preop);
1878: strcat(tmpout,fileres);
1879: strcat(tmpout,postop);
1880: return tmpout;
1881: }
1882:
1.162 brouard 1883: char *asc_diff_time(long time_sec, char ascdiff[])
1884: {
1885: long sec_left, days, hours, minutes;
1886: days = (time_sec) / (60*60*24);
1887: sec_left = (time_sec) % (60*60*24);
1888: hours = (sec_left) / (60*60) ;
1889: sec_left = (sec_left) %(60*60);
1890: minutes = (sec_left) /60;
1891: sec_left = (sec_left) % (60);
1892: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1893: return ascdiff;
1894: }
1895:
1.126 brouard 1896: /***************** f1dim *************************/
1897: extern int ncom;
1898: extern double *pcom,*xicom;
1899: extern double (*nrfunc)(double []);
1900:
1901: double f1dim(double x)
1902: {
1903: int j;
1904: double f;
1905: double *xt;
1906:
1907: xt=vector(1,ncom);
1908: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1909: f=(*nrfunc)(xt);
1910: free_vector(xt,1,ncom);
1911: return f;
1912: }
1913:
1914: /*****************brent *************************/
1915: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1916: {
1917: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1918: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1919: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1920: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1921: * returned function value.
1922: */
1.126 brouard 1923: int iter;
1924: double a,b,d,etemp;
1.159 brouard 1925: double fu=0,fv,fw,fx;
1.164 brouard 1926: double ftemp=0.;
1.126 brouard 1927: double p,q,r,tol1,tol2,u,v,w,x,xm;
1928: double e=0.0;
1929:
1930: a=(ax < cx ? ax : cx);
1931: b=(ax > cx ? ax : cx);
1932: x=w=v=bx;
1933: fw=fv=fx=(*f)(x);
1934: for (iter=1;iter<=ITMAX;iter++) {
1935: xm=0.5*(a+b);
1936: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1937: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1938: printf(".");fflush(stdout);
1939: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1940: #ifdef DEBUGBRENT
1.126 brouard 1941: 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);
1942: 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);
1943: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1944: #endif
1945: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1946: *xmin=x;
1947: return fx;
1948: }
1949: ftemp=fu;
1950: if (fabs(e) > tol1) {
1951: r=(x-w)*(fx-fv);
1952: q=(x-v)*(fx-fw);
1953: p=(x-v)*q-(x-w)*r;
1954: q=2.0*(q-r);
1955: if (q > 0.0) p = -p;
1956: q=fabs(q);
1957: etemp=e;
1958: e=d;
1959: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1960: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1961: else {
1.224 brouard 1962: d=p/q;
1963: u=x+d;
1964: if (u-a < tol2 || b-u < tol2)
1965: d=SIGN(tol1,xm-x);
1.126 brouard 1966: }
1967: } else {
1968: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1969: }
1970: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1971: fu=(*f)(u);
1972: if (fu <= fx) {
1973: if (u >= x) a=x; else b=x;
1974: SHFT(v,w,x,u)
1.183 brouard 1975: SHFT(fv,fw,fx,fu)
1976: } else {
1977: if (u < x) a=u; else b=u;
1978: if (fu <= fw || w == x) {
1.224 brouard 1979: v=w;
1980: w=u;
1981: fv=fw;
1982: fw=fu;
1.183 brouard 1983: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1984: v=u;
1985: fv=fu;
1.183 brouard 1986: }
1987: }
1.126 brouard 1988: }
1989: nrerror("Too many iterations in brent");
1990: *xmin=x;
1991: return fx;
1992: }
1993:
1994: /****************** mnbrak ***********************/
1995:
1996: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1997: double (*func)(double))
1.183 brouard 1998: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1999: the downhill direction (defined by the function as evaluated at the initial points) and returns
2000: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2001: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2002: */
1.126 brouard 2003: double ulim,u,r,q, dum;
2004: double fu;
1.187 brouard 2005:
2006: double scale=10.;
2007: int iterscale=0;
2008:
2009: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2010: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2011:
2012:
2013: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2014: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2015: /* *bx = *ax - (*ax - *bx)/scale; */
2016: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2017: /* } */
2018:
1.126 brouard 2019: if (*fb > *fa) {
2020: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2021: SHFT(dum,*fb,*fa,dum)
2022: }
1.126 brouard 2023: *cx=(*bx)+GOLD*(*bx-*ax);
2024: *fc=(*func)(*cx);
1.183 brouard 2025: #ifdef DEBUG
1.224 brouard 2026: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2027: 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 2028: #endif
1.224 brouard 2029: 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 2030: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2031: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2032: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2033: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2034: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2035: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2036: fu=(*func)(u);
1.163 brouard 2037: #ifdef DEBUG
2038: /* f(x)=A(x-u)**2+f(u) */
2039: double A, fparabu;
2040: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2041: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2042: 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);
2043: 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 2044: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2045: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2046: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2047: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2048: #endif
1.184 brouard 2049: #ifdef MNBRAKORIGINAL
1.183 brouard 2050: #else
1.191 brouard 2051: /* if (fu > *fc) { */
2052: /* #ifdef DEBUG */
2053: /* printf("mnbrak4 fu > fc \n"); */
2054: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2055: /* #endif */
2056: /* /\* 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 *\\/ *\/ */
2057: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2058: /* dum=u; /\* Shifting c and u *\/ */
2059: /* u = *cx; */
2060: /* *cx = dum; */
2061: /* dum = fu; */
2062: /* fu = *fc; */
2063: /* *fc =dum; */
2064: /* } else { /\* end *\/ */
2065: /* #ifdef DEBUG */
2066: /* printf("mnbrak3 fu < fc \n"); */
2067: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2068: /* #endif */
2069: /* dum=u; /\* Shifting c and u *\/ */
2070: /* u = *cx; */
2071: /* *cx = dum; */
2072: /* dum = fu; */
2073: /* fu = *fc; */
2074: /* *fc =dum; */
2075: /* } */
1.224 brouard 2076: #ifdef DEBUGMNBRAK
2077: double A, fparabu;
2078: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2079: fparabu= *fa - A*(*ax-u)*(*ax-u);
2080: 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);
2081: 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 2082: #endif
1.191 brouard 2083: dum=u; /* Shifting c and u */
2084: u = *cx;
2085: *cx = dum;
2086: dum = fu;
2087: fu = *fc;
2088: *fc =dum;
1.183 brouard 2089: #endif
1.162 brouard 2090: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2091: #ifdef DEBUG
1.224 brouard 2092: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2093: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2094: #endif
1.126 brouard 2095: fu=(*func)(u);
2096: if (fu < *fc) {
1.183 brouard 2097: #ifdef DEBUG
1.224 brouard 2098: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2099: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2100: #endif
2101: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2102: SHFT(*fb,*fc,fu,(*func)(u))
2103: #ifdef DEBUG
2104: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2105: #endif
2106: }
1.162 brouard 2107: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2108: #ifdef DEBUG
1.224 brouard 2109: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2110: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2111: #endif
1.126 brouard 2112: u=ulim;
2113: fu=(*func)(u);
1.183 brouard 2114: } else { /* u could be left to b (if r > q parabola has a maximum) */
2115: #ifdef DEBUG
1.224 brouard 2116: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2117: 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 2118: #endif
1.126 brouard 2119: u=(*cx)+GOLD*(*cx-*bx);
2120: fu=(*func)(u);
1.224 brouard 2121: #ifdef DEBUG
2122: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2123: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2124: #endif
1.183 brouard 2125: } /* end tests */
1.126 brouard 2126: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2127: SHFT(*fa,*fb,*fc,fu)
2128: #ifdef DEBUG
1.224 brouard 2129: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2130: 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 2131: #endif
2132: } /* 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 2133: }
2134:
2135: /*************** linmin ************************/
1.162 brouard 2136: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2137: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2138: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2139: the value of func at the returned location p . This is actually all accomplished by calling the
2140: routines mnbrak and brent .*/
1.126 brouard 2141: int ncom;
2142: double *pcom,*xicom;
2143: double (*nrfunc)(double []);
2144:
1.224 brouard 2145: #ifdef LINMINORIGINAL
1.126 brouard 2146: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2147: #else
2148: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2149: #endif
1.126 brouard 2150: {
2151: double brent(double ax, double bx, double cx,
2152: double (*f)(double), double tol, double *xmin);
2153: double f1dim(double x);
2154: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2155: double *fc, double (*func)(double));
2156: int j;
2157: double xx,xmin,bx,ax;
2158: double fx,fb,fa;
1.187 brouard 2159:
1.203 brouard 2160: #ifdef LINMINORIGINAL
2161: #else
2162: double scale=10., axs, xxs; /* Scale added for infinity */
2163: #endif
2164:
1.126 brouard 2165: ncom=n;
2166: pcom=vector(1,n);
2167: xicom=vector(1,n);
2168: nrfunc=func;
2169: for (j=1;j<=n;j++) {
2170: pcom[j]=p[j];
1.202 brouard 2171: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2172: }
1.187 brouard 2173:
1.203 brouard 2174: #ifdef LINMINORIGINAL
2175: xx=1.;
2176: #else
2177: axs=0.0;
2178: xxs=1.;
2179: do{
2180: xx= xxs;
2181: #endif
1.187 brouard 2182: ax=0.;
2183: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2184: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2185: /* 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)) */
2186: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2187: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2188: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2189: /* 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 2190: #ifdef LINMINORIGINAL
2191: #else
2192: if (fx != fx){
1.224 brouard 2193: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2194: printf("|");
2195: fprintf(ficlog,"|");
1.203 brouard 2196: #ifdef DEBUGLINMIN
1.224 brouard 2197: 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 2198: #endif
2199: }
1.224 brouard 2200: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2201: #endif
2202:
1.191 brouard 2203: #ifdef DEBUGLINMIN
2204: 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 2205: 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 2206: #endif
1.224 brouard 2207: #ifdef LINMINORIGINAL
2208: #else
2209: if(fb == fx){ /* Flat function in the direction */
2210: xmin=xx;
2211: *flat=1;
2212: }else{
2213: *flat=0;
2214: #endif
2215: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2216: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2217: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2218: /* fmin = f(p[j] + xmin * xi[j]) */
2219: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2220: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2221: #ifdef DEBUG
1.224 brouard 2222: 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);
2223: 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);
2224: #endif
2225: #ifdef LINMINORIGINAL
2226: #else
2227: }
1.126 brouard 2228: #endif
1.191 brouard 2229: #ifdef DEBUGLINMIN
2230: printf("linmin end ");
1.202 brouard 2231: fprintf(ficlog,"linmin end ");
1.191 brouard 2232: #endif
1.126 brouard 2233: for (j=1;j<=n;j++) {
1.203 brouard 2234: #ifdef LINMINORIGINAL
2235: xi[j] *= xmin;
2236: #else
2237: #ifdef DEBUGLINMIN
2238: if(xxs <1.0)
2239: printf(" before xi[%d]=%12.8f", j,xi[j]);
2240: #endif
2241: 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) */
2242: #ifdef DEBUGLINMIN
2243: if(xxs <1.0)
2244: 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 );
2245: #endif
2246: #endif
1.187 brouard 2247: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2248: }
1.191 brouard 2249: #ifdef DEBUGLINMIN
1.203 brouard 2250: printf("\n");
1.191 brouard 2251: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2252: 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 2253: for (j=1;j<=n;j++) {
1.202 brouard 2254: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2255: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2256: if(j % ncovmodel == 0){
1.191 brouard 2257: printf("\n");
1.202 brouard 2258: fprintf(ficlog,"\n");
2259: }
1.191 brouard 2260: }
1.203 brouard 2261: #else
1.191 brouard 2262: #endif
1.126 brouard 2263: free_vector(xicom,1,n);
2264: free_vector(pcom,1,n);
2265: }
2266:
2267:
2268: /*************** powell ************************/
1.162 brouard 2269: /*
2270: Minimization of a function func of n variables. Input consists of an initial starting point
2271: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2272: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2273: such that failure to decrease by more than this amount on one iteration signals doneness. On
2274: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2275: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2276: */
1.224 brouard 2277: #ifdef LINMINORIGINAL
2278: #else
2279: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2280: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2281: #endif
1.126 brouard 2282: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2283: double (*func)(double []))
2284: {
1.224 brouard 2285: #ifdef LINMINORIGINAL
2286: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2287: double (*func)(double []));
1.224 brouard 2288: #else
1.241 brouard 2289: void linmin(double p[], double xi[], int n, double *fret,
2290: double (*func)(double []),int *flat);
1.224 brouard 2291: #endif
1.239 brouard 2292: int i,ibig,j,jk,k;
1.126 brouard 2293: double del,t,*pt,*ptt,*xit;
1.181 brouard 2294: double directest;
1.126 brouard 2295: double fp,fptt;
2296: double *xits;
2297: int niterf, itmp;
1.224 brouard 2298: #ifdef LINMINORIGINAL
2299: #else
2300:
2301: flatdir=ivector(1,n);
2302: for (j=1;j<=n;j++) flatdir[j]=0;
2303: #endif
1.126 brouard 2304:
2305: pt=vector(1,n);
2306: ptt=vector(1,n);
2307: xit=vector(1,n);
2308: xits=vector(1,n);
2309: *fret=(*func)(p);
2310: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2311: rcurr_time = time(NULL);
1.126 brouard 2312: for (*iter=1;;++(*iter)) {
1.187 brouard 2313: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2314: ibig=0;
2315: del=0.0;
1.157 brouard 2316: rlast_time=rcurr_time;
2317: /* (void) gettimeofday(&curr_time,&tzp); */
2318: rcurr_time = time(NULL);
2319: curr_time = *localtime(&rcurr_time);
2320: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2321: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2322: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2323: for (i=1;i<=n;i++) {
1.126 brouard 2324: fprintf(ficrespow," %.12lf", p[i]);
2325: }
1.239 brouard 2326: fprintf(ficrespow,"\n");fflush(ficrespow);
2327: printf("\n#model= 1 + age ");
2328: fprintf(ficlog,"\n#model= 1 + age ");
2329: if(nagesqr==1){
1.241 brouard 2330: printf(" + age*age ");
2331: fprintf(ficlog," + age*age ");
1.239 brouard 2332: }
2333: for(j=1;j <=ncovmodel-2;j++){
2334: if(Typevar[j]==0) {
2335: printf(" + V%d ",Tvar[j]);
2336: fprintf(ficlog," + V%d ",Tvar[j]);
2337: }else if(Typevar[j]==1) {
2338: printf(" + V%d*age ",Tvar[j]);
2339: fprintf(ficlog," + V%d*age ",Tvar[j]);
2340: }else if(Typevar[j]==2) {
2341: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2342: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2343: }
2344: }
1.126 brouard 2345: printf("\n");
1.239 brouard 2346: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2347: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2348: fprintf(ficlog,"\n");
1.239 brouard 2349: for(i=1,jk=1; i <=nlstate; i++){
2350: for(k=1; k <=(nlstate+ndeath); k++){
2351: if (k != i) {
2352: printf("%d%d ",i,k);
2353: fprintf(ficlog,"%d%d ",i,k);
2354: for(j=1; j <=ncovmodel; j++){
2355: printf("%12.7f ",p[jk]);
2356: fprintf(ficlog,"%12.7f ",p[jk]);
2357: jk++;
2358: }
2359: printf("\n");
2360: fprintf(ficlog,"\n");
2361: }
2362: }
2363: }
1.241 brouard 2364: if(*iter <=3 && *iter >1){
1.157 brouard 2365: tml = *localtime(&rcurr_time);
2366: strcpy(strcurr,asctime(&tml));
2367: rforecast_time=rcurr_time;
1.126 brouard 2368: itmp = strlen(strcurr);
2369: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2370: strcurr[itmp-1]='\0';
1.162 brouard 2371: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2372: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2373: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2374: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2375: forecast_time = *localtime(&rforecast_time);
2376: strcpy(strfor,asctime(&forecast_time));
2377: itmp = strlen(strfor);
2378: if(strfor[itmp-1]=='\n')
2379: strfor[itmp-1]='\0';
2380: 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);
2381: 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 2382: }
2383: }
1.187 brouard 2384: for (i=1;i<=n;i++) { /* For each direction i */
2385: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2386: fptt=(*fret);
2387: #ifdef DEBUG
1.203 brouard 2388: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2389: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2390: #endif
1.203 brouard 2391: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2392: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2393: #ifdef LINMINORIGINAL
1.188 brouard 2394: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2395: #else
2396: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2397: flatdir[i]=flat; /* Function is vanishing in that direction i */
2398: #endif
2399: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2400: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2401: /* because that direction will be replaced unless the gain del is small */
2402: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2403: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2404: /* with the new direction. */
2405: del=fabs(fptt-(*fret));
2406: ibig=i;
1.126 brouard 2407: }
2408: #ifdef DEBUG
2409: printf("%d %.12e",i,(*fret));
2410: fprintf(ficlog,"%d %.12e",i,(*fret));
2411: for (j=1;j<=n;j++) {
1.224 brouard 2412: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2413: printf(" x(%d)=%.12e",j,xit[j]);
2414: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2415: }
2416: for(j=1;j<=n;j++) {
1.225 brouard 2417: printf(" p(%d)=%.12e",j,p[j]);
2418: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2419: }
2420: printf("\n");
2421: fprintf(ficlog,"\n");
2422: #endif
1.187 brouard 2423: } /* end loop on each direction i */
2424: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2425: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2426: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2427: for(j=1;j<=n;j++) {
1.302 brouard 2428: if(flatdir[j] >0){
2429: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2430: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2431: }
2432: /* printf("\n"); */
2433: /* fprintf(ficlog,"\n"); */
2434: }
1.243 brouard 2435: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2436: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2437: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2438: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2439: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2440: /* decreased of more than 3.84 */
2441: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2442: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2443: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2444:
1.188 brouard 2445: /* Starting the program with initial values given by a former maximization will simply change */
2446: /* the scales of the directions and the directions, because the are reset to canonical directions */
2447: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2448: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2449: #ifdef DEBUG
2450: int k[2],l;
2451: k[0]=1;
2452: k[1]=-1;
2453: printf("Max: %.12e",(*func)(p));
2454: fprintf(ficlog,"Max: %.12e",(*func)(p));
2455: for (j=1;j<=n;j++) {
2456: printf(" %.12e",p[j]);
2457: fprintf(ficlog," %.12e",p[j]);
2458: }
2459: printf("\n");
2460: fprintf(ficlog,"\n");
2461: for(l=0;l<=1;l++) {
2462: for (j=1;j<=n;j++) {
2463: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2464: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2465: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2466: }
2467: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2468: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2469: }
2470: #endif
2471:
1.224 brouard 2472: #ifdef LINMINORIGINAL
2473: #else
2474: free_ivector(flatdir,1,n);
2475: #endif
1.126 brouard 2476: free_vector(xit,1,n);
2477: free_vector(xits,1,n);
2478: free_vector(ptt,1,n);
2479: free_vector(pt,1,n);
2480: return;
1.192 brouard 2481: } /* enough precision */
1.240 brouard 2482: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2483: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2484: ptt[j]=2.0*p[j]-pt[j];
2485: xit[j]=p[j]-pt[j];
2486: pt[j]=p[j];
2487: }
1.181 brouard 2488: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2489: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2490: if (*iter <=4) {
1.225 brouard 2491: #else
2492: #endif
1.224 brouard 2493: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2494: #else
1.161 brouard 2495: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2496: #endif
1.162 brouard 2497: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2498: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2499: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2500: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2501: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2502: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2503: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2504: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2505: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2506: /* Even if f3 <f1, directest can be negative and t >0 */
2507: /* mu² and del² are equal when f3=f1 */
2508: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2509: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2510: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2511: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2512: #ifdef NRCORIGINAL
2513: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2514: #else
2515: 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 2516: t= t- del*SQR(fp-fptt);
1.183 brouard 2517: #endif
1.202 brouard 2518: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2519: #ifdef DEBUG
1.181 brouard 2520: 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);
2521: 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 2522: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2523: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2524: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2525: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2526: 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);
2527: 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);
2528: #endif
1.183 brouard 2529: #ifdef POWELLORIGINAL
2530: if (t < 0.0) { /* Then we use it for new direction */
2531: #else
1.182 brouard 2532: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2533: 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 2534: 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 2535: 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 2536: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2537: }
1.181 brouard 2538: if (directest < 0.0) { /* Then we use it for new direction */
2539: #endif
1.191 brouard 2540: #ifdef DEBUGLINMIN
1.234 brouard 2541: printf("Before linmin in direction P%d-P0\n",n);
2542: for (j=1;j<=n;j++) {
2543: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2544: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2545: if(j % ncovmodel == 0){
2546: printf("\n");
2547: fprintf(ficlog,"\n");
2548: }
2549: }
1.224 brouard 2550: #endif
2551: #ifdef LINMINORIGINAL
1.234 brouard 2552: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2553: #else
1.234 brouard 2554: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2555: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2556: #endif
1.234 brouard 2557:
1.191 brouard 2558: #ifdef DEBUGLINMIN
1.234 brouard 2559: for (j=1;j<=n;j++) {
2560: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2561: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2562: if(j % ncovmodel == 0){
2563: printf("\n");
2564: fprintf(ficlog,"\n");
2565: }
2566: }
1.224 brouard 2567: #endif
1.234 brouard 2568: for (j=1;j<=n;j++) {
2569: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2570: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2571: }
1.224 brouard 2572: #ifdef LINMINORIGINAL
2573: #else
1.234 brouard 2574: for (j=1, flatd=0;j<=n;j++) {
2575: if(flatdir[j]>0)
2576: flatd++;
2577: }
2578: if(flatd >0){
1.255 brouard 2579: printf("%d flat directions: ",flatd);
2580: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2581: for (j=1;j<=n;j++) {
2582: if(flatdir[j]>0){
2583: printf("%d ",j);
2584: fprintf(ficlog,"%d ",j);
2585: }
2586: }
2587: printf("\n");
2588: fprintf(ficlog,"\n");
2589: }
1.191 brouard 2590: #endif
1.234 brouard 2591: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2592: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2593:
1.126 brouard 2594: #ifdef DEBUG
1.234 brouard 2595: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2596: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2597: for(j=1;j<=n;j++){
2598: printf(" %lf",xit[j]);
2599: fprintf(ficlog," %lf",xit[j]);
2600: }
2601: printf("\n");
2602: fprintf(ficlog,"\n");
1.126 brouard 2603: #endif
1.192 brouard 2604: } /* end of t or directest negative */
1.224 brouard 2605: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2606: #else
1.234 brouard 2607: } /* end if (fptt < fp) */
1.192 brouard 2608: #endif
1.225 brouard 2609: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2610: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2611: #else
1.224 brouard 2612: #endif
1.234 brouard 2613: } /* loop iteration */
1.126 brouard 2614: }
1.234 brouard 2615:
1.126 brouard 2616: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2617:
1.235 brouard 2618: 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 2619: {
1.279 brouard 2620: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2621: * (and selected quantitative values in nres)
2622: * by left multiplying the unit
2623: * matrix by transitions matrix until convergence is reached with precision ftolpl
2624: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2625: * Wx is row vector: population in state 1, population in state 2, population dead
2626: * or prevalence in state 1, prevalence in state 2, 0
2627: * newm is the matrix after multiplications, its rows are identical at a factor.
2628: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2629: * Output is prlim.
2630: * Initial matrix pimij
2631: */
1.206 brouard 2632: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2633: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2634: /* 0, 0 , 1} */
2635: /*
2636: * and after some iteration: */
2637: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2638: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2639: /* 0, 0 , 1} */
2640: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2641: /* {0.51571254859325999, 0.4842874514067399, */
2642: /* 0.51326036147820708, 0.48673963852179264} */
2643: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2644:
1.126 brouard 2645: int i, ii,j,k;
1.209 brouard 2646: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2647: /* double **matprod2(); */ /* test */
1.218 brouard 2648: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2649: double **newm;
1.209 brouard 2650: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2651: int ncvloop=0;
1.288 brouard 2652: int first=0;
1.169 brouard 2653:
1.209 brouard 2654: min=vector(1,nlstate);
2655: max=vector(1,nlstate);
2656: meandiff=vector(1,nlstate);
2657:
1.218 brouard 2658: /* Starting with matrix unity */
1.126 brouard 2659: for (ii=1;ii<=nlstate+ndeath;ii++)
2660: for (j=1;j<=nlstate+ndeath;j++){
2661: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2662: }
1.169 brouard 2663:
2664: cov[1]=1.;
2665:
2666: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2667: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2668: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2669: ncvloop++;
1.126 brouard 2670: newm=savm;
2671: /* Covariates have to be included here again */
1.138 brouard 2672: cov[2]=agefin;
1.187 brouard 2673: if(nagesqr==1)
2674: cov[3]= agefin*agefin;;
1.234 brouard 2675: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2676: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2677: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2678: /* 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 2679: }
2680: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2681: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2682: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2683: /* 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 2684: }
1.237 brouard 2685: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2686: if(Dummy[Tvar[Tage[k]]]){
2687: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2688: } else{
1.235 brouard 2689: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2690: }
1.235 brouard 2691: /* 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 2692: }
1.237 brouard 2693: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2694: /* 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 2695: if(Dummy[Tvard[k][1]==0]){
2696: if(Dummy[Tvard[k][2]==0]){
2697: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2698: }else{
2699: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2700: }
2701: }else{
2702: if(Dummy[Tvard[k][2]==0]){
2703: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2704: }else{
2705: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2706: }
2707: }
1.234 brouard 2708: }
1.138 brouard 2709: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2710: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2711: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2712: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2713: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2714: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2715: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2716:
1.126 brouard 2717: savm=oldm;
2718: oldm=newm;
1.209 brouard 2719:
2720: for(j=1; j<=nlstate; j++){
2721: max[j]=0.;
2722: min[j]=1.;
2723: }
2724: for(i=1;i<=nlstate;i++){
2725: sumnew=0;
2726: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2727: for(j=1; j<=nlstate; j++){
2728: prlim[i][j]= newm[i][j]/(1-sumnew);
2729: max[j]=FMAX(max[j],prlim[i][j]);
2730: min[j]=FMIN(min[j],prlim[i][j]);
2731: }
2732: }
2733:
1.126 brouard 2734: maxmax=0.;
1.209 brouard 2735: for(j=1; j<=nlstate; j++){
2736: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2737: maxmax=FMAX(maxmax,meandiff[j]);
2738: /* 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 2739: } /* j loop */
1.203 brouard 2740: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2741: /* 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 2742: if(maxmax < ftolpl){
1.209 brouard 2743: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2744: free_vector(min,1,nlstate);
2745: free_vector(max,1,nlstate);
2746: free_vector(meandiff,1,nlstate);
1.126 brouard 2747: return prlim;
2748: }
1.288 brouard 2749: } /* agefin loop */
1.208 brouard 2750: /* After some age loop it doesn't converge */
1.288 brouard 2751: if(!first){
2752: first=1;
2753: 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);
2754: }
2755: 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);
2756:
1.209 brouard 2757: /* 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); */
2758: free_vector(min,1,nlstate);
2759: free_vector(max,1,nlstate);
2760: free_vector(meandiff,1,nlstate);
1.208 brouard 2761:
1.169 brouard 2762: return prlim; /* should not reach here */
1.126 brouard 2763: }
2764:
1.217 brouard 2765:
2766: /**** Back Prevalence limit (stable or period prevalence) ****************/
2767:
1.218 brouard 2768: /* 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) */
2769: /* 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 2770: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2771: {
1.264 brouard 2772: /* 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 2773: matrix by transitions matrix until convergence is reached with precision ftolpl */
2774: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2775: /* Wx is row vector: population in state 1, population in state 2, population dead */
2776: /* or prevalence in state 1, prevalence in state 2, 0 */
2777: /* newm is the matrix after multiplications, its rows are identical at a factor */
2778: /* Initial matrix pimij */
2779: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2780: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2781: /* 0, 0 , 1} */
2782: /*
2783: * and after some iteration: */
2784: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2785: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2786: /* 0, 0 , 1} */
2787: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2788: /* {0.51571254859325999, 0.4842874514067399, */
2789: /* 0.51326036147820708, 0.48673963852179264} */
2790: /* If we start from prlim again, prlim tends to a constant matrix */
2791:
2792: int i, ii,j,k;
1.247 brouard 2793: int first=0;
1.217 brouard 2794: double *min, *max, *meandiff, maxmax,sumnew=0.;
2795: /* double **matprod2(); */ /* test */
2796: double **out, cov[NCOVMAX+1], **bmij();
2797: double **newm;
1.218 brouard 2798: double **dnewm, **doldm, **dsavm; /* for use */
2799: double **oldm, **savm; /* for use */
2800:
1.217 brouard 2801: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2802: int ncvloop=0;
2803:
2804: min=vector(1,nlstate);
2805: max=vector(1,nlstate);
2806: meandiff=vector(1,nlstate);
2807:
1.266 brouard 2808: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2809: oldm=oldms; savm=savms;
2810:
2811: /* Starting with matrix unity */
2812: for (ii=1;ii<=nlstate+ndeath;ii++)
2813: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2814: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2815: }
2816:
2817: cov[1]=1.;
2818:
2819: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2820: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2821: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2822: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2823: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2824: ncvloop++;
1.218 brouard 2825: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2826: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2827: /* Covariates have to be included here again */
2828: cov[2]=agefin;
2829: if(nagesqr==1)
2830: cov[3]= agefin*agefin;;
1.242 brouard 2831: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2832: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2833: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2834: /* 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 2835: }
2836: /* for (k=1; k<=cptcovn;k++) { */
2837: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2838: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2839: /* /\* 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])]); *\/ */
2840: /* } */
2841: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2842: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2843: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2844: /* 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]); */
2845: }
2846: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2847: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2848: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2849: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2850: for (k=1; k<=cptcovage;k++){ /* For product with age */
2851: if(Dummy[Tvar[Tage[k]]]){
2852: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2853: } else{
2854: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2855: }
2856: /* 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]); */
2857: }
2858: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2859: /* 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]); */
2860: if(Dummy[Tvard[k][1]==0]){
2861: if(Dummy[Tvard[k][2]==0]){
2862: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2863: }else{
2864: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2865: }
2866: }else{
2867: if(Dummy[Tvard[k][2]==0]){
2868: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2869: }else{
2870: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2871: }
2872: }
1.217 brouard 2873: }
2874:
2875: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2876: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2877: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2878: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2879: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2880: /* ij should be linked to the correct index of cov */
2881: /* age and covariate values ij are in 'cov', but we need to pass
2882: * ij for the observed prevalence at age and status and covariate
2883: * number: prevacurrent[(int)agefin][ii][ij]
2884: */
2885: /* 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 *\/ */
2886: /* 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 *\/ */
2887: 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 2888: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2889: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2890: /* for(i=1; i<=nlstate+ndeath; i++) { */
2891: /* printf("%d newm= ",i); */
2892: /* for(j=1;j<=nlstate+ndeath;j++) { */
2893: /* printf("%f ",newm[i][j]); */
2894: /* } */
2895: /* printf("oldm * "); */
2896: /* for(j=1;j<=nlstate+ndeath;j++) { */
2897: /* printf("%f ",oldm[i][j]); */
2898: /* } */
1.268 brouard 2899: /* printf(" bmmij "); */
1.266 brouard 2900: /* for(j=1;j<=nlstate+ndeath;j++) { */
2901: /* printf("%f ",pmmij[i][j]); */
2902: /* } */
2903: /* printf("\n"); */
2904: /* } */
2905: /* } */
1.217 brouard 2906: savm=oldm;
2907: oldm=newm;
1.266 brouard 2908:
1.217 brouard 2909: for(j=1; j<=nlstate; j++){
2910: max[j]=0.;
2911: min[j]=1.;
2912: }
2913: for(j=1; j<=nlstate; j++){
2914: for(i=1;i<=nlstate;i++){
1.234 brouard 2915: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2916: bprlim[i][j]= newm[i][j];
2917: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2918: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2919: }
2920: }
1.218 brouard 2921:
1.217 brouard 2922: maxmax=0.;
2923: for(i=1; i<=nlstate; i++){
2924: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2925: maxmax=FMAX(maxmax,meandiff[i]);
2926: /* 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 2927: } /* i loop */
1.217 brouard 2928: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2929: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2930: if(maxmax < ftolpl){
1.220 brouard 2931: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2932: free_vector(min,1,nlstate);
2933: free_vector(max,1,nlstate);
2934: free_vector(meandiff,1,nlstate);
2935: return bprlim;
2936: }
1.288 brouard 2937: } /* agefin loop */
1.217 brouard 2938: /* After some age loop it doesn't converge */
1.288 brouard 2939: if(!first){
1.247 brouard 2940: first=1;
2941: 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\
2942: 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);
2943: }
2944: 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 2945: 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);
2946: /* 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); */
2947: free_vector(min,1,nlstate);
2948: free_vector(max,1,nlstate);
2949: free_vector(meandiff,1,nlstate);
2950:
2951: return bprlim; /* should not reach here */
2952: }
2953:
1.126 brouard 2954: /*************** transition probabilities ***************/
2955:
2956: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2957: {
1.138 brouard 2958: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2959: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2960: model to the ncovmodel covariates (including constant and age).
2961: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2962: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2963: ncth covariate in the global vector x is given by the formula:
2964: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2965: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2966: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2967: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2968: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2969: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2970: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2971: */
2972: double s1, lnpijopii;
1.126 brouard 2973: /*double t34;*/
1.164 brouard 2974: int i,j, nc, ii, jj;
1.126 brouard 2975:
1.223 brouard 2976: for(i=1; i<= nlstate; i++){
2977: for(j=1; j<i;j++){
2978: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2979: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2980: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2981: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2982: }
2983: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2984: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2985: }
2986: for(j=i+1; j<=nlstate+ndeath;j++){
2987: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2988: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2989: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2990: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2991: }
2992: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2993: }
2994: }
1.218 brouard 2995:
1.223 brouard 2996: for(i=1; i<= nlstate; i++){
2997: s1=0;
2998: for(j=1; j<i; j++){
2999: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3000: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3001: }
3002: for(j=i+1; j<=nlstate+ndeath; j++){
3003: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3004: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3005: }
3006: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3007: ps[i][i]=1./(s1+1.);
3008: /* Computing other pijs */
3009: for(j=1; j<i; j++)
3010: ps[i][j]= exp(ps[i][j])*ps[i][i];
3011: for(j=i+1; j<=nlstate+ndeath; j++)
3012: ps[i][j]= exp(ps[i][j])*ps[i][i];
3013: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3014: } /* end i */
1.218 brouard 3015:
1.223 brouard 3016: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3017: for(jj=1; jj<= nlstate+ndeath; jj++){
3018: ps[ii][jj]=0;
3019: ps[ii][ii]=1;
3020: }
3021: }
1.294 brouard 3022:
3023:
1.223 brouard 3024: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3025: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3026: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3027: /* } */
3028: /* printf("\n "); */
3029: /* } */
3030: /* printf("\n ");printf("%lf ",cov[2]);*/
3031: /*
3032: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3033: goto end;*/
1.266 brouard 3034: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3035: }
3036:
1.218 brouard 3037: /*************** backward transition probabilities ***************/
3038:
3039: /* 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 ) */
3040: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3041: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3042: {
1.302 brouard 3043: /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
1.266 brouard 3044: * 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 3045: */
1.218 brouard 3046: int i, ii, j,k;
1.222 brouard 3047:
3048: double **out, **pmij();
3049: double sumnew=0.;
1.218 brouard 3050: double agefin;
1.292 brouard 3051: double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
1.222 brouard 3052: double **dnewm, **dsavm, **doldm;
3053: double **bbmij;
3054:
1.218 brouard 3055: doldm=ddoldms; /* global pointers */
1.222 brouard 3056: dnewm=ddnewms;
3057: dsavm=ddsavms;
3058:
3059: agefin=cov[2];
1.268 brouard 3060: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3061: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3062: the observed prevalence (with this covariate ij) at beginning of transition */
3063: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3064:
3065: /* P_x */
1.266 brouard 3066: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3067: /* outputs pmmij which is a stochastic matrix in row */
3068:
3069: /* Diag(w_x) */
1.292 brouard 3070: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3071: sumnew=0.;
1.269 brouard 3072: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3073: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3074: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3075: sumnew+=prevacurrent[(int)agefin][ii][ij];
3076: }
3077: if(sumnew >0.01){ /* At least some value in the prevalence */
3078: for (ii=1;ii<=nlstate+ndeath;ii++){
3079: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3080: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3081: }
3082: }else{
3083: for (ii=1;ii<=nlstate+ndeath;ii++){
3084: for (j=1;j<=nlstate+ndeath;j++)
3085: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3086: }
3087: /* if(sumnew <0.9){ */
3088: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3089: /* } */
3090: }
3091: k3=0.0; /* We put the last diagonal to 0 */
3092: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3093: doldm[ii][ii]= k3;
3094: }
3095: /* End doldm, At the end doldm is diag[(w_i)] */
3096:
1.292 brouard 3097: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3098: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3099:
1.292 brouard 3100: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3101: /* 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 3102: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3103: sumnew=0.;
1.222 brouard 3104: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3105: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3106: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3107: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3108: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3109: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3110: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3111: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3112: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3113: /* }else */
1.268 brouard 3114: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3115: } /*End ii */
3116: } /* 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 */
3117:
1.292 brouard 3118: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3119: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3120: /* end bmij */
1.266 brouard 3121: return ps; /*pointer is unchanged */
1.218 brouard 3122: }
1.217 brouard 3123: /*************** transition probabilities ***************/
3124:
1.218 brouard 3125: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3126: {
3127: /* According to parameters values stored in x and the covariate's values stored in cov,
3128: computes the probability to be observed in state j being in state i by appying the
3129: model to the ncovmodel covariates (including constant and age).
3130: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3131: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3132: ncth covariate in the global vector x is given by the formula:
3133: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3134: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3135: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3136: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3137: Outputs ps[i][j] the probability to be observed in j being in j according to
3138: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3139: */
3140: double s1, lnpijopii;
3141: /*double t34;*/
3142: int i,j, nc, ii, jj;
3143:
1.234 brouard 3144: for(i=1; i<= nlstate; i++){
3145: for(j=1; j<i;j++){
3146: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3147: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3148: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3149: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3150: }
3151: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3152: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3153: }
3154: for(j=i+1; j<=nlstate+ndeath;j++){
3155: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3156: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3157: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3158: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3159: }
3160: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3161: }
3162: }
3163:
3164: for(i=1; i<= nlstate; i++){
3165: s1=0;
3166: for(j=1; j<i; j++){
3167: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3168: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3169: }
3170: for(j=i+1; j<=nlstate+ndeath; j++){
3171: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3172: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3173: }
3174: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3175: ps[i][i]=1./(s1+1.);
3176: /* Computing other pijs */
3177: for(j=1; j<i; j++)
3178: ps[i][j]= exp(ps[i][j])*ps[i][i];
3179: for(j=i+1; j<=nlstate+ndeath; j++)
3180: ps[i][j]= exp(ps[i][j])*ps[i][i];
3181: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3182: } /* end i */
3183:
3184: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3185: for(jj=1; jj<= nlstate+ndeath; jj++){
3186: ps[ii][jj]=0;
3187: ps[ii][ii]=1;
3188: }
3189: }
1.296 brouard 3190: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3191: for(jj=1; jj<= nlstate+ndeath; jj++){
3192: s1=0.;
3193: for(ii=1; ii<= nlstate+ndeath; ii++){
3194: s1+=ps[ii][jj];
3195: }
3196: for(ii=1; ii<= nlstate; ii++){
3197: ps[ii][jj]=ps[ii][jj]/s1;
3198: }
3199: }
3200: /* Transposition */
3201: for(jj=1; jj<= nlstate+ndeath; jj++){
3202: for(ii=jj; ii<= nlstate+ndeath; ii++){
3203: s1=ps[ii][jj];
3204: ps[ii][jj]=ps[jj][ii];
3205: ps[jj][ii]=s1;
3206: }
3207: }
3208: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3209: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3210: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3211: /* } */
3212: /* printf("\n "); */
3213: /* } */
3214: /* printf("\n ");printf("%lf ",cov[2]);*/
3215: /*
3216: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3217: goto end;*/
3218: return ps;
1.217 brouard 3219: }
3220:
3221:
1.126 brouard 3222: /**************** Product of 2 matrices ******************/
3223:
1.145 brouard 3224: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3225: {
3226: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3227: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3228: /* in, b, out are matrice of pointers which should have been initialized
3229: before: only the contents of out is modified. The function returns
3230: a pointer to pointers identical to out */
1.145 brouard 3231: int i, j, k;
1.126 brouard 3232: for(i=nrl; i<= nrh; i++)
1.145 brouard 3233: for(k=ncolol; k<=ncoloh; k++){
3234: out[i][k]=0.;
3235: for(j=ncl; j<=nch; j++)
3236: out[i][k] +=in[i][j]*b[j][k];
3237: }
1.126 brouard 3238: return out;
3239: }
3240:
3241:
3242: /************* Higher Matrix Product ***************/
3243:
1.235 brouard 3244: 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 3245: {
1.218 brouard 3246: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3247: 'nhstepm*hstepm*stepm' months (i.e. until
3248: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3249: nhstepm*hstepm matrices.
3250: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3251: (typically every 2 years instead of every month which is too big
3252: for the memory).
3253: Model is determined by parameters x and covariates have to be
3254: included manually here.
3255:
3256: */
3257:
3258: int i, j, d, h, k;
1.131 brouard 3259: double **out, cov[NCOVMAX+1];
1.126 brouard 3260: double **newm;
1.187 brouard 3261: double agexact;
1.214 brouard 3262: double agebegin, ageend;
1.126 brouard 3263:
3264: /* Hstepm could be zero and should return the unit matrix */
3265: for (i=1;i<=nlstate+ndeath;i++)
3266: for (j=1;j<=nlstate+ndeath;j++){
3267: oldm[i][j]=(i==j ? 1.0 : 0.0);
3268: po[i][j][0]=(i==j ? 1.0 : 0.0);
3269: }
3270: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3271: for(h=1; h <=nhstepm; h++){
3272: for(d=1; d <=hstepm; d++){
3273: newm=savm;
3274: /* Covariates have to be included here again */
3275: cov[1]=1.;
1.214 brouard 3276: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3277: cov[2]=agexact;
3278: if(nagesqr==1)
1.227 brouard 3279: cov[3]= agexact*agexact;
1.235 brouard 3280: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3281: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3282: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3283: /* 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)); */
3284: }
3285: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3286: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3287: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3288: /* 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]); */
3289: }
3290: for (k=1; k<=cptcovage;k++){
3291: if(Dummy[Tvar[Tage[k]]]){
3292: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3293: } else{
3294: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3295: }
3296: /* 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]); */
3297: }
3298: for (k=1; k<=cptcovprod;k++){ /* */
3299: /* 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]); */
3300: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3301: }
3302: /* for (k=1; k<=cptcovn;k++) */
3303: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3304: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3305: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3306: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3307: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3308:
3309:
1.126 brouard 3310: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3311: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3312: /* right multiplication of oldm by the current matrix */
1.126 brouard 3313: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3314: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3315: /* if((int)age == 70){ */
3316: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3317: /* for(i=1; i<=nlstate+ndeath; i++) { */
3318: /* printf("%d pmmij ",i); */
3319: /* for(j=1;j<=nlstate+ndeath;j++) { */
3320: /* printf("%f ",pmmij[i][j]); */
3321: /* } */
3322: /* printf(" oldm "); */
3323: /* for(j=1;j<=nlstate+ndeath;j++) { */
3324: /* printf("%f ",oldm[i][j]); */
3325: /* } */
3326: /* printf("\n"); */
3327: /* } */
3328: /* } */
1.126 brouard 3329: savm=oldm;
3330: oldm=newm;
3331: }
3332: for(i=1; i<=nlstate+ndeath; i++)
3333: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3334: po[i][j][h]=newm[i][j];
3335: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3336: }
1.128 brouard 3337: /*printf("h=%d ",h);*/
1.126 brouard 3338: } /* end h */
1.267 brouard 3339: /* printf("\n H=%d \n",h); */
1.126 brouard 3340: return po;
3341: }
3342:
1.217 brouard 3343: /************* Higher Back Matrix Product ***************/
1.218 brouard 3344: /* 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 3345: 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 3346: {
1.266 brouard 3347: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3348: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3349: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3350: nhstepm*hstepm matrices.
3351: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3352: (typically every 2 years instead of every month which is too big
1.217 brouard 3353: for the memory).
1.218 brouard 3354: Model is determined by parameters x and covariates have to be
1.266 brouard 3355: included manually here. Then we use a call to bmij(x and cov)
3356: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3357: */
1.217 brouard 3358:
3359: int i, j, d, h, k;
1.266 brouard 3360: double **out, cov[NCOVMAX+1], **bmij();
3361: double **newm, ***newmm;
1.217 brouard 3362: double agexact;
3363: double agebegin, ageend;
1.222 brouard 3364: double **oldm, **savm;
1.217 brouard 3365:
1.266 brouard 3366: newmm=po; /* To be saved */
3367: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3368: /* Hstepm could be zero and should return the unit matrix */
3369: for (i=1;i<=nlstate+ndeath;i++)
3370: for (j=1;j<=nlstate+ndeath;j++){
3371: oldm[i][j]=(i==j ? 1.0 : 0.0);
3372: po[i][j][0]=(i==j ? 1.0 : 0.0);
3373: }
3374: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3375: for(h=1; h <=nhstepm; h++){
3376: for(d=1; d <=hstepm; d++){
3377: newm=savm;
3378: /* Covariates have to be included here again */
3379: cov[1]=1.;
1.271 brouard 3380: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3381: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3382: cov[2]=agexact;
3383: if(nagesqr==1)
1.222 brouard 3384: cov[3]= agexact*agexact;
1.266 brouard 3385: for (k=1; k<=cptcovn;k++){
3386: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3387: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3388: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3389: /* 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)); */
3390: }
1.267 brouard 3391: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3392: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3393: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3394: /* 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]); */
3395: }
3396: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3397: if(Dummy[Tvar[Tage[k]]]){
3398: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3399: } else{
3400: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3401: }
3402: /* 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]); */
3403: }
3404: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3405: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3406: }
1.217 brouard 3407: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3408: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3409:
1.218 brouard 3410: /* Careful transposed matrix */
1.266 brouard 3411: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3412: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3413: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3414: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3415: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3416: /* if((int)age == 70){ */
3417: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3418: /* for(i=1; i<=nlstate+ndeath; i++) { */
3419: /* printf("%d pmmij ",i); */
3420: /* for(j=1;j<=nlstate+ndeath;j++) { */
3421: /* printf("%f ",pmmij[i][j]); */
3422: /* } */
3423: /* printf(" oldm "); */
3424: /* for(j=1;j<=nlstate+ndeath;j++) { */
3425: /* printf("%f ",oldm[i][j]); */
3426: /* } */
3427: /* printf("\n"); */
3428: /* } */
3429: /* } */
3430: savm=oldm;
3431: oldm=newm;
3432: }
3433: for(i=1; i<=nlstate+ndeath; i++)
3434: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3435: po[i][j][h]=newm[i][j];
1.268 brouard 3436: /* if(h==nhstepm) */
3437: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3438: }
1.268 brouard 3439: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3440: } /* end h */
1.268 brouard 3441: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3442: return po;
3443: }
3444:
3445:
1.162 brouard 3446: #ifdef NLOPT
3447: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3448: double fret;
3449: double *xt;
3450: int j;
3451: myfunc_data *d2 = (myfunc_data *) pd;
3452: /* xt = (p1-1); */
3453: xt=vector(1,n);
3454: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3455:
3456: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3457: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3458: printf("Function = %.12lf ",fret);
3459: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3460: printf("\n");
3461: free_vector(xt,1,n);
3462: return fret;
3463: }
3464: #endif
1.126 brouard 3465:
3466: /*************** log-likelihood *************/
3467: double func( double *x)
3468: {
1.226 brouard 3469: int i, ii, j, k, mi, d, kk;
3470: int ioffset=0;
3471: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3472: double **out;
3473: double lli; /* Individual log likelihood */
3474: int s1, s2;
1.228 brouard 3475: 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 3476: double bbh, survp;
3477: long ipmx;
3478: double agexact;
3479: /*extern weight */
3480: /* We are differentiating ll according to initial status */
3481: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3482: /*for(i=1;i<imx;i++)
3483: printf(" %d\n",s[4][i]);
3484: */
1.162 brouard 3485:
1.226 brouard 3486: ++countcallfunc;
1.162 brouard 3487:
1.226 brouard 3488: cov[1]=1.;
1.126 brouard 3489:
1.226 brouard 3490: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3491: ioffset=0;
1.226 brouard 3492: if(mle==1){
3493: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3494: /* Computes the values of the ncovmodel covariates of the model
3495: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3496: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3497: to be observed in j being in i according to the model.
3498: */
1.243 brouard 3499: ioffset=2+nagesqr ;
1.233 brouard 3500: /* Fixed */
1.234 brouard 3501: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3502: 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)*/
3503: }
1.226 brouard 3504: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3505: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3506: has been calculated etc */
3507: /* For an individual i, wav[i] gives the number of effective waves */
3508: /* We compute the contribution to Likelihood of each effective transition
3509: mw[mi][i] is real wave of the mi th effectve wave */
3510: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3511: s2=s[mw[mi+1][i]][i];
3512: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3513: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3514: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3515: */
3516: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3517: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3518: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3519: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3520: }
3521: for (ii=1;ii<=nlstate+ndeath;ii++)
3522: for (j=1;j<=nlstate+ndeath;j++){
3523: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3524: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3525: }
3526: for(d=0; d<dh[mi][i]; d++){
3527: newm=savm;
3528: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3529: cov[2]=agexact;
3530: if(nagesqr==1)
3531: cov[3]= agexact*agexact; /* Should be changed here */
3532: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3533: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3534: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3535: else
3536: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3537: }
3538: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3539: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3540: savm=oldm;
3541: oldm=newm;
3542: } /* end mult */
3543:
3544: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3545: /* But now since version 0.9 we anticipate for bias at large stepm.
3546: * If stepm is larger than one month (smallest stepm) and if the exact delay
3547: * (in months) between two waves is not a multiple of stepm, we rounded to
3548: * the nearest (and in case of equal distance, to the lowest) interval but now
3549: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3550: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3551: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3552: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3553: * -stepm/2 to stepm/2 .
3554: * For stepm=1 the results are the same as for previous versions of Imach.
3555: * For stepm > 1 the results are less biased than in previous versions.
3556: */
1.234 brouard 3557: s1=s[mw[mi][i]][i];
3558: s2=s[mw[mi+1][i]][i];
3559: bbh=(double)bh[mi][i]/(double)stepm;
3560: /* bias bh is positive if real duration
3561: * is higher than the multiple of stepm and negative otherwise.
3562: */
3563: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3564: if( s2 > nlstate){
3565: /* i.e. if s2 is a death state and if the date of death is known
3566: then the contribution to the likelihood is the probability to
3567: die between last step unit time and current step unit time,
3568: which is also equal to probability to die before dh
3569: minus probability to die before dh-stepm .
3570: In version up to 0.92 likelihood was computed
3571: as if date of death was unknown. Death was treated as any other
3572: health state: the date of the interview describes the actual state
3573: and not the date of a change in health state. The former idea was
3574: to consider that at each interview the state was recorded
3575: (healthy, disable or death) and IMaCh was corrected; but when we
3576: introduced the exact date of death then we should have modified
3577: the contribution of an exact death to the likelihood. This new
3578: contribution is smaller and very dependent of the step unit
3579: stepm. It is no more the probability to die between last interview
3580: and month of death but the probability to survive from last
3581: interview up to one month before death multiplied by the
3582: probability to die within a month. Thanks to Chris
3583: Jackson for correcting this bug. Former versions increased
3584: mortality artificially. The bad side is that we add another loop
3585: which slows down the processing. The difference can be up to 10%
3586: lower mortality.
3587: */
3588: /* If, at the beginning of the maximization mostly, the
3589: cumulative probability or probability to be dead is
3590: constant (ie = 1) over time d, the difference is equal to
3591: 0. out[s1][3] = savm[s1][3]: probability, being at state
3592: s1 at precedent wave, to be dead a month before current
3593: wave is equal to probability, being at state s1 at
3594: precedent wave, to be dead at mont of the current
3595: wave. Then the observed probability (that this person died)
3596: is null according to current estimated parameter. In fact,
3597: it should be very low but not zero otherwise the log go to
3598: infinity.
3599: */
1.183 brouard 3600: /* #ifdef INFINITYORIGINAL */
3601: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3602: /* #else */
3603: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3604: /* lli=log(mytinydouble); */
3605: /* else */
3606: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3607: /* #endif */
1.226 brouard 3608: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3609:
1.226 brouard 3610: } else if ( s2==-1 ) { /* alive */
3611: for (j=1,survp=0. ; j<=nlstate; j++)
3612: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3613: /*survp += out[s1][j]; */
3614: lli= log(survp);
3615: }
3616: else if (s2==-4) {
3617: for (j=3,survp=0. ; j<=nlstate; j++)
3618: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3619: lli= log(survp);
3620: }
3621: else if (s2==-5) {
3622: for (j=1,survp=0. ; j<=2; j++)
3623: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3624: lli= log(survp);
3625: }
3626: else{
3627: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3628: /* 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 */
3629: }
3630: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3631: /*if(lli ==000.0)*/
3632: /*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); */
3633: ipmx +=1;
3634: sw += weight[i];
3635: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3636: /* if (lli < log(mytinydouble)){ */
3637: /* 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); */
3638: /* 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]); */
3639: /* } */
3640: } /* end of wave */
3641: } /* end of individual */
3642: } else if(mle==2){
3643: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3644: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3645: for(mi=1; mi<= wav[i]-1; mi++){
3646: for (ii=1;ii<=nlstate+ndeath;ii++)
3647: for (j=1;j<=nlstate+ndeath;j++){
3648: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3649: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3650: }
3651: for(d=0; d<=dh[mi][i]; d++){
3652: newm=savm;
3653: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3654: cov[2]=agexact;
3655: if(nagesqr==1)
3656: cov[3]= agexact*agexact;
3657: for (kk=1; kk<=cptcovage;kk++) {
3658: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3659: }
3660: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3661: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3662: savm=oldm;
3663: oldm=newm;
3664: } /* end mult */
3665:
3666: s1=s[mw[mi][i]][i];
3667: s2=s[mw[mi+1][i]][i];
3668: bbh=(double)bh[mi][i]/(double)stepm;
3669: 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 */
3670: ipmx +=1;
3671: sw += weight[i];
3672: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3673: } /* end of wave */
3674: } /* end of individual */
3675: } else if(mle==3){ /* exponential inter-extrapolation */
3676: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3677: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3678: for(mi=1; mi<= wav[i]-1; mi++){
3679: for (ii=1;ii<=nlstate+ndeath;ii++)
3680: for (j=1;j<=nlstate+ndeath;j++){
3681: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3682: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3683: }
3684: for(d=0; d<dh[mi][i]; d++){
3685: newm=savm;
3686: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3687: cov[2]=agexact;
3688: if(nagesqr==1)
3689: cov[3]= agexact*agexact;
3690: for (kk=1; kk<=cptcovage;kk++) {
3691: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3692: }
3693: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3694: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3695: savm=oldm;
3696: oldm=newm;
3697: } /* end mult */
3698:
3699: s1=s[mw[mi][i]][i];
3700: s2=s[mw[mi+1][i]][i];
3701: bbh=(double)bh[mi][i]/(double)stepm;
3702: 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 */
3703: ipmx +=1;
3704: sw += weight[i];
3705: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3706: } /* end of wave */
3707: } /* end of individual */
3708: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3709: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3710: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3711: for(mi=1; mi<= wav[i]-1; mi++){
3712: for (ii=1;ii<=nlstate+ndeath;ii++)
3713: for (j=1;j<=nlstate+ndeath;j++){
3714: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3715: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3716: }
3717: for(d=0; d<dh[mi][i]; d++){
3718: newm=savm;
3719: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3720: cov[2]=agexact;
3721: if(nagesqr==1)
3722: cov[3]= agexact*agexact;
3723: for (kk=1; kk<=cptcovage;kk++) {
3724: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3725: }
1.126 brouard 3726:
1.226 brouard 3727: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3728: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3729: savm=oldm;
3730: oldm=newm;
3731: } /* end mult */
3732:
3733: s1=s[mw[mi][i]][i];
3734: s2=s[mw[mi+1][i]][i];
3735: if( s2 > nlstate){
3736: lli=log(out[s1][s2] - savm[s1][s2]);
3737: } else if ( s2==-1 ) { /* alive */
3738: for (j=1,survp=0. ; j<=nlstate; j++)
3739: survp += out[s1][j];
3740: lli= log(survp);
3741: }else{
3742: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3743: }
3744: ipmx +=1;
3745: sw += weight[i];
3746: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3747: /* 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 3748: } /* end of wave */
3749: } /* end of individual */
3750: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3751: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3752: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3753: for(mi=1; mi<= wav[i]-1; mi++){
3754: for (ii=1;ii<=nlstate+ndeath;ii++)
3755: for (j=1;j<=nlstate+ndeath;j++){
3756: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3757: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3758: }
3759: for(d=0; d<dh[mi][i]; d++){
3760: newm=savm;
3761: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3762: cov[2]=agexact;
3763: if(nagesqr==1)
3764: cov[3]= agexact*agexact;
3765: for (kk=1; kk<=cptcovage;kk++) {
3766: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3767: }
1.126 brouard 3768:
1.226 brouard 3769: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3770: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3771: savm=oldm;
3772: oldm=newm;
3773: } /* end mult */
3774:
3775: s1=s[mw[mi][i]][i];
3776: s2=s[mw[mi+1][i]][i];
3777: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3778: ipmx +=1;
3779: sw += weight[i];
3780: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3781: /*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]);*/
3782: } /* end of wave */
3783: } /* end of individual */
3784: } /* End of if */
3785: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3786: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3787: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3788: return -l;
1.126 brouard 3789: }
3790:
3791: /*************** log-likelihood *************/
3792: double funcone( double *x)
3793: {
1.228 brouard 3794: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3795: int i, ii, j, k, mi, d, kk;
1.228 brouard 3796: int ioffset=0;
1.131 brouard 3797: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3798: double **out;
3799: double lli; /* Individual log likelihood */
3800: double llt;
3801: int s1, s2;
1.228 brouard 3802: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3803:
1.126 brouard 3804: double bbh, survp;
1.187 brouard 3805: double agexact;
1.214 brouard 3806: double agebegin, ageend;
1.126 brouard 3807: /*extern weight */
3808: /* We are differentiating ll according to initial status */
3809: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3810: /*for(i=1;i<imx;i++)
3811: printf(" %d\n",s[4][i]);
3812: */
3813: cov[1]=1.;
3814:
3815: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3816: ioffset=0;
3817: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3818: /* ioffset=2+nagesqr+cptcovage; */
3819: ioffset=2+nagesqr;
1.232 brouard 3820: /* Fixed */
1.224 brouard 3821: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3822: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3823: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3824: 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)*/
3825: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3826: /* cov[2+6]=covar[Tvar[6]][i]; */
3827: /* cov[2+6]=covar[2][i]; V2 */
3828: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3829: /* cov[2+7]=covar[Tvar[7]][i]; */
3830: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3831: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3832: /* cov[2+9]=covar[Tvar[9]][i]; */
3833: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3834: }
1.232 brouard 3835: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3836: /* 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?)*\/ */
3837: /* } */
1.231 brouard 3838: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3839: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3840: /* } */
1.225 brouard 3841:
1.233 brouard 3842:
3843: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3844: /* Wave varying (but not age varying) */
3845: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3846: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3847: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3848: }
1.232 brouard 3849: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3850: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3851: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3852: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3853: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3854: /* 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 3855: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3856: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3857: /* /\* 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]); *\/ */
3858: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3859: /* } */
1.126 brouard 3860: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3861: for (j=1;j<=nlstate+ndeath;j++){
3862: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3863: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3864: }
1.214 brouard 3865:
3866: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3867: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3868: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3869: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3870: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3871: and mw[mi+1][i]. dh depends on stepm.*/
3872: newm=savm;
1.247 brouard 3873: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3874: cov[2]=agexact;
3875: if(nagesqr==1)
3876: cov[3]= agexact*agexact;
3877: for (kk=1; kk<=cptcovage;kk++) {
3878: if(!FixedV[Tvar[Tage[kk]]])
3879: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3880: else
3881: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3882: }
3883: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3884: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3885: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3886: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3887: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3888: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3889: savm=oldm;
3890: oldm=newm;
1.126 brouard 3891: } /* end mult */
3892:
3893: s1=s[mw[mi][i]][i];
3894: s2=s[mw[mi+1][i]][i];
1.217 brouard 3895: /* if(s2==-1){ */
1.268 brouard 3896: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3897: /* /\* exit(1); *\/ */
3898: /* } */
1.126 brouard 3899: bbh=(double)bh[mi][i]/(double)stepm;
3900: /* bias is positive if real duration
3901: * is higher than the multiple of stepm and negative otherwise.
3902: */
3903: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3904: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3905: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3906: for (j=1,survp=0. ; j<=nlstate; j++)
3907: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3908: lli= log(survp);
1.126 brouard 3909: }else if (mle==1){
1.242 brouard 3910: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3911: } else if(mle==2){
1.242 brouard 3912: 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 3913: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3914: 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 3915: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3916: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3917: } else{ /* mle=0 back to 1 */
1.242 brouard 3918: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3919: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3920: } /* End of if */
3921: ipmx +=1;
3922: sw += weight[i];
3923: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3924: /*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 3925: if(globpr){
1.246 brouard 3926: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3927: %11.6f %11.6f %11.6f ", \
1.242 brouard 3928: 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 3929: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3930: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3931: llt +=ll[k]*gipmx/gsw;
3932: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3933: }
3934: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3935: }
1.232 brouard 3936: } /* end of wave */
3937: } /* end of individual */
3938: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3939: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3940: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3941: if(globpr==0){ /* First time we count the contributions and weights */
3942: gipmx=ipmx;
3943: gsw=sw;
3944: }
3945: return -l;
1.126 brouard 3946: }
3947:
3948:
3949: /*************** function likelione ***********/
1.292 brouard 3950: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3951: {
3952: /* This routine should help understanding what is done with
3953: the selection of individuals/waves and
3954: to check the exact contribution to the likelihood.
3955: Plotting could be done.
3956: */
3957: int k;
3958:
3959: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3960: strcpy(fileresilk,"ILK_");
1.202 brouard 3961: strcat(fileresilk,fileresu);
1.126 brouard 3962: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3963: printf("Problem with resultfile: %s\n", fileresilk);
3964: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3965: }
1.214 brouard 3966: 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");
3967: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3968: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3969: for(k=1; k<=nlstate; k++)
3970: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3971: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3972: }
3973:
1.292 brouard 3974: *fretone=(*func)(p);
1.126 brouard 3975: if(*globpri !=0){
3976: fclose(ficresilk);
1.205 brouard 3977: if (mle ==0)
3978: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3979: else if(mle >=1)
3980: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3981: 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 3982: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3983:
3984: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3985: 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 3986: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3987: }
1.207 brouard 3988: 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 3989: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3990: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3991: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3992: fflush(fichtm);
1.205 brouard 3993: }
1.126 brouard 3994: return;
3995: }
3996:
3997:
3998: /*********** Maximum Likelihood Estimation ***************/
3999:
4000: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4001: {
1.165 brouard 4002: int i,j, iter=0;
1.126 brouard 4003: double **xi;
4004: double fret;
4005: double fretone; /* Only one call to likelihood */
4006: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4007:
4008: #ifdef NLOPT
4009: int creturn;
4010: nlopt_opt opt;
4011: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4012: double *lb;
4013: double minf; /* the minimum objective value, upon return */
4014: double * p1; /* Shifted parameters from 0 instead of 1 */
4015: myfunc_data dinst, *d = &dinst;
4016: #endif
4017:
4018:
1.126 brouard 4019: xi=matrix(1,npar,1,npar);
4020: for (i=1;i<=npar;i++)
4021: for (j=1;j<=npar;j++)
4022: xi[i][j]=(i==j ? 1.0 : 0.0);
4023: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4024: strcpy(filerespow,"POW_");
1.126 brouard 4025: strcat(filerespow,fileres);
4026: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4027: printf("Problem with resultfile: %s\n", filerespow);
4028: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4029: }
4030: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4031: for (i=1;i<=nlstate;i++)
4032: for(j=1;j<=nlstate+ndeath;j++)
4033: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4034: fprintf(ficrespow,"\n");
1.162 brouard 4035: #ifdef POWELL
1.126 brouard 4036: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4037: #endif
1.126 brouard 4038:
1.162 brouard 4039: #ifdef NLOPT
4040: #ifdef NEWUOA
4041: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4042: #else
4043: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4044: #endif
4045: lb=vector(0,npar-1);
4046: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4047: nlopt_set_lower_bounds(opt, lb);
4048: nlopt_set_initial_step1(opt, 0.1);
4049:
4050: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4051: d->function = func;
4052: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4053: nlopt_set_min_objective(opt, myfunc, d);
4054: nlopt_set_xtol_rel(opt, ftol);
4055: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4056: printf("nlopt failed! %d\n",creturn);
4057: }
4058: else {
4059: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4060: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4061: iter=1; /* not equal */
4062: }
4063: nlopt_destroy(opt);
4064: #endif
1.126 brouard 4065: free_matrix(xi,1,npar,1,npar);
4066: fclose(ficrespow);
1.203 brouard 4067: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4068: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4069: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4070:
4071: }
4072:
4073: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4074: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4075: {
4076: double **a,**y,*x,pd;
1.203 brouard 4077: /* double **hess; */
1.164 brouard 4078: int i, j;
1.126 brouard 4079: int *indx;
4080:
4081: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4082: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4083: void lubksb(double **a, int npar, int *indx, double b[]) ;
4084: void ludcmp(double **a, int npar, int *indx, double *d) ;
4085: double gompertz(double p[]);
1.203 brouard 4086: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4087:
4088: printf("\nCalculation of the hessian matrix. Wait...\n");
4089: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4090: for (i=1;i<=npar;i++){
1.203 brouard 4091: printf("%d-",i);fflush(stdout);
4092: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4093:
4094: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4095:
4096: /* printf(" %f ",p[i]);
4097: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4098: }
4099:
4100: for (i=1;i<=npar;i++) {
4101: for (j=1;j<=npar;j++) {
4102: if (j>i) {
1.203 brouard 4103: printf(".%d-%d",i,j);fflush(stdout);
4104: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4105: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4106:
4107: hess[j][i]=hess[i][j];
4108: /*printf(" %lf ",hess[i][j]);*/
4109: }
4110: }
4111: }
4112: printf("\n");
4113: fprintf(ficlog,"\n");
4114:
4115: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4116: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4117:
4118: a=matrix(1,npar,1,npar);
4119: y=matrix(1,npar,1,npar);
4120: x=vector(1,npar);
4121: indx=ivector(1,npar);
4122: for (i=1;i<=npar;i++)
4123: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4124: ludcmp(a,npar,indx,&pd);
4125:
4126: for (j=1;j<=npar;j++) {
4127: for (i=1;i<=npar;i++) x[i]=0;
4128: x[j]=1;
4129: lubksb(a,npar,indx,x);
4130: for (i=1;i<=npar;i++){
4131: matcov[i][j]=x[i];
4132: }
4133: }
4134:
4135: printf("\n#Hessian matrix#\n");
4136: fprintf(ficlog,"\n#Hessian matrix#\n");
4137: for (i=1;i<=npar;i++) {
4138: for (j=1;j<=npar;j++) {
1.203 brouard 4139: printf("%.6e ",hess[i][j]);
4140: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4141: }
4142: printf("\n");
4143: fprintf(ficlog,"\n");
4144: }
4145:
1.203 brouard 4146: /* printf("\n#Covariance matrix#\n"); */
4147: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4148: /* for (i=1;i<=npar;i++) { */
4149: /* for (j=1;j<=npar;j++) { */
4150: /* printf("%.6e ",matcov[i][j]); */
4151: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4152: /* } */
4153: /* printf("\n"); */
4154: /* fprintf(ficlog,"\n"); */
4155: /* } */
4156:
1.126 brouard 4157: /* Recompute Inverse */
1.203 brouard 4158: /* for (i=1;i<=npar;i++) */
4159: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4160: /* ludcmp(a,npar,indx,&pd); */
4161:
4162: /* printf("\n#Hessian matrix recomputed#\n"); */
4163:
4164: /* for (j=1;j<=npar;j++) { */
4165: /* for (i=1;i<=npar;i++) x[i]=0; */
4166: /* x[j]=1; */
4167: /* lubksb(a,npar,indx,x); */
4168: /* for (i=1;i<=npar;i++){ */
4169: /* y[i][j]=x[i]; */
4170: /* printf("%.3e ",y[i][j]); */
4171: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4172: /* } */
4173: /* printf("\n"); */
4174: /* fprintf(ficlog,"\n"); */
4175: /* } */
4176:
4177: /* Verifying the inverse matrix */
4178: #ifdef DEBUGHESS
4179: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4180:
1.203 brouard 4181: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4182: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4183:
4184: for (j=1;j<=npar;j++) {
4185: for (i=1;i<=npar;i++){
1.203 brouard 4186: printf("%.2f ",y[i][j]);
4187: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4188: }
4189: printf("\n");
4190: fprintf(ficlog,"\n");
4191: }
1.203 brouard 4192: #endif
1.126 brouard 4193:
4194: free_matrix(a,1,npar,1,npar);
4195: free_matrix(y,1,npar,1,npar);
4196: free_vector(x,1,npar);
4197: free_ivector(indx,1,npar);
1.203 brouard 4198: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4199:
4200:
4201: }
4202:
4203: /*************** hessian matrix ****************/
4204: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4205: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4206: int i;
4207: int l=1, lmax=20;
1.203 brouard 4208: double k1,k2, res, fx;
1.132 brouard 4209: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4210: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4211: int k=0,kmax=10;
4212: double l1;
4213:
4214: fx=func(x);
4215: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4216: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4217: l1=pow(10,l);
4218: delts=delt;
4219: for(k=1 ; k <kmax; k=k+1){
4220: delt = delta*(l1*k);
4221: p2[theta]=x[theta] +delt;
1.145 brouard 4222: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4223: p2[theta]=x[theta]-delt;
4224: k2=func(p2)-fx;
4225: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4226: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4227:
1.203 brouard 4228: #ifdef DEBUGHESSII
1.126 brouard 4229: 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);
4230: 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);
4231: #endif
4232: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4233: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4234: k=kmax;
4235: }
4236: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4237: k=kmax; l=lmax*10;
1.126 brouard 4238: }
4239: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4240: delts=delt;
4241: }
1.203 brouard 4242: } /* End loop k */
1.126 brouard 4243: }
4244: delti[theta]=delts;
4245: return res;
4246:
4247: }
4248:
1.203 brouard 4249: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4250: {
4251: int i;
1.164 brouard 4252: int l=1, lmax=20;
1.126 brouard 4253: double k1,k2,k3,k4,res,fx;
1.132 brouard 4254: double p2[MAXPARM+1];
1.203 brouard 4255: int k, kmax=1;
4256: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4257:
4258: int firstime=0;
1.203 brouard 4259:
1.126 brouard 4260: fx=func(x);
1.203 brouard 4261: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4262: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4263: p2[thetai]=x[thetai]+delti[thetai]*k;
4264: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4265: k1=func(p2)-fx;
4266:
1.203 brouard 4267: p2[thetai]=x[thetai]+delti[thetai]*k;
4268: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4269: k2=func(p2)-fx;
4270:
1.203 brouard 4271: p2[thetai]=x[thetai]-delti[thetai]*k;
4272: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4273: k3=func(p2)-fx;
4274:
1.203 brouard 4275: p2[thetai]=x[thetai]-delti[thetai]*k;
4276: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4277: k4=func(p2)-fx;
1.203 brouard 4278: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4279: if(k1*k2*k3*k4 <0.){
1.208 brouard 4280: firstime=1;
1.203 brouard 4281: kmax=kmax+10;
1.208 brouard 4282: }
4283: if(kmax >=10 || firstime ==1){
1.246 brouard 4284: 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);
4285: 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 4286: 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);
4287: 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);
4288: }
4289: #ifdef DEBUGHESSIJ
4290: v1=hess[thetai][thetai];
4291: v2=hess[thetaj][thetaj];
4292: cv12=res;
4293: /* Computing eigen value of Hessian matrix */
4294: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4295: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4296: if ((lc2 <0) || (lc1 <0) ){
4297: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4298: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4299: 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);
4300: 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);
4301: }
1.126 brouard 4302: #endif
4303: }
4304: return res;
4305: }
4306:
1.203 brouard 4307: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4308: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4309: /* { */
4310: /* int i; */
4311: /* int l=1, lmax=20; */
4312: /* double k1,k2,k3,k4,res,fx; */
4313: /* double p2[MAXPARM+1]; */
4314: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4315: /* int k=0,kmax=10; */
4316: /* double l1; */
4317:
4318: /* fx=func(x); */
4319: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4320: /* l1=pow(10,l); */
4321: /* delts=delt; */
4322: /* for(k=1 ; k <kmax; k=k+1){ */
4323: /* delt = delti*(l1*k); */
4324: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4325: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4326: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4327: /* k1=func(p2)-fx; */
4328:
4329: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4330: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4331: /* k2=func(p2)-fx; */
4332:
4333: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4334: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4335: /* k3=func(p2)-fx; */
4336:
4337: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4338: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4339: /* k4=func(p2)-fx; */
4340: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4341: /* #ifdef DEBUGHESSIJ */
4342: /* 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); */
4343: /* 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); */
4344: /* #endif */
4345: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4346: /* k=kmax; */
4347: /* } */
4348: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4349: /* k=kmax; l=lmax*10; */
4350: /* } */
4351: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4352: /* delts=delt; */
4353: /* } */
4354: /* } /\* End loop k *\/ */
4355: /* } */
4356: /* delti[theta]=delts; */
4357: /* return res; */
4358: /* } */
4359:
4360:
1.126 brouard 4361: /************** Inverse of matrix **************/
4362: void ludcmp(double **a, int n, int *indx, double *d)
4363: {
4364: int i,imax,j,k;
4365: double big,dum,sum,temp;
4366: double *vv;
4367:
4368: vv=vector(1,n);
4369: *d=1.0;
4370: for (i=1;i<=n;i++) {
4371: big=0.0;
4372: for (j=1;j<=n;j++)
4373: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4374: if (big == 0.0){
4375: printf(" Singular Hessian matrix at row %d:\n",i);
4376: for (j=1;j<=n;j++) {
4377: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4378: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4379: }
4380: fflush(ficlog);
4381: fclose(ficlog);
4382: nrerror("Singular matrix in routine ludcmp");
4383: }
1.126 brouard 4384: vv[i]=1.0/big;
4385: }
4386: for (j=1;j<=n;j++) {
4387: for (i=1;i<j;i++) {
4388: sum=a[i][j];
4389: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4390: a[i][j]=sum;
4391: }
4392: big=0.0;
4393: for (i=j;i<=n;i++) {
4394: sum=a[i][j];
4395: for (k=1;k<j;k++)
4396: sum -= a[i][k]*a[k][j];
4397: a[i][j]=sum;
4398: if ( (dum=vv[i]*fabs(sum)) >= big) {
4399: big=dum;
4400: imax=i;
4401: }
4402: }
4403: if (j != imax) {
4404: for (k=1;k<=n;k++) {
4405: dum=a[imax][k];
4406: a[imax][k]=a[j][k];
4407: a[j][k]=dum;
4408: }
4409: *d = -(*d);
4410: vv[imax]=vv[j];
4411: }
4412: indx[j]=imax;
4413: if (a[j][j] == 0.0) a[j][j]=TINY;
4414: if (j != n) {
4415: dum=1.0/(a[j][j]);
4416: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4417: }
4418: }
4419: free_vector(vv,1,n); /* Doesn't work */
4420: ;
4421: }
4422:
4423: void lubksb(double **a, int n, int *indx, double b[])
4424: {
4425: int i,ii=0,ip,j;
4426: double sum;
4427:
4428: for (i=1;i<=n;i++) {
4429: ip=indx[i];
4430: sum=b[ip];
4431: b[ip]=b[i];
4432: if (ii)
4433: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4434: else if (sum) ii=i;
4435: b[i]=sum;
4436: }
4437: for (i=n;i>=1;i--) {
4438: sum=b[i];
4439: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4440: b[i]=sum/a[i][i];
4441: }
4442: }
4443:
4444: void pstamp(FILE *fichier)
4445: {
1.196 brouard 4446: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4447: }
4448:
1.297 brouard 4449: void date2dmy(double date,double *day, double *month, double *year){
4450: double yp=0., yp1=0., yp2=0.;
4451:
4452: yp1=modf(date,&yp);/* extracts integral of date in yp and
4453: fractional in yp1 */
4454: *year=yp;
4455: yp2=modf((yp1*12),&yp);
4456: *month=yp;
4457: yp1=modf((yp2*30.5),&yp);
4458: *day=yp;
4459: if(*day==0) *day=1;
4460: if(*month==0) *month=1;
4461: }
4462:
1.253 brouard 4463:
4464:
1.126 brouard 4465: /************ Frequencies ********************/
1.251 brouard 4466: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4467: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4468: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4469: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4470:
1.265 brouard 4471: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4472: int iind=0, iage=0;
4473: int mi; /* Effective wave */
4474: int first;
4475: double ***freq; /* Frequencies */
1.268 brouard 4476: 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 */
4477: 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 4478: double *meanq, *stdq, *idq;
1.226 brouard 4479: double **meanqt;
4480: double *pp, **prop, *posprop, *pospropt;
4481: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4482: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4483: double agebegin, ageend;
4484:
4485: pp=vector(1,nlstate);
1.251 brouard 4486: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4487: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4488: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4489: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4490: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4491: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4492: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4493: meanqt=matrix(1,lastpass,1,nqtveff);
4494: strcpy(fileresp,"P_");
4495: strcat(fileresp,fileresu);
4496: /*strcat(fileresphtm,fileresu);*/
4497: if((ficresp=fopen(fileresp,"w"))==NULL) {
4498: printf("Problem with prevalence resultfile: %s\n", fileresp);
4499: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4500: exit(0);
4501: }
1.240 brouard 4502:
1.226 brouard 4503: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4504: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4505: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4506: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4507: fflush(ficlog);
4508: exit(70);
4509: }
4510: else{
4511: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4512: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4513: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4514: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4515: }
1.237 brouard 4516: 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 4517:
1.226 brouard 4518: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4519: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4520: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4521: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4522: fflush(ficlog);
4523: exit(70);
1.240 brouard 4524: } else{
1.226 brouard 4525: 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 4526: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4527: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4528: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4529: }
1.240 brouard 4530: 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);
4531:
1.253 brouard 4532: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4533: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4534: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4535: j1=0;
1.126 brouard 4536:
1.227 brouard 4537: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4538: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4539: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4540:
4541:
1.226 brouard 4542: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4543: reference=low_education V1=0,V2=0
4544: med_educ V1=1 V2=0,
4545: high_educ V1=0 V2=1
4546: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4547: */
1.249 brouard 4548: dateintsum=0;
4549: k2cpt=0;
4550:
1.253 brouard 4551: if(cptcoveff == 0 )
1.265 brouard 4552: nl=1; /* Constant and age model only */
1.253 brouard 4553: else
4554: nl=2;
1.265 brouard 4555:
4556: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4557: /* Loop on nj=1 or 2 if dummy covariates j!=0
4558: * Loop on j1(1 to 2**cptcoveff) covariate combination
4559: * freq[s1][s2][iage] =0.
4560: * Loop on iind
4561: * ++freq[s1][s2][iage] weighted
4562: * end iind
4563: * if covariate and j!0
4564: * headers Variable on one line
4565: * endif cov j!=0
4566: * header of frequency table by age
4567: * Loop on age
4568: * pp[s1]+=freq[s1][s2][iage] weighted
4569: * pos+=freq[s1][s2][iage] weighted
4570: * Loop on s1 initial state
4571: * fprintf(ficresp
4572: * end s1
4573: * end age
4574: * if j!=0 computes starting values
4575: * end compute starting values
4576: * end j1
4577: * end nl
4578: */
1.253 brouard 4579: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4580: if(nj==1)
4581: j=0; /* First pass for the constant */
1.265 brouard 4582: else{
1.253 brouard 4583: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4584: }
1.251 brouard 4585: first=1;
1.265 brouard 4586: 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 4587: posproptt=0.;
4588: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4589: scanf("%d", i);*/
4590: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4591: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4592: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4593: freq[i][s2][m]=0;
1.251 brouard 4594:
4595: for (i=1; i<=nlstate; i++) {
1.240 brouard 4596: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4597: prop[i][m]=0;
4598: posprop[i]=0;
4599: pospropt[i]=0;
4600: }
1.283 brouard 4601: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4602: idq[z1]=0.;
4603: meanq[z1]=0.;
4604: stdq[z1]=0.;
1.283 brouard 4605: }
4606: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4607: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4608: /* meanqt[m][z1]=0.; */
4609: /* } */
4610: /* } */
1.251 brouard 4611: /* dateintsum=0; */
4612: /* k2cpt=0; */
4613:
1.265 brouard 4614: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4615: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4616: bool=1;
4617: if(j !=0){
4618: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4619: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4620: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4621: /* if(Tvaraff[z1] ==-20){ */
4622: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4623: /* }else if(Tvaraff[z1] ==-10){ */
4624: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4625: /* }else */
4626: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4627: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4628: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4629: /* 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",
4630: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4631: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4632: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4633: } /* Onlyf fixed */
4634: } /* end z1 */
4635: } /* cptcovn > 0 */
4636: } /* end any */
4637: }/* end j==0 */
1.265 brouard 4638: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4639: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4640: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4641: m=mw[mi][iind];
4642: if(j!=0){
4643: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4644: for (z1=1; z1<=cptcoveff; z1++) {
4645: if( Fixed[Tmodelind[z1]]==1){
4646: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4647: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4648: value is -1, we don't select. It differs from the
4649: constant and age model which counts them. */
4650: bool=0; /* not selected */
4651: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4652: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4653: bool=0;
4654: }
4655: }
4656: }
4657: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4658: } /* end j==0 */
4659: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4660: if(bool==1){ /*Selected */
1.251 brouard 4661: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4662: and mw[mi+1][iind]. dh depends on stepm. */
4663: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4664: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4665: if(m >=firstpass && m <=lastpass){
4666: k2=anint[m][iind]+(mint[m][iind]/12.);
4667: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4668: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4669: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4670: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4671: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4672: if (m<lastpass) {
4673: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4674: /* 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]); */
4675: if(s[m][iind]==-1)
4676: 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.));
4677: 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 4678: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4679: idq[z1]=idq[z1]+weight[iind];
4680: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4681: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4682: }
1.251 brouard 4683: /* if((int)agev[m][iind] == 55) */
4684: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4685: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4686: 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 4687: }
1.251 brouard 4688: } /* end if between passes */
4689: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4690: dateintsum=dateintsum+k2; /* on all covariates ?*/
4691: k2cpt++;
4692: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4693: }
1.251 brouard 4694: }else{
4695: bool=1;
4696: }/* end bool 2 */
4697: } /* end m */
1.284 brouard 4698: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4699: /* idq[z1]=idq[z1]+weight[iind]; */
4700: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4701: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4702: /* } */
1.251 brouard 4703: } /* end bool */
4704: } /* end iind = 1 to imx */
4705: /* prop[s][age] is feeded for any initial and valid live state as well as
4706: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4707:
4708:
4709: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4710: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4711: pstamp(ficresp);
1.251 brouard 4712: if (cptcoveff>0 && j!=0){
1.265 brouard 4713: pstamp(ficresp);
1.251 brouard 4714: printf( "\n#********** Variable ");
4715: fprintf(ficresp, "\n#********** Variable ");
4716: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4717: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4718: fprintf(ficlog, "\n#********** Variable ");
4719: for (z1=1; z1<=cptcoveff; z1++){
4720: if(!FixedV[Tvaraff[z1]]){
4721: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4722: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4723: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4724: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4725: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4726: }else{
1.251 brouard 4727: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4728: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4729: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4730: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4731: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4732: }
4733: }
4734: printf( "**********\n#");
4735: fprintf(ficresp, "**********\n#");
4736: fprintf(ficresphtm, "**********</h3>\n");
4737: fprintf(ficresphtmfr, "**********</h3>\n");
4738: fprintf(ficlog, "**********\n");
4739: }
1.284 brouard 4740: /*
4741: Printing means of quantitative variables if any
4742: */
4743: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4744: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4745: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4746: if(weightopt==1){
4747: printf(" Weighted mean and standard deviation of");
4748: fprintf(ficlog," Weighted mean and standard deviation of");
4749: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4750: }
1.285 brouard 4751: 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]));
4752: 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]));
4753: 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 4754: }
4755: /* for (z1=1; z1<= nqtveff; z1++) { */
4756: /* for(m=1;m<=lastpass;m++){ */
4757: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4758: /* } */
4759: /* } */
1.283 brouard 4760:
1.251 brouard 4761: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4762: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4763: fprintf(ficresp, " Age");
4764: 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 4765: for(i=1; i<=nlstate;i++) {
1.265 brouard 4766: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4767: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4768: }
1.265 brouard 4769: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4770: fprintf(ficresphtm, "\n");
4771:
4772: /* Header of frequency table by age */
4773: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4774: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4775: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4776: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4777: if(s2!=0 && m!=0)
4778: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4779: }
1.226 brouard 4780: }
1.251 brouard 4781: fprintf(ficresphtmfr, "\n");
4782:
4783: /* For each age */
4784: for(iage=iagemin; iage <= iagemax+3; iage++){
4785: fprintf(ficresphtm,"<tr>");
4786: if(iage==iagemax+1){
4787: fprintf(ficlog,"1");
4788: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4789: }else if(iage==iagemax+2){
4790: fprintf(ficlog,"0");
4791: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4792: }else if(iage==iagemax+3){
4793: fprintf(ficlog,"Total");
4794: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4795: }else{
1.240 brouard 4796: if(first==1){
1.251 brouard 4797: first=0;
4798: printf("See log file for details...\n");
4799: }
4800: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4801: fprintf(ficlog,"Age %d", iage);
4802: }
1.265 brouard 4803: for(s1=1; s1 <=nlstate ; s1++){
4804: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4805: pp[s1] += freq[s1][m][iage];
1.251 brouard 4806: }
1.265 brouard 4807: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4808: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4809: pos += freq[s1][m][iage];
4810: if(pp[s1]>=1.e-10){
1.251 brouard 4811: if(first==1){
1.265 brouard 4812: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4813: }
1.265 brouard 4814: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4815: }else{
4816: if(first==1)
1.265 brouard 4817: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4818: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4819: }
4820: }
4821:
1.265 brouard 4822: for(s1=1; s1 <=nlstate ; s1++){
4823: /* posprop[s1]=0; */
4824: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4825: pp[s1] += freq[s1][m][iage];
4826: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4827:
4828: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4829: pos += pp[s1]; /* pos is the total number of transitions until this age */
4830: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4831: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4832: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4833: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4834: }
4835:
4836: /* Writing ficresp */
4837: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4838: if( iage <= iagemax){
4839: fprintf(ficresp," %d",iage);
4840: }
4841: }else if( nj==2){
4842: if( iage <= iagemax){
4843: fprintf(ficresp," %d",iage);
4844: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4845: }
1.240 brouard 4846: }
1.265 brouard 4847: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4848: if(pos>=1.e-5){
1.251 brouard 4849: if(first==1)
1.265 brouard 4850: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4851: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4852: }else{
4853: if(first==1)
1.265 brouard 4854: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4855: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4856: }
4857: if( iage <= iagemax){
4858: if(pos>=1.e-5){
1.265 brouard 4859: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4860: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4861: }else if( nj==2){
4862: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4863: }
4864: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4865: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4866: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4867: } else{
4868: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4869: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4870: }
1.240 brouard 4871: }
1.265 brouard 4872: pospropt[s1] +=posprop[s1];
4873: } /* end loop s1 */
1.251 brouard 4874: /* pospropt=0.; */
1.265 brouard 4875: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4876: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4877: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4878: if(first==1){
1.265 brouard 4879: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4880: }
1.265 brouard 4881: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4882: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4883: }
1.265 brouard 4884: if(s1!=0 && m!=0)
4885: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4886: }
1.265 brouard 4887: } /* end loop s1 */
1.251 brouard 4888: posproptt=0.;
1.265 brouard 4889: for(s1=1; s1 <=nlstate; s1++){
4890: posproptt += pospropt[s1];
1.251 brouard 4891: }
4892: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4893: fprintf(ficresphtm,"</tr>\n");
4894: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4895: if(iage <= iagemax)
4896: fprintf(ficresp,"\n");
1.240 brouard 4897: }
1.251 brouard 4898: if(first==1)
4899: printf("Others in log...\n");
4900: fprintf(ficlog,"\n");
4901: } /* end loop age iage */
1.265 brouard 4902:
1.251 brouard 4903: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4904: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4905: if(posproptt < 1.e-5){
1.265 brouard 4906: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4907: }else{
1.265 brouard 4908: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4909: }
1.226 brouard 4910: }
1.251 brouard 4911: fprintf(ficresphtm,"</tr>\n");
4912: fprintf(ficresphtm,"</table>\n");
4913: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4914: if(posproptt < 1.e-5){
1.251 brouard 4915: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4916: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4917: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4918: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4919: invalidvarcomb[j1]=1;
1.226 brouard 4920: }else{
1.251 brouard 4921: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4922: invalidvarcomb[j1]=0;
1.226 brouard 4923: }
1.251 brouard 4924: fprintf(ficresphtmfr,"</table>\n");
4925: fprintf(ficlog,"\n");
4926: if(j!=0){
4927: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4928: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4929: for(k=1; k <=(nlstate+ndeath); k++){
4930: if (k != i) {
1.265 brouard 4931: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4932: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4933: if(j1==1){ /* All dummy covariates to zero */
4934: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4935: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4936: printf("%d%d ",i,k);
4937: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4938: 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]));
4939: 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]));
4940: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4941: }
1.253 brouard 4942: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4943: for(iage=iagemin; iage <= iagemax+3; iage++){
4944: x[iage]= (double)iage;
4945: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4946: /* 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 4947: }
1.268 brouard 4948: /* Some are not finite, but linreg will ignore these ages */
4949: no=0;
1.253 brouard 4950: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4951: pstart[s1]=b;
4952: pstart[s1-1]=a;
1.252 brouard 4953: }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 */
4954: 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]);
4955: 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 4956: 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 4957: printf("%d%d ",i,k);
4958: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4959: 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 4960: }else{ /* Other cases, like quantitative fixed or varying covariates */
4961: ;
4962: }
4963: /* printf("%12.7f )", param[i][jj][k]); */
4964: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4965: s1++;
1.251 brouard 4966: } /* end jj */
4967: } /* end k!= i */
4968: } /* end k */
1.265 brouard 4969: } /* end i, s1 */
1.251 brouard 4970: } /* end j !=0 */
4971: } /* end selected combination of covariate j1 */
4972: if(j==0){ /* We can estimate starting values from the occurences in each case */
4973: printf("#Freqsummary: Starting values for the constants:\n");
4974: fprintf(ficlog,"\n");
1.265 brouard 4975: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4976: for(k=1; k <=(nlstate+ndeath); k++){
4977: if (k != i) {
4978: printf("%d%d ",i,k);
4979: fprintf(ficlog,"%d%d ",i,k);
4980: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4981: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4982: if(jj==1){ /* Age has to be done */
1.265 brouard 4983: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4984: 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]));
4985: 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 4986: }
4987: /* printf("%12.7f )", param[i][jj][k]); */
4988: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4989: s1++;
1.250 brouard 4990: }
1.251 brouard 4991: printf("\n");
4992: fprintf(ficlog,"\n");
1.250 brouard 4993: }
4994: }
1.284 brouard 4995: } /* end of state i */
1.251 brouard 4996: printf("#Freqsummary\n");
4997: fprintf(ficlog,"\n");
1.265 brouard 4998: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4999: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5000: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5001: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5002: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5003: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5004: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5005: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5006: /* } */
5007: }
1.265 brouard 5008: } /* end loop s1 */
1.251 brouard 5009:
5010: printf("\n");
5011: fprintf(ficlog,"\n");
5012: } /* end j=0 */
1.249 brouard 5013: } /* end j */
1.252 brouard 5014:
1.253 brouard 5015: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5016: for(i=1, jk=1; i <=nlstate; i++){
5017: for(j=1; j <=nlstate+ndeath; j++){
5018: if(j!=i){
5019: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5020: printf("%1d%1d",i,j);
5021: fprintf(ficparo,"%1d%1d",i,j);
5022: for(k=1; k<=ncovmodel;k++){
5023: /* printf(" %lf",param[i][j][k]); */
5024: /* fprintf(ficparo," %lf",param[i][j][k]); */
5025: p[jk]=pstart[jk];
5026: printf(" %f ",pstart[jk]);
5027: fprintf(ficparo," %f ",pstart[jk]);
5028: jk++;
5029: }
5030: printf("\n");
5031: fprintf(ficparo,"\n");
5032: }
5033: }
5034: }
5035: } /* end mle=-2 */
1.226 brouard 5036: dateintmean=dateintsum/k2cpt;
1.296 brouard 5037: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5038:
1.226 brouard 5039: fclose(ficresp);
5040: fclose(ficresphtm);
5041: fclose(ficresphtmfr);
1.283 brouard 5042: free_vector(idq,1,nqfveff);
1.226 brouard 5043: free_vector(meanq,1,nqfveff);
1.284 brouard 5044: free_vector(stdq,1,nqfveff);
1.226 brouard 5045: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5046: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5047: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5048: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5049: free_vector(pospropt,1,nlstate);
5050: free_vector(posprop,1,nlstate);
1.251 brouard 5051: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5052: free_vector(pp,1,nlstate);
5053: /* End of freqsummary */
5054: }
1.126 brouard 5055:
1.268 brouard 5056: /* Simple linear regression */
5057: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5058:
5059: /* y=a+bx regression */
5060: double sumx = 0.0; /* sum of x */
5061: double sumx2 = 0.0; /* sum of x**2 */
5062: double sumxy = 0.0; /* sum of x * y */
5063: double sumy = 0.0; /* sum of y */
5064: double sumy2 = 0.0; /* sum of y**2 */
5065: double sume2 = 0.0; /* sum of square or residuals */
5066: double yhat;
5067:
5068: double denom=0;
5069: int i;
5070: int ne=*no;
5071:
5072: for ( i=ifi, ne=0;i<=ila;i++) {
5073: if(!isfinite(x[i]) || !isfinite(y[i])){
5074: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5075: continue;
5076: }
5077: ne=ne+1;
5078: sumx += x[i];
5079: sumx2 += x[i]*x[i];
5080: sumxy += x[i] * y[i];
5081: sumy += y[i];
5082: sumy2 += y[i]*y[i];
5083: denom = (ne * sumx2 - sumx*sumx);
5084: /* 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); */
5085: }
5086:
5087: denom = (ne * sumx2 - sumx*sumx);
5088: if (denom == 0) {
5089: // vertical, slope m is infinity
5090: *b = INFINITY;
5091: *a = 0;
5092: if (r) *r = 0;
5093: return 1;
5094: }
5095:
5096: *b = (ne * sumxy - sumx * sumy) / denom;
5097: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5098: if (r!=NULL) {
5099: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5100: sqrt((sumx2 - sumx*sumx/ne) *
5101: (sumy2 - sumy*sumy/ne));
5102: }
5103: *no=ne;
5104: for ( i=ifi, ne=0;i<=ila;i++) {
5105: if(!isfinite(x[i]) || !isfinite(y[i])){
5106: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5107: continue;
5108: }
5109: ne=ne+1;
5110: yhat = y[i] - *a -*b* x[i];
5111: sume2 += yhat * yhat ;
5112:
5113: denom = (ne * sumx2 - sumx*sumx);
5114: /* 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); */
5115: }
5116: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5117: *sa= *sb * sqrt(sumx2/ne);
5118:
5119: return 0;
5120: }
5121:
1.126 brouard 5122: /************ Prevalence ********************/
1.227 brouard 5123: 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)
5124: {
5125: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5126: in each health status at the date of interview (if between dateprev1 and dateprev2).
5127: We still use firstpass and lastpass as another selection.
5128: */
1.126 brouard 5129:
1.227 brouard 5130: int i, m, jk, j1, bool, z1,j, iv;
5131: int mi; /* Effective wave */
5132: int iage;
5133: double agebegin, ageend;
5134:
5135: double **prop;
5136: double posprop;
5137: double y2; /* in fractional years */
5138: int iagemin, iagemax;
5139: int first; /** to stop verbosity which is redirected to log file */
5140:
5141: iagemin= (int) agemin;
5142: iagemax= (int) agemax;
5143: /*pp=vector(1,nlstate);*/
1.251 brouard 5144: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5145: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5146: j1=0;
1.222 brouard 5147:
1.227 brouard 5148: /*j=cptcoveff;*/
5149: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5150:
1.288 brouard 5151: first=0;
1.227 brouard 5152: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5153: for (i=1; i<=nlstate; i++)
1.251 brouard 5154: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5155: prop[i][iage]=0.0;
5156: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5157: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5158: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5159:
5160: for (i=1; i<=imx; i++) { /* Each individual */
5161: bool=1;
5162: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5163: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5164: m=mw[mi][i];
5165: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5166: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5167: for (z1=1; z1<=cptcoveff; z1++){
5168: if( Fixed[Tmodelind[z1]]==1){
5169: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5170: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5171: bool=0;
5172: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5173: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5174: bool=0;
5175: }
5176: }
5177: if(bool==1){ /* Otherwise we skip that wave/person */
5178: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5179: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5180: if(m >=firstpass && m <=lastpass){
5181: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5182: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5183: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5184: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5185: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5186: 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);
5187: exit(1);
5188: }
5189: if (s[m][i]>0 && s[m][i]<=nlstate) {
5190: /*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]]);*/
5191: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5192: prop[s[m][i]][iagemax+3] += weight[i];
5193: } /* end valid statuses */
5194: } /* end selection of dates */
5195: } /* end selection of waves */
5196: } /* end bool */
5197: } /* end wave */
5198: } /* end individual */
5199: for(i=iagemin; i <= iagemax+3; i++){
5200: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5201: posprop += prop[jk][i];
5202: }
5203:
5204: for(jk=1; jk <=nlstate ; jk++){
5205: if( i <= iagemax){
5206: if(posprop>=1.e-5){
5207: probs[i][jk][j1]= prop[jk][i]/posprop;
5208: } else{
1.288 brouard 5209: if(!first){
5210: first=1;
1.266 brouard 5211: 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]);
5212: }else{
1.288 brouard 5213: 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 5214: }
5215: }
5216: }
5217: }/* end jk */
5218: }/* end i */
1.222 brouard 5219: /*} *//* end i1 */
1.227 brouard 5220: } /* end j1 */
1.222 brouard 5221:
1.227 brouard 5222: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5223: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5224: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5225: } /* End of prevalence */
1.126 brouard 5226:
5227: /************* Waves Concatenation ***************/
5228:
5229: 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)
5230: {
1.298 brouard 5231: /* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
1.126 brouard 5232: Death is a valid wave (if date is known).
5233: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5234: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5235: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5236: */
1.126 brouard 5237:
1.224 brouard 5238: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5239: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5240: double sum=0., jmean=0.;*/
1.224 brouard 5241: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5242: int j, k=0,jk, ju, jl;
5243: double sum=0.;
5244: first=0;
1.214 brouard 5245: firstwo=0;
1.217 brouard 5246: firsthree=0;
1.218 brouard 5247: firstfour=0;
1.164 brouard 5248: jmin=100000;
1.126 brouard 5249: jmax=-1;
5250: jmean=0.;
1.224 brouard 5251:
5252: /* Treating live states */
1.214 brouard 5253: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5254: mi=0; /* First valid wave */
1.227 brouard 5255: mli=0; /* Last valid wave */
1.126 brouard 5256: m=firstpass;
1.214 brouard 5257: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5258: 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 */
5259: mli=m-1;/* mw[++mi][i]=m-1; */
5260: }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 */
5261: mw[++mi][i]=m;
5262: mli=m;
1.224 brouard 5263: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5264: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5265: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5266: }
1.227 brouard 5267: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5268: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5269: break;
1.224 brouard 5270: #else
1.227 brouard 5271: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5272: if(firsthree == 0){
1.302 brouard 5273: 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 5274: firsthree=1;
5275: }
1.302 brouard 5276: 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 5277: mw[++mi][i]=m;
5278: mli=m;
5279: }
5280: if(s[m][i]==-2){ /* Vital status is really unknown */
5281: nbwarn++;
5282: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5283: 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);
5284: 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);
5285: }
5286: break;
5287: }
5288: break;
1.224 brouard 5289: #endif
1.227 brouard 5290: }/* End m >= lastpass */
1.126 brouard 5291: }/* end while */
1.224 brouard 5292:
1.227 brouard 5293: /* 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 5294: /* After last pass */
1.224 brouard 5295: /* Treating death states */
1.214 brouard 5296: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5297: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5298: /* } */
1.126 brouard 5299: mi++; /* Death is another wave */
5300: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5301: /* Only death is a correct wave */
1.126 brouard 5302: mw[mi][i]=m;
1.257 brouard 5303: } /* else not in a death state */
1.224 brouard 5304: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5305: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5306: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5307: 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 */
5308: nbwarn++;
5309: if(firstfiv==0){
5310: 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 );
5311: firstfiv=1;
5312: }else{
5313: 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 );
5314: }
5315: }else{ /* Death occured afer last wave potential bias */
5316: nberr++;
5317: if(firstwo==0){
1.257 brouard 5318: 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 5319: firstwo=1;
5320: }
1.257 brouard 5321: 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 5322: }
1.257 brouard 5323: }else{ /* if date of interview is unknown */
1.227 brouard 5324: /* death is known but not confirmed by death status at any wave */
5325: if(firstfour==0){
5326: 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 );
5327: firstfour=1;
5328: }
5329: 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 5330: }
1.224 brouard 5331: } /* end if date of death is known */
5332: #endif
5333: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5334: /* wav[i]=mw[mi][i]; */
1.126 brouard 5335: if(mi==0){
5336: nbwarn++;
5337: if(first==0){
1.227 brouard 5338: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5339: first=1;
1.126 brouard 5340: }
5341: if(first==1){
1.227 brouard 5342: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5343: }
5344: } /* end mi==0 */
5345: } /* End individuals */
1.214 brouard 5346: /* wav and mw are no more changed */
1.223 brouard 5347:
1.214 brouard 5348:
1.126 brouard 5349: for(i=1; i<=imx; i++){
5350: for(mi=1; mi<wav[i];mi++){
5351: if (stepm <=0)
1.227 brouard 5352: dh[mi][i]=1;
1.126 brouard 5353: else{
1.260 brouard 5354: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5355: if (agedc[i] < 2*AGESUP) {
5356: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5357: if(j==0) j=1; /* Survives at least one month after exam */
5358: else if(j<0){
5359: nberr++;
5360: 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]);
5361: j=1; /* Temporary Dangerous patch */
5362: 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);
5363: 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]);
5364: 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);
5365: }
5366: k=k+1;
5367: if (j >= jmax){
5368: jmax=j;
5369: ijmax=i;
5370: }
5371: if (j <= jmin){
5372: jmin=j;
5373: ijmin=i;
5374: }
5375: sum=sum+j;
5376: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5377: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5378: }
5379: }
5380: else{
5381: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5382: /* 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 5383:
1.227 brouard 5384: k=k+1;
5385: if (j >= jmax) {
5386: jmax=j;
5387: ijmax=i;
5388: }
5389: else if (j <= jmin){
5390: jmin=j;
5391: ijmin=i;
5392: }
5393: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5394: /*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]);*/
5395: if(j<0){
5396: nberr++;
5397: 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]);
5398: 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]);
5399: }
5400: sum=sum+j;
5401: }
5402: jk= j/stepm;
5403: jl= j -jk*stepm;
5404: ju= j -(jk+1)*stepm;
5405: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5406: if(jl==0){
5407: dh[mi][i]=jk;
5408: bh[mi][i]=0;
5409: }else{ /* We want a negative bias in order to only have interpolation ie
5410: * to avoid the price of an extra matrix product in likelihood */
5411: dh[mi][i]=jk+1;
5412: bh[mi][i]=ju;
5413: }
5414: }else{
5415: if(jl <= -ju){
5416: dh[mi][i]=jk;
5417: bh[mi][i]=jl; /* bias is positive if real duration
5418: * is higher than the multiple of stepm and negative otherwise.
5419: */
5420: }
5421: else{
5422: dh[mi][i]=jk+1;
5423: bh[mi][i]=ju;
5424: }
5425: if(dh[mi][i]==0){
5426: dh[mi][i]=1; /* At least one step */
5427: bh[mi][i]=ju; /* At least one step */
5428: /* 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);*/
5429: }
5430: } /* end if mle */
1.126 brouard 5431: }
5432: } /* end wave */
5433: }
5434: jmean=sum/k;
5435: 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 5436: 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 5437: }
1.126 brouard 5438:
5439: /*********** Tricode ****************************/
1.220 brouard 5440: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5441: {
5442: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5443: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5444: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5445: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5446: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5447: */
1.130 brouard 5448:
1.242 brouard 5449: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5450: int modmaxcovj=0; /* Modality max of covariates j */
5451: int cptcode=0; /* Modality max of covariates j */
5452: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5453:
5454:
1.242 brouard 5455: /* cptcoveff=0; */
5456: /* *cptcov=0; */
1.126 brouard 5457:
1.242 brouard 5458: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5459: for (k=1; k <= maxncov; k++)
5460: for(j=1; j<=2; j++)
5461: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5462:
1.242 brouard 5463: /* Loop on covariates without age and products and no quantitative variable */
5464: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5465: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5466: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5467: switch(Fixed[k]) {
5468: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5469: 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*/
5470: ij=(int)(covar[Tvar[k]][i]);
5471: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5472: * If product of Vn*Vm, still boolean *:
5473: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5474: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5475: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5476: modality of the nth covariate of individual i. */
5477: if (ij > modmaxcovj)
5478: modmaxcovj=ij;
5479: else if (ij < modmincovj)
5480: modmincovj=ij;
1.287 brouard 5481: if (ij <0 || ij >1 ){
5482: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5483: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5484: }
5485: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5486: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5487: exit(1);
5488: }else
5489: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5490: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5491: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5492: /* getting the maximum value of the modality of the covariate
5493: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5494: female ies 1, then modmaxcovj=1.
5495: */
5496: } /* end for loop on individuals i */
5497: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5498: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5499: cptcode=modmaxcovj;
5500: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5501: /*for (i=0; i<=cptcode; i++) {*/
5502: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5503: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5504: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5505: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5506: if( j != -1){
5507: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5508: covariate for which somebody answered excluding
5509: undefined. Usually 2: 0 and 1. */
5510: }
5511: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5512: covariate for which somebody answered including
5513: undefined. Usually 3: -1, 0 and 1. */
5514: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5515: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5516: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5517:
1.242 brouard 5518: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5519: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5520: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5521: /* modmincovj=3; modmaxcovj = 7; */
5522: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5523: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5524: /* defining two dummy variables: variables V1_1 and V1_2.*/
5525: /* nbcode[Tvar[j]][ij]=k; */
5526: /* nbcode[Tvar[j]][1]=0; */
5527: /* nbcode[Tvar[j]][2]=1; */
5528: /* nbcode[Tvar[j]][3]=2; */
5529: /* To be continued (not working yet). */
5530: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5531:
5532: /* 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*/
5533: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5534: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5535: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5536: /*, could be restored in the future */
5537: 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 5538: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5539: break;
5540: }
5541: ij++;
1.287 brouard 5542: 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 5543: cptcode = ij; /* New max modality for covar j */
5544: } /* end of loop on modality i=-1 to 1 or more */
5545: break;
5546: case 1: /* Testing on varying covariate, could be simple and
5547: * should look at waves or product of fixed *
5548: * varying. No time to test -1, assuming 0 and 1 only */
5549: ij=0;
5550: for(i=0; i<=1;i++){
5551: nbcode[Tvar[k]][++ij]=i;
5552: }
5553: break;
5554: default:
5555: break;
5556: } /* end switch */
5557: } /* end dummy test */
1.287 brouard 5558: } /* 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 5559:
5560: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5561: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5562: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5563: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5564: 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 */
5565: 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 */
5566: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5567: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5568:
5569: ij=0;
5570: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5571: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5572: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5573: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5574: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5575: /* If product not in single variable we don't print results */
5576: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5577: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5578: 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*/
5579: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5580: 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 */
5581: if(Fixed[k]!=0)
5582: anyvaryingduminmodel=1;
5583: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5584: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5585: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5586: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5587: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5588: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5589: }
5590: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5591: /* ij--; */
5592: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5593: *cptcov=ij; /*Number of total real effective covariates: effective
5594: * because they can be excluded from the model and real
5595: * if in the model but excluded because missing values, but how to get k from ij?*/
5596: for(j=ij+1; j<= cptcovt; j++){
5597: Tvaraff[j]=0;
5598: Tmodelind[j]=0;
5599: }
5600: for(j=ntveff+1; j<= cptcovt; j++){
5601: TmodelInvind[j]=0;
5602: }
5603: /* To be sorted */
5604: ;
5605: }
1.126 brouard 5606:
1.145 brouard 5607:
1.126 brouard 5608: /*********** Health Expectancies ****************/
5609:
1.235 brouard 5610: 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 5611:
5612: {
5613: /* Health expectancies, no variances */
1.164 brouard 5614: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5615: int nhstepma, nstepma; /* Decreasing with age */
5616: double age, agelim, hf;
5617: double ***p3mat;
5618: double eip;
5619:
1.238 brouard 5620: /* pstamp(ficreseij); */
1.126 brouard 5621: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5622: fprintf(ficreseij,"# Age");
5623: for(i=1; i<=nlstate;i++){
5624: for(j=1; j<=nlstate;j++){
5625: fprintf(ficreseij," e%1d%1d ",i,j);
5626: }
5627: fprintf(ficreseij," e%1d. ",i);
5628: }
5629: fprintf(ficreseij,"\n");
5630:
5631:
5632: if(estepm < stepm){
5633: printf ("Problem %d lower than %d\n",estepm, stepm);
5634: }
5635: else hstepm=estepm;
5636: /* We compute the life expectancy from trapezoids spaced every estepm months
5637: * This is mainly to measure the difference between two models: for example
5638: * if stepm=24 months pijx are given only every 2 years and by summing them
5639: * we are calculating an estimate of the Life Expectancy assuming a linear
5640: * progression in between and thus overestimating or underestimating according
5641: * to the curvature of the survival function. If, for the same date, we
5642: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5643: * to compare the new estimate of Life expectancy with the same linear
5644: * hypothesis. A more precise result, taking into account a more precise
5645: * curvature will be obtained if estepm is as small as stepm. */
5646:
5647: /* For example we decided to compute the life expectancy with the smallest unit */
5648: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5649: nhstepm is the number of hstepm from age to agelim
5650: nstepm is the number of stepm from age to agelin.
1.270 brouard 5651: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5652: and note for a fixed period like estepm months */
5653: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5654: survival function given by stepm (the optimization length). Unfortunately it
5655: means that if the survival funtion is printed only each two years of age and if
5656: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5657: results. So we changed our mind and took the option of the best precision.
5658: */
5659: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5660:
5661: agelim=AGESUP;
5662: /* If stepm=6 months */
5663: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5664: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5665:
5666: /* nhstepm age range expressed in number of stepm */
5667: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5668: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5669: /* if (stepm >= YEARM) hstepm=1;*/
5670: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5671: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5672:
5673: for (age=bage; age<=fage; age ++){
5674: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5675: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5676: /* if (stepm >= YEARM) hstepm=1;*/
5677: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5678:
5679: /* If stepm=6 months */
5680: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5681: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5682:
1.235 brouard 5683: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5684:
5685: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5686:
5687: printf("%d|",(int)age);fflush(stdout);
5688: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5689:
5690: /* Computing expectancies */
5691: for(i=1; i<=nlstate;i++)
5692: for(j=1; j<=nlstate;j++)
5693: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5694: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5695:
5696: /* 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]);*/
5697:
5698: }
5699:
5700: fprintf(ficreseij,"%3.0f",age );
5701: for(i=1; i<=nlstate;i++){
5702: eip=0;
5703: for(j=1; j<=nlstate;j++){
5704: eip +=eij[i][j][(int)age];
5705: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5706: }
5707: fprintf(ficreseij,"%9.4f", eip );
5708: }
5709: fprintf(ficreseij,"\n");
5710:
5711: }
5712: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5713: printf("\n");
5714: fprintf(ficlog,"\n");
5715:
5716: }
5717:
1.235 brouard 5718: 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 5719:
5720: {
5721: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5722: to initial status i, ei. .
1.126 brouard 5723: */
5724: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5725: int nhstepma, nstepma; /* Decreasing with age */
5726: double age, agelim, hf;
5727: double ***p3matp, ***p3matm, ***varhe;
5728: double **dnewm,**doldm;
5729: double *xp, *xm;
5730: double **gp, **gm;
5731: double ***gradg, ***trgradg;
5732: int theta;
5733:
5734: double eip, vip;
5735:
5736: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5737: xp=vector(1,npar);
5738: xm=vector(1,npar);
5739: dnewm=matrix(1,nlstate*nlstate,1,npar);
5740: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5741:
5742: pstamp(ficresstdeij);
5743: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5744: fprintf(ficresstdeij,"# Age");
5745: for(i=1; i<=nlstate;i++){
5746: for(j=1; j<=nlstate;j++)
5747: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5748: fprintf(ficresstdeij," e%1d. ",i);
5749: }
5750: fprintf(ficresstdeij,"\n");
5751:
5752: pstamp(ficrescveij);
5753: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5754: fprintf(ficrescveij,"# Age");
5755: for(i=1; i<=nlstate;i++)
5756: for(j=1; j<=nlstate;j++){
5757: cptj= (j-1)*nlstate+i;
5758: for(i2=1; i2<=nlstate;i2++)
5759: for(j2=1; j2<=nlstate;j2++){
5760: cptj2= (j2-1)*nlstate+i2;
5761: if(cptj2 <= cptj)
5762: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5763: }
5764: }
5765: fprintf(ficrescveij,"\n");
5766:
5767: if(estepm < stepm){
5768: printf ("Problem %d lower than %d\n",estepm, stepm);
5769: }
5770: else hstepm=estepm;
5771: /* We compute the life expectancy from trapezoids spaced every estepm months
5772: * This is mainly to measure the difference between two models: for example
5773: * if stepm=24 months pijx are given only every 2 years and by summing them
5774: * we are calculating an estimate of the Life Expectancy assuming a linear
5775: * progression in between and thus overestimating or underestimating according
5776: * to the curvature of the survival function. If, for the same date, we
5777: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5778: * to compare the new estimate of Life expectancy with the same linear
5779: * hypothesis. A more precise result, taking into account a more precise
5780: * curvature will be obtained if estepm is as small as stepm. */
5781:
5782: /* For example we decided to compute the life expectancy with the smallest unit */
5783: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5784: nhstepm is the number of hstepm from age to agelim
5785: nstepm is the number of stepm from age to agelin.
5786: Look at hpijx to understand the reason of that which relies in memory size
5787: and note for a fixed period like estepm months */
5788: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5789: survival function given by stepm (the optimization length). Unfortunately it
5790: means that if the survival funtion is printed only each two years of age and if
5791: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5792: results. So we changed our mind and took the option of the best precision.
5793: */
5794: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5795:
5796: /* If stepm=6 months */
5797: /* nhstepm age range expressed in number of stepm */
5798: agelim=AGESUP;
5799: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5800: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5801: /* if (stepm >= YEARM) hstepm=1;*/
5802: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5803:
5804: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5805: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5806: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5807: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5808: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5809: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5810:
5811: for (age=bage; age<=fage; age ++){
5812: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5813: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5814: /* if (stepm >= YEARM) hstepm=1;*/
5815: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5816:
1.126 brouard 5817: /* If stepm=6 months */
5818: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5819: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5820:
5821: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5822:
1.126 brouard 5823: /* Computing Variances of health expectancies */
5824: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5825: decrease memory allocation */
5826: for(theta=1; theta <=npar; theta++){
5827: for(i=1; i<=npar; i++){
1.222 brouard 5828: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5829: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5830: }
1.235 brouard 5831: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5832: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5833:
1.126 brouard 5834: for(j=1; j<= nlstate; j++){
1.222 brouard 5835: for(i=1; i<=nlstate; i++){
5836: for(h=0; h<=nhstepm-1; h++){
5837: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5838: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5839: }
5840: }
1.126 brouard 5841: }
1.218 brouard 5842:
1.126 brouard 5843: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5844: for(h=0; h<=nhstepm-1; h++){
5845: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5846: }
1.126 brouard 5847: }/* End theta */
5848:
5849:
5850: for(h=0; h<=nhstepm-1; h++)
5851: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5852: for(theta=1; theta <=npar; theta++)
5853: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5854:
1.218 brouard 5855:
1.222 brouard 5856: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5857: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5858: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5859:
1.222 brouard 5860: printf("%d|",(int)age);fflush(stdout);
5861: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5862: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5863: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5864: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5865: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5866: for(ij=1;ij<=nlstate*nlstate;ij++)
5867: for(ji=1;ji<=nlstate*nlstate;ji++)
5868: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5869: }
5870: }
1.218 brouard 5871:
1.126 brouard 5872: /* Computing expectancies */
1.235 brouard 5873: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5874: for(i=1; i<=nlstate;i++)
5875: for(j=1; j<=nlstate;j++)
1.222 brouard 5876: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5877: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5878:
1.222 brouard 5879: /* 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 5880:
1.222 brouard 5881: }
1.269 brouard 5882:
5883: /* Standard deviation of expectancies ij */
1.126 brouard 5884: fprintf(ficresstdeij,"%3.0f",age );
5885: for(i=1; i<=nlstate;i++){
5886: eip=0.;
5887: vip=0.;
5888: for(j=1; j<=nlstate;j++){
1.222 brouard 5889: eip += eij[i][j][(int)age];
5890: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5891: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5892: 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 5893: }
5894: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5895: }
5896: fprintf(ficresstdeij,"\n");
1.218 brouard 5897:
1.269 brouard 5898: /* Variance of expectancies ij */
1.126 brouard 5899: fprintf(ficrescveij,"%3.0f",age );
5900: for(i=1; i<=nlstate;i++)
5901: for(j=1; j<=nlstate;j++){
1.222 brouard 5902: cptj= (j-1)*nlstate+i;
5903: for(i2=1; i2<=nlstate;i2++)
5904: for(j2=1; j2<=nlstate;j2++){
5905: cptj2= (j2-1)*nlstate+i2;
5906: if(cptj2 <= cptj)
5907: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5908: }
1.126 brouard 5909: }
5910: fprintf(ficrescveij,"\n");
1.218 brouard 5911:
1.126 brouard 5912: }
5913: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5914: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5915: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5916: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5917: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5918: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5919: printf("\n");
5920: fprintf(ficlog,"\n");
1.218 brouard 5921:
1.126 brouard 5922: free_vector(xm,1,npar);
5923: free_vector(xp,1,npar);
5924: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5925: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5926: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5927: }
1.218 brouard 5928:
1.126 brouard 5929: /************ Variance ******************/
1.235 brouard 5930: 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 5931: {
1.279 brouard 5932: /** Variance of health expectancies
5933: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5934: * double **newm;
5935: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5936: */
1.218 brouard 5937:
5938: /* int movingaverage(); */
5939: double **dnewm,**doldm;
5940: double **dnewmp,**doldmp;
5941: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5942: int first=0;
1.218 brouard 5943: int k;
5944: double *xp;
1.279 brouard 5945: double **gp, **gm; /**< for var eij */
5946: double ***gradg, ***trgradg; /**< for var eij */
5947: double **gradgp, **trgradgp; /**< for var p point j */
5948: double *gpp, *gmp; /**< for var p point j */
5949: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5950: double ***p3mat;
5951: double age,agelim, hf;
5952: /* double ***mobaverage; */
5953: int theta;
5954: char digit[4];
5955: char digitp[25];
5956:
5957: char fileresprobmorprev[FILENAMELENGTH];
5958:
5959: if(popbased==1){
5960: if(mobilav!=0)
5961: strcpy(digitp,"-POPULBASED-MOBILAV_");
5962: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5963: }
5964: else
5965: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5966:
1.218 brouard 5967: /* if (mobilav!=0) { */
5968: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5969: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5970: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5971: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5972: /* } */
5973: /* } */
5974:
5975: strcpy(fileresprobmorprev,"PRMORPREV-");
5976: sprintf(digit,"%-d",ij);
5977: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5978: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5979: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5980: strcat(fileresprobmorprev,fileresu);
5981: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5982: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5983: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5984: }
5985: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5986: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5987: pstamp(ficresprobmorprev);
5988: 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 5989: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5990: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5991: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5992: }
5993: for(j=1;j<=cptcoveff;j++)
5994: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5995: fprintf(ficresprobmorprev,"\n");
5996:
1.218 brouard 5997: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5998: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5999: fprintf(ficresprobmorprev," p.%-d SE",j);
6000: for(i=1; i<=nlstate;i++)
6001: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6002: }
6003: fprintf(ficresprobmorprev,"\n");
6004:
6005: fprintf(ficgp,"\n# Routine varevsij");
6006: fprintf(ficgp,"\nunset title \n");
6007: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6008: 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");
6009: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6010:
1.218 brouard 6011: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6012: pstamp(ficresvij);
6013: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6014: if(popbased==1)
6015: 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);
6016: else
6017: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6018: fprintf(ficresvij,"# Age");
6019: for(i=1; i<=nlstate;i++)
6020: for(j=1; j<=nlstate;j++)
6021: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6022: fprintf(ficresvij,"\n");
6023:
6024: xp=vector(1,npar);
6025: dnewm=matrix(1,nlstate,1,npar);
6026: doldm=matrix(1,nlstate,1,nlstate);
6027: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6028: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6029:
6030: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6031: gpp=vector(nlstate+1,nlstate+ndeath);
6032: gmp=vector(nlstate+1,nlstate+ndeath);
6033: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6034:
1.218 brouard 6035: if(estepm < stepm){
6036: printf ("Problem %d lower than %d\n",estepm, stepm);
6037: }
6038: else hstepm=estepm;
6039: /* For example we decided to compute the life expectancy with the smallest unit */
6040: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6041: nhstepm is the number of hstepm from age to agelim
6042: nstepm is the number of stepm from age to agelim.
6043: Look at function hpijx to understand why because of memory size limitations,
6044: we decided (b) to get a life expectancy respecting the most precise curvature of the
6045: survival function given by stepm (the optimization length). Unfortunately it
6046: means that if the survival funtion is printed every two years of age and if
6047: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6048: results. So we changed our mind and took the option of the best precision.
6049: */
6050: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6051: agelim = AGESUP;
6052: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6053: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6054: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6055: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6056: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6057: gp=matrix(0,nhstepm,1,nlstate);
6058: gm=matrix(0,nhstepm,1,nlstate);
6059:
6060:
6061: for(theta=1; theta <=npar; theta++){
6062: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6063: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6064: }
1.279 brouard 6065: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6066: * returns into prlim .
1.288 brouard 6067: */
1.242 brouard 6068: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6069:
6070: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6071: if (popbased==1) {
6072: if(mobilav ==0){
6073: for(i=1; i<=nlstate;i++)
6074: prlim[i][i]=probs[(int)age][i][ij];
6075: }else{ /* mobilav */
6076: for(i=1; i<=nlstate;i++)
6077: prlim[i][i]=mobaverage[(int)age][i][ij];
6078: }
6079: }
1.295 brouard 6080: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6081: */
6082: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
1.292 brouard 6083: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
1.279 brouard 6084: * at horizon h in state j including mortality.
6085: */
1.218 brouard 6086: for(j=1; j<= nlstate; j++){
6087: for(h=0; h<=nhstepm; h++){
6088: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6089: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6090: }
6091: }
1.279 brouard 6092: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6093: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6094: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6095: */
6096: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6097: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6098: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6099: }
6100:
6101: /* Again with minus shift */
1.218 brouard 6102:
6103: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6104: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6105:
1.242 brouard 6106: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6107:
6108: if (popbased==1) {
6109: if(mobilav ==0){
6110: for(i=1; i<=nlstate;i++)
6111: prlim[i][i]=probs[(int)age][i][ij];
6112: }else{ /* mobilav */
6113: for(i=1; i<=nlstate;i++)
6114: prlim[i][i]=mobaverage[(int)age][i][ij];
6115: }
6116: }
6117:
1.235 brouard 6118: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6119:
6120: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6121: for(h=0; h<=nhstepm; h++){
6122: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6123: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6124: }
6125: }
6126: /* This for computing probability of death (h=1 means
6127: computed over hstepm matrices product = hstepm*stepm months)
6128: as a weighted average of prlim.
6129: */
6130: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6131: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6132: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6133: }
1.279 brouard 6134: /* end shifting computations */
6135:
6136: /**< Computing gradient matrix at horizon h
6137: */
1.218 brouard 6138: for(j=1; j<= nlstate; j++) /* vareij */
6139: for(h=0; h<=nhstepm; h++){
6140: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6141: }
1.279 brouard 6142: /**< Gradient of overall mortality p.3 (or p.j)
6143: */
6144: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6145: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6146: }
6147:
6148: } /* End theta */
1.279 brouard 6149:
6150: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6151: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6152:
6153: for(h=0; h<=nhstepm; h++) /* veij */
6154: for(j=1; j<=nlstate;j++)
6155: for(theta=1; theta <=npar; theta++)
6156: trgradg[h][j][theta]=gradg[h][theta][j];
6157:
6158: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6159: for(theta=1; theta <=npar; theta++)
6160: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6161: /**< as well as its transposed matrix
6162: */
1.218 brouard 6163:
6164: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6165: for(i=1;i<=nlstate;i++)
6166: for(j=1;j<=nlstate;j++)
6167: vareij[i][j][(int)age] =0.;
1.279 brouard 6168:
6169: /* Computing trgradg by matcov by gradg at age and summing over h
6170: * and k (nhstepm) formula 15 of article
6171: * Lievre-Brouard-Heathcote
6172: */
6173:
1.218 brouard 6174: for(h=0;h<=nhstepm;h++){
6175: for(k=0;k<=nhstepm;k++){
6176: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6177: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6178: for(i=1;i<=nlstate;i++)
6179: for(j=1;j<=nlstate;j++)
6180: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6181: }
6182: }
6183:
1.279 brouard 6184: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6185: * p.j overall mortality formula 49 but computed directly because
6186: * we compute the grad (wix pijx) instead of grad (pijx),even if
6187: * wix is independent of theta.
6188: */
1.218 brouard 6189: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6190: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6191: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6192: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6193: varppt[j][i]=doldmp[j][i];
6194: /* end ppptj */
6195: /* x centered again */
6196:
1.242 brouard 6197: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6198:
6199: if (popbased==1) {
6200: if(mobilav ==0){
6201: for(i=1; i<=nlstate;i++)
6202: prlim[i][i]=probs[(int)age][i][ij];
6203: }else{ /* mobilav */
6204: for(i=1; i<=nlstate;i++)
6205: prlim[i][i]=mobaverage[(int)age][i][ij];
6206: }
6207: }
6208:
6209: /* This for computing probability of death (h=1 means
6210: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6211: as a weighted average of prlim.
6212: */
1.235 brouard 6213: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6214: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6215: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6216: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6217: }
6218: /* end probability of death */
6219:
6220: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6221: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6222: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6223: for(i=1; i<=nlstate;i++){
6224: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6225: }
6226: }
6227: fprintf(ficresprobmorprev,"\n");
6228:
6229: fprintf(ficresvij,"%.0f ",age );
6230: for(i=1; i<=nlstate;i++)
6231: for(j=1; j<=nlstate;j++){
6232: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6233: }
6234: fprintf(ficresvij,"\n");
6235: free_matrix(gp,0,nhstepm,1,nlstate);
6236: free_matrix(gm,0,nhstepm,1,nlstate);
6237: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6238: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6239: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6240: } /* End age */
6241: free_vector(gpp,nlstate+1,nlstate+ndeath);
6242: free_vector(gmp,nlstate+1,nlstate+ndeath);
6243: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6244: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6245: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6246: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6247: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6248: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6249: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6250: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6251: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6252: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6253: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6254: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6255: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6256: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6257: 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);
6258: /* 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 6259: */
1.218 brouard 6260: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6261: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6262:
1.218 brouard 6263: free_vector(xp,1,npar);
6264: free_matrix(doldm,1,nlstate,1,nlstate);
6265: free_matrix(dnewm,1,nlstate,1,npar);
6266: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6267: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6268: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6269: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6270: fclose(ficresprobmorprev);
6271: fflush(ficgp);
6272: fflush(fichtm);
6273: } /* end varevsij */
1.126 brouard 6274:
6275: /************ Variance of prevlim ******************/
1.269 brouard 6276: 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 6277: {
1.205 brouard 6278: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6279: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6280:
1.268 brouard 6281: double **dnewmpar,**doldm;
1.126 brouard 6282: int i, j, nhstepm, hstepm;
6283: double *xp;
6284: double *gp, *gm;
6285: double **gradg, **trgradg;
1.208 brouard 6286: double **mgm, **mgp;
1.126 brouard 6287: double age,agelim;
6288: int theta;
6289:
6290: pstamp(ficresvpl);
1.288 brouard 6291: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6292: fprintf(ficresvpl,"# Age ");
6293: if(nresult >=1)
6294: fprintf(ficresvpl," Result# ");
1.126 brouard 6295: for(i=1; i<=nlstate;i++)
6296: fprintf(ficresvpl," %1d-%1d",i,i);
6297: fprintf(ficresvpl,"\n");
6298:
6299: xp=vector(1,npar);
1.268 brouard 6300: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6301: doldm=matrix(1,nlstate,1,nlstate);
6302:
6303: hstepm=1*YEARM; /* Every year of age */
6304: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6305: agelim = AGESUP;
6306: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6307: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6308: if (stepm >= YEARM) hstepm=1;
6309: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6310: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6311: mgp=matrix(1,npar,1,nlstate);
6312: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6313: gp=vector(1,nlstate);
6314: gm=vector(1,nlstate);
6315:
6316: for(theta=1; theta <=npar; theta++){
6317: for(i=1; i<=npar; i++){ /* Computes gradient */
6318: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6319: }
1.288 brouard 6320: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6321: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6322: /* else */
6323: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6324: for(i=1;i<=nlstate;i++){
1.126 brouard 6325: gp[i] = prlim[i][i];
1.208 brouard 6326: mgp[theta][i] = prlim[i][i];
6327: }
1.126 brouard 6328: for(i=1; i<=npar; i++) /* Computes gradient */
6329: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6330: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6331: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6332: /* else */
6333: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6334: for(i=1;i<=nlstate;i++){
1.126 brouard 6335: gm[i] = prlim[i][i];
1.208 brouard 6336: mgm[theta][i] = prlim[i][i];
6337: }
1.126 brouard 6338: for(i=1;i<=nlstate;i++)
6339: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6340: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6341: } /* End theta */
6342:
6343: trgradg =matrix(1,nlstate,1,npar);
6344:
6345: for(j=1; j<=nlstate;j++)
6346: for(theta=1; theta <=npar; theta++)
6347: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6348: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6349: /* printf("\nmgm mgp %d ",(int)age); */
6350: /* for(j=1; j<=nlstate;j++){ */
6351: /* printf(" %d ",j); */
6352: /* for(theta=1; theta <=npar; theta++) */
6353: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6354: /* printf("\n "); */
6355: /* } */
6356: /* } */
6357: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6358: /* printf("\n gradg %d ",(int)age); */
6359: /* for(j=1; j<=nlstate;j++){ */
6360: /* printf("%d ",j); */
6361: /* for(theta=1; theta <=npar; theta++) */
6362: /* printf("%d %lf ",theta,gradg[theta][j]); */
6363: /* printf("\n "); */
6364: /* } */
6365: /* } */
1.126 brouard 6366:
6367: for(i=1;i<=nlstate;i++)
6368: varpl[i][(int)age] =0.;
1.209 brouard 6369: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6370: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6371: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6372: }else{
1.268 brouard 6373: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6374: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6375: }
1.126 brouard 6376: for(i=1;i<=nlstate;i++)
6377: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6378:
6379: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6380: if(nresult >=1)
6381: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6382: for(i=1; i<=nlstate;i++){
1.126 brouard 6383: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6384: /* for(j=1;j<=nlstate;j++) */
6385: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6386: }
1.126 brouard 6387: fprintf(ficresvpl,"\n");
6388: free_vector(gp,1,nlstate);
6389: free_vector(gm,1,nlstate);
1.208 brouard 6390: free_matrix(mgm,1,npar,1,nlstate);
6391: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6392: free_matrix(gradg,1,npar,1,nlstate);
6393: free_matrix(trgradg,1,nlstate,1,npar);
6394: } /* End age */
6395:
6396: free_vector(xp,1,npar);
6397: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6398: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6399:
6400: }
6401:
6402:
6403: /************ Variance of backprevalence limit ******************/
1.269 brouard 6404: 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 6405: {
6406: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6407: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6408:
6409: double **dnewmpar,**doldm;
6410: int i, j, nhstepm, hstepm;
6411: double *xp;
6412: double *gp, *gm;
6413: double **gradg, **trgradg;
6414: double **mgm, **mgp;
6415: double age,agelim;
6416: int theta;
6417:
6418: pstamp(ficresvbl);
6419: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6420: fprintf(ficresvbl,"# Age ");
6421: if(nresult >=1)
6422: fprintf(ficresvbl," Result# ");
6423: for(i=1; i<=nlstate;i++)
6424: fprintf(ficresvbl," %1d-%1d",i,i);
6425: fprintf(ficresvbl,"\n");
6426:
6427: xp=vector(1,npar);
6428: dnewmpar=matrix(1,nlstate,1,npar);
6429: doldm=matrix(1,nlstate,1,nlstate);
6430:
6431: hstepm=1*YEARM; /* Every year of age */
6432: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6433: agelim = AGEINF;
6434: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6435: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6436: if (stepm >= YEARM) hstepm=1;
6437: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6438: gradg=matrix(1,npar,1,nlstate);
6439: mgp=matrix(1,npar,1,nlstate);
6440: mgm=matrix(1,npar,1,nlstate);
6441: gp=vector(1,nlstate);
6442: gm=vector(1,nlstate);
6443:
6444: for(theta=1; theta <=npar; theta++){
6445: for(i=1; i<=npar; i++){ /* Computes gradient */
6446: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6447: }
6448: if(mobilavproj > 0 )
6449: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6450: else
6451: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6452: for(i=1;i<=nlstate;i++){
6453: gp[i] = bprlim[i][i];
6454: mgp[theta][i] = bprlim[i][i];
6455: }
6456: for(i=1; i<=npar; i++) /* Computes gradient */
6457: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6458: if(mobilavproj > 0 )
6459: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6460: else
6461: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6462: for(i=1;i<=nlstate;i++){
6463: gm[i] = bprlim[i][i];
6464: mgm[theta][i] = bprlim[i][i];
6465: }
6466: for(i=1;i<=nlstate;i++)
6467: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6468: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6469: } /* End theta */
6470:
6471: trgradg =matrix(1,nlstate,1,npar);
6472:
6473: for(j=1; j<=nlstate;j++)
6474: for(theta=1; theta <=npar; theta++)
6475: trgradg[j][theta]=gradg[theta][j];
6476: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6477: /* printf("\nmgm mgp %d ",(int)age); */
6478: /* for(j=1; j<=nlstate;j++){ */
6479: /* printf(" %d ",j); */
6480: /* for(theta=1; theta <=npar; theta++) */
6481: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6482: /* printf("\n "); */
6483: /* } */
6484: /* } */
6485: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6486: /* printf("\n gradg %d ",(int)age); */
6487: /* for(j=1; j<=nlstate;j++){ */
6488: /* printf("%d ",j); */
6489: /* for(theta=1; theta <=npar; theta++) */
6490: /* printf("%d %lf ",theta,gradg[theta][j]); */
6491: /* printf("\n "); */
6492: /* } */
6493: /* } */
6494:
6495: for(i=1;i<=nlstate;i++)
6496: varbpl[i][(int)age] =0.;
6497: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6498: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6499: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6500: }else{
6501: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6502: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6503: }
6504: for(i=1;i<=nlstate;i++)
6505: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6506:
6507: fprintf(ficresvbl,"%.0f ",age );
6508: if(nresult >=1)
6509: fprintf(ficresvbl,"%d ",nres );
6510: for(i=1; i<=nlstate;i++)
6511: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6512: fprintf(ficresvbl,"\n");
6513: free_vector(gp,1,nlstate);
6514: free_vector(gm,1,nlstate);
6515: free_matrix(mgm,1,npar,1,nlstate);
6516: free_matrix(mgp,1,npar,1,nlstate);
6517: free_matrix(gradg,1,npar,1,nlstate);
6518: free_matrix(trgradg,1,nlstate,1,npar);
6519: } /* End age */
6520:
6521: free_vector(xp,1,npar);
6522: free_matrix(doldm,1,nlstate,1,npar);
6523: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6524:
6525: }
6526:
6527: /************ Variance of one-step probabilities ******************/
6528: 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 6529: {
6530: int i, j=0, k1, l1, tj;
6531: int k2, l2, j1, z1;
6532: int k=0, l;
6533: int first=1, first1, first2;
6534: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6535: double **dnewm,**doldm;
6536: double *xp;
6537: double *gp, *gm;
6538: double **gradg, **trgradg;
6539: double **mu;
6540: double age, cov[NCOVMAX+1];
6541: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6542: int theta;
6543: char fileresprob[FILENAMELENGTH];
6544: char fileresprobcov[FILENAMELENGTH];
6545: char fileresprobcor[FILENAMELENGTH];
6546: double ***varpij;
6547:
6548: strcpy(fileresprob,"PROB_");
6549: strcat(fileresprob,fileres);
6550: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6551: printf("Problem with resultfile: %s\n", fileresprob);
6552: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6553: }
6554: strcpy(fileresprobcov,"PROBCOV_");
6555: strcat(fileresprobcov,fileresu);
6556: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6557: printf("Problem with resultfile: %s\n", fileresprobcov);
6558: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6559: }
6560: strcpy(fileresprobcor,"PROBCOR_");
6561: strcat(fileresprobcor,fileresu);
6562: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6563: printf("Problem with resultfile: %s\n", fileresprobcor);
6564: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6565: }
6566: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6567: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6568: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6569: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6570: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6571: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6572: pstamp(ficresprob);
6573: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6574: fprintf(ficresprob,"# Age");
6575: pstamp(ficresprobcov);
6576: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6577: fprintf(ficresprobcov,"# Age");
6578: pstamp(ficresprobcor);
6579: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6580: fprintf(ficresprobcor,"# Age");
1.126 brouard 6581:
6582:
1.222 brouard 6583: for(i=1; i<=nlstate;i++)
6584: for(j=1; j<=(nlstate+ndeath);j++){
6585: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6586: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6587: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6588: }
6589: /* fprintf(ficresprob,"\n");
6590: fprintf(ficresprobcov,"\n");
6591: fprintf(ficresprobcor,"\n");
6592: */
6593: xp=vector(1,npar);
6594: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6595: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6596: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6597: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6598: first=1;
6599: fprintf(ficgp,"\n# Routine varprob");
6600: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6601: fprintf(fichtm,"\n");
6602:
1.288 brouard 6603: 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 6604: 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);
6605: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6606: and drawn. It helps understanding how is the covariance between two incidences.\
6607: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6608: 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 6609: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6610: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6611: standard deviations wide on each axis. <br>\
6612: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6613: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6614: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6615:
1.222 brouard 6616: cov[1]=1;
6617: /* tj=cptcoveff; */
1.225 brouard 6618: tj = (int) pow(2,cptcoveff);
1.222 brouard 6619: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6620: j1=0;
1.224 brouard 6621: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6622: if (cptcovn>0) {
6623: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6624: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6625: fprintf(ficresprob, "**********\n#\n");
6626: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6627: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6628: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6629:
1.222 brouard 6630: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6631: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6632: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6633:
6634:
1.222 brouard 6635: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6636: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6637: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6638:
1.222 brouard 6639: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6640: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6641: fprintf(ficresprobcor, "**********\n#");
6642: if(invalidvarcomb[j1]){
6643: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6644: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6645: continue;
6646: }
6647: }
6648: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6649: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6650: gp=vector(1,(nlstate)*(nlstate+ndeath));
6651: gm=vector(1,(nlstate)*(nlstate+ndeath));
6652: for (age=bage; age<=fage; age ++){
6653: cov[2]=age;
6654: if(nagesqr==1)
6655: cov[3]= age*age;
6656: for (k=1; k<=cptcovn;k++) {
6657: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6658: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6659: * 1 1 1 1 1
6660: * 2 2 1 1 1
6661: * 3 1 2 1 1
6662: */
6663: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6664: }
6665: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6666: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6667: for (k=1; k<=cptcovprod;k++)
6668: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6669:
6670:
1.222 brouard 6671: for(theta=1; theta <=npar; theta++){
6672: for(i=1; i<=npar; i++)
6673: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6674:
1.222 brouard 6675: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6676:
1.222 brouard 6677: k=0;
6678: for(i=1; i<= (nlstate); i++){
6679: for(j=1; j<=(nlstate+ndeath);j++){
6680: k=k+1;
6681: gp[k]=pmmij[i][j];
6682: }
6683: }
1.220 brouard 6684:
1.222 brouard 6685: for(i=1; i<=npar; i++)
6686: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6687:
1.222 brouard 6688: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6689: k=0;
6690: for(i=1; i<=(nlstate); i++){
6691: for(j=1; j<=(nlstate+ndeath);j++){
6692: k=k+1;
6693: gm[k]=pmmij[i][j];
6694: }
6695: }
1.220 brouard 6696:
1.222 brouard 6697: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6698: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6699: }
1.126 brouard 6700:
1.222 brouard 6701: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6702: for(theta=1; theta <=npar; theta++)
6703: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6704:
1.222 brouard 6705: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6706: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6707:
1.222 brouard 6708: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6709:
1.222 brouard 6710: k=0;
6711: for(i=1; i<=(nlstate); i++){
6712: for(j=1; j<=(nlstate+ndeath);j++){
6713: k=k+1;
6714: mu[k][(int) age]=pmmij[i][j];
6715: }
6716: }
6717: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6718: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6719: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6720:
1.222 brouard 6721: /*printf("\n%d ",(int)age);
6722: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6723: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6724: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6725: }*/
1.220 brouard 6726:
1.222 brouard 6727: fprintf(ficresprob,"\n%d ",(int)age);
6728: fprintf(ficresprobcov,"\n%d ",(int)age);
6729: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6730:
1.222 brouard 6731: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6732: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6733: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6734: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6735: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6736: }
6737: i=0;
6738: for (k=1; k<=(nlstate);k++){
6739: for (l=1; l<=(nlstate+ndeath);l++){
6740: i++;
6741: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6742: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6743: for (j=1; j<=i;j++){
6744: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6745: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6746: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6747: }
6748: }
6749: }/* end of loop for state */
6750: } /* end of loop for age */
6751: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6752: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6753: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6754: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6755:
6756: /* Confidence intervalle of pij */
6757: /*
6758: fprintf(ficgp,"\nunset parametric;unset label");
6759: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6760: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6761: 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);
6762: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6763: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6764: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6765: */
6766:
6767: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6768: first1=1;first2=2;
6769: for (k2=1; k2<=(nlstate);k2++){
6770: for (l2=1; l2<=(nlstate+ndeath);l2++){
6771: if(l2==k2) continue;
6772: j=(k2-1)*(nlstate+ndeath)+l2;
6773: for (k1=1; k1<=(nlstate);k1++){
6774: for (l1=1; l1<=(nlstate+ndeath);l1++){
6775: if(l1==k1) continue;
6776: i=(k1-1)*(nlstate+ndeath)+l1;
6777: if(i<=j) continue;
6778: for (age=bage; age<=fage; age ++){
6779: if ((int)age %5==0){
6780: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6781: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6782: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6783: mu1=mu[i][(int) age]/stepm*YEARM ;
6784: mu2=mu[j][(int) age]/stepm*YEARM;
6785: c12=cv12/sqrt(v1*v2);
6786: /* Computing eigen value of matrix of covariance */
6787: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6788: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6789: if ((lc2 <0) || (lc1 <0) ){
6790: if(first2==1){
6791: first1=0;
6792: 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);
6793: }
6794: 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);
6795: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6796: /* lc2=fabs(lc2); */
6797: }
1.220 brouard 6798:
1.222 brouard 6799: /* Eigen vectors */
1.280 brouard 6800: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6801: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6802: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6803: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6804: }else
6805: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6806: /*v21=sqrt(1.-v11*v11); *//* error */
6807: v21=(lc1-v1)/cv12*v11;
6808: v12=-v21;
6809: v22=v11;
6810: tnalp=v21/v11;
6811: if(first1==1){
6812: first1=0;
6813: 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);
6814: }
6815: 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);
6816: /*printf(fignu*/
6817: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6818: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6819: if(first==1){
6820: first=0;
6821: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6822: fprintf(ficgp,"\nset parametric;unset label");
6823: 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);
6824: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6825: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6826: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6827: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6828: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6829: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6830: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6831: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6832: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6833: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6834: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6835: 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 6836: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6837: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6838: }else{
6839: first=0;
6840: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6841: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6842: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6843: 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 6844: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6845: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6846: }/* if first */
6847: } /* age mod 5 */
6848: } /* end loop age */
6849: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6850: first=1;
6851: } /*l12 */
6852: } /* k12 */
6853: } /*l1 */
6854: }/* k1 */
6855: } /* loop on combination of covariates j1 */
6856: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6857: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6858: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6859: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6860: free_vector(xp,1,npar);
6861: fclose(ficresprob);
6862: fclose(ficresprobcov);
6863: fclose(ficresprobcor);
6864: fflush(ficgp);
6865: fflush(fichtmcov);
6866: }
1.126 brouard 6867:
6868:
6869: /******************* Printing html file ***********/
1.201 brouard 6870: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6871: int lastpass, int stepm, int weightopt, char model[],\
6872: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6873: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6874: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6875: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6876: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6877:
6878: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6879: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6880: </ul>");
1.237 brouard 6881: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6882: </ul>", model);
1.214 brouard 6883: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6884: 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",
6885: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6886: 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 6887: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6888: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6889: fprintf(fichtm,"\
6890: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6891: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6892: fprintf(fichtm,"\
1.217 brouard 6893: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6894: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6895: fprintf(fichtm,"\
1.288 brouard 6896: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6897: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6898: fprintf(fichtm,"\
1.288 brouard 6899: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6900: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6901: fprintf(fichtm,"\
1.211 brouard 6902: - (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 6903: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6904: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6905: if(prevfcast==1){
6906: fprintf(fichtm,"\
6907: - Prevalence projections by age and states: \
1.201 brouard 6908: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6909: }
1.126 brouard 6910:
6911:
1.225 brouard 6912: m=pow(2,cptcoveff);
1.222 brouard 6913: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6914:
1.264 brouard 6915: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6916:
6917: jj1=0;
6918:
6919: fprintf(fichtm," \n<ul>");
6920: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6921: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6922: if(m != 1 && TKresult[nres]!= k1)
6923: continue;
6924: jj1++;
6925: if (cptcovn > 0) {
6926: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6927: for (cpt=1; cpt<=cptcoveff;cpt++){
6928: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6929: }
6930: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6931: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6932: }
6933: fprintf(fichtm,"\">");
6934:
6935: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6936: fprintf(fichtm,"************ Results for covariates");
6937: for (cpt=1; cpt<=cptcoveff;cpt++){
6938: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6939: }
6940: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6941: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6942: }
6943: if(invalidvarcomb[k1]){
6944: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6945: continue;
6946: }
6947: fprintf(fichtm,"</a></li>");
6948: } /* cptcovn >0 */
6949: }
6950: fprintf(fichtm," \n</ul>");
6951:
1.222 brouard 6952: jj1=0;
1.237 brouard 6953:
6954: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6955: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6956: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6957: continue;
1.220 brouard 6958:
1.222 brouard 6959: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6960: jj1++;
6961: if (cptcovn > 0) {
1.264 brouard 6962: fprintf(fichtm,"\n<p><a name=\"rescov");
6963: for (cpt=1; cpt<=cptcoveff;cpt++){
6964: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6965: }
6966: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6967: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6968: }
6969: fprintf(fichtm,"\"</a>");
6970:
1.222 brouard 6971: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6972: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6973: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6974: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6975: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6976: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6977: }
1.237 brouard 6978: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6979: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6980: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6981: }
6982:
1.230 brouard 6983: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6984: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6985: if(invalidvarcomb[k1]){
6986: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6987: printf("\nCombination (%d) ignored because no cases \n",k1);
6988: continue;
6989: }
6990: }
6991: /* aij, bij */
1.259 brouard 6992: 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 6993: <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 6994: /* Pij */
1.241 brouard 6995: 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> \
6996: <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 6997: /* Quasi-incidences */
6998: 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 6999: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7000: 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 7001: 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> \
7002: <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 7003: /* Survival functions (period) in state j */
7004: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7005: fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241 brouard 7006: <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 7007: }
7008: /* State specific survival functions (period) */
7009: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7010: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7011: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7012: <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 7013: }
1.288 brouard 7014: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7015: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7016: 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> \
7017: <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 7018: }
1.296 brouard 7019: if(prevbcast==1){
1.288 brouard 7020: /* Backward prevalence in each health state */
1.222 brouard 7021: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7022: 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 7023: <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 7024: }
1.217 brouard 7025: }
1.222 brouard 7026: if(prevfcast==1){
1.288 brouard 7027: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7028: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7029: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.296 brouard 7030: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 7031: }
7032: }
1.296 brouard 7033: if(prevbcast==1){
1.268 brouard 7034: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7035: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7036: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7037: 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 \
7038: 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) \
7039: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7040: <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 7041: }
7042: }
1.220 brouard 7043:
1.222 brouard 7044: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7045: 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> \
7046: <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 7047: }
7048: /* } /\* end i1 *\/ */
7049: }/* End k1 */
7050: fprintf(fichtm,"</ul>");
1.126 brouard 7051:
1.222 brouard 7052: fprintf(fichtm,"\
1.126 brouard 7053: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7054: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7055: - 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 7056: But because parameters are usually highly correlated (a higher incidence of disability \
7057: and a higher incidence of recovery can give very close observed transition) it might \
7058: be very useful to look not only at linear confidence intervals estimated from the \
7059: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7060: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7061: covariance matrix of the one-step probabilities. \
7062: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7063:
1.222 brouard 7064: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7065: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7066: fprintf(fichtm,"\
1.126 brouard 7067: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7068: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7069:
1.222 brouard 7070: fprintf(fichtm,"\
1.126 brouard 7071: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7072: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7073: fprintf(fichtm,"\
1.126 brouard 7074: - 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): \
7075: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7076: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7077: fprintf(fichtm,"\
1.126 brouard 7078: - (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): \
7079: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7080: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7081: fprintf(fichtm,"\
1.288 brouard 7082: - 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 7083: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7084: fprintf(fichtm,"\
1.128 brouard 7085: - 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 7086: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7087: fprintf(fichtm,"\
1.288 brouard 7088: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7089: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7090:
7091: /* if(popforecast==1) fprintf(fichtm,"\n */
7092: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7093: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7094: /* <br>",fileres,fileres,fileres,fileres); */
7095: /* else */
7096: /* 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 7097: fflush(fichtm);
7098: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7099:
1.225 brouard 7100: m=pow(2,cptcoveff);
1.222 brouard 7101: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7102:
1.222 brouard 7103: jj1=0;
1.237 brouard 7104:
1.241 brouard 7105: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7106: for(k1=1; k1<=m;k1++){
1.253 brouard 7107: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7108: continue;
1.222 brouard 7109: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7110: jj1++;
1.126 brouard 7111: if (cptcovn > 0) {
7112: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7113: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7114: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7115: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7116: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7117: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7118: }
7119:
1.126 brouard 7120: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7121:
1.222 brouard 7122: if(invalidvarcomb[k1]){
7123: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7124: continue;
7125: }
1.126 brouard 7126: }
7127: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7128: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7129: 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 7130: <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 7131: }
7132: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7133: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7134: true period expectancies (those weighted with period prevalences are also\
7135: drawn in addition to the population based expectancies computed using\
1.241 brouard 7136: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7137: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7138: /* } /\* end i1 *\/ */
7139: }/* End k1 */
1.241 brouard 7140: }/* End nres */
1.222 brouard 7141: fprintf(fichtm,"</ul>");
7142: fflush(fichtm);
1.126 brouard 7143: }
7144:
7145: /******************* Gnuplot file **************/
1.296 brouard 7146: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
1.126 brouard 7147:
7148: char dirfileres[132],optfileres[132];
1.264 brouard 7149: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7150: 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 7151: int lv=0, vlv=0, kl=0;
1.130 brouard 7152: int ng=0;
1.201 brouard 7153: int vpopbased;
1.223 brouard 7154: int ioffset; /* variable offset for columns */
1.270 brouard 7155: int iyearc=1; /* variable column for year of projection */
7156: int iagec=1; /* variable column for age of projection */
1.235 brouard 7157: int nres=0; /* Index of resultline */
1.266 brouard 7158: int istart=1; /* For starting graphs in projections */
1.219 brouard 7159:
1.126 brouard 7160: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7161: /* printf("Problem with file %s",optionfilegnuplot); */
7162: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7163: /* } */
7164:
7165: /*#ifdef windows */
7166: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7167: /*#endif */
1.225 brouard 7168: m=pow(2,cptcoveff);
1.126 brouard 7169:
1.274 brouard 7170: /* diagram of the model */
7171: fprintf(ficgp,"\n#Diagram of the model \n");
7172: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7173: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7174: 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);
7175:
7176: 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);
7177: fprintf(ficgp,"\n#show arrow\nunset label\n");
7178: 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);
7179: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7180: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7181: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7182: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7183:
1.202 brouard 7184: /* Contribution to likelihood */
7185: /* Plot the probability implied in the likelihood */
1.223 brouard 7186: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7187: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7188: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7189: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7190: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7191: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7192: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7193: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7194: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7195: 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));
7196: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7197: 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));
7198: for (i=1; i<= nlstate ; i ++) {
7199: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7200: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7201: 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);
7202: for (j=2; j<= nlstate+ndeath ; j ++) {
7203: 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);
7204: }
7205: fprintf(ficgp,";\nset out; unset ylabel;\n");
7206: }
7207: /* 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 */
7208: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7209: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7210: fprintf(ficgp,"\nset out;unset log\n");
7211: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7212:
1.126 brouard 7213: strcpy(dirfileres,optionfilefiname);
7214: strcpy(optfileres,"vpl");
1.223 brouard 7215: /* 1eme*/
1.238 brouard 7216: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7217: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7218: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7219: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7220: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7221: continue;
7222: /* We are interested in selected combination by the resultline */
1.246 brouard 7223: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7224: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7225: strcpy(gplotlabel,"(");
1.238 brouard 7226: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7227: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7228: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7229: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7230: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7231: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7232: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7233: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7234: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7235: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7236: }
7237: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7238: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7239: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7240: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7241: }
7242: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7243: /* printf("\n#\n"); */
1.238 brouard 7244: fprintf(ficgp,"\n#\n");
7245: if(invalidvarcomb[k1]){
1.260 brouard 7246: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7247: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7248: continue;
7249: }
1.235 brouard 7250:
1.241 brouard 7251: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7252: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7253: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7254: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7255: 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);
7256: /* 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); */
7257: /* k1-1 error should be nres-1*/
1.238 brouard 7258: for (i=1; i<= nlstate ; i ++) {
7259: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7260: else fprintf(ficgp," %%*lf (%%*lf)");
7261: }
1.288 brouard 7262: 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 7263: for (i=1; i<= nlstate ; i ++) {
7264: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7265: else fprintf(ficgp," %%*lf (%%*lf)");
7266: }
1.260 brouard 7267: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7268: for (i=1; i<= nlstate ; i ++) {
7269: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7270: else fprintf(ficgp," %%*lf (%%*lf)");
7271: }
1.265 brouard 7272: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7273:
7274: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7275: if(cptcoveff ==0){
1.271 brouard 7276: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7277: }else{
7278: kl=0;
7279: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7280: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7281: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7282: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7283: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7284: vlv= nbcode[Tvaraff[k]][lv];
7285: kl++;
7286: /* 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 *\/ */
7287: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7288: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7289: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7290: if(k==cptcoveff){
7291: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7292: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7293: }else{
7294: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7295: kl++;
7296: }
7297: } /* end covariate */
7298: } /* end if no covariate */
7299:
1.296 brouard 7300: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7301: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7302: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7303: if(cptcoveff ==0){
1.245 brouard 7304: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7305: }else{
7306: kl=0;
7307: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7308: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7309: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7310: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7311: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7312: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7313: kl++;
1.238 brouard 7314: /* 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 *\/ */
7315: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7316: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7317: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7318: if(k==cptcoveff){
1.245 brouard 7319: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7320: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7321: }else{
7322: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7323: kl++;
7324: }
7325: } /* end covariate */
7326: } /* end if no covariate */
1.296 brouard 7327: if(prevbcast == 1){
1.268 brouard 7328: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7329: /* k1-1 error should be nres-1*/
7330: for (i=1; i<= nlstate ; i ++) {
7331: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7332: else fprintf(ficgp," %%*lf (%%*lf)");
7333: }
1.271 brouard 7334: 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 7335: for (i=1; i<= nlstate ; i ++) {
7336: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7337: else fprintf(ficgp," %%*lf (%%*lf)");
7338: }
1.276 brouard 7339: 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 7340: for (i=1; i<= nlstate ; i ++) {
7341: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7342: else fprintf(ficgp," %%*lf (%%*lf)");
7343: }
1.274 brouard 7344: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7345: } /* end if backprojcast */
1.296 brouard 7346: } /* end if prevbcast */
1.276 brouard 7347: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7348: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7349: } /* nres */
1.201 brouard 7350: } /* k1 */
7351: } /* cpt */
1.235 brouard 7352:
7353:
1.126 brouard 7354: /*2 eme*/
1.238 brouard 7355: for (k1=1; k1<= m ; k1 ++){
7356: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7357: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7358: continue;
7359: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7360: strcpy(gplotlabel,"(");
1.238 brouard 7361: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7362: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7363: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7364: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7365: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7366: vlv= nbcode[Tvaraff[k]][lv];
7367: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7368: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7369: }
1.237 brouard 7370: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7371: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7372: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7373: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7374: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7375: }
1.264 brouard 7376: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7377: fprintf(ficgp,"\n#\n");
1.223 brouard 7378: if(invalidvarcomb[k1]){
7379: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7380: continue;
7381: }
1.219 brouard 7382:
1.241 brouard 7383: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7384: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7385: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7386: if(vpopbased==0){
1.238 brouard 7387: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7388: }else
1.238 brouard 7389: fprintf(ficgp,"\nreplot ");
7390: for (i=1; i<= nlstate+1 ; i ++) {
7391: k=2*i;
1.261 brouard 7392: 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 7393: for (j=1; j<= nlstate+1 ; j ++) {
7394: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7395: else fprintf(ficgp," %%*lf (%%*lf)");
7396: }
7397: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7398: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7399: 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 7400: for (j=1; j<= nlstate+1 ; j ++) {
7401: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7402: else fprintf(ficgp," %%*lf (%%*lf)");
7403: }
7404: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7405: 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 7406: for (j=1; j<= nlstate+1 ; j ++) {
7407: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7408: else fprintf(ficgp," %%*lf (%%*lf)");
7409: }
7410: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7411: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7412: } /* state */
7413: } /* vpopbased */
1.264 brouard 7414: 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 7415: } /* end nres */
7416: } /* k1 end 2 eme*/
7417:
7418:
7419: /*3eme*/
7420: for (k1=1; k1<= m ; k1 ++){
7421: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7422: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7423: continue;
7424:
7425: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7426: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7427: strcpy(gplotlabel,"(");
1.238 brouard 7428: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7429: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7430: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7431: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7432: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7433: vlv= nbcode[Tvaraff[k]][lv];
7434: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7435: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7436: }
7437: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7438: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7439: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7440: }
1.264 brouard 7441: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7442: fprintf(ficgp,"\n#\n");
7443: if(invalidvarcomb[k1]){
7444: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7445: continue;
7446: }
7447:
7448: /* k=2+nlstate*(2*cpt-2); */
7449: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7450: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7451: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7452: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7453: 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 7454: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7455: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7456: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7457: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7458: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7459: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7460:
1.238 brouard 7461: */
7462: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7463: 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 7464: /* 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 7465:
1.238 brouard 7466: }
1.261 brouard 7467: 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 7468: }
1.264 brouard 7469: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7470: } /* end nres */
7471: } /* end kl 3eme */
1.126 brouard 7472:
1.223 brouard 7473: /* 4eme */
1.201 brouard 7474: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7475: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7476: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7477: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7478: continue;
1.238 brouard 7479: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7480: strcpy(gplotlabel,"(");
1.238 brouard 7481: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7482: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7483: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7484: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7485: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7486: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7487: vlv= nbcode[Tvaraff[k]][lv];
7488: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7489: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7490: }
7491: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7492: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7493: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7494: }
1.264 brouard 7495: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7496: fprintf(ficgp,"\n#\n");
7497: if(invalidvarcomb[k1]){
7498: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7499: continue;
1.223 brouard 7500: }
1.238 brouard 7501:
1.241 brouard 7502: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7503: 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 7504: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7505: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7506: k=3;
7507: for (i=1; i<= nlstate ; i ++){
7508: if(i==1){
7509: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7510: }else{
7511: fprintf(ficgp,", '' ");
7512: }
7513: l=(nlstate+ndeath)*(i-1)+1;
7514: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7515: for (j=2; j<= nlstate+ndeath ; j ++)
7516: fprintf(ficgp,"+$%d",k+l+j-1);
7517: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7518: } /* nlstate */
1.264 brouard 7519: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7520: } /* end cpt state*/
7521: } /* end nres */
7522: } /* end covariate k1 */
7523:
1.220 brouard 7524: /* 5eme */
1.201 brouard 7525: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7526: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7527: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7528: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7529: continue;
1.238 brouard 7530: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7531: strcpy(gplotlabel,"(");
1.238 brouard 7532: 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);
7533: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7534: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7535: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7536: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7537: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7538: vlv= nbcode[Tvaraff[k]][lv];
7539: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7540: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7541: }
7542: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7543: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7544: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7545: }
1.264 brouard 7546: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7547: fprintf(ficgp,"\n#\n");
7548: if(invalidvarcomb[k1]){
7549: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7550: continue;
7551: }
1.227 brouard 7552:
1.241 brouard 7553: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7554: 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 7555: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7556: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7557: k=3;
7558: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7559: if(j==1)
7560: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7561: else
7562: fprintf(ficgp,", '' ");
7563: l=(nlstate+ndeath)*(cpt-1) +j;
7564: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7565: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7566: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7567: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7568: } /* nlstate */
7569: fprintf(ficgp,", '' ");
7570: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7571: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7572: l=(nlstate+ndeath)*(cpt-1) +j;
7573: if(j < nlstate)
7574: fprintf(ficgp,"$%d +",k+l);
7575: else
7576: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7577: }
1.264 brouard 7578: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7579: } /* end cpt state*/
7580: } /* end covariate */
7581: } /* end nres */
1.227 brouard 7582:
1.220 brouard 7583: /* 6eme */
1.202 brouard 7584: /* CV preval stable (period) for each covariate */
1.237 brouard 7585: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7586: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7587: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7588: continue;
1.255 brouard 7589: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7590: strcpy(gplotlabel,"(");
1.288 brouard 7591: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7592: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7593: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7594: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7595: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7596: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7597: vlv= nbcode[Tvaraff[k]][lv];
7598: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7599: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7600: }
1.237 brouard 7601: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7602: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7603: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7604: }
1.264 brouard 7605: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7606: fprintf(ficgp,"\n#\n");
1.223 brouard 7607: if(invalidvarcomb[k1]){
1.227 brouard 7608: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7609: continue;
1.223 brouard 7610: }
1.227 brouard 7611:
1.241 brouard 7612: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7613: 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 7614: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7615: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7616: k=3; /* Offset */
1.255 brouard 7617: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7618: if(i==1)
7619: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7620: else
7621: fprintf(ficgp,", '' ");
1.255 brouard 7622: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7623: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7624: for (j=2; j<= nlstate ; j ++)
7625: fprintf(ficgp,"+$%d",k+l+j-1);
7626: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7627: } /* nlstate */
1.264 brouard 7628: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7629: } /* end cpt state*/
7630: } /* end covariate */
1.227 brouard 7631:
7632:
1.220 brouard 7633: /* 7eme */
1.296 brouard 7634: if(prevbcast == 1){
1.288 brouard 7635: /* CV backward prevalence for each covariate */
1.237 brouard 7636: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7637: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7638: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7639: continue;
1.268 brouard 7640: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7641: strcpy(gplotlabel,"(");
1.288 brouard 7642: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7643: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7644: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7645: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7646: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7647: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7648: vlv= nbcode[Tvaraff[k]][lv];
7649: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7650: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7651: }
1.237 brouard 7652: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7653: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7654: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7655: }
1.264 brouard 7656: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7657: fprintf(ficgp,"\n#\n");
7658: if(invalidvarcomb[k1]){
7659: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7660: continue;
7661: }
7662:
1.241 brouard 7663: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7664: 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 7665: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7666: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7667: k=3; /* Offset */
1.268 brouard 7668: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7669: if(i==1)
7670: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7671: else
7672: fprintf(ficgp,", '' ");
7673: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7674: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7675: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7676: /* 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 7677: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7678: /* for (j=2; j<= nlstate ; j ++) */
7679: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7680: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7681: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7682: } /* nlstate */
1.264 brouard 7683: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7684: } /* end cpt state*/
7685: } /* end covariate */
1.296 brouard 7686: } /* End if prevbcast */
1.218 brouard 7687:
1.223 brouard 7688: /* 8eme */
1.218 brouard 7689: if(prevfcast==1){
1.288 brouard 7690: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7691:
1.237 brouard 7692: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7693: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7694: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7695: continue;
1.211 brouard 7696: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7697: strcpy(gplotlabel,"(");
1.288 brouard 7698: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7699: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7700: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7701: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7702: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7703: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7704: vlv= nbcode[Tvaraff[k]][lv];
7705: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7706: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7707: }
1.237 brouard 7708: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7709: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7710: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7711: }
1.264 brouard 7712: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7713: fprintf(ficgp,"\n#\n");
7714: if(invalidvarcomb[k1]){
7715: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7716: continue;
7717: }
7718:
7719: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7720: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7721: 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 7722: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7723: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7724:
7725: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7726: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7727: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7728: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7729: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7730: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7731: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7732: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7733: if(i==istart){
1.227 brouard 7734: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7735: }else{
7736: fprintf(ficgp,",\\\n '' ");
7737: }
7738: if(cptcoveff ==0){ /* No covariate */
7739: ioffset=2; /* Age is in 2 */
7740: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7741: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7742: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7743: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7744: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7745: if(i==nlstate+1){
1.270 brouard 7746: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7747: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7748: fprintf(ficgp,",\\\n '' ");
7749: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7750: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7751: offyear, \
1.268 brouard 7752: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7753: }else
1.227 brouard 7754: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7755: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7756: }else{ /* more than 2 covariates */
1.270 brouard 7757: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7758: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7759: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7760: iyearc=ioffset-1;
7761: iagec=ioffset;
1.227 brouard 7762: fprintf(ficgp," u %d:(",ioffset);
7763: kl=0;
7764: strcpy(gplotcondition,"(");
7765: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7766: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7767: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7768: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7769: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7770: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7771: kl++;
7772: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7773: kl++;
7774: if(k <cptcoveff && cptcoveff>1)
7775: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7776: }
7777: strcpy(gplotcondition+strlen(gplotcondition),")");
7778: /* 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 *\/ */
7779: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7780: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7781: /* '' 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*/
7782: if(i==nlstate+1){
1.270 brouard 7783: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7784: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7785: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7786: fprintf(ficgp," u %d:(",iagec);
7787: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7788: iyearc, iagec, offyear, \
7789: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7790: /* '' 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 7791: }else{
7792: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7793: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7794: }
7795: } /* end if covariate */
7796: } /* nlstate */
1.264 brouard 7797: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7798: } /* end cpt state*/
7799: } /* end covariate */
7800: } /* End if prevfcast */
1.227 brouard 7801:
1.296 brouard 7802: if(prevbcast==1){
1.268 brouard 7803: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7804:
7805: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7806: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7807: if(m != 1 && TKresult[nres]!= k1)
7808: continue;
7809: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7810: strcpy(gplotlabel,"(");
7811: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7812: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7813: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7814: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7815: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7816: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7817: vlv= nbcode[Tvaraff[k]][lv];
7818: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7819: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7820: }
7821: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7822: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7823: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7824: }
7825: strcpy(gplotlabel+strlen(gplotlabel),")");
7826: fprintf(ficgp,"\n#\n");
7827: if(invalidvarcomb[k1]){
7828: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7829: continue;
7830: }
7831:
7832: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7833: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7834: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7835: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7836: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7837:
7838: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7839: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7840: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7841: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7842: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7843: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7844: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7845: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7846: if(i==istart){
7847: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7848: }else{
7849: fprintf(ficgp,",\\\n '' ");
7850: }
7851: if(cptcoveff ==0){ /* No covariate */
7852: ioffset=2; /* Age is in 2 */
7853: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7854: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7855: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7856: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7857: fprintf(ficgp," u %d:(", ioffset);
7858: if(i==nlstate+1){
1.270 brouard 7859: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7860: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7861: fprintf(ficgp,",\\\n '' ");
7862: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7863: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7864: offbyear, \
7865: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7866: }else
7867: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7868: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7869: }else{ /* more than 2 covariates */
1.270 brouard 7870: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7871: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7872: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7873: iyearc=ioffset-1;
7874: iagec=ioffset;
1.268 brouard 7875: fprintf(ficgp," u %d:(",ioffset);
7876: kl=0;
7877: strcpy(gplotcondition,"(");
7878: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7879: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7880: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7881: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7882: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7883: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7884: kl++;
7885: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7886: kl++;
7887: if(k <cptcoveff && cptcoveff>1)
7888: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7889: }
7890: strcpy(gplotcondition+strlen(gplotcondition),")");
7891: /* 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 *\/ */
7892: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7893: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7894: /* '' 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*/
7895: if(i==nlstate+1){
1.270 brouard 7896: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7897: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7898: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7899: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7900: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7901: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7902: iyearc,iagec,offbyear, \
7903: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7904: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7905: }else{
7906: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7907: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7908: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7909: }
7910: } /* end if covariate */
7911: } /* nlstate */
7912: fprintf(ficgp,"\nset out; unset label;\n");
7913: } /* end cpt state*/
7914: } /* end covariate */
1.296 brouard 7915: } /* End if prevbcast */
1.268 brouard 7916:
1.227 brouard 7917:
1.238 brouard 7918: /* 9eme writing MLE parameters */
7919: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7920: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7921: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7922: for(k=1; k <=(nlstate+ndeath); k++){
7923: if (k != i) {
1.227 brouard 7924: fprintf(ficgp,"# current state %d\n",k);
7925: for(j=1; j <=ncovmodel; j++){
7926: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7927: jk++;
7928: }
7929: fprintf(ficgp,"\n");
1.126 brouard 7930: }
7931: }
1.223 brouard 7932: }
1.187 brouard 7933: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7934:
1.145 brouard 7935: /*goto avoid;*/
1.238 brouard 7936: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7937: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7938: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7939: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7940: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7941: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7942: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7943: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7944: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7945: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7946: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7947: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7948: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7949: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7950: fprintf(ficgp,"#\n");
1.223 brouard 7951: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7952: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7953: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7954: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7955: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7956: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7957: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7958: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7959: continue;
1.264 brouard 7960: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7961: strcpy(gplotlabel,"(");
1.276 brouard 7962: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7963: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7964: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7965: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7966: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7967: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7968: vlv= nbcode[Tvaraff[k]][lv];
7969: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7970: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7971: }
1.237 brouard 7972: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7973: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7974: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7975: }
1.264 brouard 7976: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7977: fprintf(ficgp,"\n#\n");
1.264 brouard 7978: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7979: fprintf(ficgp,"\nset key outside ");
7980: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7981: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7982: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7983: if (ng==1){
7984: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7985: fprintf(ficgp,"\nunset log y");
7986: }else if (ng==2){
7987: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7988: fprintf(ficgp,"\nset log y");
7989: }else if (ng==3){
7990: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7991: fprintf(ficgp,"\nset log y");
7992: }else
7993: fprintf(ficgp,"\nunset title ");
7994: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7995: i=1;
7996: for(k2=1; k2<=nlstate; k2++) {
7997: k3=i;
7998: for(k=1; k<=(nlstate+ndeath); k++) {
7999: if (k != k2){
8000: switch( ng) {
8001: case 1:
8002: if(nagesqr==0)
8003: fprintf(ficgp," p%d+p%d*x",i,i+1);
8004: else /* nagesqr =1 */
8005: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8006: break;
8007: case 2: /* ng=2 */
8008: if(nagesqr==0)
8009: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8010: else /* nagesqr =1 */
8011: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8012: break;
8013: case 3:
8014: if(nagesqr==0)
8015: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8016: else /* nagesqr =1 */
8017: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8018: break;
8019: }
8020: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8021: ijp=1; /* product no age */
8022: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8023: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8024: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8025: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8026: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8027: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8028: if(DummyV[j]==0){
8029: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8030: }else{ /* quantitative */
8031: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8032: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8033: }
8034: ij++;
1.237 brouard 8035: }
1.268 brouard 8036: }
8037: }else if(cptcovprod >0){
8038: if(j==Tprod[ijp]) { /* */
8039: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8040: if(ijp <=cptcovprod) { /* Product */
8041: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8042: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8043: /* 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)]); */
8044: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8045: }else{ /* Vn is dummy and Vm is quanti */
8046: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8047: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8048: }
8049: }else{ /* Vn*Vm Vn is quanti */
8050: if(DummyV[Tvard[ijp][2]]==0){
8051: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8052: }else{ /* Both quanti */
8053: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8054: }
1.237 brouard 8055: }
1.268 brouard 8056: ijp++;
1.237 brouard 8057: }
1.268 brouard 8058: } /* end Tprod */
1.237 brouard 8059: } else{ /* simple covariate */
1.264 brouard 8060: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8061: if(Dummy[j]==0){
8062: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8063: }else{ /* quantitative */
8064: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8065: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8066: }
1.237 brouard 8067: } /* end simple */
8068: } /* end j */
1.223 brouard 8069: }else{
8070: i=i-ncovmodel;
8071: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8072: fprintf(ficgp," (1.");
8073: }
1.227 brouard 8074:
1.223 brouard 8075: if(ng != 1){
8076: fprintf(ficgp,")/(1");
1.227 brouard 8077:
1.264 brouard 8078: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8079: if(nagesqr==0)
1.264 brouard 8080: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8081: else /* nagesqr =1 */
1.264 brouard 8082: 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 8083:
1.223 brouard 8084: ij=1;
8085: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8086: if(cptcovage >0){
8087: if((j-2)==Tage[ij]) { /* Bug valgrind */
8088: if(ij <=cptcovage) { /* Bug valgrind */
8089: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8090: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8091: ij++;
8092: }
8093: }
8094: }else
8095: 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 8096: }
8097: fprintf(ficgp,")");
8098: }
8099: fprintf(ficgp,")");
8100: if(ng ==2)
1.276 brouard 8101: 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 8102: else /* ng= 3 */
1.276 brouard 8103: 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 8104: }else{ /* end ng <> 1 */
8105: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8106: 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 8107: }
8108: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8109: fprintf(ficgp,",");
8110: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8111: fprintf(ficgp,",");
8112: i=i+ncovmodel;
8113: } /* end k */
8114: } /* end k2 */
1.276 brouard 8115: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8116: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8117: } /* end k1 */
1.223 brouard 8118: } /* end ng */
8119: /* avoid: */
8120: fflush(ficgp);
1.126 brouard 8121: } /* end gnuplot */
8122:
8123:
8124: /*************** Moving average **************/
1.219 brouard 8125: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8126: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8127:
1.222 brouard 8128: int i, cpt, cptcod;
8129: int modcovmax =1;
8130: int mobilavrange, mob;
8131: int iage=0;
1.288 brouard 8132: int firstA1=0, firstA2=0;
1.222 brouard 8133:
1.266 brouard 8134: double sum=0., sumr=0.;
1.222 brouard 8135: double age;
1.266 brouard 8136: double *sumnewp, *sumnewm, *sumnewmr;
8137: double *agemingood, *agemaxgood;
8138: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8139:
8140:
1.278 brouard 8141: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8142: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8143:
8144: sumnewp = vector(1,ncovcombmax);
8145: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8146: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8147: agemingood = vector(1,ncovcombmax);
1.266 brouard 8148: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8149: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8150: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8151:
8152: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8153: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8154: sumnewp[cptcod]=0.;
1.266 brouard 8155: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8156: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8157: }
8158: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8159:
1.266 brouard 8160: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8161: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8162: else mobilavrange=mobilav;
8163: for (age=bage; age<=fage; age++)
8164: for (i=1; i<=nlstate;i++)
8165: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8166: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8167: /* We keep the original values on the extreme ages bage, fage and for
8168: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8169: we use a 5 terms etc. until the borders are no more concerned.
8170: */
8171: for (mob=3;mob <=mobilavrange;mob=mob+2){
8172: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8173: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8174: sumnewm[cptcod]=0.;
8175: for (i=1; i<=nlstate;i++){
1.222 brouard 8176: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8177: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8178: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8179: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8180: }
8181: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8182: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8183: } /* end i */
8184: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8185: } /* end cptcod */
1.222 brouard 8186: }/* end age */
8187: }/* end mob */
1.266 brouard 8188: }else{
8189: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8190: return -1;
1.266 brouard 8191: }
8192:
8193: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8194: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8195: if(invalidvarcomb[cptcod]){
8196: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8197: continue;
8198: }
1.219 brouard 8199:
1.266 brouard 8200: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8201: sumnewm[cptcod]=0.;
8202: sumnewmr[cptcod]=0.;
8203: for (i=1; i<=nlstate;i++){
8204: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8205: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8206: }
8207: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8208: agemingoodr[cptcod]=age;
8209: }
8210: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8211: agemingood[cptcod]=age;
8212: }
8213: } /* age */
8214: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8215: sumnewm[cptcod]=0.;
1.266 brouard 8216: sumnewmr[cptcod]=0.;
1.222 brouard 8217: for (i=1; i<=nlstate;i++){
8218: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8219: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8220: }
8221: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8222: agemaxgoodr[cptcod]=age;
1.222 brouard 8223: }
8224: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8225: agemaxgood[cptcod]=age;
8226: }
8227: } /* age */
8228: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8229: /* but they will change */
1.288 brouard 8230: firstA1=0;firstA2=0;
1.266 brouard 8231: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8232: sumnewm[cptcod]=0.;
8233: sumnewmr[cptcod]=0.;
8234: for (i=1; i<=nlstate;i++){
8235: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8236: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8237: }
8238: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8239: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8240: agemaxgoodr[cptcod]=age; /* age min */
8241: for (i=1; i<=nlstate;i++)
8242: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8243: }else{ /* bad we change the value with the values of good ages */
8244: for (i=1; i<=nlstate;i++){
8245: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8246: } /* i */
8247: } /* end bad */
8248: }else{
8249: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8250: agemaxgood[cptcod]=age;
8251: }else{ /* bad we change the value with the values of good ages */
8252: for (i=1; i<=nlstate;i++){
8253: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8254: } /* i */
8255: } /* end bad */
8256: }/* end else */
8257: sum=0.;sumr=0.;
8258: for (i=1; i<=nlstate;i++){
8259: sum+=mobaverage[(int)age][i][cptcod];
8260: sumr+=probs[(int)age][i][cptcod];
8261: }
8262: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8263: if(!firstA1){
8264: firstA1=1;
8265: 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);
8266: }
8267: 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 8268: } /* end bad */
8269: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8270: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8271: if(!firstA2){
8272: firstA2=1;
8273: 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);
8274: }
8275: 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 8276: } /* end bad */
8277: }/* age */
1.266 brouard 8278:
8279: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8280: sumnewm[cptcod]=0.;
1.266 brouard 8281: sumnewmr[cptcod]=0.;
1.222 brouard 8282: for (i=1; i<=nlstate;i++){
8283: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8284: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8285: }
8286: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8287: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8288: agemingoodr[cptcod]=age;
8289: for (i=1; i<=nlstate;i++)
8290: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8291: }else{ /* bad we change the value with the values of good ages */
8292: for (i=1; i<=nlstate;i++){
8293: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8294: } /* i */
8295: } /* end bad */
8296: }else{
8297: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8298: agemingood[cptcod]=age;
8299: }else{ /* bad */
8300: for (i=1; i<=nlstate;i++){
8301: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8302: } /* i */
8303: } /* end bad */
8304: }/* end else */
8305: sum=0.;sumr=0.;
8306: for (i=1; i<=nlstate;i++){
8307: sum+=mobaverage[(int)age][i][cptcod];
8308: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8309: }
1.266 brouard 8310: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8311: 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 8312: } /* end bad */
8313: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8314: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8315: 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 8316: } /* end bad */
8317: }/* age */
1.266 brouard 8318:
1.222 brouard 8319:
8320: for (age=bage; age<=fage; age++){
1.235 brouard 8321: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8322: sumnewp[cptcod]=0.;
8323: sumnewm[cptcod]=0.;
8324: for (i=1; i<=nlstate;i++){
8325: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8326: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8327: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8328: }
8329: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8330: }
8331: /* printf("\n"); */
8332: /* } */
1.266 brouard 8333:
1.222 brouard 8334: /* brutal averaging */
1.266 brouard 8335: /* for (i=1; i<=nlstate;i++){ */
8336: /* for (age=1; age<=bage; age++){ */
8337: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8338: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8339: /* } */
8340: /* for (age=fage; age<=AGESUP; age++){ */
8341: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8342: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8343: /* } */
8344: /* } /\* end i status *\/ */
8345: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8346: /* for (age=1; age<=AGESUP; age++){ */
8347: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8348: /* mobaverage[(int)age][i][cptcod]=0.; */
8349: /* } */
8350: /* } */
1.222 brouard 8351: }/* end cptcod */
1.266 brouard 8352: free_vector(agemaxgoodr,1, ncovcombmax);
8353: free_vector(agemaxgood,1, ncovcombmax);
8354: free_vector(agemingood,1, ncovcombmax);
8355: free_vector(agemingoodr,1, ncovcombmax);
8356: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8357: free_vector(sumnewm,1, ncovcombmax);
8358: free_vector(sumnewp,1, ncovcombmax);
8359: return 0;
8360: }/* End movingaverage */
1.218 brouard 8361:
1.126 brouard 8362:
1.296 brouard 8363:
1.126 brouard 8364: /************** Forecasting ******************/
1.296 brouard 8365: /* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)*/
8366: void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
8367: /* dateintemean, mean date of interviews
8368: dateprojd, year, month, day of starting projection
8369: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8370: agemin, agemax range of age
8371: dateprev1 dateprev2 range of dates during which prevalence is computed
8372: */
1.296 brouard 8373: /* double anprojd, mprojd, jprojd; */
8374: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8375: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8376: double agec; /* generic age */
1.296 brouard 8377: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8378: double *popeffectif,*popcount;
8379: double ***p3mat;
1.218 brouard 8380: /* double ***mobaverage; */
1.126 brouard 8381: char fileresf[FILENAMELENGTH];
8382:
8383: agelim=AGESUP;
1.211 brouard 8384: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8385: in each health status at the date of interview (if between dateprev1 and dateprev2).
8386: We still use firstpass and lastpass as another selection.
8387: */
1.214 brouard 8388: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8389: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8390:
1.201 brouard 8391: strcpy(fileresf,"F_");
8392: strcat(fileresf,fileresu);
1.126 brouard 8393: if((ficresf=fopen(fileresf,"w"))==NULL) {
8394: printf("Problem with forecast resultfile: %s\n", fileresf);
8395: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8396: }
1.235 brouard 8397: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8398: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8399:
1.225 brouard 8400: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8401:
8402:
8403: stepsize=(int) (stepm+YEARM-1)/YEARM;
8404: if (stepm<=12) stepsize=1;
8405: if(estepm < stepm){
8406: printf ("Problem %d lower than %d\n",estepm, stepm);
8407: }
1.270 brouard 8408: else{
8409: hstepm=estepm;
8410: }
8411: if(estepm > stepm){ /* Yes every two year */
8412: stepsize=2;
8413: }
1.296 brouard 8414: hstepm=hstepm/stepm;
1.126 brouard 8415:
1.296 brouard 8416:
8417: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8418: /* fractional in yp1 *\/ */
8419: /* aintmean=yp; */
8420: /* yp2=modf((yp1*12),&yp); */
8421: /* mintmean=yp; */
8422: /* yp1=modf((yp2*30.5),&yp); */
8423: /* jintmean=yp; */
8424: /* if(jintmean==0) jintmean=1; */
8425: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8426:
1.296 brouard 8427:
8428: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8429: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8430: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8431: i1=pow(2,cptcoveff);
1.126 brouard 8432: if (cptcovn < 1){i1=1;}
8433:
1.296 brouard 8434: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8435:
8436: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8437:
1.126 brouard 8438: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8439: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8440: for(k=1; k<=i1;k++){
1.253 brouard 8441: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8442: continue;
1.227 brouard 8443: if(invalidvarcomb[k]){
8444: printf("\nCombination (%d) projection ignored because no cases \n",k);
8445: continue;
8446: }
8447: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8448: for(j=1;j<=cptcoveff;j++) {
8449: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8450: }
1.235 brouard 8451: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8452: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8453: }
1.227 brouard 8454: fprintf(ficresf," yearproj age");
8455: for(j=1; j<=nlstate+ndeath;j++){
8456: for(i=1; i<=nlstate;i++)
8457: fprintf(ficresf," p%d%d",i,j);
8458: fprintf(ficresf," wp.%d",j);
8459: }
1.296 brouard 8460: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8461: fprintf(ficresf,"\n");
1.296 brouard 8462: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8463: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8464: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8465: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8466: nhstepm = nhstepm/hstepm;
8467: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8468: oldm=oldms;savm=savms;
1.268 brouard 8469: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8470: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8471: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8472: for (h=0; h<=nhstepm; h++){
8473: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8474: break;
8475: }
8476: }
8477: fprintf(ficresf,"\n");
8478: for(j=1;j<=cptcoveff;j++)
8479: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8480: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8481:
8482: for(j=1; j<=nlstate+ndeath;j++) {
8483: ppij=0.;
8484: for(i=1; i<=nlstate;i++) {
1.278 brouard 8485: if (mobilav>=1)
8486: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8487: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8488: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8489: }
1.268 brouard 8490: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8491: } /* end i */
8492: fprintf(ficresf," %.3f", ppij);
8493: }/* end j */
1.227 brouard 8494: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8495: } /* end agec */
1.266 brouard 8496: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8497: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8498: } /* end yearp */
8499: } /* end k */
1.219 brouard 8500:
1.126 brouard 8501: fclose(ficresf);
1.215 brouard 8502: printf("End of Computing forecasting \n");
8503: fprintf(ficlog,"End of Computing forecasting\n");
8504:
1.126 brouard 8505: }
8506:
1.269 brouard 8507: /************** Back Forecasting ******************/
1.296 brouard 8508: /* 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){ */
8509: void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
8510: /* back1, year, month, day of starting backprojection
1.267 brouard 8511: agemin, agemax range of age
8512: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8513: anback2 year of end of backprojection (same day and month as back1).
8514: prevacurrent and prev are prevalences.
1.267 brouard 8515: */
8516: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8517: double agec; /* generic age */
1.302 brouard 8518: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8519: double *popeffectif,*popcount;
8520: double ***p3mat;
8521: /* double ***mobaverage; */
8522: char fileresfb[FILENAMELENGTH];
8523:
1.268 brouard 8524: agelim=AGEINF;
1.267 brouard 8525: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8526: in each health status at the date of interview (if between dateprev1 and dateprev2).
8527: We still use firstpass and lastpass as another selection.
8528: */
8529: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8530: /* firstpass, lastpass, stepm, weightopt, model); */
8531:
8532: /*Do we need to compute prevalence again?*/
8533:
8534: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8535:
8536: strcpy(fileresfb,"FB_");
8537: strcat(fileresfb,fileresu);
8538: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8539: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8540: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8541: }
8542: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8543: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8544:
8545: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8546:
8547:
8548: stepsize=(int) (stepm+YEARM-1)/YEARM;
8549: if (stepm<=12) stepsize=1;
8550: if(estepm < stepm){
8551: printf ("Problem %d lower than %d\n",estepm, stepm);
8552: }
1.270 brouard 8553: else{
8554: hstepm=estepm;
8555: }
8556: if(estepm >= stepm){ /* Yes every two year */
8557: stepsize=2;
8558: }
1.267 brouard 8559:
8560: hstepm=hstepm/stepm;
1.296 brouard 8561: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8562: /* fractional in yp1 *\/ */
8563: /* aintmean=yp; */
8564: /* yp2=modf((yp1*12),&yp); */
8565: /* mintmean=yp; */
8566: /* yp1=modf((yp2*30.5),&yp); */
8567: /* jintmean=yp; */
8568: /* if(jintmean==0) jintmean=1; */
8569: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8570:
8571: i1=pow(2,cptcoveff);
8572: if (cptcovn < 1){i1=1;}
8573:
1.296 brouard 8574: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8575: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8576:
8577: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8578:
8579: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8580: for(k=1; k<=i1;k++){
8581: if(i1 != 1 && TKresult[nres]!= k)
8582: continue;
8583: if(invalidvarcomb[k]){
8584: printf("\nCombination (%d) projection ignored because no cases \n",k);
8585: continue;
8586: }
1.268 brouard 8587: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8588: for(j=1;j<=cptcoveff;j++) {
8589: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8590: }
8591: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8592: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8593: }
8594: fprintf(ficresfb," yearbproj age");
8595: for(j=1; j<=nlstate+ndeath;j++){
8596: for(i=1; i<=nlstate;i++)
1.268 brouard 8597: fprintf(ficresfb," b%d%d",i,j);
8598: fprintf(ficresfb," b.%d",j);
1.267 brouard 8599: }
1.296 brouard 8600: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8601: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8602: fprintf(ficresfb,"\n");
1.296 brouard 8603: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8604: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8605: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8606: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8607: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8608: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8609: nhstepm = nhstepm/hstepm;
8610: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8611: oldm=oldms;savm=savms;
1.268 brouard 8612: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8613: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8614: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8615: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8616: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8617: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8618: for (h=0; h<=nhstepm; h++){
1.268 brouard 8619: if (h*hstepm/YEARM*stepm ==-yearp) {
8620: break;
8621: }
8622: }
8623: fprintf(ficresfb,"\n");
8624: for(j=1;j<=cptcoveff;j++)
8625: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8626: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8627: for(i=1; i<=nlstate+ndeath;i++) {
8628: ppij=0.;ppi=0.;
8629: for(j=1; j<=nlstate;j++) {
8630: /* if (mobilav==1) */
1.269 brouard 8631: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8632: ppi=ppi+prevacurrent[(int)agec][j][k];
8633: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8634: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8635: /* else { */
8636: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8637: /* } */
1.268 brouard 8638: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8639: } /* end j */
8640: if(ppi <0.99){
8641: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8642: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8643: }
8644: fprintf(ficresfb," %.3f", ppij);
8645: }/* end j */
1.267 brouard 8646: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8647: } /* end agec */
8648: } /* end yearp */
8649: } /* end k */
1.217 brouard 8650:
1.267 brouard 8651: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8652:
1.267 brouard 8653: fclose(ficresfb);
8654: printf("End of Computing Back forecasting \n");
8655: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8656:
1.267 brouard 8657: }
1.217 brouard 8658:
1.269 brouard 8659: /* Variance of prevalence limit: varprlim */
8660: 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 8661: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8662:
8663: char fileresvpl[FILENAMELENGTH];
8664: FILE *ficresvpl;
8665: double **oldm, **savm;
8666: double **varpl; /* Variances of prevalence limits by age */
8667: int i1, k, nres, j ;
8668:
8669: strcpy(fileresvpl,"VPL_");
8670: strcat(fileresvpl,fileresu);
8671: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8672: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8673: exit(0);
8674: }
1.288 brouard 8675: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8676: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8677:
8678: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8679: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8680:
8681: i1=pow(2,cptcoveff);
8682: if (cptcovn < 1){i1=1;}
8683:
8684: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8685: for(k=1; k<=i1;k++){
8686: if(i1 != 1 && TKresult[nres]!= k)
8687: continue;
8688: fprintf(ficresvpl,"\n#****** ");
8689: printf("\n#****** ");
8690: fprintf(ficlog,"\n#****** ");
8691: for(j=1;j<=cptcoveff;j++) {
8692: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8693: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8694: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8695: }
8696: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8697: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8698: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8699: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8700: }
8701: fprintf(ficresvpl,"******\n");
8702: printf("******\n");
8703: fprintf(ficlog,"******\n");
8704:
8705: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8706: oldm=oldms;savm=savms;
8707: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8708: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8709: /*}*/
8710: }
8711:
8712: fclose(ficresvpl);
1.288 brouard 8713: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8714: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8715:
8716: }
8717: /* Variance of back prevalence: varbprlim */
8718: 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){
8719: /*------- Variance of back (stable) prevalence------*/
8720:
8721: char fileresvbl[FILENAMELENGTH];
8722: FILE *ficresvbl;
8723:
8724: double **oldm, **savm;
8725: double **varbpl; /* Variances of back prevalence limits by age */
8726: int i1, k, nres, j ;
8727:
8728: strcpy(fileresvbl,"VBL_");
8729: strcat(fileresvbl,fileresu);
8730: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8731: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8732: exit(0);
8733: }
8734: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8735: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8736:
8737:
8738: i1=pow(2,cptcoveff);
8739: if (cptcovn < 1){i1=1;}
8740:
8741: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8742: for(k=1; k<=i1;k++){
8743: if(i1 != 1 && TKresult[nres]!= k)
8744: continue;
8745: fprintf(ficresvbl,"\n#****** ");
8746: printf("\n#****** ");
8747: fprintf(ficlog,"\n#****** ");
8748: for(j=1;j<=cptcoveff;j++) {
8749: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8750: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8751: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8752: }
8753: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8754: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8755: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8756: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8757: }
8758: fprintf(ficresvbl,"******\n");
8759: printf("******\n");
8760: fprintf(ficlog,"******\n");
8761:
8762: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8763: oldm=oldms;savm=savms;
8764:
8765: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8766: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8767: /*}*/
8768: }
8769:
8770: fclose(ficresvbl);
8771: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8772: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8773:
8774: } /* End of varbprlim */
8775:
1.126 brouard 8776: /************** Forecasting *****not tested NB*************/
1.227 brouard 8777: /* 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 8778:
1.227 brouard 8779: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8780: /* int *popage; */
8781: /* double calagedatem, agelim, kk1, kk2; */
8782: /* double *popeffectif,*popcount; */
8783: /* double ***p3mat,***tabpop,***tabpopprev; */
8784: /* /\* double ***mobaverage; *\/ */
8785: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8786:
1.227 brouard 8787: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8788: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8789: /* agelim=AGESUP; */
8790: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8791:
1.227 brouard 8792: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8793:
8794:
1.227 brouard 8795: /* strcpy(filerespop,"POP_"); */
8796: /* strcat(filerespop,fileresu); */
8797: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8798: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8799: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8800: /* } */
8801: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8802: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8803:
1.227 brouard 8804: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8805:
1.227 brouard 8806: /* /\* if (mobilav!=0) { *\/ */
8807: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8808: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8809: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8810: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8811: /* /\* } *\/ */
8812: /* /\* } *\/ */
1.126 brouard 8813:
1.227 brouard 8814: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8815: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8816:
1.227 brouard 8817: /* agelim=AGESUP; */
1.126 brouard 8818:
1.227 brouard 8819: /* hstepm=1; */
8820: /* hstepm=hstepm/stepm; */
1.218 brouard 8821:
1.227 brouard 8822: /* if (popforecast==1) { */
8823: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8824: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8825: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8826: /* } */
8827: /* popage=ivector(0,AGESUP); */
8828: /* popeffectif=vector(0,AGESUP); */
8829: /* popcount=vector(0,AGESUP); */
1.126 brouard 8830:
1.227 brouard 8831: /* i=1; */
8832: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8833:
1.227 brouard 8834: /* imx=i; */
8835: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8836: /* } */
1.218 brouard 8837:
1.227 brouard 8838: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8839: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8840: /* k=k+1; */
8841: /* fprintf(ficrespop,"\n#******"); */
8842: /* for(j=1;j<=cptcoveff;j++) { */
8843: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8844: /* } */
8845: /* fprintf(ficrespop,"******\n"); */
8846: /* fprintf(ficrespop,"# Age"); */
8847: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8848: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8849:
1.227 brouard 8850: /* for (cpt=0; cpt<=0;cpt++) { */
8851: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8852:
1.227 brouard 8853: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8854: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8855: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8856:
1.227 brouard 8857: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8858: /* oldm=oldms;savm=savms; */
8859: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8860:
1.227 brouard 8861: /* for (h=0; h<=nhstepm; h++){ */
8862: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8863: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8864: /* } */
8865: /* for(j=1; j<=nlstate+ndeath;j++) { */
8866: /* kk1=0.;kk2=0; */
8867: /* for(i=1; i<=nlstate;i++) { */
8868: /* if (mobilav==1) */
8869: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8870: /* else { */
8871: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8872: /* } */
8873: /* } */
8874: /* if (h==(int)(calagedatem+12*cpt)){ */
8875: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8876: /* /\*fprintf(ficrespop," %.3f", kk1); */
8877: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8878: /* } */
8879: /* } */
8880: /* for(i=1; i<=nlstate;i++){ */
8881: /* kk1=0.; */
8882: /* for(j=1; j<=nlstate;j++){ */
8883: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8884: /* } */
8885: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8886: /* } */
1.218 brouard 8887:
1.227 brouard 8888: /* if (h==(int)(calagedatem+12*cpt)) */
8889: /* for(j=1; j<=nlstate;j++) */
8890: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8891: /* } */
8892: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8893: /* } */
8894: /* } */
1.218 brouard 8895:
1.227 brouard 8896: /* /\******\/ */
1.218 brouard 8897:
1.227 brouard 8898: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8899: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8900: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8901: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8902: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8903:
1.227 brouard 8904: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8905: /* oldm=oldms;savm=savms; */
8906: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8907: /* for (h=0; h<=nhstepm; h++){ */
8908: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8909: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8910: /* } */
8911: /* for(j=1; j<=nlstate+ndeath;j++) { */
8912: /* kk1=0.;kk2=0; */
8913: /* for(i=1; i<=nlstate;i++) { */
8914: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8915: /* } */
8916: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8917: /* } */
8918: /* } */
8919: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8920: /* } */
8921: /* } */
8922: /* } */
8923: /* } */
1.218 brouard 8924:
1.227 brouard 8925: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8926:
1.227 brouard 8927: /* if (popforecast==1) { */
8928: /* free_ivector(popage,0,AGESUP); */
8929: /* free_vector(popeffectif,0,AGESUP); */
8930: /* free_vector(popcount,0,AGESUP); */
8931: /* } */
8932: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8933: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8934: /* fclose(ficrespop); */
8935: /* } /\* End of popforecast *\/ */
1.218 brouard 8936:
1.126 brouard 8937: int fileappend(FILE *fichier, char *optionfich)
8938: {
8939: if((fichier=fopen(optionfich,"a"))==NULL) {
8940: printf("Problem with file: %s\n", optionfich);
8941: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8942: return (0);
8943: }
8944: fflush(fichier);
8945: return (1);
8946: }
8947:
8948:
8949: /**************** function prwizard **********************/
8950: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8951: {
8952:
8953: /* Wizard to print covariance matrix template */
8954:
1.164 brouard 8955: char ca[32], cb[32];
8956: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8957: int numlinepar;
8958:
8959: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8960: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8961: for(i=1; i <=nlstate; i++){
8962: jj=0;
8963: for(j=1; j <=nlstate+ndeath; j++){
8964: if(j==i) continue;
8965: jj++;
8966: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8967: printf("%1d%1d",i,j);
8968: fprintf(ficparo,"%1d%1d",i,j);
8969: for(k=1; k<=ncovmodel;k++){
8970: /* printf(" %lf",param[i][j][k]); */
8971: /* fprintf(ficparo," %lf",param[i][j][k]); */
8972: printf(" 0.");
8973: fprintf(ficparo," 0.");
8974: }
8975: printf("\n");
8976: fprintf(ficparo,"\n");
8977: }
8978: }
8979: printf("# Scales (for hessian or gradient estimation)\n");
8980: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8981: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8982: for(i=1; i <=nlstate; i++){
8983: jj=0;
8984: for(j=1; j <=nlstate+ndeath; j++){
8985: if(j==i) continue;
8986: jj++;
8987: fprintf(ficparo,"%1d%1d",i,j);
8988: printf("%1d%1d",i,j);
8989: fflush(stdout);
8990: for(k=1; k<=ncovmodel;k++){
8991: /* printf(" %le",delti3[i][j][k]); */
8992: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8993: printf(" 0.");
8994: fprintf(ficparo," 0.");
8995: }
8996: numlinepar++;
8997: printf("\n");
8998: fprintf(ficparo,"\n");
8999: }
9000: }
9001: printf("# Covariance matrix\n");
9002: /* # 121 Var(a12)\n\ */
9003: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9004: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9005: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9006: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9007: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9008: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9009: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9010: fflush(stdout);
9011: fprintf(ficparo,"# Covariance matrix\n");
9012: /* # 121 Var(a12)\n\ */
9013: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9014: /* # ...\n\ */
9015: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9016:
9017: for(itimes=1;itimes<=2;itimes++){
9018: jj=0;
9019: for(i=1; i <=nlstate; i++){
9020: for(j=1; j <=nlstate+ndeath; j++){
9021: if(j==i) continue;
9022: for(k=1; k<=ncovmodel;k++){
9023: jj++;
9024: ca[0]= k+'a'-1;ca[1]='\0';
9025: if(itimes==1){
9026: printf("#%1d%1d%d",i,j,k);
9027: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9028: }else{
9029: printf("%1d%1d%d",i,j,k);
9030: fprintf(ficparo,"%1d%1d%d",i,j,k);
9031: /* printf(" %.5le",matcov[i][j]); */
9032: }
9033: ll=0;
9034: for(li=1;li <=nlstate; li++){
9035: for(lj=1;lj <=nlstate+ndeath; lj++){
9036: if(lj==li) continue;
9037: for(lk=1;lk<=ncovmodel;lk++){
9038: ll++;
9039: if(ll<=jj){
9040: cb[0]= lk +'a'-1;cb[1]='\0';
9041: if(ll<jj){
9042: if(itimes==1){
9043: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9044: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9045: }else{
9046: printf(" 0.");
9047: fprintf(ficparo," 0.");
9048: }
9049: }else{
9050: if(itimes==1){
9051: printf(" Var(%s%1d%1d)",ca,i,j);
9052: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9053: }else{
9054: printf(" 0.");
9055: fprintf(ficparo," 0.");
9056: }
9057: }
9058: }
9059: } /* end lk */
9060: } /* end lj */
9061: } /* end li */
9062: printf("\n");
9063: fprintf(ficparo,"\n");
9064: numlinepar++;
9065: } /* end k*/
9066: } /*end j */
9067: } /* end i */
9068: } /* end itimes */
9069:
9070: } /* end of prwizard */
9071: /******************* Gompertz Likelihood ******************************/
9072: double gompertz(double x[])
9073: {
1.302 brouard 9074: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9075: int i,n=0; /* n is the size of the sample */
9076:
1.220 brouard 9077: for (i=1;i<=imx ; i++) {
1.126 brouard 9078: sump=sump+weight[i];
9079: /* sump=sump+1;*/
9080: num=num+1;
9081: }
1.302 brouard 9082: L=0.0;
9083: /* agegomp=AGEGOMP; */
1.126 brouard 9084: /* for (i=0; i<=imx; i++)
9085: 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]);*/
9086:
1.302 brouard 9087: for (i=1;i<=imx ; i++) {
9088: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9089: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9090: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9091: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9092: * +
9093: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9094: */
9095: if (wav[i] > 1 || agedc[i] < AGESUP) {
9096: if (cens[i] == 1){
9097: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9098: } else if (cens[i] == 0){
1.126 brouard 9099: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9100: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9101: } else
9102: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9103: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9104: L=L+A*weight[i];
1.126 brouard 9105: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
1.302 brouard 9106: }
9107: }
1.126 brouard 9108:
1.302 brouard 9109: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9110:
9111: return -2*L*num/sump;
9112: }
9113:
1.136 brouard 9114: #ifdef GSL
9115: /******************* Gompertz_f Likelihood ******************************/
9116: double gompertz_f(const gsl_vector *v, void *params)
9117: {
1.302 brouard 9118: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9119: double *x= (double *) v->data;
9120: int i,n=0; /* n is the size of the sample */
9121:
9122: for (i=0;i<=imx-1 ; i++) {
9123: sump=sump+weight[i];
9124: /* sump=sump+1;*/
9125: num=num+1;
9126: }
9127:
9128:
9129: /* for (i=0; i<=imx; i++)
9130: 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]);*/
9131: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9132: for (i=1;i<=imx ; i++)
9133: {
9134: if (cens[i] == 1 && wav[i]>1)
9135: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9136:
9137: if (cens[i] == 0 && wav[i]>1)
9138: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9139: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9140:
9141: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9142: if (wav[i] > 1 ) { /* ??? */
9143: LL=LL+A*weight[i];
9144: /* 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]);*/
9145: }
9146: }
9147:
9148: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9149: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9150:
9151: return -2*LL*num/sump;
9152: }
9153: #endif
9154:
1.126 brouard 9155: /******************* Printing html file ***********/
1.201 brouard 9156: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9157: int lastpass, int stepm, int weightopt, char model[],\
9158: int imx, double p[],double **matcov,double agemortsup){
9159: int i,k;
9160:
9161: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9162: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9163: for (i=1;i<=2;i++)
9164: 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 9165: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9166: fprintf(fichtm,"</ul>");
9167:
9168: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9169:
9170: 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>");
9171:
9172: for (k=agegomp;k<(agemortsup-2);k++)
9173: 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]);
9174:
9175:
9176: fflush(fichtm);
9177: }
9178:
9179: /******************* Gnuplot file **************/
1.201 brouard 9180: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9181:
9182: char dirfileres[132],optfileres[132];
1.164 brouard 9183:
1.126 brouard 9184: int ng;
9185:
9186:
9187: /*#ifdef windows */
9188: fprintf(ficgp,"cd \"%s\" \n",pathc);
9189: /*#endif */
9190:
9191:
9192: strcpy(dirfileres,optionfilefiname);
9193: strcpy(optfileres,"vpl");
1.199 brouard 9194: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9195: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9196: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9197: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9198: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9199:
9200: }
9201:
1.136 brouard 9202: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9203: {
1.126 brouard 9204:
1.136 brouard 9205: /*-------- data file ----------*/
9206: FILE *fic;
9207: char dummy[]=" ";
1.240 brouard 9208: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9209: int lstra;
1.136 brouard 9210: int linei, month, year,iout;
1.302 brouard 9211: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9212: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9213: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9214: char *stratrunc;
1.223 brouard 9215:
1.240 brouard 9216: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9217: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9218:
1.240 brouard 9219: for(v=1; v <=ncovcol;v++){
9220: DummyV[v]=0;
9221: FixedV[v]=0;
9222: }
9223: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9224: DummyV[v]=1;
9225: FixedV[v]=0;
9226: }
9227: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9228: DummyV[v]=0;
9229: FixedV[v]=1;
9230: }
9231: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9232: DummyV[v]=1;
9233: FixedV[v]=1;
9234: }
9235: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9236: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9237: 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]);
9238: }
1.126 brouard 9239:
1.136 brouard 9240: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9241: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9242: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9243: }
1.126 brouard 9244:
1.302 brouard 9245: /* Is it a BOM UTF-8 Windows file? */
9246: /* First data line */
9247: linei=0;
9248: while(fgets(line, MAXLINE, fic)) {
9249: noffset=0;
9250: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9251: {
9252: noffset=noffset+3;
9253: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9254: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9255: fflush(ficlog); return 1;
9256: }
9257: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9258: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9259: {
9260: noffset=noffset+2;
1.304 brouard 9261: printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
9262: fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302 brouard 9263: fflush(ficlog); return 1;
9264: }
9265: else if( line[0] == 0 && line[1] == 0)
9266: {
9267: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9268: noffset=noffset+4;
1.304 brouard 9269: printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
9270: fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
1.302 brouard 9271: fflush(ficlog); return 1;
9272: }
9273: } else{
9274: ;/*printf(" Not a BOM file\n");*/
9275: }
9276: /* If line starts with a # it is a comment */
9277: if (line[noffset] == '#') {
9278: linei=linei+1;
9279: break;
9280: }else{
9281: break;
9282: }
9283: }
9284: fclose(fic);
9285: if((fic=fopen(datafile,"r"))==NULL) {
9286: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9287: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9288: }
9289: /* Not a Bom file */
9290:
1.136 brouard 9291: i=1;
9292: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9293: linei=linei+1;
9294: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9295: if(line[j] == '\t')
9296: line[j] = ' ';
9297: }
9298: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9299: ;
9300: };
9301: line[j+1]=0; /* Trims blanks at end of line */
9302: if(line[0]=='#'){
9303: fprintf(ficlog,"Comment line\n%s\n",line);
9304: printf("Comment line\n%s\n",line);
9305: continue;
9306: }
9307: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9308: strcpy(line, linetmp);
1.223 brouard 9309:
9310: /* Loops on waves */
9311: for (j=maxwav;j>=1;j--){
9312: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9313: cutv(stra, strb, line, ' ');
9314: if(strb[0]=='.') { /* Missing value */
9315: lval=-1;
9316: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9317: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9318: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9319: 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);
9320: 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);
9321: return 1;
9322: }
9323: }else{
9324: errno=0;
9325: /* what_kind_of_number(strb); */
9326: dval=strtod(strb,&endptr);
9327: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9328: /* if(strb != endptr && *endptr == '\0') */
9329: /* dval=dlval; */
9330: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9331: if( strb[0]=='\0' || (*endptr != '\0')){
9332: 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);
9333: 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);
9334: return 1;
9335: }
9336: cotqvar[j][iv][i]=dval;
9337: cotvar[j][ntv+iv][i]=dval;
9338: }
9339: strcpy(line,stra);
1.223 brouard 9340: }/* end loop ntqv */
1.225 brouard 9341:
1.223 brouard 9342: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9343: cutv(stra, strb, line, ' ');
9344: if(strb[0]=='.') { /* Missing value */
9345: lval=-1;
9346: }else{
9347: errno=0;
9348: lval=strtol(strb,&endptr,10);
9349: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9350: if( strb[0]=='\0' || (*endptr != '\0')){
9351: 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);
9352: 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);
9353: return 1;
9354: }
9355: }
9356: if(lval <-1 || lval >1){
9357: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9358: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9359: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9360: For example, for multinomial values like 1, 2 and 3,\n \
9361: build V1=0 V2=0 for the reference value (1),\n \
9362: V1=1 V2=0 for (2) \n \
1.223 brouard 9363: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9364: output of IMaCh is often meaningless.\n \
1.223 brouard 9365: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9366: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9367: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9368: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9369: For example, for multinomial values like 1, 2 and 3,\n \
9370: build V1=0 V2=0 for the reference value (1),\n \
9371: V1=1 V2=0 for (2) \n \
1.223 brouard 9372: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9373: output of IMaCh is often meaningless.\n \
1.223 brouard 9374: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9375: return 1;
9376: }
9377: cotvar[j][iv][i]=(double)(lval);
9378: strcpy(line,stra);
1.223 brouard 9379: }/* end loop ntv */
1.225 brouard 9380:
1.223 brouard 9381: /* Statuses at wave */
1.137 brouard 9382: cutv(stra, strb, line, ' ');
1.223 brouard 9383: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9384: lval=-1;
1.136 brouard 9385: }else{
1.238 brouard 9386: errno=0;
9387: lval=strtol(strb,&endptr,10);
9388: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9389: if( strb[0]=='\0' || (*endptr != '\0')){
9390: 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);
9391: 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);
9392: return 1;
9393: }
1.136 brouard 9394: }
1.225 brouard 9395:
1.136 brouard 9396: s[j][i]=lval;
1.225 brouard 9397:
1.223 brouard 9398: /* Date of Interview */
1.136 brouard 9399: strcpy(line,stra);
9400: cutv(stra, strb,line,' ');
1.169 brouard 9401: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9402: }
1.169 brouard 9403: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9404: month=99;
9405: year=9999;
1.136 brouard 9406: }else{
1.225 brouard 9407: 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);
9408: 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);
9409: return 1;
1.136 brouard 9410: }
9411: anint[j][i]= (double) year;
1.302 brouard 9412: mint[j][i]= (double)month;
9413: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9414: /* printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
9415: /* fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
9416: /* } */
1.136 brouard 9417: strcpy(line,stra);
1.223 brouard 9418: } /* End loop on waves */
1.225 brouard 9419:
1.223 brouard 9420: /* Date of death */
1.136 brouard 9421: cutv(stra, strb,line,' ');
1.169 brouard 9422: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9423: }
1.169 brouard 9424: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9425: month=99;
9426: year=9999;
9427: }else{
1.141 brouard 9428: 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 9429: 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);
9430: return 1;
1.136 brouard 9431: }
9432: andc[i]=(double) year;
9433: moisdc[i]=(double) month;
9434: strcpy(line,stra);
9435:
1.223 brouard 9436: /* Date of birth */
1.136 brouard 9437: cutv(stra, strb,line,' ');
1.169 brouard 9438: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9439: }
1.169 brouard 9440: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9441: month=99;
9442: year=9999;
9443: }else{
1.141 brouard 9444: 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);
9445: 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 9446: return 1;
1.136 brouard 9447: }
9448: if (year==9999) {
1.141 brouard 9449: 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);
9450: 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 9451: return 1;
9452:
1.136 brouard 9453: }
9454: annais[i]=(double)(year);
1.302 brouard 9455: moisnais[i]=(double)(month);
9456: for (j=1;j<=maxwav;j++){
9457: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9458: printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
9459: fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
9460: }
9461: }
9462:
1.136 brouard 9463: strcpy(line,stra);
1.225 brouard 9464:
1.223 brouard 9465: /* Sample weight */
1.136 brouard 9466: cutv(stra, strb,line,' ');
9467: errno=0;
9468: dval=strtod(strb,&endptr);
9469: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9470: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9471: 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 9472: fflush(ficlog);
9473: return 1;
9474: }
9475: weight[i]=dval;
9476: strcpy(line,stra);
1.225 brouard 9477:
1.223 brouard 9478: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9479: cutv(stra, strb, line, ' ');
9480: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9481: lval=-1;
1.223 brouard 9482: }else{
1.225 brouard 9483: errno=0;
9484: /* what_kind_of_number(strb); */
9485: dval=strtod(strb,&endptr);
9486: /* if(strb != endptr && *endptr == '\0') */
9487: /* dval=dlval; */
9488: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9489: if( strb[0]=='\0' || (*endptr != '\0')){
9490: 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);
9491: 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);
9492: return 1;
9493: }
9494: coqvar[iv][i]=dval;
1.226 brouard 9495: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9496: }
9497: strcpy(line,stra);
9498: }/* end loop nqv */
1.136 brouard 9499:
1.223 brouard 9500: /* Covariate values */
1.136 brouard 9501: for (j=ncovcol;j>=1;j--){
9502: cutv(stra, strb,line,' ');
1.223 brouard 9503: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9504: lval=-1;
1.136 brouard 9505: }else{
1.225 brouard 9506: errno=0;
9507: lval=strtol(strb,&endptr,10);
9508: if( strb[0]=='\0' || (*endptr != '\0')){
9509: 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);
9510: 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);
9511: return 1;
9512: }
1.136 brouard 9513: }
9514: if(lval <-1 || lval >1){
1.225 brouard 9515: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9516: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9517: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9518: For example, for multinomial values like 1, 2 and 3,\n \
9519: build V1=0 V2=0 for the reference value (1),\n \
9520: V1=1 V2=0 for (2) \n \
1.136 brouard 9521: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9522: output of IMaCh is often meaningless.\n \
1.136 brouard 9523: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9524: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9525: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9526: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9527: For example, for multinomial values like 1, 2 and 3,\n \
9528: build V1=0 V2=0 for the reference value (1),\n \
9529: V1=1 V2=0 for (2) \n \
1.136 brouard 9530: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9531: output of IMaCh is often meaningless.\n \
1.136 brouard 9532: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9533: return 1;
1.136 brouard 9534: }
9535: covar[j][i]=(double)(lval);
9536: strcpy(line,stra);
9537: }
9538: lstra=strlen(stra);
1.225 brouard 9539:
1.136 brouard 9540: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9541: stratrunc = &(stra[lstra-9]);
9542: num[i]=atol(stratrunc);
9543: }
9544: else
9545: num[i]=atol(stra);
9546: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9547: 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;}*/
9548:
9549: i=i+1;
9550: } /* End loop reading data */
1.225 brouard 9551:
1.136 brouard 9552: *imax=i-1; /* Number of individuals */
9553: fclose(fic);
1.225 brouard 9554:
1.136 brouard 9555: return (0);
1.164 brouard 9556: /* endread: */
1.225 brouard 9557: printf("Exiting readdata: ");
9558: fclose(fic);
9559: return (1);
1.223 brouard 9560: }
1.126 brouard 9561:
1.234 brouard 9562: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9563: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9564: while (*p2 == ' ')
1.234 brouard 9565: p2++;
9566: /* while ((*p1++ = *p2++) !=0) */
9567: /* ; */
9568: /* do */
9569: /* while (*p2 == ' ') */
9570: /* p2++; */
9571: /* while (*p1++ == *p2++); */
9572: *stri=p2;
1.145 brouard 9573: }
9574:
1.235 brouard 9575: int decoderesult ( char resultline[], int nres)
1.230 brouard 9576: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9577: {
1.235 brouard 9578: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9579: char resultsav[MAXLINE];
1.234 brouard 9580: int resultmodel[MAXLINE];
9581: int modelresult[MAXLINE];
1.230 brouard 9582: char stra[80], strb[80], strc[80], strd[80],stre[80];
9583:
1.234 brouard 9584: removefirstspace(&resultline);
1.233 brouard 9585: printf("decoderesult:%s\n",resultline);
1.230 brouard 9586:
9587: if (strstr(resultline,"v") !=0){
9588: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9589: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9590: return 1;
9591: }
9592: trimbb(resultsav, resultline);
9593: if (strlen(resultsav) >1){
9594: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9595: }
1.253 brouard 9596: if(j == 0){ /* Resultline but no = */
9597: TKresult[nres]=0; /* Combination for the nresult and the model */
9598: return (0);
9599: }
9600:
1.234 brouard 9601: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9602: 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);
9603: 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);
9604: }
9605: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9606: if(nbocc(resultsav,'=') >1){
9607: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9608: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9609: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9610: }else
9611: cutl(strc,strd,resultsav,'=');
1.230 brouard 9612: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9613:
1.230 brouard 9614: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9615: Tvarsel[k]=atoi(strc);
9616: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9617: /* cptcovsel++; */
9618: if (nbocc(stra,'=') >0)
9619: strcpy(resultsav,stra); /* and analyzes it */
9620: }
1.235 brouard 9621: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9622: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9623: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9624: match=0;
1.236 brouard 9625: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9626: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9627: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9628: match=1;
9629: break;
9630: }
9631: }
9632: if(match == 0){
9633: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9634: }
9635: }
9636: }
1.235 brouard 9637: /* Checking for missing or useless values in comparison of current model needs */
9638: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9639: match=0;
1.235 brouard 9640: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9641: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9642: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9643: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9644: ++match;
9645: }
9646: }
9647: }
9648: if(match == 0){
9649: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9650: }else if(match > 1){
9651: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9652: }
9653: }
1.235 brouard 9654:
1.234 brouard 9655: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9656: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9657: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9658: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9659: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9660: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9661: /* 1 0 0 0 */
9662: /* 2 1 0 0 */
9663: /* 3 0 1 0 */
9664: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9665: /* 5 0 0 1 */
9666: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9667: /* 7 0 1 1 */
9668: /* 8 1 1 1 */
1.237 brouard 9669: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9670: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9671: /* V5*age V5 known which value for nres? */
9672: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9673: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9674: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9675: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9676: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9677: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9678: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9679: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9680: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9681: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9682: k4++;;
9683: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9684: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9685: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9686: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9687: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9688: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9689: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9690: k4q++;;
9691: }
9692: }
1.234 brouard 9693:
1.235 brouard 9694: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9695: return (0);
9696: }
1.235 brouard 9697:
1.230 brouard 9698: int decodemodel( char model[], int lastobs)
9699: /**< This routine decodes the model and returns:
1.224 brouard 9700: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9701: * - nagesqr = 1 if age*age in the model, otherwise 0.
9702: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9703: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9704: * - cptcovage number of covariates with age*products =2
9705: * - cptcovs number of simple covariates
9706: * - 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
9707: * which is a new column after the 9 (ncovcol) variables.
9708: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9709: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9710: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9711: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9712: */
1.136 brouard 9713: {
1.238 brouard 9714: int i, j, k, ks, v;
1.227 brouard 9715: int j1, k1, k2, k3, k4;
1.136 brouard 9716: char modelsav[80];
1.145 brouard 9717: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9718: char *strpt;
1.136 brouard 9719:
1.145 brouard 9720: /*removespace(model);*/
1.136 brouard 9721: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9722: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9723: if (strstr(model,"AGE") !=0){
1.192 brouard 9724: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9725: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9726: return 1;
9727: }
1.141 brouard 9728: if (strstr(model,"v") !=0){
9729: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9730: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9731: return 1;
9732: }
1.187 brouard 9733: strcpy(modelsav,model);
9734: if ((strpt=strstr(model,"age*age")) !=0){
9735: printf(" strpt=%s, model=%s\n",strpt, model);
9736: if(strpt != model){
1.234 brouard 9737: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9738: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9739: corresponding column of parameters.\n",model);
1.234 brouard 9740: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9741: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9742: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9743: return 1;
1.225 brouard 9744: }
1.187 brouard 9745: nagesqr=1;
9746: if (strstr(model,"+age*age") !=0)
1.234 brouard 9747: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9748: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9749: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9750: else
1.234 brouard 9751: substrchaine(modelsav, model, "age*age");
1.187 brouard 9752: }else
9753: nagesqr=0;
9754: if (strlen(modelsav) >1){
9755: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9756: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9757: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9758: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9759: * cst, age and age*age
9760: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9761: /* including age products which are counted in cptcovage.
9762: * but the covariates which are products must be treated
9763: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9764: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9765: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9766:
9767:
1.187 brouard 9768: /* Design
9769: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9770: * < ncovcol=8 >
9771: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9772: * k= 1 2 3 4 5 6 7 8
9773: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9774: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9775: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9776: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9777: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9778: * Tage[++cptcovage]=k
9779: * if products, new covar are created after ncovcol with k1
9780: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9781: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9782: * 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
9783: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9784: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9785: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9786: * < ncovcol=8 >
9787: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9788: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9789: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9790: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9791: * p Tprod[1]@2={ 6, 5}
9792: *p Tvard[1][1]@4= {7, 8, 5, 6}
9793: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9794: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9795: *How to reorganize?
9796: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9797: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9798: * {2, 1, 4, 8, 5, 6, 3, 7}
9799: * Struct []
9800: */
1.225 brouard 9801:
1.187 brouard 9802: /* This loop fills the array Tvar from the string 'model'.*/
9803: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9804: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9805: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9806: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9807: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9808: /* k=1 Tvar[1]=2 (from V2) */
9809: /* k=5 Tvar[5] */
9810: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9811: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9812: /* } */
1.198 brouard 9813: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9814: /*
9815: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9816: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9817: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9818: }
1.187 brouard 9819: cptcovage=0;
9820: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9821: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9822: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9823: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9824: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9825: /*scanf("%d",i);*/
9826: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9827: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9828: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9829: /* covar is not filled and then is empty */
9830: cptcovprod--;
9831: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9832: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9833: Typevar[k]=1; /* 1 for age product */
9834: cptcovage++; /* Sums the number of covariates which include age as a product */
9835: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9836: /*printf("stre=%s ", stre);*/
9837: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9838: cptcovprod--;
9839: cutl(stre,strb,strc,'V');
9840: Tvar[k]=atoi(stre);
9841: Typevar[k]=1; /* 1 for age product */
9842: cptcovage++;
9843: Tage[cptcovage]=k;
9844: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9845: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9846: cptcovn++;
9847: cptcovprodnoage++;k1++;
9848: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9849: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9850: because this model-covariate is a construction we invent a new column
9851: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9852: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9853: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9854: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9855: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9856: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9857: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9858: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9859: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9860: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9861: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9862: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9863: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9864: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9865: for (i=1; i<=lastobs;i++){
9866: /* Computes the new covariate which is a product of
9867: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9868: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9869: }
9870: } /* End age is not in the model */
9871: } /* End if model includes a product */
9872: else { /* no more sum */
9873: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9874: /* scanf("%d",i);*/
9875: cutl(strd,strc,strb,'V');
9876: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9877: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9878: Tvar[k]=atoi(strd);
9879: Typevar[k]=0; /* 0 for simple covariates */
9880: }
9881: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9882: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9883: scanf("%d",i);*/
1.187 brouard 9884: } /* end of loop + on total covariates */
9885: } /* end if strlen(modelsave == 0) age*age might exist */
9886: } /* end if strlen(model == 0) */
1.136 brouard 9887:
9888: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9889: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9890:
1.136 brouard 9891: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9892: printf("cptcovprod=%d ", cptcovprod);
9893: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9894: scanf("%d ",i);*/
9895:
9896:
1.230 brouard 9897: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9898: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9899: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9900: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9901: k = 1 2 3 4 5 6 7 8 9
9902: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9903: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9904: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9905: Dummy[k] 1 0 0 0 3 1 1 2 3
9906: Tmodelind[combination of covar]=k;
1.225 brouard 9907: */
9908: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9909: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9910: /* 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 9911: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9912: printf("Model=%s\n\
9913: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9914: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9915: 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);
9916: fprintf(ficlog,"Model=%s\n\
9917: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9918: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9919: 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 9920: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9921: 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 */
9922: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9923: Fixed[k]= 0;
9924: Dummy[k]= 0;
1.225 brouard 9925: ncoveff++;
1.232 brouard 9926: ncovf++;
1.234 brouard 9927: nsd++;
9928: modell[k].maintype= FTYPE;
9929: TvarsD[nsd]=Tvar[k];
9930: TvarsDind[nsd]=k;
9931: TvarF[ncovf]=Tvar[k];
9932: TvarFind[ncovf]=k;
9933: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9934: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9935: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9936: Fixed[k]= 0;
9937: Dummy[k]= 0;
9938: ncoveff++;
9939: ncovf++;
9940: modell[k].maintype= FTYPE;
9941: TvarF[ncovf]=Tvar[k];
9942: TvarFind[ncovf]=k;
1.230 brouard 9943: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9944: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9945: }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 9946: Fixed[k]= 0;
9947: Dummy[k]= 1;
1.230 brouard 9948: nqfveff++;
1.234 brouard 9949: modell[k].maintype= FTYPE;
9950: modell[k].subtype= FQ;
9951: nsq++;
9952: TvarsQ[nsq]=Tvar[k];
9953: TvarsQind[nsq]=k;
1.232 brouard 9954: ncovf++;
1.234 brouard 9955: TvarF[ncovf]=Tvar[k];
9956: TvarFind[ncovf]=k;
1.231 brouard 9957: 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 9958: 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 9959: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9960: Fixed[k]= 1;
9961: Dummy[k]= 0;
1.225 brouard 9962: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9963: modell[k].maintype= VTYPE;
9964: modell[k].subtype= VD;
9965: nsd++;
9966: TvarsD[nsd]=Tvar[k];
9967: TvarsDind[nsd]=k;
9968: ncovv++; /* Only simple time varying variables */
9969: TvarV[ncovv]=Tvar[k];
1.242 brouard 9970: 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 9971: 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 */
9972: 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 9973: 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);
9974: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9975: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9976: Fixed[k]= 1;
9977: Dummy[k]= 1;
9978: nqtveff++;
9979: modell[k].maintype= VTYPE;
9980: modell[k].subtype= VQ;
9981: ncovv++; /* Only simple time varying variables */
9982: nsq++;
9983: TvarsQ[nsq]=Tvar[k];
9984: TvarsQind[nsq]=k;
9985: TvarV[ncovv]=Tvar[k];
1.242 brouard 9986: 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 9987: 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 */
9988: 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 9989: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9990: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9991: 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 9992: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9993: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9994: ncova++;
9995: TvarA[ncova]=Tvar[k];
9996: TvarAind[ncova]=k;
1.231 brouard 9997: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9998: Fixed[k]= 2;
9999: Dummy[k]= 2;
10000: modell[k].maintype= ATYPE;
10001: modell[k].subtype= APFD;
10002: /* ncoveff++; */
1.227 brouard 10003: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10004: Fixed[k]= 2;
10005: Dummy[k]= 3;
10006: modell[k].maintype= ATYPE;
10007: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10008: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10009: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10010: Fixed[k]= 3;
10011: Dummy[k]= 2;
10012: modell[k].maintype= ATYPE;
10013: modell[k].subtype= APVD; /* Product age * varying dummy */
10014: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10015: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10016: Fixed[k]= 3;
10017: Dummy[k]= 3;
10018: modell[k].maintype= ATYPE;
10019: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10020: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10021: }
10022: }else if (Typevar[k] == 2) { /* product without age */
10023: k1=Tposprod[k];
10024: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10025: if(Tvard[k1][2] <=ncovcol){
10026: Fixed[k]= 1;
10027: Dummy[k]= 0;
10028: modell[k].maintype= FTYPE;
10029: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10030: ncovf++; /* Fixed variables without age */
10031: TvarF[ncovf]=Tvar[k];
10032: TvarFind[ncovf]=k;
10033: }else if(Tvard[k1][2] <=ncovcol+nqv){
10034: Fixed[k]= 0; /* or 2 ?*/
10035: Dummy[k]= 1;
10036: modell[k].maintype= FTYPE;
10037: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10038: ncovf++; /* Varying variables without age */
10039: TvarF[ncovf]=Tvar[k];
10040: TvarFind[ncovf]=k;
10041: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10042: Fixed[k]= 1;
10043: Dummy[k]= 0;
10044: modell[k].maintype= VTYPE;
10045: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10046: ncovv++; /* Varying variables without age */
10047: TvarV[ncovv]=Tvar[k];
10048: TvarVind[ncovv]=k;
10049: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10050: Fixed[k]= 1;
10051: Dummy[k]= 1;
10052: modell[k].maintype= VTYPE;
10053: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10054: ncovv++; /* Varying variables without age */
10055: TvarV[ncovv]=Tvar[k];
10056: TvarVind[ncovv]=k;
10057: }
1.227 brouard 10058: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10059: if(Tvard[k1][2] <=ncovcol){
10060: Fixed[k]= 0; /* or 2 ?*/
10061: Dummy[k]= 1;
10062: modell[k].maintype= FTYPE;
10063: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10064: ncovf++; /* Fixed variables without age */
10065: TvarF[ncovf]=Tvar[k];
10066: TvarFind[ncovf]=k;
10067: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10068: Fixed[k]= 1;
10069: Dummy[k]= 1;
10070: modell[k].maintype= VTYPE;
10071: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10072: ncovv++; /* Varying variables without age */
10073: TvarV[ncovv]=Tvar[k];
10074: TvarVind[ncovv]=k;
10075: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10076: Fixed[k]= 1;
10077: Dummy[k]= 1;
10078: modell[k].maintype= VTYPE;
10079: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10080: ncovv++; /* Varying variables without age */
10081: TvarV[ncovv]=Tvar[k];
10082: TvarVind[ncovv]=k;
10083: ncovv++; /* Varying variables without age */
10084: TvarV[ncovv]=Tvar[k];
10085: TvarVind[ncovv]=k;
10086: }
1.227 brouard 10087: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10088: if(Tvard[k1][2] <=ncovcol){
10089: Fixed[k]= 1;
10090: Dummy[k]= 1;
10091: modell[k].maintype= VTYPE;
10092: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10093: ncovv++; /* Varying variables without age */
10094: TvarV[ncovv]=Tvar[k];
10095: TvarVind[ncovv]=k;
10096: }else if(Tvard[k1][2] <=ncovcol+nqv){
10097: Fixed[k]= 1;
10098: Dummy[k]= 1;
10099: modell[k].maintype= VTYPE;
10100: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10101: ncovv++; /* Varying variables without age */
10102: TvarV[ncovv]=Tvar[k];
10103: TvarVind[ncovv]=k;
10104: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10105: Fixed[k]= 1;
10106: Dummy[k]= 0;
10107: modell[k].maintype= VTYPE;
10108: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10109: ncovv++; /* Varying variables without age */
10110: TvarV[ncovv]=Tvar[k];
10111: TvarVind[ncovv]=k;
10112: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10113: Fixed[k]= 1;
10114: Dummy[k]= 1;
10115: modell[k].maintype= VTYPE;
10116: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10117: ncovv++; /* Varying variables without age */
10118: TvarV[ncovv]=Tvar[k];
10119: TvarVind[ncovv]=k;
10120: }
1.227 brouard 10121: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10122: if(Tvard[k1][2] <=ncovcol){
10123: Fixed[k]= 1;
10124: Dummy[k]= 1;
10125: modell[k].maintype= VTYPE;
10126: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10127: ncovv++; /* Varying variables without age */
10128: TvarV[ncovv]=Tvar[k];
10129: TvarVind[ncovv]=k;
10130: }else if(Tvard[k1][2] <=ncovcol+nqv){
10131: Fixed[k]= 1;
10132: Dummy[k]= 1;
10133: modell[k].maintype= VTYPE;
10134: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10135: ncovv++; /* Varying variables without age */
10136: TvarV[ncovv]=Tvar[k];
10137: TvarVind[ncovv]=k;
10138: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10139: Fixed[k]= 1;
10140: Dummy[k]= 1;
10141: modell[k].maintype= VTYPE;
10142: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10143: ncovv++; /* Varying variables without age */
10144: TvarV[ncovv]=Tvar[k];
10145: TvarVind[ncovv]=k;
10146: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10147: Fixed[k]= 1;
10148: Dummy[k]= 1;
10149: modell[k].maintype= VTYPE;
10150: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10151: ncovv++; /* Varying variables without age */
10152: TvarV[ncovv]=Tvar[k];
10153: TvarVind[ncovv]=k;
10154: }
1.227 brouard 10155: }else{
1.240 brouard 10156: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10157: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10158: } /*end k1*/
1.225 brouard 10159: }else{
1.226 brouard 10160: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10161: 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 10162: }
1.227 brouard 10163: 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 10164: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10165: 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]);
10166: }
10167: /* Searching for doublons in the model */
10168: for(k1=1; k1<= cptcovt;k1++){
10169: for(k2=1; k2 <k1;k2++){
1.285 brouard 10170: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10171: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10172: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10173: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10174: 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]);
10175: 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 10176: return(1);
10177: }
10178: }else if (Typevar[k1] ==2){
10179: k3=Tposprod[k1];
10180: k4=Tposprod[k2];
10181: 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])) ){
10182: 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]]);
10183: 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);
10184: return(1);
10185: }
10186: }
1.227 brouard 10187: }
10188: }
1.225 brouard 10189: }
10190: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10191: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10192: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10193: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10194: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10195: /*endread:*/
1.225 brouard 10196: printf("Exiting decodemodel: ");
10197: return (1);
1.136 brouard 10198: }
10199:
1.169 brouard 10200: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10201: {/* Check ages at death */
1.136 brouard 10202: int i, m;
1.218 brouard 10203: int firstone=0;
10204:
1.136 brouard 10205: for (i=1; i<=imx; i++) {
10206: for(m=2; (m<= maxwav); m++) {
10207: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10208: anint[m][i]=9999;
1.216 brouard 10209: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10210: s[m][i]=-1;
1.136 brouard 10211: }
10212: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10213: *nberr = *nberr + 1;
1.218 brouard 10214: if(firstone == 0){
10215: firstone=1;
1.260 brouard 10216: 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 10217: }
1.262 brouard 10218: 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 10219: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10220: }
10221: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10222: (*nberr)++;
1.259 brouard 10223: 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 10224: 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 10225: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10226: }
10227: }
10228: }
10229:
10230: for (i=1; i<=imx; i++) {
10231: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10232: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10233: 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 10234: if (s[m][i] >= nlstate+1) {
1.169 brouard 10235: if(agedc[i]>0){
10236: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10237: agev[m][i]=agedc[i];
1.214 brouard 10238: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10239: }else {
1.136 brouard 10240: if ((int)andc[i]!=9999){
10241: nbwarn++;
10242: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10243: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10244: agev[m][i]=-1;
10245: }
10246: }
1.169 brouard 10247: } /* agedc > 0 */
1.214 brouard 10248: } /* end if */
1.136 brouard 10249: else if(s[m][i] !=9){ /* Standard case, age in fractional
10250: years but with the precision of a month */
10251: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10252: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10253: agev[m][i]=1;
10254: else if(agev[m][i] < *agemin){
10255: *agemin=agev[m][i];
10256: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10257: }
10258: else if(agev[m][i] >*agemax){
10259: *agemax=agev[m][i];
1.156 brouard 10260: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10261: }
10262: /*agev[m][i]=anint[m][i]-annais[i];*/
10263: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10264: } /* en if 9*/
1.136 brouard 10265: else { /* =9 */
1.214 brouard 10266: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10267: agev[m][i]=1;
10268: s[m][i]=-1;
10269: }
10270: }
1.214 brouard 10271: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10272: agev[m][i]=1;
1.214 brouard 10273: else{
10274: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10275: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10276: agev[m][i]=0;
10277: }
10278: } /* End for lastpass */
10279: }
1.136 brouard 10280:
10281: for (i=1; i<=imx; i++) {
10282: for(m=firstpass; (m<=lastpass); m++){
10283: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10284: (*nberr)++;
1.136 brouard 10285: 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);
10286: 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);
10287: return 1;
10288: }
10289: }
10290: }
10291:
10292: /*for (i=1; i<=imx; i++){
10293: for (m=firstpass; (m<lastpass); m++){
10294: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10295: }
10296:
10297: }*/
10298:
10299:
1.139 brouard 10300: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10301: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10302:
10303: return (0);
1.164 brouard 10304: /* endread:*/
1.136 brouard 10305: printf("Exiting calandcheckages: ");
10306: return (1);
10307: }
10308:
1.172 brouard 10309: #if defined(_MSC_VER)
10310: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10311: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10312: //#include "stdafx.h"
10313: //#include <stdio.h>
10314: //#include <tchar.h>
10315: //#include <windows.h>
10316: //#include <iostream>
10317: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10318:
10319: LPFN_ISWOW64PROCESS fnIsWow64Process;
10320:
10321: BOOL IsWow64()
10322: {
10323: BOOL bIsWow64 = FALSE;
10324:
10325: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10326: // (HANDLE, PBOOL);
10327:
10328: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10329:
10330: HMODULE module = GetModuleHandle(_T("kernel32"));
10331: const char funcName[] = "IsWow64Process";
10332: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10333: GetProcAddress(module, funcName);
10334:
10335: if (NULL != fnIsWow64Process)
10336: {
10337: if (!fnIsWow64Process(GetCurrentProcess(),
10338: &bIsWow64))
10339: //throw std::exception("Unknown error");
10340: printf("Unknown error\n");
10341: }
10342: return bIsWow64 != FALSE;
10343: }
10344: #endif
1.177 brouard 10345:
1.191 brouard 10346: void syscompilerinfo(int logged)
1.292 brouard 10347: {
10348: #include <stdint.h>
10349:
10350: /* #include "syscompilerinfo.h"*/
1.185 brouard 10351: /* command line Intel compiler 32bit windows, XP compatible:*/
10352: /* /GS /W3 /Gy
10353: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10354: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10355: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10356: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10357: */
10358: /* 64 bits */
1.185 brouard 10359: /*
10360: /GS /W3 /Gy
10361: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10362: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10363: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10364: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10365: /* Optimization are useless and O3 is slower than O2 */
10366: /*
10367: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10368: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10369: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10370: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10371: */
1.186 brouard 10372: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10373: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10374: /PDB:"visual studio
10375: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10376: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10377: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10378: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10379: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10380: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10381: uiAccess='false'"
10382: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10383: /NOLOGO /TLBID:1
10384: */
1.292 brouard 10385:
10386:
1.177 brouard 10387: #if defined __INTEL_COMPILER
1.178 brouard 10388: #if defined(__GNUC__)
10389: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10390: #endif
1.177 brouard 10391: #elif defined(__GNUC__)
1.179 brouard 10392: #ifndef __APPLE__
1.174 brouard 10393: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10394: #endif
1.177 brouard 10395: struct utsname sysInfo;
1.178 brouard 10396: int cross = CROSS;
10397: if (cross){
10398: printf("Cross-");
1.191 brouard 10399: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10400: }
1.174 brouard 10401: #endif
10402:
1.191 brouard 10403: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10404: #if defined(__clang__)
1.191 brouard 10405: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10406: #endif
10407: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10408: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10409: #endif
10410: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10411: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10412: #endif
10413: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10414: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10415: #endif
10416: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10417: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10418: #endif
10419: #if defined(_MSC_VER)
1.191 brouard 10420: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10421: #endif
10422: #if defined(__PGI)
1.191 brouard 10423: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10424: #endif
10425: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10426: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10427: #endif
1.191 brouard 10428: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10429:
1.167 brouard 10430: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10431: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10432: // Windows (x64 and x86)
1.191 brouard 10433: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10434: #elif __unix__ // all unices, not all compilers
10435: // Unix
1.191 brouard 10436: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10437: #elif __linux__
10438: // linux
1.191 brouard 10439: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10440: #elif __APPLE__
1.174 brouard 10441: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10442: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10443: #endif
10444:
10445: /* __MINGW32__ */
10446: /* __CYGWIN__ */
10447: /* __MINGW64__ */
10448: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10449: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10450: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10451: /* _WIN64 // Defined for applications for Win64. */
10452: /* _M_X64 // Defined for compilations that target x64 processors. */
10453: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10454:
1.167 brouard 10455: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10456: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10457: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10458: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10459: #else
1.191 brouard 10460: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10461: #endif
10462:
1.169 brouard 10463: #if defined(__GNUC__)
10464: # if defined(__GNUC_PATCHLEVEL__)
10465: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10466: + __GNUC_MINOR__ * 100 \
10467: + __GNUC_PATCHLEVEL__)
10468: # else
10469: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10470: + __GNUC_MINOR__ * 100)
10471: # endif
1.174 brouard 10472: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10473: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10474:
10475: if (uname(&sysInfo) != -1) {
10476: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10477: 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 10478: }
10479: else
10480: perror("uname() error");
1.179 brouard 10481: //#ifndef __INTEL_COMPILER
10482: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10483: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10484: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10485: #endif
1.169 brouard 10486: #endif
1.172 brouard 10487:
1.286 brouard 10488: // void main ()
1.172 brouard 10489: // {
1.169 brouard 10490: #if defined(_MSC_VER)
1.174 brouard 10491: if (IsWow64()){
1.191 brouard 10492: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10493: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10494: }
10495: else{
1.191 brouard 10496: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10497: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10498: }
1.172 brouard 10499: // printf("\nPress Enter to continue...");
10500: // getchar();
10501: // }
10502:
1.169 brouard 10503: #endif
10504:
1.167 brouard 10505:
1.219 brouard 10506: }
1.136 brouard 10507:
1.219 brouard 10508: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10509: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10510: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10511: /* double ftolpl = 1.e-10; */
1.180 brouard 10512: double age, agebase, agelim;
1.203 brouard 10513: double tot;
1.180 brouard 10514:
1.202 brouard 10515: strcpy(filerespl,"PL_");
10516: strcat(filerespl,fileresu);
10517: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10518: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10519: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10520: }
1.288 brouard 10521: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10522: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10523: pstamp(ficrespl);
1.288 brouard 10524: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10525: fprintf(ficrespl,"#Age ");
10526: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10527: fprintf(ficrespl,"\n");
1.180 brouard 10528:
1.219 brouard 10529: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10530:
1.219 brouard 10531: agebase=ageminpar;
10532: agelim=agemaxpar;
1.180 brouard 10533:
1.227 brouard 10534: /* i1=pow(2,ncoveff); */
1.234 brouard 10535: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10536: if (cptcovn < 1){i1=1;}
1.180 brouard 10537:
1.238 brouard 10538: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10539: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10540: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10541: continue;
1.235 brouard 10542:
1.238 brouard 10543: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10544: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10545: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10546: /* k=k+1; */
10547: /* to clean */
10548: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10549: fprintf(ficrespl,"#******");
10550: printf("#******");
10551: fprintf(ficlog,"#******");
10552: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10553: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10554: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10555: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10556: }
10557: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10558: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10559: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10560: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10561: }
10562: fprintf(ficrespl,"******\n");
10563: printf("******\n");
10564: fprintf(ficlog,"******\n");
10565: if(invalidvarcomb[k]){
10566: printf("\nCombination (%d) ignored because no case \n",k);
10567: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10568: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10569: continue;
10570: }
1.219 brouard 10571:
1.238 brouard 10572: fprintf(ficrespl,"#Age ");
10573: for(j=1;j<=cptcoveff;j++) {
10574: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10575: }
10576: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10577: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10578:
1.238 brouard 10579: for (age=agebase; age<=agelim; age++){
10580: /* for (age=agebase; age<=agebase; age++){ */
10581: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10582: fprintf(ficrespl,"%.0f ",age );
10583: for(j=1;j<=cptcoveff;j++)
10584: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10585: tot=0.;
10586: for(i=1; i<=nlstate;i++){
10587: tot += prlim[i][i];
10588: fprintf(ficrespl," %.5f", prlim[i][i]);
10589: }
10590: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10591: } /* Age */
10592: /* was end of cptcod */
10593: } /* cptcov */
10594: } /* nres */
1.219 brouard 10595: return 0;
1.180 brouard 10596: }
10597:
1.218 brouard 10598: 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 10599: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10600:
10601: /* Computes the back prevalence limit for any combination of covariate values
10602: * at any age between ageminpar and agemaxpar
10603: */
1.235 brouard 10604: int i, j, k, i1, nres=0 ;
1.217 brouard 10605: /* double ftolpl = 1.e-10; */
10606: double age, agebase, agelim;
10607: double tot;
1.218 brouard 10608: /* double ***mobaverage; */
10609: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10610:
10611: strcpy(fileresplb,"PLB_");
10612: strcat(fileresplb,fileresu);
10613: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10614: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10615: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10616: }
1.288 brouard 10617: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10618: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10619: pstamp(ficresplb);
1.288 brouard 10620: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10621: fprintf(ficresplb,"#Age ");
10622: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10623: fprintf(ficresplb,"\n");
10624:
1.218 brouard 10625:
10626: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10627:
10628: agebase=ageminpar;
10629: agelim=agemaxpar;
10630:
10631:
1.227 brouard 10632: i1=pow(2,cptcoveff);
1.218 brouard 10633: if (cptcovn < 1){i1=1;}
1.227 brouard 10634:
1.238 brouard 10635: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10636: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10637: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10638: continue;
10639: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10640: fprintf(ficresplb,"#******");
10641: printf("#******");
10642: fprintf(ficlog,"#******");
10643: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10644: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10645: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10646: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10647: }
10648: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10649: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10650: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10651: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10652: }
10653: fprintf(ficresplb,"******\n");
10654: printf("******\n");
10655: fprintf(ficlog,"******\n");
10656: if(invalidvarcomb[k]){
10657: printf("\nCombination (%d) ignored because no cases \n",k);
10658: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10659: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10660: continue;
10661: }
1.218 brouard 10662:
1.238 brouard 10663: fprintf(ficresplb,"#Age ");
10664: for(j=1;j<=cptcoveff;j++) {
10665: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10666: }
10667: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10668: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10669:
10670:
1.238 brouard 10671: for (age=agebase; age<=agelim; age++){
10672: /* for (age=agebase; age<=agebase; age++){ */
10673: if(mobilavproj > 0){
10674: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10675: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10676: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10677: }else if (mobilavproj == 0){
10678: 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);
10679: 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);
10680: exit(1);
10681: }else{
10682: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10683: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10684: /* printf("TOTOT\n"); */
10685: /* exit(1); */
1.238 brouard 10686: }
10687: fprintf(ficresplb,"%.0f ",age );
10688: for(j=1;j<=cptcoveff;j++)
10689: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10690: tot=0.;
10691: for(i=1; i<=nlstate;i++){
10692: tot += bprlim[i][i];
10693: fprintf(ficresplb," %.5f", bprlim[i][i]);
10694: }
10695: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10696: } /* Age */
10697: /* was end of cptcod */
1.255 brouard 10698: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10699: } /* end of any combination */
10700: } /* end of nres */
1.218 brouard 10701: /* hBijx(p, bage, fage); */
10702: /* fclose(ficrespijb); */
10703:
10704: return 0;
1.217 brouard 10705: }
1.218 brouard 10706:
1.180 brouard 10707: int hPijx(double *p, int bage, int fage){
10708: /*------------- h Pij x at various ages ------------*/
10709:
10710: int stepsize;
10711: int agelim;
10712: int hstepm;
10713: int nhstepm;
1.235 brouard 10714: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10715:
10716: double agedeb;
10717: double ***p3mat;
10718:
1.201 brouard 10719: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10720: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10721: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10722: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10723: }
10724: printf("Computing pij: result on file '%s' \n", filerespij);
10725: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10726:
10727: stepsize=(int) (stepm+YEARM-1)/YEARM;
10728: /*if (stepm<=24) stepsize=2;*/
10729:
10730: agelim=AGESUP;
10731: hstepm=stepsize*YEARM; /* Every year of age */
10732: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10733:
1.180 brouard 10734: /* hstepm=1; aff par mois*/
10735: pstamp(ficrespij);
10736: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10737: i1= pow(2,cptcoveff);
1.218 brouard 10738: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10739: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10740: /* k=k+1; */
1.235 brouard 10741: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10742: for(k=1; k<=i1;k++){
1.253 brouard 10743: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10744: continue;
1.183 brouard 10745: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10746: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10747: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10748: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10749: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10750: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10751: }
1.183 brouard 10752: fprintf(ficrespij,"******\n");
10753:
10754: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10755: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10756: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10757:
10758: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10759:
1.183 brouard 10760: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10761: oldm=oldms;savm=savms;
1.235 brouard 10762: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10763: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10764: for(i=1; i<=nlstate;i++)
10765: for(j=1; j<=nlstate+ndeath;j++)
10766: fprintf(ficrespij," %1d-%1d",i,j);
10767: fprintf(ficrespij,"\n");
10768: for (h=0; h<=nhstepm; h++){
10769: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10770: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10771: for(i=1; i<=nlstate;i++)
10772: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10773: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10774: fprintf(ficrespij,"\n");
10775: }
1.183 brouard 10776: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10777: fprintf(ficrespij,"\n");
10778: }
1.180 brouard 10779: /*}*/
10780: }
1.218 brouard 10781: return 0;
1.180 brouard 10782: }
1.218 brouard 10783:
10784: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10785: /*------------- h Bij x at various ages ------------*/
10786:
10787: int stepsize;
1.218 brouard 10788: /* int agelim; */
10789: int ageminl;
1.217 brouard 10790: int hstepm;
10791: int nhstepm;
1.238 brouard 10792: int h, i, i1, j, k, nres;
1.218 brouard 10793:
1.217 brouard 10794: double agedeb;
10795: double ***p3mat;
1.218 brouard 10796:
10797: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10798: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10799: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10800: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10801: }
10802: printf("Computing pij back: result on file '%s' \n", filerespijb);
10803: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10804:
10805: stepsize=(int) (stepm+YEARM-1)/YEARM;
10806: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10807:
1.218 brouard 10808: /* agelim=AGESUP; */
1.289 brouard 10809: ageminl=AGEINF; /* was 30 */
1.218 brouard 10810: hstepm=stepsize*YEARM; /* Every year of age */
10811: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10812:
10813: /* hstepm=1; aff par mois*/
10814: pstamp(ficrespijb);
1.255 brouard 10815: 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 10816: i1= pow(2,cptcoveff);
1.218 brouard 10817: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10818: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10819: /* k=k+1; */
1.238 brouard 10820: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10821: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10822: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10823: continue;
10824: fprintf(ficrespijb,"\n#****** ");
10825: for(j=1;j<=cptcoveff;j++)
10826: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10827: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10828: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10829: }
10830: fprintf(ficrespijb,"******\n");
1.264 brouard 10831: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10832: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10833: continue;
10834: }
10835:
10836: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10837: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10838: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10839: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
10840: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10841:
10842: /* nhstepm=nhstepm*YEARM; aff par mois*/
10843:
1.266 brouard 10844: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10845: /* and memory limitations if stepm is small */
10846:
1.238 brouard 10847: /* oldm=oldms;savm=savms; */
10848: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10849: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10850: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10851: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10852: for(i=1; i<=nlstate;i++)
10853: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10854: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10855: fprintf(ficrespijb,"\n");
1.238 brouard 10856: for (h=0; h<=nhstepm; h++){
10857: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10858: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10859: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10860: for(i=1; i<=nlstate;i++)
10861: for(j=1; j<=nlstate+ndeath;j++)
10862: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10863: fprintf(ficrespijb,"\n");
10864: }
10865: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10866: fprintf(ficrespijb,"\n");
10867: } /* end age deb */
10868: } /* end combination */
10869: } /* end nres */
1.218 brouard 10870: return 0;
10871: } /* hBijx */
1.217 brouard 10872:
1.180 brouard 10873:
1.136 brouard 10874: /***********************************************/
10875: /**************** Main Program *****************/
10876: /***********************************************/
10877:
10878: int main(int argc, char *argv[])
10879: {
10880: #ifdef GSL
10881: const gsl_multimin_fminimizer_type *T;
10882: size_t iteri = 0, it;
10883: int rval = GSL_CONTINUE;
10884: int status = GSL_SUCCESS;
10885: double ssval;
10886: #endif
10887: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10888: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10889: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10890: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10891: int jj, ll, li, lj, lk;
1.136 brouard 10892: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10893: int num_filled;
1.136 brouard 10894: int itimes;
10895: int NDIM=2;
10896: int vpopbased=0;
1.235 brouard 10897: int nres=0;
1.258 brouard 10898: int endishere=0;
1.277 brouard 10899: int noffset=0;
1.274 brouard 10900: int ncurrv=0; /* Temporary variable */
10901:
1.164 brouard 10902: char ca[32], cb[32];
1.136 brouard 10903: /* FILE *fichtm; *//* Html File */
10904: /* FILE *ficgp;*/ /*Gnuplot File */
10905: struct stat info;
1.191 brouard 10906: double agedeb=0.;
1.194 brouard 10907:
10908: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10909: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10910:
1.165 brouard 10911: double fret;
1.191 brouard 10912: double dum=0.; /* Dummy variable */
1.136 brouard 10913: double ***p3mat;
1.218 brouard 10914: /* double ***mobaverage; */
1.164 brouard 10915:
10916: char line[MAXLINE];
1.197 brouard 10917: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10918:
1.234 brouard 10919: char modeltemp[MAXLINE];
1.230 brouard 10920: char resultline[MAXLINE];
10921:
1.136 brouard 10922: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10923: char *tok, *val; /* pathtot */
1.290 brouard 10924: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10925: int c, h , cpt, c2;
1.191 brouard 10926: int jl=0;
10927: int i1, j1, jk, stepsize=0;
1.194 brouard 10928: int count=0;
10929:
1.164 brouard 10930: int *tab;
1.136 brouard 10931: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10932: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10933: /* double anprojf, mprojf, jprojf; */
10934: /* double jintmean,mintmean,aintmean; */
10935: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10936: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10937: double yrfproj= 10.0; /* Number of years of forward projections */
10938: double yrbproj= 10.0; /* Number of years of backward projections */
10939: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10940: int mobilav=0,popforecast=0;
1.191 brouard 10941: int hstepm=0, nhstepm=0;
1.136 brouard 10942: int agemortsup;
10943: float sumlpop=0.;
10944: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10945: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10946:
1.191 brouard 10947: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10948: double ftolpl=FTOL;
10949: double **prlim;
1.217 brouard 10950: double **bprlim;
1.136 brouard 10951: double ***param; /* Matrix of parameters */
1.251 brouard 10952: double ***paramstart; /* Matrix of starting parameter values */
10953: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10954: double **matcov; /* Matrix of covariance */
1.203 brouard 10955: double **hess; /* Hessian matrix */
1.136 brouard 10956: double ***delti3; /* Scale */
10957: double *delti; /* Scale */
10958: double ***eij, ***vareij;
10959: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10960:
1.136 brouard 10961: double *epj, vepp;
1.164 brouard 10962:
1.273 brouard 10963: double dateprev1, dateprev2;
1.296 brouard 10964: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10965: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10966:
1.217 brouard 10967:
1.136 brouard 10968: double **ximort;
1.145 brouard 10969: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10970: int *dcwave;
10971:
1.164 brouard 10972: char z[1]="c";
1.136 brouard 10973:
10974: /*char *strt;*/
10975: char strtend[80];
1.126 brouard 10976:
1.164 brouard 10977:
1.126 brouard 10978: /* setlocale (LC_ALL, ""); */
10979: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10980: /* textdomain (PACKAGE); */
10981: /* setlocale (LC_CTYPE, ""); */
10982: /* setlocale (LC_MESSAGES, ""); */
10983:
10984: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10985: rstart_time = time(NULL);
10986: /* (void) gettimeofday(&start_time,&tzp);*/
10987: start_time = *localtime(&rstart_time);
1.126 brouard 10988: curr_time=start_time;
1.157 brouard 10989: /*tml = *localtime(&start_time.tm_sec);*/
10990: /* strcpy(strstart,asctime(&tml)); */
10991: strcpy(strstart,asctime(&start_time));
1.126 brouard 10992:
10993: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10994: /* tp.tm_sec = tp.tm_sec +86400; */
10995: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10996: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10997: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10998: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10999: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11000: /* strt=asctime(&tmg); */
11001: /* printf("Time(after) =%s",strstart); */
11002: /* (void) time (&time_value);
11003: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11004: * tm = *localtime(&time_value);
11005: * strstart=asctime(&tm);
11006: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11007: */
11008:
11009: nberr=0; /* Number of errors and warnings */
11010: nbwarn=0;
1.184 brouard 11011: #ifdef WIN32
11012: _getcwd(pathcd, size);
11013: #else
1.126 brouard 11014: getcwd(pathcd, size);
1.184 brouard 11015: #endif
1.191 brouard 11016: syscompilerinfo(0);
1.196 brouard 11017: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11018: if(argc <=1){
11019: printf("\nEnter the parameter file name: ");
1.205 brouard 11020: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11021: printf("ERROR Empty parameter file name\n");
11022: goto end;
11023: }
1.126 brouard 11024: i=strlen(pathr);
11025: if(pathr[i-1]=='\n')
11026: pathr[i-1]='\0';
1.156 brouard 11027: i=strlen(pathr);
1.205 brouard 11028: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11029: pathr[i-1]='\0';
1.205 brouard 11030: }
11031: i=strlen(pathr);
11032: if( i==0 ){
11033: printf("ERROR Empty parameter file name\n");
11034: goto end;
11035: }
11036: for (tok = pathr; tok != NULL; ){
1.126 brouard 11037: printf("Pathr |%s|\n",pathr);
11038: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11039: printf("val= |%s| pathr=%s\n",val,pathr);
11040: strcpy (pathtot, val);
11041: if(pathr[0] == '\0') break; /* Dirty */
11042: }
11043: }
1.281 brouard 11044: else if (argc<=2){
11045: strcpy(pathtot,argv[1]);
11046: }
1.126 brouard 11047: else{
11048: strcpy(pathtot,argv[1]);
1.281 brouard 11049: strcpy(z,argv[2]);
11050: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11051: }
11052: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11053: /*cygwin_split_path(pathtot,path,optionfile);
11054: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11055: /* cutv(path,optionfile,pathtot,'\\');*/
11056:
11057: /* Split argv[0], imach program to get pathimach */
11058: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11059: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11060: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11061: /* strcpy(pathimach,argv[0]); */
11062: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11063: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11064: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11065: #ifdef WIN32
11066: _chdir(path); /* Can be a relative path */
11067: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11068: #else
1.126 brouard 11069: chdir(path); /* Can be a relative path */
1.184 brouard 11070: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11071: #endif
11072: printf("Current directory %s!\n",pathcd);
1.126 brouard 11073: strcpy(command,"mkdir ");
11074: strcat(command,optionfilefiname);
11075: if((outcmd=system(command)) != 0){
1.169 brouard 11076: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11077: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11078: /* fclose(ficlog); */
11079: /* exit(1); */
11080: }
11081: /* if((imk=mkdir(optionfilefiname))<0){ */
11082: /* perror("mkdir"); */
11083: /* } */
11084:
11085: /*-------- arguments in the command line --------*/
11086:
1.186 brouard 11087: /* Main Log file */
1.126 brouard 11088: strcat(filelog, optionfilefiname);
11089: strcat(filelog,".log"); /* */
11090: if((ficlog=fopen(filelog,"w"))==NULL) {
11091: printf("Problem with logfile %s\n",filelog);
11092: goto end;
11093: }
11094: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11095: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11096: fprintf(ficlog,"\nEnter the parameter file name: \n");
11097: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11098: path=%s \n\
11099: optionfile=%s\n\
11100: optionfilext=%s\n\
1.156 brouard 11101: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11102:
1.197 brouard 11103: syscompilerinfo(1);
1.167 brouard 11104:
1.126 brouard 11105: printf("Local time (at start):%s",strstart);
11106: fprintf(ficlog,"Local time (at start): %s",strstart);
11107: fflush(ficlog);
11108: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11109: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11110:
11111: /* */
11112: strcpy(fileres,"r");
11113: strcat(fileres, optionfilefiname);
1.201 brouard 11114: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11115: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11116: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11117:
1.186 brouard 11118: /* Main ---------arguments file --------*/
1.126 brouard 11119:
11120: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11121: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11122: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11123: fflush(ficlog);
1.149 brouard 11124: /* goto end; */
11125: exit(70);
1.126 brouard 11126: }
11127:
11128: strcpy(filereso,"o");
1.201 brouard 11129: strcat(filereso,fileresu);
1.126 brouard 11130: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11131: printf("Problem with Output resultfile: %s\n", filereso);
11132: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11133: fflush(ficlog);
11134: goto end;
11135: }
1.278 brouard 11136: /*-------- Rewriting parameter file ----------*/
11137: strcpy(rfileres,"r"); /* "Rparameterfile */
11138: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11139: strcat(rfileres,"."); /* */
11140: strcat(rfileres,optionfilext); /* Other files have txt extension */
11141: if((ficres =fopen(rfileres,"w"))==NULL) {
11142: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11143: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11144: fflush(ficlog);
11145: goto end;
11146: }
11147: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11148:
1.278 brouard 11149:
1.126 brouard 11150: /* Reads comments: lines beginning with '#' */
11151: numlinepar=0;
1.277 brouard 11152: /* Is it a BOM UTF-8 Windows file? */
11153: /* First parameter line */
1.197 brouard 11154: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11155: noffset=0;
11156: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11157: {
11158: noffset=noffset+3;
11159: printf("# File is an UTF8 Bom.\n"); // 0xBF
11160: }
1.302 brouard 11161: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11162: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11163: {
11164: noffset=noffset+2;
11165: printf("# File is an UTF16BE BOM file\n");
11166: }
11167: else if( line[0] == 0 && line[1] == 0)
11168: {
11169: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11170: noffset=noffset+4;
11171: printf("# File is an UTF16BE BOM file\n");
11172: }
11173: } else{
11174: ;/*printf(" Not a BOM file\n");*/
11175: }
11176:
1.197 brouard 11177: /* If line starts with a # it is a comment */
1.277 brouard 11178: if (line[noffset] == '#') {
1.197 brouard 11179: numlinepar++;
11180: fputs(line,stdout);
11181: fputs(line,ficparo);
1.278 brouard 11182: fputs(line,ficres);
1.197 brouard 11183: fputs(line,ficlog);
11184: continue;
11185: }else
11186: break;
11187: }
11188: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11189: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11190: if (num_filled != 5) {
11191: printf("Should be 5 parameters\n");
1.283 brouard 11192: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11193: }
1.126 brouard 11194: numlinepar++;
1.197 brouard 11195: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11196: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11197: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11198: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11199: }
11200: /* Second parameter line */
11201: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11202: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11203: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11204: if (line[0] == '#') {
11205: numlinepar++;
1.283 brouard 11206: printf("%s",line);
11207: fprintf(ficres,"%s",line);
11208: fprintf(ficparo,"%s",line);
11209: fprintf(ficlog,"%s",line);
1.197 brouard 11210: continue;
11211: }else
11212: break;
11213: }
1.223 brouard 11214: 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", \
11215: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11216: if (num_filled != 11) {
11217: 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 11218: printf("but line=%s\n",line);
1.283 brouard 11219: 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");
11220: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11221: }
1.286 brouard 11222: if( lastpass > maxwav){
11223: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11224: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11225: fflush(ficlog);
11226: goto end;
11227: }
11228: 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 11229: 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 11230: 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 11231: 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 11232: }
1.203 brouard 11233: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11234: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11235: /* Third parameter line */
11236: while(fgets(line, MAXLINE, ficpar)) {
11237: /* If line starts with a # it is a comment */
11238: if (line[0] == '#') {
11239: numlinepar++;
1.283 brouard 11240: printf("%s",line);
11241: fprintf(ficres,"%s",line);
11242: fprintf(ficparo,"%s",line);
11243: fprintf(ficlog,"%s",line);
1.197 brouard 11244: continue;
11245: }else
11246: break;
11247: }
1.201 brouard 11248: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11249: if (num_filled != 1){
1.302 brouard 11250: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11251: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11252: model[0]='\0';
11253: goto end;
11254: }
11255: else{
11256: if (model[0]=='+'){
11257: for(i=1; i<=strlen(model);i++)
11258: modeltemp[i-1]=model[i];
1.201 brouard 11259: strcpy(model,modeltemp);
1.197 brouard 11260: }
11261: }
1.199 brouard 11262: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11263: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11264: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11265: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11266: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11267: }
11268: /* 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); */
11269: /* numlinepar=numlinepar+3; /\* In general *\/ */
11270: /* 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 11271: /* 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); */
11272: /* 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 11273: fflush(ficlog);
1.190 brouard 11274: /* if(model[0]=='#'|| model[0]== '\0'){ */
11275: if(model[0]=='#'){
1.279 brouard 11276: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11277: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11278: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11279: if(mle != -1){
1.279 brouard 11280: 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 11281: exit(1);
11282: }
11283: }
1.126 brouard 11284: while((c=getc(ficpar))=='#' && c!= EOF){
11285: ungetc(c,ficpar);
11286: fgets(line, MAXLINE, ficpar);
11287: numlinepar++;
1.195 brouard 11288: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11289: z[0]=line[1];
11290: }
11291: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11292: fputs(line, stdout);
11293: //puts(line);
1.126 brouard 11294: fputs(line,ficparo);
11295: fputs(line,ficlog);
11296: }
11297: ungetc(c,ficpar);
11298:
11299:
1.290 brouard 11300: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11301: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11302: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11303: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11304: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11305: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11306: v1+v2*age+v2*v3 makes cptcovn = 3
11307: */
11308: if (strlen(model)>1)
1.187 brouard 11309: 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 11310: else
1.187 brouard 11311: ncovmodel=2; /* Constant and age */
1.133 brouard 11312: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11313: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11314: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11315: 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);
11316: 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);
11317: fflush(stdout);
11318: fclose (ficlog);
11319: goto end;
11320: }
1.126 brouard 11321: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11322: delti=delti3[1][1];
11323: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11324: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11325: /* We could also provide initial parameters values giving by simple logistic regression
11326: * only one way, that is without matrix product. We will have nlstate maximizations */
11327: /* for(i=1;i<nlstate;i++){ */
11328: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11329: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11330: /* } */
1.126 brouard 11331: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11332: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11333: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11334: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11335: fclose (ficparo);
11336: fclose (ficlog);
11337: goto end;
11338: exit(0);
1.220 brouard 11339: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11340: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11341: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11342: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11343: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11344: matcov=matrix(1,npar,1,npar);
1.203 brouard 11345: hess=matrix(1,npar,1,npar);
1.220 brouard 11346: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11347: /* Read guessed parameters */
1.126 brouard 11348: /* Reads comments: lines beginning with '#' */
11349: while((c=getc(ficpar))=='#' && c!= EOF){
11350: ungetc(c,ficpar);
11351: fgets(line, MAXLINE, ficpar);
11352: numlinepar++;
1.141 brouard 11353: fputs(line,stdout);
1.126 brouard 11354: fputs(line,ficparo);
11355: fputs(line,ficlog);
11356: }
11357: ungetc(c,ficpar);
11358:
11359: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11360: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11361: for(i=1; i <=nlstate; i++){
1.234 brouard 11362: j=0;
1.126 brouard 11363: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11364: if(jj==i) continue;
11365: j++;
1.292 brouard 11366: while((c=getc(ficpar))=='#' && c!= EOF){
11367: ungetc(c,ficpar);
11368: fgets(line, MAXLINE, ficpar);
11369: numlinepar++;
11370: fputs(line,stdout);
11371: fputs(line,ficparo);
11372: fputs(line,ficlog);
11373: }
11374: ungetc(c,ficpar);
1.234 brouard 11375: fscanf(ficpar,"%1d%1d",&i1,&j1);
11376: if ((i1 != i) || (j1 != jj)){
11377: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11378: It might be a problem of design; if ncovcol and the model are correct\n \
11379: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11380: exit(1);
11381: }
11382: fprintf(ficparo,"%1d%1d",i1,j1);
11383: if(mle==1)
11384: printf("%1d%1d",i,jj);
11385: fprintf(ficlog,"%1d%1d",i,jj);
11386: for(k=1; k<=ncovmodel;k++){
11387: fscanf(ficpar," %lf",¶m[i][j][k]);
11388: if(mle==1){
11389: printf(" %lf",param[i][j][k]);
11390: fprintf(ficlog," %lf",param[i][j][k]);
11391: }
11392: else
11393: fprintf(ficlog," %lf",param[i][j][k]);
11394: fprintf(ficparo," %lf",param[i][j][k]);
11395: }
11396: fscanf(ficpar,"\n");
11397: numlinepar++;
11398: if(mle==1)
11399: printf("\n");
11400: fprintf(ficlog,"\n");
11401: fprintf(ficparo,"\n");
1.126 brouard 11402: }
11403: }
11404: fflush(ficlog);
1.234 brouard 11405:
1.251 brouard 11406: /* Reads parameters values */
1.126 brouard 11407: p=param[1][1];
1.251 brouard 11408: pstart=paramstart[1][1];
1.126 brouard 11409:
11410: /* Reads comments: lines beginning with '#' */
11411: while((c=getc(ficpar))=='#' && c!= EOF){
11412: ungetc(c,ficpar);
11413: fgets(line, MAXLINE, ficpar);
11414: numlinepar++;
1.141 brouard 11415: fputs(line,stdout);
1.126 brouard 11416: fputs(line,ficparo);
11417: fputs(line,ficlog);
11418: }
11419: ungetc(c,ficpar);
11420:
11421: for(i=1; i <=nlstate; i++){
11422: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11423: fscanf(ficpar,"%1d%1d",&i1,&j1);
11424: if ( (i1-i) * (j1-j) != 0){
11425: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11426: exit(1);
11427: }
11428: printf("%1d%1d",i,j);
11429: fprintf(ficparo,"%1d%1d",i1,j1);
11430: fprintf(ficlog,"%1d%1d",i1,j1);
11431: for(k=1; k<=ncovmodel;k++){
11432: fscanf(ficpar,"%le",&delti3[i][j][k]);
11433: printf(" %le",delti3[i][j][k]);
11434: fprintf(ficparo," %le",delti3[i][j][k]);
11435: fprintf(ficlog," %le",delti3[i][j][k]);
11436: }
11437: fscanf(ficpar,"\n");
11438: numlinepar++;
11439: printf("\n");
11440: fprintf(ficparo,"\n");
11441: fprintf(ficlog,"\n");
1.126 brouard 11442: }
11443: }
11444: fflush(ficlog);
1.234 brouard 11445:
1.145 brouard 11446: /* Reads covariance matrix */
1.126 brouard 11447: delti=delti3[1][1];
1.220 brouard 11448:
11449:
1.126 brouard 11450: /* 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 11451:
1.126 brouard 11452: /* Reads comments: lines beginning with '#' */
11453: while((c=getc(ficpar))=='#' && c!= EOF){
11454: ungetc(c,ficpar);
11455: fgets(line, MAXLINE, ficpar);
11456: numlinepar++;
1.141 brouard 11457: fputs(line,stdout);
1.126 brouard 11458: fputs(line,ficparo);
11459: fputs(line,ficlog);
11460: }
11461: ungetc(c,ficpar);
1.220 brouard 11462:
1.126 brouard 11463: matcov=matrix(1,npar,1,npar);
1.203 brouard 11464: hess=matrix(1,npar,1,npar);
1.131 brouard 11465: for(i=1; i <=npar; i++)
11466: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11467:
1.194 brouard 11468: /* Scans npar lines */
1.126 brouard 11469: for(i=1; i <=npar; i++){
1.226 brouard 11470: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11471: if(count != 3){
1.226 brouard 11472: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11473: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11474: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11475: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11476: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11477: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11478: exit(1);
1.220 brouard 11479: }else{
1.226 brouard 11480: if(mle==1)
11481: printf("%1d%1d%d",i1,j1,jk);
11482: }
11483: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11484: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11485: for(j=1; j <=i; j++){
1.226 brouard 11486: fscanf(ficpar," %le",&matcov[i][j]);
11487: if(mle==1){
11488: printf(" %.5le",matcov[i][j]);
11489: }
11490: fprintf(ficlog," %.5le",matcov[i][j]);
11491: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11492: }
11493: fscanf(ficpar,"\n");
11494: numlinepar++;
11495: if(mle==1)
1.220 brouard 11496: printf("\n");
1.126 brouard 11497: fprintf(ficlog,"\n");
11498: fprintf(ficparo,"\n");
11499: }
1.194 brouard 11500: /* End of read covariance matrix npar lines */
1.126 brouard 11501: for(i=1; i <=npar; i++)
11502: for(j=i+1;j<=npar;j++)
1.226 brouard 11503: matcov[i][j]=matcov[j][i];
1.126 brouard 11504:
11505: if(mle==1)
11506: printf("\n");
11507: fprintf(ficlog,"\n");
11508:
11509: fflush(ficlog);
11510:
11511: } /* End of mle != -3 */
1.218 brouard 11512:
1.186 brouard 11513: /* Main data
11514: */
1.290 brouard 11515: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11516: /* num=lvector(1,n); */
11517: /* moisnais=vector(1,n); */
11518: /* annais=vector(1,n); */
11519: /* moisdc=vector(1,n); */
11520: /* andc=vector(1,n); */
11521: /* weight=vector(1,n); */
11522: /* agedc=vector(1,n); */
11523: /* cod=ivector(1,n); */
11524: /* for(i=1;i<=n;i++){ */
11525: num=lvector(firstobs,lastobs);
11526: moisnais=vector(firstobs,lastobs);
11527: annais=vector(firstobs,lastobs);
11528: moisdc=vector(firstobs,lastobs);
11529: andc=vector(firstobs,lastobs);
11530: weight=vector(firstobs,lastobs);
11531: agedc=vector(firstobs,lastobs);
11532: cod=ivector(firstobs,lastobs);
11533: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11534: num[i]=0;
11535: moisnais[i]=0;
11536: annais[i]=0;
11537: moisdc[i]=0;
11538: andc[i]=0;
11539: agedc[i]=0;
11540: cod[i]=0;
11541: weight[i]=1.0; /* Equal weights, 1 by default */
11542: }
1.290 brouard 11543: mint=matrix(1,maxwav,firstobs,lastobs);
11544: anint=matrix(1,maxwav,firstobs,lastobs);
11545: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11546: tab=ivector(1,NCOVMAX);
1.144 brouard 11547: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11548: 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 11549:
1.136 brouard 11550: /* Reads data from file datafile */
11551: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11552: goto end;
11553:
11554: /* Calculation of the number of parameters from char model */
1.234 brouard 11555: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11556: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11557: k=3 V4 Tvar[k=3]= 4 (from V4)
11558: k=2 V1 Tvar[k=2]= 1 (from V1)
11559: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11560: */
11561:
11562: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11563: TvarsDind=ivector(1,NCOVMAX); /* */
11564: TvarsD=ivector(1,NCOVMAX); /* */
11565: TvarsQind=ivector(1,NCOVMAX); /* */
11566: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11567: TvarF=ivector(1,NCOVMAX); /* */
11568: TvarFind=ivector(1,NCOVMAX); /* */
11569: TvarV=ivector(1,NCOVMAX); /* */
11570: TvarVind=ivector(1,NCOVMAX); /* */
11571: TvarA=ivector(1,NCOVMAX); /* */
11572: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11573: TvarFD=ivector(1,NCOVMAX); /* */
11574: TvarFDind=ivector(1,NCOVMAX); /* */
11575: TvarFQ=ivector(1,NCOVMAX); /* */
11576: TvarFQind=ivector(1,NCOVMAX); /* */
11577: TvarVD=ivector(1,NCOVMAX); /* */
11578: TvarVDind=ivector(1,NCOVMAX); /* */
11579: TvarVQ=ivector(1,NCOVMAX); /* */
11580: TvarVQind=ivector(1,NCOVMAX); /* */
11581:
1.230 brouard 11582: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11583: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11584: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11585: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11586: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11587: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11588: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11589: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11590: */
11591: /* For model-covariate k tells which data-covariate to use but
11592: because this model-covariate is a construction we invent a new column
11593: ncovcol + k1
11594: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11595: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11596: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11597: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11598: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11599: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11600: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11601: */
1.145 brouard 11602: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11603: 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 11604: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11605: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11606: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11607: 4 covariates (3 plus signs)
11608: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11609: */
1.230 brouard 11610: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11611: * individual dummy, fixed or varying:
11612: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11613: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11614: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11615: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11616: * Tmodelind[1]@9={9,0,3,2,}*/
11617: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11618: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11619: * individual quantitative, fixed or varying:
11620: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11621: * 3, 1, 0, 0, 0, 0, 0, 0},
11622: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11623: /* Main decodemodel */
11624:
1.187 brouard 11625:
1.223 brouard 11626: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11627: goto end;
11628:
1.137 brouard 11629: if((double)(lastobs-imx)/(double)imx > 1.10){
11630: nbwarn++;
11631: 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);
11632: 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);
11633: }
1.136 brouard 11634: /* if(mle==1){*/
1.137 brouard 11635: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11636: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11637: }
11638:
11639: /*-calculation of age at interview from date of interview and age at death -*/
11640: agev=matrix(1,maxwav,1,imx);
11641:
11642: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11643: goto end;
11644:
1.126 brouard 11645:
1.136 brouard 11646: agegomp=(int)agemin;
1.290 brouard 11647: free_vector(moisnais,firstobs,lastobs);
11648: free_vector(annais,firstobs,lastobs);
1.126 brouard 11649: /* free_matrix(mint,1,maxwav,1,n);
11650: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11651: /* free_vector(moisdc,1,n); */
11652: /* free_vector(andc,1,n); */
1.145 brouard 11653: /* */
11654:
1.126 brouard 11655: wav=ivector(1,imx);
1.214 brouard 11656: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11657: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11658: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11659: 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.*/
11660: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11661: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11662:
11663: /* Concatenates waves */
1.214 brouard 11664: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11665: Death is a valid wave (if date is known).
11666: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11667: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11668: and mw[mi+1][i]. dh depends on stepm.
11669: */
11670:
1.126 brouard 11671: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11672: /* Concatenates waves */
1.145 brouard 11673:
1.290 brouard 11674: free_vector(moisdc,firstobs,lastobs);
11675: free_vector(andc,firstobs,lastobs);
1.215 brouard 11676:
1.126 brouard 11677: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11678: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11679: ncodemax[1]=1;
1.145 brouard 11680: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11681: cptcoveff=0;
1.220 brouard 11682: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11683: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11684: }
11685:
11686: ncovcombmax=pow(2,cptcoveff);
11687: invalidvarcomb=ivector(1, ncovcombmax);
11688: for(i=1;i<ncovcombmax;i++)
11689: invalidvarcomb[i]=0;
11690:
1.211 brouard 11691: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11692: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11693: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11694:
1.200 brouard 11695: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11696: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11697: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11698: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11699: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11700: * (currently 0 or 1) in the data.
11701: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11702: * corresponding modality (h,j).
11703: */
11704:
1.145 brouard 11705: h=0;
11706: /*if (cptcovn > 0) */
1.126 brouard 11707: m=pow(2,cptcoveff);
11708:
1.144 brouard 11709: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11710: * For k=4 covariates, h goes from 1 to m=2**k
11711: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11712: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11713: * h\k 1 2 3 4
1.143 brouard 11714: *______________________________
11715: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11716: * 2 2 1 1 1
11717: * 3 i=2 1 2 1 1
11718: * 4 2 2 1 1
11719: * 5 i=3 1 i=2 1 2 1
11720: * 6 2 1 2 1
11721: * 7 i=4 1 2 2 1
11722: * 8 2 2 2 1
1.197 brouard 11723: * 9 i=5 1 i=3 1 i=2 1 2
11724: * 10 2 1 1 2
11725: * 11 i=6 1 2 1 2
11726: * 12 2 2 1 2
11727: * 13 i=7 1 i=4 1 2 2
11728: * 14 2 1 2 2
11729: * 15 i=8 1 2 2 2
11730: * 16 2 2 2 2
1.143 brouard 11731: */
1.212 brouard 11732: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11733: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11734: * and the value of each covariate?
11735: * V1=1, V2=1, V3=2, V4=1 ?
11736: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11737: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11738: * In order to get the real value in the data, we use nbcode
11739: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11740: * We are keeping this crazy system in order to be able (in the future?)
11741: * to have more than 2 values (0 or 1) for a covariate.
11742: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11743: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11744: * bbbbbbbb
11745: * 76543210
11746: * h-1 00000101 (6-1=5)
1.219 brouard 11747: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11748: * &
11749: * 1 00000001 (1)
1.219 brouard 11750: * 00000000 = 1 & ((h-1) >> (k-1))
11751: * +1= 00000001 =1
1.211 brouard 11752: *
11753: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11754: * h' 1101 =2^3+2^2+0x2^1+2^0
11755: * >>k' 11
11756: * & 00000001
11757: * = 00000001
11758: * +1 = 00000010=2 = codtabm(14,3)
11759: * Reverse h=6 and m=16?
11760: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11761: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11762: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11763: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11764: * V3=decodtabm(14,3,2**4)=2
11765: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11766: *(h-1) >> (j-1) 0011 =13 >> 2
11767: * &1 000000001
11768: * = 000000001
11769: * +1= 000000010 =2
11770: * 2211
11771: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11772: * V3=2
1.220 brouard 11773: * codtabm and decodtabm are identical
1.211 brouard 11774: */
11775:
1.145 brouard 11776:
11777: free_ivector(Ndum,-1,NCOVMAX);
11778:
11779:
1.126 brouard 11780:
1.186 brouard 11781: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11782: strcpy(optionfilegnuplot,optionfilefiname);
11783: if(mle==-3)
1.201 brouard 11784: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11785: strcat(optionfilegnuplot,".gp");
11786:
11787: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11788: printf("Problem with file %s",optionfilegnuplot);
11789: }
11790: else{
1.204 brouard 11791: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11792: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11793: //fprintf(ficgp,"set missing 'NaNq'\n");
11794: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11795: }
11796: /* fclose(ficgp);*/
1.186 brouard 11797:
11798:
11799: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11800:
11801: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11802: if(mle==-3)
1.201 brouard 11803: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11804: strcat(optionfilehtm,".htm");
11805: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11806: printf("Problem with %s \n",optionfilehtm);
11807: exit(0);
1.126 brouard 11808: }
11809:
11810: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11811: strcat(optionfilehtmcov,"-cov.htm");
11812: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11813: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11814: }
11815: else{
11816: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11817: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11818: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11819: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11820: }
11821:
1.213 brouard 11822: 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 11823: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11824: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11825: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11826: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11827: \n\
11828: <hr size=\"2\" color=\"#EC5E5E\">\
11829: <ul><li><h4>Parameter files</h4>\n\
11830: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11831: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11832: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11833: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11834: - Date and time at start: %s</ul>\n",\
11835: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11836: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11837: fileres,fileres,\
11838: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11839: fflush(fichtm);
11840:
11841: strcpy(pathr,path);
11842: strcat(pathr,optionfilefiname);
1.184 brouard 11843: #ifdef WIN32
11844: _chdir(optionfilefiname); /* Move to directory named optionfile */
11845: #else
1.126 brouard 11846: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11847: #endif
11848:
1.126 brouard 11849:
1.220 brouard 11850: /* Calculates basic frequencies. Computes observed prevalence at single age
11851: and for any valid combination of covariates
1.126 brouard 11852: and prints on file fileres'p'. */
1.251 brouard 11853: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11854: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11855:
11856: fprintf(fichtm,"\n");
1.286 brouard 11857: 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 11858: ftol, stepm);
11859: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11860: ncurrv=1;
11861: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11862: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11863: ncurrv=i;
11864: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11865: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11866: ncurrv=i;
11867: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11868: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11869: ncurrv=i;
11870: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11871: 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", \
11872: nlstate, ndeath, maxwav, mle, weightopt);
11873:
11874: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11875: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11876:
11877:
11878: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11879: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11880: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11881: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11882: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11883: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11884: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11885: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11886: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11887:
1.126 brouard 11888: /* For Powell, parameters are in a vector p[] starting at p[1]
11889: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11890: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11891:
11892: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11893: /* For mortality only */
1.126 brouard 11894: if (mle==-3){
1.136 brouard 11895: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11896: for(i=1;i<=NDIM;i++)
11897: for(j=1;j<=NDIM;j++)
11898: ximort[i][j]=0.;
1.186 brouard 11899: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11900: cens=ivector(firstobs,lastobs);
11901: ageexmed=vector(firstobs,lastobs);
11902: agecens=vector(firstobs,lastobs);
11903: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11904:
1.126 brouard 11905: for (i=1; i<=imx; i++){
11906: dcwave[i]=-1;
11907: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11908: if (s[m][i]>nlstate) {
11909: dcwave[i]=m;
11910: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11911: break;
11912: }
1.126 brouard 11913: }
1.226 brouard 11914:
1.126 brouard 11915: for (i=1; i<=imx; i++) {
11916: if (wav[i]>0){
1.226 brouard 11917: ageexmed[i]=agev[mw[1][i]][i];
11918: j=wav[i];
11919: agecens[i]=1.;
11920:
11921: if (ageexmed[i]> 1 && wav[i] > 0){
11922: agecens[i]=agev[mw[j][i]][i];
11923: cens[i]= 1;
11924: }else if (ageexmed[i]< 1)
11925: cens[i]= -1;
11926: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11927: cens[i]=0 ;
1.126 brouard 11928: }
11929: else cens[i]=-1;
11930: }
11931:
11932: for (i=1;i<=NDIM;i++) {
11933: for (j=1;j<=NDIM;j++)
1.226 brouard 11934: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11935: }
11936:
1.302 brouard 11937: p[1]=0.0268; p[NDIM]=0.083;
11938: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 11939:
11940:
1.136 brouard 11941: #ifdef GSL
11942: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11943: #else
1.126 brouard 11944: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11945: #endif
1.201 brouard 11946: strcpy(filerespow,"POW-MORT_");
11947: strcat(filerespow,fileresu);
1.126 brouard 11948: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11949: printf("Problem with resultfile: %s\n", filerespow);
11950: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11951: }
1.136 brouard 11952: #ifdef GSL
11953: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11954: #else
1.126 brouard 11955: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11956: #endif
1.126 brouard 11957: /* for (i=1;i<=nlstate;i++)
11958: for(j=1;j<=nlstate+ndeath;j++)
11959: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11960: */
11961: fprintf(ficrespow,"\n");
1.136 brouard 11962: #ifdef GSL
11963: /* gsl starts here */
11964: T = gsl_multimin_fminimizer_nmsimplex;
11965: gsl_multimin_fminimizer *sfm = NULL;
11966: gsl_vector *ss, *x;
11967: gsl_multimin_function minex_func;
11968:
11969: /* Initial vertex size vector */
11970: ss = gsl_vector_alloc (NDIM);
11971:
11972: if (ss == NULL){
11973: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11974: }
11975: /* Set all step sizes to 1 */
11976: gsl_vector_set_all (ss, 0.001);
11977:
11978: /* Starting point */
1.126 brouard 11979:
1.136 brouard 11980: x = gsl_vector_alloc (NDIM);
11981:
11982: if (x == NULL){
11983: gsl_vector_free(ss);
11984: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11985: }
11986:
11987: /* Initialize method and iterate */
11988: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11989: /* gsl_vector_set(x, 0, 0.0268); */
11990: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11991: gsl_vector_set(x, 0, p[1]);
11992: gsl_vector_set(x, 1, p[2]);
11993:
11994: minex_func.f = &gompertz_f;
11995: minex_func.n = NDIM;
11996: minex_func.params = (void *)&p; /* ??? */
11997:
11998: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11999: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12000:
12001: printf("Iterations beginning .....\n\n");
12002: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12003:
12004: iteri=0;
12005: while (rval == GSL_CONTINUE){
12006: iteri++;
12007: status = gsl_multimin_fminimizer_iterate(sfm);
12008:
12009: if (status) printf("error: %s\n", gsl_strerror (status));
12010: fflush(0);
12011:
12012: if (status)
12013: break;
12014:
12015: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12016: ssval = gsl_multimin_fminimizer_size (sfm);
12017:
12018: if (rval == GSL_SUCCESS)
12019: printf ("converged to a local maximum at\n");
12020:
12021: printf("%5d ", iteri);
12022: for (it = 0; it < NDIM; it++){
12023: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12024: }
12025: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12026: }
12027:
12028: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12029:
12030: gsl_vector_free(x); /* initial values */
12031: gsl_vector_free(ss); /* inital step size */
12032: for (it=0; it<NDIM; it++){
12033: p[it+1]=gsl_vector_get(sfm->x,it);
12034: fprintf(ficrespow," %.12lf", p[it]);
12035: }
12036: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12037: #endif
12038: #ifdef POWELL
12039: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12040: #endif
1.126 brouard 12041: fclose(ficrespow);
12042:
1.203 brouard 12043: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12044:
12045: for(i=1; i <=NDIM; i++)
12046: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12047: matcov[i][j]=matcov[j][i];
1.126 brouard 12048:
12049: printf("\nCovariance matrix\n ");
1.203 brouard 12050: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12051: for(i=1; i <=NDIM; i++) {
12052: for(j=1;j<=NDIM;j++){
1.220 brouard 12053: printf("%f ",matcov[i][j]);
12054: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12055: }
1.203 brouard 12056: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12057: }
12058:
12059: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12060: for (i=1;i<=NDIM;i++) {
1.126 brouard 12061: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12062: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12063: }
1.302 brouard 12064: lsurv=vector(agegomp,AGESUP);
12065: lpop=vector(agegomp,AGESUP);
12066: tpop=vector(agegomp,AGESUP);
1.126 brouard 12067: lsurv[agegomp]=100000;
12068:
12069: for (k=agegomp;k<=AGESUP;k++) {
12070: agemortsup=k;
12071: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12072: }
12073:
12074: for (k=agegomp;k<agemortsup;k++)
12075: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12076:
12077: for (k=agegomp;k<agemortsup;k++){
12078: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12079: sumlpop=sumlpop+lpop[k];
12080: }
12081:
12082: tpop[agegomp]=sumlpop;
12083: for (k=agegomp;k<(agemortsup-3);k++){
12084: /* tpop[k+1]=2;*/
12085: tpop[k+1]=tpop[k]-lpop[k];
12086: }
12087:
12088:
12089: printf("\nAge lx qx dx Lx Tx e(x)\n");
12090: for (k=agegomp;k<(agemortsup-2);k++)
12091: 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]);
12092:
12093:
12094: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12095: ageminpar=50;
12096: agemaxpar=100;
1.194 brouard 12097: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12098: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12099: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12100: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12101: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12102: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12103: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12104: }else{
12105: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12106: 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 12107: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12108: }
1.201 brouard 12109: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12110: stepm, weightopt,\
12111: model,imx,p,matcov,agemortsup);
12112:
1.302 brouard 12113: free_vector(lsurv,agegomp,AGESUP);
12114: free_vector(lpop,agegomp,AGESUP);
12115: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12116: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12117: free_ivector(dcwave,firstobs,lastobs);
12118: free_vector(agecens,firstobs,lastobs);
12119: free_vector(ageexmed,firstobs,lastobs);
12120: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12121: #ifdef GSL
1.136 brouard 12122: #endif
1.186 brouard 12123: } /* Endof if mle==-3 mortality only */
1.205 brouard 12124: /* Standard */
12125: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12126: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12127: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12128: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12129: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12130: for (k=1; k<=npar;k++)
12131: printf(" %d %8.5f",k,p[k]);
12132: printf("\n");
1.205 brouard 12133: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12134: /* mlikeli uses func not funcone */
1.247 brouard 12135: /* for(i=1;i<nlstate;i++){ */
12136: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12137: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12138: /* } */
1.205 brouard 12139: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12140: }
12141: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12142: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12143: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12144: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12145: }
12146: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12147: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12148: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12149: for (k=1; k<=npar;k++)
12150: printf(" %d %8.5f",k,p[k]);
12151: printf("\n");
12152:
12153: /*--------- results files --------------*/
1.283 brouard 12154: /* 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 12155:
12156:
12157: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12158: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12159: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12160: for(i=1,jk=1; i <=nlstate; i++){
12161: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12162: if (k != i) {
12163: printf("%d%d ",i,k);
12164: fprintf(ficlog,"%d%d ",i,k);
12165: fprintf(ficres,"%1d%1d ",i,k);
12166: for(j=1; j <=ncovmodel; j++){
12167: printf("%12.7f ",p[jk]);
12168: fprintf(ficlog,"%12.7f ",p[jk]);
12169: fprintf(ficres,"%12.7f ",p[jk]);
12170: jk++;
12171: }
12172: printf("\n");
12173: fprintf(ficlog,"\n");
12174: fprintf(ficres,"\n");
12175: }
1.126 brouard 12176: }
12177: }
1.203 brouard 12178: if(mle != 0){
12179: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12180: ftolhess=ftol; /* Usually correct */
1.203 brouard 12181: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12182: 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");
12183: 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");
12184: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12185: for(k=1; k <=(nlstate+ndeath); k++){
12186: if (k != i) {
12187: printf("%d%d ",i,k);
12188: fprintf(ficlog,"%d%d ",i,k);
12189: for(j=1; j <=ncovmodel; j++){
12190: 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]));
12191: 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]));
12192: jk++;
12193: }
12194: printf("\n");
12195: fprintf(ficlog,"\n");
12196: }
12197: }
1.193 brouard 12198: }
1.203 brouard 12199: } /* end of hesscov and Wald tests */
1.225 brouard 12200:
1.203 brouard 12201: /* */
1.126 brouard 12202: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12203: printf("# Scales (for hessian or gradient estimation)\n");
12204: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12205: for(i=1,jk=1; i <=nlstate; i++){
12206: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12207: if (j!=i) {
12208: fprintf(ficres,"%1d%1d",i,j);
12209: printf("%1d%1d",i,j);
12210: fprintf(ficlog,"%1d%1d",i,j);
12211: for(k=1; k<=ncovmodel;k++){
12212: printf(" %.5e",delti[jk]);
12213: fprintf(ficlog," %.5e",delti[jk]);
12214: fprintf(ficres," %.5e",delti[jk]);
12215: jk++;
12216: }
12217: printf("\n");
12218: fprintf(ficlog,"\n");
12219: fprintf(ficres,"\n");
12220: }
1.126 brouard 12221: }
12222: }
12223:
12224: 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 12225: if(mle >= 1) /* To big for the screen */
1.126 brouard 12226: 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");
12227: 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");
12228: /* # 121 Var(a12)\n\ */
12229: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12230: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12231: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12232: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12233: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12234: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12235: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12236:
12237:
12238: /* Just to have a covariance matrix which will be more understandable
12239: even is we still don't want to manage dictionary of variables
12240: */
12241: for(itimes=1;itimes<=2;itimes++){
12242: jj=0;
12243: for(i=1; i <=nlstate; i++){
1.225 brouard 12244: for(j=1; j <=nlstate+ndeath; j++){
12245: if(j==i) continue;
12246: for(k=1; k<=ncovmodel;k++){
12247: jj++;
12248: ca[0]= k+'a'-1;ca[1]='\0';
12249: if(itimes==1){
12250: if(mle>=1)
12251: printf("#%1d%1d%d",i,j,k);
12252: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12253: fprintf(ficres,"#%1d%1d%d",i,j,k);
12254: }else{
12255: if(mle>=1)
12256: printf("%1d%1d%d",i,j,k);
12257: fprintf(ficlog,"%1d%1d%d",i,j,k);
12258: fprintf(ficres,"%1d%1d%d",i,j,k);
12259: }
12260: ll=0;
12261: for(li=1;li <=nlstate; li++){
12262: for(lj=1;lj <=nlstate+ndeath; lj++){
12263: if(lj==li) continue;
12264: for(lk=1;lk<=ncovmodel;lk++){
12265: ll++;
12266: if(ll<=jj){
12267: cb[0]= lk +'a'-1;cb[1]='\0';
12268: if(ll<jj){
12269: if(itimes==1){
12270: if(mle>=1)
12271: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12272: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12273: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12274: }else{
12275: if(mle>=1)
12276: printf(" %.5e",matcov[jj][ll]);
12277: fprintf(ficlog," %.5e",matcov[jj][ll]);
12278: fprintf(ficres," %.5e",matcov[jj][ll]);
12279: }
12280: }else{
12281: if(itimes==1){
12282: if(mle>=1)
12283: printf(" Var(%s%1d%1d)",ca,i,j);
12284: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12285: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12286: }else{
12287: if(mle>=1)
12288: printf(" %.7e",matcov[jj][ll]);
12289: fprintf(ficlog," %.7e",matcov[jj][ll]);
12290: fprintf(ficres," %.7e",matcov[jj][ll]);
12291: }
12292: }
12293: }
12294: } /* end lk */
12295: } /* end lj */
12296: } /* end li */
12297: if(mle>=1)
12298: printf("\n");
12299: fprintf(ficlog,"\n");
12300: fprintf(ficres,"\n");
12301: numlinepar++;
12302: } /* end k*/
12303: } /*end j */
1.126 brouard 12304: } /* end i */
12305: } /* end itimes */
12306:
12307: fflush(ficlog);
12308: fflush(ficres);
1.225 brouard 12309: while(fgets(line, MAXLINE, ficpar)) {
12310: /* If line starts with a # it is a comment */
12311: if (line[0] == '#') {
12312: numlinepar++;
12313: fputs(line,stdout);
12314: fputs(line,ficparo);
12315: fputs(line,ficlog);
1.299 brouard 12316: fputs(line,ficres);
1.225 brouard 12317: continue;
12318: }else
12319: break;
12320: }
12321:
1.209 brouard 12322: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12323: /* ungetc(c,ficpar); */
12324: /* fgets(line, MAXLINE, ficpar); */
12325: /* fputs(line,stdout); */
12326: /* fputs(line,ficparo); */
12327: /* } */
12328: /* ungetc(c,ficpar); */
1.126 brouard 12329:
12330: estepm=0;
1.209 brouard 12331: 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 12332:
12333: if (num_filled != 6) {
12334: 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);
12335: 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);
12336: goto end;
12337: }
12338: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12339: }
12340: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12341: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12342:
1.209 brouard 12343: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12344: if (estepm==0 || estepm < stepm) estepm=stepm;
12345: if (fage <= 2) {
12346: bage = ageminpar;
12347: fage = agemaxpar;
12348: }
12349:
12350: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12351: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12352: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12353:
1.186 brouard 12354: /* Other stuffs, more or less useful */
1.254 brouard 12355: while(fgets(line, MAXLINE, ficpar)) {
12356: /* If line starts with a # it is a comment */
12357: if (line[0] == '#') {
12358: numlinepar++;
12359: fputs(line,stdout);
12360: fputs(line,ficparo);
12361: fputs(line,ficlog);
1.299 brouard 12362: fputs(line,ficres);
1.254 brouard 12363: continue;
12364: }else
12365: break;
12366: }
12367:
12368: 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){
12369:
12370: if (num_filled != 7) {
12371: 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);
12372: 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);
12373: goto end;
12374: }
12375: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12376: 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);
12377: 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);
12378: 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 12379: }
1.254 brouard 12380:
12381: while(fgets(line, MAXLINE, ficpar)) {
12382: /* If line starts with a # it is a comment */
12383: if (line[0] == '#') {
12384: numlinepar++;
12385: fputs(line,stdout);
12386: fputs(line,ficparo);
12387: fputs(line,ficlog);
1.299 brouard 12388: fputs(line,ficres);
1.254 brouard 12389: continue;
12390: }else
12391: break;
1.126 brouard 12392: }
12393:
12394:
12395: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12396: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12397:
1.254 brouard 12398: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12399: if (num_filled != 1) {
12400: 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);
12401: 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);
12402: goto end;
12403: }
12404: printf("pop_based=%d\n",popbased);
12405: fprintf(ficlog,"pop_based=%d\n",popbased);
12406: fprintf(ficparo,"pop_based=%d\n",popbased);
12407: fprintf(ficres,"pop_based=%d\n",popbased);
12408: }
12409:
1.258 brouard 12410: /* Results */
12411: nresult=0;
12412: do{
12413: if(!fgets(line, MAXLINE, ficpar)){
12414: endishere=1;
12415: parameterline=14;
12416: }else if (line[0] == '#') {
12417: /* If line starts with a # it is a comment */
1.254 brouard 12418: numlinepar++;
12419: fputs(line,stdout);
12420: fputs(line,ficparo);
12421: fputs(line,ficlog);
1.299 brouard 12422: fputs(line,ficres);
1.254 brouard 12423: continue;
1.258 brouard 12424: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12425: parameterline=11;
1.296 brouard 12426: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12427: parameterline=12;
12428: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12429: parameterline=13;
12430: else{
12431: parameterline=14;
1.254 brouard 12432: }
1.258 brouard 12433: switch (parameterline){
12434: case 11:
1.296 brouard 12435: if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
12436: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
1.258 brouard 12437: 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);
12438: 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);
12439: 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);
12440: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12441: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12442: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12443: prvforecast = 1;
12444: }
12445: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.302 brouard 12446: printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12447: fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12448: fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12449: prvforecast = 2;
12450: }
12451: else {
12452: printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12453: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12454: goto end;
1.258 brouard 12455: }
1.254 brouard 12456: break;
1.258 brouard 12457: case 12:
1.296 brouard 12458: if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
12459: fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12460: printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12461: fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12462: fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12463: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12464: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12465: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12466: prvbackcast = 1;
12467: }
12468: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.302 brouard 12469: printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12470: fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12471: fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12472: prvbackcast = 2;
12473: }
12474: else {
12475: printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12476: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
12477: goto end;
1.258 brouard 12478: }
1.230 brouard 12479: break;
1.258 brouard 12480: case 13:
12481: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12482: if (num_filled == 0){
12483: resultline[0]='\0';
12484: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12485: 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);
12486: break;
12487: } else if (num_filled != 1){
12488: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12489: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12490: }
12491: nresult++; /* Sum of resultlines */
12492: printf("Result %d: result=%s\n",nresult, resultline);
12493: if(nresult > MAXRESULTLINES){
12494: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12495: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12496: goto end;
12497: }
12498: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12499: fprintf(ficparo,"result: %s\n",resultline);
12500: fprintf(ficres,"result: %s\n",resultline);
12501: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12502: break;
1.303 brouard 12503: case 14:
12504: printf("Error: Unknown command '%s'\n",line);
12505: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
12506: if(ncovmodel >=2 && nresult==0 ){
1.259 brouard 12507: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.303 brouard 12508: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12509: }
1.305 ! brouard 12510: /* goto end; */
1.259 brouard 12511: break;
1.258 brouard 12512: default:
12513: nresult=1;
12514: decoderesult(".",nresult ); /* No covariate */
12515: }
12516: } /* End switch parameterline */
12517: }while(endishere==0); /* End do */
1.126 brouard 12518:
1.230 brouard 12519: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12520: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12521:
12522: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12523: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12524: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12525: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12526: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12527: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12528: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12529: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12530: }else{
1.270 brouard 12531: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12532: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12533: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12534: if(prvforecast==1){
12535: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12536: jprojd=jproj1;
12537: mprojd=mproj1;
12538: anprojd=anproj1;
12539: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12540: jprojf=jproj2;
12541: mprojf=mproj2;
12542: anprojf=anproj2;
12543: } else if(prvforecast == 2){
12544: dateprojd=dateintmean;
12545: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12546: dateprojf=dateintmean+yrfproj;
12547: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12548: }
12549: if(prvbackcast==1){
12550: datebackd=(jback1+12*mback1+365*anback1)/365;
12551: jbackd=jback1;
12552: mbackd=mback1;
12553: anbackd=anback1;
12554: datebackf=(jback2+12*mback2+365*anback2)/365;
12555: jbackf=jback2;
12556: mbackf=mback2;
12557: anbackf=anback2;
12558: } else if(prvbackcast == 2){
12559: datebackd=dateintmean;
12560: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12561: datebackf=dateintmean-yrbproj;
12562: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12563: }
12564:
12565: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12566: }
12567: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12568: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12569: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12570:
1.225 brouard 12571: /*------------ free_vector -------------*/
12572: /* chdir(path); */
1.220 brouard 12573:
1.215 brouard 12574: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12575: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12576: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12577: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12578: free_lvector(num,firstobs,lastobs);
12579: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12580: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12581: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12582: fclose(ficparo);
12583: fclose(ficres);
1.220 brouard 12584:
12585:
1.186 brouard 12586: /* Other results (useful)*/
1.220 brouard 12587:
12588:
1.126 brouard 12589: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12590: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12591: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12592: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12593: fclose(ficrespl);
12594:
12595: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12596: /*#include "hpijx.h"*/
12597: hPijx(p, bage, fage);
1.145 brouard 12598: fclose(ficrespij);
1.227 brouard 12599:
1.220 brouard 12600: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12601: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12602: k=1;
1.126 brouard 12603: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12604:
1.269 brouard 12605: /* Prevalence for each covariate combination in probs[age][status][cov] */
12606: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12607: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12608: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12609: for(k=1;k<=ncovcombmax;k++)
12610: probs[i][j][k]=0.;
1.269 brouard 12611: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12612: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12613: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12614: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12615: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12616: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12617: for(k=1;k<=ncovcombmax;k++)
12618: mobaverages[i][j][k]=0.;
1.219 brouard 12619: mobaverage=mobaverages;
12620: if (mobilav!=0) {
1.235 brouard 12621: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12622: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12623: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12624: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12625: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12626: }
1.269 brouard 12627: } else if (mobilavproj !=0) {
1.235 brouard 12628: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12629: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12630: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12631: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12632: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12633: }
1.269 brouard 12634: }else{
12635: printf("Internal error moving average\n");
12636: fflush(stdout);
12637: exit(1);
1.219 brouard 12638: }
12639: }/* end if moving average */
1.227 brouard 12640:
1.126 brouard 12641: /*---------- Forecasting ------------------*/
1.296 brouard 12642: if(prevfcast==1){
12643: /* /\* if(stepm ==1){*\/ */
12644: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12645: /*This done previously after freqsummary.*/
12646: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12647: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12648:
12649: /* } else if (prvforecast==2){ */
12650: /* /\* if(stepm ==1){*\/ */
12651: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12652: /* } */
12653: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12654: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12655: }
1.269 brouard 12656:
1.296 brouard 12657: /* Prevbcasting */
12658: if(prevbcast==1){
1.219 brouard 12659: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12660: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12661: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12662:
12663: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12664:
12665: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12666:
1.219 brouard 12667: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12668: fclose(ficresplb);
12669:
1.222 brouard 12670: hBijx(p, bage, fage, mobaverage);
12671: fclose(ficrespijb);
1.219 brouard 12672:
1.296 brouard 12673: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12674: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12675: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12676: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12677: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12678: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12679:
12680:
1.269 brouard 12681: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12682:
12683:
1.269 brouard 12684: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12685: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12686: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12687: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12688: } /* end Prevbcasting */
1.268 brouard 12689:
1.186 brouard 12690:
12691: /* ------ Other prevalence ratios------------ */
1.126 brouard 12692:
1.215 brouard 12693: free_ivector(wav,1,imx);
12694: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12695: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12696: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12697:
12698:
1.127 brouard 12699: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12700:
1.201 brouard 12701: strcpy(filerese,"E_");
12702: strcat(filerese,fileresu);
1.126 brouard 12703: if((ficreseij=fopen(filerese,"w"))==NULL) {
12704: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12705: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12706: }
1.208 brouard 12707: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12708: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12709:
12710: pstamp(ficreseij);
1.219 brouard 12711:
1.235 brouard 12712: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12713: if (cptcovn < 1){i1=1;}
12714:
12715: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12716: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12717: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12718: continue;
1.219 brouard 12719: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12720: printf("\n#****** ");
1.225 brouard 12721: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12722: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12723: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12724: }
12725: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12726: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12727: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12728: }
12729: fprintf(ficreseij,"******\n");
1.235 brouard 12730: printf("******\n");
1.219 brouard 12731:
12732: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12733: oldm=oldms;savm=savms;
1.235 brouard 12734: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12735:
1.219 brouard 12736: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12737: }
12738: fclose(ficreseij);
1.208 brouard 12739: printf("done evsij\n");fflush(stdout);
12740: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12741:
1.218 brouard 12742:
1.227 brouard 12743: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12744:
1.201 brouard 12745: strcpy(filerest,"T_");
12746: strcat(filerest,fileresu);
1.127 brouard 12747: if((ficrest=fopen(filerest,"w"))==NULL) {
12748: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12749: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12750: }
1.208 brouard 12751: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12752: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12753: strcpy(fileresstde,"STDE_");
12754: strcat(fileresstde,fileresu);
1.126 brouard 12755: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12756: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12757: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12758: }
1.227 brouard 12759: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12760: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12761:
1.201 brouard 12762: strcpy(filerescve,"CVE_");
12763: strcat(filerescve,fileresu);
1.126 brouard 12764: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12765: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12766: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12767: }
1.227 brouard 12768: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12769: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12770:
1.201 brouard 12771: strcpy(fileresv,"V_");
12772: strcat(fileresv,fileresu);
1.126 brouard 12773: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12774: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12775: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12776: }
1.227 brouard 12777: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12778: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12779:
1.235 brouard 12780: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12781: if (cptcovn < 1){i1=1;}
12782:
12783: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12784: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12785: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12786: continue;
1.242 brouard 12787: printf("\n#****** Result for:");
12788: fprintf(ficrest,"\n#****** Result for:");
12789: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12790: for(j=1;j<=cptcoveff;j++){
12791: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12792: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12793: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12794: }
1.235 brouard 12795: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12796: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12797: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12798: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12799: }
1.208 brouard 12800: fprintf(ficrest,"******\n");
1.227 brouard 12801: fprintf(ficlog,"******\n");
12802: printf("******\n");
1.208 brouard 12803:
12804: fprintf(ficresstdeij,"\n#****** ");
12805: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12806: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12807: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12808: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12809: }
1.235 brouard 12810: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12811: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12812: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12813: }
1.208 brouard 12814: fprintf(ficresstdeij,"******\n");
12815: fprintf(ficrescveij,"******\n");
12816:
12817: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12818: /* pstamp(ficresvij); */
1.225 brouard 12819: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12820: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12821: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12822: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12823: }
1.208 brouard 12824: fprintf(ficresvij,"******\n");
12825:
12826: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12827: oldm=oldms;savm=savms;
1.235 brouard 12828: printf(" cvevsij ");
12829: fprintf(ficlog, " cvevsij ");
12830: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12831: printf(" end cvevsij \n ");
12832: fprintf(ficlog, " end cvevsij \n ");
12833:
12834: /*
12835: */
12836: /* goto endfree; */
12837:
12838: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12839: pstamp(ficrest);
12840:
1.269 brouard 12841: epj=vector(1,nlstate+1);
1.208 brouard 12842: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12843: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12844: cptcod= 0; /* To be deleted */
12845: printf("varevsij vpopbased=%d \n",vpopbased);
12846: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12847: 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 12848: 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 ");
12849: if(vpopbased==1)
12850: 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);
12851: else
1.288 brouard 12852: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12853: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12854: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12855: fprintf(ficrest,"\n");
12856: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12857: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12858: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12859: for(age=bage; age <=fage ;age++){
1.235 brouard 12860: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12861: if (vpopbased==1) {
12862: if(mobilav ==0){
12863: for(i=1; i<=nlstate;i++)
12864: prlim[i][i]=probs[(int)age][i][k];
12865: }else{ /* mobilav */
12866: for(i=1; i<=nlstate;i++)
12867: prlim[i][i]=mobaverage[(int)age][i][k];
12868: }
12869: }
1.219 brouard 12870:
1.227 brouard 12871: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12872: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12873: /* printf(" age %4.0f ",age); */
12874: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12875: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12876: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12877: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12878: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12879: }
12880: epj[nlstate+1] +=epj[j];
12881: }
12882: /* printf(" age %4.0f \n",age); */
1.219 brouard 12883:
1.227 brouard 12884: for(i=1, vepp=0.;i <=nlstate;i++)
12885: for(j=1;j <=nlstate;j++)
12886: vepp += vareij[i][j][(int)age];
12887: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12888: for(j=1;j <=nlstate;j++){
12889: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12890: }
12891: fprintf(ficrest,"\n");
12892: }
1.208 brouard 12893: } /* End vpopbased */
1.269 brouard 12894: free_vector(epj,1,nlstate+1);
1.208 brouard 12895: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12896: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12897: printf("done selection\n");fflush(stdout);
12898: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12899:
1.235 brouard 12900: } /* End k selection */
1.227 brouard 12901:
12902: printf("done State-specific expectancies\n");fflush(stdout);
12903: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12904:
1.288 brouard 12905: /* variance-covariance of forward period prevalence*/
1.269 brouard 12906: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12907:
1.227 brouard 12908:
1.290 brouard 12909: free_vector(weight,firstobs,lastobs);
1.227 brouard 12910: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12911: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12912: free_matrix(anint,1,maxwav,firstobs,lastobs);
12913: free_matrix(mint,1,maxwav,firstobs,lastobs);
12914: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12915: free_ivector(tab,1,NCOVMAX);
12916: fclose(ficresstdeij);
12917: fclose(ficrescveij);
12918: fclose(ficresvij);
12919: fclose(ficrest);
12920: fclose(ficpar);
12921:
12922:
1.126 brouard 12923: /*---------- End : free ----------------*/
1.219 brouard 12924: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12925: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12926: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12927: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12928: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12929: } /* mle==-3 arrives here for freeing */
1.227 brouard 12930: /* endfree:*/
12931: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12932: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12933: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12934: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12935: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12936: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12937: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12938: free_matrix(matcov,1,npar,1,npar);
12939: free_matrix(hess,1,npar,1,npar);
12940: /*free_vector(delti,1,npar);*/
12941: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12942: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12943: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12944: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12945:
12946: free_ivector(ncodemax,1,NCOVMAX);
12947: free_ivector(ncodemaxwundef,1,NCOVMAX);
12948: free_ivector(Dummy,-1,NCOVMAX);
12949: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12950: free_ivector(DummyV,1,NCOVMAX);
12951: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12952: free_ivector(Typevar,-1,NCOVMAX);
12953: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12954: free_ivector(TvarsQ,1,NCOVMAX);
12955: free_ivector(TvarsQind,1,NCOVMAX);
12956: free_ivector(TvarsD,1,NCOVMAX);
12957: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12958: free_ivector(TvarFD,1,NCOVMAX);
12959: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12960: free_ivector(TvarF,1,NCOVMAX);
12961: free_ivector(TvarFind,1,NCOVMAX);
12962: free_ivector(TvarV,1,NCOVMAX);
12963: free_ivector(TvarVind,1,NCOVMAX);
12964: free_ivector(TvarA,1,NCOVMAX);
12965: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12966: free_ivector(TvarFQ,1,NCOVMAX);
12967: free_ivector(TvarFQind,1,NCOVMAX);
12968: free_ivector(TvarVD,1,NCOVMAX);
12969: free_ivector(TvarVDind,1,NCOVMAX);
12970: free_ivector(TvarVQ,1,NCOVMAX);
12971: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12972: free_ivector(Tvarsel,1,NCOVMAX);
12973: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12974: free_ivector(Tposprod,1,NCOVMAX);
12975: free_ivector(Tprod,1,NCOVMAX);
12976: free_ivector(Tvaraff,1,NCOVMAX);
12977: free_ivector(invalidvarcomb,1,ncovcombmax);
12978: free_ivector(Tage,1,NCOVMAX);
12979: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12980: free_ivector(TmodelInvind,1,NCOVMAX);
12981: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12982:
12983: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12984: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12985: fflush(fichtm);
12986: fflush(ficgp);
12987:
1.227 brouard 12988:
1.126 brouard 12989: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12990: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12991: 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 12992: }else{
12993: printf("End of Imach\n");
12994: fprintf(ficlog,"End of Imach\n");
12995: }
12996: printf("See log file on %s\n",filelog);
12997: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12998: /*(void) gettimeofday(&end_time,&tzp);*/
12999: rend_time = time(NULL);
13000: end_time = *localtime(&rend_time);
13001: /* tml = *localtime(&end_time.tm_sec); */
13002: strcpy(strtend,asctime(&end_time));
1.126 brouard 13003: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13004: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13005: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13006:
1.157 brouard 13007: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13008: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13009: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13010: /* printf("Total time was %d uSec.\n", total_usecs);*/
13011: /* if(fileappend(fichtm,optionfilehtm)){ */
13012: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13013: fclose(fichtm);
13014: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13015: fclose(fichtmcov);
13016: fclose(ficgp);
13017: fclose(ficlog);
13018: /*------ End -----------*/
1.227 brouard 13019:
1.281 brouard 13020:
13021: /* Executes gnuplot */
1.227 brouard 13022:
13023: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13024: #ifdef WIN32
1.227 brouard 13025: if (_chdir(pathcd) != 0)
13026: printf("Can't move to directory %s!\n",path);
13027: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13028: #else
1.227 brouard 13029: if(chdir(pathcd) != 0)
13030: printf("Can't move to directory %s!\n", path);
13031: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13032: #endif
1.126 brouard 13033: printf("Current directory %s!\n",pathcd);
13034: /*strcat(plotcmd,CHARSEPARATOR);*/
13035: sprintf(plotcmd,"gnuplot");
1.157 brouard 13036: #ifdef _WIN32
1.126 brouard 13037: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13038: #endif
13039: if(!stat(plotcmd,&info)){
1.158 brouard 13040: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13041: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13042: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13043: }else
13044: strcpy(pplotcmd,plotcmd);
1.157 brouard 13045: #ifdef __unix
1.126 brouard 13046: strcpy(plotcmd,GNUPLOTPROGRAM);
13047: if(!stat(plotcmd,&info)){
1.158 brouard 13048: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13049: }else
13050: strcpy(pplotcmd,plotcmd);
13051: #endif
13052: }else
13053: strcpy(pplotcmd,plotcmd);
13054:
13055: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13056: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13057: strcpy(pplotcmd,plotcmd);
1.227 brouard 13058:
1.126 brouard 13059: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13060: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13061: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13062: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13063: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13064: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13065: strcpy(plotcmd,pplotcmd);
13066: }
1.126 brouard 13067: }
1.158 brouard 13068: printf(" Successful, please wait...");
1.126 brouard 13069: while (z[0] != 'q') {
13070: /* chdir(path); */
1.154 brouard 13071: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13072: scanf("%s",z);
13073: /* if (z[0] == 'c') system("./imach"); */
13074: if (z[0] == 'e') {
1.158 brouard 13075: #ifdef __APPLE__
1.152 brouard 13076: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13077: #elif __linux
13078: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13079: #else
1.152 brouard 13080: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13081: #endif
13082: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13083: system(pplotcmd);
1.126 brouard 13084: }
13085: else if (z[0] == 'g') system(plotcmd);
13086: else if (z[0] == 'q') exit(0);
13087: }
1.227 brouard 13088: end:
1.126 brouard 13089: while (z[0] != 'q') {
1.195 brouard 13090: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13091: scanf("%s",z);
13092: }
1.283 brouard 13093: printf("End\n");
1.282 brouard 13094: exit(0);
1.126 brouard 13095: }
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