Annotation of imach/src/imach.c, revision 1.308
1.308 ! brouard 1: /* $Id: imach.c,v 1.307 2021/03/08 18:11:32 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.308 ! brouard 4: Revision 1.307 2021/03/08 18:11:32 brouard
! 5: Summary: 0.99r22 fixed bug on result:
! 6:
1.307 brouard 7: Revision 1.306 2021/02/20 15:44:02 brouard
8: Summary: Version 0.99r21
9:
10: * imach.c (Module): Fix bug on quitting after result lines!
11: (Module): Version 0.99r21
12:
1.306 brouard 13: Revision 1.305 2021/02/20 15:28:30 brouard
14: * imach.c (Module): Fix bug on quitting after result lines!
15:
1.305 brouard 16: Revision 1.304 2021/02/12 11:34:20 brouard
17: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
18:
1.304 brouard 19: Revision 1.303 2021/02/11 19:50:15 brouard
20: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
21:
1.303 brouard 22: Revision 1.302 2020/02/22 21:00:05 brouard
23: * (Module): imach.c Update mle=-3 (for computing Life expectancy
24: and life table from the data without any state)
25:
1.302 brouard 26: Revision 1.301 2019/06/04 13:51:20 brouard
27: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
28:
1.301 brouard 29: Revision 1.300 2019/05/22 19:09:45 brouard
30: Summary: version 0.99r19 of May 2019
31:
1.300 brouard 32: Revision 1.299 2019/05/22 18:37:08 brouard
33: Summary: Cleaned 0.99r19
34:
1.299 brouard 35: Revision 1.298 2019/05/22 18:19:56 brouard
36: *** empty log message ***
37:
1.298 brouard 38: Revision 1.297 2019/05/22 17:56:10 brouard
39: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
40:
1.297 brouard 41: Revision 1.296 2019/05/20 13:03:18 brouard
42: Summary: Projection syntax simplified
43:
44:
45: We can now start projections, forward or backward, from the mean date
46: of inteviews up to or down to a number of years of projection:
47: prevforecast=1 yearsfproj=15.3 mobil_average=0
48: or
49: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
50: or
51: prevbackcast=1 yearsbproj=12.3 mobil_average=1
52: or
53: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
54:
1.296 brouard 55: Revision 1.295 2019/05/18 09:52:50 brouard
56: Summary: doxygen tex bug
57:
1.295 brouard 58: Revision 1.294 2019/05/16 14:54:33 brouard
59: Summary: There was some wrong lines added
60:
1.294 brouard 61: Revision 1.293 2019/05/09 15:17:34 brouard
62: *** empty log message ***
63:
1.293 brouard 64: Revision 1.292 2019/05/09 14:17:20 brouard
65: Summary: Some updates
66:
1.292 brouard 67: Revision 1.291 2019/05/09 13:44:18 brouard
68: Summary: Before ncovmax
69:
1.291 brouard 70: Revision 1.290 2019/05/09 13:39:37 brouard
71: Summary: 0.99r18 unlimited number of individuals
72:
73: 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.
74:
1.290 brouard 75: Revision 1.289 2018/12/13 09:16:26 brouard
76: Summary: Bug for young ages (<-30) will be in r17
77:
1.289 brouard 78: Revision 1.288 2018/05/02 20:58:27 brouard
79: Summary: Some bugs fixed
80:
1.288 brouard 81: Revision 1.287 2018/05/01 17:57:25 brouard
82: Summary: Bug fixed by providing frequencies only for non missing covariates
83:
1.287 brouard 84: Revision 1.286 2018/04/27 14:27:04 brouard
85: Summary: some minor bugs
86:
1.286 brouard 87: Revision 1.285 2018/04/21 21:02:16 brouard
88: Summary: Some bugs fixed, valgrind tested
89:
1.285 brouard 90: Revision 1.284 2018/04/20 05:22:13 brouard
91: Summary: Computing mean and stdeviation of fixed quantitative variables
92:
1.284 brouard 93: Revision 1.283 2018/04/19 14:49:16 brouard
94: Summary: Some minor bugs fixed
95:
1.283 brouard 96: Revision 1.282 2018/02/27 22:50:02 brouard
97: *** empty log message ***
98:
1.282 brouard 99: Revision 1.281 2018/02/27 19:25:23 brouard
100: Summary: Adding second argument for quitting
101:
1.281 brouard 102: Revision 1.280 2018/02/21 07:58:13 brouard
103: Summary: 0.99r15
104:
105: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
106:
1.280 brouard 107: Revision 1.279 2017/07/20 13:35:01 brouard
108: Summary: temporary working
109:
1.279 brouard 110: Revision 1.278 2017/07/19 14:09:02 brouard
111: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
112:
1.278 brouard 113: Revision 1.277 2017/07/17 08:53:49 brouard
114: Summary: BOM files can be read now
115:
1.277 brouard 116: Revision 1.276 2017/06/30 15:48:31 brouard
117: Summary: Graphs improvements
118:
1.276 brouard 119: Revision 1.275 2017/06/30 13:39:33 brouard
120: Summary: Saito's color
121:
1.275 brouard 122: Revision 1.274 2017/06/29 09:47:08 brouard
123: Summary: Version 0.99r14
124:
1.274 brouard 125: Revision 1.273 2017/06/27 11:06:02 brouard
126: Summary: More documentation on projections
127:
1.273 brouard 128: Revision 1.272 2017/06/27 10:22:40 brouard
129: Summary: Color of backprojection changed from 6 to 5(yellow)
130:
1.272 brouard 131: Revision 1.271 2017/06/27 10:17:50 brouard
132: Summary: Some bug with rint
133:
1.271 brouard 134: Revision 1.270 2017/05/24 05:45:29 brouard
135: *** empty log message ***
136:
1.270 brouard 137: Revision 1.269 2017/05/23 08:39:25 brouard
138: Summary: Code into subroutine, cleanings
139:
1.269 brouard 140: Revision 1.268 2017/05/18 20:09:32 brouard
141: Summary: backprojection and confidence intervals of backprevalence
142:
1.268 brouard 143: Revision 1.267 2017/05/13 10:25:05 brouard
144: Summary: temporary save for backprojection
145:
1.267 brouard 146: Revision 1.266 2017/05/13 07:26:12 brouard
147: Summary: Version 0.99r13 (improvements and bugs fixed)
148:
1.266 brouard 149: Revision 1.265 2017/04/26 16:22:11 brouard
150: Summary: imach 0.99r13 Some bugs fixed
151:
1.265 brouard 152: Revision 1.264 2017/04/26 06:01:29 brouard
153: Summary: Labels in graphs
154:
1.264 brouard 155: Revision 1.263 2017/04/24 15:23:15 brouard
156: Summary: to save
157:
1.263 brouard 158: Revision 1.262 2017/04/18 16:48:12 brouard
159: *** empty log message ***
160:
1.262 brouard 161: Revision 1.261 2017/04/05 10:14:09 brouard
162: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
163:
1.261 brouard 164: Revision 1.260 2017/04/04 17:46:59 brouard
165: Summary: Gnuplot indexations fixed (humm)
166:
1.260 brouard 167: Revision 1.259 2017/04/04 13:01:16 brouard
168: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
169:
1.259 brouard 170: Revision 1.258 2017/04/03 10:17:47 brouard
171: Summary: Version 0.99r12
172:
173: Some cleanings, conformed with updated documentation.
174:
1.258 brouard 175: Revision 1.257 2017/03/29 16:53:30 brouard
176: Summary: Temp
177:
1.257 brouard 178: Revision 1.256 2017/03/27 05:50:23 brouard
179: Summary: Temporary
180:
1.256 brouard 181: Revision 1.255 2017/03/08 16:02:28 brouard
182: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
183:
1.255 brouard 184: Revision 1.254 2017/03/08 07:13:00 brouard
185: Summary: Fixing data parameter line
186:
1.254 brouard 187: Revision 1.253 2016/12/15 11:59:41 brouard
188: Summary: 0.99 in progress
189:
1.253 brouard 190: Revision 1.252 2016/09/15 21:15:37 brouard
191: *** empty log message ***
192:
1.252 brouard 193: Revision 1.251 2016/09/15 15:01:13 brouard
194: Summary: not working
195:
1.251 brouard 196: Revision 1.250 2016/09/08 16:07:27 brouard
197: Summary: continue
198:
1.250 brouard 199: Revision 1.249 2016/09/07 17:14:18 brouard
200: Summary: Starting values from frequencies
201:
1.249 brouard 202: Revision 1.248 2016/09/07 14:10:18 brouard
203: *** empty log message ***
204:
1.248 brouard 205: Revision 1.247 2016/09/02 11:11:21 brouard
206: *** empty log message ***
207:
1.247 brouard 208: Revision 1.246 2016/09/02 08:49:22 brouard
209: *** empty log message ***
210:
1.246 brouard 211: Revision 1.245 2016/09/02 07:25:01 brouard
212: *** empty log message ***
213:
1.245 brouard 214: Revision 1.244 2016/09/02 07:17:34 brouard
215: *** empty log message ***
216:
1.244 brouard 217: Revision 1.243 2016/09/02 06:45:35 brouard
218: *** empty log message ***
219:
1.243 brouard 220: Revision 1.242 2016/08/30 15:01:20 brouard
221: Summary: Fixing a lots
222:
1.242 brouard 223: Revision 1.241 2016/08/29 17:17:25 brouard
224: Summary: gnuplot problem in Back projection to fix
225:
1.241 brouard 226: Revision 1.240 2016/08/29 07:53:18 brouard
227: Summary: Better
228:
1.240 brouard 229: Revision 1.239 2016/08/26 15:51:03 brouard
230: Summary: Improvement in Powell output in order to copy and paste
231:
232: Author:
233:
1.239 brouard 234: Revision 1.238 2016/08/26 14:23:35 brouard
235: Summary: Starting tests of 0.99
236:
1.238 brouard 237: Revision 1.237 2016/08/26 09:20:19 brouard
238: Summary: to valgrind
239:
1.237 brouard 240: Revision 1.236 2016/08/25 10:50:18 brouard
241: *** empty log message ***
242:
1.236 brouard 243: Revision 1.235 2016/08/25 06:59:23 brouard
244: *** empty log message ***
245:
1.235 brouard 246: Revision 1.234 2016/08/23 16:51:20 brouard
247: *** empty log message ***
248:
1.234 brouard 249: Revision 1.233 2016/08/23 07:40:50 brouard
250: Summary: not working
251:
1.233 brouard 252: Revision 1.232 2016/08/22 14:20:21 brouard
253: Summary: not working
254:
1.232 brouard 255: Revision 1.231 2016/08/22 07:17:15 brouard
256: Summary: not working
257:
1.231 brouard 258: Revision 1.230 2016/08/22 06:55:53 brouard
259: Summary: Not working
260:
1.230 brouard 261: Revision 1.229 2016/07/23 09:45:53 brouard
262: Summary: Completing for func too
263:
1.229 brouard 264: Revision 1.228 2016/07/22 17:45:30 brouard
265: Summary: Fixing some arrays, still debugging
266:
1.227 brouard 267: Revision 1.226 2016/07/12 18:42:34 brouard
268: Summary: temp
269:
1.226 brouard 270: Revision 1.225 2016/07/12 08:40:03 brouard
271: Summary: saving but not running
272:
1.225 brouard 273: Revision 1.224 2016/07/01 13:16:01 brouard
274: Summary: Fixes
275:
1.224 brouard 276: Revision 1.223 2016/02/19 09:23:35 brouard
277: Summary: temporary
278:
1.223 brouard 279: Revision 1.222 2016/02/17 08:14:50 brouard
280: Summary: Probably last 0.98 stable version 0.98r6
281:
1.222 brouard 282: Revision 1.221 2016/02/15 23:35:36 brouard
283: Summary: minor bug
284:
1.220 brouard 285: Revision 1.219 2016/02/15 00:48:12 brouard
286: *** empty log message ***
287:
1.219 brouard 288: Revision 1.218 2016/02/12 11:29:23 brouard
289: Summary: 0.99 Back projections
290:
1.218 brouard 291: Revision 1.217 2015/12/23 17:18:31 brouard
292: Summary: Experimental backcast
293:
1.217 brouard 294: Revision 1.216 2015/12/18 17:32:11 brouard
295: Summary: 0.98r4 Warning and status=-2
296:
297: Version 0.98r4 is now:
298: - displaying an error when status is -1, date of interview unknown and date of death known;
299: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
300: Older changes concerning s=-2, dating from 2005 have been supersed.
301:
1.216 brouard 302: Revision 1.215 2015/12/16 08:52:24 brouard
303: Summary: 0.98r4 working
304:
1.215 brouard 305: Revision 1.214 2015/12/16 06:57:54 brouard
306: Summary: temporary not working
307:
1.214 brouard 308: Revision 1.213 2015/12/11 18:22:17 brouard
309: Summary: 0.98r4
310:
1.213 brouard 311: Revision 1.212 2015/11/21 12:47:24 brouard
312: Summary: minor typo
313:
1.212 brouard 314: Revision 1.211 2015/11/21 12:41:11 brouard
315: Summary: 0.98r3 with some graph of projected cross-sectional
316:
317: Author: Nicolas Brouard
318:
1.211 brouard 319: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 320: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 321: Summary: Adding ftolpl parameter
322: Author: N Brouard
323:
324: We had difficulties to get smoothed confidence intervals. It was due
325: to the period prevalence which wasn't computed accurately. The inner
326: parameter ftolpl is now an outer parameter of the .imach parameter
327: file after estepm. If ftolpl is small 1.e-4 and estepm too,
328: computation are long.
329:
1.209 brouard 330: Revision 1.208 2015/11/17 14:31:57 brouard
331: Summary: temporary
332:
1.208 brouard 333: Revision 1.207 2015/10/27 17:36:57 brouard
334: *** empty log message ***
335:
1.207 brouard 336: Revision 1.206 2015/10/24 07:14:11 brouard
337: *** empty log message ***
338:
1.206 brouard 339: Revision 1.205 2015/10/23 15:50:53 brouard
340: Summary: 0.98r3 some clarification for graphs on likelihood contributions
341:
1.205 brouard 342: Revision 1.204 2015/10/01 16:20:26 brouard
343: Summary: Some new graphs of contribution to likelihood
344:
1.204 brouard 345: Revision 1.203 2015/09/30 17:45:14 brouard
346: Summary: looking at better estimation of the hessian
347:
348: Also a better criteria for convergence to the period prevalence And
349: therefore adding the number of years needed to converge. (The
350: prevalence in any alive state shold sum to one
351:
1.203 brouard 352: Revision 1.202 2015/09/22 19:45:16 brouard
353: Summary: Adding some overall graph on contribution to likelihood. Might change
354:
1.202 brouard 355: Revision 1.201 2015/09/15 17:34:58 brouard
356: Summary: 0.98r0
357:
358: - Some new graphs like suvival functions
359: - Some bugs fixed like model=1+age+V2.
360:
1.201 brouard 361: Revision 1.200 2015/09/09 16:53:55 brouard
362: Summary: Big bug thanks to Flavia
363:
364: Even model=1+age+V2. did not work anymore
365:
1.200 brouard 366: Revision 1.199 2015/09/07 14:09:23 brouard
367: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
368:
1.199 brouard 369: Revision 1.198 2015/09/03 07:14:39 brouard
370: Summary: 0.98q5 Flavia
371:
1.198 brouard 372: Revision 1.197 2015/09/01 18:24:39 brouard
373: *** empty log message ***
374:
1.197 brouard 375: Revision 1.196 2015/08/18 23:17:52 brouard
376: Summary: 0.98q5
377:
1.196 brouard 378: Revision 1.195 2015/08/18 16:28:39 brouard
379: Summary: Adding a hack for testing purpose
380:
381: After reading the title, ftol and model lines, if the comment line has
382: a q, starting with #q, the answer at the end of the run is quit. It
383: permits to run test files in batch with ctest. The former workaround was
384: $ echo q | imach foo.imach
385:
1.195 brouard 386: Revision 1.194 2015/08/18 13:32:00 brouard
387: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
388:
1.194 brouard 389: Revision 1.193 2015/08/04 07:17:42 brouard
390: Summary: 0.98q4
391:
1.193 brouard 392: Revision 1.192 2015/07/16 16:49:02 brouard
393: Summary: Fixing some outputs
394:
1.192 brouard 395: Revision 1.191 2015/07/14 10:00:33 brouard
396: Summary: Some fixes
397:
1.191 brouard 398: Revision 1.190 2015/05/05 08:51:13 brouard
399: Summary: Adding digits in output parameters (7 digits instead of 6)
400:
401: Fix 1+age+.
402:
1.190 brouard 403: Revision 1.189 2015/04/30 14:45:16 brouard
404: Summary: 0.98q2
405:
1.189 brouard 406: Revision 1.188 2015/04/30 08:27:53 brouard
407: *** empty log message ***
408:
1.188 brouard 409: Revision 1.187 2015/04/29 09:11:15 brouard
410: *** empty log message ***
411:
1.187 brouard 412: Revision 1.186 2015/04/23 12:01:52 brouard
413: Summary: V1*age is working now, version 0.98q1
414:
415: Some codes had been disabled in order to simplify and Vn*age was
416: working in the optimization phase, ie, giving correct MLE parameters,
417: but, as usual, outputs were not correct and program core dumped.
418:
1.186 brouard 419: Revision 1.185 2015/03/11 13:26:42 brouard
420: Summary: Inclusion of compile and links command line for Intel Compiler
421:
1.185 brouard 422: Revision 1.184 2015/03/11 11:52:39 brouard
423: Summary: Back from Windows 8. Intel Compiler
424:
1.184 brouard 425: Revision 1.183 2015/03/10 20:34:32 brouard
426: Summary: 0.98q0, trying with directest, mnbrak fixed
427:
428: We use directest instead of original Powell test; probably no
429: incidence on the results, but better justifications;
430: We fixed Numerical Recipes mnbrak routine which was wrong and gave
431: wrong results.
432:
1.183 brouard 433: Revision 1.182 2015/02/12 08:19:57 brouard
434: Summary: Trying to keep directest which seems simpler and more general
435: Author: Nicolas Brouard
436:
1.182 brouard 437: Revision 1.181 2015/02/11 23:22:24 brouard
438: Summary: Comments on Powell added
439:
440: Author:
441:
1.181 brouard 442: Revision 1.180 2015/02/11 17:33:45 brouard
443: Summary: Finishing move from main to function (hpijx and prevalence_limit)
444:
1.180 brouard 445: Revision 1.179 2015/01/04 09:57:06 brouard
446: Summary: back to OS/X
447:
1.179 brouard 448: Revision 1.178 2015/01/04 09:35:48 brouard
449: *** empty log message ***
450:
1.178 brouard 451: Revision 1.177 2015/01/03 18:40:56 brouard
452: Summary: Still testing ilc32 on OSX
453:
1.177 brouard 454: Revision 1.176 2015/01/03 16:45:04 brouard
455: *** empty log message ***
456:
1.176 brouard 457: Revision 1.175 2015/01/03 16:33:42 brouard
458: *** empty log message ***
459:
1.175 brouard 460: Revision 1.174 2015/01/03 16:15:49 brouard
461: Summary: Still in cross-compilation
462:
1.174 brouard 463: Revision 1.173 2015/01/03 12:06:26 brouard
464: Summary: trying to detect cross-compilation
465:
1.173 brouard 466: Revision 1.172 2014/12/27 12:07:47 brouard
467: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
468:
1.172 brouard 469: Revision 1.171 2014/12/23 13:26:59 brouard
470: Summary: Back from Visual C
471:
472: Still problem with utsname.h on Windows
473:
1.171 brouard 474: Revision 1.170 2014/12/23 11:17:12 brouard
475: Summary: Cleaning some \%% back to %%
476:
477: The escape was mandatory for a specific compiler (which one?), but too many warnings.
478:
1.170 brouard 479: Revision 1.169 2014/12/22 23:08:31 brouard
480: Summary: 0.98p
481:
482: Outputs some informations on compiler used, OS etc. Testing on different platforms.
483:
1.169 brouard 484: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 485: Summary: update
1.169 brouard 486:
1.168 brouard 487: Revision 1.167 2014/12/22 13:50:56 brouard
488: Summary: Testing uname and compiler version and if compiled 32 or 64
489:
490: Testing on Linux 64
491:
1.167 brouard 492: Revision 1.166 2014/12/22 11:40:47 brouard
493: *** empty log message ***
494:
1.166 brouard 495: Revision 1.165 2014/12/16 11:20:36 brouard
496: Summary: After compiling on Visual C
497:
498: * imach.c (Module): Merging 1.61 to 1.162
499:
1.165 brouard 500: Revision 1.164 2014/12/16 10:52:11 brouard
501: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
502:
503: * imach.c (Module): Merging 1.61 to 1.162
504:
1.164 brouard 505: Revision 1.163 2014/12/16 10:30:11 brouard
506: * imach.c (Module): Merging 1.61 to 1.162
507:
1.163 brouard 508: Revision 1.162 2014/09/25 11:43:39 brouard
509: Summary: temporary backup 0.99!
510:
1.162 brouard 511: Revision 1.1 2014/09/16 11:06:58 brouard
512: Summary: With some code (wrong) for nlopt
513:
514: Author:
515:
516: Revision 1.161 2014/09/15 20:41:41 brouard
517: Summary: Problem with macro SQR on Intel compiler
518:
1.161 brouard 519: Revision 1.160 2014/09/02 09:24:05 brouard
520: *** empty log message ***
521:
1.160 brouard 522: Revision 1.159 2014/09/01 10:34:10 brouard
523: Summary: WIN32
524: Author: Brouard
525:
1.159 brouard 526: Revision 1.158 2014/08/27 17:11:51 brouard
527: *** empty log message ***
528:
1.158 brouard 529: Revision 1.157 2014/08/27 16:26:55 brouard
530: Summary: Preparing windows Visual studio version
531: Author: Brouard
532:
533: In order to compile on Visual studio, time.h is now correct and time_t
534: and tm struct should be used. difftime should be used but sometimes I
535: just make the differences in raw time format (time(&now).
536: Trying to suppress #ifdef LINUX
537: Add xdg-open for __linux in order to open default browser.
538:
1.157 brouard 539: Revision 1.156 2014/08/25 20:10:10 brouard
540: *** empty log message ***
541:
1.156 brouard 542: Revision 1.155 2014/08/25 18:32:34 brouard
543: Summary: New compile, minor changes
544: Author: Brouard
545:
1.155 brouard 546: Revision 1.154 2014/06/20 17:32:08 brouard
547: Summary: Outputs now all graphs of convergence to period prevalence
548:
1.154 brouard 549: Revision 1.153 2014/06/20 16:45:46 brouard
550: Summary: If 3 live state, convergence to period prevalence on same graph
551: Author: Brouard
552:
1.153 brouard 553: Revision 1.152 2014/06/18 17:54:09 brouard
554: Summary: open browser, use gnuplot on same dir than imach if not found in the path
555:
1.152 brouard 556: Revision 1.151 2014/06/18 16:43:30 brouard
557: *** empty log message ***
558:
1.151 brouard 559: Revision 1.150 2014/06/18 16:42:35 brouard
560: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
561: Author: brouard
562:
1.150 brouard 563: Revision 1.149 2014/06/18 15:51:14 brouard
564: Summary: Some fixes in parameter files errors
565: Author: Nicolas Brouard
566:
1.149 brouard 567: Revision 1.148 2014/06/17 17:38:48 brouard
568: Summary: Nothing new
569: Author: Brouard
570:
571: Just a new packaging for OS/X version 0.98nS
572:
1.148 brouard 573: Revision 1.147 2014/06/16 10:33:11 brouard
574: *** empty log message ***
575:
1.147 brouard 576: Revision 1.146 2014/06/16 10:20:28 brouard
577: Summary: Merge
578: Author: Brouard
579:
580: Merge, before building revised version.
581:
1.146 brouard 582: Revision 1.145 2014/06/10 21:23:15 brouard
583: Summary: Debugging with valgrind
584: Author: Nicolas Brouard
585:
586: Lot of changes in order to output the results with some covariates
587: After the Edimburgh REVES conference 2014, it seems mandatory to
588: improve the code.
589: No more memory valgrind error but a lot has to be done in order to
590: continue the work of splitting the code into subroutines.
591: Also, decodemodel has been improved. Tricode is still not
592: optimal. nbcode should be improved. Documentation has been added in
593: the source code.
594:
1.144 brouard 595: Revision 1.143 2014/01/26 09:45:38 brouard
596: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
597:
598: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
599: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
600:
1.143 brouard 601: Revision 1.142 2014/01/26 03:57:36 brouard
602: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
603:
604: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
605:
1.142 brouard 606: Revision 1.141 2014/01/26 02:42:01 brouard
607: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
608:
1.141 brouard 609: Revision 1.140 2011/09/02 10:37:54 brouard
610: Summary: times.h is ok with mingw32 now.
611:
1.140 brouard 612: Revision 1.139 2010/06/14 07:50:17 brouard
613: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
614: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
615:
1.139 brouard 616: Revision 1.138 2010/04/30 18:19:40 brouard
617: *** empty log message ***
618:
1.138 brouard 619: Revision 1.137 2010/04/29 18:11:38 brouard
620: (Module): Checking covariates for more complex models
621: than V1+V2. A lot of change to be done. Unstable.
622:
1.137 brouard 623: Revision 1.136 2010/04/26 20:30:53 brouard
624: (Module): merging some libgsl code. Fixing computation
625: of likelione (using inter/intrapolation if mle = 0) in order to
626: get same likelihood as if mle=1.
627: Some cleaning of code and comments added.
628:
1.136 brouard 629: Revision 1.135 2009/10/29 15:33:14 brouard
630: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
631:
1.135 brouard 632: Revision 1.134 2009/10/29 13:18:53 brouard
633: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
634:
1.134 brouard 635: Revision 1.133 2009/07/06 10:21:25 brouard
636: just nforces
637:
1.133 brouard 638: Revision 1.132 2009/07/06 08:22:05 brouard
639: Many tings
640:
1.132 brouard 641: Revision 1.131 2009/06/20 16:22:47 brouard
642: Some dimensions resccaled
643:
1.131 brouard 644: Revision 1.130 2009/05/26 06:44:34 brouard
645: (Module): Max Covariate is now set to 20 instead of 8. A
646: lot of cleaning with variables initialized to 0. Trying to make
647: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
648:
1.130 brouard 649: Revision 1.129 2007/08/31 13:49:27 lievre
650: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
651:
1.129 lievre 652: Revision 1.128 2006/06/30 13:02:05 brouard
653: (Module): Clarifications on computing e.j
654:
1.128 brouard 655: Revision 1.127 2006/04/28 18:11:50 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: (Module): In order to speed up (in case of numerous covariates) we
660: compute health expectancies (without variances) in a first step
661: and then all the health expectancies with variances or standard
662: deviation (needs data from the Hessian matrices) which slows the
663: computation.
664: In the future we should be able to stop the program is only health
665: expectancies and graph are needed without standard deviations.
666:
1.127 brouard 667: Revision 1.126 2006/04/28 17:23:28 brouard
668: (Module): Yes the sum of survivors was wrong since
669: imach-114 because nhstepm was no more computed in the age
670: loop. Now we define nhstepma in the age loop.
671: Version 0.98h
672:
1.126 brouard 673: Revision 1.125 2006/04/04 15:20:31 lievre
674: Errors in calculation of health expectancies. Age was not initialized.
675: Forecasting file added.
676:
677: Revision 1.124 2006/03/22 17:13:53 lievre
678: Parameters are printed with %lf instead of %f (more numbers after the comma).
679: The log-likelihood is printed in the log file
680:
681: Revision 1.123 2006/03/20 10:52:43 brouard
682: * imach.c (Module): <title> changed, corresponds to .htm file
683: name. <head> headers where missing.
684:
685: * imach.c (Module): Weights can have a decimal point as for
686: English (a comma might work with a correct LC_NUMERIC environment,
687: otherwise the weight is truncated).
688: Modification of warning when the covariates values are not 0 or
689: 1.
690: Version 0.98g
691:
692: Revision 1.122 2006/03/20 09:45:41 brouard
693: (Module): Weights can have a decimal point as for
694: English (a comma might work with a correct LC_NUMERIC environment,
695: otherwise the weight is truncated).
696: Modification of warning when the covariates values are not 0 or
697: 1.
698: Version 0.98g
699:
700: Revision 1.121 2006/03/16 17:45:01 lievre
701: * imach.c (Module): Comments concerning covariates added
702:
703: * imach.c (Module): refinements in the computation of lli if
704: status=-2 in order to have more reliable computation if stepm is
705: not 1 month. Version 0.98f
706:
707: Revision 1.120 2006/03/16 15:10:38 lievre
708: (Module): refinements in the computation of lli if
709: status=-2 in order to have more reliable computation if stepm is
710: not 1 month. Version 0.98f
711:
712: Revision 1.119 2006/03/15 17:42:26 brouard
713: (Module): Bug if status = -2, the loglikelihood was
714: computed as likelihood omitting the logarithm. Version O.98e
715:
716: Revision 1.118 2006/03/14 18:20:07 brouard
717: (Module): varevsij Comments added explaining the second
718: table of variances if popbased=1 .
719: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
720: (Module): Function pstamp added
721: (Module): Version 0.98d
722:
723: Revision 1.117 2006/03/14 17:16:22 brouard
724: (Module): varevsij Comments added explaining the second
725: table of variances if popbased=1 .
726: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
727: (Module): Function pstamp added
728: (Module): Version 0.98d
729:
730: Revision 1.116 2006/03/06 10:29:27 brouard
731: (Module): Variance-covariance wrong links and
732: varian-covariance of ej. is needed (Saito).
733:
734: Revision 1.115 2006/02/27 12:17:45 brouard
735: (Module): One freematrix added in mlikeli! 0.98c
736:
737: Revision 1.114 2006/02/26 12:57:58 brouard
738: (Module): Some improvements in processing parameter
739: filename with strsep.
740:
741: Revision 1.113 2006/02/24 14:20:24 brouard
742: (Module): Memory leaks checks with valgrind and:
743: datafile was not closed, some imatrix were not freed and on matrix
744: allocation too.
745:
746: Revision 1.112 2006/01/30 09:55:26 brouard
747: (Module): Back to gnuplot.exe instead of wgnuplot.exe
748:
749: Revision 1.111 2006/01/25 20:38:18 brouard
750: (Module): Lots of cleaning and bugs added (Gompertz)
751: (Module): Comments can be added in data file. Missing date values
752: can be a simple dot '.'.
753:
754: Revision 1.110 2006/01/25 00:51:50 brouard
755: (Module): Lots of cleaning and bugs added (Gompertz)
756:
757: Revision 1.109 2006/01/24 19:37:15 brouard
758: (Module): Comments (lines starting with a #) are allowed in data.
759:
760: Revision 1.108 2006/01/19 18:05:42 lievre
761: Gnuplot problem appeared...
762: To be fixed
763:
764: Revision 1.107 2006/01/19 16:20:37 brouard
765: Test existence of gnuplot in imach path
766:
767: Revision 1.106 2006/01/19 13:24:36 brouard
768: Some cleaning and links added in html output
769:
770: Revision 1.105 2006/01/05 20:23:19 lievre
771: *** empty log message ***
772:
773: Revision 1.104 2005/09/30 16:11:43 lievre
774: (Module): sump fixed, loop imx fixed, and simplifications.
775: (Module): If the status is missing at the last wave but we know
776: that the person is alive, then we can code his/her status as -2
777: (instead of missing=-1 in earlier versions) and his/her
778: contributions to the likelihood is 1 - Prob of dying from last
779: health status (= 1-p13= p11+p12 in the easiest case of somebody in
780: the healthy state at last known wave). Version is 0.98
781:
782: Revision 1.103 2005/09/30 15:54:49 lievre
783: (Module): sump fixed, loop imx fixed, and simplifications.
784:
785: Revision 1.102 2004/09/15 17:31:30 brouard
786: Add the possibility to read data file including tab characters.
787:
788: Revision 1.101 2004/09/15 10:38:38 brouard
789: Fix on curr_time
790:
791: Revision 1.100 2004/07/12 18:29:06 brouard
792: Add version for Mac OS X. Just define UNIX in Makefile
793:
794: Revision 1.99 2004/06/05 08:57:40 brouard
795: *** empty log message ***
796:
797: Revision 1.98 2004/05/16 15:05:56 brouard
798: New version 0.97 . First attempt to estimate force of mortality
799: directly from the data i.e. without the need of knowing the health
800: state at each age, but using a Gompertz model: log u =a + b*age .
801: This is the basic analysis of mortality and should be done before any
802: other analysis, in order to test if the mortality estimated from the
803: cross-longitudinal survey is different from the mortality estimated
804: from other sources like vital statistic data.
805:
806: The same imach parameter file can be used but the option for mle should be -3.
807:
1.133 brouard 808: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 809: former routines in order to include the new code within the former code.
810:
811: The output is very simple: only an estimate of the intercept and of
812: the slope with 95% confident intervals.
813:
814: Current limitations:
815: A) Even if you enter covariates, i.e. with the
816: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
817: B) There is no computation of Life Expectancy nor Life Table.
818:
819: Revision 1.97 2004/02/20 13:25:42 lievre
820: Version 0.96d. Population forecasting command line is (temporarily)
821: suppressed.
822:
823: Revision 1.96 2003/07/15 15:38:55 brouard
824: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
825: rewritten within the same printf. Workaround: many printfs.
826:
827: Revision 1.95 2003/07/08 07:54:34 brouard
828: * imach.c (Repository):
829: (Repository): Using imachwizard code to output a more meaningful covariance
830: matrix (cov(a12,c31) instead of numbers.
831:
832: Revision 1.94 2003/06/27 13:00:02 brouard
833: Just cleaning
834:
835: Revision 1.93 2003/06/25 16:33:55 brouard
836: (Module): On windows (cygwin) function asctime_r doesn't
837: exist so I changed back to asctime which exists.
838: (Module): Version 0.96b
839:
840: Revision 1.92 2003/06/25 16:30:45 brouard
841: (Module): On windows (cygwin) function asctime_r doesn't
842: exist so I changed back to asctime which exists.
843:
844: Revision 1.91 2003/06/25 15:30:29 brouard
845: * imach.c (Repository): Duplicated warning errors corrected.
846: (Repository): Elapsed time after each iteration is now output. It
847: helps to forecast when convergence will be reached. Elapsed time
848: is stamped in powell. We created a new html file for the graphs
849: concerning matrix of covariance. It has extension -cov.htm.
850:
851: Revision 1.90 2003/06/24 12:34:15 brouard
852: (Module): Some bugs corrected for windows. Also, when
853: mle=-1 a template is output in file "or"mypar.txt with the design
854: of the covariance matrix to be input.
855:
856: Revision 1.89 2003/06/24 12:30:52 brouard
857: (Module): Some bugs corrected for windows. Also, when
858: mle=-1 a template is output in file "or"mypar.txt with the design
859: of the covariance matrix to be input.
860:
861: Revision 1.88 2003/06/23 17:54:56 brouard
862: * 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.
863:
864: Revision 1.87 2003/06/18 12:26:01 brouard
865: Version 0.96
866:
867: Revision 1.86 2003/06/17 20:04:08 brouard
868: (Module): Change position of html and gnuplot routines and added
869: routine fileappend.
870:
871: Revision 1.85 2003/06/17 13:12:43 brouard
872: * imach.c (Repository): Check when date of death was earlier that
873: current date of interview. It may happen when the death was just
874: prior to the death. In this case, dh was negative and likelihood
875: was wrong (infinity). We still send an "Error" but patch by
876: assuming that the date of death was just one stepm after the
877: interview.
878: (Repository): Because some people have very long ID (first column)
879: we changed int to long in num[] and we added a new lvector for
880: memory allocation. But we also truncated to 8 characters (left
881: truncation)
882: (Repository): No more line truncation errors.
883:
884: Revision 1.84 2003/06/13 21:44:43 brouard
885: * imach.c (Repository): Replace "freqsummary" at a correct
886: place. It differs from routine "prevalence" which may be called
887: many times. Probs is memory consuming and must be used with
888: parcimony.
889: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
890:
891: Revision 1.83 2003/06/10 13:39:11 lievre
892: *** empty log message ***
893:
894: Revision 1.82 2003/06/05 15:57:20 brouard
895: Add log in imach.c and fullversion number is now printed.
896:
897: */
898: /*
899: Interpolated Markov Chain
900:
901: Short summary of the programme:
902:
1.227 brouard 903: This program computes Healthy Life Expectancies or State-specific
904: (if states aren't health statuses) Expectancies from
905: cross-longitudinal data. Cross-longitudinal data consist in:
906:
907: -1- a first survey ("cross") where individuals from different ages
908: are interviewed on their health status or degree of disability (in
909: the case of a health survey which is our main interest)
910:
911: -2- at least a second wave of interviews ("longitudinal") which
912: measure each change (if any) in individual health status. Health
913: expectancies are computed from the time spent in each health state
914: according to a model. More health states you consider, more time is
915: necessary to reach the Maximum Likelihood of the parameters involved
916: in the model. The simplest model is the multinomial logistic model
917: where pij is the probability to be observed in state j at the second
918: wave conditional to be observed in state i at the first
919: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
920: etc , where 'age' is age and 'sex' is a covariate. If you want to
921: have a more complex model than "constant and age", you should modify
922: the program where the markup *Covariates have to be included here
923: again* invites you to do it. More covariates you add, slower the
1.126 brouard 924: convergence.
925:
926: The advantage of this computer programme, compared to a simple
927: multinomial logistic model, is clear when the delay between waves is not
928: identical for each individual. Also, if a individual missed an
929: intermediate interview, the information is lost, but taken into
930: account using an interpolation or extrapolation.
931:
932: hPijx is the probability to be observed in state i at age x+h
933: conditional to the observed state i at age x. The delay 'h' can be
934: split into an exact number (nh*stepm) of unobserved intermediate
935: states. This elementary transition (by month, quarter,
936: semester or year) is modelled as a multinomial logistic. The hPx
937: matrix is simply the matrix product of nh*stepm elementary matrices
938: and the contribution of each individual to the likelihood is simply
939: hPijx.
940:
941: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 942: of the life expectancies. It also computes the period (stable) prevalence.
943:
944: Back prevalence and projections:
1.227 brouard 945:
946: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
947: double agemaxpar, double ftolpl, int *ncvyearp, double
948: dateprev1,double dateprev2, int firstpass, int lastpass, int
949: mobilavproj)
950:
951: Computes the back prevalence limit for any combination of
952: covariate values k at any age between ageminpar and agemaxpar and
953: returns it in **bprlim. In the loops,
954:
955: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
956: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
957:
958: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 959: Computes for any combination of covariates k and any age between bage and fage
960: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
961: oldm=oldms;savm=savms;
1.227 brouard 962:
1.267 brouard 963: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 964: Computes the transition matrix starting at age 'age' over
965: 'nhstepm*hstepm*stepm' months (i.e. until
966: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 967: nhstepm*hstepm matrices.
968:
969: Returns p3mat[i][j][h] after calling
970: p3mat[i][j][h]=matprod2(newm,
971: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
972: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
973: oldm);
1.226 brouard 974:
975: Important routines
976:
977: - func (or funcone), computes logit (pij) distinguishing
978: o fixed variables (single or product dummies or quantitative);
979: o varying variables by:
980: (1) wave (single, product dummies, quantitative),
981: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
982: % fixed dummy (treated) or quantitative (not done because time-consuming);
983: % varying dummy (not done) or quantitative (not done);
984: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
985: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
986: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
987: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
988: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 989:
1.226 brouard 990:
991:
1.133 brouard 992: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
993: Institut national d'études démographiques, Paris.
1.126 brouard 994: This software have been partly granted by Euro-REVES, a concerted action
995: from the European Union.
996: It is copyrighted identically to a GNU software product, ie programme and
997: software can be distributed freely for non commercial use. Latest version
998: can be accessed at http://euroreves.ined.fr/imach .
999:
1000: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
1001: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
1002:
1003: **********************************************************************/
1004: /*
1005: main
1006: read parameterfile
1007: read datafile
1008: concatwav
1009: freqsummary
1010: if (mle >= 1)
1011: mlikeli
1012: print results files
1013: if mle==1
1014: computes hessian
1015: read end of parameter file: agemin, agemax, bage, fage, estepm
1016: begin-prev-date,...
1017: open gnuplot file
1018: open html file
1.145 brouard 1019: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1020: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1021: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1022: freexexit2 possible for memory heap.
1023:
1024: h Pij x | pij_nom ficrestpij
1025: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1026: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1027: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1028:
1029: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1030: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1031: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1032: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1033: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1034:
1.126 brouard 1035: forecasting if prevfcast==1 prevforecast call prevalence()
1036: health expectancies
1037: Variance-covariance of DFLE
1038: prevalence()
1039: movingaverage()
1040: varevsij()
1041: if popbased==1 varevsij(,popbased)
1042: total life expectancies
1043: Variance of period (stable) prevalence
1044: end
1045: */
1046:
1.187 brouard 1047: /* #define DEBUG */
1048: /* #define DEBUGBRENT */
1.203 brouard 1049: /* #define DEBUGLINMIN */
1050: /* #define DEBUGHESS */
1051: #define DEBUGHESSIJ
1.224 brouard 1052: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1053: #define POWELL /* Instead of NLOPT */
1.224 brouard 1054: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1055: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1056: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1057:
1058: #include <math.h>
1059: #include <stdio.h>
1060: #include <stdlib.h>
1061: #include <string.h>
1.226 brouard 1062: #include <ctype.h>
1.159 brouard 1063:
1064: #ifdef _WIN32
1065: #include <io.h>
1.172 brouard 1066: #include <windows.h>
1067: #include <tchar.h>
1.159 brouard 1068: #else
1.126 brouard 1069: #include <unistd.h>
1.159 brouard 1070: #endif
1.126 brouard 1071:
1072: #include <limits.h>
1073: #include <sys/types.h>
1.171 brouard 1074:
1075: #if defined(__GNUC__)
1076: #include <sys/utsname.h> /* Doesn't work on Windows */
1077: #endif
1078:
1.126 brouard 1079: #include <sys/stat.h>
1080: #include <errno.h>
1.159 brouard 1081: /* extern int errno; */
1.126 brouard 1082:
1.157 brouard 1083: /* #ifdef LINUX */
1084: /* #include <time.h> */
1085: /* #include "timeval.h" */
1086: /* #else */
1087: /* #include <sys/time.h> */
1088: /* #endif */
1089:
1.126 brouard 1090: #include <time.h>
1091:
1.136 brouard 1092: #ifdef GSL
1093: #include <gsl/gsl_errno.h>
1094: #include <gsl/gsl_multimin.h>
1095: #endif
1096:
1.167 brouard 1097:
1.162 brouard 1098: #ifdef NLOPT
1099: #include <nlopt.h>
1100: typedef struct {
1101: double (* function)(double [] );
1102: } myfunc_data ;
1103: #endif
1104:
1.126 brouard 1105: /* #include <libintl.h> */
1106: /* #define _(String) gettext (String) */
1107:
1.251 brouard 1108: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1109:
1110: #define GNUPLOTPROGRAM "gnuplot"
1111: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1112: #define FILENAMELENGTH 132
1113:
1114: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1115: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1116:
1.144 brouard 1117: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1118: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1119:
1120: #define NINTERVMAX 8
1.144 brouard 1121: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1122: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1123: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1124: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1125: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1126: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1127: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1128: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1129: /* #define AGESUP 130 */
1.288 brouard 1130: /* #define AGESUP 150 */
1131: #define AGESUP 200
1.268 brouard 1132: #define AGEINF 0
1.218 brouard 1133: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1134: #define AGEBASE 40
1.194 brouard 1135: #define AGEOVERFLOW 1.e20
1.164 brouard 1136: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1137: #ifdef _WIN32
1138: #define DIRSEPARATOR '\\'
1139: #define CHARSEPARATOR "\\"
1140: #define ODIRSEPARATOR '/'
1141: #else
1.126 brouard 1142: #define DIRSEPARATOR '/'
1143: #define CHARSEPARATOR "/"
1144: #define ODIRSEPARATOR '\\'
1145: #endif
1146:
1.308 ! brouard 1147: /* $Id: imach.c,v 1.307 2021/03/08 18:11:32 brouard Exp $ */
1.126 brouard 1148: /* $State: Exp $ */
1.196 brouard 1149: #include "version.h"
1150: char version[]=__IMACH_VERSION__;
1.308 ! brouard 1151: char copyright[]="March 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021, INED 2000-2021";
! 1152: char fullversion[]="$Revision: 1.307 $ $Date: 2021/03/08 18:11:32 $";
1.126 brouard 1153: char strstart[80];
1154: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1155: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1156: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1157: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1158: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1159: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1160: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1161: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1162: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1163: int cptcovprodnoage=0; /**< Number of covariate products without age */
1164: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1165: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1166: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1167: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1168: int nsd=0; /**< Total number of single dummy variables (output) */
1169: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1170: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1171: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1172: int ntveff=0; /**< ntveff number of effective time varying variables */
1173: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1174: int cptcov=0; /* Working variable */
1.290 brouard 1175: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1176: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1177: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1178: int nlstate=2; /* Number of live states */
1179: int ndeath=1; /* Number of dead states */
1.130 brouard 1180: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1181: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1182: int popbased=0;
1183:
1184: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1185: int maxwav=0; /* Maxim number of waves */
1186: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1187: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1188: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1189: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1190: int mle=1, weightopt=0;
1.126 brouard 1191: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1192: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1193: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1194: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1195: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1196: int selected(int kvar); /* Is covariate kvar selected for printing results */
1197:
1.130 brouard 1198: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1199: double **matprod2(); /* test */
1.126 brouard 1200: double **oldm, **newm, **savm; /* Working pointers to matrices */
1201: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1202: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1203:
1.136 brouard 1204: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1205: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1206: FILE *ficlog, *ficrespow;
1.130 brouard 1207: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1208: double fretone; /* Only one call to likelihood */
1.130 brouard 1209: long ipmx=0; /* Number of contributions */
1.126 brouard 1210: double sw; /* Sum of weights */
1211: char filerespow[FILENAMELENGTH];
1212: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1213: FILE *ficresilk;
1214: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1215: FILE *ficresprobmorprev;
1216: FILE *fichtm, *fichtmcov; /* Html File */
1217: FILE *ficreseij;
1218: char filerese[FILENAMELENGTH];
1219: FILE *ficresstdeij;
1220: char fileresstde[FILENAMELENGTH];
1221: FILE *ficrescveij;
1222: char filerescve[FILENAMELENGTH];
1223: FILE *ficresvij;
1224: char fileresv[FILENAMELENGTH];
1.269 brouard 1225:
1.126 brouard 1226: char title[MAXLINE];
1.234 brouard 1227: char model[MAXLINE]; /**< The model line */
1.217 brouard 1228: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1229: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1230: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1231: char command[FILENAMELENGTH];
1232: int outcmd=0;
1233:
1.217 brouard 1234: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1235: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1236: char filelog[FILENAMELENGTH]; /* Log file */
1237: char filerest[FILENAMELENGTH];
1238: char fileregp[FILENAMELENGTH];
1239: char popfile[FILENAMELENGTH];
1240:
1241: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1242:
1.157 brouard 1243: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1244: /* struct timezone tzp; */
1245: /* extern int gettimeofday(); */
1246: struct tm tml, *gmtime(), *localtime();
1247:
1248: extern time_t time();
1249:
1250: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1251: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1252: struct tm tm;
1253:
1.126 brouard 1254: char strcurr[80], strfor[80];
1255:
1256: char *endptr;
1257: long lval;
1258: double dval;
1259:
1260: #define NR_END 1
1261: #define FREE_ARG char*
1262: #define FTOL 1.0e-10
1263:
1264: #define NRANSI
1.240 brouard 1265: #define ITMAX 200
1266: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1267:
1268: #define TOL 2.0e-4
1269:
1270: #define CGOLD 0.3819660
1271: #define ZEPS 1.0e-10
1272: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1273:
1274: #define GOLD 1.618034
1275: #define GLIMIT 100.0
1276: #define TINY 1.0e-20
1277:
1278: static double maxarg1,maxarg2;
1279: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1280: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1281:
1282: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1283: #define rint(a) floor(a+0.5)
1.166 brouard 1284: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1285: #define mytinydouble 1.0e-16
1.166 brouard 1286: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1287: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1288: /* static double dsqrarg; */
1289: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1290: static double sqrarg;
1291: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1292: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1293: int agegomp= AGEGOMP;
1294:
1295: int imx;
1296: int stepm=1;
1297: /* Stepm, step in month: minimum step interpolation*/
1298:
1299: int estepm;
1300: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1301:
1302: int m,nb;
1303: long *num;
1.197 brouard 1304: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1305: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1306: covariate for which somebody answered excluding
1307: undefined. Usually 2: 0 and 1. */
1308: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1309: covariate for which somebody answered including
1310: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1311: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1312: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1313: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1314: double *ageexmed,*agecens;
1315: double dateintmean=0;
1.296 brouard 1316: double anprojd, mprojd, jprojd; /* For eventual projections */
1317: double anprojf, mprojf, jprojf;
1.126 brouard 1318:
1.296 brouard 1319: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1320: double anbackf, mbackf, jbackf;
1321: double jintmean,mintmean,aintmean;
1.126 brouard 1322: double *weight;
1323: int **s; /* Status */
1.141 brouard 1324: double *agedc;
1.145 brouard 1325: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1326: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1327: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1328: double **coqvar; /* Fixed quantitative covariate nqv */
1329: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1330: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1331: double idx;
1332: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1333: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1334: /*k 1 2 3 4 5 6 7 8 9 */
1335: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1336: /* Tndvar[k] 1 2 3 4 5 */
1337: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1338: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1339: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1340: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1341: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1342: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1343: /* Tprod[i]=k 4 7 */
1344: /* Tage[i]=k 5 8 */
1345: /* */
1346: /* Type */
1347: /* V 1 2 3 4 5 */
1348: /* F F V V V */
1349: /* D Q D D Q */
1350: /* */
1351: int *TvarsD;
1352: int *TvarsDind;
1353: int *TvarsQ;
1354: int *TvarsQind;
1355:
1.235 brouard 1356: #define MAXRESULTLINES 10
1357: int nresult=0;
1.258 brouard 1358: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1359: int TKresult[MAXRESULTLINES];
1.237 brouard 1360: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1361: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1362: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1363: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1364: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1365: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1366:
1.234 brouard 1367: /* 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 1368: 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 */
1369: 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 */
1370: 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 */
1371: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1372: 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 */
1373: 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 1374: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1375: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1376: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1377: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1378: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1379: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1380: 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 */
1381: 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 */
1382:
1.230 brouard 1383: int *Tvarsel; /**< Selected covariates for output */
1384: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1385: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1386: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1387: 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 1388: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1389: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1390: int *Tage;
1.227 brouard 1391: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1392: 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 1393: 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*/
1394: 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 1395: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1396: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1397: int **Tvard;
1398: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1399: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1400: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1401: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1402: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1403: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1404: double *lsurv, *lpop, *tpop;
1405:
1.231 brouard 1406: #define FD 1; /* Fixed dummy covariate */
1407: #define FQ 2; /* Fixed quantitative covariate */
1408: #define FP 3; /* Fixed product covariate */
1409: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1410: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1411: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1412: #define VD 10; /* Varying dummy covariate */
1413: #define VQ 11; /* Varying quantitative covariate */
1414: #define VP 12; /* Varying product covariate */
1415: #define VPDD 13; /* Varying product dummy*dummy covariate */
1416: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1417: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1418: #define APFD 16; /* Age product * fixed dummy covariate */
1419: #define APFQ 17; /* Age product * fixed quantitative covariate */
1420: #define APVD 18; /* Age product * varying dummy covariate */
1421: #define APVQ 19; /* Age product * varying quantitative covariate */
1422:
1423: #define FTYPE 1; /* Fixed covariate */
1424: #define VTYPE 2; /* Varying covariate (loop in wave) */
1425: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1426:
1427: struct kmodel{
1428: int maintype; /* main type */
1429: int subtype; /* subtype */
1430: };
1431: struct kmodel modell[NCOVMAX];
1432:
1.143 brouard 1433: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1434: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1435:
1436: /**************** split *************************/
1437: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1438: {
1439: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1440: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1441: */
1442: char *ss; /* pointer */
1.186 brouard 1443: int l1=0, l2=0; /* length counters */
1.126 brouard 1444:
1445: l1 = strlen(path ); /* length of path */
1446: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1447: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1448: if ( ss == NULL ) { /* no directory, so determine current directory */
1449: strcpy( name, path ); /* we got the fullname name because no directory */
1450: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1451: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1452: /* get current working directory */
1453: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1454: #ifdef WIN32
1455: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1456: #else
1457: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1458: #endif
1.126 brouard 1459: return( GLOCK_ERROR_GETCWD );
1460: }
1461: /* got dirc from getcwd*/
1462: printf(" DIRC = %s \n",dirc);
1.205 brouard 1463: } else { /* strip directory from path */
1.126 brouard 1464: ss++; /* after this, the filename */
1465: l2 = strlen( ss ); /* length of filename */
1466: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1467: strcpy( name, ss ); /* save file name */
1468: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1469: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1470: printf(" DIRC2 = %s \n",dirc);
1471: }
1472: /* We add a separator at the end of dirc if not exists */
1473: l1 = strlen( dirc ); /* length of directory */
1474: if( dirc[l1-1] != DIRSEPARATOR ){
1475: dirc[l1] = DIRSEPARATOR;
1476: dirc[l1+1] = 0;
1477: printf(" DIRC3 = %s \n",dirc);
1478: }
1479: ss = strrchr( name, '.' ); /* find last / */
1480: if (ss >0){
1481: ss++;
1482: strcpy(ext,ss); /* save extension */
1483: l1= strlen( name);
1484: l2= strlen(ss)+1;
1485: strncpy( finame, name, l1-l2);
1486: finame[l1-l2]= 0;
1487: }
1488:
1489: return( 0 ); /* we're done */
1490: }
1491:
1492:
1493: /******************************************/
1494:
1495: void replace_back_to_slash(char *s, char*t)
1496: {
1497: int i;
1498: int lg=0;
1499: i=0;
1500: lg=strlen(t);
1501: for(i=0; i<= lg; i++) {
1502: (s[i] = t[i]);
1503: if (t[i]== '\\') s[i]='/';
1504: }
1505: }
1506:
1.132 brouard 1507: char *trimbb(char *out, char *in)
1.137 brouard 1508: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1509: char *s;
1510: s=out;
1511: while (*in != '\0'){
1.137 brouard 1512: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1513: in++;
1514: }
1515: *out++ = *in++;
1516: }
1517: *out='\0';
1518: return s;
1519: }
1520:
1.187 brouard 1521: /* char *substrchaine(char *out, char *in, char *chain) */
1522: /* { */
1523: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1524: /* char *s, *t; */
1525: /* t=in;s=out; */
1526: /* while ((*in != *chain) && (*in != '\0')){ */
1527: /* *out++ = *in++; */
1528: /* } */
1529:
1530: /* /\* *in matches *chain *\/ */
1531: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1532: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1533: /* } */
1534: /* in--; chain--; */
1535: /* while ( (*in != '\0')){ */
1536: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1537: /* *out++ = *in++; */
1538: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1539: /* } */
1540: /* *out='\0'; */
1541: /* out=s; */
1542: /* return out; */
1543: /* } */
1544: char *substrchaine(char *out, char *in, char *chain)
1545: {
1546: /* Substract chain 'chain' from 'in', return and output 'out' */
1547: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1548:
1549: char *strloc;
1550:
1551: strcpy (out, in);
1552: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1553: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1554: if(strloc != NULL){
1555: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1556: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1557: /* strcpy (strloc, strloc +strlen(chain));*/
1558: }
1559: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1560: return out;
1561: }
1562:
1563:
1.145 brouard 1564: char *cutl(char *blocc, char *alocc, char *in, char occ)
1565: {
1.187 brouard 1566: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1567: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1568: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1569: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1570: */
1.160 brouard 1571: char *s, *t;
1.145 brouard 1572: t=in;s=in;
1573: while ((*in != occ) && (*in != '\0')){
1574: *alocc++ = *in++;
1575: }
1576: if( *in == occ){
1577: *(alocc)='\0';
1578: s=++in;
1579: }
1580:
1581: if (s == t) {/* occ not found */
1582: *(alocc-(in-s))='\0';
1583: in=s;
1584: }
1585: while ( *in != '\0'){
1586: *blocc++ = *in++;
1587: }
1588:
1589: *blocc='\0';
1590: return t;
1591: }
1.137 brouard 1592: char *cutv(char *blocc, char *alocc, char *in, char occ)
1593: {
1.187 brouard 1594: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1595: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1596: gives blocc="abcdef2ghi" and alocc="j".
1597: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1598: */
1599: char *s, *t;
1600: t=in;s=in;
1601: while (*in != '\0'){
1602: while( *in == occ){
1603: *blocc++ = *in++;
1604: s=in;
1605: }
1606: *blocc++ = *in++;
1607: }
1608: if (s == t) /* occ not found */
1609: *(blocc-(in-s))='\0';
1610: else
1611: *(blocc-(in-s)-1)='\0';
1612: in=s;
1613: while ( *in != '\0'){
1614: *alocc++ = *in++;
1615: }
1616:
1617: *alocc='\0';
1618: return s;
1619: }
1620:
1.126 brouard 1621: int nbocc(char *s, char occ)
1622: {
1623: int i,j=0;
1624: int lg=20;
1625: i=0;
1626: lg=strlen(s);
1627: for(i=0; i<= lg; i++) {
1.234 brouard 1628: if (s[i] == occ ) j++;
1.126 brouard 1629: }
1630: return j;
1631: }
1632:
1.137 brouard 1633: /* void cutv(char *u,char *v, char*t, char occ) */
1634: /* { */
1635: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1636: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1637: /* gives u="abcdef2ghi" and v="j" *\/ */
1638: /* int i,lg,j,p=0; */
1639: /* i=0; */
1640: /* lg=strlen(t); */
1641: /* for(j=0; j<=lg-1; j++) { */
1642: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1643: /* } */
1.126 brouard 1644:
1.137 brouard 1645: /* for(j=0; j<p; j++) { */
1646: /* (u[j] = t[j]); */
1647: /* } */
1648: /* u[p]='\0'; */
1.126 brouard 1649:
1.137 brouard 1650: /* for(j=0; j<= lg; j++) { */
1651: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1652: /* } */
1653: /* } */
1.126 brouard 1654:
1.160 brouard 1655: #ifdef _WIN32
1656: char * strsep(char **pp, const char *delim)
1657: {
1658: char *p, *q;
1659:
1660: if ((p = *pp) == NULL)
1661: return 0;
1662: if ((q = strpbrk (p, delim)) != NULL)
1663: {
1664: *pp = q + 1;
1665: *q = '\0';
1666: }
1667: else
1668: *pp = 0;
1669: return p;
1670: }
1671: #endif
1672:
1.126 brouard 1673: /********************** nrerror ********************/
1674:
1675: void nrerror(char error_text[])
1676: {
1677: fprintf(stderr,"ERREUR ...\n");
1678: fprintf(stderr,"%s\n",error_text);
1679: exit(EXIT_FAILURE);
1680: }
1681: /*********************** vector *******************/
1682: double *vector(int nl, int nh)
1683: {
1684: double *v;
1685: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1686: if (!v) nrerror("allocation failure in vector");
1687: return v-nl+NR_END;
1688: }
1689:
1690: /************************ free vector ******************/
1691: void free_vector(double*v, int nl, int nh)
1692: {
1693: free((FREE_ARG)(v+nl-NR_END));
1694: }
1695:
1696: /************************ivector *******************************/
1697: int *ivector(long nl,long nh)
1698: {
1699: int *v;
1700: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1701: if (!v) nrerror("allocation failure in ivector");
1702: return v-nl+NR_END;
1703: }
1704:
1705: /******************free ivector **************************/
1706: void free_ivector(int *v, long nl, long nh)
1707: {
1708: free((FREE_ARG)(v+nl-NR_END));
1709: }
1710:
1711: /************************lvector *******************************/
1712: long *lvector(long nl,long nh)
1713: {
1714: long *v;
1715: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1716: if (!v) nrerror("allocation failure in ivector");
1717: return v-nl+NR_END;
1718: }
1719:
1720: /******************free lvector **************************/
1721: void free_lvector(long *v, long nl, long nh)
1722: {
1723: free((FREE_ARG)(v+nl-NR_END));
1724: }
1725:
1726: /******************* imatrix *******************************/
1727: int **imatrix(long nrl, long nrh, long ncl, long nch)
1728: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1729: {
1730: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1731: int **m;
1732:
1733: /* allocate pointers to rows */
1734: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1735: if (!m) nrerror("allocation failure 1 in matrix()");
1736: m += NR_END;
1737: m -= nrl;
1738:
1739:
1740: /* allocate rows and set pointers to them */
1741: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1742: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1743: m[nrl] += NR_END;
1744: m[nrl] -= ncl;
1745:
1746: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1747:
1748: /* return pointer to array of pointers to rows */
1749: return m;
1750: }
1751:
1752: /****************** free_imatrix *************************/
1753: void free_imatrix(m,nrl,nrh,ncl,nch)
1754: int **m;
1755: long nch,ncl,nrh,nrl;
1756: /* free an int matrix allocated by imatrix() */
1757: {
1758: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1759: free((FREE_ARG) (m+nrl-NR_END));
1760: }
1761:
1762: /******************* matrix *******************************/
1763: double **matrix(long nrl, long nrh, long ncl, long nch)
1764: {
1765: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1766: double **m;
1767:
1768: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1769: if (!m) nrerror("allocation failure 1 in matrix()");
1770: m += NR_END;
1771: m -= nrl;
1772:
1773: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1774: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1775: m[nrl] += NR_END;
1776: m[nrl] -= ncl;
1777:
1778: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1779: return m;
1.145 brouard 1780: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1781: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1782: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1783: */
1784: }
1785:
1786: /*************************free matrix ************************/
1787: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1788: {
1789: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1790: free((FREE_ARG)(m+nrl-NR_END));
1791: }
1792:
1793: /******************* ma3x *******************************/
1794: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1795: {
1796: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1797: double ***m;
1798:
1799: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1800: if (!m) nrerror("allocation failure 1 in matrix()");
1801: m += NR_END;
1802: m -= nrl;
1803:
1804: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1805: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1806: m[nrl] += NR_END;
1807: m[nrl] -= ncl;
1808:
1809: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1810:
1811: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1812: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1813: m[nrl][ncl] += NR_END;
1814: m[nrl][ncl] -= nll;
1815: for (j=ncl+1; j<=nch; j++)
1816: m[nrl][j]=m[nrl][j-1]+nlay;
1817:
1818: for (i=nrl+1; i<=nrh; i++) {
1819: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1820: for (j=ncl+1; j<=nch; j++)
1821: m[i][j]=m[i][j-1]+nlay;
1822: }
1823: return m;
1824: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1825: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1826: */
1827: }
1828:
1829: /*************************free ma3x ************************/
1830: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1831: {
1832: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1833: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1834: free((FREE_ARG)(m+nrl-NR_END));
1835: }
1836:
1837: /*************** function subdirf ***********/
1838: char *subdirf(char fileres[])
1839: {
1840: /* Caution optionfilefiname is hidden */
1841: strcpy(tmpout,optionfilefiname);
1842: strcat(tmpout,"/"); /* Add to the right */
1843: strcat(tmpout,fileres);
1844: return tmpout;
1845: }
1846:
1847: /*************** function subdirf2 ***********/
1848: char *subdirf2(char fileres[], char *preop)
1849: {
1850:
1851: /* Caution optionfilefiname is hidden */
1852: strcpy(tmpout,optionfilefiname);
1853: strcat(tmpout,"/");
1854: strcat(tmpout,preop);
1855: strcat(tmpout,fileres);
1856: return tmpout;
1857: }
1858:
1859: /*************** function subdirf3 ***********/
1860: char *subdirf3(char fileres[], char *preop, char *preop2)
1861: {
1862:
1863: /* Caution optionfilefiname is hidden */
1864: strcpy(tmpout,optionfilefiname);
1865: strcat(tmpout,"/");
1866: strcat(tmpout,preop);
1867: strcat(tmpout,preop2);
1868: strcat(tmpout,fileres);
1869: return tmpout;
1870: }
1.213 brouard 1871:
1872: /*************** function subdirfext ***********/
1873: char *subdirfext(char fileres[], char *preop, char *postop)
1874: {
1875:
1876: strcpy(tmpout,preop);
1877: strcat(tmpout,fileres);
1878: strcat(tmpout,postop);
1879: return tmpout;
1880: }
1.126 brouard 1881:
1.213 brouard 1882: /*************** function subdirfext3 ***********/
1883: char *subdirfext3(char fileres[], char *preop, char *postop)
1884: {
1885:
1886: /* Caution optionfilefiname is hidden */
1887: strcpy(tmpout,optionfilefiname);
1888: strcat(tmpout,"/");
1889: strcat(tmpout,preop);
1890: strcat(tmpout,fileres);
1891: strcat(tmpout,postop);
1892: return tmpout;
1893: }
1894:
1.162 brouard 1895: char *asc_diff_time(long time_sec, char ascdiff[])
1896: {
1897: long sec_left, days, hours, minutes;
1898: days = (time_sec) / (60*60*24);
1899: sec_left = (time_sec) % (60*60*24);
1900: hours = (sec_left) / (60*60) ;
1901: sec_left = (sec_left) %(60*60);
1902: minutes = (sec_left) /60;
1903: sec_left = (sec_left) % (60);
1904: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1905: return ascdiff;
1906: }
1907:
1.126 brouard 1908: /***************** f1dim *************************/
1909: extern int ncom;
1910: extern double *pcom,*xicom;
1911: extern double (*nrfunc)(double []);
1912:
1913: double f1dim(double x)
1914: {
1915: int j;
1916: double f;
1917: double *xt;
1918:
1919: xt=vector(1,ncom);
1920: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1921: f=(*nrfunc)(xt);
1922: free_vector(xt,1,ncom);
1923: return f;
1924: }
1925:
1926: /*****************brent *************************/
1927: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1928: {
1929: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1930: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1931: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1932: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1933: * returned function value.
1934: */
1.126 brouard 1935: int iter;
1936: double a,b,d,etemp;
1.159 brouard 1937: double fu=0,fv,fw,fx;
1.164 brouard 1938: double ftemp=0.;
1.126 brouard 1939: double p,q,r,tol1,tol2,u,v,w,x,xm;
1940: double e=0.0;
1941:
1942: a=(ax < cx ? ax : cx);
1943: b=(ax > cx ? ax : cx);
1944: x=w=v=bx;
1945: fw=fv=fx=(*f)(x);
1946: for (iter=1;iter<=ITMAX;iter++) {
1947: xm=0.5*(a+b);
1948: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1949: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1950: printf(".");fflush(stdout);
1951: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1952: #ifdef DEBUGBRENT
1.126 brouard 1953: 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);
1954: 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);
1955: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1956: #endif
1957: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1958: *xmin=x;
1959: return fx;
1960: }
1961: ftemp=fu;
1962: if (fabs(e) > tol1) {
1963: r=(x-w)*(fx-fv);
1964: q=(x-v)*(fx-fw);
1965: p=(x-v)*q-(x-w)*r;
1966: q=2.0*(q-r);
1967: if (q > 0.0) p = -p;
1968: q=fabs(q);
1969: etemp=e;
1970: e=d;
1971: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1972: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1973: else {
1.224 brouard 1974: d=p/q;
1975: u=x+d;
1976: if (u-a < tol2 || b-u < tol2)
1977: d=SIGN(tol1,xm-x);
1.126 brouard 1978: }
1979: } else {
1980: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1981: }
1982: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1983: fu=(*f)(u);
1984: if (fu <= fx) {
1985: if (u >= x) a=x; else b=x;
1986: SHFT(v,w,x,u)
1.183 brouard 1987: SHFT(fv,fw,fx,fu)
1988: } else {
1989: if (u < x) a=u; else b=u;
1990: if (fu <= fw || w == x) {
1.224 brouard 1991: v=w;
1992: w=u;
1993: fv=fw;
1994: fw=fu;
1.183 brouard 1995: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1996: v=u;
1997: fv=fu;
1.183 brouard 1998: }
1999: }
1.126 brouard 2000: }
2001: nrerror("Too many iterations in brent");
2002: *xmin=x;
2003: return fx;
2004: }
2005:
2006: /****************** mnbrak ***********************/
2007:
2008: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2009: double (*func)(double))
1.183 brouard 2010: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2011: the downhill direction (defined by the function as evaluated at the initial points) and returns
2012: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2013: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2014: */
1.126 brouard 2015: double ulim,u,r,q, dum;
2016: double fu;
1.187 brouard 2017:
2018: double scale=10.;
2019: int iterscale=0;
2020:
2021: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2022: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2023:
2024:
2025: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2026: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2027: /* *bx = *ax - (*ax - *bx)/scale; */
2028: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2029: /* } */
2030:
1.126 brouard 2031: if (*fb > *fa) {
2032: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2033: SHFT(dum,*fb,*fa,dum)
2034: }
1.126 brouard 2035: *cx=(*bx)+GOLD*(*bx-*ax);
2036: *fc=(*func)(*cx);
1.183 brouard 2037: #ifdef DEBUG
1.224 brouard 2038: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2039: 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 2040: #endif
1.224 brouard 2041: 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 2042: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2043: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2044: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2045: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2046: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2047: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2048: fu=(*func)(u);
1.163 brouard 2049: #ifdef DEBUG
2050: /* f(x)=A(x-u)**2+f(u) */
2051: double A, fparabu;
2052: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2053: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2054: 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);
2055: 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 2056: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2057: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2058: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2059: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2060: #endif
1.184 brouard 2061: #ifdef MNBRAKORIGINAL
1.183 brouard 2062: #else
1.191 brouard 2063: /* if (fu > *fc) { */
2064: /* #ifdef DEBUG */
2065: /* printf("mnbrak4 fu > fc \n"); */
2066: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2067: /* #endif */
2068: /* /\* 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 *\\/ *\/ */
2069: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2070: /* dum=u; /\* Shifting c and u *\/ */
2071: /* u = *cx; */
2072: /* *cx = dum; */
2073: /* dum = fu; */
2074: /* fu = *fc; */
2075: /* *fc =dum; */
2076: /* } else { /\* end *\/ */
2077: /* #ifdef DEBUG */
2078: /* printf("mnbrak3 fu < fc \n"); */
2079: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2080: /* #endif */
2081: /* dum=u; /\* Shifting c and u *\/ */
2082: /* u = *cx; */
2083: /* *cx = dum; */
2084: /* dum = fu; */
2085: /* fu = *fc; */
2086: /* *fc =dum; */
2087: /* } */
1.224 brouard 2088: #ifdef DEBUGMNBRAK
2089: double A, fparabu;
2090: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2091: fparabu= *fa - A*(*ax-u)*(*ax-u);
2092: 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);
2093: 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 2094: #endif
1.191 brouard 2095: dum=u; /* Shifting c and u */
2096: u = *cx;
2097: *cx = dum;
2098: dum = fu;
2099: fu = *fc;
2100: *fc =dum;
1.183 brouard 2101: #endif
1.162 brouard 2102: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2103: #ifdef DEBUG
1.224 brouard 2104: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2105: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2106: #endif
1.126 brouard 2107: fu=(*func)(u);
2108: if (fu < *fc) {
1.183 brouard 2109: #ifdef DEBUG
1.224 brouard 2110: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2111: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2112: #endif
2113: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2114: SHFT(*fb,*fc,fu,(*func)(u))
2115: #ifdef DEBUG
2116: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2117: #endif
2118: }
1.162 brouard 2119: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2120: #ifdef DEBUG
1.224 brouard 2121: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2122: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2123: #endif
1.126 brouard 2124: u=ulim;
2125: fu=(*func)(u);
1.183 brouard 2126: } else { /* u could be left to b (if r > q parabola has a maximum) */
2127: #ifdef DEBUG
1.224 brouard 2128: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2129: 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 2130: #endif
1.126 brouard 2131: u=(*cx)+GOLD*(*cx-*bx);
2132: fu=(*func)(u);
1.224 brouard 2133: #ifdef DEBUG
2134: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2135: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2136: #endif
1.183 brouard 2137: } /* end tests */
1.126 brouard 2138: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2139: SHFT(*fa,*fb,*fc,fu)
2140: #ifdef DEBUG
1.224 brouard 2141: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2142: 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 2143: #endif
2144: } /* 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 2145: }
2146:
2147: /*************** linmin ************************/
1.162 brouard 2148: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2149: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2150: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2151: the value of func at the returned location p . This is actually all accomplished by calling the
2152: routines mnbrak and brent .*/
1.126 brouard 2153: int ncom;
2154: double *pcom,*xicom;
2155: double (*nrfunc)(double []);
2156:
1.224 brouard 2157: #ifdef LINMINORIGINAL
1.126 brouard 2158: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2159: #else
2160: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2161: #endif
1.126 brouard 2162: {
2163: double brent(double ax, double bx, double cx,
2164: double (*f)(double), double tol, double *xmin);
2165: double f1dim(double x);
2166: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2167: double *fc, double (*func)(double));
2168: int j;
2169: double xx,xmin,bx,ax;
2170: double fx,fb,fa;
1.187 brouard 2171:
1.203 brouard 2172: #ifdef LINMINORIGINAL
2173: #else
2174: double scale=10., axs, xxs; /* Scale added for infinity */
2175: #endif
2176:
1.126 brouard 2177: ncom=n;
2178: pcom=vector(1,n);
2179: xicom=vector(1,n);
2180: nrfunc=func;
2181: for (j=1;j<=n;j++) {
2182: pcom[j]=p[j];
1.202 brouard 2183: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2184: }
1.187 brouard 2185:
1.203 brouard 2186: #ifdef LINMINORIGINAL
2187: xx=1.;
2188: #else
2189: axs=0.0;
2190: xxs=1.;
2191: do{
2192: xx= xxs;
2193: #endif
1.187 brouard 2194: ax=0.;
2195: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2196: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2197: /* 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)) */
2198: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2199: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2200: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2201: /* 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 2202: #ifdef LINMINORIGINAL
2203: #else
2204: if (fx != fx){
1.224 brouard 2205: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2206: printf("|");
2207: fprintf(ficlog,"|");
1.203 brouard 2208: #ifdef DEBUGLINMIN
1.224 brouard 2209: 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 2210: #endif
2211: }
1.224 brouard 2212: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2213: #endif
2214:
1.191 brouard 2215: #ifdef DEBUGLINMIN
2216: 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 2217: 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 2218: #endif
1.224 brouard 2219: #ifdef LINMINORIGINAL
2220: #else
2221: if(fb == fx){ /* Flat function in the direction */
2222: xmin=xx;
2223: *flat=1;
2224: }else{
2225: *flat=0;
2226: #endif
2227: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2228: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2229: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2230: /* fmin = f(p[j] + xmin * xi[j]) */
2231: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2232: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2233: #ifdef DEBUG
1.224 brouard 2234: 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);
2235: 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);
2236: #endif
2237: #ifdef LINMINORIGINAL
2238: #else
2239: }
1.126 brouard 2240: #endif
1.191 brouard 2241: #ifdef DEBUGLINMIN
2242: printf("linmin end ");
1.202 brouard 2243: fprintf(ficlog,"linmin end ");
1.191 brouard 2244: #endif
1.126 brouard 2245: for (j=1;j<=n;j++) {
1.203 brouard 2246: #ifdef LINMINORIGINAL
2247: xi[j] *= xmin;
2248: #else
2249: #ifdef DEBUGLINMIN
2250: if(xxs <1.0)
2251: printf(" before xi[%d]=%12.8f", j,xi[j]);
2252: #endif
2253: 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) */
2254: #ifdef DEBUGLINMIN
2255: if(xxs <1.0)
2256: 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 );
2257: #endif
2258: #endif
1.187 brouard 2259: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2260: }
1.191 brouard 2261: #ifdef DEBUGLINMIN
1.203 brouard 2262: printf("\n");
1.191 brouard 2263: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2264: 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 2265: for (j=1;j<=n;j++) {
1.202 brouard 2266: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2267: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2268: if(j % ncovmodel == 0){
1.191 brouard 2269: printf("\n");
1.202 brouard 2270: fprintf(ficlog,"\n");
2271: }
1.191 brouard 2272: }
1.203 brouard 2273: #else
1.191 brouard 2274: #endif
1.126 brouard 2275: free_vector(xicom,1,n);
2276: free_vector(pcom,1,n);
2277: }
2278:
2279:
2280: /*************** powell ************************/
1.162 brouard 2281: /*
2282: Minimization of a function func of n variables. Input consists of an initial starting point
2283: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2284: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2285: such that failure to decrease by more than this amount on one iteration signals doneness. On
2286: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2287: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2288: */
1.224 brouard 2289: #ifdef LINMINORIGINAL
2290: #else
2291: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2292: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2293: #endif
1.126 brouard 2294: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2295: double (*func)(double []))
2296: {
1.224 brouard 2297: #ifdef LINMINORIGINAL
2298: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2299: double (*func)(double []));
1.224 brouard 2300: #else
1.241 brouard 2301: void linmin(double p[], double xi[], int n, double *fret,
2302: double (*func)(double []),int *flat);
1.224 brouard 2303: #endif
1.239 brouard 2304: int i,ibig,j,jk,k;
1.126 brouard 2305: double del,t,*pt,*ptt,*xit;
1.181 brouard 2306: double directest;
1.126 brouard 2307: double fp,fptt;
2308: double *xits;
2309: int niterf, itmp;
1.224 brouard 2310: #ifdef LINMINORIGINAL
2311: #else
2312:
2313: flatdir=ivector(1,n);
2314: for (j=1;j<=n;j++) flatdir[j]=0;
2315: #endif
1.126 brouard 2316:
2317: pt=vector(1,n);
2318: ptt=vector(1,n);
2319: xit=vector(1,n);
2320: xits=vector(1,n);
2321: *fret=(*func)(p);
2322: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2323: rcurr_time = time(NULL);
1.126 brouard 2324: for (*iter=1;;++(*iter)) {
1.187 brouard 2325: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2326: ibig=0;
2327: del=0.0;
1.157 brouard 2328: rlast_time=rcurr_time;
2329: /* (void) gettimeofday(&curr_time,&tzp); */
2330: rcurr_time = time(NULL);
2331: curr_time = *localtime(&rcurr_time);
2332: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2333: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2334: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2335: for (i=1;i<=n;i++) {
1.126 brouard 2336: fprintf(ficrespow," %.12lf", p[i]);
2337: }
1.239 brouard 2338: fprintf(ficrespow,"\n");fflush(ficrespow);
2339: printf("\n#model= 1 + age ");
2340: fprintf(ficlog,"\n#model= 1 + age ");
2341: if(nagesqr==1){
1.241 brouard 2342: printf(" + age*age ");
2343: fprintf(ficlog," + age*age ");
1.239 brouard 2344: }
2345: for(j=1;j <=ncovmodel-2;j++){
2346: if(Typevar[j]==0) {
2347: printf(" + V%d ",Tvar[j]);
2348: fprintf(ficlog," + V%d ",Tvar[j]);
2349: }else if(Typevar[j]==1) {
2350: printf(" + V%d*age ",Tvar[j]);
2351: fprintf(ficlog," + V%d*age ",Tvar[j]);
2352: }else if(Typevar[j]==2) {
2353: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2354: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2355: }
2356: }
1.126 brouard 2357: printf("\n");
1.239 brouard 2358: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2359: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2360: fprintf(ficlog,"\n");
1.239 brouard 2361: for(i=1,jk=1; i <=nlstate; i++){
2362: for(k=1; k <=(nlstate+ndeath); k++){
2363: if (k != i) {
2364: printf("%d%d ",i,k);
2365: fprintf(ficlog,"%d%d ",i,k);
2366: for(j=1; j <=ncovmodel; j++){
2367: printf("%12.7f ",p[jk]);
2368: fprintf(ficlog,"%12.7f ",p[jk]);
2369: jk++;
2370: }
2371: printf("\n");
2372: fprintf(ficlog,"\n");
2373: }
2374: }
2375: }
1.241 brouard 2376: if(*iter <=3 && *iter >1){
1.157 brouard 2377: tml = *localtime(&rcurr_time);
2378: strcpy(strcurr,asctime(&tml));
2379: rforecast_time=rcurr_time;
1.126 brouard 2380: itmp = strlen(strcurr);
2381: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2382: strcurr[itmp-1]='\0';
1.162 brouard 2383: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2384: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2385: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2386: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2387: forecast_time = *localtime(&rforecast_time);
2388: strcpy(strfor,asctime(&forecast_time));
2389: itmp = strlen(strfor);
2390: if(strfor[itmp-1]=='\n')
2391: strfor[itmp-1]='\0';
2392: 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);
2393: 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 2394: }
2395: }
1.187 brouard 2396: for (i=1;i<=n;i++) { /* For each direction i */
2397: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2398: fptt=(*fret);
2399: #ifdef DEBUG
1.203 brouard 2400: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2401: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2402: #endif
1.203 brouard 2403: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2404: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2405: #ifdef LINMINORIGINAL
1.188 brouard 2406: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2407: #else
2408: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2409: flatdir[i]=flat; /* Function is vanishing in that direction i */
2410: #endif
2411: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2412: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2413: /* because that direction will be replaced unless the gain del is small */
2414: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2415: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2416: /* with the new direction. */
2417: del=fabs(fptt-(*fret));
2418: ibig=i;
1.126 brouard 2419: }
2420: #ifdef DEBUG
2421: printf("%d %.12e",i,(*fret));
2422: fprintf(ficlog,"%d %.12e",i,(*fret));
2423: for (j=1;j<=n;j++) {
1.224 brouard 2424: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2425: printf(" x(%d)=%.12e",j,xit[j]);
2426: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2427: }
2428: for(j=1;j<=n;j++) {
1.225 brouard 2429: printf(" p(%d)=%.12e",j,p[j]);
2430: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2431: }
2432: printf("\n");
2433: fprintf(ficlog,"\n");
2434: #endif
1.187 brouard 2435: } /* end loop on each direction i */
2436: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2437: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2438: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2439: for(j=1;j<=n;j++) {
1.302 brouard 2440: if(flatdir[j] >0){
2441: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2442: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2443: }
2444: /* printf("\n"); */
2445: /* fprintf(ficlog,"\n"); */
2446: }
1.243 brouard 2447: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2448: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2449: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2450: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2451: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2452: /* decreased of more than 3.84 */
2453: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2454: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2455: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2456:
1.188 brouard 2457: /* Starting the program with initial values given by a former maximization will simply change */
2458: /* the scales of the directions and the directions, because the are reset to canonical directions */
2459: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2460: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2461: #ifdef DEBUG
2462: int k[2],l;
2463: k[0]=1;
2464: k[1]=-1;
2465: printf("Max: %.12e",(*func)(p));
2466: fprintf(ficlog,"Max: %.12e",(*func)(p));
2467: for (j=1;j<=n;j++) {
2468: printf(" %.12e",p[j]);
2469: fprintf(ficlog," %.12e",p[j]);
2470: }
2471: printf("\n");
2472: fprintf(ficlog,"\n");
2473: for(l=0;l<=1;l++) {
2474: for (j=1;j<=n;j++) {
2475: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2476: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2477: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2478: }
2479: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2480: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2481: }
2482: #endif
2483:
1.224 brouard 2484: #ifdef LINMINORIGINAL
2485: #else
2486: free_ivector(flatdir,1,n);
2487: #endif
1.126 brouard 2488: free_vector(xit,1,n);
2489: free_vector(xits,1,n);
2490: free_vector(ptt,1,n);
2491: free_vector(pt,1,n);
2492: return;
1.192 brouard 2493: } /* enough precision */
1.240 brouard 2494: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2495: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2496: ptt[j]=2.0*p[j]-pt[j];
2497: xit[j]=p[j]-pt[j];
2498: pt[j]=p[j];
2499: }
1.181 brouard 2500: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2501: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2502: if (*iter <=4) {
1.225 brouard 2503: #else
2504: #endif
1.224 brouard 2505: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2506: #else
1.161 brouard 2507: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2508: #endif
1.162 brouard 2509: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2510: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2511: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2512: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2513: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2514: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2515: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2516: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2517: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2518: /* Even if f3 <f1, directest can be negative and t >0 */
2519: /* mu² and del² are equal when f3=f1 */
2520: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2521: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2522: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2523: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2524: #ifdef NRCORIGINAL
2525: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2526: #else
2527: 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 2528: t= t- del*SQR(fp-fptt);
1.183 brouard 2529: #endif
1.202 brouard 2530: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2531: #ifdef DEBUG
1.181 brouard 2532: 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);
2533: 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 2534: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2535: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2536: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2537: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2538: 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);
2539: 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);
2540: #endif
1.183 brouard 2541: #ifdef POWELLORIGINAL
2542: if (t < 0.0) { /* Then we use it for new direction */
2543: #else
1.182 brouard 2544: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2545: 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 2546: 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 2547: 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 2548: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2549: }
1.181 brouard 2550: if (directest < 0.0) { /* Then we use it for new direction */
2551: #endif
1.191 brouard 2552: #ifdef DEBUGLINMIN
1.234 brouard 2553: printf("Before linmin in direction P%d-P0\n",n);
2554: for (j=1;j<=n;j++) {
2555: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2556: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2557: if(j % ncovmodel == 0){
2558: printf("\n");
2559: fprintf(ficlog,"\n");
2560: }
2561: }
1.224 brouard 2562: #endif
2563: #ifdef LINMINORIGINAL
1.234 brouard 2564: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2565: #else
1.234 brouard 2566: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2567: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2568: #endif
1.234 brouard 2569:
1.191 brouard 2570: #ifdef DEBUGLINMIN
1.234 brouard 2571: for (j=1;j<=n;j++) {
2572: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2573: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2574: if(j % ncovmodel == 0){
2575: printf("\n");
2576: fprintf(ficlog,"\n");
2577: }
2578: }
1.224 brouard 2579: #endif
1.234 brouard 2580: for (j=1;j<=n;j++) {
2581: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2582: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2583: }
1.224 brouard 2584: #ifdef LINMINORIGINAL
2585: #else
1.234 brouard 2586: for (j=1, flatd=0;j<=n;j++) {
2587: if(flatdir[j]>0)
2588: flatd++;
2589: }
2590: if(flatd >0){
1.255 brouard 2591: printf("%d flat directions: ",flatd);
2592: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2593: for (j=1;j<=n;j++) {
2594: if(flatdir[j]>0){
2595: printf("%d ",j);
2596: fprintf(ficlog,"%d ",j);
2597: }
2598: }
2599: printf("\n");
2600: fprintf(ficlog,"\n");
2601: }
1.191 brouard 2602: #endif
1.234 brouard 2603: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2604: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2605:
1.126 brouard 2606: #ifdef DEBUG
1.234 brouard 2607: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2608: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2609: for(j=1;j<=n;j++){
2610: printf(" %lf",xit[j]);
2611: fprintf(ficlog," %lf",xit[j]);
2612: }
2613: printf("\n");
2614: fprintf(ficlog,"\n");
1.126 brouard 2615: #endif
1.192 brouard 2616: } /* end of t or directest negative */
1.224 brouard 2617: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2618: #else
1.234 brouard 2619: } /* end if (fptt < fp) */
1.192 brouard 2620: #endif
1.225 brouard 2621: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2622: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2623: #else
1.224 brouard 2624: #endif
1.234 brouard 2625: } /* loop iteration */
1.126 brouard 2626: }
1.234 brouard 2627:
1.126 brouard 2628: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2629:
1.235 brouard 2630: 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 2631: {
1.279 brouard 2632: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2633: * (and selected quantitative values in nres)
2634: * by left multiplying the unit
2635: * matrix by transitions matrix until convergence is reached with precision ftolpl
2636: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2637: * Wx is row vector: population in state 1, population in state 2, population dead
2638: * or prevalence in state 1, prevalence in state 2, 0
2639: * newm is the matrix after multiplications, its rows are identical at a factor.
2640: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2641: * Output is prlim.
2642: * Initial matrix pimij
2643: */
1.206 brouard 2644: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2645: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2646: /* 0, 0 , 1} */
2647: /*
2648: * and after some iteration: */
2649: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2650: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2651: /* 0, 0 , 1} */
2652: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2653: /* {0.51571254859325999, 0.4842874514067399, */
2654: /* 0.51326036147820708, 0.48673963852179264} */
2655: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2656:
1.126 brouard 2657: int i, ii,j,k;
1.209 brouard 2658: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2659: /* double **matprod2(); */ /* test */
1.218 brouard 2660: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2661: double **newm;
1.209 brouard 2662: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2663: int ncvloop=0;
1.288 brouard 2664: int first=0;
1.169 brouard 2665:
1.209 brouard 2666: min=vector(1,nlstate);
2667: max=vector(1,nlstate);
2668: meandiff=vector(1,nlstate);
2669:
1.218 brouard 2670: /* Starting with matrix unity */
1.126 brouard 2671: for (ii=1;ii<=nlstate+ndeath;ii++)
2672: for (j=1;j<=nlstate+ndeath;j++){
2673: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2674: }
1.169 brouard 2675:
2676: cov[1]=1.;
2677:
2678: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2679: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2680: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2681: ncvloop++;
1.126 brouard 2682: newm=savm;
2683: /* Covariates have to be included here again */
1.138 brouard 2684: cov[2]=agefin;
1.187 brouard 2685: if(nagesqr==1)
2686: cov[3]= agefin*agefin;;
1.234 brouard 2687: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2688: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2689: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2690: /* 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 2691: }
2692: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2693: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2694: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2695: /* 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 2696: }
1.237 brouard 2697: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2698: if(Dummy[Tvar[Tage[k]]]){
2699: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2700: } else{
1.235 brouard 2701: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2702: }
1.235 brouard 2703: /* 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 2704: }
1.237 brouard 2705: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2706: /* 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 2707: if(Dummy[Tvard[k][1]==0]){
2708: if(Dummy[Tvard[k][2]==0]){
2709: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2710: }else{
2711: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2712: }
2713: }else{
2714: if(Dummy[Tvard[k][2]==0]){
2715: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2716: }else{
2717: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2718: }
2719: }
1.234 brouard 2720: }
1.138 brouard 2721: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2722: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2723: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2724: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2725: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2726: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2727: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2728:
1.126 brouard 2729: savm=oldm;
2730: oldm=newm;
1.209 brouard 2731:
2732: for(j=1; j<=nlstate; j++){
2733: max[j]=0.;
2734: min[j]=1.;
2735: }
2736: for(i=1;i<=nlstate;i++){
2737: sumnew=0;
2738: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2739: for(j=1; j<=nlstate; j++){
2740: prlim[i][j]= newm[i][j]/(1-sumnew);
2741: max[j]=FMAX(max[j],prlim[i][j]);
2742: min[j]=FMIN(min[j],prlim[i][j]);
2743: }
2744: }
2745:
1.126 brouard 2746: maxmax=0.;
1.209 brouard 2747: for(j=1; j<=nlstate; j++){
2748: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2749: maxmax=FMAX(maxmax,meandiff[j]);
2750: /* 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 2751: } /* j loop */
1.203 brouard 2752: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2753: /* 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 2754: if(maxmax < ftolpl){
1.209 brouard 2755: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2756: free_vector(min,1,nlstate);
2757: free_vector(max,1,nlstate);
2758: free_vector(meandiff,1,nlstate);
1.126 brouard 2759: return prlim;
2760: }
1.288 brouard 2761: } /* agefin loop */
1.208 brouard 2762: /* After some age loop it doesn't converge */
1.288 brouard 2763: if(!first){
2764: first=1;
2765: 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);
2766: }
2767: 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);
2768:
1.209 brouard 2769: /* 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); */
2770: free_vector(min,1,nlstate);
2771: free_vector(max,1,nlstate);
2772: free_vector(meandiff,1,nlstate);
1.208 brouard 2773:
1.169 brouard 2774: return prlim; /* should not reach here */
1.126 brouard 2775: }
2776:
1.217 brouard 2777:
2778: /**** Back Prevalence limit (stable or period prevalence) ****************/
2779:
1.218 brouard 2780: /* 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) */
2781: /* 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 2782: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2783: {
1.264 brouard 2784: /* 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 2785: matrix by transitions matrix until convergence is reached with precision ftolpl */
2786: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2787: /* Wx is row vector: population in state 1, population in state 2, population dead */
2788: /* or prevalence in state 1, prevalence in state 2, 0 */
2789: /* newm is the matrix after multiplications, its rows are identical at a factor */
2790: /* Initial matrix pimij */
2791: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2792: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2793: /* 0, 0 , 1} */
2794: /*
2795: * and after some iteration: */
2796: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2797: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2798: /* 0, 0 , 1} */
2799: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2800: /* {0.51571254859325999, 0.4842874514067399, */
2801: /* 0.51326036147820708, 0.48673963852179264} */
2802: /* If we start from prlim again, prlim tends to a constant matrix */
2803:
2804: int i, ii,j,k;
1.247 brouard 2805: int first=0;
1.217 brouard 2806: double *min, *max, *meandiff, maxmax,sumnew=0.;
2807: /* double **matprod2(); */ /* test */
2808: double **out, cov[NCOVMAX+1], **bmij();
2809: double **newm;
1.218 brouard 2810: double **dnewm, **doldm, **dsavm; /* for use */
2811: double **oldm, **savm; /* for use */
2812:
1.217 brouard 2813: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2814: int ncvloop=0;
2815:
2816: min=vector(1,nlstate);
2817: max=vector(1,nlstate);
2818: meandiff=vector(1,nlstate);
2819:
1.266 brouard 2820: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2821: oldm=oldms; savm=savms;
2822:
2823: /* Starting with matrix unity */
2824: for (ii=1;ii<=nlstate+ndeath;ii++)
2825: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2826: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2827: }
2828:
2829: cov[1]=1.;
2830:
2831: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2832: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2833: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2834: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2835: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2836: ncvloop++;
1.218 brouard 2837: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2838: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2839: /* Covariates have to be included here again */
2840: cov[2]=agefin;
2841: if(nagesqr==1)
2842: cov[3]= agefin*agefin;;
1.242 brouard 2843: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2844: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2845: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2846: /* 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 2847: }
2848: /* for (k=1; k<=cptcovn;k++) { */
2849: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2850: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2851: /* /\* 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])]); *\/ */
2852: /* } */
2853: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2854: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2855: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2856: /* 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]); */
2857: }
2858: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2859: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2860: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2861: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2862: for (k=1; k<=cptcovage;k++){ /* For product with age */
2863: if(Dummy[Tvar[Tage[k]]]){
2864: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2865: } else{
2866: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2867: }
2868: /* 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]); */
2869: }
2870: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2871: /* 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]); */
2872: if(Dummy[Tvard[k][1]==0]){
2873: if(Dummy[Tvard[k][2]==0]){
2874: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2875: }else{
2876: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2877: }
2878: }else{
2879: if(Dummy[Tvard[k][2]==0]){
2880: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2881: }else{
2882: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2883: }
2884: }
1.217 brouard 2885: }
2886:
2887: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2888: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2889: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2890: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2891: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2892: /* ij should be linked to the correct index of cov */
2893: /* age and covariate values ij are in 'cov', but we need to pass
2894: * ij for the observed prevalence at age and status and covariate
2895: * number: prevacurrent[(int)agefin][ii][ij]
2896: */
2897: /* 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 *\/ */
2898: /* 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 *\/ */
2899: 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 2900: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2901: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2902: /* for(i=1; i<=nlstate+ndeath; i++) { */
2903: /* printf("%d newm= ",i); */
2904: /* for(j=1;j<=nlstate+ndeath;j++) { */
2905: /* printf("%f ",newm[i][j]); */
2906: /* } */
2907: /* printf("oldm * "); */
2908: /* for(j=1;j<=nlstate+ndeath;j++) { */
2909: /* printf("%f ",oldm[i][j]); */
2910: /* } */
1.268 brouard 2911: /* printf(" bmmij "); */
1.266 brouard 2912: /* for(j=1;j<=nlstate+ndeath;j++) { */
2913: /* printf("%f ",pmmij[i][j]); */
2914: /* } */
2915: /* printf("\n"); */
2916: /* } */
2917: /* } */
1.217 brouard 2918: savm=oldm;
2919: oldm=newm;
1.266 brouard 2920:
1.217 brouard 2921: for(j=1; j<=nlstate; j++){
2922: max[j]=0.;
2923: min[j]=1.;
2924: }
2925: for(j=1; j<=nlstate; j++){
2926: for(i=1;i<=nlstate;i++){
1.234 brouard 2927: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2928: bprlim[i][j]= newm[i][j];
2929: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2930: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2931: }
2932: }
1.218 brouard 2933:
1.217 brouard 2934: maxmax=0.;
2935: for(i=1; i<=nlstate; i++){
2936: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2937: maxmax=FMAX(maxmax,meandiff[i]);
2938: /* 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 2939: } /* i loop */
1.217 brouard 2940: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2941: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2942: if(maxmax < ftolpl){
1.220 brouard 2943: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2944: free_vector(min,1,nlstate);
2945: free_vector(max,1,nlstate);
2946: free_vector(meandiff,1,nlstate);
2947: return bprlim;
2948: }
1.288 brouard 2949: } /* agefin loop */
1.217 brouard 2950: /* After some age loop it doesn't converge */
1.288 brouard 2951: if(!first){
1.247 brouard 2952: first=1;
2953: 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\
2954: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
2955: }
2956: 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 2957: 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);
2958: /* 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); */
2959: free_vector(min,1,nlstate);
2960: free_vector(max,1,nlstate);
2961: free_vector(meandiff,1,nlstate);
2962:
2963: return bprlim; /* should not reach here */
2964: }
2965:
1.126 brouard 2966: /*************** transition probabilities ***************/
2967:
2968: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2969: {
1.138 brouard 2970: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2971: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2972: model to the ncovmodel covariates (including constant and age).
2973: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2974: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2975: ncth covariate in the global vector x is given by the formula:
2976: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2977: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2978: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2979: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2980: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2981: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2982: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2983: */
2984: double s1, lnpijopii;
1.126 brouard 2985: /*double t34;*/
1.164 brouard 2986: int i,j, nc, ii, jj;
1.126 brouard 2987:
1.223 brouard 2988: for(i=1; i<= nlstate; i++){
2989: for(j=1; j<i;j++){
2990: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2991: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2992: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2993: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2994: }
2995: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2996: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2997: }
2998: for(j=i+1; j<=nlstate+ndeath;j++){
2999: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3000: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3001: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3002: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3003: }
3004: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3005: }
3006: }
1.218 brouard 3007:
1.223 brouard 3008: for(i=1; i<= nlstate; i++){
3009: s1=0;
3010: for(j=1; j<i; j++){
3011: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3012: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3013: }
3014: for(j=i+1; j<=nlstate+ndeath; j++){
3015: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3016: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3017: }
3018: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3019: ps[i][i]=1./(s1+1.);
3020: /* Computing other pijs */
3021: for(j=1; j<i; j++)
3022: ps[i][j]= exp(ps[i][j])*ps[i][i];
3023: for(j=i+1; j<=nlstate+ndeath; j++)
3024: ps[i][j]= exp(ps[i][j])*ps[i][i];
3025: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3026: } /* end i */
1.218 brouard 3027:
1.223 brouard 3028: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3029: for(jj=1; jj<= nlstate+ndeath; jj++){
3030: ps[ii][jj]=0;
3031: ps[ii][ii]=1;
3032: }
3033: }
1.294 brouard 3034:
3035:
1.223 brouard 3036: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3037: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3038: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3039: /* } */
3040: /* printf("\n "); */
3041: /* } */
3042: /* printf("\n ");printf("%lf ",cov[2]);*/
3043: /*
3044: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3045: goto end;*/
1.266 brouard 3046: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3047: }
3048:
1.218 brouard 3049: /*************** backward transition probabilities ***************/
3050:
3051: /* 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 ) */
3052: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3053: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3054: {
1.302 brouard 3055: /* 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 3056: * 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 3057: */
1.218 brouard 3058: int i, ii, j,k;
1.222 brouard 3059:
3060: double **out, **pmij();
3061: double sumnew=0.;
1.218 brouard 3062: double agefin;
1.292 brouard 3063: 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 3064: double **dnewm, **dsavm, **doldm;
3065: double **bbmij;
3066:
1.218 brouard 3067: doldm=ddoldms; /* global pointers */
1.222 brouard 3068: dnewm=ddnewms;
3069: dsavm=ddsavms;
3070:
3071: agefin=cov[2];
1.268 brouard 3072: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3073: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3074: the observed prevalence (with this covariate ij) at beginning of transition */
3075: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3076:
3077: /* P_x */
1.266 brouard 3078: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3079: /* outputs pmmij which is a stochastic matrix in row */
3080:
3081: /* Diag(w_x) */
1.292 brouard 3082: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3083: sumnew=0.;
1.269 brouard 3084: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3085: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3086: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3087: sumnew+=prevacurrent[(int)agefin][ii][ij];
3088: }
3089: if(sumnew >0.01){ /* At least some value in the prevalence */
3090: for (ii=1;ii<=nlstate+ndeath;ii++){
3091: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3092: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3093: }
3094: }else{
3095: for (ii=1;ii<=nlstate+ndeath;ii++){
3096: for (j=1;j<=nlstate+ndeath;j++)
3097: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3098: }
3099: /* if(sumnew <0.9){ */
3100: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3101: /* } */
3102: }
3103: k3=0.0; /* We put the last diagonal to 0 */
3104: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3105: doldm[ii][ii]= k3;
3106: }
3107: /* End doldm, At the end doldm is diag[(w_i)] */
3108:
1.292 brouard 3109: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3110: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3111:
1.292 brouard 3112: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3113: /* 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 3114: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3115: sumnew=0.;
1.222 brouard 3116: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3117: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3118: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3119: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3120: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3121: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3122: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3123: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3124: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3125: /* }else */
1.268 brouard 3126: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3127: } /*End ii */
3128: } /* 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 */
3129:
1.292 brouard 3130: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3131: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3132: /* end bmij */
1.266 brouard 3133: return ps; /*pointer is unchanged */
1.218 brouard 3134: }
1.217 brouard 3135: /*************** transition probabilities ***************/
3136:
1.218 brouard 3137: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3138: {
3139: /* According to parameters values stored in x and the covariate's values stored in cov,
3140: computes the probability to be observed in state j being in state i by appying the
3141: model to the ncovmodel covariates (including constant and age).
3142: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3143: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3144: ncth covariate in the global vector x is given by the formula:
3145: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3146: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3147: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3148: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3149: Outputs ps[i][j] the probability to be observed in j being in j according to
3150: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3151: */
3152: double s1, lnpijopii;
3153: /*double t34;*/
3154: int i,j, nc, ii, jj;
3155:
1.234 brouard 3156: for(i=1; i<= nlstate; i++){
3157: for(j=1; j<i;j++){
3158: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3159: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3160: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3161: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3162: }
3163: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3164: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3165: }
3166: for(j=i+1; j<=nlstate+ndeath;j++){
3167: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3168: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3169: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3170: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3171: }
3172: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3173: }
3174: }
3175:
3176: for(i=1; i<= nlstate; i++){
3177: s1=0;
3178: for(j=1; j<i; j++){
3179: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3180: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3181: }
3182: for(j=i+1; j<=nlstate+ndeath; j++){
3183: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3184: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3185: }
3186: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3187: ps[i][i]=1./(s1+1.);
3188: /* Computing other pijs */
3189: for(j=1; j<i; j++)
3190: ps[i][j]= exp(ps[i][j])*ps[i][i];
3191: for(j=i+1; j<=nlstate+ndeath; j++)
3192: ps[i][j]= exp(ps[i][j])*ps[i][i];
3193: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3194: } /* end i */
3195:
3196: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3197: for(jj=1; jj<= nlstate+ndeath; jj++){
3198: ps[ii][jj]=0;
3199: ps[ii][ii]=1;
3200: }
3201: }
1.296 brouard 3202: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3203: for(jj=1; jj<= nlstate+ndeath; jj++){
3204: s1=0.;
3205: for(ii=1; ii<= nlstate+ndeath; ii++){
3206: s1+=ps[ii][jj];
3207: }
3208: for(ii=1; ii<= nlstate; ii++){
3209: ps[ii][jj]=ps[ii][jj]/s1;
3210: }
3211: }
3212: /* Transposition */
3213: for(jj=1; jj<= nlstate+ndeath; jj++){
3214: for(ii=jj; ii<= nlstate+ndeath; ii++){
3215: s1=ps[ii][jj];
3216: ps[ii][jj]=ps[jj][ii];
3217: ps[jj][ii]=s1;
3218: }
3219: }
3220: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3221: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3222: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3223: /* } */
3224: /* printf("\n "); */
3225: /* } */
3226: /* printf("\n ");printf("%lf ",cov[2]);*/
3227: /*
3228: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3229: goto end;*/
3230: return ps;
1.217 brouard 3231: }
3232:
3233:
1.126 brouard 3234: /**************** Product of 2 matrices ******************/
3235:
1.145 brouard 3236: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3237: {
3238: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3239: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3240: /* in, b, out are matrice of pointers which should have been initialized
3241: before: only the contents of out is modified. The function returns
3242: a pointer to pointers identical to out */
1.145 brouard 3243: int i, j, k;
1.126 brouard 3244: for(i=nrl; i<= nrh; i++)
1.145 brouard 3245: for(k=ncolol; k<=ncoloh; k++){
3246: out[i][k]=0.;
3247: for(j=ncl; j<=nch; j++)
3248: out[i][k] +=in[i][j]*b[j][k];
3249: }
1.126 brouard 3250: return out;
3251: }
3252:
3253:
3254: /************* Higher Matrix Product ***************/
3255:
1.235 brouard 3256: 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 3257: {
1.218 brouard 3258: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3259: 'nhstepm*hstepm*stepm' months (i.e. until
3260: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3261: nhstepm*hstepm matrices.
3262: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3263: (typically every 2 years instead of every month which is too big
3264: for the memory).
3265: Model is determined by parameters x and covariates have to be
3266: included manually here.
3267:
3268: */
3269:
3270: int i, j, d, h, k;
1.131 brouard 3271: double **out, cov[NCOVMAX+1];
1.126 brouard 3272: double **newm;
1.187 brouard 3273: double agexact;
1.214 brouard 3274: double agebegin, ageend;
1.126 brouard 3275:
3276: /* Hstepm could be zero and should return the unit matrix */
3277: for (i=1;i<=nlstate+ndeath;i++)
3278: for (j=1;j<=nlstate+ndeath;j++){
3279: oldm[i][j]=(i==j ? 1.0 : 0.0);
3280: po[i][j][0]=(i==j ? 1.0 : 0.0);
3281: }
3282: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3283: for(h=1; h <=nhstepm; h++){
3284: for(d=1; d <=hstepm; d++){
3285: newm=savm;
3286: /* Covariates have to be included here again */
3287: cov[1]=1.;
1.214 brouard 3288: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3289: cov[2]=agexact;
3290: if(nagesqr==1)
1.227 brouard 3291: cov[3]= agexact*agexact;
1.235 brouard 3292: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3293: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3294: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3295: /* 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)); */
3296: }
3297: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3298: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3299: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3300: /* 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]); */
3301: }
3302: for (k=1; k<=cptcovage;k++){
3303: if(Dummy[Tvar[Tage[k]]]){
3304: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3305: } else{
3306: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3307: }
3308: /* 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]); */
3309: }
3310: for (k=1; k<=cptcovprod;k++){ /* */
3311: /* 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]); */
3312: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3313: }
3314: /* for (k=1; k<=cptcovn;k++) */
3315: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3316: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3317: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3318: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3319: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3320:
3321:
1.126 brouard 3322: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3323: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3324: /* right multiplication of oldm by the current matrix */
1.126 brouard 3325: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3326: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3327: /* if((int)age == 70){ */
3328: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3329: /* for(i=1; i<=nlstate+ndeath; i++) { */
3330: /* printf("%d pmmij ",i); */
3331: /* for(j=1;j<=nlstate+ndeath;j++) { */
3332: /* printf("%f ",pmmij[i][j]); */
3333: /* } */
3334: /* printf(" oldm "); */
3335: /* for(j=1;j<=nlstate+ndeath;j++) { */
3336: /* printf("%f ",oldm[i][j]); */
3337: /* } */
3338: /* printf("\n"); */
3339: /* } */
3340: /* } */
1.126 brouard 3341: savm=oldm;
3342: oldm=newm;
3343: }
3344: for(i=1; i<=nlstate+ndeath; i++)
3345: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3346: po[i][j][h]=newm[i][j];
3347: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3348: }
1.128 brouard 3349: /*printf("h=%d ",h);*/
1.126 brouard 3350: } /* end h */
1.267 brouard 3351: /* printf("\n H=%d \n",h); */
1.126 brouard 3352: return po;
3353: }
3354:
1.217 brouard 3355: /************* Higher Back Matrix Product ***************/
1.218 brouard 3356: /* 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 3357: 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 3358: {
1.266 brouard 3359: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3360: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3361: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3362: nhstepm*hstepm matrices.
3363: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3364: (typically every 2 years instead of every month which is too big
1.217 brouard 3365: for the memory).
1.218 brouard 3366: Model is determined by parameters x and covariates have to be
1.266 brouard 3367: included manually here. Then we use a call to bmij(x and cov)
3368: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3369: */
1.217 brouard 3370:
3371: int i, j, d, h, k;
1.266 brouard 3372: double **out, cov[NCOVMAX+1], **bmij();
3373: double **newm, ***newmm;
1.217 brouard 3374: double agexact;
3375: double agebegin, ageend;
1.222 brouard 3376: double **oldm, **savm;
1.217 brouard 3377:
1.266 brouard 3378: newmm=po; /* To be saved */
3379: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3380: /* Hstepm could be zero and should return the unit matrix */
3381: for (i=1;i<=nlstate+ndeath;i++)
3382: for (j=1;j<=nlstate+ndeath;j++){
3383: oldm[i][j]=(i==j ? 1.0 : 0.0);
3384: po[i][j][0]=(i==j ? 1.0 : 0.0);
3385: }
3386: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3387: for(h=1; h <=nhstepm; h++){
3388: for(d=1; d <=hstepm; d++){
3389: newm=savm;
3390: /* Covariates have to be included here again */
3391: cov[1]=1.;
1.271 brouard 3392: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3393: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3394: cov[2]=agexact;
3395: if(nagesqr==1)
1.222 brouard 3396: cov[3]= agexact*agexact;
1.266 brouard 3397: for (k=1; k<=cptcovn;k++){
3398: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3399: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3400: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3401: /* 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)); */
3402: }
1.267 brouard 3403: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3404: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3405: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3406: /* 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]); */
3407: }
3408: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3409: if(Dummy[Tvar[Tage[k]]]){
3410: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3411: } else{
3412: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3413: }
3414: /* 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]); */
3415: }
3416: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3417: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3418: }
1.217 brouard 3419: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3420: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3421:
1.218 brouard 3422: /* Careful transposed matrix */
1.266 brouard 3423: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3424: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3425: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3426: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3427: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3428: /* if((int)age == 70){ */
3429: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3430: /* for(i=1; i<=nlstate+ndeath; i++) { */
3431: /* printf("%d pmmij ",i); */
3432: /* for(j=1;j<=nlstate+ndeath;j++) { */
3433: /* printf("%f ",pmmij[i][j]); */
3434: /* } */
3435: /* printf(" oldm "); */
3436: /* for(j=1;j<=nlstate+ndeath;j++) { */
3437: /* printf("%f ",oldm[i][j]); */
3438: /* } */
3439: /* printf("\n"); */
3440: /* } */
3441: /* } */
3442: savm=oldm;
3443: oldm=newm;
3444: }
3445: for(i=1; i<=nlstate+ndeath; i++)
3446: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3447: po[i][j][h]=newm[i][j];
1.268 brouard 3448: /* if(h==nhstepm) */
3449: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3450: }
1.268 brouard 3451: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3452: } /* end h */
1.268 brouard 3453: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3454: return po;
3455: }
3456:
3457:
1.162 brouard 3458: #ifdef NLOPT
3459: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3460: double fret;
3461: double *xt;
3462: int j;
3463: myfunc_data *d2 = (myfunc_data *) pd;
3464: /* xt = (p1-1); */
3465: xt=vector(1,n);
3466: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3467:
3468: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3469: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3470: printf("Function = %.12lf ",fret);
3471: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3472: printf("\n");
3473: free_vector(xt,1,n);
3474: return fret;
3475: }
3476: #endif
1.126 brouard 3477:
3478: /*************** log-likelihood *************/
3479: double func( double *x)
3480: {
1.226 brouard 3481: int i, ii, j, k, mi, d, kk;
3482: int ioffset=0;
3483: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3484: double **out;
3485: double lli; /* Individual log likelihood */
3486: int s1, s2;
1.228 brouard 3487: 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 3488: double bbh, survp;
3489: long ipmx;
3490: double agexact;
3491: /*extern weight */
3492: /* We are differentiating ll according to initial status */
3493: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3494: /*for(i=1;i<imx;i++)
3495: printf(" %d\n",s[4][i]);
3496: */
1.162 brouard 3497:
1.226 brouard 3498: ++countcallfunc;
1.162 brouard 3499:
1.226 brouard 3500: cov[1]=1.;
1.126 brouard 3501:
1.226 brouard 3502: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3503: ioffset=0;
1.226 brouard 3504: if(mle==1){
3505: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3506: /* Computes the values of the ncovmodel covariates of the model
3507: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3508: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3509: to be observed in j being in i according to the model.
3510: */
1.243 brouard 3511: ioffset=2+nagesqr ;
1.233 brouard 3512: /* Fixed */
1.234 brouard 3513: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3514: 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)*/
3515: }
1.226 brouard 3516: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3517: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3518: has been calculated etc */
3519: /* For an individual i, wav[i] gives the number of effective waves */
3520: /* We compute the contribution to Likelihood of each effective transition
3521: mw[mi][i] is real wave of the mi th effectve wave */
3522: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3523: s2=s[mw[mi+1][i]][i];
3524: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3525: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3526: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3527: */
3528: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3529: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3530: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3531: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3532: }
3533: for (ii=1;ii<=nlstate+ndeath;ii++)
3534: for (j=1;j<=nlstate+ndeath;j++){
3535: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3536: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3537: }
3538: for(d=0; d<dh[mi][i]; d++){
3539: newm=savm;
3540: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3541: cov[2]=agexact;
3542: if(nagesqr==1)
3543: cov[3]= agexact*agexact; /* Should be changed here */
3544: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3545: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3546: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3547: else
3548: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3549: }
3550: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3551: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3552: savm=oldm;
3553: oldm=newm;
3554: } /* end mult */
3555:
3556: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3557: /* But now since version 0.9 we anticipate for bias at large stepm.
3558: * If stepm is larger than one month (smallest stepm) and if the exact delay
3559: * (in months) between two waves is not a multiple of stepm, we rounded to
3560: * the nearest (and in case of equal distance, to the lowest) interval but now
3561: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3562: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3563: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3564: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3565: * -stepm/2 to stepm/2 .
3566: * For stepm=1 the results are the same as for previous versions of Imach.
3567: * For stepm > 1 the results are less biased than in previous versions.
3568: */
1.234 brouard 3569: s1=s[mw[mi][i]][i];
3570: s2=s[mw[mi+1][i]][i];
3571: bbh=(double)bh[mi][i]/(double)stepm;
3572: /* bias bh is positive if real duration
3573: * is higher than the multiple of stepm and negative otherwise.
3574: */
3575: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3576: if( s2 > nlstate){
3577: /* i.e. if s2 is a death state and if the date of death is known
3578: then the contribution to the likelihood is the probability to
3579: die between last step unit time and current step unit time,
3580: which is also equal to probability to die before dh
3581: minus probability to die before dh-stepm .
3582: In version up to 0.92 likelihood was computed
3583: as if date of death was unknown. Death was treated as any other
3584: health state: the date of the interview describes the actual state
3585: and not the date of a change in health state. The former idea was
3586: to consider that at each interview the state was recorded
3587: (healthy, disable or death) and IMaCh was corrected; but when we
3588: introduced the exact date of death then we should have modified
3589: the contribution of an exact death to the likelihood. This new
3590: contribution is smaller and very dependent of the step unit
3591: stepm. It is no more the probability to die between last interview
3592: and month of death but the probability to survive from last
3593: interview up to one month before death multiplied by the
3594: probability to die within a month. Thanks to Chris
3595: Jackson for correcting this bug. Former versions increased
3596: mortality artificially. The bad side is that we add another loop
3597: which slows down the processing. The difference can be up to 10%
3598: lower mortality.
3599: */
3600: /* If, at the beginning of the maximization mostly, the
3601: cumulative probability or probability to be dead is
3602: constant (ie = 1) over time d, the difference is equal to
3603: 0. out[s1][3] = savm[s1][3]: probability, being at state
3604: s1 at precedent wave, to be dead a month before current
3605: wave is equal to probability, being at state s1 at
3606: precedent wave, to be dead at mont of the current
3607: wave. Then the observed probability (that this person died)
3608: is null according to current estimated parameter. In fact,
3609: it should be very low but not zero otherwise the log go to
3610: infinity.
3611: */
1.183 brouard 3612: /* #ifdef INFINITYORIGINAL */
3613: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3614: /* #else */
3615: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3616: /* lli=log(mytinydouble); */
3617: /* else */
3618: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3619: /* #endif */
1.226 brouard 3620: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3621:
1.226 brouard 3622: } else if ( s2==-1 ) { /* alive */
3623: for (j=1,survp=0. ; j<=nlstate; j++)
3624: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3625: /*survp += out[s1][j]; */
3626: lli= log(survp);
3627: }
3628: else if (s2==-4) {
3629: for (j=3,survp=0. ; j<=nlstate; j++)
3630: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3631: lli= log(survp);
3632: }
3633: else if (s2==-5) {
3634: for (j=1,survp=0. ; j<=2; j++)
3635: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3636: lli= log(survp);
3637: }
3638: else{
3639: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3640: /* 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 */
3641: }
3642: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3643: /*if(lli ==000.0)*/
3644: /*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); */
3645: ipmx +=1;
3646: sw += weight[i];
3647: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3648: /* if (lli < log(mytinydouble)){ */
3649: /* 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); */
3650: /* 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]); */
3651: /* } */
3652: } /* end of wave */
3653: } /* end of individual */
3654: } else if(mle==2){
3655: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3656: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3657: for(mi=1; mi<= wav[i]-1; mi++){
3658: for (ii=1;ii<=nlstate+ndeath;ii++)
3659: for (j=1;j<=nlstate+ndeath;j++){
3660: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3661: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3662: }
3663: for(d=0; d<=dh[mi][i]; d++){
3664: newm=savm;
3665: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3666: cov[2]=agexact;
3667: if(nagesqr==1)
3668: cov[3]= agexact*agexact;
3669: for (kk=1; kk<=cptcovage;kk++) {
3670: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3671: }
3672: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3673: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3674: savm=oldm;
3675: oldm=newm;
3676: } /* end mult */
3677:
3678: s1=s[mw[mi][i]][i];
3679: s2=s[mw[mi+1][i]][i];
3680: bbh=(double)bh[mi][i]/(double)stepm;
3681: 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 */
3682: ipmx +=1;
3683: sw += weight[i];
3684: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3685: } /* end of wave */
3686: } /* end of individual */
3687: } else if(mle==3){ /* exponential inter-extrapolation */
3688: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3689: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3690: for(mi=1; mi<= wav[i]-1; mi++){
3691: for (ii=1;ii<=nlstate+ndeath;ii++)
3692: for (j=1;j<=nlstate+ndeath;j++){
3693: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3694: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3695: }
3696: for(d=0; d<dh[mi][i]; d++){
3697: newm=savm;
3698: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3699: cov[2]=agexact;
3700: if(nagesqr==1)
3701: cov[3]= agexact*agexact;
3702: for (kk=1; kk<=cptcovage;kk++) {
3703: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3704: }
3705: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3706: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3707: savm=oldm;
3708: oldm=newm;
3709: } /* end mult */
3710:
3711: s1=s[mw[mi][i]][i];
3712: s2=s[mw[mi+1][i]][i];
3713: bbh=(double)bh[mi][i]/(double)stepm;
3714: 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 */
3715: ipmx +=1;
3716: sw += weight[i];
3717: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3718: } /* end of wave */
3719: } /* end of individual */
3720: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3721: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3722: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3723: for(mi=1; mi<= wav[i]-1; mi++){
3724: for (ii=1;ii<=nlstate+ndeath;ii++)
3725: for (j=1;j<=nlstate+ndeath;j++){
3726: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3727: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3728: }
3729: for(d=0; d<dh[mi][i]; d++){
3730: newm=savm;
3731: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3732: cov[2]=agexact;
3733: if(nagesqr==1)
3734: cov[3]= agexact*agexact;
3735: for (kk=1; kk<=cptcovage;kk++) {
3736: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3737: }
1.126 brouard 3738:
1.226 brouard 3739: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3740: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3741: savm=oldm;
3742: oldm=newm;
3743: } /* end mult */
3744:
3745: s1=s[mw[mi][i]][i];
3746: s2=s[mw[mi+1][i]][i];
3747: if( s2 > nlstate){
3748: lli=log(out[s1][s2] - savm[s1][s2]);
3749: } else if ( s2==-1 ) { /* alive */
3750: for (j=1,survp=0. ; j<=nlstate; j++)
3751: survp += out[s1][j];
3752: lli= log(survp);
3753: }else{
3754: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3755: }
3756: ipmx +=1;
3757: sw += weight[i];
3758: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3759: /* 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 3760: } /* end of wave */
3761: } /* end of individual */
3762: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3763: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3764: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3765: for(mi=1; mi<= wav[i]-1; mi++){
3766: for (ii=1;ii<=nlstate+ndeath;ii++)
3767: for (j=1;j<=nlstate+ndeath;j++){
3768: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3769: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3770: }
3771: for(d=0; d<dh[mi][i]; d++){
3772: newm=savm;
3773: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3774: cov[2]=agexact;
3775: if(nagesqr==1)
3776: cov[3]= agexact*agexact;
3777: for (kk=1; kk<=cptcovage;kk++) {
3778: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3779: }
1.126 brouard 3780:
1.226 brouard 3781: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3782: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3783: savm=oldm;
3784: oldm=newm;
3785: } /* end mult */
3786:
3787: s1=s[mw[mi][i]][i];
3788: s2=s[mw[mi+1][i]][i];
3789: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3790: ipmx +=1;
3791: sw += weight[i];
3792: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3793: /*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]);*/
3794: } /* end of wave */
3795: } /* end of individual */
3796: } /* End of if */
3797: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3798: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3799: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3800: return -l;
1.126 brouard 3801: }
3802:
3803: /*************** log-likelihood *************/
3804: double funcone( double *x)
3805: {
1.228 brouard 3806: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3807: int i, ii, j, k, mi, d, kk;
1.228 brouard 3808: int ioffset=0;
1.131 brouard 3809: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3810: double **out;
3811: double lli; /* Individual log likelihood */
3812: double llt;
3813: int s1, s2;
1.228 brouard 3814: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3815:
1.126 brouard 3816: double bbh, survp;
1.187 brouard 3817: double agexact;
1.214 brouard 3818: double agebegin, ageend;
1.126 brouard 3819: /*extern weight */
3820: /* We are differentiating ll according to initial status */
3821: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3822: /*for(i=1;i<imx;i++)
3823: printf(" %d\n",s[4][i]);
3824: */
3825: cov[1]=1.;
3826:
3827: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3828: ioffset=0;
3829: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3830: /* ioffset=2+nagesqr+cptcovage; */
3831: ioffset=2+nagesqr;
1.232 brouard 3832: /* Fixed */
1.224 brouard 3833: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3834: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3835: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3836: 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)*/
3837: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3838: /* cov[2+6]=covar[Tvar[6]][i]; */
3839: /* cov[2+6]=covar[2][i]; V2 */
3840: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3841: /* cov[2+7]=covar[Tvar[7]][i]; */
3842: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3843: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3844: /* cov[2+9]=covar[Tvar[9]][i]; */
3845: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3846: }
1.232 brouard 3847: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3848: /* 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?)*\/ */
3849: /* } */
1.231 brouard 3850: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3851: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3852: /* } */
1.225 brouard 3853:
1.233 brouard 3854:
3855: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3856: /* Wave varying (but not age varying) */
3857: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3858: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3859: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3860: }
1.232 brouard 3861: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3862: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3863: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3864: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3865: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3866: /* 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 3867: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3868: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3869: /* /\* 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]); *\/ */
3870: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3871: /* } */
1.126 brouard 3872: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3873: for (j=1;j<=nlstate+ndeath;j++){
3874: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3875: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3876: }
1.214 brouard 3877:
3878: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3879: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3880: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3881: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3882: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3883: and mw[mi+1][i]. dh depends on stepm.*/
3884: newm=savm;
1.247 brouard 3885: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3886: cov[2]=agexact;
3887: if(nagesqr==1)
3888: cov[3]= agexact*agexact;
3889: for (kk=1; kk<=cptcovage;kk++) {
3890: if(!FixedV[Tvar[Tage[kk]]])
3891: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3892: else
3893: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3894: }
3895: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3896: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3897: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3898: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3899: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3900: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3901: savm=oldm;
3902: oldm=newm;
1.126 brouard 3903: } /* end mult */
3904:
3905: s1=s[mw[mi][i]][i];
3906: s2=s[mw[mi+1][i]][i];
1.217 brouard 3907: /* if(s2==-1){ */
1.268 brouard 3908: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3909: /* /\* exit(1); *\/ */
3910: /* } */
1.126 brouard 3911: bbh=(double)bh[mi][i]/(double)stepm;
3912: /* bias is positive if real duration
3913: * is higher than the multiple of stepm and negative otherwise.
3914: */
3915: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3916: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3917: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3918: for (j=1,survp=0. ; j<=nlstate; j++)
3919: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3920: lli= log(survp);
1.126 brouard 3921: }else if (mle==1){
1.242 brouard 3922: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3923: } else if(mle==2){
1.242 brouard 3924: 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 3925: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3926: 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 3927: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3928: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3929: } else{ /* mle=0 back to 1 */
1.242 brouard 3930: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3931: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3932: } /* End of if */
3933: ipmx +=1;
3934: sw += weight[i];
3935: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3936: /*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 3937: if(globpr){
1.246 brouard 3938: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3939: %11.6f %11.6f %11.6f ", \
1.242 brouard 3940: 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 3941: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3942: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3943: llt +=ll[k]*gipmx/gsw;
3944: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3945: }
3946: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3947: }
1.232 brouard 3948: } /* end of wave */
3949: } /* end of individual */
3950: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3951: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3952: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3953: if(globpr==0){ /* First time we count the contributions and weights */
3954: gipmx=ipmx;
3955: gsw=sw;
3956: }
3957: return -l;
1.126 brouard 3958: }
3959:
3960:
3961: /*************** function likelione ***********/
1.292 brouard 3962: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3963: {
3964: /* This routine should help understanding what is done with
3965: the selection of individuals/waves and
3966: to check the exact contribution to the likelihood.
3967: Plotting could be done.
3968: */
3969: int k;
3970:
3971: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3972: strcpy(fileresilk,"ILK_");
1.202 brouard 3973: strcat(fileresilk,fileresu);
1.126 brouard 3974: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3975: printf("Problem with resultfile: %s\n", fileresilk);
3976: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3977: }
1.214 brouard 3978: 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");
3979: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3980: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3981: for(k=1; k<=nlstate; k++)
3982: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3983: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3984: }
3985:
1.292 brouard 3986: *fretone=(*func)(p);
1.126 brouard 3987: if(*globpri !=0){
3988: fclose(ficresilk);
1.205 brouard 3989: if (mle ==0)
3990: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3991: else if(mle >=1)
3992: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3993: 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 3994: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3995:
3996: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3997: 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 3998: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3999: }
1.207 brouard 4000: 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 4001: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4002: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 4003: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 4004: fflush(fichtm);
1.205 brouard 4005: }
1.126 brouard 4006: return;
4007: }
4008:
4009:
4010: /*********** Maximum Likelihood Estimation ***************/
4011:
4012: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4013: {
1.165 brouard 4014: int i,j, iter=0;
1.126 brouard 4015: double **xi;
4016: double fret;
4017: double fretone; /* Only one call to likelihood */
4018: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4019:
4020: #ifdef NLOPT
4021: int creturn;
4022: nlopt_opt opt;
4023: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4024: double *lb;
4025: double minf; /* the minimum objective value, upon return */
4026: double * p1; /* Shifted parameters from 0 instead of 1 */
4027: myfunc_data dinst, *d = &dinst;
4028: #endif
4029:
4030:
1.126 brouard 4031: xi=matrix(1,npar,1,npar);
4032: for (i=1;i<=npar;i++)
4033: for (j=1;j<=npar;j++)
4034: xi[i][j]=(i==j ? 1.0 : 0.0);
4035: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4036: strcpy(filerespow,"POW_");
1.126 brouard 4037: strcat(filerespow,fileres);
4038: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4039: printf("Problem with resultfile: %s\n", filerespow);
4040: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4041: }
4042: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4043: for (i=1;i<=nlstate;i++)
4044: for(j=1;j<=nlstate+ndeath;j++)
4045: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4046: fprintf(ficrespow,"\n");
1.162 brouard 4047: #ifdef POWELL
1.126 brouard 4048: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4049: #endif
1.126 brouard 4050:
1.162 brouard 4051: #ifdef NLOPT
4052: #ifdef NEWUOA
4053: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4054: #else
4055: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4056: #endif
4057: lb=vector(0,npar-1);
4058: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4059: nlopt_set_lower_bounds(opt, lb);
4060: nlopt_set_initial_step1(opt, 0.1);
4061:
4062: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4063: d->function = func;
4064: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4065: nlopt_set_min_objective(opt, myfunc, d);
4066: nlopt_set_xtol_rel(opt, ftol);
4067: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4068: printf("nlopt failed! %d\n",creturn);
4069: }
4070: else {
4071: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4072: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4073: iter=1; /* not equal */
4074: }
4075: nlopt_destroy(opt);
4076: #endif
1.126 brouard 4077: free_matrix(xi,1,npar,1,npar);
4078: fclose(ficrespow);
1.203 brouard 4079: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4080: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4081: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4082:
4083: }
4084:
4085: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4086: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4087: {
4088: double **a,**y,*x,pd;
1.203 brouard 4089: /* double **hess; */
1.164 brouard 4090: int i, j;
1.126 brouard 4091: int *indx;
4092:
4093: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4094: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4095: void lubksb(double **a, int npar, int *indx, double b[]) ;
4096: void ludcmp(double **a, int npar, int *indx, double *d) ;
4097: double gompertz(double p[]);
1.203 brouard 4098: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4099:
4100: printf("\nCalculation of the hessian matrix. Wait...\n");
4101: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4102: for (i=1;i<=npar;i++){
1.203 brouard 4103: printf("%d-",i);fflush(stdout);
4104: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4105:
4106: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4107:
4108: /* printf(" %f ",p[i]);
4109: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4110: }
4111:
4112: for (i=1;i<=npar;i++) {
4113: for (j=1;j<=npar;j++) {
4114: if (j>i) {
1.203 brouard 4115: printf(".%d-%d",i,j);fflush(stdout);
4116: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4117: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4118:
4119: hess[j][i]=hess[i][j];
4120: /*printf(" %lf ",hess[i][j]);*/
4121: }
4122: }
4123: }
4124: printf("\n");
4125: fprintf(ficlog,"\n");
4126:
4127: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4128: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4129:
4130: a=matrix(1,npar,1,npar);
4131: y=matrix(1,npar,1,npar);
4132: x=vector(1,npar);
4133: indx=ivector(1,npar);
4134: for (i=1;i<=npar;i++)
4135: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4136: ludcmp(a,npar,indx,&pd);
4137:
4138: for (j=1;j<=npar;j++) {
4139: for (i=1;i<=npar;i++) x[i]=0;
4140: x[j]=1;
4141: lubksb(a,npar,indx,x);
4142: for (i=1;i<=npar;i++){
4143: matcov[i][j]=x[i];
4144: }
4145: }
4146:
4147: printf("\n#Hessian matrix#\n");
4148: fprintf(ficlog,"\n#Hessian matrix#\n");
4149: for (i=1;i<=npar;i++) {
4150: for (j=1;j<=npar;j++) {
1.203 brouard 4151: printf("%.6e ",hess[i][j]);
4152: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4153: }
4154: printf("\n");
4155: fprintf(ficlog,"\n");
4156: }
4157:
1.203 brouard 4158: /* printf("\n#Covariance matrix#\n"); */
4159: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4160: /* for (i=1;i<=npar;i++) { */
4161: /* for (j=1;j<=npar;j++) { */
4162: /* printf("%.6e ",matcov[i][j]); */
4163: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4164: /* } */
4165: /* printf("\n"); */
4166: /* fprintf(ficlog,"\n"); */
4167: /* } */
4168:
1.126 brouard 4169: /* Recompute Inverse */
1.203 brouard 4170: /* for (i=1;i<=npar;i++) */
4171: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4172: /* ludcmp(a,npar,indx,&pd); */
4173:
4174: /* printf("\n#Hessian matrix recomputed#\n"); */
4175:
4176: /* for (j=1;j<=npar;j++) { */
4177: /* for (i=1;i<=npar;i++) x[i]=0; */
4178: /* x[j]=1; */
4179: /* lubksb(a,npar,indx,x); */
4180: /* for (i=1;i<=npar;i++){ */
4181: /* y[i][j]=x[i]; */
4182: /* printf("%.3e ",y[i][j]); */
4183: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4184: /* } */
4185: /* printf("\n"); */
4186: /* fprintf(ficlog,"\n"); */
4187: /* } */
4188:
4189: /* Verifying the inverse matrix */
4190: #ifdef DEBUGHESS
4191: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4192:
1.203 brouard 4193: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4194: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4195:
4196: for (j=1;j<=npar;j++) {
4197: for (i=1;i<=npar;i++){
1.203 brouard 4198: printf("%.2f ",y[i][j]);
4199: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4200: }
4201: printf("\n");
4202: fprintf(ficlog,"\n");
4203: }
1.203 brouard 4204: #endif
1.126 brouard 4205:
4206: free_matrix(a,1,npar,1,npar);
4207: free_matrix(y,1,npar,1,npar);
4208: free_vector(x,1,npar);
4209: free_ivector(indx,1,npar);
1.203 brouard 4210: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4211:
4212:
4213: }
4214:
4215: /*************** hessian matrix ****************/
4216: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4217: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4218: int i;
4219: int l=1, lmax=20;
1.203 brouard 4220: double k1,k2, res, fx;
1.132 brouard 4221: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4222: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4223: int k=0,kmax=10;
4224: double l1;
4225:
4226: fx=func(x);
4227: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4228: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4229: l1=pow(10,l);
4230: delts=delt;
4231: for(k=1 ; k <kmax; k=k+1){
4232: delt = delta*(l1*k);
4233: p2[theta]=x[theta] +delt;
1.145 brouard 4234: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4235: p2[theta]=x[theta]-delt;
4236: k2=func(p2)-fx;
4237: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4238: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4239:
1.203 brouard 4240: #ifdef DEBUGHESSII
1.126 brouard 4241: 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);
4242: 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);
4243: #endif
4244: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4245: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4246: k=kmax;
4247: }
4248: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4249: k=kmax; l=lmax*10;
1.126 brouard 4250: }
4251: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4252: delts=delt;
4253: }
1.203 brouard 4254: } /* End loop k */
1.126 brouard 4255: }
4256: delti[theta]=delts;
4257: return res;
4258:
4259: }
4260:
1.203 brouard 4261: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4262: {
4263: int i;
1.164 brouard 4264: int l=1, lmax=20;
1.126 brouard 4265: double k1,k2,k3,k4,res,fx;
1.132 brouard 4266: double p2[MAXPARM+1];
1.203 brouard 4267: int k, kmax=1;
4268: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4269:
4270: int firstime=0;
1.203 brouard 4271:
1.126 brouard 4272: fx=func(x);
1.203 brouard 4273: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4274: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4275: p2[thetai]=x[thetai]+delti[thetai]*k;
4276: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4277: k1=func(p2)-fx;
4278:
1.203 brouard 4279: p2[thetai]=x[thetai]+delti[thetai]*k;
4280: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4281: k2=func(p2)-fx;
4282:
1.203 brouard 4283: p2[thetai]=x[thetai]-delti[thetai]*k;
4284: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4285: k3=func(p2)-fx;
4286:
1.203 brouard 4287: p2[thetai]=x[thetai]-delti[thetai]*k;
4288: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4289: k4=func(p2)-fx;
1.203 brouard 4290: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4291: if(k1*k2*k3*k4 <0.){
1.208 brouard 4292: firstime=1;
1.203 brouard 4293: kmax=kmax+10;
1.208 brouard 4294: }
4295: if(kmax >=10 || firstime ==1){
1.246 brouard 4296: 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);
4297: 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 4298: 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);
4299: 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);
4300: }
4301: #ifdef DEBUGHESSIJ
4302: v1=hess[thetai][thetai];
4303: v2=hess[thetaj][thetaj];
4304: cv12=res;
4305: /* Computing eigen value of Hessian matrix */
4306: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4307: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4308: if ((lc2 <0) || (lc1 <0) ){
4309: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4310: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4311: 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);
4312: 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);
4313: }
1.126 brouard 4314: #endif
4315: }
4316: return res;
4317: }
4318:
1.203 brouard 4319: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4320: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4321: /* { */
4322: /* int i; */
4323: /* int l=1, lmax=20; */
4324: /* double k1,k2,k3,k4,res,fx; */
4325: /* double p2[MAXPARM+1]; */
4326: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4327: /* int k=0,kmax=10; */
4328: /* double l1; */
4329:
4330: /* fx=func(x); */
4331: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4332: /* l1=pow(10,l); */
4333: /* delts=delt; */
4334: /* for(k=1 ; k <kmax; k=k+1){ */
4335: /* delt = delti*(l1*k); */
4336: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4337: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4338: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4339: /* k1=func(p2)-fx; */
4340:
4341: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4342: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4343: /* k2=func(p2)-fx; */
4344:
4345: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4346: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4347: /* k3=func(p2)-fx; */
4348:
4349: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4350: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4351: /* k4=func(p2)-fx; */
4352: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4353: /* #ifdef DEBUGHESSIJ */
4354: /* 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); */
4355: /* 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); */
4356: /* #endif */
4357: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4358: /* k=kmax; */
4359: /* } */
4360: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4361: /* k=kmax; l=lmax*10; */
4362: /* } */
4363: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4364: /* delts=delt; */
4365: /* } */
4366: /* } /\* End loop k *\/ */
4367: /* } */
4368: /* delti[theta]=delts; */
4369: /* return res; */
4370: /* } */
4371:
4372:
1.126 brouard 4373: /************** Inverse of matrix **************/
4374: void ludcmp(double **a, int n, int *indx, double *d)
4375: {
4376: int i,imax,j,k;
4377: double big,dum,sum,temp;
4378: double *vv;
4379:
4380: vv=vector(1,n);
4381: *d=1.0;
4382: for (i=1;i<=n;i++) {
4383: big=0.0;
4384: for (j=1;j<=n;j++)
4385: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4386: if (big == 0.0){
4387: printf(" Singular Hessian matrix at row %d:\n",i);
4388: for (j=1;j<=n;j++) {
4389: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4390: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4391: }
4392: fflush(ficlog);
4393: fclose(ficlog);
4394: nrerror("Singular matrix in routine ludcmp");
4395: }
1.126 brouard 4396: vv[i]=1.0/big;
4397: }
4398: for (j=1;j<=n;j++) {
4399: for (i=1;i<j;i++) {
4400: sum=a[i][j];
4401: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4402: a[i][j]=sum;
4403: }
4404: big=0.0;
4405: for (i=j;i<=n;i++) {
4406: sum=a[i][j];
4407: for (k=1;k<j;k++)
4408: sum -= a[i][k]*a[k][j];
4409: a[i][j]=sum;
4410: if ( (dum=vv[i]*fabs(sum)) >= big) {
4411: big=dum;
4412: imax=i;
4413: }
4414: }
4415: if (j != imax) {
4416: for (k=1;k<=n;k++) {
4417: dum=a[imax][k];
4418: a[imax][k]=a[j][k];
4419: a[j][k]=dum;
4420: }
4421: *d = -(*d);
4422: vv[imax]=vv[j];
4423: }
4424: indx[j]=imax;
4425: if (a[j][j] == 0.0) a[j][j]=TINY;
4426: if (j != n) {
4427: dum=1.0/(a[j][j]);
4428: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4429: }
4430: }
4431: free_vector(vv,1,n); /* Doesn't work */
4432: ;
4433: }
4434:
4435: void lubksb(double **a, int n, int *indx, double b[])
4436: {
4437: int i,ii=0,ip,j;
4438: double sum;
4439:
4440: for (i=1;i<=n;i++) {
4441: ip=indx[i];
4442: sum=b[ip];
4443: b[ip]=b[i];
4444: if (ii)
4445: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4446: else if (sum) ii=i;
4447: b[i]=sum;
4448: }
4449: for (i=n;i>=1;i--) {
4450: sum=b[i];
4451: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4452: b[i]=sum/a[i][i];
4453: }
4454: }
4455:
4456: void pstamp(FILE *fichier)
4457: {
1.196 brouard 4458: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4459: }
4460:
1.297 brouard 4461: void date2dmy(double date,double *day, double *month, double *year){
4462: double yp=0., yp1=0., yp2=0.;
4463:
4464: yp1=modf(date,&yp);/* extracts integral of date in yp and
4465: fractional in yp1 */
4466: *year=yp;
4467: yp2=modf((yp1*12),&yp);
4468: *month=yp;
4469: yp1=modf((yp2*30.5),&yp);
4470: *day=yp;
4471: if(*day==0) *day=1;
4472: if(*month==0) *month=1;
4473: }
4474:
1.253 brouard 4475:
4476:
1.126 brouard 4477: /************ Frequencies ********************/
1.251 brouard 4478: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4479: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4480: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4481: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4482:
1.265 brouard 4483: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4484: int iind=0, iage=0;
4485: int mi; /* Effective wave */
4486: int first;
4487: double ***freq; /* Frequencies */
1.268 brouard 4488: 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 */
4489: 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 4490: double *meanq, *stdq, *idq;
1.226 brouard 4491: double **meanqt;
4492: double *pp, **prop, *posprop, *pospropt;
4493: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4494: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4495: double agebegin, ageend;
4496:
4497: pp=vector(1,nlstate);
1.251 brouard 4498: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4499: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4500: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4501: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4502: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4503: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4504: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4505: meanqt=matrix(1,lastpass,1,nqtveff);
4506: strcpy(fileresp,"P_");
4507: strcat(fileresp,fileresu);
4508: /*strcat(fileresphtm,fileresu);*/
4509: if((ficresp=fopen(fileresp,"w"))==NULL) {
4510: printf("Problem with prevalence resultfile: %s\n", fileresp);
4511: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4512: exit(0);
4513: }
1.240 brouard 4514:
1.226 brouard 4515: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4516: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4517: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4518: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4519: fflush(ficlog);
4520: exit(70);
4521: }
4522: else{
4523: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4524: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4525: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4526: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4527: }
1.237 brouard 4528: 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 4529:
1.226 brouard 4530: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4531: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4532: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4533: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4534: fflush(ficlog);
4535: exit(70);
1.240 brouard 4536: } else{
1.226 brouard 4537: 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 4538: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4539: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4540: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4541: }
1.240 brouard 4542: 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);
4543:
1.253 brouard 4544: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4545: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4546: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4547: j1=0;
1.126 brouard 4548:
1.227 brouard 4549: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4550: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4551: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4552:
4553:
1.226 brouard 4554: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4555: reference=low_education V1=0,V2=0
4556: med_educ V1=1 V2=0,
4557: high_educ V1=0 V2=1
4558: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4559: */
1.249 brouard 4560: dateintsum=0;
4561: k2cpt=0;
4562:
1.253 brouard 4563: if(cptcoveff == 0 )
1.265 brouard 4564: nl=1; /* Constant and age model only */
1.253 brouard 4565: else
4566: nl=2;
1.265 brouard 4567:
4568: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4569: /* Loop on nj=1 or 2 if dummy covariates j!=0
4570: * Loop on j1(1 to 2**cptcoveff) covariate combination
4571: * freq[s1][s2][iage] =0.
4572: * Loop on iind
4573: * ++freq[s1][s2][iage] weighted
4574: * end iind
4575: * if covariate and j!0
4576: * headers Variable on one line
4577: * endif cov j!=0
4578: * header of frequency table by age
4579: * Loop on age
4580: * pp[s1]+=freq[s1][s2][iage] weighted
4581: * pos+=freq[s1][s2][iage] weighted
4582: * Loop on s1 initial state
4583: * fprintf(ficresp
4584: * end s1
4585: * end age
4586: * if j!=0 computes starting values
4587: * end compute starting values
4588: * end j1
4589: * end nl
4590: */
1.253 brouard 4591: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4592: if(nj==1)
4593: j=0; /* First pass for the constant */
1.265 brouard 4594: else{
1.253 brouard 4595: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4596: }
1.251 brouard 4597: first=1;
1.265 brouard 4598: 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 4599: posproptt=0.;
4600: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4601: scanf("%d", i);*/
4602: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4603: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4604: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4605: freq[i][s2][m]=0;
1.251 brouard 4606:
4607: for (i=1; i<=nlstate; i++) {
1.240 brouard 4608: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4609: prop[i][m]=0;
4610: posprop[i]=0;
4611: pospropt[i]=0;
4612: }
1.283 brouard 4613: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4614: idq[z1]=0.;
4615: meanq[z1]=0.;
4616: stdq[z1]=0.;
1.283 brouard 4617: }
4618: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4619: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4620: /* meanqt[m][z1]=0.; */
4621: /* } */
4622: /* } */
1.251 brouard 4623: /* dateintsum=0; */
4624: /* k2cpt=0; */
4625:
1.265 brouard 4626: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4627: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4628: bool=1;
4629: if(j !=0){
4630: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4631: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4632: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4633: /* if(Tvaraff[z1] ==-20){ */
4634: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4635: /* }else if(Tvaraff[z1] ==-10){ */
4636: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4637: /* }else */
4638: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4639: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4640: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4641: /* 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",
4642: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4643: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4644: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4645: } /* Onlyf fixed */
4646: } /* end z1 */
4647: } /* cptcovn > 0 */
4648: } /* end any */
4649: }/* end j==0 */
1.265 brouard 4650: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4651: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4652: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4653: m=mw[mi][iind];
4654: if(j!=0){
4655: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4656: for (z1=1; z1<=cptcoveff; z1++) {
4657: if( Fixed[Tmodelind[z1]]==1){
4658: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4659: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4660: value is -1, we don't select. It differs from the
4661: constant and age model which counts them. */
4662: bool=0; /* not selected */
4663: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4664: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4665: bool=0;
4666: }
4667: }
4668: }
4669: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4670: } /* end j==0 */
4671: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4672: if(bool==1){ /*Selected */
1.251 brouard 4673: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4674: and mw[mi+1][iind]. dh depends on stepm. */
4675: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4676: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4677: if(m >=firstpass && m <=lastpass){
4678: k2=anint[m][iind]+(mint[m][iind]/12.);
4679: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4680: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4681: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4682: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4683: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4684: if (m<lastpass) {
4685: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4686: /* 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]); */
4687: if(s[m][iind]==-1)
4688: 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.));
4689: 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 4690: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4691: idq[z1]=idq[z1]+weight[iind];
4692: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4693: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4694: }
1.251 brouard 4695: /* if((int)agev[m][iind] == 55) */
4696: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4697: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4698: 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 4699: }
1.251 brouard 4700: } /* end if between passes */
4701: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4702: dateintsum=dateintsum+k2; /* on all covariates ?*/
4703: k2cpt++;
4704: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4705: }
1.251 brouard 4706: }else{
4707: bool=1;
4708: }/* end bool 2 */
4709: } /* end m */
1.284 brouard 4710: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4711: /* idq[z1]=idq[z1]+weight[iind]; */
4712: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4713: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4714: /* } */
1.251 brouard 4715: } /* end bool */
4716: } /* end iind = 1 to imx */
4717: /* prop[s][age] is feeded for any initial and valid live state as well as
4718: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4719:
4720:
4721: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4722: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4723: pstamp(ficresp);
1.251 brouard 4724: if (cptcoveff>0 && j!=0){
1.265 brouard 4725: pstamp(ficresp);
1.251 brouard 4726: printf( "\n#********** Variable ");
4727: fprintf(ficresp, "\n#********** Variable ");
4728: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4729: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4730: fprintf(ficlog, "\n#********** Variable ");
4731: for (z1=1; z1<=cptcoveff; z1++){
4732: if(!FixedV[Tvaraff[z1]]){
4733: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4734: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4735: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4736: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4737: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4738: }else{
1.251 brouard 4739: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4740: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4741: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4742: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4743: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4744: }
4745: }
4746: printf( "**********\n#");
4747: fprintf(ficresp, "**********\n#");
4748: fprintf(ficresphtm, "**********</h3>\n");
4749: fprintf(ficresphtmfr, "**********</h3>\n");
4750: fprintf(ficlog, "**********\n");
4751: }
1.284 brouard 4752: /*
4753: Printing means of quantitative variables if any
4754: */
4755: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4756: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4757: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4758: if(weightopt==1){
4759: printf(" Weighted mean and standard deviation of");
4760: fprintf(ficlog," Weighted mean and standard deviation of");
4761: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4762: }
1.285 brouard 4763: 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]));
4764: 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]));
4765: 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 4766: }
4767: /* for (z1=1; z1<= nqtveff; z1++) { */
4768: /* for(m=1;m<=lastpass;m++){ */
4769: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4770: /* } */
4771: /* } */
1.283 brouard 4772:
1.251 brouard 4773: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4774: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4775: fprintf(ficresp, " Age");
4776: 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 4777: for(i=1; i<=nlstate;i++) {
1.265 brouard 4778: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4779: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4780: }
1.265 brouard 4781: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4782: fprintf(ficresphtm, "\n");
4783:
4784: /* Header of frequency table by age */
4785: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4786: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4787: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4788: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4789: if(s2!=0 && m!=0)
4790: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4791: }
1.226 brouard 4792: }
1.251 brouard 4793: fprintf(ficresphtmfr, "\n");
4794:
4795: /* For each age */
4796: for(iage=iagemin; iage <= iagemax+3; iage++){
4797: fprintf(ficresphtm,"<tr>");
4798: if(iage==iagemax+1){
4799: fprintf(ficlog,"1");
4800: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4801: }else if(iage==iagemax+2){
4802: fprintf(ficlog,"0");
4803: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4804: }else if(iage==iagemax+3){
4805: fprintf(ficlog,"Total");
4806: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4807: }else{
1.240 brouard 4808: if(first==1){
1.251 brouard 4809: first=0;
4810: printf("See log file for details...\n");
4811: }
4812: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4813: fprintf(ficlog,"Age %d", iage);
4814: }
1.265 brouard 4815: for(s1=1; s1 <=nlstate ; s1++){
4816: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4817: pp[s1] += freq[s1][m][iage];
1.251 brouard 4818: }
1.265 brouard 4819: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4820: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4821: pos += freq[s1][m][iage];
4822: if(pp[s1]>=1.e-10){
1.251 brouard 4823: if(first==1){
1.265 brouard 4824: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4825: }
1.265 brouard 4826: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4827: }else{
4828: if(first==1)
1.265 brouard 4829: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4830: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4831: }
4832: }
4833:
1.265 brouard 4834: for(s1=1; s1 <=nlstate ; s1++){
4835: /* posprop[s1]=0; */
4836: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4837: pp[s1] += freq[s1][m][iage];
4838: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4839:
4840: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4841: pos += pp[s1]; /* pos is the total number of transitions until this age */
4842: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4843: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4844: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4845: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4846: }
4847:
4848: /* Writing ficresp */
4849: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4850: if( iage <= iagemax){
4851: fprintf(ficresp," %d",iage);
4852: }
4853: }else if( nj==2){
4854: if( iage <= iagemax){
4855: fprintf(ficresp," %d",iage);
4856: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4857: }
1.240 brouard 4858: }
1.265 brouard 4859: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4860: if(pos>=1.e-5){
1.251 brouard 4861: if(first==1)
1.265 brouard 4862: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4863: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4864: }else{
4865: if(first==1)
1.265 brouard 4866: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4867: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4868: }
4869: if( iage <= iagemax){
4870: if(pos>=1.e-5){
1.265 brouard 4871: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4872: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4873: }else if( nj==2){
4874: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4875: }
4876: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4877: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4878: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4879: } else{
4880: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4881: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4882: }
1.240 brouard 4883: }
1.265 brouard 4884: pospropt[s1] +=posprop[s1];
4885: } /* end loop s1 */
1.251 brouard 4886: /* pospropt=0.; */
1.265 brouard 4887: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4888: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4889: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4890: if(first==1){
1.265 brouard 4891: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4892: }
1.265 brouard 4893: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4894: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4895: }
1.265 brouard 4896: if(s1!=0 && m!=0)
4897: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4898: }
1.265 brouard 4899: } /* end loop s1 */
1.251 brouard 4900: posproptt=0.;
1.265 brouard 4901: for(s1=1; s1 <=nlstate; s1++){
4902: posproptt += pospropt[s1];
1.251 brouard 4903: }
4904: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4905: fprintf(ficresphtm,"</tr>\n");
4906: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4907: if(iage <= iagemax)
4908: fprintf(ficresp,"\n");
1.240 brouard 4909: }
1.251 brouard 4910: if(first==1)
4911: printf("Others in log...\n");
4912: fprintf(ficlog,"\n");
4913: } /* end loop age iage */
1.265 brouard 4914:
1.251 brouard 4915: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4916: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4917: if(posproptt < 1.e-5){
1.265 brouard 4918: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4919: }else{
1.265 brouard 4920: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4921: }
1.226 brouard 4922: }
1.251 brouard 4923: fprintf(ficresphtm,"</tr>\n");
4924: fprintf(ficresphtm,"</table>\n");
4925: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4926: if(posproptt < 1.e-5){
1.251 brouard 4927: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4928: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4929: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4930: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4931: invalidvarcomb[j1]=1;
1.226 brouard 4932: }else{
1.251 brouard 4933: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4934: invalidvarcomb[j1]=0;
1.226 brouard 4935: }
1.251 brouard 4936: fprintf(ficresphtmfr,"</table>\n");
4937: fprintf(ficlog,"\n");
4938: if(j!=0){
4939: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4940: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4941: for(k=1; k <=(nlstate+ndeath); k++){
4942: if (k != i) {
1.265 brouard 4943: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4944: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4945: if(j1==1){ /* All dummy covariates to zero */
4946: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4947: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4948: printf("%d%d ",i,k);
4949: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4950: 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]));
4951: 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]));
4952: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4953: }
1.253 brouard 4954: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4955: for(iage=iagemin; iage <= iagemax+3; iage++){
4956: x[iage]= (double)iage;
4957: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4958: /* 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 4959: }
1.268 brouard 4960: /* Some are not finite, but linreg will ignore these ages */
4961: no=0;
1.253 brouard 4962: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4963: pstart[s1]=b;
4964: pstart[s1-1]=a;
1.252 brouard 4965: }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 */
4966: 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]);
4967: 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 4968: 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 4969: printf("%d%d ",i,k);
4970: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4971: 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 4972: }else{ /* Other cases, like quantitative fixed or varying covariates */
4973: ;
4974: }
4975: /* printf("%12.7f )", param[i][jj][k]); */
4976: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4977: s1++;
1.251 brouard 4978: } /* end jj */
4979: } /* end k!= i */
4980: } /* end k */
1.265 brouard 4981: } /* end i, s1 */
1.251 brouard 4982: } /* end j !=0 */
4983: } /* end selected combination of covariate j1 */
4984: if(j==0){ /* We can estimate starting values from the occurences in each case */
4985: printf("#Freqsummary: Starting values for the constants:\n");
4986: fprintf(ficlog,"\n");
1.265 brouard 4987: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4988: for(k=1; k <=(nlstate+ndeath); k++){
4989: if (k != i) {
4990: printf("%d%d ",i,k);
4991: fprintf(ficlog,"%d%d ",i,k);
4992: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4993: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4994: if(jj==1){ /* Age has to be done */
1.265 brouard 4995: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4996: 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]));
4997: 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 4998: }
4999: /* printf("%12.7f )", param[i][jj][k]); */
5000: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 5001: s1++;
1.250 brouard 5002: }
1.251 brouard 5003: printf("\n");
5004: fprintf(ficlog,"\n");
1.250 brouard 5005: }
5006: }
1.284 brouard 5007: } /* end of state i */
1.251 brouard 5008: printf("#Freqsummary\n");
5009: fprintf(ficlog,"\n");
1.265 brouard 5010: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5011: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5012: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5013: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5014: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5015: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5016: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5017: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5018: /* } */
5019: }
1.265 brouard 5020: } /* end loop s1 */
1.251 brouard 5021:
5022: printf("\n");
5023: fprintf(ficlog,"\n");
5024: } /* end j=0 */
1.249 brouard 5025: } /* end j */
1.252 brouard 5026:
1.253 brouard 5027: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5028: for(i=1, jk=1; i <=nlstate; i++){
5029: for(j=1; j <=nlstate+ndeath; j++){
5030: if(j!=i){
5031: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5032: printf("%1d%1d",i,j);
5033: fprintf(ficparo,"%1d%1d",i,j);
5034: for(k=1; k<=ncovmodel;k++){
5035: /* printf(" %lf",param[i][j][k]); */
5036: /* fprintf(ficparo," %lf",param[i][j][k]); */
5037: p[jk]=pstart[jk];
5038: printf(" %f ",pstart[jk]);
5039: fprintf(ficparo," %f ",pstart[jk]);
5040: jk++;
5041: }
5042: printf("\n");
5043: fprintf(ficparo,"\n");
5044: }
5045: }
5046: }
5047: } /* end mle=-2 */
1.226 brouard 5048: dateintmean=dateintsum/k2cpt;
1.296 brouard 5049: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5050:
1.226 brouard 5051: fclose(ficresp);
5052: fclose(ficresphtm);
5053: fclose(ficresphtmfr);
1.283 brouard 5054: free_vector(idq,1,nqfveff);
1.226 brouard 5055: free_vector(meanq,1,nqfveff);
1.284 brouard 5056: free_vector(stdq,1,nqfveff);
1.226 brouard 5057: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5058: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5059: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5060: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5061: free_vector(pospropt,1,nlstate);
5062: free_vector(posprop,1,nlstate);
1.251 brouard 5063: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5064: free_vector(pp,1,nlstate);
5065: /* End of freqsummary */
5066: }
1.126 brouard 5067:
1.268 brouard 5068: /* Simple linear regression */
5069: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5070:
5071: /* y=a+bx regression */
5072: double sumx = 0.0; /* sum of x */
5073: double sumx2 = 0.0; /* sum of x**2 */
5074: double sumxy = 0.0; /* sum of x * y */
5075: double sumy = 0.0; /* sum of y */
5076: double sumy2 = 0.0; /* sum of y**2 */
5077: double sume2 = 0.0; /* sum of square or residuals */
5078: double yhat;
5079:
5080: double denom=0;
5081: int i;
5082: int ne=*no;
5083:
5084: for ( i=ifi, ne=0;i<=ila;i++) {
5085: if(!isfinite(x[i]) || !isfinite(y[i])){
5086: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5087: continue;
5088: }
5089: ne=ne+1;
5090: sumx += x[i];
5091: sumx2 += x[i]*x[i];
5092: sumxy += x[i] * y[i];
5093: sumy += y[i];
5094: sumy2 += y[i]*y[i];
5095: denom = (ne * sumx2 - sumx*sumx);
5096: /* 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); */
5097: }
5098:
5099: denom = (ne * sumx2 - sumx*sumx);
5100: if (denom == 0) {
5101: // vertical, slope m is infinity
5102: *b = INFINITY;
5103: *a = 0;
5104: if (r) *r = 0;
5105: return 1;
5106: }
5107:
5108: *b = (ne * sumxy - sumx * sumy) / denom;
5109: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5110: if (r!=NULL) {
5111: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5112: sqrt((sumx2 - sumx*sumx/ne) *
5113: (sumy2 - sumy*sumy/ne));
5114: }
5115: *no=ne;
5116: for ( i=ifi, ne=0;i<=ila;i++) {
5117: if(!isfinite(x[i]) || !isfinite(y[i])){
5118: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5119: continue;
5120: }
5121: ne=ne+1;
5122: yhat = y[i] - *a -*b* x[i];
5123: sume2 += yhat * yhat ;
5124:
5125: denom = (ne * sumx2 - sumx*sumx);
5126: /* 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); */
5127: }
5128: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5129: *sa= *sb * sqrt(sumx2/ne);
5130:
5131: return 0;
5132: }
5133:
1.126 brouard 5134: /************ Prevalence ********************/
1.227 brouard 5135: 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)
5136: {
5137: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5138: in each health status at the date of interview (if between dateprev1 and dateprev2).
5139: We still use firstpass and lastpass as another selection.
5140: */
1.126 brouard 5141:
1.227 brouard 5142: int i, m, jk, j1, bool, z1,j, iv;
5143: int mi; /* Effective wave */
5144: int iage;
5145: double agebegin, ageend;
5146:
5147: double **prop;
5148: double posprop;
5149: double y2; /* in fractional years */
5150: int iagemin, iagemax;
5151: int first; /** to stop verbosity which is redirected to log file */
5152:
5153: iagemin= (int) agemin;
5154: iagemax= (int) agemax;
5155: /*pp=vector(1,nlstate);*/
1.251 brouard 5156: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5157: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5158: j1=0;
1.222 brouard 5159:
1.227 brouard 5160: /*j=cptcoveff;*/
5161: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5162:
1.288 brouard 5163: first=0;
1.227 brouard 5164: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5165: for (i=1; i<=nlstate; i++)
1.251 brouard 5166: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5167: prop[i][iage]=0.0;
5168: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5169: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5170: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5171:
5172: for (i=1; i<=imx; i++) { /* Each individual */
5173: bool=1;
5174: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5175: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5176: m=mw[mi][i];
5177: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5178: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5179: for (z1=1; z1<=cptcoveff; z1++){
5180: if( Fixed[Tmodelind[z1]]==1){
5181: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5182: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5183: bool=0;
5184: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5185: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5186: bool=0;
5187: }
5188: }
5189: if(bool==1){ /* Otherwise we skip that wave/person */
5190: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5191: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5192: if(m >=firstpass && m <=lastpass){
5193: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5194: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5195: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5196: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5197: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5198: 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);
5199: exit(1);
5200: }
5201: if (s[m][i]>0 && s[m][i]<=nlstate) {
5202: /*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]]);*/
5203: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5204: prop[s[m][i]][iagemax+3] += weight[i];
5205: } /* end valid statuses */
5206: } /* end selection of dates */
5207: } /* end selection of waves */
5208: } /* end bool */
5209: } /* end wave */
5210: } /* end individual */
5211: for(i=iagemin; i <= iagemax+3; i++){
5212: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5213: posprop += prop[jk][i];
5214: }
5215:
5216: for(jk=1; jk <=nlstate ; jk++){
5217: if( i <= iagemax){
5218: if(posprop>=1.e-5){
5219: probs[i][jk][j1]= prop[jk][i]/posprop;
5220: } else{
1.288 brouard 5221: if(!first){
5222: first=1;
1.266 brouard 5223: 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]);
5224: }else{
1.288 brouard 5225: 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 5226: }
5227: }
5228: }
5229: }/* end jk */
5230: }/* end i */
1.222 brouard 5231: /*} *//* end i1 */
1.227 brouard 5232: } /* end j1 */
1.222 brouard 5233:
1.227 brouard 5234: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5235: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5236: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5237: } /* End of prevalence */
1.126 brouard 5238:
5239: /************* Waves Concatenation ***************/
5240:
5241: 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)
5242: {
1.298 brouard 5243: /* 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 5244: Death is a valid wave (if date is known).
5245: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5246: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5247: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5248: */
1.126 brouard 5249:
1.224 brouard 5250: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5251: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5252: double sum=0., jmean=0.;*/
1.224 brouard 5253: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5254: int j, k=0,jk, ju, jl;
5255: double sum=0.;
5256: first=0;
1.214 brouard 5257: firstwo=0;
1.217 brouard 5258: firsthree=0;
1.218 brouard 5259: firstfour=0;
1.164 brouard 5260: jmin=100000;
1.126 brouard 5261: jmax=-1;
5262: jmean=0.;
1.224 brouard 5263:
5264: /* Treating live states */
1.214 brouard 5265: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5266: mi=0; /* First valid wave */
1.227 brouard 5267: mli=0; /* Last valid wave */
1.126 brouard 5268: m=firstpass;
1.214 brouard 5269: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5270: 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 */
5271: mli=m-1;/* mw[++mi][i]=m-1; */
5272: }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 */
5273: mw[++mi][i]=m;
5274: mli=m;
1.224 brouard 5275: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5276: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5277: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5278: }
1.227 brouard 5279: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5280: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5281: break;
1.224 brouard 5282: #else
1.227 brouard 5283: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5284: if(firsthree == 0){
1.302 brouard 5285: 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 5286: firsthree=1;
5287: }
1.302 brouard 5288: 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 5289: mw[++mi][i]=m;
5290: mli=m;
5291: }
5292: if(s[m][i]==-2){ /* Vital status is really unknown */
5293: nbwarn++;
5294: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5295: 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);
5296: 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);
5297: }
5298: break;
5299: }
5300: break;
1.224 brouard 5301: #endif
1.227 brouard 5302: }/* End m >= lastpass */
1.126 brouard 5303: }/* end while */
1.224 brouard 5304:
1.227 brouard 5305: /* 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 5306: /* After last pass */
1.224 brouard 5307: /* Treating death states */
1.214 brouard 5308: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5309: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5310: /* } */
1.126 brouard 5311: mi++; /* Death is another wave */
5312: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5313: /* Only death is a correct wave */
1.126 brouard 5314: mw[mi][i]=m;
1.257 brouard 5315: } /* else not in a death state */
1.224 brouard 5316: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5317: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5318: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5319: 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 */
5320: nbwarn++;
5321: if(firstfiv==0){
5322: 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 );
5323: firstfiv=1;
5324: }else{
5325: 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 );
5326: }
5327: }else{ /* Death occured afer last wave potential bias */
5328: nberr++;
5329: if(firstwo==0){
1.257 brouard 5330: 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 5331: firstwo=1;
5332: }
1.257 brouard 5333: 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 5334: }
1.257 brouard 5335: }else{ /* if date of interview is unknown */
1.227 brouard 5336: /* death is known but not confirmed by death status at any wave */
5337: if(firstfour==0){
5338: 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 );
5339: firstfour=1;
5340: }
5341: 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 5342: }
1.224 brouard 5343: } /* end if date of death is known */
5344: #endif
5345: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5346: /* wav[i]=mw[mi][i]; */
1.126 brouard 5347: if(mi==0){
5348: nbwarn++;
5349: if(first==0){
1.227 brouard 5350: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5351: first=1;
1.126 brouard 5352: }
5353: if(first==1){
1.227 brouard 5354: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5355: }
5356: } /* end mi==0 */
5357: } /* End individuals */
1.214 brouard 5358: /* wav and mw are no more changed */
1.223 brouard 5359:
1.214 brouard 5360:
1.126 brouard 5361: for(i=1; i<=imx; i++){
5362: for(mi=1; mi<wav[i];mi++){
5363: if (stepm <=0)
1.227 brouard 5364: dh[mi][i]=1;
1.126 brouard 5365: else{
1.260 brouard 5366: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5367: if (agedc[i] < 2*AGESUP) {
5368: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5369: if(j==0) j=1; /* Survives at least one month after exam */
5370: else if(j<0){
5371: nberr++;
5372: 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]);
5373: j=1; /* Temporary Dangerous patch */
5374: 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);
5375: 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]);
5376: 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);
5377: }
5378: k=k+1;
5379: if (j >= jmax){
5380: jmax=j;
5381: ijmax=i;
5382: }
5383: if (j <= jmin){
5384: jmin=j;
5385: ijmin=i;
5386: }
5387: sum=sum+j;
5388: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5389: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5390: }
5391: }
5392: else{
5393: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5394: /* 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 5395:
1.227 brouard 5396: k=k+1;
5397: if (j >= jmax) {
5398: jmax=j;
5399: ijmax=i;
5400: }
5401: else if (j <= jmin){
5402: jmin=j;
5403: ijmin=i;
5404: }
5405: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5406: /*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]);*/
5407: if(j<0){
5408: nberr++;
5409: 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]);
5410: 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]);
5411: }
5412: sum=sum+j;
5413: }
5414: jk= j/stepm;
5415: jl= j -jk*stepm;
5416: ju= j -(jk+1)*stepm;
5417: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5418: if(jl==0){
5419: dh[mi][i]=jk;
5420: bh[mi][i]=0;
5421: }else{ /* We want a negative bias in order to only have interpolation ie
5422: * to avoid the price of an extra matrix product in likelihood */
5423: dh[mi][i]=jk+1;
5424: bh[mi][i]=ju;
5425: }
5426: }else{
5427: if(jl <= -ju){
5428: dh[mi][i]=jk;
5429: bh[mi][i]=jl; /* bias is positive if real duration
5430: * is higher than the multiple of stepm and negative otherwise.
5431: */
5432: }
5433: else{
5434: dh[mi][i]=jk+1;
5435: bh[mi][i]=ju;
5436: }
5437: if(dh[mi][i]==0){
5438: dh[mi][i]=1; /* At least one step */
5439: bh[mi][i]=ju; /* At least one step */
5440: /* 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);*/
5441: }
5442: } /* end if mle */
1.126 brouard 5443: }
5444: } /* end wave */
5445: }
5446: jmean=sum/k;
5447: 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 5448: 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 5449: }
1.126 brouard 5450:
5451: /*********** Tricode ****************************/
1.220 brouard 5452: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5453: {
5454: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5455: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5456: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5457: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5458: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5459: */
1.130 brouard 5460:
1.242 brouard 5461: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5462: int modmaxcovj=0; /* Modality max of covariates j */
5463: int cptcode=0; /* Modality max of covariates j */
5464: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5465:
5466:
1.242 brouard 5467: /* cptcoveff=0; */
5468: /* *cptcov=0; */
1.126 brouard 5469:
1.242 brouard 5470: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5471: for (k=1; k <= maxncov; k++)
5472: for(j=1; j<=2; j++)
5473: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5474:
1.242 brouard 5475: /* Loop on covariates without age and products and no quantitative variable */
5476: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5477: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5478: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5479: switch(Fixed[k]) {
5480: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5481: 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*/
5482: ij=(int)(covar[Tvar[k]][i]);
5483: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5484: * If product of Vn*Vm, still boolean *:
5485: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5486: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5487: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5488: modality of the nth covariate of individual i. */
5489: if (ij > modmaxcovj)
5490: modmaxcovj=ij;
5491: else if (ij < modmincovj)
5492: modmincovj=ij;
1.287 brouard 5493: if (ij <0 || ij >1 ){
5494: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5495: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5496: }
5497: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5498: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5499: exit(1);
5500: }else
5501: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5502: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5503: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5504: /* getting the maximum value of the modality of the covariate
5505: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5506: female ies 1, then modmaxcovj=1.
5507: */
5508: } /* end for loop on individuals i */
5509: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5510: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5511: cptcode=modmaxcovj;
5512: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5513: /*for (i=0; i<=cptcode; i++) {*/
5514: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5515: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5516: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5517: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5518: if( j != -1){
5519: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5520: covariate for which somebody answered excluding
5521: undefined. Usually 2: 0 and 1. */
5522: }
5523: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5524: covariate for which somebody answered including
5525: undefined. Usually 3: -1, 0 and 1. */
5526: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5527: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5528: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5529:
1.242 brouard 5530: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5531: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5532: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5533: /* modmincovj=3; modmaxcovj = 7; */
5534: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5535: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5536: /* defining two dummy variables: variables V1_1 and V1_2.*/
5537: /* nbcode[Tvar[j]][ij]=k; */
5538: /* nbcode[Tvar[j]][1]=0; */
5539: /* nbcode[Tvar[j]][2]=1; */
5540: /* nbcode[Tvar[j]][3]=2; */
5541: /* To be continued (not working yet). */
5542: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5543:
5544: /* 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*/
5545: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5546: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5547: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5548: /*, could be restored in the future */
5549: 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 5550: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5551: break;
5552: }
5553: ij++;
1.287 brouard 5554: 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 5555: cptcode = ij; /* New max modality for covar j */
5556: } /* end of loop on modality i=-1 to 1 or more */
5557: break;
5558: case 1: /* Testing on varying covariate, could be simple and
5559: * should look at waves or product of fixed *
5560: * varying. No time to test -1, assuming 0 and 1 only */
5561: ij=0;
5562: for(i=0; i<=1;i++){
5563: nbcode[Tvar[k]][++ij]=i;
5564: }
5565: break;
5566: default:
5567: break;
5568: } /* end switch */
5569: } /* end dummy test */
1.287 brouard 5570: } /* 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 5571:
5572: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5573: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5574: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5575: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5576: 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 */
5577: 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 */
5578: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5579: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5580:
5581: ij=0;
5582: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5583: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5584: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5585: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5586: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5587: /* If product not in single variable we don't print results */
5588: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5589: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5590: 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*/
5591: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5592: 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 */
5593: if(Fixed[k]!=0)
5594: anyvaryingduminmodel=1;
5595: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5596: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5597: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5598: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5599: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5600: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5601: }
5602: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5603: /* ij--; */
5604: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5605: *cptcov=ij; /*Number of total real effective covariates: effective
5606: * because they can be excluded from the model and real
5607: * if in the model but excluded because missing values, but how to get k from ij?*/
5608: for(j=ij+1; j<= cptcovt; j++){
5609: Tvaraff[j]=0;
5610: Tmodelind[j]=0;
5611: }
5612: for(j=ntveff+1; j<= cptcovt; j++){
5613: TmodelInvind[j]=0;
5614: }
5615: /* To be sorted */
5616: ;
5617: }
1.126 brouard 5618:
1.145 brouard 5619:
1.126 brouard 5620: /*********** Health Expectancies ****************/
5621:
1.235 brouard 5622: 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 5623:
5624: {
5625: /* Health expectancies, no variances */
1.164 brouard 5626: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5627: int nhstepma, nstepma; /* Decreasing with age */
5628: double age, agelim, hf;
5629: double ***p3mat;
5630: double eip;
5631:
1.238 brouard 5632: /* pstamp(ficreseij); */
1.126 brouard 5633: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5634: fprintf(ficreseij,"# Age");
5635: for(i=1; i<=nlstate;i++){
5636: for(j=1; j<=nlstate;j++){
5637: fprintf(ficreseij," e%1d%1d ",i,j);
5638: }
5639: fprintf(ficreseij," e%1d. ",i);
5640: }
5641: fprintf(ficreseij,"\n");
5642:
5643:
5644: if(estepm < stepm){
5645: printf ("Problem %d lower than %d\n",estepm, stepm);
5646: }
5647: else hstepm=estepm;
5648: /* We compute the life expectancy from trapezoids spaced every estepm months
5649: * This is mainly to measure the difference between two models: for example
5650: * if stepm=24 months pijx are given only every 2 years and by summing them
5651: * we are calculating an estimate of the Life Expectancy assuming a linear
5652: * progression in between and thus overestimating or underestimating according
5653: * to the curvature of the survival function. If, for the same date, we
5654: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5655: * to compare the new estimate of Life expectancy with the same linear
5656: * hypothesis. A more precise result, taking into account a more precise
5657: * curvature will be obtained if estepm is as small as stepm. */
5658:
5659: /* For example we decided to compute the life expectancy with the smallest unit */
5660: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5661: nhstepm is the number of hstepm from age to agelim
5662: nstepm is the number of stepm from age to agelin.
1.270 brouard 5663: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5664: and note for a fixed period like estepm months */
5665: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5666: survival function given by stepm (the optimization length). Unfortunately it
5667: means that if the survival funtion is printed only each two years of age and if
5668: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5669: results. So we changed our mind and took the option of the best precision.
5670: */
5671: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5672:
5673: agelim=AGESUP;
5674: /* If stepm=6 months */
5675: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5676: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5677:
5678: /* nhstepm age range expressed in number of stepm */
5679: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5680: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5681: /* if (stepm >= YEARM) hstepm=1;*/
5682: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5683: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5684:
5685: for (age=bage; age<=fage; age ++){
5686: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5687: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5688: /* if (stepm >= YEARM) hstepm=1;*/
5689: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5690:
5691: /* If stepm=6 months */
5692: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5693: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5694:
1.235 brouard 5695: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5696:
5697: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5698:
5699: printf("%d|",(int)age);fflush(stdout);
5700: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5701:
5702: /* Computing expectancies */
5703: for(i=1; i<=nlstate;i++)
5704: for(j=1; j<=nlstate;j++)
5705: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5706: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5707:
5708: /* 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]);*/
5709:
5710: }
5711:
5712: fprintf(ficreseij,"%3.0f",age );
5713: for(i=1; i<=nlstate;i++){
5714: eip=0;
5715: for(j=1; j<=nlstate;j++){
5716: eip +=eij[i][j][(int)age];
5717: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5718: }
5719: fprintf(ficreseij,"%9.4f", eip );
5720: }
5721: fprintf(ficreseij,"\n");
5722:
5723: }
5724: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5725: printf("\n");
5726: fprintf(ficlog,"\n");
5727:
5728: }
5729:
1.235 brouard 5730: 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 5731:
5732: {
5733: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5734: to initial status i, ei. .
1.126 brouard 5735: */
5736: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5737: int nhstepma, nstepma; /* Decreasing with age */
5738: double age, agelim, hf;
5739: double ***p3matp, ***p3matm, ***varhe;
5740: double **dnewm,**doldm;
5741: double *xp, *xm;
5742: double **gp, **gm;
5743: double ***gradg, ***trgradg;
5744: int theta;
5745:
5746: double eip, vip;
5747:
5748: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5749: xp=vector(1,npar);
5750: xm=vector(1,npar);
5751: dnewm=matrix(1,nlstate*nlstate,1,npar);
5752: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5753:
5754: pstamp(ficresstdeij);
5755: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5756: fprintf(ficresstdeij,"# Age");
5757: for(i=1; i<=nlstate;i++){
5758: for(j=1; j<=nlstate;j++)
5759: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5760: fprintf(ficresstdeij," e%1d. ",i);
5761: }
5762: fprintf(ficresstdeij,"\n");
5763:
5764: pstamp(ficrescveij);
5765: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5766: fprintf(ficrescveij,"# Age");
5767: for(i=1; i<=nlstate;i++)
5768: for(j=1; j<=nlstate;j++){
5769: cptj= (j-1)*nlstate+i;
5770: for(i2=1; i2<=nlstate;i2++)
5771: for(j2=1; j2<=nlstate;j2++){
5772: cptj2= (j2-1)*nlstate+i2;
5773: if(cptj2 <= cptj)
5774: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5775: }
5776: }
5777: fprintf(ficrescveij,"\n");
5778:
5779: if(estepm < stepm){
5780: printf ("Problem %d lower than %d\n",estepm, stepm);
5781: }
5782: else hstepm=estepm;
5783: /* We compute the life expectancy from trapezoids spaced every estepm months
5784: * This is mainly to measure the difference between two models: for example
5785: * if stepm=24 months pijx are given only every 2 years and by summing them
5786: * we are calculating an estimate of the Life Expectancy assuming a linear
5787: * progression in between and thus overestimating or underestimating according
5788: * to the curvature of the survival function. If, for the same date, we
5789: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5790: * to compare the new estimate of Life expectancy with the same linear
5791: * hypothesis. A more precise result, taking into account a more precise
5792: * curvature will be obtained if estepm is as small as stepm. */
5793:
5794: /* For example we decided to compute the life expectancy with the smallest unit */
5795: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5796: nhstepm is the number of hstepm from age to agelim
5797: nstepm is the number of stepm from age to agelin.
5798: Look at hpijx to understand the reason of that which relies in memory size
5799: and note for a fixed period like estepm months */
5800: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5801: survival function given by stepm (the optimization length). Unfortunately it
5802: means that if the survival funtion is printed only each two years of age and if
5803: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5804: results. So we changed our mind and took the option of the best precision.
5805: */
5806: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5807:
5808: /* If stepm=6 months */
5809: /* nhstepm age range expressed in number of stepm */
5810: agelim=AGESUP;
5811: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5812: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5813: /* if (stepm >= YEARM) hstepm=1;*/
5814: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5815:
5816: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5817: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5818: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5819: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5820: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5821: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5822:
5823: for (age=bage; age<=fage; age ++){
5824: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5825: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5826: /* if (stepm >= YEARM) hstepm=1;*/
5827: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5828:
1.126 brouard 5829: /* If stepm=6 months */
5830: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5831: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5832:
5833: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5834:
1.126 brouard 5835: /* Computing Variances of health expectancies */
5836: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5837: decrease memory allocation */
5838: for(theta=1; theta <=npar; theta++){
5839: for(i=1; i<=npar; i++){
1.222 brouard 5840: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5841: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5842: }
1.235 brouard 5843: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5844: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5845:
1.126 brouard 5846: for(j=1; j<= nlstate; j++){
1.222 brouard 5847: for(i=1; i<=nlstate; i++){
5848: for(h=0; h<=nhstepm-1; h++){
5849: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5850: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5851: }
5852: }
1.126 brouard 5853: }
1.218 brouard 5854:
1.126 brouard 5855: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5856: for(h=0; h<=nhstepm-1; h++){
5857: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5858: }
1.126 brouard 5859: }/* End theta */
5860:
5861:
5862: for(h=0; h<=nhstepm-1; h++)
5863: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5864: for(theta=1; theta <=npar; theta++)
5865: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5866:
1.218 brouard 5867:
1.222 brouard 5868: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5869: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5870: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5871:
1.222 brouard 5872: printf("%d|",(int)age);fflush(stdout);
5873: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5874: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5875: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5876: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5877: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5878: for(ij=1;ij<=nlstate*nlstate;ij++)
5879: for(ji=1;ji<=nlstate*nlstate;ji++)
5880: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5881: }
5882: }
1.218 brouard 5883:
1.126 brouard 5884: /* Computing expectancies */
1.235 brouard 5885: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5886: for(i=1; i<=nlstate;i++)
5887: for(j=1; j<=nlstate;j++)
1.222 brouard 5888: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5889: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5890:
1.222 brouard 5891: /* 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 5892:
1.222 brouard 5893: }
1.269 brouard 5894:
5895: /* Standard deviation of expectancies ij */
1.126 brouard 5896: fprintf(ficresstdeij,"%3.0f",age );
5897: for(i=1; i<=nlstate;i++){
5898: eip=0.;
5899: vip=0.;
5900: for(j=1; j<=nlstate;j++){
1.222 brouard 5901: eip += eij[i][j][(int)age];
5902: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5903: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5904: 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 5905: }
5906: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5907: }
5908: fprintf(ficresstdeij,"\n");
1.218 brouard 5909:
1.269 brouard 5910: /* Variance of expectancies ij */
1.126 brouard 5911: fprintf(ficrescveij,"%3.0f",age );
5912: for(i=1; i<=nlstate;i++)
5913: for(j=1; j<=nlstate;j++){
1.222 brouard 5914: cptj= (j-1)*nlstate+i;
5915: for(i2=1; i2<=nlstate;i2++)
5916: for(j2=1; j2<=nlstate;j2++){
5917: cptj2= (j2-1)*nlstate+i2;
5918: if(cptj2 <= cptj)
5919: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5920: }
1.126 brouard 5921: }
5922: fprintf(ficrescveij,"\n");
1.218 brouard 5923:
1.126 brouard 5924: }
5925: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5926: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5927: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5928: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5929: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5930: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5931: printf("\n");
5932: fprintf(ficlog,"\n");
1.218 brouard 5933:
1.126 brouard 5934: free_vector(xm,1,npar);
5935: free_vector(xp,1,npar);
5936: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5937: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5938: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5939: }
1.218 brouard 5940:
1.126 brouard 5941: /************ Variance ******************/
1.235 brouard 5942: 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 5943: {
1.279 brouard 5944: /** Variance of health expectancies
5945: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5946: * double **newm;
5947: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5948: */
1.218 brouard 5949:
5950: /* int movingaverage(); */
5951: double **dnewm,**doldm;
5952: double **dnewmp,**doldmp;
5953: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5954: int first=0;
1.218 brouard 5955: int k;
5956: double *xp;
1.279 brouard 5957: double **gp, **gm; /**< for var eij */
5958: double ***gradg, ***trgradg; /**< for var eij */
5959: double **gradgp, **trgradgp; /**< for var p point j */
5960: double *gpp, *gmp; /**< for var p point j */
5961: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5962: double ***p3mat;
5963: double age,agelim, hf;
5964: /* double ***mobaverage; */
5965: int theta;
5966: char digit[4];
5967: char digitp[25];
5968:
5969: char fileresprobmorprev[FILENAMELENGTH];
5970:
5971: if(popbased==1){
5972: if(mobilav!=0)
5973: strcpy(digitp,"-POPULBASED-MOBILAV_");
5974: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5975: }
5976: else
5977: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5978:
1.218 brouard 5979: /* if (mobilav!=0) { */
5980: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5981: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5982: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5983: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5984: /* } */
5985: /* } */
5986:
5987: strcpy(fileresprobmorprev,"PRMORPREV-");
5988: sprintf(digit,"%-d",ij);
5989: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5990: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5991: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5992: strcat(fileresprobmorprev,fileresu);
5993: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5994: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5995: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5996: }
5997: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5998: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5999: pstamp(ficresprobmorprev);
6000: 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 6001: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
6002: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
6003: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
6004: }
6005: for(j=1;j<=cptcoveff;j++)
6006: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
6007: fprintf(ficresprobmorprev,"\n");
6008:
1.218 brouard 6009: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6010: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6011: fprintf(ficresprobmorprev," p.%-d SE",j);
6012: for(i=1; i<=nlstate;i++)
6013: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6014: }
6015: fprintf(ficresprobmorprev,"\n");
6016:
6017: fprintf(ficgp,"\n# Routine varevsij");
6018: fprintf(ficgp,"\nunset title \n");
6019: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6020: 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");
6021: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6022:
1.218 brouard 6023: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6024: pstamp(ficresvij);
6025: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6026: if(popbased==1)
6027: 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);
6028: else
6029: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6030: fprintf(ficresvij,"# Age");
6031: for(i=1; i<=nlstate;i++)
6032: for(j=1; j<=nlstate;j++)
6033: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6034: fprintf(ficresvij,"\n");
6035:
6036: xp=vector(1,npar);
6037: dnewm=matrix(1,nlstate,1,npar);
6038: doldm=matrix(1,nlstate,1,nlstate);
6039: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6040: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6041:
6042: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6043: gpp=vector(nlstate+1,nlstate+ndeath);
6044: gmp=vector(nlstate+1,nlstate+ndeath);
6045: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6046:
1.218 brouard 6047: if(estepm < stepm){
6048: printf ("Problem %d lower than %d\n",estepm, stepm);
6049: }
6050: else hstepm=estepm;
6051: /* For example we decided to compute the life expectancy with the smallest unit */
6052: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6053: nhstepm is the number of hstepm from age to agelim
6054: nstepm is the number of stepm from age to agelim.
6055: Look at function hpijx to understand why because of memory size limitations,
6056: we decided (b) to get a life expectancy respecting the most precise curvature of the
6057: survival function given by stepm (the optimization length). Unfortunately it
6058: means that if the survival funtion is printed every two years of age and if
6059: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6060: results. So we changed our mind and took the option of the best precision.
6061: */
6062: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6063: agelim = AGESUP;
6064: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6065: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6066: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6067: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6068: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6069: gp=matrix(0,nhstepm,1,nlstate);
6070: gm=matrix(0,nhstepm,1,nlstate);
6071:
6072:
6073: for(theta=1; theta <=npar; theta++){
6074: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6075: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6076: }
1.279 brouard 6077: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6078: * returns into prlim .
1.288 brouard 6079: */
1.242 brouard 6080: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6081:
6082: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6083: if (popbased==1) {
6084: if(mobilav ==0){
6085: for(i=1; i<=nlstate;i++)
6086: prlim[i][i]=probs[(int)age][i][ij];
6087: }else{ /* mobilav */
6088: for(i=1; i<=nlstate;i++)
6089: prlim[i][i]=mobaverage[(int)age][i][ij];
6090: }
6091: }
1.295 brouard 6092: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6093: */
6094: 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 6095: /**< 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 6096: * at horizon h in state j including mortality.
6097: */
1.218 brouard 6098: for(j=1; j<= nlstate; j++){
6099: for(h=0; h<=nhstepm; h++){
6100: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6101: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6102: }
6103: }
1.279 brouard 6104: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6105: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6106: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6107: */
6108: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6109: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6110: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6111: }
6112:
6113: /* Again with minus shift */
1.218 brouard 6114:
6115: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6116: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6117:
1.242 brouard 6118: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6119:
6120: if (popbased==1) {
6121: if(mobilav ==0){
6122: for(i=1; i<=nlstate;i++)
6123: prlim[i][i]=probs[(int)age][i][ij];
6124: }else{ /* mobilav */
6125: for(i=1; i<=nlstate;i++)
6126: prlim[i][i]=mobaverage[(int)age][i][ij];
6127: }
6128: }
6129:
1.235 brouard 6130: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6131:
6132: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6133: for(h=0; h<=nhstepm; h++){
6134: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6135: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6136: }
6137: }
6138: /* This for computing probability of death (h=1 means
6139: computed over hstepm matrices product = hstepm*stepm months)
6140: as a weighted average of prlim.
6141: */
6142: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6143: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6144: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6145: }
1.279 brouard 6146: /* end shifting computations */
6147:
6148: /**< Computing gradient matrix at horizon h
6149: */
1.218 brouard 6150: for(j=1; j<= nlstate; j++) /* vareij */
6151: for(h=0; h<=nhstepm; h++){
6152: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6153: }
1.279 brouard 6154: /**< Gradient of overall mortality p.3 (or p.j)
6155: */
6156: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6157: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6158: }
6159:
6160: } /* End theta */
1.279 brouard 6161:
6162: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6163: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6164:
6165: for(h=0; h<=nhstepm; h++) /* veij */
6166: for(j=1; j<=nlstate;j++)
6167: for(theta=1; theta <=npar; theta++)
6168: trgradg[h][j][theta]=gradg[h][theta][j];
6169:
6170: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6171: for(theta=1; theta <=npar; theta++)
6172: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6173: /**< as well as its transposed matrix
6174: */
1.218 brouard 6175:
6176: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6177: for(i=1;i<=nlstate;i++)
6178: for(j=1;j<=nlstate;j++)
6179: vareij[i][j][(int)age] =0.;
1.279 brouard 6180:
6181: /* Computing trgradg by matcov by gradg at age and summing over h
6182: * and k (nhstepm) formula 15 of article
6183: * Lievre-Brouard-Heathcote
6184: */
6185:
1.218 brouard 6186: for(h=0;h<=nhstepm;h++){
6187: for(k=0;k<=nhstepm;k++){
6188: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6189: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6190: for(i=1;i<=nlstate;i++)
6191: for(j=1;j<=nlstate;j++)
6192: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6193: }
6194: }
6195:
1.279 brouard 6196: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6197: * p.j overall mortality formula 49 but computed directly because
6198: * we compute the grad (wix pijx) instead of grad (pijx),even if
6199: * wix is independent of theta.
6200: */
1.218 brouard 6201: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6202: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6203: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6204: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6205: varppt[j][i]=doldmp[j][i];
6206: /* end ppptj */
6207: /* x centered again */
6208:
1.242 brouard 6209: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6210:
6211: if (popbased==1) {
6212: if(mobilav ==0){
6213: for(i=1; i<=nlstate;i++)
6214: prlim[i][i]=probs[(int)age][i][ij];
6215: }else{ /* mobilav */
6216: for(i=1; i<=nlstate;i++)
6217: prlim[i][i]=mobaverage[(int)age][i][ij];
6218: }
6219: }
6220:
6221: /* This for computing probability of death (h=1 means
6222: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6223: as a weighted average of prlim.
6224: */
1.235 brouard 6225: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6226: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6227: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6228: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6229: }
6230: /* end probability of death */
6231:
6232: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6233: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6234: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6235: for(i=1; i<=nlstate;i++){
6236: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6237: }
6238: }
6239: fprintf(ficresprobmorprev,"\n");
6240:
6241: fprintf(ficresvij,"%.0f ",age );
6242: for(i=1; i<=nlstate;i++)
6243: for(j=1; j<=nlstate;j++){
6244: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6245: }
6246: fprintf(ficresvij,"\n");
6247: free_matrix(gp,0,nhstepm,1,nlstate);
6248: free_matrix(gm,0,nhstepm,1,nlstate);
6249: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6250: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6251: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6252: } /* End age */
6253: free_vector(gpp,nlstate+1,nlstate+ndeath);
6254: free_vector(gmp,nlstate+1,nlstate+ndeath);
6255: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6256: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6257: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6258: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6259: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6260: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6261: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6262: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6263: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6264: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6265: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6266: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6267: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6268: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6269: 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);
6270: /* 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 6271: */
1.218 brouard 6272: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6273: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6274:
1.218 brouard 6275: free_vector(xp,1,npar);
6276: free_matrix(doldm,1,nlstate,1,nlstate);
6277: free_matrix(dnewm,1,nlstate,1,npar);
6278: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6279: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6280: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6281: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6282: fclose(ficresprobmorprev);
6283: fflush(ficgp);
6284: fflush(fichtm);
6285: } /* end varevsij */
1.126 brouard 6286:
6287: /************ Variance of prevlim ******************/
1.269 brouard 6288: 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 6289: {
1.205 brouard 6290: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6291: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6292:
1.268 brouard 6293: double **dnewmpar,**doldm;
1.126 brouard 6294: int i, j, nhstepm, hstepm;
6295: double *xp;
6296: double *gp, *gm;
6297: double **gradg, **trgradg;
1.208 brouard 6298: double **mgm, **mgp;
1.126 brouard 6299: double age,agelim;
6300: int theta;
6301:
6302: pstamp(ficresvpl);
1.288 brouard 6303: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6304: fprintf(ficresvpl,"# Age ");
6305: if(nresult >=1)
6306: fprintf(ficresvpl," Result# ");
1.126 brouard 6307: for(i=1; i<=nlstate;i++)
6308: fprintf(ficresvpl," %1d-%1d",i,i);
6309: fprintf(ficresvpl,"\n");
6310:
6311: xp=vector(1,npar);
1.268 brouard 6312: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6313: doldm=matrix(1,nlstate,1,nlstate);
6314:
6315: hstepm=1*YEARM; /* Every year of age */
6316: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6317: agelim = AGESUP;
6318: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6319: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6320: if (stepm >= YEARM) hstepm=1;
6321: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6322: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6323: mgp=matrix(1,npar,1,nlstate);
6324: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6325: gp=vector(1,nlstate);
6326: gm=vector(1,nlstate);
6327:
6328: for(theta=1; theta <=npar; theta++){
6329: for(i=1; i<=npar; i++){ /* Computes gradient */
6330: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6331: }
1.288 brouard 6332: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6333: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6334: /* else */
6335: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6336: for(i=1;i<=nlstate;i++){
1.126 brouard 6337: gp[i] = prlim[i][i];
1.208 brouard 6338: mgp[theta][i] = prlim[i][i];
6339: }
1.126 brouard 6340: for(i=1; i<=npar; i++) /* Computes gradient */
6341: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6342: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6343: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6344: /* else */
6345: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6346: for(i=1;i<=nlstate;i++){
1.126 brouard 6347: gm[i] = prlim[i][i];
1.208 brouard 6348: mgm[theta][i] = prlim[i][i];
6349: }
1.126 brouard 6350: for(i=1;i<=nlstate;i++)
6351: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6352: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6353: } /* End theta */
6354:
6355: trgradg =matrix(1,nlstate,1,npar);
6356:
6357: for(j=1; j<=nlstate;j++)
6358: for(theta=1; theta <=npar; theta++)
6359: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6360: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6361: /* printf("\nmgm mgp %d ",(int)age); */
6362: /* for(j=1; j<=nlstate;j++){ */
6363: /* printf(" %d ",j); */
6364: /* for(theta=1; theta <=npar; theta++) */
6365: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6366: /* printf("\n "); */
6367: /* } */
6368: /* } */
6369: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6370: /* printf("\n gradg %d ",(int)age); */
6371: /* for(j=1; j<=nlstate;j++){ */
6372: /* printf("%d ",j); */
6373: /* for(theta=1; theta <=npar; theta++) */
6374: /* printf("%d %lf ",theta,gradg[theta][j]); */
6375: /* printf("\n "); */
6376: /* } */
6377: /* } */
1.126 brouard 6378:
6379: for(i=1;i<=nlstate;i++)
6380: varpl[i][(int)age] =0.;
1.209 brouard 6381: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6382: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6383: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6384: }else{
1.268 brouard 6385: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6386: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6387: }
1.126 brouard 6388: for(i=1;i<=nlstate;i++)
6389: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6390:
6391: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6392: if(nresult >=1)
6393: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6394: for(i=1; i<=nlstate;i++){
1.126 brouard 6395: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6396: /* for(j=1;j<=nlstate;j++) */
6397: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6398: }
1.126 brouard 6399: fprintf(ficresvpl,"\n");
6400: free_vector(gp,1,nlstate);
6401: free_vector(gm,1,nlstate);
1.208 brouard 6402: free_matrix(mgm,1,npar,1,nlstate);
6403: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6404: free_matrix(gradg,1,npar,1,nlstate);
6405: free_matrix(trgradg,1,nlstate,1,npar);
6406: } /* End age */
6407:
6408: free_vector(xp,1,npar);
6409: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6410: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6411:
6412: }
6413:
6414:
6415: /************ Variance of backprevalence limit ******************/
1.269 brouard 6416: 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 6417: {
6418: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6419: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6420:
6421: double **dnewmpar,**doldm;
6422: int i, j, nhstepm, hstepm;
6423: double *xp;
6424: double *gp, *gm;
6425: double **gradg, **trgradg;
6426: double **mgm, **mgp;
6427: double age,agelim;
6428: int theta;
6429:
6430: pstamp(ficresvbl);
6431: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6432: fprintf(ficresvbl,"# Age ");
6433: if(nresult >=1)
6434: fprintf(ficresvbl," Result# ");
6435: for(i=1; i<=nlstate;i++)
6436: fprintf(ficresvbl," %1d-%1d",i,i);
6437: fprintf(ficresvbl,"\n");
6438:
6439: xp=vector(1,npar);
6440: dnewmpar=matrix(1,nlstate,1,npar);
6441: doldm=matrix(1,nlstate,1,nlstate);
6442:
6443: hstepm=1*YEARM; /* Every year of age */
6444: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6445: agelim = AGEINF;
6446: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6447: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6448: if (stepm >= YEARM) hstepm=1;
6449: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6450: gradg=matrix(1,npar,1,nlstate);
6451: mgp=matrix(1,npar,1,nlstate);
6452: mgm=matrix(1,npar,1,nlstate);
6453: gp=vector(1,nlstate);
6454: gm=vector(1,nlstate);
6455:
6456: for(theta=1; theta <=npar; theta++){
6457: for(i=1; i<=npar; i++){ /* Computes gradient */
6458: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6459: }
6460: if(mobilavproj > 0 )
6461: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6462: else
6463: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6464: for(i=1;i<=nlstate;i++){
6465: gp[i] = bprlim[i][i];
6466: mgp[theta][i] = bprlim[i][i];
6467: }
6468: for(i=1; i<=npar; i++) /* Computes gradient */
6469: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6470: if(mobilavproj > 0 )
6471: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6472: else
6473: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6474: for(i=1;i<=nlstate;i++){
6475: gm[i] = bprlim[i][i];
6476: mgm[theta][i] = bprlim[i][i];
6477: }
6478: for(i=1;i<=nlstate;i++)
6479: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6480: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6481: } /* End theta */
6482:
6483: trgradg =matrix(1,nlstate,1,npar);
6484:
6485: for(j=1; j<=nlstate;j++)
6486: for(theta=1; theta <=npar; theta++)
6487: trgradg[j][theta]=gradg[theta][j];
6488: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6489: /* printf("\nmgm mgp %d ",(int)age); */
6490: /* for(j=1; j<=nlstate;j++){ */
6491: /* printf(" %d ",j); */
6492: /* for(theta=1; theta <=npar; theta++) */
6493: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6494: /* printf("\n "); */
6495: /* } */
6496: /* } */
6497: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6498: /* printf("\n gradg %d ",(int)age); */
6499: /* for(j=1; j<=nlstate;j++){ */
6500: /* printf("%d ",j); */
6501: /* for(theta=1; theta <=npar; theta++) */
6502: /* printf("%d %lf ",theta,gradg[theta][j]); */
6503: /* printf("\n "); */
6504: /* } */
6505: /* } */
6506:
6507: for(i=1;i<=nlstate;i++)
6508: varbpl[i][(int)age] =0.;
6509: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6510: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6511: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6512: }else{
6513: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6514: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6515: }
6516: for(i=1;i<=nlstate;i++)
6517: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6518:
6519: fprintf(ficresvbl,"%.0f ",age );
6520: if(nresult >=1)
6521: fprintf(ficresvbl,"%d ",nres );
6522: for(i=1; i<=nlstate;i++)
6523: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6524: fprintf(ficresvbl,"\n");
6525: free_vector(gp,1,nlstate);
6526: free_vector(gm,1,nlstate);
6527: free_matrix(mgm,1,npar,1,nlstate);
6528: free_matrix(mgp,1,npar,1,nlstate);
6529: free_matrix(gradg,1,npar,1,nlstate);
6530: free_matrix(trgradg,1,nlstate,1,npar);
6531: } /* End age */
6532:
6533: free_vector(xp,1,npar);
6534: free_matrix(doldm,1,nlstate,1,npar);
6535: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6536:
6537: }
6538:
6539: /************ Variance of one-step probabilities ******************/
6540: 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 6541: {
6542: int i, j=0, k1, l1, tj;
6543: int k2, l2, j1, z1;
6544: int k=0, l;
6545: int first=1, first1, first2;
6546: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6547: double **dnewm,**doldm;
6548: double *xp;
6549: double *gp, *gm;
6550: double **gradg, **trgradg;
6551: double **mu;
6552: double age, cov[NCOVMAX+1];
6553: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6554: int theta;
6555: char fileresprob[FILENAMELENGTH];
6556: char fileresprobcov[FILENAMELENGTH];
6557: char fileresprobcor[FILENAMELENGTH];
6558: double ***varpij;
6559:
6560: strcpy(fileresprob,"PROB_");
6561: strcat(fileresprob,fileres);
6562: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6563: printf("Problem with resultfile: %s\n", fileresprob);
6564: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6565: }
6566: strcpy(fileresprobcov,"PROBCOV_");
6567: strcat(fileresprobcov,fileresu);
6568: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6569: printf("Problem with resultfile: %s\n", fileresprobcov);
6570: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6571: }
6572: strcpy(fileresprobcor,"PROBCOR_");
6573: strcat(fileresprobcor,fileresu);
6574: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6575: printf("Problem with resultfile: %s\n", fileresprobcor);
6576: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6577: }
6578: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6579: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6580: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6581: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6582: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6583: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6584: pstamp(ficresprob);
6585: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6586: fprintf(ficresprob,"# Age");
6587: pstamp(ficresprobcov);
6588: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6589: fprintf(ficresprobcov,"# Age");
6590: pstamp(ficresprobcor);
6591: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6592: fprintf(ficresprobcor,"# Age");
1.126 brouard 6593:
6594:
1.222 brouard 6595: for(i=1; i<=nlstate;i++)
6596: for(j=1; j<=(nlstate+ndeath);j++){
6597: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6598: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6599: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6600: }
6601: /* fprintf(ficresprob,"\n");
6602: fprintf(ficresprobcov,"\n");
6603: fprintf(ficresprobcor,"\n");
6604: */
6605: xp=vector(1,npar);
6606: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6607: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6608: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6609: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6610: first=1;
6611: fprintf(ficgp,"\n# Routine varprob");
6612: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6613: fprintf(fichtm,"\n");
6614:
1.288 brouard 6615: 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 6616: 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);
6617: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6618: and drawn. It helps understanding how is the covariance between two incidences.\
6619: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6620: 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 6621: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6622: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6623: standard deviations wide on each axis. <br>\
6624: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6625: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6626: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6627:
1.222 brouard 6628: cov[1]=1;
6629: /* tj=cptcoveff; */
1.225 brouard 6630: tj = (int) pow(2,cptcoveff);
1.222 brouard 6631: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6632: j1=0;
1.224 brouard 6633: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6634: if (cptcovn>0) {
6635: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6636: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6637: fprintf(ficresprob, "**********\n#\n");
6638: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6639: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6640: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6641:
1.222 brouard 6642: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6643: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6644: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6645:
6646:
1.222 brouard 6647: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6648: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6649: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6650:
1.222 brouard 6651: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6652: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6653: fprintf(ficresprobcor, "**********\n#");
6654: if(invalidvarcomb[j1]){
6655: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6656: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6657: continue;
6658: }
6659: }
6660: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6661: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6662: gp=vector(1,(nlstate)*(nlstate+ndeath));
6663: gm=vector(1,(nlstate)*(nlstate+ndeath));
6664: for (age=bage; age<=fage; age ++){
6665: cov[2]=age;
6666: if(nagesqr==1)
6667: cov[3]= age*age;
6668: for (k=1; k<=cptcovn;k++) {
6669: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6670: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6671: * 1 1 1 1 1
6672: * 2 2 1 1 1
6673: * 3 1 2 1 1
6674: */
6675: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6676: }
6677: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6678: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6679: for (k=1; k<=cptcovprod;k++)
6680: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6681:
6682:
1.222 brouard 6683: for(theta=1; theta <=npar; theta++){
6684: for(i=1; i<=npar; i++)
6685: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6686:
1.222 brouard 6687: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6688:
1.222 brouard 6689: k=0;
6690: for(i=1; i<= (nlstate); i++){
6691: for(j=1; j<=(nlstate+ndeath);j++){
6692: k=k+1;
6693: gp[k]=pmmij[i][j];
6694: }
6695: }
1.220 brouard 6696:
1.222 brouard 6697: for(i=1; i<=npar; i++)
6698: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6699:
1.222 brouard 6700: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6701: k=0;
6702: for(i=1; i<=(nlstate); i++){
6703: for(j=1; j<=(nlstate+ndeath);j++){
6704: k=k+1;
6705: gm[k]=pmmij[i][j];
6706: }
6707: }
1.220 brouard 6708:
1.222 brouard 6709: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6710: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6711: }
1.126 brouard 6712:
1.222 brouard 6713: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6714: for(theta=1; theta <=npar; theta++)
6715: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6716:
1.222 brouard 6717: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6718: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6719:
1.222 brouard 6720: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6721:
1.222 brouard 6722: k=0;
6723: for(i=1; i<=(nlstate); i++){
6724: for(j=1; j<=(nlstate+ndeath);j++){
6725: k=k+1;
6726: mu[k][(int) age]=pmmij[i][j];
6727: }
6728: }
6729: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6730: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6731: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6732:
1.222 brouard 6733: /*printf("\n%d ",(int)age);
6734: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6735: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6736: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6737: }*/
1.220 brouard 6738:
1.222 brouard 6739: fprintf(ficresprob,"\n%d ",(int)age);
6740: fprintf(ficresprobcov,"\n%d ",(int)age);
6741: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6742:
1.222 brouard 6743: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6744: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6745: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6746: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6747: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6748: }
6749: i=0;
6750: for (k=1; k<=(nlstate);k++){
6751: for (l=1; l<=(nlstate+ndeath);l++){
6752: i++;
6753: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6754: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6755: for (j=1; j<=i;j++){
6756: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6757: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6758: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6759: }
6760: }
6761: }/* end of loop for state */
6762: } /* end of loop for age */
6763: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6764: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6765: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6766: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6767:
6768: /* Confidence intervalle of pij */
6769: /*
6770: fprintf(ficgp,"\nunset parametric;unset label");
6771: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6772: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6773: 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);
6774: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6775: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6776: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6777: */
6778:
6779: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6780: first1=1;first2=2;
6781: for (k2=1; k2<=(nlstate);k2++){
6782: for (l2=1; l2<=(nlstate+ndeath);l2++){
6783: if(l2==k2) continue;
6784: j=(k2-1)*(nlstate+ndeath)+l2;
6785: for (k1=1; k1<=(nlstate);k1++){
6786: for (l1=1; l1<=(nlstate+ndeath);l1++){
6787: if(l1==k1) continue;
6788: i=(k1-1)*(nlstate+ndeath)+l1;
6789: if(i<=j) continue;
6790: for (age=bage; age<=fage; age ++){
6791: if ((int)age %5==0){
6792: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6793: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6794: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6795: mu1=mu[i][(int) age]/stepm*YEARM ;
6796: mu2=mu[j][(int) age]/stepm*YEARM;
6797: c12=cv12/sqrt(v1*v2);
6798: /* Computing eigen value of matrix of covariance */
6799: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6800: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6801: if ((lc2 <0) || (lc1 <0) ){
6802: if(first2==1){
6803: first1=0;
6804: 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);
6805: }
6806: 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);
6807: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6808: /* lc2=fabs(lc2); */
6809: }
1.220 brouard 6810:
1.222 brouard 6811: /* Eigen vectors */
1.280 brouard 6812: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6813: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6814: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6815: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6816: }else
6817: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6818: /*v21=sqrt(1.-v11*v11); *//* error */
6819: v21=(lc1-v1)/cv12*v11;
6820: v12=-v21;
6821: v22=v11;
6822: tnalp=v21/v11;
6823: if(first1==1){
6824: first1=0;
6825: 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);
6826: }
6827: 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);
6828: /*printf(fignu*/
6829: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6830: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6831: if(first==1){
6832: first=0;
6833: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6834: fprintf(ficgp,"\nset parametric;unset label");
6835: 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);
6836: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6837: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6838: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6839: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6840: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6841: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6842: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6843: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6844: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6845: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6846: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6847: 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 6848: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6849: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6850: }else{
6851: first=0;
6852: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6853: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6854: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6855: 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 6856: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6857: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6858: }/* if first */
6859: } /* age mod 5 */
6860: } /* end loop age */
6861: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6862: first=1;
6863: } /*l12 */
6864: } /* k12 */
6865: } /*l1 */
6866: }/* k1 */
6867: } /* loop on combination of covariates j1 */
6868: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6869: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6870: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6871: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6872: free_vector(xp,1,npar);
6873: fclose(ficresprob);
6874: fclose(ficresprobcov);
6875: fclose(ficresprobcor);
6876: fflush(ficgp);
6877: fflush(fichtmcov);
6878: }
1.126 brouard 6879:
6880:
6881: /******************* Printing html file ***********/
1.201 brouard 6882: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6883: int lastpass, int stepm, int weightopt, char model[],\
6884: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6885: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6886: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6887: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6888: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6889:
6890: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6891: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6892: </ul>");
1.237 brouard 6893: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6894: </ul>", model);
1.214 brouard 6895: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6896: 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",
6897: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6898: 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 6899: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6900: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6901: fprintf(fichtm,"\
6902: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6903: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6904: fprintf(fichtm,"\
1.217 brouard 6905: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6906: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6907: fprintf(fichtm,"\
1.288 brouard 6908: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6909: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6910: fprintf(fichtm,"\
1.288 brouard 6911: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6912: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6913: fprintf(fichtm,"\
1.211 brouard 6914: - (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 6915: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6916: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6917: if(prevfcast==1){
6918: fprintf(fichtm,"\
6919: - Prevalence projections by age and states: \
1.201 brouard 6920: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6921: }
1.126 brouard 6922:
6923:
1.225 brouard 6924: m=pow(2,cptcoveff);
1.222 brouard 6925: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6926:
1.264 brouard 6927: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6928:
6929: jj1=0;
6930:
6931: fprintf(fichtm," \n<ul>");
6932: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6933: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6934: if(m != 1 && TKresult[nres]!= k1)
6935: continue;
6936: jj1++;
6937: if (cptcovn > 0) {
6938: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6939: for (cpt=1; cpt<=cptcoveff;cpt++){
6940: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6941: }
6942: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6943: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6944: }
6945: fprintf(fichtm,"\">");
6946:
6947: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6948: fprintf(fichtm,"************ Results for covariates");
6949: for (cpt=1; cpt<=cptcoveff;cpt++){
6950: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6951: }
6952: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6953: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6954: }
6955: if(invalidvarcomb[k1]){
6956: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6957: continue;
6958: }
6959: fprintf(fichtm,"</a></li>");
6960: } /* cptcovn >0 */
6961: }
6962: fprintf(fichtm," \n</ul>");
6963:
1.222 brouard 6964: jj1=0;
1.237 brouard 6965:
6966: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6967: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6968: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6969: continue;
1.220 brouard 6970:
1.222 brouard 6971: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6972: jj1++;
6973: if (cptcovn > 0) {
1.264 brouard 6974: fprintf(fichtm,"\n<p><a name=\"rescov");
6975: for (cpt=1; cpt<=cptcoveff;cpt++){
6976: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6977: }
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: }
6981: fprintf(fichtm,"\"</a>");
6982:
1.222 brouard 6983: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6984: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6985: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6986: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6987: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6988: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6989: }
1.237 brouard 6990: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6991: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6992: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6993: }
6994:
1.230 brouard 6995: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6996: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6997: if(invalidvarcomb[k1]){
6998: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6999: printf("\nCombination (%d) ignored because no cases \n",k1);
7000: continue;
7001: }
7002: }
7003: /* aij, bij */
1.259 brouard 7004: 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 7005: <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 7006: /* Pij */
1.241 brouard 7007: 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> \
7008: <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 7009: /* Quasi-incidences */
7010: 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 7011: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7012: 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 7013: 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> \
7014: <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 7015: /* Survival functions (period) in state j */
7016: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7017: 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 7018: <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 7019: }
7020: /* State specific survival functions (period) */
7021: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7022: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7023: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7024: <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 7025: }
1.288 brouard 7026: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7027: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7028: 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> \
7029: <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 7030: }
1.296 brouard 7031: if(prevbcast==1){
1.288 brouard 7032: /* Backward prevalence in each health state */
1.222 brouard 7033: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7034: 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 7035: <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 7036: }
1.217 brouard 7037: }
1.222 brouard 7038: if(prevfcast==1){
1.288 brouard 7039: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7040: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7041: 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 7042: <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 7043: }
7044: }
1.296 brouard 7045: if(prevbcast==1){
1.268 brouard 7046: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7047: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7048: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7049: 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 \
7050: 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) \
7051: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7052: <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 7053: }
7054: }
1.220 brouard 7055:
1.222 brouard 7056: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7057: 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> \
7058: <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 7059: }
7060: /* } /\* end i1 *\/ */
7061: }/* End k1 */
7062: fprintf(fichtm,"</ul>");
1.126 brouard 7063:
1.222 brouard 7064: fprintf(fichtm,"\
1.126 brouard 7065: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7066: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7067: - 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 7068: But because parameters are usually highly correlated (a higher incidence of disability \
7069: and a higher incidence of recovery can give very close observed transition) it might \
7070: be very useful to look not only at linear confidence intervals estimated from the \
7071: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7072: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7073: covariance matrix of the one-step probabilities. \
7074: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7075:
1.222 brouard 7076: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7077: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7078: fprintf(fichtm,"\
1.126 brouard 7079: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7080: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7081:
1.222 brouard 7082: fprintf(fichtm,"\
1.126 brouard 7083: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7084: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7085: fprintf(fichtm,"\
1.126 brouard 7086: - 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): \
7087: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7088: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7089: fprintf(fichtm,"\
1.126 brouard 7090: - (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): \
7091: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7092: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7093: fprintf(fichtm,"\
1.288 brouard 7094: - 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 7095: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7096: fprintf(fichtm,"\
1.128 brouard 7097: - 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 7098: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7099: fprintf(fichtm,"\
1.288 brouard 7100: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7101: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7102:
7103: /* if(popforecast==1) fprintf(fichtm,"\n */
7104: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7105: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7106: /* <br>",fileres,fileres,fileres,fileres); */
7107: /* else */
7108: /* 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 7109: fflush(fichtm);
7110: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7111:
1.225 brouard 7112: m=pow(2,cptcoveff);
1.222 brouard 7113: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7114:
1.222 brouard 7115: jj1=0;
1.237 brouard 7116:
1.241 brouard 7117: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7118: for(k1=1; k1<=m;k1++){
1.253 brouard 7119: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7120: continue;
1.222 brouard 7121: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7122: jj1++;
1.126 brouard 7123: if (cptcovn > 0) {
7124: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7125: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7126: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7127: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7128: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7129: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7130: }
7131:
1.126 brouard 7132: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7133:
1.222 brouard 7134: if(invalidvarcomb[k1]){
7135: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7136: continue;
7137: }
1.126 brouard 7138: }
7139: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7140: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7141: 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 7142: <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 7143: }
7144: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7145: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7146: true period expectancies (those weighted with period prevalences are also\
7147: drawn in addition to the population based expectancies computed using\
1.241 brouard 7148: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7149: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7150: /* } /\* end i1 *\/ */
7151: }/* End k1 */
1.241 brouard 7152: }/* End nres */
1.222 brouard 7153: fprintf(fichtm,"</ul>");
7154: fflush(fichtm);
1.126 brouard 7155: }
7156:
7157: /******************* Gnuplot file **************/
1.296 brouard 7158: 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 7159:
7160: char dirfileres[132],optfileres[132];
1.264 brouard 7161: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7162: 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 7163: int lv=0, vlv=0, kl=0;
1.130 brouard 7164: int ng=0;
1.201 brouard 7165: int vpopbased;
1.223 brouard 7166: int ioffset; /* variable offset for columns */
1.270 brouard 7167: int iyearc=1; /* variable column for year of projection */
7168: int iagec=1; /* variable column for age of projection */
1.235 brouard 7169: int nres=0; /* Index of resultline */
1.266 brouard 7170: int istart=1; /* For starting graphs in projections */
1.219 brouard 7171:
1.126 brouard 7172: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7173: /* printf("Problem with file %s",optionfilegnuplot); */
7174: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7175: /* } */
7176:
7177: /*#ifdef windows */
7178: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7179: /*#endif */
1.225 brouard 7180: m=pow(2,cptcoveff);
1.126 brouard 7181:
1.274 brouard 7182: /* diagram of the model */
7183: fprintf(ficgp,"\n#Diagram of the model \n");
7184: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7185: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7186: 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);
7187:
7188: 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);
7189: fprintf(ficgp,"\n#show arrow\nunset label\n");
7190: 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);
7191: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7192: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7193: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7194: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7195:
1.202 brouard 7196: /* Contribution to likelihood */
7197: /* Plot the probability implied in the likelihood */
1.223 brouard 7198: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7199: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7200: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7201: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7202: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7203: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7204: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7205: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7206: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7207: 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));
7208: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7209: 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));
7210: for (i=1; i<= nlstate ; i ++) {
7211: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7212: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7213: 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);
7214: for (j=2; j<= nlstate+ndeath ; j ++) {
7215: 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);
7216: }
7217: fprintf(ficgp,";\nset out; unset ylabel;\n");
7218: }
7219: /* 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 */
7220: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7221: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7222: fprintf(ficgp,"\nset out;unset log\n");
7223: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7224:
1.126 brouard 7225: strcpy(dirfileres,optionfilefiname);
7226: strcpy(optfileres,"vpl");
1.223 brouard 7227: /* 1eme*/
1.238 brouard 7228: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7229: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7230: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7231: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7232: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7233: continue;
7234: /* We are interested in selected combination by the resultline */
1.246 brouard 7235: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7236: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7237: strcpy(gplotlabel,"(");
1.238 brouard 7238: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7239: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7240: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7241: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7242: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7243: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7244: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7245: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7246: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7247: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7248: }
7249: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7250: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7251: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7252: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7253: }
7254: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7255: /* printf("\n#\n"); */
1.238 brouard 7256: fprintf(ficgp,"\n#\n");
7257: if(invalidvarcomb[k1]){
1.260 brouard 7258: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7259: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7260: continue;
7261: }
1.235 brouard 7262:
1.241 brouard 7263: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7264: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7265: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7266: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7267: 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);
7268: /* 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); */
7269: /* k1-1 error should be nres-1*/
1.238 brouard 7270: for (i=1; i<= nlstate ; i ++) {
7271: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7272: else fprintf(ficgp," %%*lf (%%*lf)");
7273: }
1.288 brouard 7274: 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 7275: for (i=1; i<= nlstate ; i ++) {
7276: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7277: else fprintf(ficgp," %%*lf (%%*lf)");
7278: }
1.260 brouard 7279: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7280: for (i=1; i<= nlstate ; i ++) {
7281: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7282: else fprintf(ficgp," %%*lf (%%*lf)");
7283: }
1.265 brouard 7284: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7285:
7286: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7287: if(cptcoveff ==0){
1.271 brouard 7288: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7289: }else{
7290: kl=0;
7291: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7292: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7293: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7294: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7295: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7296: vlv= nbcode[Tvaraff[k]][lv];
7297: kl++;
7298: /* 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 *\/ */
7299: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7300: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7301: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7302: if(k==cptcoveff){
7303: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7304: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7305: }else{
7306: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7307: kl++;
7308: }
7309: } /* end covariate */
7310: } /* end if no covariate */
7311:
1.296 brouard 7312: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7313: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7314: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7315: if(cptcoveff ==0){
1.245 brouard 7316: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7317: }else{
7318: kl=0;
7319: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7320: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7321: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7322: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7323: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7324: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7325: kl++;
1.238 brouard 7326: /* 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 *\/ */
7327: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7328: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7329: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7330: if(k==cptcoveff){
1.245 brouard 7331: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7332: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7333: }else{
7334: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7335: kl++;
7336: }
7337: } /* end covariate */
7338: } /* end if no covariate */
1.296 brouard 7339: if(prevbcast == 1){
1.268 brouard 7340: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7341: /* k1-1 error should be nres-1*/
7342: for (i=1; i<= nlstate ; i ++) {
7343: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7344: else fprintf(ficgp," %%*lf (%%*lf)");
7345: }
1.271 brouard 7346: 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 7347: for (i=1; i<= nlstate ; i ++) {
7348: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7349: else fprintf(ficgp," %%*lf (%%*lf)");
7350: }
1.276 brouard 7351: 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 7352: for (i=1; i<= nlstate ; i ++) {
7353: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7354: else fprintf(ficgp," %%*lf (%%*lf)");
7355: }
1.274 brouard 7356: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7357: } /* end if backprojcast */
1.296 brouard 7358: } /* end if prevbcast */
1.276 brouard 7359: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7360: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7361: } /* nres */
1.201 brouard 7362: } /* k1 */
7363: } /* cpt */
1.235 brouard 7364:
7365:
1.126 brouard 7366: /*2 eme*/
1.238 brouard 7367: for (k1=1; k1<= m ; k1 ++){
7368: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7369: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7370: continue;
7371: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7372: strcpy(gplotlabel,"(");
1.238 brouard 7373: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7374: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7375: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7376: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7377: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7378: vlv= nbcode[Tvaraff[k]][lv];
7379: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7380: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7381: }
1.237 brouard 7382: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7383: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7384: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7385: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7386: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7387: }
1.264 brouard 7388: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7389: fprintf(ficgp,"\n#\n");
1.223 brouard 7390: if(invalidvarcomb[k1]){
7391: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7392: continue;
7393: }
1.219 brouard 7394:
1.241 brouard 7395: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7396: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7397: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7398: if(vpopbased==0){
1.238 brouard 7399: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7400: }else
1.238 brouard 7401: fprintf(ficgp,"\nreplot ");
7402: for (i=1; i<= nlstate+1 ; i ++) {
7403: k=2*i;
1.261 brouard 7404: 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 7405: for (j=1; j<= nlstate+1 ; j ++) {
7406: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7407: else fprintf(ficgp," %%*lf (%%*lf)");
7408: }
7409: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7410: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7411: 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 7412: for (j=1; j<= nlstate+1 ; j ++) {
7413: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7414: else fprintf(ficgp," %%*lf (%%*lf)");
7415: }
7416: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7417: 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 7418: for (j=1; j<= nlstate+1 ; j ++) {
7419: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7420: else fprintf(ficgp," %%*lf (%%*lf)");
7421: }
7422: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7423: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7424: } /* state */
7425: } /* vpopbased */
1.264 brouard 7426: 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 7427: } /* end nres */
7428: } /* k1 end 2 eme*/
7429:
7430:
7431: /*3eme*/
7432: for (k1=1; k1<= m ; k1 ++){
7433: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7434: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7435: continue;
7436:
7437: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7438: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7439: strcpy(gplotlabel,"(");
1.238 brouard 7440: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7441: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7442: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7443: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7444: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7445: vlv= nbcode[Tvaraff[k]][lv];
7446: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7447: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7448: }
7449: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7450: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7451: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7452: }
1.264 brouard 7453: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7454: fprintf(ficgp,"\n#\n");
7455: if(invalidvarcomb[k1]){
7456: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7457: continue;
7458: }
7459:
7460: /* k=2+nlstate*(2*cpt-2); */
7461: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7462: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7463: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7464: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7465: 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 7466: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7467: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7468: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7469: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7470: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7471: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7472:
1.238 brouard 7473: */
7474: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7475: 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 7476: /* 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 7477:
1.238 brouard 7478: }
1.261 brouard 7479: 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 7480: }
1.264 brouard 7481: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7482: } /* end nres */
7483: } /* end kl 3eme */
1.126 brouard 7484:
1.223 brouard 7485: /* 4eme */
1.201 brouard 7486: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7487: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7488: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7489: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7490: continue;
1.238 brouard 7491: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7492: strcpy(gplotlabel,"(");
1.238 brouard 7493: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7494: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7495: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7496: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7497: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7498: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7499: vlv= nbcode[Tvaraff[k]][lv];
7500: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7501: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7502: }
7503: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7504: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7505: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7506: }
1.264 brouard 7507: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7508: fprintf(ficgp,"\n#\n");
7509: if(invalidvarcomb[k1]){
7510: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7511: continue;
1.223 brouard 7512: }
1.238 brouard 7513:
1.241 brouard 7514: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7515: 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 7516: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7517: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7518: k=3;
7519: for (i=1; i<= nlstate ; i ++){
7520: if(i==1){
7521: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7522: }else{
7523: fprintf(ficgp,", '' ");
7524: }
7525: l=(nlstate+ndeath)*(i-1)+1;
7526: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7527: for (j=2; j<= nlstate+ndeath ; j ++)
7528: fprintf(ficgp,"+$%d",k+l+j-1);
7529: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7530: } /* nlstate */
1.264 brouard 7531: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7532: } /* end cpt state*/
7533: } /* end nres */
7534: } /* end covariate k1 */
7535:
1.220 brouard 7536: /* 5eme */
1.201 brouard 7537: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7538: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7539: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7540: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7541: continue;
1.238 brouard 7542: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7543: strcpy(gplotlabel,"(");
1.238 brouard 7544: 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);
7545: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7546: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7547: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7548: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7549: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7550: vlv= nbcode[Tvaraff[k]][lv];
7551: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7552: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7553: }
7554: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7555: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7556: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7557: }
1.264 brouard 7558: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7559: fprintf(ficgp,"\n#\n");
7560: if(invalidvarcomb[k1]){
7561: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7562: continue;
7563: }
1.227 brouard 7564:
1.241 brouard 7565: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7566: 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 7567: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7568: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7569: k=3;
7570: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7571: if(j==1)
7572: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7573: else
7574: fprintf(ficgp,", '' ");
7575: l=(nlstate+ndeath)*(cpt-1) +j;
7576: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7577: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7578: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7579: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7580: } /* nlstate */
7581: fprintf(ficgp,", '' ");
7582: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7583: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7584: l=(nlstate+ndeath)*(cpt-1) +j;
7585: if(j < nlstate)
7586: fprintf(ficgp,"$%d +",k+l);
7587: else
7588: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7589: }
1.264 brouard 7590: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7591: } /* end cpt state*/
7592: } /* end covariate */
7593: } /* end nres */
1.227 brouard 7594:
1.220 brouard 7595: /* 6eme */
1.202 brouard 7596: /* CV preval stable (period) for each covariate */
1.237 brouard 7597: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7598: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7599: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7600: continue;
1.255 brouard 7601: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7602: strcpy(gplotlabel,"(");
1.288 brouard 7603: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7604: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7605: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7606: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7607: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7608: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7609: vlv= nbcode[Tvaraff[k]][lv];
7610: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7611: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7612: }
1.237 brouard 7613: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7614: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7615: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7616: }
1.264 brouard 7617: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7618: fprintf(ficgp,"\n#\n");
1.223 brouard 7619: if(invalidvarcomb[k1]){
1.227 brouard 7620: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7621: continue;
1.223 brouard 7622: }
1.227 brouard 7623:
1.241 brouard 7624: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7625: 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 7626: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7627: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7628: k=3; /* Offset */
1.255 brouard 7629: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7630: if(i==1)
7631: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7632: else
7633: fprintf(ficgp,", '' ");
1.255 brouard 7634: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7635: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7636: for (j=2; j<= nlstate ; j ++)
7637: fprintf(ficgp,"+$%d",k+l+j-1);
7638: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7639: } /* nlstate */
1.264 brouard 7640: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7641: } /* end cpt state*/
7642: } /* end covariate */
1.227 brouard 7643:
7644:
1.220 brouard 7645: /* 7eme */
1.296 brouard 7646: if(prevbcast == 1){
1.288 brouard 7647: /* CV backward prevalence for each covariate */
1.237 brouard 7648: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7649: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7650: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7651: continue;
1.268 brouard 7652: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7653: strcpy(gplotlabel,"(");
1.288 brouard 7654: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7655: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7656: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7657: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7658: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7659: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7660: vlv= nbcode[Tvaraff[k]][lv];
7661: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7662: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7663: }
1.237 brouard 7664: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7665: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7666: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7667: }
1.264 brouard 7668: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7669: fprintf(ficgp,"\n#\n");
7670: if(invalidvarcomb[k1]){
7671: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7672: continue;
7673: }
7674:
1.241 brouard 7675: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7676: 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 7677: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7678: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7679: k=3; /* Offset */
1.268 brouard 7680: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7681: if(i==1)
7682: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7683: else
7684: fprintf(ficgp,", '' ");
7685: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7686: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7687: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7688: /* 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 7689: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7690: /* for (j=2; j<= nlstate ; j ++) */
7691: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7692: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7693: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7694: } /* nlstate */
1.264 brouard 7695: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7696: } /* end cpt state*/
7697: } /* end covariate */
1.296 brouard 7698: } /* End if prevbcast */
1.218 brouard 7699:
1.223 brouard 7700: /* 8eme */
1.218 brouard 7701: if(prevfcast==1){
1.288 brouard 7702: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7703:
1.237 brouard 7704: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7705: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7706: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7707: continue;
1.211 brouard 7708: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7709: strcpy(gplotlabel,"(");
1.288 brouard 7710: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7711: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7712: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7713: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7714: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7715: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7716: vlv= nbcode[Tvaraff[k]][lv];
7717: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7718: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7719: }
1.237 brouard 7720: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7721: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7722: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7723: }
1.264 brouard 7724: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7725: fprintf(ficgp,"\n#\n");
7726: if(invalidvarcomb[k1]){
7727: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7728: continue;
7729: }
7730:
7731: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7732: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7733: 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 7734: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7735: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7736:
7737: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7738: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7739: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7740: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7741: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7742: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7743: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7744: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7745: if(i==istart){
1.227 brouard 7746: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7747: }else{
7748: fprintf(ficgp,",\\\n '' ");
7749: }
7750: if(cptcoveff ==0){ /* No covariate */
7751: ioffset=2; /* Age is in 2 */
7752: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7753: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7754: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7755: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7756: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7757: if(i==nlstate+1){
1.270 brouard 7758: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7759: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7760: fprintf(ficgp,",\\\n '' ");
7761: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7762: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7763: offyear, \
1.268 brouard 7764: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7765: }else
1.227 brouard 7766: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7767: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7768: }else{ /* more than 2 covariates */
1.270 brouard 7769: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7770: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7771: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7772: iyearc=ioffset-1;
7773: iagec=ioffset;
1.227 brouard 7774: fprintf(ficgp," u %d:(",ioffset);
7775: kl=0;
7776: strcpy(gplotcondition,"(");
7777: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7778: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7779: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7780: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7781: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7782: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7783: kl++;
7784: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7785: kl++;
7786: if(k <cptcoveff && cptcoveff>1)
7787: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7788: }
7789: strcpy(gplotcondition+strlen(gplotcondition),")");
7790: /* 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 *\/ */
7791: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7792: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7793: /* '' 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*/
7794: if(i==nlstate+1){
1.270 brouard 7795: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7796: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7797: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7798: fprintf(ficgp," u %d:(",iagec);
7799: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7800: iyearc, iagec, offyear, \
7801: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7802: /* '' 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 7803: }else{
7804: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7805: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7806: }
7807: } /* end if covariate */
7808: } /* nlstate */
1.264 brouard 7809: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7810: } /* end cpt state*/
7811: } /* end covariate */
7812: } /* End if prevfcast */
1.227 brouard 7813:
1.296 brouard 7814: if(prevbcast==1){
1.268 brouard 7815: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7816:
7817: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7818: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7819: if(m != 1 && TKresult[nres]!= k1)
7820: continue;
7821: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7822: strcpy(gplotlabel,"(");
7823: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7824: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7825: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7826: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7827: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7828: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7829: vlv= nbcode[Tvaraff[k]][lv];
7830: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7831: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7832: }
7833: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7834: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7835: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7836: }
7837: strcpy(gplotlabel+strlen(gplotlabel),")");
7838: fprintf(ficgp,"\n#\n");
7839: if(invalidvarcomb[k1]){
7840: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7841: continue;
7842: }
7843:
7844: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7845: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7846: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7847: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7848: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7849:
7850: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7851: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7852: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7853: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7854: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7855: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7856: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7857: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7858: if(i==istart){
7859: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7860: }else{
7861: fprintf(ficgp,",\\\n '' ");
7862: }
7863: if(cptcoveff ==0){ /* No covariate */
7864: ioffset=2; /* Age is in 2 */
7865: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7866: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7867: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7868: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7869: fprintf(ficgp," u %d:(", ioffset);
7870: if(i==nlstate+1){
1.270 brouard 7871: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7872: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7873: fprintf(ficgp,",\\\n '' ");
7874: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7875: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7876: offbyear, \
7877: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7878: }else
7879: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7880: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7881: }else{ /* more than 2 covariates */
1.270 brouard 7882: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7883: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7884: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7885: iyearc=ioffset-1;
7886: iagec=ioffset;
1.268 brouard 7887: fprintf(ficgp," u %d:(",ioffset);
7888: kl=0;
7889: strcpy(gplotcondition,"(");
7890: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7891: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7892: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7893: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7894: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7895: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7896: kl++;
7897: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7898: kl++;
7899: if(k <cptcoveff && cptcoveff>1)
7900: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7901: }
7902: strcpy(gplotcondition+strlen(gplotcondition),")");
7903: /* 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 *\/ */
7904: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7905: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7906: /* '' 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*/
7907: if(i==nlstate+1){
1.270 brouard 7908: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7909: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7910: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7911: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7912: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7913: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7914: iyearc,iagec,offbyear, \
7915: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7916: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7917: }else{
7918: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7919: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7920: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7921: }
7922: } /* end if covariate */
7923: } /* nlstate */
7924: fprintf(ficgp,"\nset out; unset label;\n");
7925: } /* end cpt state*/
7926: } /* end covariate */
1.296 brouard 7927: } /* End if prevbcast */
1.268 brouard 7928:
1.227 brouard 7929:
1.238 brouard 7930: /* 9eme writing MLE parameters */
7931: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7932: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7933: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7934: for(k=1; k <=(nlstate+ndeath); k++){
7935: if (k != i) {
1.227 brouard 7936: fprintf(ficgp,"# current state %d\n",k);
7937: for(j=1; j <=ncovmodel; j++){
7938: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7939: jk++;
7940: }
7941: fprintf(ficgp,"\n");
1.126 brouard 7942: }
7943: }
1.223 brouard 7944: }
1.187 brouard 7945: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7946:
1.145 brouard 7947: /*goto avoid;*/
1.238 brouard 7948: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7949: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7950: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7951: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7952: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7953: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7954: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7955: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7956: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7957: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7958: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7959: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7960: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7961: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7962: fprintf(ficgp,"#\n");
1.223 brouard 7963: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7964: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7965: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7966: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7967: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7968: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7969: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7970: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7971: continue;
1.264 brouard 7972: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7973: strcpy(gplotlabel,"(");
1.276 brouard 7974: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7975: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7976: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7977: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7978: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7979: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7980: vlv= nbcode[Tvaraff[k]][lv];
7981: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7982: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7983: }
1.237 brouard 7984: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7985: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7986: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7987: }
1.264 brouard 7988: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7989: fprintf(ficgp,"\n#\n");
1.264 brouard 7990: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7991: fprintf(ficgp,"\nset key outside ");
7992: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7993: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7994: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7995: if (ng==1){
7996: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7997: fprintf(ficgp,"\nunset log y");
7998: }else if (ng==2){
7999: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
8000: fprintf(ficgp,"\nset log y");
8001: }else if (ng==3){
8002: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
8003: fprintf(ficgp,"\nset log y");
8004: }else
8005: fprintf(ficgp,"\nunset title ");
8006: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
8007: i=1;
8008: for(k2=1; k2<=nlstate; k2++) {
8009: k3=i;
8010: for(k=1; k<=(nlstate+ndeath); k++) {
8011: if (k != k2){
8012: switch( ng) {
8013: case 1:
8014: if(nagesqr==0)
8015: fprintf(ficgp," p%d+p%d*x",i,i+1);
8016: else /* nagesqr =1 */
8017: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8018: break;
8019: case 2: /* ng=2 */
8020: if(nagesqr==0)
8021: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8022: else /* nagesqr =1 */
8023: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8024: break;
8025: case 3:
8026: if(nagesqr==0)
8027: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8028: else /* nagesqr =1 */
8029: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8030: break;
8031: }
8032: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8033: ijp=1; /* product no age */
8034: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8035: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8036: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8037: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8038: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8039: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8040: if(DummyV[j]==0){
8041: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8042: }else{ /* quantitative */
8043: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8044: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8045: }
8046: ij++;
1.237 brouard 8047: }
1.268 brouard 8048: }
8049: }else if(cptcovprod >0){
8050: if(j==Tprod[ijp]) { /* */
8051: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8052: if(ijp <=cptcovprod) { /* Product */
8053: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8054: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8055: /* 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)]); */
8056: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8057: }else{ /* Vn is dummy and Vm is quanti */
8058: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8059: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8060: }
8061: }else{ /* Vn*Vm Vn is quanti */
8062: if(DummyV[Tvard[ijp][2]]==0){
8063: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8064: }else{ /* Both quanti */
8065: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8066: }
1.237 brouard 8067: }
1.268 brouard 8068: ijp++;
1.237 brouard 8069: }
1.268 brouard 8070: } /* end Tprod */
1.237 brouard 8071: } else{ /* simple covariate */
1.264 brouard 8072: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8073: if(Dummy[j]==0){
8074: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8075: }else{ /* quantitative */
8076: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8077: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8078: }
1.237 brouard 8079: } /* end simple */
8080: } /* end j */
1.223 brouard 8081: }else{
8082: i=i-ncovmodel;
8083: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8084: fprintf(ficgp," (1.");
8085: }
1.227 brouard 8086:
1.223 brouard 8087: if(ng != 1){
8088: fprintf(ficgp,")/(1");
1.227 brouard 8089:
1.264 brouard 8090: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8091: if(nagesqr==0)
1.264 brouard 8092: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8093: else /* nagesqr =1 */
1.264 brouard 8094: 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 8095:
1.223 brouard 8096: ij=1;
8097: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8098: if(cptcovage >0){
8099: if((j-2)==Tage[ij]) { /* Bug valgrind */
8100: if(ij <=cptcovage) { /* Bug valgrind */
8101: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8102: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8103: ij++;
8104: }
8105: }
8106: }else
8107: 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 8108: }
8109: fprintf(ficgp,")");
8110: }
8111: fprintf(ficgp,")");
8112: if(ng ==2)
1.276 brouard 8113: 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 8114: else /* ng= 3 */
1.276 brouard 8115: 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 8116: }else{ /* end ng <> 1 */
8117: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8118: 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 8119: }
8120: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8121: fprintf(ficgp,",");
8122: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8123: fprintf(ficgp,",");
8124: i=i+ncovmodel;
8125: } /* end k */
8126: } /* end k2 */
1.276 brouard 8127: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8128: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8129: } /* end k1 */
1.223 brouard 8130: } /* end ng */
8131: /* avoid: */
8132: fflush(ficgp);
1.126 brouard 8133: } /* end gnuplot */
8134:
8135:
8136: /*************** Moving average **************/
1.219 brouard 8137: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8138: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8139:
1.222 brouard 8140: int i, cpt, cptcod;
8141: int modcovmax =1;
8142: int mobilavrange, mob;
8143: int iage=0;
1.288 brouard 8144: int firstA1=0, firstA2=0;
1.222 brouard 8145:
1.266 brouard 8146: double sum=0., sumr=0.;
1.222 brouard 8147: double age;
1.266 brouard 8148: double *sumnewp, *sumnewm, *sumnewmr;
8149: double *agemingood, *agemaxgood;
8150: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8151:
8152:
1.278 brouard 8153: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8154: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8155:
8156: sumnewp = vector(1,ncovcombmax);
8157: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8158: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8159: agemingood = vector(1,ncovcombmax);
1.266 brouard 8160: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8161: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8162: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8163:
8164: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8165: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8166: sumnewp[cptcod]=0.;
1.266 brouard 8167: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8168: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8169: }
8170: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8171:
1.266 brouard 8172: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8173: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8174: else mobilavrange=mobilav;
8175: for (age=bage; age<=fage; age++)
8176: for (i=1; i<=nlstate;i++)
8177: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8178: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8179: /* We keep the original values on the extreme ages bage, fage and for
8180: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8181: we use a 5 terms etc. until the borders are no more concerned.
8182: */
8183: for (mob=3;mob <=mobilavrange;mob=mob+2){
8184: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8185: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8186: sumnewm[cptcod]=0.;
8187: for (i=1; i<=nlstate;i++){
1.222 brouard 8188: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8189: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8190: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8191: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8192: }
8193: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8194: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8195: } /* end i */
8196: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8197: } /* end cptcod */
1.222 brouard 8198: }/* end age */
8199: }/* end mob */
1.266 brouard 8200: }else{
8201: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8202: return -1;
1.266 brouard 8203: }
8204:
8205: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8206: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8207: if(invalidvarcomb[cptcod]){
8208: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8209: continue;
8210: }
1.219 brouard 8211:
1.266 brouard 8212: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8213: sumnewm[cptcod]=0.;
8214: sumnewmr[cptcod]=0.;
8215: for (i=1; i<=nlstate;i++){
8216: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8217: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8218: }
8219: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8220: agemingoodr[cptcod]=age;
8221: }
8222: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8223: agemingood[cptcod]=age;
8224: }
8225: } /* age */
8226: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8227: sumnewm[cptcod]=0.;
1.266 brouard 8228: sumnewmr[cptcod]=0.;
1.222 brouard 8229: for (i=1; i<=nlstate;i++){
8230: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8231: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8232: }
8233: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8234: agemaxgoodr[cptcod]=age;
1.222 brouard 8235: }
8236: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8237: agemaxgood[cptcod]=age;
8238: }
8239: } /* age */
8240: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8241: /* but they will change */
1.288 brouard 8242: firstA1=0;firstA2=0;
1.266 brouard 8243: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8244: sumnewm[cptcod]=0.;
8245: sumnewmr[cptcod]=0.;
8246: for (i=1; i<=nlstate;i++){
8247: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8248: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8249: }
8250: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8251: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8252: agemaxgoodr[cptcod]=age; /* age min */
8253: for (i=1; i<=nlstate;i++)
8254: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8255: }else{ /* bad we change the value with the values of good ages */
8256: for (i=1; i<=nlstate;i++){
8257: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8258: } /* i */
8259: } /* end bad */
8260: }else{
8261: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8262: agemaxgood[cptcod]=age;
8263: }else{ /* bad we change the value with the values of good ages */
8264: for (i=1; i<=nlstate;i++){
8265: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8266: } /* i */
8267: } /* end bad */
8268: }/* end else */
8269: sum=0.;sumr=0.;
8270: for (i=1; i<=nlstate;i++){
8271: sum+=mobaverage[(int)age][i][cptcod];
8272: sumr+=probs[(int)age][i][cptcod];
8273: }
8274: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8275: if(!firstA1){
8276: firstA1=1;
8277: 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);
8278: }
8279: 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 8280: } /* end bad */
8281: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8282: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8283: if(!firstA2){
8284: firstA2=1;
8285: 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);
8286: }
8287: 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 8288: } /* end bad */
8289: }/* age */
1.266 brouard 8290:
8291: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8292: sumnewm[cptcod]=0.;
1.266 brouard 8293: sumnewmr[cptcod]=0.;
1.222 brouard 8294: for (i=1; i<=nlstate;i++){
8295: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8296: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8297: }
8298: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8299: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8300: agemingoodr[cptcod]=age;
8301: for (i=1; i<=nlstate;i++)
8302: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8303: }else{ /* bad we change the value with the values of good ages */
8304: for (i=1; i<=nlstate;i++){
8305: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8306: } /* i */
8307: } /* end bad */
8308: }else{
8309: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8310: agemingood[cptcod]=age;
8311: }else{ /* bad */
8312: for (i=1; i<=nlstate;i++){
8313: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8314: } /* i */
8315: } /* end bad */
8316: }/* end else */
8317: sum=0.;sumr=0.;
8318: for (i=1; i<=nlstate;i++){
8319: sum+=mobaverage[(int)age][i][cptcod];
8320: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8321: }
1.266 brouard 8322: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8323: 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 8324: } /* end bad */
8325: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8326: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8327: 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 8328: } /* end bad */
8329: }/* age */
1.266 brouard 8330:
1.222 brouard 8331:
8332: for (age=bage; age<=fage; age++){
1.235 brouard 8333: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8334: sumnewp[cptcod]=0.;
8335: sumnewm[cptcod]=0.;
8336: for (i=1; i<=nlstate;i++){
8337: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8338: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8339: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8340: }
8341: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8342: }
8343: /* printf("\n"); */
8344: /* } */
1.266 brouard 8345:
1.222 brouard 8346: /* brutal averaging */
1.266 brouard 8347: /* for (i=1; i<=nlstate;i++){ */
8348: /* for (age=1; age<=bage; age++){ */
8349: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8350: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8351: /* } */
8352: /* for (age=fage; age<=AGESUP; age++){ */
8353: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8354: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8355: /* } */
8356: /* } /\* end i status *\/ */
8357: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8358: /* for (age=1; age<=AGESUP; age++){ */
8359: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8360: /* mobaverage[(int)age][i][cptcod]=0.; */
8361: /* } */
8362: /* } */
1.222 brouard 8363: }/* end cptcod */
1.266 brouard 8364: free_vector(agemaxgoodr,1, ncovcombmax);
8365: free_vector(agemaxgood,1, ncovcombmax);
8366: free_vector(agemingood,1, ncovcombmax);
8367: free_vector(agemingoodr,1, ncovcombmax);
8368: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8369: free_vector(sumnewm,1, ncovcombmax);
8370: free_vector(sumnewp,1, ncovcombmax);
8371: return 0;
8372: }/* End movingaverage */
1.218 brouard 8373:
1.126 brouard 8374:
1.296 brouard 8375:
1.126 brouard 8376: /************** Forecasting ******************/
1.296 brouard 8377: /* 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)*/
8378: 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){
8379: /* dateintemean, mean date of interviews
8380: dateprojd, year, month, day of starting projection
8381: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8382: agemin, agemax range of age
8383: dateprev1 dateprev2 range of dates during which prevalence is computed
8384: */
1.296 brouard 8385: /* double anprojd, mprojd, jprojd; */
8386: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8387: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8388: double agec; /* generic age */
1.296 brouard 8389: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8390: double *popeffectif,*popcount;
8391: double ***p3mat;
1.218 brouard 8392: /* double ***mobaverage; */
1.126 brouard 8393: char fileresf[FILENAMELENGTH];
8394:
8395: agelim=AGESUP;
1.211 brouard 8396: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8397: in each health status at the date of interview (if between dateprev1 and dateprev2).
8398: We still use firstpass and lastpass as another selection.
8399: */
1.214 brouard 8400: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8401: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8402:
1.201 brouard 8403: strcpy(fileresf,"F_");
8404: strcat(fileresf,fileresu);
1.126 brouard 8405: if((ficresf=fopen(fileresf,"w"))==NULL) {
8406: printf("Problem with forecast resultfile: %s\n", fileresf);
8407: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8408: }
1.235 brouard 8409: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8410: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8411:
1.225 brouard 8412: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8413:
8414:
8415: stepsize=(int) (stepm+YEARM-1)/YEARM;
8416: if (stepm<=12) stepsize=1;
8417: if(estepm < stepm){
8418: printf ("Problem %d lower than %d\n",estepm, stepm);
8419: }
1.270 brouard 8420: else{
8421: hstepm=estepm;
8422: }
8423: if(estepm > stepm){ /* Yes every two year */
8424: stepsize=2;
8425: }
1.296 brouard 8426: hstepm=hstepm/stepm;
1.126 brouard 8427:
1.296 brouard 8428:
8429: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8430: /* fractional in yp1 *\/ */
8431: /* aintmean=yp; */
8432: /* yp2=modf((yp1*12),&yp); */
8433: /* mintmean=yp; */
8434: /* yp1=modf((yp2*30.5),&yp); */
8435: /* jintmean=yp; */
8436: /* if(jintmean==0) jintmean=1; */
8437: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8438:
1.296 brouard 8439:
8440: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8441: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8442: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8443: i1=pow(2,cptcoveff);
1.126 brouard 8444: if (cptcovn < 1){i1=1;}
8445:
1.296 brouard 8446: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8447:
8448: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8449:
1.126 brouard 8450: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8451: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8452: for(k=1; k<=i1;k++){
1.253 brouard 8453: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8454: continue;
1.227 brouard 8455: if(invalidvarcomb[k]){
8456: printf("\nCombination (%d) projection ignored because no cases \n",k);
8457: continue;
8458: }
8459: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8460: for(j=1;j<=cptcoveff;j++) {
8461: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8462: }
1.235 brouard 8463: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8464: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8465: }
1.227 brouard 8466: fprintf(ficresf," yearproj age");
8467: for(j=1; j<=nlstate+ndeath;j++){
8468: for(i=1; i<=nlstate;i++)
8469: fprintf(ficresf," p%d%d",i,j);
8470: fprintf(ficresf," wp.%d",j);
8471: }
1.296 brouard 8472: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8473: fprintf(ficresf,"\n");
1.296 brouard 8474: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8475: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8476: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8477: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8478: nhstepm = nhstepm/hstepm;
8479: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8480: oldm=oldms;savm=savms;
1.268 brouard 8481: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8482: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8483: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8484: for (h=0; h<=nhstepm; h++){
8485: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8486: break;
8487: }
8488: }
8489: fprintf(ficresf,"\n");
8490: for(j=1;j<=cptcoveff;j++)
8491: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8492: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8493:
8494: for(j=1; j<=nlstate+ndeath;j++) {
8495: ppij=0.;
8496: for(i=1; i<=nlstate;i++) {
1.278 brouard 8497: if (mobilav>=1)
8498: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8499: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8500: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8501: }
1.268 brouard 8502: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8503: } /* end i */
8504: fprintf(ficresf," %.3f", ppij);
8505: }/* end j */
1.227 brouard 8506: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8507: } /* end agec */
1.266 brouard 8508: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8509: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8510: } /* end yearp */
8511: } /* end k */
1.219 brouard 8512:
1.126 brouard 8513: fclose(ficresf);
1.215 brouard 8514: printf("End of Computing forecasting \n");
8515: fprintf(ficlog,"End of Computing forecasting\n");
8516:
1.126 brouard 8517: }
8518:
1.269 brouard 8519: /************** Back Forecasting ******************/
1.296 brouard 8520: /* 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){ */
8521: 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){
8522: /* back1, year, month, day of starting backprojection
1.267 brouard 8523: agemin, agemax range of age
8524: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8525: anback2 year of end of backprojection (same day and month as back1).
8526: prevacurrent and prev are prevalences.
1.267 brouard 8527: */
8528: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8529: double agec; /* generic age */
1.302 brouard 8530: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8531: double *popeffectif,*popcount;
8532: double ***p3mat;
8533: /* double ***mobaverage; */
8534: char fileresfb[FILENAMELENGTH];
8535:
1.268 brouard 8536: agelim=AGEINF;
1.267 brouard 8537: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8538: in each health status at the date of interview (if between dateprev1 and dateprev2).
8539: We still use firstpass and lastpass as another selection.
8540: */
8541: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8542: /* firstpass, lastpass, stepm, weightopt, model); */
8543:
8544: /*Do we need to compute prevalence again?*/
8545:
8546: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8547:
8548: strcpy(fileresfb,"FB_");
8549: strcat(fileresfb,fileresu);
8550: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8551: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8552: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8553: }
8554: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8555: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8556:
8557: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8558:
8559:
8560: stepsize=(int) (stepm+YEARM-1)/YEARM;
8561: if (stepm<=12) stepsize=1;
8562: if(estepm < stepm){
8563: printf ("Problem %d lower than %d\n",estepm, stepm);
8564: }
1.270 brouard 8565: else{
8566: hstepm=estepm;
8567: }
8568: if(estepm >= stepm){ /* Yes every two year */
8569: stepsize=2;
8570: }
1.267 brouard 8571:
8572: hstepm=hstepm/stepm;
1.296 brouard 8573: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8574: /* fractional in yp1 *\/ */
8575: /* aintmean=yp; */
8576: /* yp2=modf((yp1*12),&yp); */
8577: /* mintmean=yp; */
8578: /* yp1=modf((yp2*30.5),&yp); */
8579: /* jintmean=yp; */
8580: /* if(jintmean==0) jintmean=1; */
8581: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8582:
8583: i1=pow(2,cptcoveff);
8584: if (cptcovn < 1){i1=1;}
8585:
1.296 brouard 8586: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8587: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8588:
8589: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8590:
8591: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8592: for(k=1; k<=i1;k++){
8593: if(i1 != 1 && TKresult[nres]!= k)
8594: continue;
8595: if(invalidvarcomb[k]){
8596: printf("\nCombination (%d) projection ignored because no cases \n",k);
8597: continue;
8598: }
1.268 brouard 8599: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8600: for(j=1;j<=cptcoveff;j++) {
8601: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8602: }
8603: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8604: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8605: }
8606: fprintf(ficresfb," yearbproj age");
8607: for(j=1; j<=nlstate+ndeath;j++){
8608: for(i=1; i<=nlstate;i++)
1.268 brouard 8609: fprintf(ficresfb," b%d%d",i,j);
8610: fprintf(ficresfb," b.%d",j);
1.267 brouard 8611: }
1.296 brouard 8612: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8613: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8614: fprintf(ficresfb,"\n");
1.296 brouard 8615: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8616: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8617: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8618: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8619: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8620: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8621: nhstepm = nhstepm/hstepm;
8622: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8623: oldm=oldms;savm=savms;
1.268 brouard 8624: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8625: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8626: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8627: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8628: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8629: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8630: for (h=0; h<=nhstepm; h++){
1.268 brouard 8631: if (h*hstepm/YEARM*stepm ==-yearp) {
8632: break;
8633: }
8634: }
8635: fprintf(ficresfb,"\n");
8636: for(j=1;j<=cptcoveff;j++)
8637: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8638: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8639: for(i=1; i<=nlstate+ndeath;i++) {
8640: ppij=0.;ppi=0.;
8641: for(j=1; j<=nlstate;j++) {
8642: /* if (mobilav==1) */
1.269 brouard 8643: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8644: ppi=ppi+prevacurrent[(int)agec][j][k];
8645: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8646: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8647: /* else { */
8648: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8649: /* } */
1.268 brouard 8650: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8651: } /* end j */
8652: if(ppi <0.99){
8653: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8654: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8655: }
8656: fprintf(ficresfb," %.3f", ppij);
8657: }/* end j */
1.267 brouard 8658: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8659: } /* end agec */
8660: } /* end yearp */
8661: } /* end k */
1.217 brouard 8662:
1.267 brouard 8663: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8664:
1.267 brouard 8665: fclose(ficresfb);
8666: printf("End of Computing Back forecasting \n");
8667: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8668:
1.267 brouard 8669: }
1.217 brouard 8670:
1.269 brouard 8671: /* Variance of prevalence limit: varprlim */
8672: 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 8673: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8674:
8675: char fileresvpl[FILENAMELENGTH];
8676: FILE *ficresvpl;
8677: double **oldm, **savm;
8678: double **varpl; /* Variances of prevalence limits by age */
8679: int i1, k, nres, j ;
8680:
8681: strcpy(fileresvpl,"VPL_");
8682: strcat(fileresvpl,fileresu);
8683: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8684: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8685: exit(0);
8686: }
1.288 brouard 8687: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8688: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8689:
8690: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8691: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8692:
8693: i1=pow(2,cptcoveff);
8694: if (cptcovn < 1){i1=1;}
8695:
8696: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8697: for(k=1; k<=i1;k++){
8698: if(i1 != 1 && TKresult[nres]!= k)
8699: continue;
8700: fprintf(ficresvpl,"\n#****** ");
8701: printf("\n#****** ");
8702: fprintf(ficlog,"\n#****** ");
8703: for(j=1;j<=cptcoveff;j++) {
8704: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8705: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8706: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8707: }
8708: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8709: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8710: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8711: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8712: }
8713: fprintf(ficresvpl,"******\n");
8714: printf("******\n");
8715: fprintf(ficlog,"******\n");
8716:
8717: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8718: oldm=oldms;savm=savms;
8719: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8720: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8721: /*}*/
8722: }
8723:
8724: fclose(ficresvpl);
1.288 brouard 8725: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8726: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8727:
8728: }
8729: /* Variance of back prevalence: varbprlim */
8730: 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){
8731: /*------- Variance of back (stable) prevalence------*/
8732:
8733: char fileresvbl[FILENAMELENGTH];
8734: FILE *ficresvbl;
8735:
8736: double **oldm, **savm;
8737: double **varbpl; /* Variances of back prevalence limits by age */
8738: int i1, k, nres, j ;
8739:
8740: strcpy(fileresvbl,"VBL_");
8741: strcat(fileresvbl,fileresu);
8742: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8743: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8744: exit(0);
8745: }
8746: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8747: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8748:
8749:
8750: i1=pow(2,cptcoveff);
8751: if (cptcovn < 1){i1=1;}
8752:
8753: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8754: for(k=1; k<=i1;k++){
8755: if(i1 != 1 && TKresult[nres]!= k)
8756: continue;
8757: fprintf(ficresvbl,"\n#****** ");
8758: printf("\n#****** ");
8759: fprintf(ficlog,"\n#****** ");
8760: for(j=1;j<=cptcoveff;j++) {
8761: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8762: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8763: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8764: }
8765: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8766: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8767: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8768: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8769: }
8770: fprintf(ficresvbl,"******\n");
8771: printf("******\n");
8772: fprintf(ficlog,"******\n");
8773:
8774: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8775: oldm=oldms;savm=savms;
8776:
8777: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8778: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8779: /*}*/
8780: }
8781:
8782: fclose(ficresvbl);
8783: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8784: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8785:
8786: } /* End of varbprlim */
8787:
1.126 brouard 8788: /************** Forecasting *****not tested NB*************/
1.227 brouard 8789: /* 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 8790:
1.227 brouard 8791: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8792: /* int *popage; */
8793: /* double calagedatem, agelim, kk1, kk2; */
8794: /* double *popeffectif,*popcount; */
8795: /* double ***p3mat,***tabpop,***tabpopprev; */
8796: /* /\* double ***mobaverage; *\/ */
8797: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8798:
1.227 brouard 8799: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8800: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8801: /* agelim=AGESUP; */
8802: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8803:
1.227 brouard 8804: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8805:
8806:
1.227 brouard 8807: /* strcpy(filerespop,"POP_"); */
8808: /* strcat(filerespop,fileresu); */
8809: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8810: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8811: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8812: /* } */
8813: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8814: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8815:
1.227 brouard 8816: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8817:
1.227 brouard 8818: /* /\* if (mobilav!=0) { *\/ */
8819: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8820: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8821: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8822: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8823: /* /\* } *\/ */
8824: /* /\* } *\/ */
1.126 brouard 8825:
1.227 brouard 8826: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8827: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8828:
1.227 brouard 8829: /* agelim=AGESUP; */
1.126 brouard 8830:
1.227 brouard 8831: /* hstepm=1; */
8832: /* hstepm=hstepm/stepm; */
1.218 brouard 8833:
1.227 brouard 8834: /* if (popforecast==1) { */
8835: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8836: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8837: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8838: /* } */
8839: /* popage=ivector(0,AGESUP); */
8840: /* popeffectif=vector(0,AGESUP); */
8841: /* popcount=vector(0,AGESUP); */
1.126 brouard 8842:
1.227 brouard 8843: /* i=1; */
8844: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8845:
1.227 brouard 8846: /* imx=i; */
8847: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8848: /* } */
1.218 brouard 8849:
1.227 brouard 8850: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8851: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8852: /* k=k+1; */
8853: /* fprintf(ficrespop,"\n#******"); */
8854: /* for(j=1;j<=cptcoveff;j++) { */
8855: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8856: /* } */
8857: /* fprintf(ficrespop,"******\n"); */
8858: /* fprintf(ficrespop,"# Age"); */
8859: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8860: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8861:
1.227 brouard 8862: /* for (cpt=0; cpt<=0;cpt++) { */
8863: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8864:
1.227 brouard 8865: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8866: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8867: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8868:
1.227 brouard 8869: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8870: /* oldm=oldms;savm=savms; */
8871: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8872:
1.227 brouard 8873: /* for (h=0; h<=nhstepm; h++){ */
8874: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8875: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8876: /* } */
8877: /* for(j=1; j<=nlstate+ndeath;j++) { */
8878: /* kk1=0.;kk2=0; */
8879: /* for(i=1; i<=nlstate;i++) { */
8880: /* if (mobilav==1) */
8881: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8882: /* else { */
8883: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8884: /* } */
8885: /* } */
8886: /* if (h==(int)(calagedatem+12*cpt)){ */
8887: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8888: /* /\*fprintf(ficrespop," %.3f", kk1); */
8889: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8890: /* } */
8891: /* } */
8892: /* for(i=1; i<=nlstate;i++){ */
8893: /* kk1=0.; */
8894: /* for(j=1; j<=nlstate;j++){ */
8895: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8896: /* } */
8897: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8898: /* } */
1.218 brouard 8899:
1.227 brouard 8900: /* if (h==(int)(calagedatem+12*cpt)) */
8901: /* for(j=1; j<=nlstate;j++) */
8902: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8903: /* } */
8904: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8905: /* } */
8906: /* } */
1.218 brouard 8907:
1.227 brouard 8908: /* /\******\/ */
1.218 brouard 8909:
1.227 brouard 8910: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8911: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8912: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8913: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8914: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8915:
1.227 brouard 8916: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8917: /* oldm=oldms;savm=savms; */
8918: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8919: /* for (h=0; h<=nhstepm; h++){ */
8920: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8921: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8922: /* } */
8923: /* for(j=1; j<=nlstate+ndeath;j++) { */
8924: /* kk1=0.;kk2=0; */
8925: /* for(i=1; i<=nlstate;i++) { */
8926: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8927: /* } */
8928: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8929: /* } */
8930: /* } */
8931: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8932: /* } */
8933: /* } */
8934: /* } */
8935: /* } */
1.218 brouard 8936:
1.227 brouard 8937: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8938:
1.227 brouard 8939: /* if (popforecast==1) { */
8940: /* free_ivector(popage,0,AGESUP); */
8941: /* free_vector(popeffectif,0,AGESUP); */
8942: /* free_vector(popcount,0,AGESUP); */
8943: /* } */
8944: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8945: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8946: /* fclose(ficrespop); */
8947: /* } /\* End of popforecast *\/ */
1.218 brouard 8948:
1.126 brouard 8949: int fileappend(FILE *fichier, char *optionfich)
8950: {
8951: if((fichier=fopen(optionfich,"a"))==NULL) {
8952: printf("Problem with file: %s\n", optionfich);
8953: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8954: return (0);
8955: }
8956: fflush(fichier);
8957: return (1);
8958: }
8959:
8960:
8961: /**************** function prwizard **********************/
8962: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8963: {
8964:
8965: /* Wizard to print covariance matrix template */
8966:
1.164 brouard 8967: char ca[32], cb[32];
8968: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8969: int numlinepar;
8970:
8971: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8972: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8973: for(i=1; i <=nlstate; i++){
8974: jj=0;
8975: for(j=1; j <=nlstate+ndeath; j++){
8976: if(j==i) continue;
8977: jj++;
8978: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8979: printf("%1d%1d",i,j);
8980: fprintf(ficparo,"%1d%1d",i,j);
8981: for(k=1; k<=ncovmodel;k++){
8982: /* printf(" %lf",param[i][j][k]); */
8983: /* fprintf(ficparo," %lf",param[i][j][k]); */
8984: printf(" 0.");
8985: fprintf(ficparo," 0.");
8986: }
8987: printf("\n");
8988: fprintf(ficparo,"\n");
8989: }
8990: }
8991: printf("# Scales (for hessian or gradient estimation)\n");
8992: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8993: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8994: for(i=1; i <=nlstate; i++){
8995: jj=0;
8996: for(j=1; j <=nlstate+ndeath; j++){
8997: if(j==i) continue;
8998: jj++;
8999: fprintf(ficparo,"%1d%1d",i,j);
9000: printf("%1d%1d",i,j);
9001: fflush(stdout);
9002: for(k=1; k<=ncovmodel;k++){
9003: /* printf(" %le",delti3[i][j][k]); */
9004: /* fprintf(ficparo," %le",delti3[i][j][k]); */
9005: printf(" 0.");
9006: fprintf(ficparo," 0.");
9007: }
9008: numlinepar++;
9009: printf("\n");
9010: fprintf(ficparo,"\n");
9011: }
9012: }
9013: printf("# Covariance matrix\n");
9014: /* # 121 Var(a12)\n\ */
9015: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9016: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9017: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9018: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9019: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9020: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9021: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9022: fflush(stdout);
9023: fprintf(ficparo,"# Covariance matrix\n");
9024: /* # 121 Var(a12)\n\ */
9025: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9026: /* # ...\n\ */
9027: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9028:
9029: for(itimes=1;itimes<=2;itimes++){
9030: jj=0;
9031: for(i=1; i <=nlstate; i++){
9032: for(j=1; j <=nlstate+ndeath; j++){
9033: if(j==i) continue;
9034: for(k=1; k<=ncovmodel;k++){
9035: jj++;
9036: ca[0]= k+'a'-1;ca[1]='\0';
9037: if(itimes==1){
9038: printf("#%1d%1d%d",i,j,k);
9039: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9040: }else{
9041: printf("%1d%1d%d",i,j,k);
9042: fprintf(ficparo,"%1d%1d%d",i,j,k);
9043: /* printf(" %.5le",matcov[i][j]); */
9044: }
9045: ll=0;
9046: for(li=1;li <=nlstate; li++){
9047: for(lj=1;lj <=nlstate+ndeath; lj++){
9048: if(lj==li) continue;
9049: for(lk=1;lk<=ncovmodel;lk++){
9050: ll++;
9051: if(ll<=jj){
9052: cb[0]= lk +'a'-1;cb[1]='\0';
9053: if(ll<jj){
9054: if(itimes==1){
9055: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9056: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9057: }else{
9058: printf(" 0.");
9059: fprintf(ficparo," 0.");
9060: }
9061: }else{
9062: if(itimes==1){
9063: printf(" Var(%s%1d%1d)",ca,i,j);
9064: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9065: }else{
9066: printf(" 0.");
9067: fprintf(ficparo," 0.");
9068: }
9069: }
9070: }
9071: } /* end lk */
9072: } /* end lj */
9073: } /* end li */
9074: printf("\n");
9075: fprintf(ficparo,"\n");
9076: numlinepar++;
9077: } /* end k*/
9078: } /*end j */
9079: } /* end i */
9080: } /* end itimes */
9081:
9082: } /* end of prwizard */
9083: /******************* Gompertz Likelihood ******************************/
9084: double gompertz(double x[])
9085: {
1.302 brouard 9086: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9087: int i,n=0; /* n is the size of the sample */
9088:
1.220 brouard 9089: for (i=1;i<=imx ; i++) {
1.126 brouard 9090: sump=sump+weight[i];
9091: /* sump=sump+1;*/
9092: num=num+1;
9093: }
1.302 brouard 9094: L=0.0;
9095: /* agegomp=AGEGOMP; */
1.126 brouard 9096: /* for (i=0; i<=imx; i++)
9097: 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]);*/
9098:
1.302 brouard 9099: for (i=1;i<=imx ; i++) {
9100: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9101: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9102: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9103: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9104: * +
9105: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9106: */
9107: if (wav[i] > 1 || agedc[i] < AGESUP) {
9108: if (cens[i] == 1){
9109: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9110: } else if (cens[i] == 0){
1.126 brouard 9111: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9112: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9113: } else
9114: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9115: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9116: L=L+A*weight[i];
1.126 brouard 9117: /* 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 9118: }
9119: }
1.126 brouard 9120:
1.302 brouard 9121: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9122:
9123: return -2*L*num/sump;
9124: }
9125:
1.136 brouard 9126: #ifdef GSL
9127: /******************* Gompertz_f Likelihood ******************************/
9128: double gompertz_f(const gsl_vector *v, void *params)
9129: {
1.302 brouard 9130: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9131: double *x= (double *) v->data;
9132: int i,n=0; /* n is the size of the sample */
9133:
9134: for (i=0;i<=imx-1 ; i++) {
9135: sump=sump+weight[i];
9136: /* sump=sump+1;*/
9137: num=num+1;
9138: }
9139:
9140:
9141: /* for (i=0; i<=imx; i++)
9142: 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]);*/
9143: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9144: for (i=1;i<=imx ; i++)
9145: {
9146: if (cens[i] == 1 && wav[i]>1)
9147: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9148:
9149: if (cens[i] == 0 && wav[i]>1)
9150: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9151: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9152:
9153: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9154: if (wav[i] > 1 ) { /* ??? */
9155: LL=LL+A*weight[i];
9156: /* 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]);*/
9157: }
9158: }
9159:
9160: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9161: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9162:
9163: return -2*LL*num/sump;
9164: }
9165: #endif
9166:
1.126 brouard 9167: /******************* Printing html file ***********/
1.201 brouard 9168: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9169: int lastpass, int stepm, int weightopt, char model[],\
9170: int imx, double p[],double **matcov,double agemortsup){
9171: int i,k;
9172:
9173: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9174: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9175: for (i=1;i<=2;i++)
9176: 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 9177: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9178: fprintf(fichtm,"</ul>");
9179:
9180: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9181:
9182: 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>");
9183:
9184: for (k=agegomp;k<(agemortsup-2);k++)
9185: 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]);
9186:
9187:
9188: fflush(fichtm);
9189: }
9190:
9191: /******************* Gnuplot file **************/
1.201 brouard 9192: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9193:
9194: char dirfileres[132],optfileres[132];
1.164 brouard 9195:
1.126 brouard 9196: int ng;
9197:
9198:
9199: /*#ifdef windows */
9200: fprintf(ficgp,"cd \"%s\" \n",pathc);
9201: /*#endif */
9202:
9203:
9204: strcpy(dirfileres,optionfilefiname);
9205: strcpy(optfileres,"vpl");
1.199 brouard 9206: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9207: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9208: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9209: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9210: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9211:
9212: }
9213:
1.136 brouard 9214: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9215: {
1.126 brouard 9216:
1.136 brouard 9217: /*-------- data file ----------*/
9218: FILE *fic;
9219: char dummy[]=" ";
1.240 brouard 9220: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9221: int lstra;
1.136 brouard 9222: int linei, month, year,iout;
1.302 brouard 9223: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9224: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9225: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9226: char *stratrunc;
1.223 brouard 9227:
1.240 brouard 9228: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9229: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9230:
1.240 brouard 9231: for(v=1; v <=ncovcol;v++){
9232: DummyV[v]=0;
9233: FixedV[v]=0;
9234: }
9235: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9236: DummyV[v]=1;
9237: FixedV[v]=0;
9238: }
9239: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9240: DummyV[v]=0;
9241: FixedV[v]=1;
9242: }
9243: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9244: DummyV[v]=1;
9245: FixedV[v]=1;
9246: }
9247: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9248: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9249: 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]);
9250: }
1.126 brouard 9251:
1.136 brouard 9252: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9253: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9254: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9255: }
1.126 brouard 9256:
1.302 brouard 9257: /* Is it a BOM UTF-8 Windows file? */
9258: /* First data line */
9259: linei=0;
9260: while(fgets(line, MAXLINE, fic)) {
9261: noffset=0;
9262: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9263: {
9264: noffset=noffset+3;
9265: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9266: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9267: fflush(ficlog); return 1;
9268: }
9269: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9270: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9271: {
9272: noffset=noffset+2;
1.304 brouard 9273: 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);
9274: 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 9275: fflush(ficlog); return 1;
9276: }
9277: else if( line[0] == 0 && line[1] == 0)
9278: {
9279: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9280: noffset=noffset+4;
1.304 brouard 9281: 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);
9282: 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 9283: fflush(ficlog); return 1;
9284: }
9285: } else{
9286: ;/*printf(" Not a BOM file\n");*/
9287: }
9288: /* If line starts with a # it is a comment */
9289: if (line[noffset] == '#') {
9290: linei=linei+1;
9291: break;
9292: }else{
9293: break;
9294: }
9295: }
9296: fclose(fic);
9297: if((fic=fopen(datafile,"r"))==NULL) {
9298: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9299: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9300: }
9301: /* Not a Bom file */
9302:
1.136 brouard 9303: i=1;
9304: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9305: linei=linei+1;
9306: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9307: if(line[j] == '\t')
9308: line[j] = ' ';
9309: }
9310: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9311: ;
9312: };
9313: line[j+1]=0; /* Trims blanks at end of line */
9314: if(line[0]=='#'){
9315: fprintf(ficlog,"Comment line\n%s\n",line);
9316: printf("Comment line\n%s\n",line);
9317: continue;
9318: }
9319: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9320: strcpy(line, linetmp);
1.223 brouard 9321:
9322: /* Loops on waves */
9323: for (j=maxwav;j>=1;j--){
9324: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9325: cutv(stra, strb, line, ' ');
9326: if(strb[0]=='.') { /* Missing value */
9327: lval=-1;
9328: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9329: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9330: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9331: 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);
9332: 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);
9333: return 1;
9334: }
9335: }else{
9336: errno=0;
9337: /* what_kind_of_number(strb); */
9338: dval=strtod(strb,&endptr);
9339: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9340: /* if(strb != endptr && *endptr == '\0') */
9341: /* dval=dlval; */
9342: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9343: if( strb[0]=='\0' || (*endptr != '\0')){
9344: 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);
9345: 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);
9346: return 1;
9347: }
9348: cotqvar[j][iv][i]=dval;
9349: cotvar[j][ntv+iv][i]=dval;
9350: }
9351: strcpy(line,stra);
1.223 brouard 9352: }/* end loop ntqv */
1.225 brouard 9353:
1.223 brouard 9354: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9355: cutv(stra, strb, line, ' ');
9356: if(strb[0]=='.') { /* Missing value */
9357: lval=-1;
9358: }else{
9359: errno=0;
9360: lval=strtol(strb,&endptr,10);
9361: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9362: if( strb[0]=='\0' || (*endptr != '\0')){
9363: 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);
9364: 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);
9365: return 1;
9366: }
9367: }
9368: if(lval <-1 || lval >1){
9369: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9370: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9371: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9372: For example, for multinomial values like 1, 2 and 3,\n \
9373: build V1=0 V2=0 for the reference value (1),\n \
9374: V1=1 V2=0 for (2) \n \
1.223 brouard 9375: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9376: output of IMaCh is often meaningless.\n \
1.223 brouard 9377: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9378: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9379: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9380: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9381: For example, for multinomial values like 1, 2 and 3,\n \
9382: build V1=0 V2=0 for the reference value (1),\n \
9383: V1=1 V2=0 for (2) \n \
1.223 brouard 9384: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9385: output of IMaCh is often meaningless.\n \
1.223 brouard 9386: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9387: return 1;
9388: }
9389: cotvar[j][iv][i]=(double)(lval);
9390: strcpy(line,stra);
1.223 brouard 9391: }/* end loop ntv */
1.225 brouard 9392:
1.223 brouard 9393: /* Statuses at wave */
1.137 brouard 9394: cutv(stra, strb, line, ' ');
1.223 brouard 9395: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9396: lval=-1;
1.136 brouard 9397: }else{
1.238 brouard 9398: errno=0;
9399: lval=strtol(strb,&endptr,10);
9400: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9401: if( strb[0]=='\0' || (*endptr != '\0')){
9402: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
9403: 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);
9404: return 1;
9405: }
1.136 brouard 9406: }
1.225 brouard 9407:
1.136 brouard 9408: s[j][i]=lval;
1.225 brouard 9409:
1.223 brouard 9410: /* Date of Interview */
1.136 brouard 9411: strcpy(line,stra);
9412: cutv(stra, strb,line,' ');
1.169 brouard 9413: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9414: }
1.169 brouard 9415: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9416: month=99;
9417: year=9999;
1.136 brouard 9418: }else{
1.225 brouard 9419: 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);
9420: 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);
9421: return 1;
1.136 brouard 9422: }
9423: anint[j][i]= (double) year;
1.302 brouard 9424: mint[j][i]= (double)month;
9425: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9426: /* 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]); */
9427: /* 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]); */
9428: /* } */
1.136 brouard 9429: strcpy(line,stra);
1.223 brouard 9430: } /* End loop on waves */
1.225 brouard 9431:
1.223 brouard 9432: /* Date of death */
1.136 brouard 9433: cutv(stra, strb,line,' ');
1.169 brouard 9434: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9435: }
1.169 brouard 9436: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9437: month=99;
9438: year=9999;
9439: }else{
1.141 brouard 9440: 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 9441: 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);
9442: return 1;
1.136 brouard 9443: }
9444: andc[i]=(double) year;
9445: moisdc[i]=(double) month;
9446: strcpy(line,stra);
9447:
1.223 brouard 9448: /* Date of birth */
1.136 brouard 9449: cutv(stra, strb,line,' ');
1.169 brouard 9450: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9451: }
1.169 brouard 9452: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9453: month=99;
9454: year=9999;
9455: }else{
1.141 brouard 9456: 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);
9457: 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 9458: return 1;
1.136 brouard 9459: }
9460: if (year==9999) {
1.141 brouard 9461: 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);
9462: 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 9463: return 1;
9464:
1.136 brouard 9465: }
9466: annais[i]=(double)(year);
1.302 brouard 9467: moisnais[i]=(double)(month);
9468: for (j=1;j<=maxwav;j++){
9469: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9470: 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]);
9471: 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]);
9472: }
9473: }
9474:
1.136 brouard 9475: strcpy(line,stra);
1.225 brouard 9476:
1.223 brouard 9477: /* Sample weight */
1.136 brouard 9478: cutv(stra, strb,line,' ');
9479: errno=0;
9480: dval=strtod(strb,&endptr);
9481: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9482: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9483: 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 9484: fflush(ficlog);
9485: return 1;
9486: }
9487: weight[i]=dval;
9488: strcpy(line,stra);
1.225 brouard 9489:
1.223 brouard 9490: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9491: cutv(stra, strb, line, ' ');
9492: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9493: lval=-1;
1.223 brouard 9494: }else{
1.225 brouard 9495: errno=0;
9496: /* what_kind_of_number(strb); */
9497: dval=strtod(strb,&endptr);
9498: /* if(strb != endptr && *endptr == '\0') */
9499: /* dval=dlval; */
9500: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9501: if( strb[0]=='\0' || (*endptr != '\0')){
9502: 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);
9503: 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);
9504: return 1;
9505: }
9506: coqvar[iv][i]=dval;
1.226 brouard 9507: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9508: }
9509: strcpy(line,stra);
9510: }/* end loop nqv */
1.136 brouard 9511:
1.223 brouard 9512: /* Covariate values */
1.136 brouard 9513: for (j=ncovcol;j>=1;j--){
9514: cutv(stra, strb,line,' ');
1.223 brouard 9515: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9516: lval=-1;
1.136 brouard 9517: }else{
1.225 brouard 9518: errno=0;
9519: lval=strtol(strb,&endptr,10);
9520: if( strb[0]=='\0' || (*endptr != '\0')){
9521: 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);
9522: 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);
9523: return 1;
9524: }
1.136 brouard 9525: }
9526: if(lval <-1 || lval >1){
1.225 brouard 9527: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9528: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9529: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9530: For example, for multinomial values like 1, 2 and 3,\n \
9531: build V1=0 V2=0 for the reference value (1),\n \
9532: V1=1 V2=0 for (2) \n \
1.136 brouard 9533: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9534: output of IMaCh is often meaningless.\n \
1.136 brouard 9535: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9536: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9537: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9538: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9539: For example, for multinomial values like 1, 2 and 3,\n \
9540: build V1=0 V2=0 for the reference value (1),\n \
9541: V1=1 V2=0 for (2) \n \
1.136 brouard 9542: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9543: output of IMaCh is often meaningless.\n \
1.136 brouard 9544: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9545: return 1;
1.136 brouard 9546: }
9547: covar[j][i]=(double)(lval);
9548: strcpy(line,stra);
9549: }
9550: lstra=strlen(stra);
1.225 brouard 9551:
1.136 brouard 9552: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9553: stratrunc = &(stra[lstra-9]);
9554: num[i]=atol(stratrunc);
9555: }
9556: else
9557: num[i]=atol(stra);
9558: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9559: 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;}*/
9560:
9561: i=i+1;
9562: } /* End loop reading data */
1.225 brouard 9563:
1.136 brouard 9564: *imax=i-1; /* Number of individuals */
9565: fclose(fic);
1.225 brouard 9566:
1.136 brouard 9567: return (0);
1.164 brouard 9568: /* endread: */
1.225 brouard 9569: printf("Exiting readdata: ");
9570: fclose(fic);
9571: return (1);
1.223 brouard 9572: }
1.126 brouard 9573:
1.234 brouard 9574: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9575: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9576: while (*p2 == ' ')
1.234 brouard 9577: p2++;
9578: /* while ((*p1++ = *p2++) !=0) */
9579: /* ; */
9580: /* do */
9581: /* while (*p2 == ' ') */
9582: /* p2++; */
9583: /* while (*p1++ == *p2++); */
9584: *stri=p2;
1.145 brouard 9585: }
9586:
1.235 brouard 9587: int decoderesult ( char resultline[], int nres)
1.230 brouard 9588: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9589: {
1.235 brouard 9590: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9591: char resultsav[MAXLINE];
1.234 brouard 9592: int resultmodel[MAXLINE];
9593: int modelresult[MAXLINE];
1.230 brouard 9594: char stra[80], strb[80], strc[80], strd[80],stre[80];
9595:
1.234 brouard 9596: removefirstspace(&resultline);
1.230 brouard 9597:
9598: if (strstr(resultline,"v") !=0){
9599: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9600: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9601: return 1;
9602: }
9603: trimbb(resultsav, resultline);
9604: if (strlen(resultsav) >1){
9605: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9606: }
1.253 brouard 9607: if(j == 0){ /* Resultline but no = */
9608: TKresult[nres]=0; /* Combination for the nresult and the model */
9609: return (0);
9610: }
1.234 brouard 9611: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9612: 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);
9613: 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);
9614: }
9615: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9616: if(nbocc(resultsav,'=') >1){
9617: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9618: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9619: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9620: }else
9621: cutl(strc,strd,resultsav,'=');
1.230 brouard 9622: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9623:
1.230 brouard 9624: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9625: Tvarsel[k]=atoi(strc);
9626: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9627: /* cptcovsel++; */
9628: if (nbocc(stra,'=') >0)
9629: strcpy(resultsav,stra); /* and analyzes it */
9630: }
1.235 brouard 9631: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9632: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9633: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9634: match=0;
1.236 brouard 9635: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9636: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9637: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9638: match=1;
9639: break;
9640: }
9641: }
9642: if(match == 0){
9643: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9644: }
9645: }
9646: }
1.235 brouard 9647: /* Checking for missing or useless values in comparison of current model needs */
9648: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9649: match=0;
1.235 brouard 9650: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9651: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9652: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9653: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9654: ++match;
9655: }
9656: }
9657: }
9658: if(match == 0){
9659: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9660: }else if(match > 1){
9661: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9662: }
9663: }
1.235 brouard 9664:
1.234 brouard 9665: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9666: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9667: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9668: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9669: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9670: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9671: /* 1 0 0 0 */
9672: /* 2 1 0 0 */
9673: /* 3 0 1 0 */
9674: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9675: /* 5 0 0 1 */
9676: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9677: /* 7 0 1 1 */
9678: /* 8 1 1 1 */
1.237 brouard 9679: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9680: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9681: /* V5*age V5 known which value for nres? */
9682: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9683: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9684: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9685: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9686: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9687: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9688: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9689: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9690: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9691: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9692: k4++;;
9693: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9694: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9695: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9696: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9697: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9698: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9699: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9700: k4q++;;
9701: }
9702: }
1.234 brouard 9703:
1.235 brouard 9704: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9705: return (0);
9706: }
1.235 brouard 9707:
1.230 brouard 9708: int decodemodel( char model[], int lastobs)
9709: /**< This routine decodes the model and returns:
1.224 brouard 9710: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9711: * - nagesqr = 1 if age*age in the model, otherwise 0.
9712: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9713: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9714: * - cptcovage number of covariates with age*products =2
9715: * - cptcovs number of simple covariates
9716: * - 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
9717: * which is a new column after the 9 (ncovcol) variables.
9718: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9719: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9720: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9721: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9722: */
1.136 brouard 9723: {
1.238 brouard 9724: int i, j, k, ks, v;
1.227 brouard 9725: int j1, k1, k2, k3, k4;
1.136 brouard 9726: char modelsav[80];
1.145 brouard 9727: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9728: char *strpt;
1.136 brouard 9729:
1.145 brouard 9730: /*removespace(model);*/
1.136 brouard 9731: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9732: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9733: if (strstr(model,"AGE") !=0){
1.192 brouard 9734: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9735: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9736: return 1;
9737: }
1.141 brouard 9738: if (strstr(model,"v") !=0){
9739: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9740: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9741: return 1;
9742: }
1.187 brouard 9743: strcpy(modelsav,model);
9744: if ((strpt=strstr(model,"age*age")) !=0){
9745: printf(" strpt=%s, model=%s\n",strpt, model);
9746: if(strpt != model){
1.234 brouard 9747: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9748: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9749: corresponding column of parameters.\n",model);
1.234 brouard 9750: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9751: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9752: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9753: return 1;
1.225 brouard 9754: }
1.187 brouard 9755: nagesqr=1;
9756: if (strstr(model,"+age*age") !=0)
1.234 brouard 9757: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9758: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9759: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9760: else
1.234 brouard 9761: substrchaine(modelsav, model, "age*age");
1.187 brouard 9762: }else
9763: nagesqr=0;
9764: if (strlen(modelsav) >1){
9765: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9766: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9767: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9768: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9769: * cst, age and age*age
9770: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9771: /* including age products which are counted in cptcovage.
9772: * but the covariates which are products must be treated
9773: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9774: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9775: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9776:
9777:
1.187 brouard 9778: /* Design
9779: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9780: * < ncovcol=8 >
9781: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9782: * k= 1 2 3 4 5 6 7 8
9783: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9784: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9785: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9786: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9787: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9788: * Tage[++cptcovage]=k
9789: * if products, new covar are created after ncovcol with k1
9790: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9791: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9792: * 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
9793: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9794: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9795: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9796: * < ncovcol=8 >
9797: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9798: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9799: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9800: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9801: * p Tprod[1]@2={ 6, 5}
9802: *p Tvard[1][1]@4= {7, 8, 5, 6}
9803: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9804: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9805: *How to reorganize?
9806: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9807: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9808: * {2, 1, 4, 8, 5, 6, 3, 7}
9809: * Struct []
9810: */
1.225 brouard 9811:
1.187 brouard 9812: /* This loop fills the array Tvar from the string 'model'.*/
9813: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9814: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9815: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9816: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9817: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9818: /* k=1 Tvar[1]=2 (from V2) */
9819: /* k=5 Tvar[5] */
9820: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9821: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9822: /* } */
1.198 brouard 9823: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9824: /*
9825: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9826: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9827: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9828: }
1.187 brouard 9829: cptcovage=0;
9830: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9831: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9832: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9833: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9834: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9835: /*scanf("%d",i);*/
9836: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9837: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9838: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9839: /* covar is not filled and then is empty */
9840: cptcovprod--;
9841: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9842: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9843: Typevar[k]=1; /* 1 for age product */
9844: cptcovage++; /* Sums the number of covariates which include age as a product */
9845: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9846: /*printf("stre=%s ", stre);*/
9847: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9848: cptcovprod--;
9849: cutl(stre,strb,strc,'V');
9850: Tvar[k]=atoi(stre);
9851: Typevar[k]=1; /* 1 for age product */
9852: cptcovage++;
9853: Tage[cptcovage]=k;
9854: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9855: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9856: cptcovn++;
9857: cptcovprodnoage++;k1++;
9858: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9859: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9860: because this model-covariate is a construction we invent a new column
9861: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9862: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9863: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9864: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9865: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9866: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9867: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9868: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9869: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9870: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9871: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9872: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9873: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9874: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9875: for (i=1; i<=lastobs;i++){
9876: /* Computes the new covariate which is a product of
9877: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9878: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9879: }
9880: } /* End age is not in the model */
9881: } /* End if model includes a product */
9882: else { /* no more sum */
9883: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9884: /* scanf("%d",i);*/
9885: cutl(strd,strc,strb,'V');
9886: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9887: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9888: Tvar[k]=atoi(strd);
9889: Typevar[k]=0; /* 0 for simple covariates */
9890: }
9891: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9892: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9893: scanf("%d",i);*/
1.187 brouard 9894: } /* end of loop + on total covariates */
9895: } /* end if strlen(modelsave == 0) age*age might exist */
9896: } /* end if strlen(model == 0) */
1.136 brouard 9897:
9898: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9899: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9900:
1.136 brouard 9901: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9902: printf("cptcovprod=%d ", cptcovprod);
9903: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9904: scanf("%d ",i);*/
9905:
9906:
1.230 brouard 9907: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9908: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9909: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9910: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9911: k = 1 2 3 4 5 6 7 8 9
9912: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9913: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9914: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9915: Dummy[k] 1 0 0 0 3 1 1 2 3
9916: Tmodelind[combination of covar]=k;
1.225 brouard 9917: */
9918: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9919: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9920: /* 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 9921: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9922: printf("Model=%s\n\
9923: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9924: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9925: 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);
9926: fprintf(ficlog,"Model=%s\n\
9927: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9928: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9929: 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 9930: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9931: 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 */
9932: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9933: Fixed[k]= 0;
9934: Dummy[k]= 0;
1.225 brouard 9935: ncoveff++;
1.232 brouard 9936: ncovf++;
1.234 brouard 9937: nsd++;
9938: modell[k].maintype= FTYPE;
9939: TvarsD[nsd]=Tvar[k];
9940: TvarsDind[nsd]=k;
9941: TvarF[ncovf]=Tvar[k];
9942: TvarFind[ncovf]=k;
9943: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9944: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9945: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9946: Fixed[k]= 0;
9947: Dummy[k]= 0;
9948: ncoveff++;
9949: ncovf++;
9950: modell[k].maintype= FTYPE;
9951: TvarF[ncovf]=Tvar[k];
9952: TvarFind[ncovf]=k;
1.230 brouard 9953: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9954: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9955: }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 9956: Fixed[k]= 0;
9957: Dummy[k]= 1;
1.230 brouard 9958: nqfveff++;
1.234 brouard 9959: modell[k].maintype= FTYPE;
9960: modell[k].subtype= FQ;
9961: nsq++;
9962: TvarsQ[nsq]=Tvar[k];
9963: TvarsQind[nsq]=k;
1.232 brouard 9964: ncovf++;
1.234 brouard 9965: TvarF[ncovf]=Tvar[k];
9966: TvarFind[ncovf]=k;
1.231 brouard 9967: 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 9968: 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 9969: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9970: Fixed[k]= 1;
9971: Dummy[k]= 0;
1.225 brouard 9972: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9973: modell[k].maintype= VTYPE;
9974: modell[k].subtype= VD;
9975: nsd++;
9976: TvarsD[nsd]=Tvar[k];
9977: TvarsDind[nsd]=k;
9978: ncovv++; /* Only simple time varying variables */
9979: TvarV[ncovv]=Tvar[k];
1.242 brouard 9980: 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 9981: 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 */
9982: 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 9983: 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);
9984: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9985: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9986: Fixed[k]= 1;
9987: Dummy[k]= 1;
9988: nqtveff++;
9989: modell[k].maintype= VTYPE;
9990: modell[k].subtype= VQ;
9991: ncovv++; /* Only simple time varying variables */
9992: nsq++;
9993: TvarsQ[nsq]=Tvar[k];
9994: TvarsQind[nsq]=k;
9995: TvarV[ncovv]=Tvar[k];
1.242 brouard 9996: 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 9997: 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 */
9998: 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 9999: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
10000: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
10001: 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 10002: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 10003: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 10004: ncova++;
10005: TvarA[ncova]=Tvar[k];
10006: TvarAind[ncova]=k;
1.231 brouard 10007: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10008: Fixed[k]= 2;
10009: Dummy[k]= 2;
10010: modell[k].maintype= ATYPE;
10011: modell[k].subtype= APFD;
10012: /* ncoveff++; */
1.227 brouard 10013: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10014: Fixed[k]= 2;
10015: Dummy[k]= 3;
10016: modell[k].maintype= ATYPE;
10017: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10018: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10019: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10020: Fixed[k]= 3;
10021: Dummy[k]= 2;
10022: modell[k].maintype= ATYPE;
10023: modell[k].subtype= APVD; /* Product age * varying dummy */
10024: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10025: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10026: Fixed[k]= 3;
10027: Dummy[k]= 3;
10028: modell[k].maintype= ATYPE;
10029: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10030: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10031: }
10032: }else if (Typevar[k] == 2) { /* product without age */
10033: k1=Tposprod[k];
10034: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10035: if(Tvard[k1][2] <=ncovcol){
10036: Fixed[k]= 1;
10037: Dummy[k]= 0;
10038: modell[k].maintype= FTYPE;
10039: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10040: ncovf++; /* Fixed variables without age */
10041: TvarF[ncovf]=Tvar[k];
10042: TvarFind[ncovf]=k;
10043: }else if(Tvard[k1][2] <=ncovcol+nqv){
10044: Fixed[k]= 0; /* or 2 ?*/
10045: Dummy[k]= 1;
10046: modell[k].maintype= FTYPE;
10047: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10048: ncovf++; /* Varying variables without age */
10049: TvarF[ncovf]=Tvar[k];
10050: TvarFind[ncovf]=k;
10051: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10052: Fixed[k]= 1;
10053: Dummy[k]= 0;
10054: modell[k].maintype= VTYPE;
10055: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10056: ncovv++; /* Varying variables without age */
10057: TvarV[ncovv]=Tvar[k];
10058: TvarVind[ncovv]=k;
10059: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10060: Fixed[k]= 1;
10061: Dummy[k]= 1;
10062: modell[k].maintype= VTYPE;
10063: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10064: ncovv++; /* Varying variables without age */
10065: TvarV[ncovv]=Tvar[k];
10066: TvarVind[ncovv]=k;
10067: }
1.227 brouard 10068: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10069: if(Tvard[k1][2] <=ncovcol){
10070: Fixed[k]= 0; /* or 2 ?*/
10071: Dummy[k]= 1;
10072: modell[k].maintype= FTYPE;
10073: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10074: ncovf++; /* Fixed variables without age */
10075: TvarF[ncovf]=Tvar[k];
10076: TvarFind[ncovf]=k;
10077: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10078: Fixed[k]= 1;
10079: Dummy[k]= 1;
10080: modell[k].maintype= VTYPE;
10081: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10082: ncovv++; /* Varying variables without age */
10083: TvarV[ncovv]=Tvar[k];
10084: TvarVind[ncovv]=k;
10085: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10086: Fixed[k]= 1;
10087: Dummy[k]= 1;
10088: modell[k].maintype= VTYPE;
10089: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10090: ncovv++; /* Varying variables without age */
10091: TvarV[ncovv]=Tvar[k];
10092: TvarVind[ncovv]=k;
10093: ncovv++; /* Varying variables without age */
10094: TvarV[ncovv]=Tvar[k];
10095: TvarVind[ncovv]=k;
10096: }
1.227 brouard 10097: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10098: if(Tvard[k1][2] <=ncovcol){
10099: Fixed[k]= 1;
10100: Dummy[k]= 1;
10101: modell[k].maintype= VTYPE;
10102: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10103: ncovv++; /* Varying variables without age */
10104: TvarV[ncovv]=Tvar[k];
10105: TvarVind[ncovv]=k;
10106: }else if(Tvard[k1][2] <=ncovcol+nqv){
10107: Fixed[k]= 1;
10108: Dummy[k]= 1;
10109: modell[k].maintype= VTYPE;
10110: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10111: ncovv++; /* Varying variables without age */
10112: TvarV[ncovv]=Tvar[k];
10113: TvarVind[ncovv]=k;
10114: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10115: Fixed[k]= 1;
10116: Dummy[k]= 0;
10117: modell[k].maintype= VTYPE;
10118: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10119: ncovv++; /* Varying variables without age */
10120: TvarV[ncovv]=Tvar[k];
10121: TvarVind[ncovv]=k;
10122: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10123: Fixed[k]= 1;
10124: Dummy[k]= 1;
10125: modell[k].maintype= VTYPE;
10126: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10127: ncovv++; /* Varying variables without age */
10128: TvarV[ncovv]=Tvar[k];
10129: TvarVind[ncovv]=k;
10130: }
1.227 brouard 10131: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10132: if(Tvard[k1][2] <=ncovcol){
10133: Fixed[k]= 1;
10134: Dummy[k]= 1;
10135: modell[k].maintype= VTYPE;
10136: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10137: ncovv++; /* Varying variables without age */
10138: TvarV[ncovv]=Tvar[k];
10139: TvarVind[ncovv]=k;
10140: }else if(Tvard[k1][2] <=ncovcol+nqv){
10141: Fixed[k]= 1;
10142: Dummy[k]= 1;
10143: modell[k].maintype= VTYPE;
10144: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10145: ncovv++; /* Varying variables without age */
10146: TvarV[ncovv]=Tvar[k];
10147: TvarVind[ncovv]=k;
10148: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10149: Fixed[k]= 1;
10150: Dummy[k]= 1;
10151: modell[k].maintype= VTYPE;
10152: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10153: ncovv++; /* Varying variables without age */
10154: TvarV[ncovv]=Tvar[k];
10155: TvarVind[ncovv]=k;
10156: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10157: Fixed[k]= 1;
10158: Dummy[k]= 1;
10159: modell[k].maintype= VTYPE;
10160: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10161: ncovv++; /* Varying variables without age */
10162: TvarV[ncovv]=Tvar[k];
10163: TvarVind[ncovv]=k;
10164: }
1.227 brouard 10165: }else{
1.240 brouard 10166: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10167: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10168: } /*end k1*/
1.225 brouard 10169: }else{
1.226 brouard 10170: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10171: 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 10172: }
1.227 brouard 10173: 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 10174: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10175: 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]);
10176: }
10177: /* Searching for doublons in the model */
10178: for(k1=1; k1<= cptcovt;k1++){
10179: for(k2=1; k2 <k1;k2++){
1.285 brouard 10180: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10181: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10182: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10183: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10184: 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]);
10185: 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 10186: return(1);
10187: }
10188: }else if (Typevar[k1] ==2){
10189: k3=Tposprod[k1];
10190: k4=Tposprod[k2];
10191: 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])) ){
10192: 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]]);
10193: 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);
10194: return(1);
10195: }
10196: }
1.227 brouard 10197: }
10198: }
1.225 brouard 10199: }
10200: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10201: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10202: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10203: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10204: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10205: /*endread:*/
1.225 brouard 10206: printf("Exiting decodemodel: ");
10207: return (1);
1.136 brouard 10208: }
10209:
1.169 brouard 10210: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10211: {/* Check ages at death */
1.136 brouard 10212: int i, m;
1.218 brouard 10213: int firstone=0;
10214:
1.136 brouard 10215: for (i=1; i<=imx; i++) {
10216: for(m=2; (m<= maxwav); m++) {
10217: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10218: anint[m][i]=9999;
1.216 brouard 10219: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10220: s[m][i]=-1;
1.136 brouard 10221: }
10222: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10223: *nberr = *nberr + 1;
1.218 brouard 10224: if(firstone == 0){
10225: firstone=1;
1.260 brouard 10226: 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 10227: }
1.262 brouard 10228: 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 10229: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10230: }
10231: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10232: (*nberr)++;
1.259 brouard 10233: 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 10234: 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 10235: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10236: }
10237: }
10238: }
10239:
10240: for (i=1; i<=imx; i++) {
10241: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10242: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10243: 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 10244: if (s[m][i] >= nlstate+1) {
1.169 brouard 10245: if(agedc[i]>0){
10246: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10247: agev[m][i]=agedc[i];
1.214 brouard 10248: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10249: }else {
1.136 brouard 10250: if ((int)andc[i]!=9999){
10251: nbwarn++;
10252: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10253: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10254: agev[m][i]=-1;
10255: }
10256: }
1.169 brouard 10257: } /* agedc > 0 */
1.214 brouard 10258: } /* end if */
1.136 brouard 10259: else if(s[m][i] !=9){ /* Standard case, age in fractional
10260: years but with the precision of a month */
10261: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10262: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10263: agev[m][i]=1;
10264: else if(agev[m][i] < *agemin){
10265: *agemin=agev[m][i];
10266: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10267: }
10268: else if(agev[m][i] >*agemax){
10269: *agemax=agev[m][i];
1.156 brouard 10270: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10271: }
10272: /*agev[m][i]=anint[m][i]-annais[i];*/
10273: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10274: } /* en if 9*/
1.136 brouard 10275: else { /* =9 */
1.214 brouard 10276: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10277: agev[m][i]=1;
10278: s[m][i]=-1;
10279: }
10280: }
1.214 brouard 10281: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10282: agev[m][i]=1;
1.214 brouard 10283: else{
10284: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10285: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10286: agev[m][i]=0;
10287: }
10288: } /* End for lastpass */
10289: }
1.136 brouard 10290:
10291: for (i=1; i<=imx; i++) {
10292: for(m=firstpass; (m<=lastpass); m++){
10293: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10294: (*nberr)++;
1.136 brouard 10295: 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);
10296: 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);
10297: return 1;
10298: }
10299: }
10300: }
10301:
10302: /*for (i=1; i<=imx; i++){
10303: for (m=firstpass; (m<lastpass); m++){
10304: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10305: }
10306:
10307: }*/
10308:
10309:
1.139 brouard 10310: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10311: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10312:
10313: return (0);
1.164 brouard 10314: /* endread:*/
1.136 brouard 10315: printf("Exiting calandcheckages: ");
10316: return (1);
10317: }
10318:
1.172 brouard 10319: #if defined(_MSC_VER)
10320: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10321: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10322: //#include "stdafx.h"
10323: //#include <stdio.h>
10324: //#include <tchar.h>
10325: //#include <windows.h>
10326: //#include <iostream>
10327: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10328:
10329: LPFN_ISWOW64PROCESS fnIsWow64Process;
10330:
10331: BOOL IsWow64()
10332: {
10333: BOOL bIsWow64 = FALSE;
10334:
10335: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10336: // (HANDLE, PBOOL);
10337:
10338: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10339:
10340: HMODULE module = GetModuleHandle(_T("kernel32"));
10341: const char funcName[] = "IsWow64Process";
10342: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10343: GetProcAddress(module, funcName);
10344:
10345: if (NULL != fnIsWow64Process)
10346: {
10347: if (!fnIsWow64Process(GetCurrentProcess(),
10348: &bIsWow64))
10349: //throw std::exception("Unknown error");
10350: printf("Unknown error\n");
10351: }
10352: return bIsWow64 != FALSE;
10353: }
10354: #endif
1.177 brouard 10355:
1.191 brouard 10356: void syscompilerinfo(int logged)
1.292 brouard 10357: {
10358: #include <stdint.h>
10359:
10360: /* #include "syscompilerinfo.h"*/
1.185 brouard 10361: /* command line Intel compiler 32bit windows, XP compatible:*/
10362: /* /GS /W3 /Gy
10363: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10364: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10365: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10366: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10367: */
10368: /* 64 bits */
1.185 brouard 10369: /*
10370: /GS /W3 /Gy
10371: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10372: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10373: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10374: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10375: /* Optimization are useless and O3 is slower than O2 */
10376: /*
10377: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10378: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10379: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10380: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10381: */
1.186 brouard 10382: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10383: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10384: /PDB:"visual studio
10385: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10386: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10387: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10388: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10389: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10390: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10391: uiAccess='false'"
10392: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10393: /NOLOGO /TLBID:1
10394: */
1.292 brouard 10395:
10396:
1.177 brouard 10397: #if defined __INTEL_COMPILER
1.178 brouard 10398: #if defined(__GNUC__)
10399: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10400: #endif
1.177 brouard 10401: #elif defined(__GNUC__)
1.179 brouard 10402: #ifndef __APPLE__
1.174 brouard 10403: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10404: #endif
1.177 brouard 10405: struct utsname sysInfo;
1.178 brouard 10406: int cross = CROSS;
10407: if (cross){
10408: printf("Cross-");
1.191 brouard 10409: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10410: }
1.174 brouard 10411: #endif
10412:
1.191 brouard 10413: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10414: #if defined(__clang__)
1.191 brouard 10415: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10416: #endif
10417: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10418: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10419: #endif
10420: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10421: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10422: #endif
10423: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10424: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10425: #endif
10426: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10427: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10428: #endif
10429: #if defined(_MSC_VER)
1.191 brouard 10430: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10431: #endif
10432: #if defined(__PGI)
1.191 brouard 10433: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10434: #endif
10435: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10436: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10437: #endif
1.191 brouard 10438: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10439:
1.167 brouard 10440: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10441: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10442: // Windows (x64 and x86)
1.191 brouard 10443: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10444: #elif __unix__ // all unices, not all compilers
10445: // Unix
1.191 brouard 10446: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10447: #elif __linux__
10448: // linux
1.191 brouard 10449: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10450: #elif __APPLE__
1.174 brouard 10451: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10452: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10453: #endif
10454:
10455: /* __MINGW32__ */
10456: /* __CYGWIN__ */
10457: /* __MINGW64__ */
10458: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10459: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10460: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10461: /* _WIN64 // Defined for applications for Win64. */
10462: /* _M_X64 // Defined for compilations that target x64 processors. */
10463: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10464:
1.167 brouard 10465: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10466: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10467: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10468: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10469: #else
1.191 brouard 10470: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10471: #endif
10472:
1.169 brouard 10473: #if defined(__GNUC__)
10474: # if defined(__GNUC_PATCHLEVEL__)
10475: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10476: + __GNUC_MINOR__ * 100 \
10477: + __GNUC_PATCHLEVEL__)
10478: # else
10479: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10480: + __GNUC_MINOR__ * 100)
10481: # endif
1.174 brouard 10482: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10483: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10484:
10485: if (uname(&sysInfo) != -1) {
10486: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10487: 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 10488: }
10489: else
10490: perror("uname() error");
1.179 brouard 10491: //#ifndef __INTEL_COMPILER
10492: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10493: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10494: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10495: #endif
1.169 brouard 10496: #endif
1.172 brouard 10497:
1.286 brouard 10498: // void main ()
1.172 brouard 10499: // {
1.169 brouard 10500: #if defined(_MSC_VER)
1.174 brouard 10501: if (IsWow64()){
1.191 brouard 10502: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10503: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10504: }
10505: else{
1.191 brouard 10506: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10507: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10508: }
1.172 brouard 10509: // printf("\nPress Enter to continue...");
10510: // getchar();
10511: // }
10512:
1.169 brouard 10513: #endif
10514:
1.167 brouard 10515:
1.219 brouard 10516: }
1.136 brouard 10517:
1.219 brouard 10518: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10519: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10520: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10521: /* double ftolpl = 1.e-10; */
1.180 brouard 10522: double age, agebase, agelim;
1.203 brouard 10523: double tot;
1.180 brouard 10524:
1.202 brouard 10525: strcpy(filerespl,"PL_");
10526: strcat(filerespl,fileresu);
10527: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10528: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10529: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10530: }
1.288 brouard 10531: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10532: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10533: pstamp(ficrespl);
1.288 brouard 10534: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10535: fprintf(ficrespl,"#Age ");
10536: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10537: fprintf(ficrespl,"\n");
1.180 brouard 10538:
1.219 brouard 10539: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10540:
1.219 brouard 10541: agebase=ageminpar;
10542: agelim=agemaxpar;
1.180 brouard 10543:
1.227 brouard 10544: /* i1=pow(2,ncoveff); */
1.234 brouard 10545: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10546: if (cptcovn < 1){i1=1;}
1.180 brouard 10547:
1.238 brouard 10548: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10549: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10550: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10551: continue;
1.235 brouard 10552:
1.238 brouard 10553: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10554: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10555: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10556: /* k=k+1; */
10557: /* to clean */
10558: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10559: fprintf(ficrespl,"#******");
10560: printf("#******");
10561: fprintf(ficlog,"#******");
10562: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10563: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10564: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10565: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10566: }
10567: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10568: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10569: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10570: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10571: }
10572: fprintf(ficrespl,"******\n");
10573: printf("******\n");
10574: fprintf(ficlog,"******\n");
10575: if(invalidvarcomb[k]){
10576: printf("\nCombination (%d) ignored because no case \n",k);
10577: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10578: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10579: continue;
10580: }
1.219 brouard 10581:
1.238 brouard 10582: fprintf(ficrespl,"#Age ");
10583: for(j=1;j<=cptcoveff;j++) {
10584: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10585: }
10586: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10587: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10588:
1.238 brouard 10589: for (age=agebase; age<=agelim; age++){
10590: /* for (age=agebase; age<=agebase; age++){ */
10591: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10592: fprintf(ficrespl,"%.0f ",age );
10593: for(j=1;j<=cptcoveff;j++)
10594: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10595: tot=0.;
10596: for(i=1; i<=nlstate;i++){
10597: tot += prlim[i][i];
10598: fprintf(ficrespl," %.5f", prlim[i][i]);
10599: }
10600: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10601: } /* Age */
10602: /* was end of cptcod */
10603: } /* cptcov */
10604: } /* nres */
1.219 brouard 10605: return 0;
1.180 brouard 10606: }
10607:
1.218 brouard 10608: 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 10609: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10610:
10611: /* Computes the back prevalence limit for any combination of covariate values
10612: * at any age between ageminpar and agemaxpar
10613: */
1.235 brouard 10614: int i, j, k, i1, nres=0 ;
1.217 brouard 10615: /* double ftolpl = 1.e-10; */
10616: double age, agebase, agelim;
10617: double tot;
1.218 brouard 10618: /* double ***mobaverage; */
10619: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10620:
10621: strcpy(fileresplb,"PLB_");
10622: strcat(fileresplb,fileresu);
10623: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10624: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10625: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10626: }
1.288 brouard 10627: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10628: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10629: pstamp(ficresplb);
1.288 brouard 10630: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10631: fprintf(ficresplb,"#Age ");
10632: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10633: fprintf(ficresplb,"\n");
10634:
1.218 brouard 10635:
10636: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10637:
10638: agebase=ageminpar;
10639: agelim=agemaxpar;
10640:
10641:
1.227 brouard 10642: i1=pow(2,cptcoveff);
1.218 brouard 10643: if (cptcovn < 1){i1=1;}
1.227 brouard 10644:
1.238 brouard 10645: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10646: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10647: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10648: continue;
10649: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10650: fprintf(ficresplb,"#******");
10651: printf("#******");
10652: fprintf(ficlog,"#******");
10653: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10654: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10655: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10656: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10657: }
10658: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10659: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10660: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10661: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10662: }
10663: fprintf(ficresplb,"******\n");
10664: printf("******\n");
10665: fprintf(ficlog,"******\n");
10666: if(invalidvarcomb[k]){
10667: printf("\nCombination (%d) ignored because no cases \n",k);
10668: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10669: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10670: continue;
10671: }
1.218 brouard 10672:
1.238 brouard 10673: fprintf(ficresplb,"#Age ");
10674: for(j=1;j<=cptcoveff;j++) {
10675: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10676: }
10677: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10678: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10679:
10680:
1.238 brouard 10681: for (age=agebase; age<=agelim; age++){
10682: /* for (age=agebase; age<=agebase; age++){ */
10683: if(mobilavproj > 0){
10684: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10685: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10686: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10687: }else if (mobilavproj == 0){
10688: 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);
10689: 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);
10690: exit(1);
10691: }else{
10692: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10693: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10694: /* printf("TOTOT\n"); */
10695: /* exit(1); */
1.238 brouard 10696: }
10697: fprintf(ficresplb,"%.0f ",age );
10698: for(j=1;j<=cptcoveff;j++)
10699: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10700: tot=0.;
10701: for(i=1; i<=nlstate;i++){
10702: tot += bprlim[i][i];
10703: fprintf(ficresplb," %.5f", bprlim[i][i]);
10704: }
10705: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10706: } /* Age */
10707: /* was end of cptcod */
1.255 brouard 10708: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10709: } /* end of any combination */
10710: } /* end of nres */
1.218 brouard 10711: /* hBijx(p, bage, fage); */
10712: /* fclose(ficrespijb); */
10713:
10714: return 0;
1.217 brouard 10715: }
1.218 brouard 10716:
1.180 brouard 10717: int hPijx(double *p, int bage, int fage){
10718: /*------------- h Pij x at various ages ------------*/
10719:
10720: int stepsize;
10721: int agelim;
10722: int hstepm;
10723: int nhstepm;
1.235 brouard 10724: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10725:
10726: double agedeb;
10727: double ***p3mat;
10728:
1.201 brouard 10729: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10730: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10731: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10732: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10733: }
10734: printf("Computing pij: result on file '%s' \n", filerespij);
10735: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10736:
10737: stepsize=(int) (stepm+YEARM-1)/YEARM;
10738: /*if (stepm<=24) stepsize=2;*/
10739:
10740: agelim=AGESUP;
10741: hstepm=stepsize*YEARM; /* Every year of age */
10742: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10743:
1.180 brouard 10744: /* hstepm=1; aff par mois*/
10745: pstamp(ficrespij);
10746: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10747: i1= pow(2,cptcoveff);
1.218 brouard 10748: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10749: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10750: /* k=k+1; */
1.235 brouard 10751: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10752: for(k=1; k<=i1;k++){
1.253 brouard 10753: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10754: continue;
1.183 brouard 10755: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10756: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10757: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10758: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10759: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10760: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10761: }
1.183 brouard 10762: fprintf(ficrespij,"******\n");
10763:
10764: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10765: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10766: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10767:
10768: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10769:
1.183 brouard 10770: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10771: oldm=oldms;savm=savms;
1.235 brouard 10772: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10773: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10774: for(i=1; i<=nlstate;i++)
10775: for(j=1; j<=nlstate+ndeath;j++)
10776: fprintf(ficrespij," %1d-%1d",i,j);
10777: fprintf(ficrespij,"\n");
10778: for (h=0; h<=nhstepm; h++){
10779: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10780: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10781: for(i=1; i<=nlstate;i++)
10782: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10783: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10784: fprintf(ficrespij,"\n");
10785: }
1.183 brouard 10786: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10787: fprintf(ficrespij,"\n");
10788: }
1.180 brouard 10789: /*}*/
10790: }
1.218 brouard 10791: return 0;
1.180 brouard 10792: }
1.218 brouard 10793:
10794: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10795: /*------------- h Bij x at various ages ------------*/
10796:
10797: int stepsize;
1.218 brouard 10798: /* int agelim; */
10799: int ageminl;
1.217 brouard 10800: int hstepm;
10801: int nhstepm;
1.238 brouard 10802: int h, i, i1, j, k, nres;
1.218 brouard 10803:
1.217 brouard 10804: double agedeb;
10805: double ***p3mat;
1.218 brouard 10806:
10807: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10808: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10809: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10810: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10811: }
10812: printf("Computing pij back: result on file '%s' \n", filerespijb);
10813: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10814:
10815: stepsize=(int) (stepm+YEARM-1)/YEARM;
10816: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10817:
1.218 brouard 10818: /* agelim=AGESUP; */
1.289 brouard 10819: ageminl=AGEINF; /* was 30 */
1.218 brouard 10820: hstepm=stepsize*YEARM; /* Every year of age */
10821: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10822:
10823: /* hstepm=1; aff par mois*/
10824: pstamp(ficrespijb);
1.255 brouard 10825: 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 10826: i1= pow(2,cptcoveff);
1.218 brouard 10827: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10828: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10829: /* k=k+1; */
1.238 brouard 10830: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10831: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10832: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10833: continue;
10834: fprintf(ficrespijb,"\n#****** ");
10835: for(j=1;j<=cptcoveff;j++)
10836: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10837: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10838: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10839: }
10840: fprintf(ficrespijb,"******\n");
1.264 brouard 10841: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10842: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10843: continue;
10844: }
10845:
10846: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10847: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10848: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10849: 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 */
10850: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10851:
10852: /* nhstepm=nhstepm*YEARM; aff par mois*/
10853:
1.266 brouard 10854: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10855: /* and memory limitations if stepm is small */
10856:
1.238 brouard 10857: /* oldm=oldms;savm=savms; */
10858: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10859: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10860: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10861: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10862: for(i=1; i<=nlstate;i++)
10863: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10864: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10865: fprintf(ficrespijb,"\n");
1.238 brouard 10866: for (h=0; h<=nhstepm; h++){
10867: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10868: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10869: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10870: for(i=1; i<=nlstate;i++)
10871: for(j=1; j<=nlstate+ndeath;j++)
10872: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10873: fprintf(ficrespijb,"\n");
10874: }
10875: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10876: fprintf(ficrespijb,"\n");
10877: } /* end age deb */
10878: } /* end combination */
10879: } /* end nres */
1.218 brouard 10880: return 0;
10881: } /* hBijx */
1.217 brouard 10882:
1.180 brouard 10883:
1.136 brouard 10884: /***********************************************/
10885: /**************** Main Program *****************/
10886: /***********************************************/
10887:
10888: int main(int argc, char *argv[])
10889: {
10890: #ifdef GSL
10891: const gsl_multimin_fminimizer_type *T;
10892: size_t iteri = 0, it;
10893: int rval = GSL_CONTINUE;
10894: int status = GSL_SUCCESS;
10895: double ssval;
10896: #endif
10897: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10898: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10899: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10900: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10901: int jj, ll, li, lj, lk;
1.136 brouard 10902: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10903: int num_filled;
1.136 brouard 10904: int itimes;
10905: int NDIM=2;
10906: int vpopbased=0;
1.235 brouard 10907: int nres=0;
1.258 brouard 10908: int endishere=0;
1.277 brouard 10909: int noffset=0;
1.274 brouard 10910: int ncurrv=0; /* Temporary variable */
10911:
1.164 brouard 10912: char ca[32], cb[32];
1.136 brouard 10913: /* FILE *fichtm; *//* Html File */
10914: /* FILE *ficgp;*/ /*Gnuplot File */
10915: struct stat info;
1.191 brouard 10916: double agedeb=0.;
1.194 brouard 10917:
10918: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10919: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10920:
1.165 brouard 10921: double fret;
1.191 brouard 10922: double dum=0.; /* Dummy variable */
1.136 brouard 10923: double ***p3mat;
1.218 brouard 10924: /* double ***mobaverage; */
1.164 brouard 10925:
10926: char line[MAXLINE];
1.197 brouard 10927: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10928:
1.234 brouard 10929: char modeltemp[MAXLINE];
1.230 brouard 10930: char resultline[MAXLINE];
10931:
1.136 brouard 10932: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10933: char *tok, *val; /* pathtot */
1.290 brouard 10934: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10935: int c, h , cpt, c2;
1.191 brouard 10936: int jl=0;
10937: int i1, j1, jk, stepsize=0;
1.194 brouard 10938: int count=0;
10939:
1.164 brouard 10940: int *tab;
1.136 brouard 10941: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10942: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10943: /* double anprojf, mprojf, jprojf; */
10944: /* double jintmean,mintmean,aintmean; */
10945: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10946: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10947: double yrfproj= 10.0; /* Number of years of forward projections */
10948: double yrbproj= 10.0; /* Number of years of backward projections */
10949: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10950: int mobilav=0,popforecast=0;
1.191 brouard 10951: int hstepm=0, nhstepm=0;
1.136 brouard 10952: int agemortsup;
10953: float sumlpop=0.;
10954: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10955: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10956:
1.191 brouard 10957: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10958: double ftolpl=FTOL;
10959: double **prlim;
1.217 brouard 10960: double **bprlim;
1.136 brouard 10961: double ***param; /* Matrix of parameters */
1.251 brouard 10962: double ***paramstart; /* Matrix of starting parameter values */
10963: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10964: double **matcov; /* Matrix of covariance */
1.203 brouard 10965: double **hess; /* Hessian matrix */
1.136 brouard 10966: double ***delti3; /* Scale */
10967: double *delti; /* Scale */
10968: double ***eij, ***vareij;
10969: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10970:
1.136 brouard 10971: double *epj, vepp;
1.164 brouard 10972:
1.273 brouard 10973: double dateprev1, dateprev2;
1.296 brouard 10974: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10975: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10976:
1.217 brouard 10977:
1.136 brouard 10978: double **ximort;
1.145 brouard 10979: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10980: int *dcwave;
10981:
1.164 brouard 10982: char z[1]="c";
1.136 brouard 10983:
10984: /*char *strt;*/
10985: char strtend[80];
1.126 brouard 10986:
1.164 brouard 10987:
1.126 brouard 10988: /* setlocale (LC_ALL, ""); */
10989: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10990: /* textdomain (PACKAGE); */
10991: /* setlocale (LC_CTYPE, ""); */
10992: /* setlocale (LC_MESSAGES, ""); */
10993:
10994: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10995: rstart_time = time(NULL);
10996: /* (void) gettimeofday(&start_time,&tzp);*/
10997: start_time = *localtime(&rstart_time);
1.126 brouard 10998: curr_time=start_time;
1.157 brouard 10999: /*tml = *localtime(&start_time.tm_sec);*/
11000: /* strcpy(strstart,asctime(&tml)); */
11001: strcpy(strstart,asctime(&start_time));
1.126 brouard 11002:
11003: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 11004: /* tp.tm_sec = tp.tm_sec +86400; */
11005: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 11006: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11007: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11008: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11009: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11010: /* strt=asctime(&tmg); */
11011: /* printf("Time(after) =%s",strstart); */
11012: /* (void) time (&time_value);
11013: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11014: * tm = *localtime(&time_value);
11015: * strstart=asctime(&tm);
11016: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11017: */
11018:
11019: nberr=0; /* Number of errors and warnings */
11020: nbwarn=0;
1.184 brouard 11021: #ifdef WIN32
11022: _getcwd(pathcd, size);
11023: #else
1.126 brouard 11024: getcwd(pathcd, size);
1.184 brouard 11025: #endif
1.191 brouard 11026: syscompilerinfo(0);
1.196 brouard 11027: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11028: if(argc <=1){
11029: printf("\nEnter the parameter file name: ");
1.205 brouard 11030: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11031: printf("ERROR Empty parameter file name\n");
11032: goto end;
11033: }
1.126 brouard 11034: i=strlen(pathr);
11035: if(pathr[i-1]=='\n')
11036: pathr[i-1]='\0';
1.156 brouard 11037: i=strlen(pathr);
1.205 brouard 11038: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11039: pathr[i-1]='\0';
1.205 brouard 11040: }
11041: i=strlen(pathr);
11042: if( i==0 ){
11043: printf("ERROR Empty parameter file name\n");
11044: goto end;
11045: }
11046: for (tok = pathr; tok != NULL; ){
1.126 brouard 11047: printf("Pathr |%s|\n",pathr);
11048: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11049: printf("val= |%s| pathr=%s\n",val,pathr);
11050: strcpy (pathtot, val);
11051: if(pathr[0] == '\0') break; /* Dirty */
11052: }
11053: }
1.281 brouard 11054: else if (argc<=2){
11055: strcpy(pathtot,argv[1]);
11056: }
1.126 brouard 11057: else{
11058: strcpy(pathtot,argv[1]);
1.281 brouard 11059: strcpy(z,argv[2]);
11060: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11061: }
11062: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11063: /*cygwin_split_path(pathtot,path,optionfile);
11064: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11065: /* cutv(path,optionfile,pathtot,'\\');*/
11066:
11067: /* Split argv[0], imach program to get pathimach */
11068: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11069: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11070: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11071: /* strcpy(pathimach,argv[0]); */
11072: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11073: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11074: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11075: #ifdef WIN32
11076: _chdir(path); /* Can be a relative path */
11077: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11078: #else
1.126 brouard 11079: chdir(path); /* Can be a relative path */
1.184 brouard 11080: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11081: #endif
11082: printf("Current directory %s!\n",pathcd);
1.126 brouard 11083: strcpy(command,"mkdir ");
11084: strcat(command,optionfilefiname);
11085: if((outcmd=system(command)) != 0){
1.169 brouard 11086: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11087: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11088: /* fclose(ficlog); */
11089: /* exit(1); */
11090: }
11091: /* if((imk=mkdir(optionfilefiname))<0){ */
11092: /* perror("mkdir"); */
11093: /* } */
11094:
11095: /*-------- arguments in the command line --------*/
11096:
1.186 brouard 11097: /* Main Log file */
1.126 brouard 11098: strcat(filelog, optionfilefiname);
11099: strcat(filelog,".log"); /* */
11100: if((ficlog=fopen(filelog,"w"))==NULL) {
11101: printf("Problem with logfile %s\n",filelog);
11102: goto end;
11103: }
11104: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11105: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11106: fprintf(ficlog,"\nEnter the parameter file name: \n");
11107: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11108: path=%s \n\
11109: optionfile=%s\n\
11110: optionfilext=%s\n\
1.156 brouard 11111: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11112:
1.197 brouard 11113: syscompilerinfo(1);
1.167 brouard 11114:
1.126 brouard 11115: printf("Local time (at start):%s",strstart);
11116: fprintf(ficlog,"Local time (at start): %s",strstart);
11117: fflush(ficlog);
11118: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11119: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11120:
11121: /* */
11122: strcpy(fileres,"r");
11123: strcat(fileres, optionfilefiname);
1.201 brouard 11124: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11125: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11126: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11127:
1.186 brouard 11128: /* Main ---------arguments file --------*/
1.126 brouard 11129:
11130: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11131: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11132: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11133: fflush(ficlog);
1.149 brouard 11134: /* goto end; */
11135: exit(70);
1.126 brouard 11136: }
11137:
11138: strcpy(filereso,"o");
1.201 brouard 11139: strcat(filereso,fileresu);
1.126 brouard 11140: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11141: printf("Problem with Output resultfile: %s\n", filereso);
11142: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11143: fflush(ficlog);
11144: goto end;
11145: }
1.278 brouard 11146: /*-------- Rewriting parameter file ----------*/
11147: strcpy(rfileres,"r"); /* "Rparameterfile */
11148: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11149: strcat(rfileres,"."); /* */
11150: strcat(rfileres,optionfilext); /* Other files have txt extension */
11151: if((ficres =fopen(rfileres,"w"))==NULL) {
11152: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11153: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11154: fflush(ficlog);
11155: goto end;
11156: }
11157: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11158:
1.278 brouard 11159:
1.126 brouard 11160: /* Reads comments: lines beginning with '#' */
11161: numlinepar=0;
1.277 brouard 11162: /* Is it a BOM UTF-8 Windows file? */
11163: /* First parameter line */
1.197 brouard 11164: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11165: noffset=0;
11166: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11167: {
11168: noffset=noffset+3;
11169: printf("# File is an UTF8 Bom.\n"); // 0xBF
11170: }
1.302 brouard 11171: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11172: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11173: {
11174: noffset=noffset+2;
11175: printf("# File is an UTF16BE BOM file\n");
11176: }
11177: else if( line[0] == 0 && line[1] == 0)
11178: {
11179: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11180: noffset=noffset+4;
11181: printf("# File is an UTF16BE BOM file\n");
11182: }
11183: } else{
11184: ;/*printf(" Not a BOM file\n");*/
11185: }
11186:
1.197 brouard 11187: /* If line starts with a # it is a comment */
1.277 brouard 11188: if (line[noffset] == '#') {
1.197 brouard 11189: numlinepar++;
11190: fputs(line,stdout);
11191: fputs(line,ficparo);
1.278 brouard 11192: fputs(line,ficres);
1.197 brouard 11193: fputs(line,ficlog);
11194: continue;
11195: }else
11196: break;
11197: }
11198: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11199: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11200: if (num_filled != 5) {
11201: printf("Should be 5 parameters\n");
1.283 brouard 11202: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11203: }
1.126 brouard 11204: numlinepar++;
1.197 brouard 11205: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11206: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11207: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11208: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11209: }
11210: /* Second parameter line */
11211: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11212: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11213: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11214: if (line[0] == '#') {
11215: numlinepar++;
1.283 brouard 11216: printf("%s",line);
11217: fprintf(ficres,"%s",line);
11218: fprintf(ficparo,"%s",line);
11219: fprintf(ficlog,"%s",line);
1.197 brouard 11220: continue;
11221: }else
11222: break;
11223: }
1.223 brouard 11224: 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", \
11225: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11226: if (num_filled != 11) {
11227: 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 11228: printf("but line=%s\n",line);
1.283 brouard 11229: 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");
11230: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11231: }
1.286 brouard 11232: if( lastpass > maxwav){
11233: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11234: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11235: fflush(ficlog);
11236: goto end;
11237: }
11238: 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 11239: 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 11240: 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 11241: 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 11242: }
1.203 brouard 11243: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11244: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11245: /* Third parameter line */
11246: while(fgets(line, MAXLINE, ficpar)) {
11247: /* If line starts with a # it is a comment */
11248: if (line[0] == '#') {
11249: numlinepar++;
1.283 brouard 11250: printf("%s",line);
11251: fprintf(ficres,"%s",line);
11252: fprintf(ficparo,"%s",line);
11253: fprintf(ficlog,"%s",line);
1.197 brouard 11254: continue;
11255: }else
11256: break;
11257: }
1.201 brouard 11258: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11259: if (num_filled != 1){
1.302 brouard 11260: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11261: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11262: model[0]='\0';
11263: goto end;
11264: }
11265: else{
11266: if (model[0]=='+'){
11267: for(i=1; i<=strlen(model);i++)
11268: modeltemp[i-1]=model[i];
1.201 brouard 11269: strcpy(model,modeltemp);
1.197 brouard 11270: }
11271: }
1.199 brouard 11272: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11273: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11274: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11275: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11276: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11277: }
11278: /* 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); */
11279: /* numlinepar=numlinepar+3; /\* In general *\/ */
11280: /* 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 11281: /* 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); */
11282: /* 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 11283: fflush(ficlog);
1.190 brouard 11284: /* if(model[0]=='#'|| model[0]== '\0'){ */
11285: if(model[0]=='#'){
1.279 brouard 11286: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11287: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11288: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11289: if(mle != -1){
1.279 brouard 11290: 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 11291: exit(1);
11292: }
11293: }
1.126 brouard 11294: while((c=getc(ficpar))=='#' && c!= EOF){
11295: ungetc(c,ficpar);
11296: fgets(line, MAXLINE, ficpar);
11297: numlinepar++;
1.195 brouard 11298: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11299: z[0]=line[1];
11300: }
11301: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11302: fputs(line, stdout);
11303: //puts(line);
1.126 brouard 11304: fputs(line,ficparo);
11305: fputs(line,ficlog);
11306: }
11307: ungetc(c,ficpar);
11308:
11309:
1.290 brouard 11310: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11311: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11312: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11313: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11314: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11315: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11316: v1+v2*age+v2*v3 makes cptcovn = 3
11317: */
11318: if (strlen(model)>1)
1.187 brouard 11319: 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 11320: else
1.187 brouard 11321: ncovmodel=2; /* Constant and age */
1.133 brouard 11322: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11323: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11324: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11325: 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);
11326: 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);
11327: fflush(stdout);
11328: fclose (ficlog);
11329: goto end;
11330: }
1.126 brouard 11331: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11332: delti=delti3[1][1];
11333: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11334: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11335: /* We could also provide initial parameters values giving by simple logistic regression
11336: * only one way, that is without matrix product. We will have nlstate maximizations */
11337: /* for(i=1;i<nlstate;i++){ */
11338: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11339: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11340: /* } */
1.126 brouard 11341: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11342: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11343: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11344: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11345: fclose (ficparo);
11346: fclose (ficlog);
11347: goto end;
11348: exit(0);
1.220 brouard 11349: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11350: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11351: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11352: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11353: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11354: matcov=matrix(1,npar,1,npar);
1.203 brouard 11355: hess=matrix(1,npar,1,npar);
1.220 brouard 11356: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11357: /* Read guessed parameters */
1.126 brouard 11358: /* Reads comments: lines beginning with '#' */
11359: while((c=getc(ficpar))=='#' && c!= EOF){
11360: ungetc(c,ficpar);
11361: fgets(line, MAXLINE, ficpar);
11362: numlinepar++;
1.141 brouard 11363: fputs(line,stdout);
1.126 brouard 11364: fputs(line,ficparo);
11365: fputs(line,ficlog);
11366: }
11367: ungetc(c,ficpar);
11368:
11369: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11370: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11371: for(i=1; i <=nlstate; i++){
1.234 brouard 11372: j=0;
1.126 brouard 11373: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11374: if(jj==i) continue;
11375: j++;
1.292 brouard 11376: while((c=getc(ficpar))=='#' && c!= EOF){
11377: ungetc(c,ficpar);
11378: fgets(line, MAXLINE, ficpar);
11379: numlinepar++;
11380: fputs(line,stdout);
11381: fputs(line,ficparo);
11382: fputs(line,ficlog);
11383: }
11384: ungetc(c,ficpar);
1.234 brouard 11385: fscanf(ficpar,"%1d%1d",&i1,&j1);
11386: if ((i1 != i) || (j1 != jj)){
11387: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11388: It might be a problem of design; if ncovcol and the model are correct\n \
11389: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11390: exit(1);
11391: }
11392: fprintf(ficparo,"%1d%1d",i1,j1);
11393: if(mle==1)
11394: printf("%1d%1d",i,jj);
11395: fprintf(ficlog,"%1d%1d",i,jj);
11396: for(k=1; k<=ncovmodel;k++){
11397: fscanf(ficpar," %lf",¶m[i][j][k]);
11398: if(mle==1){
11399: printf(" %lf",param[i][j][k]);
11400: fprintf(ficlog," %lf",param[i][j][k]);
11401: }
11402: else
11403: fprintf(ficlog," %lf",param[i][j][k]);
11404: fprintf(ficparo," %lf",param[i][j][k]);
11405: }
11406: fscanf(ficpar,"\n");
11407: numlinepar++;
11408: if(mle==1)
11409: printf("\n");
11410: fprintf(ficlog,"\n");
11411: fprintf(ficparo,"\n");
1.126 brouard 11412: }
11413: }
11414: fflush(ficlog);
1.234 brouard 11415:
1.251 brouard 11416: /* Reads parameters values */
1.126 brouard 11417: p=param[1][1];
1.251 brouard 11418: pstart=paramstart[1][1];
1.126 brouard 11419:
11420: /* Reads comments: lines beginning with '#' */
11421: while((c=getc(ficpar))=='#' && c!= EOF){
11422: ungetc(c,ficpar);
11423: fgets(line, MAXLINE, ficpar);
11424: numlinepar++;
1.141 brouard 11425: fputs(line,stdout);
1.126 brouard 11426: fputs(line,ficparo);
11427: fputs(line,ficlog);
11428: }
11429: ungetc(c,ficpar);
11430:
11431: for(i=1; i <=nlstate; i++){
11432: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11433: fscanf(ficpar,"%1d%1d",&i1,&j1);
11434: if ( (i1-i) * (j1-j) != 0){
11435: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11436: exit(1);
11437: }
11438: printf("%1d%1d",i,j);
11439: fprintf(ficparo,"%1d%1d",i1,j1);
11440: fprintf(ficlog,"%1d%1d",i1,j1);
11441: for(k=1; k<=ncovmodel;k++){
11442: fscanf(ficpar,"%le",&delti3[i][j][k]);
11443: printf(" %le",delti3[i][j][k]);
11444: fprintf(ficparo," %le",delti3[i][j][k]);
11445: fprintf(ficlog," %le",delti3[i][j][k]);
11446: }
11447: fscanf(ficpar,"\n");
11448: numlinepar++;
11449: printf("\n");
11450: fprintf(ficparo,"\n");
11451: fprintf(ficlog,"\n");
1.126 brouard 11452: }
11453: }
11454: fflush(ficlog);
1.234 brouard 11455:
1.145 brouard 11456: /* Reads covariance matrix */
1.126 brouard 11457: delti=delti3[1][1];
1.220 brouard 11458:
11459:
1.126 brouard 11460: /* 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 11461:
1.126 brouard 11462: /* Reads comments: lines beginning with '#' */
11463: while((c=getc(ficpar))=='#' && c!= EOF){
11464: ungetc(c,ficpar);
11465: fgets(line, MAXLINE, ficpar);
11466: numlinepar++;
1.141 brouard 11467: fputs(line,stdout);
1.126 brouard 11468: fputs(line,ficparo);
11469: fputs(line,ficlog);
11470: }
11471: ungetc(c,ficpar);
1.220 brouard 11472:
1.126 brouard 11473: matcov=matrix(1,npar,1,npar);
1.203 brouard 11474: hess=matrix(1,npar,1,npar);
1.131 brouard 11475: for(i=1; i <=npar; i++)
11476: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11477:
1.194 brouard 11478: /* Scans npar lines */
1.126 brouard 11479: for(i=1; i <=npar; i++){
1.226 brouard 11480: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11481: if(count != 3){
1.226 brouard 11482: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11483: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11484: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11485: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11486: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11487: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11488: exit(1);
1.220 brouard 11489: }else{
1.226 brouard 11490: if(mle==1)
11491: printf("%1d%1d%d",i1,j1,jk);
11492: }
11493: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11494: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11495: for(j=1; j <=i; j++){
1.226 brouard 11496: fscanf(ficpar," %le",&matcov[i][j]);
11497: if(mle==1){
11498: printf(" %.5le",matcov[i][j]);
11499: }
11500: fprintf(ficlog," %.5le",matcov[i][j]);
11501: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11502: }
11503: fscanf(ficpar,"\n");
11504: numlinepar++;
11505: if(mle==1)
1.220 brouard 11506: printf("\n");
1.126 brouard 11507: fprintf(ficlog,"\n");
11508: fprintf(ficparo,"\n");
11509: }
1.194 brouard 11510: /* End of read covariance matrix npar lines */
1.126 brouard 11511: for(i=1; i <=npar; i++)
11512: for(j=i+1;j<=npar;j++)
1.226 brouard 11513: matcov[i][j]=matcov[j][i];
1.126 brouard 11514:
11515: if(mle==1)
11516: printf("\n");
11517: fprintf(ficlog,"\n");
11518:
11519: fflush(ficlog);
11520:
11521: } /* End of mle != -3 */
1.218 brouard 11522:
1.186 brouard 11523: /* Main data
11524: */
1.290 brouard 11525: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11526: /* num=lvector(1,n); */
11527: /* moisnais=vector(1,n); */
11528: /* annais=vector(1,n); */
11529: /* moisdc=vector(1,n); */
11530: /* andc=vector(1,n); */
11531: /* weight=vector(1,n); */
11532: /* agedc=vector(1,n); */
11533: /* cod=ivector(1,n); */
11534: /* for(i=1;i<=n;i++){ */
11535: num=lvector(firstobs,lastobs);
11536: moisnais=vector(firstobs,lastobs);
11537: annais=vector(firstobs,lastobs);
11538: moisdc=vector(firstobs,lastobs);
11539: andc=vector(firstobs,lastobs);
11540: weight=vector(firstobs,lastobs);
11541: agedc=vector(firstobs,lastobs);
11542: cod=ivector(firstobs,lastobs);
11543: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11544: num[i]=0;
11545: moisnais[i]=0;
11546: annais[i]=0;
11547: moisdc[i]=0;
11548: andc[i]=0;
11549: agedc[i]=0;
11550: cod[i]=0;
11551: weight[i]=1.0; /* Equal weights, 1 by default */
11552: }
1.290 brouard 11553: mint=matrix(1,maxwav,firstobs,lastobs);
11554: anint=matrix(1,maxwav,firstobs,lastobs);
11555: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11556: tab=ivector(1,NCOVMAX);
1.144 brouard 11557: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11558: 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 11559:
1.136 brouard 11560: /* Reads data from file datafile */
11561: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11562: goto end;
11563:
11564: /* Calculation of the number of parameters from char model */
1.234 brouard 11565: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11566: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11567: k=3 V4 Tvar[k=3]= 4 (from V4)
11568: k=2 V1 Tvar[k=2]= 1 (from V1)
11569: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11570: */
11571:
11572: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11573: TvarsDind=ivector(1,NCOVMAX); /* */
11574: TvarsD=ivector(1,NCOVMAX); /* */
11575: TvarsQind=ivector(1,NCOVMAX); /* */
11576: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11577: TvarF=ivector(1,NCOVMAX); /* */
11578: TvarFind=ivector(1,NCOVMAX); /* */
11579: TvarV=ivector(1,NCOVMAX); /* */
11580: TvarVind=ivector(1,NCOVMAX); /* */
11581: TvarA=ivector(1,NCOVMAX); /* */
11582: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11583: TvarFD=ivector(1,NCOVMAX); /* */
11584: TvarFDind=ivector(1,NCOVMAX); /* */
11585: TvarFQ=ivector(1,NCOVMAX); /* */
11586: TvarFQind=ivector(1,NCOVMAX); /* */
11587: TvarVD=ivector(1,NCOVMAX); /* */
11588: TvarVDind=ivector(1,NCOVMAX); /* */
11589: TvarVQ=ivector(1,NCOVMAX); /* */
11590: TvarVQind=ivector(1,NCOVMAX); /* */
11591:
1.230 brouard 11592: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11593: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11594: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11595: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11596: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11597: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11598: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11599: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11600: */
11601: /* For model-covariate k tells which data-covariate to use but
11602: because this model-covariate is a construction we invent a new column
11603: ncovcol + k1
11604: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11605: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11606: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11607: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11608: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11609: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11610: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11611: */
1.145 brouard 11612: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11613: 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 11614: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11615: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11616: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11617: 4 covariates (3 plus signs)
11618: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11619: */
1.230 brouard 11620: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11621: * individual dummy, fixed or varying:
11622: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11623: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11624: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11625: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11626: * Tmodelind[1]@9={9,0,3,2,}*/
11627: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11628: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11629: * individual quantitative, fixed or varying:
11630: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11631: * 3, 1, 0, 0, 0, 0, 0, 0},
11632: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11633: /* Main decodemodel */
11634:
1.187 brouard 11635:
1.223 brouard 11636: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11637: goto end;
11638:
1.137 brouard 11639: if((double)(lastobs-imx)/(double)imx > 1.10){
11640: nbwarn++;
11641: 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);
11642: 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);
11643: }
1.136 brouard 11644: /* if(mle==1){*/
1.137 brouard 11645: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11646: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11647: }
11648:
11649: /*-calculation of age at interview from date of interview and age at death -*/
11650: agev=matrix(1,maxwav,1,imx);
11651:
11652: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11653: goto end;
11654:
1.126 brouard 11655:
1.136 brouard 11656: agegomp=(int)agemin;
1.290 brouard 11657: free_vector(moisnais,firstobs,lastobs);
11658: free_vector(annais,firstobs,lastobs);
1.126 brouard 11659: /* free_matrix(mint,1,maxwav,1,n);
11660: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11661: /* free_vector(moisdc,1,n); */
11662: /* free_vector(andc,1,n); */
1.145 brouard 11663: /* */
11664:
1.126 brouard 11665: wav=ivector(1,imx);
1.214 brouard 11666: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11667: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11668: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11669: 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.*/
11670: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11671: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11672:
11673: /* Concatenates waves */
1.214 brouard 11674: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11675: Death is a valid wave (if date is known).
11676: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11677: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11678: and mw[mi+1][i]. dh depends on stepm.
11679: */
11680:
1.126 brouard 11681: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11682: /* Concatenates waves */
1.145 brouard 11683:
1.290 brouard 11684: free_vector(moisdc,firstobs,lastobs);
11685: free_vector(andc,firstobs,lastobs);
1.215 brouard 11686:
1.126 brouard 11687: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11688: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11689: ncodemax[1]=1;
1.145 brouard 11690: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11691: cptcoveff=0;
1.220 brouard 11692: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11693: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11694: }
11695:
11696: ncovcombmax=pow(2,cptcoveff);
11697: invalidvarcomb=ivector(1, ncovcombmax);
11698: for(i=1;i<ncovcombmax;i++)
11699: invalidvarcomb[i]=0;
11700:
1.211 brouard 11701: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11702: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11703: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11704:
1.200 brouard 11705: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11706: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11707: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11708: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11709: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11710: * (currently 0 or 1) in the data.
11711: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11712: * corresponding modality (h,j).
11713: */
11714:
1.145 brouard 11715: h=0;
11716: /*if (cptcovn > 0) */
1.126 brouard 11717: m=pow(2,cptcoveff);
11718:
1.144 brouard 11719: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11720: * For k=4 covariates, h goes from 1 to m=2**k
11721: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11722: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11723: * h\k 1 2 3 4
1.143 brouard 11724: *______________________________
11725: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11726: * 2 2 1 1 1
11727: * 3 i=2 1 2 1 1
11728: * 4 2 2 1 1
11729: * 5 i=3 1 i=2 1 2 1
11730: * 6 2 1 2 1
11731: * 7 i=4 1 2 2 1
11732: * 8 2 2 2 1
1.197 brouard 11733: * 9 i=5 1 i=3 1 i=2 1 2
11734: * 10 2 1 1 2
11735: * 11 i=6 1 2 1 2
11736: * 12 2 2 1 2
11737: * 13 i=7 1 i=4 1 2 2
11738: * 14 2 1 2 2
11739: * 15 i=8 1 2 2 2
11740: * 16 2 2 2 2
1.143 brouard 11741: */
1.212 brouard 11742: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11743: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11744: * and the value of each covariate?
11745: * V1=1, V2=1, V3=2, V4=1 ?
11746: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11747: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11748: * In order to get the real value in the data, we use nbcode
11749: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11750: * We are keeping this crazy system in order to be able (in the future?)
11751: * to have more than 2 values (0 or 1) for a covariate.
11752: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11753: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11754: * bbbbbbbb
11755: * 76543210
11756: * h-1 00000101 (6-1=5)
1.219 brouard 11757: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11758: * &
11759: * 1 00000001 (1)
1.219 brouard 11760: * 00000000 = 1 & ((h-1) >> (k-1))
11761: * +1= 00000001 =1
1.211 brouard 11762: *
11763: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11764: * h' 1101 =2^3+2^2+0x2^1+2^0
11765: * >>k' 11
11766: * & 00000001
11767: * = 00000001
11768: * +1 = 00000010=2 = codtabm(14,3)
11769: * Reverse h=6 and m=16?
11770: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11771: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11772: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11773: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11774: * V3=decodtabm(14,3,2**4)=2
11775: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11776: *(h-1) >> (j-1) 0011 =13 >> 2
11777: * &1 000000001
11778: * = 000000001
11779: * +1= 000000010 =2
11780: * 2211
11781: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11782: * V3=2
1.220 brouard 11783: * codtabm and decodtabm are identical
1.211 brouard 11784: */
11785:
1.145 brouard 11786:
11787: free_ivector(Ndum,-1,NCOVMAX);
11788:
11789:
1.126 brouard 11790:
1.186 brouard 11791: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11792: strcpy(optionfilegnuplot,optionfilefiname);
11793: if(mle==-3)
1.201 brouard 11794: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11795: strcat(optionfilegnuplot,".gp");
11796:
11797: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11798: printf("Problem with file %s",optionfilegnuplot);
11799: }
11800: else{
1.204 brouard 11801: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11802: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11803: //fprintf(ficgp,"set missing 'NaNq'\n");
11804: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11805: }
11806: /* fclose(ficgp);*/
1.186 brouard 11807:
11808:
11809: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11810:
11811: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11812: if(mle==-3)
1.201 brouard 11813: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11814: strcat(optionfilehtm,".htm");
11815: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11816: printf("Problem with %s \n",optionfilehtm);
11817: exit(0);
1.126 brouard 11818: }
11819:
11820: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11821: strcat(optionfilehtmcov,"-cov.htm");
11822: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11823: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11824: }
11825: else{
11826: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11827: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11828: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11829: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11830: }
11831:
1.213 brouard 11832: 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å¦è¡“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 11833: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11834: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11835: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11836: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11837: \n\
11838: <hr size=\"2\" color=\"#EC5E5E\">\
11839: <ul><li><h4>Parameter files</h4>\n\
11840: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11841: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11842: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11843: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11844: - Date and time at start: %s</ul>\n",\
11845: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11846: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11847: fileres,fileres,\
11848: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11849: fflush(fichtm);
11850:
11851: strcpy(pathr,path);
11852: strcat(pathr,optionfilefiname);
1.184 brouard 11853: #ifdef WIN32
11854: _chdir(optionfilefiname); /* Move to directory named optionfile */
11855: #else
1.126 brouard 11856: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11857: #endif
11858:
1.126 brouard 11859:
1.220 brouard 11860: /* Calculates basic frequencies. Computes observed prevalence at single age
11861: and for any valid combination of covariates
1.126 brouard 11862: and prints on file fileres'p'. */
1.251 brouard 11863: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11864: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11865:
11866: fprintf(fichtm,"\n");
1.286 brouard 11867: 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 11868: ftol, stepm);
11869: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11870: ncurrv=1;
11871: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11872: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11873: ncurrv=i;
11874: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11875: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11876: ncurrv=i;
11877: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11878: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11879: ncurrv=i;
11880: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11881: 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", \
11882: nlstate, ndeath, maxwav, mle, weightopt);
11883:
11884: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11885: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11886:
11887:
11888: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11889: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11890: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11891: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11892: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11893: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11894: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11895: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11896: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11897:
1.126 brouard 11898: /* For Powell, parameters are in a vector p[] starting at p[1]
11899: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11900: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11901:
11902: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11903: /* For mortality only */
1.126 brouard 11904: if (mle==-3){
1.136 brouard 11905: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11906: for(i=1;i<=NDIM;i++)
11907: for(j=1;j<=NDIM;j++)
11908: ximort[i][j]=0.;
1.186 brouard 11909: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11910: cens=ivector(firstobs,lastobs);
11911: ageexmed=vector(firstobs,lastobs);
11912: agecens=vector(firstobs,lastobs);
11913: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11914:
1.126 brouard 11915: for (i=1; i<=imx; i++){
11916: dcwave[i]=-1;
11917: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11918: if (s[m][i]>nlstate) {
11919: dcwave[i]=m;
11920: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11921: break;
11922: }
1.126 brouard 11923: }
1.226 brouard 11924:
1.126 brouard 11925: for (i=1; i<=imx; i++) {
11926: if (wav[i]>0){
1.226 brouard 11927: ageexmed[i]=agev[mw[1][i]][i];
11928: j=wav[i];
11929: agecens[i]=1.;
11930:
11931: if (ageexmed[i]> 1 && wav[i] > 0){
11932: agecens[i]=agev[mw[j][i]][i];
11933: cens[i]= 1;
11934: }else if (ageexmed[i]< 1)
11935: cens[i]= -1;
11936: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11937: cens[i]=0 ;
1.126 brouard 11938: }
11939: else cens[i]=-1;
11940: }
11941:
11942: for (i=1;i<=NDIM;i++) {
11943: for (j=1;j<=NDIM;j++)
1.226 brouard 11944: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11945: }
11946:
1.302 brouard 11947: p[1]=0.0268; p[NDIM]=0.083;
11948: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 11949:
11950:
1.136 brouard 11951: #ifdef GSL
11952: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11953: #else
1.126 brouard 11954: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11955: #endif
1.201 brouard 11956: strcpy(filerespow,"POW-MORT_");
11957: strcat(filerespow,fileresu);
1.126 brouard 11958: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11959: printf("Problem with resultfile: %s\n", filerespow);
11960: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11961: }
1.136 brouard 11962: #ifdef GSL
11963: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11964: #else
1.126 brouard 11965: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11966: #endif
1.126 brouard 11967: /* for (i=1;i<=nlstate;i++)
11968: for(j=1;j<=nlstate+ndeath;j++)
11969: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11970: */
11971: fprintf(ficrespow,"\n");
1.136 brouard 11972: #ifdef GSL
11973: /* gsl starts here */
11974: T = gsl_multimin_fminimizer_nmsimplex;
11975: gsl_multimin_fminimizer *sfm = NULL;
11976: gsl_vector *ss, *x;
11977: gsl_multimin_function minex_func;
11978:
11979: /* Initial vertex size vector */
11980: ss = gsl_vector_alloc (NDIM);
11981:
11982: if (ss == NULL){
11983: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11984: }
11985: /* Set all step sizes to 1 */
11986: gsl_vector_set_all (ss, 0.001);
11987:
11988: /* Starting point */
1.126 brouard 11989:
1.136 brouard 11990: x = gsl_vector_alloc (NDIM);
11991:
11992: if (x == NULL){
11993: gsl_vector_free(ss);
11994: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11995: }
11996:
11997: /* Initialize method and iterate */
11998: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11999: /* gsl_vector_set(x, 0, 0.0268); */
12000: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 12001: gsl_vector_set(x, 0, p[1]);
12002: gsl_vector_set(x, 1, p[2]);
12003:
12004: minex_func.f = &gompertz_f;
12005: minex_func.n = NDIM;
12006: minex_func.params = (void *)&p; /* ??? */
12007:
12008: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12009: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12010:
12011: printf("Iterations beginning .....\n\n");
12012: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12013:
12014: iteri=0;
12015: while (rval == GSL_CONTINUE){
12016: iteri++;
12017: status = gsl_multimin_fminimizer_iterate(sfm);
12018:
12019: if (status) printf("error: %s\n", gsl_strerror (status));
12020: fflush(0);
12021:
12022: if (status)
12023: break;
12024:
12025: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12026: ssval = gsl_multimin_fminimizer_size (sfm);
12027:
12028: if (rval == GSL_SUCCESS)
12029: printf ("converged to a local maximum at\n");
12030:
12031: printf("%5d ", iteri);
12032: for (it = 0; it < NDIM; it++){
12033: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12034: }
12035: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12036: }
12037:
12038: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12039:
12040: gsl_vector_free(x); /* initial values */
12041: gsl_vector_free(ss); /* inital step size */
12042: for (it=0; it<NDIM; it++){
12043: p[it+1]=gsl_vector_get(sfm->x,it);
12044: fprintf(ficrespow," %.12lf", p[it]);
12045: }
12046: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12047: #endif
12048: #ifdef POWELL
12049: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12050: #endif
1.126 brouard 12051: fclose(ficrespow);
12052:
1.203 brouard 12053: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12054:
12055: for(i=1; i <=NDIM; i++)
12056: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12057: matcov[i][j]=matcov[j][i];
1.126 brouard 12058:
12059: printf("\nCovariance matrix\n ");
1.203 brouard 12060: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12061: for(i=1; i <=NDIM; i++) {
12062: for(j=1;j<=NDIM;j++){
1.220 brouard 12063: printf("%f ",matcov[i][j]);
12064: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12065: }
1.203 brouard 12066: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12067: }
12068:
12069: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12070: for (i=1;i<=NDIM;i++) {
1.126 brouard 12071: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12072: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12073: }
1.302 brouard 12074: lsurv=vector(agegomp,AGESUP);
12075: lpop=vector(agegomp,AGESUP);
12076: tpop=vector(agegomp,AGESUP);
1.126 brouard 12077: lsurv[agegomp]=100000;
12078:
12079: for (k=agegomp;k<=AGESUP;k++) {
12080: agemortsup=k;
12081: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12082: }
12083:
12084: for (k=agegomp;k<agemortsup;k++)
12085: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12086:
12087: for (k=agegomp;k<agemortsup;k++){
12088: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12089: sumlpop=sumlpop+lpop[k];
12090: }
12091:
12092: tpop[agegomp]=sumlpop;
12093: for (k=agegomp;k<(agemortsup-3);k++){
12094: /* tpop[k+1]=2;*/
12095: tpop[k+1]=tpop[k]-lpop[k];
12096: }
12097:
12098:
12099: printf("\nAge lx qx dx Lx Tx e(x)\n");
12100: for (k=agegomp;k<(agemortsup-2);k++)
12101: 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]);
12102:
12103:
12104: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12105: ageminpar=50;
12106: agemaxpar=100;
1.194 brouard 12107: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12108: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12109: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12110: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12111: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12112: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12113: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12114: }else{
12115: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12116: 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 12117: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12118: }
1.201 brouard 12119: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12120: stepm, weightopt,\
12121: model,imx,p,matcov,agemortsup);
12122:
1.302 brouard 12123: free_vector(lsurv,agegomp,AGESUP);
12124: free_vector(lpop,agegomp,AGESUP);
12125: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12126: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12127: free_ivector(dcwave,firstobs,lastobs);
12128: free_vector(agecens,firstobs,lastobs);
12129: free_vector(ageexmed,firstobs,lastobs);
12130: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12131: #ifdef GSL
1.136 brouard 12132: #endif
1.186 brouard 12133: } /* Endof if mle==-3 mortality only */
1.205 brouard 12134: /* Standard */
12135: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12136: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12137: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12138: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12139: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12140: for (k=1; k<=npar;k++)
12141: printf(" %d %8.5f",k,p[k]);
12142: printf("\n");
1.205 brouard 12143: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12144: /* mlikeli uses func not funcone */
1.247 brouard 12145: /* for(i=1;i<nlstate;i++){ */
12146: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12147: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12148: /* } */
1.205 brouard 12149: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12150: }
12151: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12152: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12153: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12154: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12155: }
12156: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12157: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12158: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12159: for (k=1; k<=npar;k++)
12160: printf(" %d %8.5f",k,p[k]);
12161: printf("\n");
12162:
12163: /*--------- results files --------------*/
1.283 brouard 12164: /* 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 12165:
12166:
12167: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12168: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12169: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12170: for(i=1,jk=1; i <=nlstate; i++){
12171: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12172: if (k != i) {
12173: printf("%d%d ",i,k);
12174: fprintf(ficlog,"%d%d ",i,k);
12175: fprintf(ficres,"%1d%1d ",i,k);
12176: for(j=1; j <=ncovmodel; j++){
12177: printf("%12.7f ",p[jk]);
12178: fprintf(ficlog,"%12.7f ",p[jk]);
12179: fprintf(ficres,"%12.7f ",p[jk]);
12180: jk++;
12181: }
12182: printf("\n");
12183: fprintf(ficlog,"\n");
12184: fprintf(ficres,"\n");
12185: }
1.126 brouard 12186: }
12187: }
1.203 brouard 12188: if(mle != 0){
12189: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12190: ftolhess=ftol; /* Usually correct */
1.203 brouard 12191: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12192: 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");
12193: 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");
12194: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12195: for(k=1; k <=(nlstate+ndeath); k++){
12196: if (k != i) {
12197: printf("%d%d ",i,k);
12198: fprintf(ficlog,"%d%d ",i,k);
12199: for(j=1; j <=ncovmodel; j++){
12200: 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]));
12201: 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]));
12202: jk++;
12203: }
12204: printf("\n");
12205: fprintf(ficlog,"\n");
12206: }
12207: }
1.193 brouard 12208: }
1.203 brouard 12209: } /* end of hesscov and Wald tests */
1.225 brouard 12210:
1.203 brouard 12211: /* */
1.126 brouard 12212: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12213: printf("# Scales (for hessian or gradient estimation)\n");
12214: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12215: for(i=1,jk=1; i <=nlstate; i++){
12216: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12217: if (j!=i) {
12218: fprintf(ficres,"%1d%1d",i,j);
12219: printf("%1d%1d",i,j);
12220: fprintf(ficlog,"%1d%1d",i,j);
12221: for(k=1; k<=ncovmodel;k++){
12222: printf(" %.5e",delti[jk]);
12223: fprintf(ficlog," %.5e",delti[jk]);
12224: fprintf(ficres," %.5e",delti[jk]);
12225: jk++;
12226: }
12227: printf("\n");
12228: fprintf(ficlog,"\n");
12229: fprintf(ficres,"\n");
12230: }
1.126 brouard 12231: }
12232: }
12233:
12234: 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 12235: if(mle >= 1) /* To big for the screen */
1.126 brouard 12236: 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");
12237: 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");
12238: /* # 121 Var(a12)\n\ */
12239: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12240: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12241: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12242: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12243: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12244: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12245: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12246:
12247:
12248: /* Just to have a covariance matrix which will be more understandable
12249: even is we still don't want to manage dictionary of variables
12250: */
12251: for(itimes=1;itimes<=2;itimes++){
12252: jj=0;
12253: for(i=1; i <=nlstate; i++){
1.225 brouard 12254: for(j=1; j <=nlstate+ndeath; j++){
12255: if(j==i) continue;
12256: for(k=1; k<=ncovmodel;k++){
12257: jj++;
12258: ca[0]= k+'a'-1;ca[1]='\0';
12259: if(itimes==1){
12260: if(mle>=1)
12261: printf("#%1d%1d%d",i,j,k);
12262: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12263: fprintf(ficres,"#%1d%1d%d",i,j,k);
12264: }else{
12265: if(mle>=1)
12266: printf("%1d%1d%d",i,j,k);
12267: fprintf(ficlog,"%1d%1d%d",i,j,k);
12268: fprintf(ficres,"%1d%1d%d",i,j,k);
12269: }
12270: ll=0;
12271: for(li=1;li <=nlstate; li++){
12272: for(lj=1;lj <=nlstate+ndeath; lj++){
12273: if(lj==li) continue;
12274: for(lk=1;lk<=ncovmodel;lk++){
12275: ll++;
12276: if(ll<=jj){
12277: cb[0]= lk +'a'-1;cb[1]='\0';
12278: if(ll<jj){
12279: if(itimes==1){
12280: if(mle>=1)
12281: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12282: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12283: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12284: }else{
12285: if(mle>=1)
12286: printf(" %.5e",matcov[jj][ll]);
12287: fprintf(ficlog," %.5e",matcov[jj][ll]);
12288: fprintf(ficres," %.5e",matcov[jj][ll]);
12289: }
12290: }else{
12291: if(itimes==1){
12292: if(mle>=1)
12293: printf(" Var(%s%1d%1d)",ca,i,j);
12294: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12295: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12296: }else{
12297: if(mle>=1)
12298: printf(" %.7e",matcov[jj][ll]);
12299: fprintf(ficlog," %.7e",matcov[jj][ll]);
12300: fprintf(ficres," %.7e",matcov[jj][ll]);
12301: }
12302: }
12303: }
12304: } /* end lk */
12305: } /* end lj */
12306: } /* end li */
12307: if(mle>=1)
12308: printf("\n");
12309: fprintf(ficlog,"\n");
12310: fprintf(ficres,"\n");
12311: numlinepar++;
12312: } /* end k*/
12313: } /*end j */
1.126 brouard 12314: } /* end i */
12315: } /* end itimes */
12316:
12317: fflush(ficlog);
12318: fflush(ficres);
1.225 brouard 12319: while(fgets(line, MAXLINE, ficpar)) {
12320: /* If line starts with a # it is a comment */
12321: if (line[0] == '#') {
12322: numlinepar++;
12323: fputs(line,stdout);
12324: fputs(line,ficparo);
12325: fputs(line,ficlog);
1.299 brouard 12326: fputs(line,ficres);
1.225 brouard 12327: continue;
12328: }else
12329: break;
12330: }
12331:
1.209 brouard 12332: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12333: /* ungetc(c,ficpar); */
12334: /* fgets(line, MAXLINE, ficpar); */
12335: /* fputs(line,stdout); */
12336: /* fputs(line,ficparo); */
12337: /* } */
12338: /* ungetc(c,ficpar); */
1.126 brouard 12339:
12340: estepm=0;
1.209 brouard 12341: 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 12342:
12343: if (num_filled != 6) {
12344: 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);
12345: 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);
12346: goto end;
12347: }
12348: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12349: }
12350: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12351: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12352:
1.209 brouard 12353: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12354: if (estepm==0 || estepm < stepm) estepm=stepm;
12355: if (fage <= 2) {
12356: bage = ageminpar;
12357: fage = agemaxpar;
12358: }
12359:
12360: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12361: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12362: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12363:
1.186 brouard 12364: /* Other stuffs, more or less useful */
1.254 brouard 12365: while(fgets(line, MAXLINE, ficpar)) {
12366: /* If line starts with a # it is a comment */
12367: if (line[0] == '#') {
12368: numlinepar++;
12369: fputs(line,stdout);
12370: fputs(line,ficparo);
12371: fputs(line,ficlog);
1.299 brouard 12372: fputs(line,ficres);
1.254 brouard 12373: continue;
12374: }else
12375: break;
12376: }
12377:
12378: 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){
12379:
12380: if (num_filled != 7) {
12381: 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);
12382: 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);
12383: goto end;
12384: }
12385: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12386: 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);
12387: 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);
12388: 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 12389: }
1.254 brouard 12390:
12391: while(fgets(line, MAXLINE, ficpar)) {
12392: /* If line starts with a # it is a comment */
12393: if (line[0] == '#') {
12394: numlinepar++;
12395: fputs(line,stdout);
12396: fputs(line,ficparo);
12397: fputs(line,ficlog);
1.299 brouard 12398: fputs(line,ficres);
1.254 brouard 12399: continue;
12400: }else
12401: break;
1.126 brouard 12402: }
12403:
12404:
12405: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12406: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12407:
1.254 brouard 12408: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12409: if (num_filled != 1) {
12410: 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);
12411: 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);
12412: goto end;
12413: }
12414: printf("pop_based=%d\n",popbased);
12415: fprintf(ficlog,"pop_based=%d\n",popbased);
12416: fprintf(ficparo,"pop_based=%d\n",popbased);
12417: fprintf(ficres,"pop_based=%d\n",popbased);
12418: }
12419:
1.258 brouard 12420: /* Results */
1.307 brouard 12421: endishere=0;
1.258 brouard 12422: nresult=0;
1.308 ! brouard 12423: parameterline=0;
1.258 brouard 12424: do{
12425: if(!fgets(line, MAXLINE, ficpar)){
12426: endishere=1;
1.308 ! brouard 12427: parameterline=15;
1.258 brouard 12428: }else if (line[0] == '#') {
12429: /* If line starts with a # it is a comment */
1.254 brouard 12430: numlinepar++;
12431: fputs(line,stdout);
12432: fputs(line,ficparo);
12433: fputs(line,ficlog);
1.299 brouard 12434: fputs(line,ficres);
1.254 brouard 12435: continue;
1.258 brouard 12436: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12437: parameterline=11;
1.296 brouard 12438: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12439: parameterline=12;
1.307 brouard 12440: else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
1.258 brouard 12441: parameterline=13;
1.307 brouard 12442: }
1.258 brouard 12443: else{
12444: parameterline=14;
1.254 brouard 12445: }
1.308 ! brouard 12446: switch (parameterline){ /* =0 only if only comments */
1.258 brouard 12447: case 11:
1.296 brouard 12448: 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)){
12449: 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 12450: 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);
12451: 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);
12452: 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);
12453: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12454: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12455: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12456: prvforecast = 1;
12457: }
12458: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.302 brouard 12459: printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12460: fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12461: fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12462: prvforecast = 2;
12463: }
12464: else {
12465: 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);
12466: 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);
12467: goto end;
1.258 brouard 12468: }
1.254 brouard 12469: break;
1.258 brouard 12470: case 12:
1.296 brouard 12471: 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)){
12472: 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);
12473: 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);
12474: 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);
12475: 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);
12476: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12477: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12478: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12479: prvbackcast = 1;
12480: }
12481: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.302 brouard 12482: printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12483: fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12484: fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12485: prvbackcast = 2;
12486: }
12487: else {
12488: 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);
12489: 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);
12490: goto end;
1.258 brouard 12491: }
1.230 brouard 12492: break;
1.258 brouard 12493: case 13:
1.307 brouard 12494: num_filled=sscanf(line,"result:%[^\n]\n",resultline);
12495: nresult++; /* Sum of resultlines */
12496: printf("Result %d: result:%s\n",nresult, resultline);
12497: if(nresult > MAXRESULTLINES){
12498: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
12499: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINES,nresult,rfileres);
12500: goto end;
12501: }
12502: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12503: fprintf(ficparo,"result: %s\n",resultline);
12504: fprintf(ficres,"result: %s\n",resultline);
12505: fprintf(ficlog,"result: %s\n",resultline);
12506: break;
12507: case 14:
12508: printf("Error: Unknown command '%s'\n",line);
12509: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
12510: if(ncovmodel >=2 && nresult==0 ){
12511: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
12512: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12513: }
1.307 brouard 12514: /* goto end; */
12515: break;
1.308 ! brouard 12516: case 15:
! 12517: printf("End of resultlines.\n");
! 12518: fprintf(ficlog,"End of resultlines.\n");
! 12519: break;
! 12520: default: /* parameterline =0 */
1.307 brouard 12521: nresult=1;
12522: decoderesult(".",nresult ); /* No covariate */
1.258 brouard 12523: } /* End switch parameterline */
12524: }while(endishere==0); /* End do */
1.126 brouard 12525:
1.230 brouard 12526: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12527: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12528:
12529: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12530: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12531: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12532: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12533: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12534: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12535: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12536: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12537: }else{
1.270 brouard 12538: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12539: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12540: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12541: if(prvforecast==1){
12542: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12543: jprojd=jproj1;
12544: mprojd=mproj1;
12545: anprojd=anproj1;
12546: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12547: jprojf=jproj2;
12548: mprojf=mproj2;
12549: anprojf=anproj2;
12550: } else if(prvforecast == 2){
12551: dateprojd=dateintmean;
12552: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12553: dateprojf=dateintmean+yrfproj;
12554: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12555: }
12556: if(prvbackcast==1){
12557: datebackd=(jback1+12*mback1+365*anback1)/365;
12558: jbackd=jback1;
12559: mbackd=mback1;
12560: anbackd=anback1;
12561: datebackf=(jback2+12*mback2+365*anback2)/365;
12562: jbackf=jback2;
12563: mbackf=mback2;
12564: anbackf=anback2;
12565: } else if(prvbackcast == 2){
12566: datebackd=dateintmean;
12567: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12568: datebackf=dateintmean-yrbproj;
12569: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12570: }
12571:
12572: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12573: }
12574: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12575: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12576: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12577:
1.225 brouard 12578: /*------------ free_vector -------------*/
12579: /* chdir(path); */
1.220 brouard 12580:
1.215 brouard 12581: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12582: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12583: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12584: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12585: free_lvector(num,firstobs,lastobs);
12586: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12587: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12588: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12589: fclose(ficparo);
12590: fclose(ficres);
1.220 brouard 12591:
12592:
1.186 brouard 12593: /* Other results (useful)*/
1.220 brouard 12594:
12595:
1.126 brouard 12596: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12597: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12598: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12599: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12600: fclose(ficrespl);
12601:
12602: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12603: /*#include "hpijx.h"*/
12604: hPijx(p, bage, fage);
1.145 brouard 12605: fclose(ficrespij);
1.227 brouard 12606:
1.220 brouard 12607: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12608: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12609: k=1;
1.126 brouard 12610: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12611:
1.269 brouard 12612: /* Prevalence for each covariate combination in probs[age][status][cov] */
12613: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12614: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12615: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12616: for(k=1;k<=ncovcombmax;k++)
12617: probs[i][j][k]=0.;
1.269 brouard 12618: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12619: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12620: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12621: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12622: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12623: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12624: for(k=1;k<=ncovcombmax;k++)
12625: mobaverages[i][j][k]=0.;
1.219 brouard 12626: mobaverage=mobaverages;
12627: if (mobilav!=0) {
1.235 brouard 12628: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12629: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12630: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12631: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12632: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12633: }
1.269 brouard 12634: } else if (mobilavproj !=0) {
1.235 brouard 12635: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12636: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12637: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12638: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12639: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12640: }
1.269 brouard 12641: }else{
12642: printf("Internal error moving average\n");
12643: fflush(stdout);
12644: exit(1);
1.219 brouard 12645: }
12646: }/* end if moving average */
1.227 brouard 12647:
1.126 brouard 12648: /*---------- Forecasting ------------------*/
1.296 brouard 12649: if(prevfcast==1){
12650: /* /\* if(stepm ==1){*\/ */
12651: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12652: /*This done previously after freqsummary.*/
12653: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12654: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12655:
12656: /* } else if (prvforecast==2){ */
12657: /* /\* if(stepm ==1){*\/ */
12658: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12659: /* } */
12660: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12661: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12662: }
1.269 brouard 12663:
1.296 brouard 12664: /* Prevbcasting */
12665: if(prevbcast==1){
1.219 brouard 12666: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12667: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12668: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12669:
12670: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12671:
12672: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12673:
1.219 brouard 12674: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12675: fclose(ficresplb);
12676:
1.222 brouard 12677: hBijx(p, bage, fage, mobaverage);
12678: fclose(ficrespijb);
1.219 brouard 12679:
1.296 brouard 12680: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12681: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12682: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12683: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12684: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12685: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12686:
12687:
1.269 brouard 12688: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12689:
12690:
1.269 brouard 12691: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12692: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12693: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12694: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12695: } /* end Prevbcasting */
1.268 brouard 12696:
1.186 brouard 12697:
12698: /* ------ Other prevalence ratios------------ */
1.126 brouard 12699:
1.215 brouard 12700: free_ivector(wav,1,imx);
12701: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12702: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12703: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12704:
12705:
1.127 brouard 12706: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12707:
1.201 brouard 12708: strcpy(filerese,"E_");
12709: strcat(filerese,fileresu);
1.126 brouard 12710: if((ficreseij=fopen(filerese,"w"))==NULL) {
12711: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12712: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12713: }
1.208 brouard 12714: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12715: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12716:
12717: pstamp(ficreseij);
1.219 brouard 12718:
1.235 brouard 12719: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12720: if (cptcovn < 1){i1=1;}
12721:
12722: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12723: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12724: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12725: continue;
1.219 brouard 12726: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12727: printf("\n#****** ");
1.225 brouard 12728: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12729: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12730: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12731: }
12732: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12733: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12734: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12735: }
12736: fprintf(ficreseij,"******\n");
1.235 brouard 12737: printf("******\n");
1.219 brouard 12738:
12739: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12740: oldm=oldms;savm=savms;
1.235 brouard 12741: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12742:
1.219 brouard 12743: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12744: }
12745: fclose(ficreseij);
1.208 brouard 12746: printf("done evsij\n");fflush(stdout);
12747: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12748:
1.218 brouard 12749:
1.227 brouard 12750: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12751:
1.201 brouard 12752: strcpy(filerest,"T_");
12753: strcat(filerest,fileresu);
1.127 brouard 12754: if((ficrest=fopen(filerest,"w"))==NULL) {
12755: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12756: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12757: }
1.208 brouard 12758: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12759: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12760: strcpy(fileresstde,"STDE_");
12761: strcat(fileresstde,fileresu);
1.126 brouard 12762: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12763: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12764: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12765: }
1.227 brouard 12766: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12767: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12768:
1.201 brouard 12769: strcpy(filerescve,"CVE_");
12770: strcat(filerescve,fileresu);
1.126 brouard 12771: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12772: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12773: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12774: }
1.227 brouard 12775: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12776: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12777:
1.201 brouard 12778: strcpy(fileresv,"V_");
12779: strcat(fileresv,fileresu);
1.126 brouard 12780: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12781: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12782: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12783: }
1.227 brouard 12784: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12785: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12786:
1.235 brouard 12787: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12788: if (cptcovn < 1){i1=1;}
12789:
12790: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12791: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12792: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12793: continue;
1.242 brouard 12794: printf("\n#****** Result for:");
12795: fprintf(ficrest,"\n#****** Result for:");
12796: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12797: for(j=1;j<=cptcoveff;j++){
12798: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12799: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12800: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12801: }
1.235 brouard 12802: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12803: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12804: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12805: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12806: }
1.208 brouard 12807: fprintf(ficrest,"******\n");
1.227 brouard 12808: fprintf(ficlog,"******\n");
12809: printf("******\n");
1.208 brouard 12810:
12811: fprintf(ficresstdeij,"\n#****** ");
12812: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12813: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12814: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12815: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12816: }
1.235 brouard 12817: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12818: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12819: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12820: }
1.208 brouard 12821: fprintf(ficresstdeij,"******\n");
12822: fprintf(ficrescveij,"******\n");
12823:
12824: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12825: /* pstamp(ficresvij); */
1.225 brouard 12826: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12827: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12828: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12829: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12830: }
1.208 brouard 12831: fprintf(ficresvij,"******\n");
12832:
12833: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12834: oldm=oldms;savm=savms;
1.235 brouard 12835: printf(" cvevsij ");
12836: fprintf(ficlog, " cvevsij ");
12837: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12838: printf(" end cvevsij \n ");
12839: fprintf(ficlog, " end cvevsij \n ");
12840:
12841: /*
12842: */
12843: /* goto endfree; */
12844:
12845: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12846: pstamp(ficrest);
12847:
1.269 brouard 12848: epj=vector(1,nlstate+1);
1.208 brouard 12849: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12850: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12851: cptcod= 0; /* To be deleted */
12852: printf("varevsij vpopbased=%d \n",vpopbased);
12853: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12854: 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 12855: 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 ");
12856: if(vpopbased==1)
12857: 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);
12858: else
1.288 brouard 12859: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12860: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12861: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12862: fprintf(ficrest,"\n");
12863: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12864: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12865: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12866: for(age=bage; age <=fage ;age++){
1.235 brouard 12867: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12868: if (vpopbased==1) {
12869: if(mobilav ==0){
12870: for(i=1; i<=nlstate;i++)
12871: prlim[i][i]=probs[(int)age][i][k];
12872: }else{ /* mobilav */
12873: for(i=1; i<=nlstate;i++)
12874: prlim[i][i]=mobaverage[(int)age][i][k];
12875: }
12876: }
1.219 brouard 12877:
1.227 brouard 12878: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12879: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12880: /* printf(" age %4.0f ",age); */
12881: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12882: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12883: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12884: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12885: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12886: }
12887: epj[nlstate+1] +=epj[j];
12888: }
12889: /* printf(" age %4.0f \n",age); */
1.219 brouard 12890:
1.227 brouard 12891: for(i=1, vepp=0.;i <=nlstate;i++)
12892: for(j=1;j <=nlstate;j++)
12893: vepp += vareij[i][j][(int)age];
12894: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12895: for(j=1;j <=nlstate;j++){
12896: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12897: }
12898: fprintf(ficrest,"\n");
12899: }
1.208 brouard 12900: } /* End vpopbased */
1.269 brouard 12901: free_vector(epj,1,nlstate+1);
1.208 brouard 12902: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12903: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12904: printf("done selection\n");fflush(stdout);
12905: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12906:
1.235 brouard 12907: } /* End k selection */
1.227 brouard 12908:
12909: printf("done State-specific expectancies\n");fflush(stdout);
12910: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12911:
1.288 brouard 12912: /* variance-covariance of forward period prevalence*/
1.269 brouard 12913: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12914:
1.227 brouard 12915:
1.290 brouard 12916: free_vector(weight,firstobs,lastobs);
1.227 brouard 12917: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12918: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12919: free_matrix(anint,1,maxwav,firstobs,lastobs);
12920: free_matrix(mint,1,maxwav,firstobs,lastobs);
12921: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12922: free_ivector(tab,1,NCOVMAX);
12923: fclose(ficresstdeij);
12924: fclose(ficrescveij);
12925: fclose(ficresvij);
12926: fclose(ficrest);
12927: fclose(ficpar);
12928:
12929:
1.126 brouard 12930: /*---------- End : free ----------------*/
1.219 brouard 12931: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12932: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12933: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12934: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12935: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12936: } /* mle==-3 arrives here for freeing */
1.227 brouard 12937: /* endfree:*/
12938: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12939: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12940: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12941: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12942: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12943: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12944: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12945: free_matrix(matcov,1,npar,1,npar);
12946: free_matrix(hess,1,npar,1,npar);
12947: /*free_vector(delti,1,npar);*/
12948: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12949: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12950: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12951: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12952:
12953: free_ivector(ncodemax,1,NCOVMAX);
12954: free_ivector(ncodemaxwundef,1,NCOVMAX);
12955: free_ivector(Dummy,-1,NCOVMAX);
12956: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12957: free_ivector(DummyV,1,NCOVMAX);
12958: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12959: free_ivector(Typevar,-1,NCOVMAX);
12960: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12961: free_ivector(TvarsQ,1,NCOVMAX);
12962: free_ivector(TvarsQind,1,NCOVMAX);
12963: free_ivector(TvarsD,1,NCOVMAX);
12964: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12965: free_ivector(TvarFD,1,NCOVMAX);
12966: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12967: free_ivector(TvarF,1,NCOVMAX);
12968: free_ivector(TvarFind,1,NCOVMAX);
12969: free_ivector(TvarV,1,NCOVMAX);
12970: free_ivector(TvarVind,1,NCOVMAX);
12971: free_ivector(TvarA,1,NCOVMAX);
12972: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12973: free_ivector(TvarFQ,1,NCOVMAX);
12974: free_ivector(TvarFQind,1,NCOVMAX);
12975: free_ivector(TvarVD,1,NCOVMAX);
12976: free_ivector(TvarVDind,1,NCOVMAX);
12977: free_ivector(TvarVQ,1,NCOVMAX);
12978: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12979: free_ivector(Tvarsel,1,NCOVMAX);
12980: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12981: free_ivector(Tposprod,1,NCOVMAX);
12982: free_ivector(Tprod,1,NCOVMAX);
12983: free_ivector(Tvaraff,1,NCOVMAX);
12984: free_ivector(invalidvarcomb,1,ncovcombmax);
12985: free_ivector(Tage,1,NCOVMAX);
12986: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12987: free_ivector(TmodelInvind,1,NCOVMAX);
12988: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12989:
12990: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12991: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12992: fflush(fichtm);
12993: fflush(ficgp);
12994:
1.227 brouard 12995:
1.126 brouard 12996: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12997: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12998: 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 12999: }else{
13000: printf("End of Imach\n");
13001: fprintf(ficlog,"End of Imach\n");
13002: }
13003: printf("See log file on %s\n",filelog);
13004: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 13005: /*(void) gettimeofday(&end_time,&tzp);*/
13006: rend_time = time(NULL);
13007: end_time = *localtime(&rend_time);
13008: /* tml = *localtime(&end_time.tm_sec); */
13009: strcpy(strtend,asctime(&end_time));
1.126 brouard 13010: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13011: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13012: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13013:
1.157 brouard 13014: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13015: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13016: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13017: /* printf("Total time was %d uSec.\n", total_usecs);*/
13018: /* if(fileappend(fichtm,optionfilehtm)){ */
13019: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13020: fclose(fichtm);
13021: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13022: fclose(fichtmcov);
13023: fclose(ficgp);
13024: fclose(ficlog);
13025: /*------ End -----------*/
1.227 brouard 13026:
1.281 brouard 13027:
13028: /* Executes gnuplot */
1.227 brouard 13029:
13030: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13031: #ifdef WIN32
1.227 brouard 13032: if (_chdir(pathcd) != 0)
13033: printf("Can't move to directory %s!\n",path);
13034: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13035: #else
1.227 brouard 13036: if(chdir(pathcd) != 0)
13037: printf("Can't move to directory %s!\n", path);
13038: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 13039: #endif
1.126 brouard 13040: printf("Current directory %s!\n",pathcd);
13041: /*strcat(plotcmd,CHARSEPARATOR);*/
13042: sprintf(plotcmd,"gnuplot");
1.157 brouard 13043: #ifdef _WIN32
1.126 brouard 13044: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13045: #endif
13046: if(!stat(plotcmd,&info)){
1.158 brouard 13047: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13048: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13049: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13050: }else
13051: strcpy(pplotcmd,plotcmd);
1.157 brouard 13052: #ifdef __unix
1.126 brouard 13053: strcpy(plotcmd,GNUPLOTPROGRAM);
13054: if(!stat(plotcmd,&info)){
1.158 brouard 13055: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13056: }else
13057: strcpy(pplotcmd,plotcmd);
13058: #endif
13059: }else
13060: strcpy(pplotcmd,plotcmd);
13061:
13062: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13063: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13064: strcpy(pplotcmd,plotcmd);
1.227 brouard 13065:
1.126 brouard 13066: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13067: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13068: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13069: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13070: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13071: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13072: strcpy(plotcmd,pplotcmd);
13073: }
1.126 brouard 13074: }
1.158 brouard 13075: printf(" Successful, please wait...");
1.126 brouard 13076: while (z[0] != 'q') {
13077: /* chdir(path); */
1.154 brouard 13078: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13079: scanf("%s",z);
13080: /* if (z[0] == 'c') system("./imach"); */
13081: if (z[0] == 'e') {
1.158 brouard 13082: #ifdef __APPLE__
1.152 brouard 13083: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13084: #elif __linux
13085: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13086: #else
1.152 brouard 13087: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13088: #endif
13089: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13090: system(pplotcmd);
1.126 brouard 13091: }
13092: else if (z[0] == 'g') system(plotcmd);
13093: else if (z[0] == 'q') exit(0);
13094: }
1.227 brouard 13095: end:
1.126 brouard 13096: while (z[0] != 'q') {
1.195 brouard 13097: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13098: scanf("%s",z);
13099: }
1.283 brouard 13100: printf("End\n");
1.282 brouard 13101: exit(0);
1.126 brouard 13102: }
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