Annotation of imach/src/imach.c, revision 1.306
1.306 ! brouard 1: /* $Id: imach.c,v 1.305 2021/02/20 15:28:30 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.306 ! brouard 4: Revision 1.305 2021/02/20 15:28:30 brouard
! 5: * imach.c (Module): Fix bug on quitting after result lines!
! 6:
1.305 brouard 7: Revision 1.304 2021/02/12 11:34:20 brouard
8: * imach.c (Module): The use of a Windows BOM (huge) file is now an error
9:
1.304 brouard 10: Revision 1.303 2021/02/11 19:50:15 brouard
11: * (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.
12:
1.303 brouard 13: Revision 1.302 2020/02/22 21:00:05 brouard
14: * (Module): imach.c Update mle=-3 (for computing Life expectancy
15: and life table from the data without any state)
16:
1.302 brouard 17: Revision 1.301 2019/06/04 13:51:20 brouard
18: Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj
19:
1.301 brouard 20: Revision 1.300 2019/05/22 19:09:45 brouard
21: Summary: version 0.99r19 of May 2019
22:
1.300 brouard 23: Revision 1.299 2019/05/22 18:37:08 brouard
24: Summary: Cleaned 0.99r19
25:
1.299 brouard 26: Revision 1.298 2019/05/22 18:19:56 brouard
27: *** empty log message ***
28:
1.298 brouard 29: Revision 1.297 2019/05/22 17:56:10 brouard
30: Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1
31:
1.297 brouard 32: Revision 1.296 2019/05/20 13:03:18 brouard
33: Summary: Projection syntax simplified
34:
35:
36: We can now start projections, forward or backward, from the mean date
37: of inteviews up to or down to a number of years of projection:
38: prevforecast=1 yearsfproj=15.3 mobil_average=0
39: or
40: prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
41: or
42: prevbackcast=1 yearsbproj=12.3 mobil_average=1
43: or
44: prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1
45:
1.296 brouard 46: Revision 1.295 2019/05/18 09:52:50 brouard
47: Summary: doxygen tex bug
48:
1.295 brouard 49: Revision 1.294 2019/05/16 14:54:33 brouard
50: Summary: There was some wrong lines added
51:
1.294 brouard 52: Revision 1.293 2019/05/09 15:17:34 brouard
53: *** empty log message ***
54:
1.293 brouard 55: Revision 1.292 2019/05/09 14:17:20 brouard
56: Summary: Some updates
57:
1.292 brouard 58: Revision 1.291 2019/05/09 13:44:18 brouard
59: Summary: Before ncovmax
60:
1.291 brouard 61: Revision 1.290 2019/05/09 13:39:37 brouard
62: Summary: 0.99r18 unlimited number of individuals
63:
64: 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.
65:
1.290 brouard 66: Revision 1.289 2018/12/13 09:16:26 brouard
67: Summary: Bug for young ages (<-30) will be in r17
68:
1.289 brouard 69: Revision 1.288 2018/05/02 20:58:27 brouard
70: Summary: Some bugs fixed
71:
1.288 brouard 72: Revision 1.287 2018/05/01 17:57:25 brouard
73: Summary: Bug fixed by providing frequencies only for non missing covariates
74:
1.287 brouard 75: Revision 1.286 2018/04/27 14:27:04 brouard
76: Summary: some minor bugs
77:
1.286 brouard 78: Revision 1.285 2018/04/21 21:02:16 brouard
79: Summary: Some bugs fixed, valgrind tested
80:
1.285 brouard 81: Revision 1.284 2018/04/20 05:22:13 brouard
82: Summary: Computing mean and stdeviation of fixed quantitative variables
83:
1.284 brouard 84: Revision 1.283 2018/04/19 14:49:16 brouard
85: Summary: Some minor bugs fixed
86:
1.283 brouard 87: Revision 1.282 2018/02/27 22:50:02 brouard
88: *** empty log message ***
89:
1.282 brouard 90: Revision 1.281 2018/02/27 19:25:23 brouard
91: Summary: Adding second argument for quitting
92:
1.281 brouard 93: Revision 1.280 2018/02/21 07:58:13 brouard
94: Summary: 0.99r15
95:
96: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
97:
1.280 brouard 98: Revision 1.279 2017/07/20 13:35:01 brouard
99: Summary: temporary working
100:
1.279 brouard 101: Revision 1.278 2017/07/19 14:09:02 brouard
102: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
103:
1.278 brouard 104: Revision 1.277 2017/07/17 08:53:49 brouard
105: Summary: BOM files can be read now
106:
1.277 brouard 107: Revision 1.276 2017/06/30 15:48:31 brouard
108: Summary: Graphs improvements
109:
1.276 brouard 110: Revision 1.275 2017/06/30 13:39:33 brouard
111: Summary: Saito's color
112:
1.275 brouard 113: Revision 1.274 2017/06/29 09:47:08 brouard
114: Summary: Version 0.99r14
115:
1.274 brouard 116: Revision 1.273 2017/06/27 11:06:02 brouard
117: Summary: More documentation on projections
118:
1.273 brouard 119: Revision 1.272 2017/06/27 10:22:40 brouard
120: Summary: Color of backprojection changed from 6 to 5(yellow)
121:
1.272 brouard 122: Revision 1.271 2017/06/27 10:17:50 brouard
123: Summary: Some bug with rint
124:
1.271 brouard 125: Revision 1.270 2017/05/24 05:45:29 brouard
126: *** empty log message ***
127:
1.270 brouard 128: Revision 1.269 2017/05/23 08:39:25 brouard
129: Summary: Code into subroutine, cleanings
130:
1.269 brouard 131: Revision 1.268 2017/05/18 20:09:32 brouard
132: Summary: backprojection and confidence intervals of backprevalence
133:
1.268 brouard 134: Revision 1.267 2017/05/13 10:25:05 brouard
135: Summary: temporary save for backprojection
136:
1.267 brouard 137: Revision 1.266 2017/05/13 07:26:12 brouard
138: Summary: Version 0.99r13 (improvements and bugs fixed)
139:
1.266 brouard 140: Revision 1.265 2017/04/26 16:22:11 brouard
141: Summary: imach 0.99r13 Some bugs fixed
142:
1.265 brouard 143: Revision 1.264 2017/04/26 06:01:29 brouard
144: Summary: Labels in graphs
145:
1.264 brouard 146: Revision 1.263 2017/04/24 15:23:15 brouard
147: Summary: to save
148:
1.263 brouard 149: Revision 1.262 2017/04/18 16:48:12 brouard
150: *** empty log message ***
151:
1.262 brouard 152: Revision 1.261 2017/04/05 10:14:09 brouard
153: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
154:
1.261 brouard 155: Revision 1.260 2017/04/04 17:46:59 brouard
156: Summary: Gnuplot indexations fixed (humm)
157:
1.260 brouard 158: Revision 1.259 2017/04/04 13:01:16 brouard
159: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
160:
1.259 brouard 161: Revision 1.258 2017/04/03 10:17:47 brouard
162: Summary: Version 0.99r12
163:
164: Some cleanings, conformed with updated documentation.
165:
1.258 brouard 166: Revision 1.257 2017/03/29 16:53:30 brouard
167: Summary: Temp
168:
1.257 brouard 169: Revision 1.256 2017/03/27 05:50:23 brouard
170: Summary: Temporary
171:
1.256 brouard 172: Revision 1.255 2017/03/08 16:02:28 brouard
173: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
174:
1.255 brouard 175: Revision 1.254 2017/03/08 07:13:00 brouard
176: Summary: Fixing data parameter line
177:
1.254 brouard 178: Revision 1.253 2016/12/15 11:59:41 brouard
179: Summary: 0.99 in progress
180:
1.253 brouard 181: Revision 1.252 2016/09/15 21:15:37 brouard
182: *** empty log message ***
183:
1.252 brouard 184: Revision 1.251 2016/09/15 15:01:13 brouard
185: Summary: not working
186:
1.251 brouard 187: Revision 1.250 2016/09/08 16:07:27 brouard
188: Summary: continue
189:
1.250 brouard 190: Revision 1.249 2016/09/07 17:14:18 brouard
191: Summary: Starting values from frequencies
192:
1.249 brouard 193: Revision 1.248 2016/09/07 14:10:18 brouard
194: *** empty log message ***
195:
1.248 brouard 196: Revision 1.247 2016/09/02 11:11:21 brouard
197: *** empty log message ***
198:
1.247 brouard 199: Revision 1.246 2016/09/02 08:49:22 brouard
200: *** empty log message ***
201:
1.246 brouard 202: Revision 1.245 2016/09/02 07:25:01 brouard
203: *** empty log message ***
204:
1.245 brouard 205: Revision 1.244 2016/09/02 07:17:34 brouard
206: *** empty log message ***
207:
1.244 brouard 208: Revision 1.243 2016/09/02 06:45:35 brouard
209: *** empty log message ***
210:
1.243 brouard 211: Revision 1.242 2016/08/30 15:01:20 brouard
212: Summary: Fixing a lots
213:
1.242 brouard 214: Revision 1.241 2016/08/29 17:17:25 brouard
215: Summary: gnuplot problem in Back projection to fix
216:
1.241 brouard 217: Revision 1.240 2016/08/29 07:53:18 brouard
218: Summary: Better
219:
1.240 brouard 220: Revision 1.239 2016/08/26 15:51:03 brouard
221: Summary: Improvement in Powell output in order to copy and paste
222:
223: Author:
224:
1.239 brouard 225: Revision 1.238 2016/08/26 14:23:35 brouard
226: Summary: Starting tests of 0.99
227:
1.238 brouard 228: Revision 1.237 2016/08/26 09:20:19 brouard
229: Summary: to valgrind
230:
1.237 brouard 231: Revision 1.236 2016/08/25 10:50:18 brouard
232: *** empty log message ***
233:
1.236 brouard 234: Revision 1.235 2016/08/25 06:59:23 brouard
235: *** empty log message ***
236:
1.235 brouard 237: Revision 1.234 2016/08/23 16:51:20 brouard
238: *** empty log message ***
239:
1.234 brouard 240: Revision 1.233 2016/08/23 07:40:50 brouard
241: Summary: not working
242:
1.233 brouard 243: Revision 1.232 2016/08/22 14:20:21 brouard
244: Summary: not working
245:
1.232 brouard 246: Revision 1.231 2016/08/22 07:17:15 brouard
247: Summary: not working
248:
1.231 brouard 249: Revision 1.230 2016/08/22 06:55:53 brouard
250: Summary: Not working
251:
1.230 brouard 252: Revision 1.229 2016/07/23 09:45:53 brouard
253: Summary: Completing for func too
254:
1.229 brouard 255: Revision 1.228 2016/07/22 17:45:30 brouard
256: Summary: Fixing some arrays, still debugging
257:
1.227 brouard 258: Revision 1.226 2016/07/12 18:42:34 brouard
259: Summary: temp
260:
1.226 brouard 261: Revision 1.225 2016/07/12 08:40:03 brouard
262: Summary: saving but not running
263:
1.225 brouard 264: Revision 1.224 2016/07/01 13:16:01 brouard
265: Summary: Fixes
266:
1.224 brouard 267: Revision 1.223 2016/02/19 09:23:35 brouard
268: Summary: temporary
269:
1.223 brouard 270: Revision 1.222 2016/02/17 08:14:50 brouard
271: Summary: Probably last 0.98 stable version 0.98r6
272:
1.222 brouard 273: Revision 1.221 2016/02/15 23:35:36 brouard
274: Summary: minor bug
275:
1.220 brouard 276: Revision 1.219 2016/02/15 00:48:12 brouard
277: *** empty log message ***
278:
1.219 brouard 279: Revision 1.218 2016/02/12 11:29:23 brouard
280: Summary: 0.99 Back projections
281:
1.218 brouard 282: Revision 1.217 2015/12/23 17:18:31 brouard
283: Summary: Experimental backcast
284:
1.217 brouard 285: Revision 1.216 2015/12/18 17:32:11 brouard
286: Summary: 0.98r4 Warning and status=-2
287:
288: Version 0.98r4 is now:
289: - displaying an error when status is -1, date of interview unknown and date of death known;
290: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
291: Older changes concerning s=-2, dating from 2005 have been supersed.
292:
1.216 brouard 293: Revision 1.215 2015/12/16 08:52:24 brouard
294: Summary: 0.98r4 working
295:
1.215 brouard 296: Revision 1.214 2015/12/16 06:57:54 brouard
297: Summary: temporary not working
298:
1.214 brouard 299: Revision 1.213 2015/12/11 18:22:17 brouard
300: Summary: 0.98r4
301:
1.213 brouard 302: Revision 1.212 2015/11/21 12:47:24 brouard
303: Summary: minor typo
304:
1.212 brouard 305: Revision 1.211 2015/11/21 12:41:11 brouard
306: Summary: 0.98r3 with some graph of projected cross-sectional
307:
308: Author: Nicolas Brouard
309:
1.211 brouard 310: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 311: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 312: Summary: Adding ftolpl parameter
313: Author: N Brouard
314:
315: We had difficulties to get smoothed confidence intervals. It was due
316: to the period prevalence which wasn't computed accurately. The inner
317: parameter ftolpl is now an outer parameter of the .imach parameter
318: file after estepm. If ftolpl is small 1.e-4 and estepm too,
319: computation are long.
320:
1.209 brouard 321: Revision 1.208 2015/11/17 14:31:57 brouard
322: Summary: temporary
323:
1.208 brouard 324: Revision 1.207 2015/10/27 17:36:57 brouard
325: *** empty log message ***
326:
1.207 brouard 327: Revision 1.206 2015/10/24 07:14:11 brouard
328: *** empty log message ***
329:
1.206 brouard 330: Revision 1.205 2015/10/23 15:50:53 brouard
331: Summary: 0.98r3 some clarification for graphs on likelihood contributions
332:
1.205 brouard 333: Revision 1.204 2015/10/01 16:20:26 brouard
334: Summary: Some new graphs of contribution to likelihood
335:
1.204 brouard 336: Revision 1.203 2015/09/30 17:45:14 brouard
337: Summary: looking at better estimation of the hessian
338:
339: Also a better criteria for convergence to the period prevalence And
340: therefore adding the number of years needed to converge. (The
341: prevalence in any alive state shold sum to one
342:
1.203 brouard 343: Revision 1.202 2015/09/22 19:45:16 brouard
344: Summary: Adding some overall graph on contribution to likelihood. Might change
345:
1.202 brouard 346: Revision 1.201 2015/09/15 17:34:58 brouard
347: Summary: 0.98r0
348:
349: - Some new graphs like suvival functions
350: - Some bugs fixed like model=1+age+V2.
351:
1.201 brouard 352: Revision 1.200 2015/09/09 16:53:55 brouard
353: Summary: Big bug thanks to Flavia
354:
355: Even model=1+age+V2. did not work anymore
356:
1.200 brouard 357: Revision 1.199 2015/09/07 14:09:23 brouard
358: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
359:
1.199 brouard 360: Revision 1.198 2015/09/03 07:14:39 brouard
361: Summary: 0.98q5 Flavia
362:
1.198 brouard 363: Revision 1.197 2015/09/01 18:24:39 brouard
364: *** empty log message ***
365:
1.197 brouard 366: Revision 1.196 2015/08/18 23:17:52 brouard
367: Summary: 0.98q5
368:
1.196 brouard 369: Revision 1.195 2015/08/18 16:28:39 brouard
370: Summary: Adding a hack for testing purpose
371:
372: After reading the title, ftol and model lines, if the comment line has
373: a q, starting with #q, the answer at the end of the run is quit. It
374: permits to run test files in batch with ctest. The former workaround was
375: $ echo q | imach foo.imach
376:
1.195 brouard 377: Revision 1.194 2015/08/18 13:32:00 brouard
378: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
379:
1.194 brouard 380: Revision 1.193 2015/08/04 07:17:42 brouard
381: Summary: 0.98q4
382:
1.193 brouard 383: Revision 1.192 2015/07/16 16:49:02 brouard
384: Summary: Fixing some outputs
385:
1.192 brouard 386: Revision 1.191 2015/07/14 10:00:33 brouard
387: Summary: Some fixes
388:
1.191 brouard 389: Revision 1.190 2015/05/05 08:51:13 brouard
390: Summary: Adding digits in output parameters (7 digits instead of 6)
391:
392: Fix 1+age+.
393:
1.190 brouard 394: Revision 1.189 2015/04/30 14:45:16 brouard
395: Summary: 0.98q2
396:
1.189 brouard 397: Revision 1.188 2015/04/30 08:27:53 brouard
398: *** empty log message ***
399:
1.188 brouard 400: Revision 1.187 2015/04/29 09:11:15 brouard
401: *** empty log message ***
402:
1.187 brouard 403: Revision 1.186 2015/04/23 12:01:52 brouard
404: Summary: V1*age is working now, version 0.98q1
405:
406: Some codes had been disabled in order to simplify and Vn*age was
407: working in the optimization phase, ie, giving correct MLE parameters,
408: but, as usual, outputs were not correct and program core dumped.
409:
1.186 brouard 410: Revision 1.185 2015/03/11 13:26:42 brouard
411: Summary: Inclusion of compile and links command line for Intel Compiler
412:
1.185 brouard 413: Revision 1.184 2015/03/11 11:52:39 brouard
414: Summary: Back from Windows 8. Intel Compiler
415:
1.184 brouard 416: Revision 1.183 2015/03/10 20:34:32 brouard
417: Summary: 0.98q0, trying with directest, mnbrak fixed
418:
419: We use directest instead of original Powell test; probably no
420: incidence on the results, but better justifications;
421: We fixed Numerical Recipes mnbrak routine which was wrong and gave
422: wrong results.
423:
1.183 brouard 424: Revision 1.182 2015/02/12 08:19:57 brouard
425: Summary: Trying to keep directest which seems simpler and more general
426: Author: Nicolas Brouard
427:
1.182 brouard 428: Revision 1.181 2015/02/11 23:22:24 brouard
429: Summary: Comments on Powell added
430:
431: Author:
432:
1.181 brouard 433: Revision 1.180 2015/02/11 17:33:45 brouard
434: Summary: Finishing move from main to function (hpijx and prevalence_limit)
435:
1.180 brouard 436: Revision 1.179 2015/01/04 09:57:06 brouard
437: Summary: back to OS/X
438:
1.179 brouard 439: Revision 1.178 2015/01/04 09:35:48 brouard
440: *** empty log message ***
441:
1.178 brouard 442: Revision 1.177 2015/01/03 18:40:56 brouard
443: Summary: Still testing ilc32 on OSX
444:
1.177 brouard 445: Revision 1.176 2015/01/03 16:45:04 brouard
446: *** empty log message ***
447:
1.176 brouard 448: Revision 1.175 2015/01/03 16:33:42 brouard
449: *** empty log message ***
450:
1.175 brouard 451: Revision 1.174 2015/01/03 16:15:49 brouard
452: Summary: Still in cross-compilation
453:
1.174 brouard 454: Revision 1.173 2015/01/03 12:06:26 brouard
455: Summary: trying to detect cross-compilation
456:
1.173 brouard 457: Revision 1.172 2014/12/27 12:07:47 brouard
458: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
459:
1.172 brouard 460: Revision 1.171 2014/12/23 13:26:59 brouard
461: Summary: Back from Visual C
462:
463: Still problem with utsname.h on Windows
464:
1.171 brouard 465: Revision 1.170 2014/12/23 11:17:12 brouard
466: Summary: Cleaning some \%% back to %%
467:
468: The escape was mandatory for a specific compiler (which one?), but too many warnings.
469:
1.170 brouard 470: Revision 1.169 2014/12/22 23:08:31 brouard
471: Summary: 0.98p
472:
473: Outputs some informations on compiler used, OS etc. Testing on different platforms.
474:
1.169 brouard 475: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 476: Summary: update
1.169 brouard 477:
1.168 brouard 478: Revision 1.167 2014/12/22 13:50:56 brouard
479: Summary: Testing uname and compiler version and if compiled 32 or 64
480:
481: Testing on Linux 64
482:
1.167 brouard 483: Revision 1.166 2014/12/22 11:40:47 brouard
484: *** empty log message ***
485:
1.166 brouard 486: Revision 1.165 2014/12/16 11:20:36 brouard
487: Summary: After compiling on Visual C
488:
489: * imach.c (Module): Merging 1.61 to 1.162
490:
1.165 brouard 491: Revision 1.164 2014/12/16 10:52:11 brouard
492: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
493:
494: * imach.c (Module): Merging 1.61 to 1.162
495:
1.164 brouard 496: Revision 1.163 2014/12/16 10:30:11 brouard
497: * imach.c (Module): Merging 1.61 to 1.162
498:
1.163 brouard 499: Revision 1.162 2014/09/25 11:43:39 brouard
500: Summary: temporary backup 0.99!
501:
1.162 brouard 502: Revision 1.1 2014/09/16 11:06:58 brouard
503: Summary: With some code (wrong) for nlopt
504:
505: Author:
506:
507: Revision 1.161 2014/09/15 20:41:41 brouard
508: Summary: Problem with macro SQR on Intel compiler
509:
1.161 brouard 510: Revision 1.160 2014/09/02 09:24:05 brouard
511: *** empty log message ***
512:
1.160 brouard 513: Revision 1.159 2014/09/01 10:34:10 brouard
514: Summary: WIN32
515: Author: Brouard
516:
1.159 brouard 517: Revision 1.158 2014/08/27 17:11:51 brouard
518: *** empty log message ***
519:
1.158 brouard 520: Revision 1.157 2014/08/27 16:26:55 brouard
521: Summary: Preparing windows Visual studio version
522: Author: Brouard
523:
524: In order to compile on Visual studio, time.h is now correct and time_t
525: and tm struct should be used. difftime should be used but sometimes I
526: just make the differences in raw time format (time(&now).
527: Trying to suppress #ifdef LINUX
528: Add xdg-open for __linux in order to open default browser.
529:
1.157 brouard 530: Revision 1.156 2014/08/25 20:10:10 brouard
531: *** empty log message ***
532:
1.156 brouard 533: Revision 1.155 2014/08/25 18:32:34 brouard
534: Summary: New compile, minor changes
535: Author: Brouard
536:
1.155 brouard 537: Revision 1.154 2014/06/20 17:32:08 brouard
538: Summary: Outputs now all graphs of convergence to period prevalence
539:
1.154 brouard 540: Revision 1.153 2014/06/20 16:45:46 brouard
541: Summary: If 3 live state, convergence to period prevalence on same graph
542: Author: Brouard
543:
1.153 brouard 544: Revision 1.152 2014/06/18 17:54:09 brouard
545: Summary: open browser, use gnuplot on same dir than imach if not found in the path
546:
1.152 brouard 547: Revision 1.151 2014/06/18 16:43:30 brouard
548: *** empty log message ***
549:
1.151 brouard 550: Revision 1.150 2014/06/18 16:42:35 brouard
551: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
552: Author: brouard
553:
1.150 brouard 554: Revision 1.149 2014/06/18 15:51:14 brouard
555: Summary: Some fixes in parameter files errors
556: Author: Nicolas Brouard
557:
1.149 brouard 558: Revision 1.148 2014/06/17 17:38:48 brouard
559: Summary: Nothing new
560: Author: Brouard
561:
562: Just a new packaging for OS/X version 0.98nS
563:
1.148 brouard 564: Revision 1.147 2014/06/16 10:33:11 brouard
565: *** empty log message ***
566:
1.147 brouard 567: Revision 1.146 2014/06/16 10:20:28 brouard
568: Summary: Merge
569: Author: Brouard
570:
571: Merge, before building revised version.
572:
1.146 brouard 573: Revision 1.145 2014/06/10 21:23:15 brouard
574: Summary: Debugging with valgrind
575: Author: Nicolas Brouard
576:
577: Lot of changes in order to output the results with some covariates
578: After the Edimburgh REVES conference 2014, it seems mandatory to
579: improve the code.
580: No more memory valgrind error but a lot has to be done in order to
581: continue the work of splitting the code into subroutines.
582: Also, decodemodel has been improved. Tricode is still not
583: optimal. nbcode should be improved. Documentation has been added in
584: the source code.
585:
1.144 brouard 586: Revision 1.143 2014/01/26 09:45:38 brouard
587: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
588:
589: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
590: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
591:
1.143 brouard 592: Revision 1.142 2014/01/26 03:57:36 brouard
593: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
594:
595: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
596:
1.142 brouard 597: Revision 1.141 2014/01/26 02:42:01 brouard
598: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
599:
1.141 brouard 600: Revision 1.140 2011/09/02 10:37:54 brouard
601: Summary: times.h is ok with mingw32 now.
602:
1.140 brouard 603: Revision 1.139 2010/06/14 07:50:17 brouard
604: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
605: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
606:
1.139 brouard 607: Revision 1.138 2010/04/30 18:19:40 brouard
608: *** empty log message ***
609:
1.138 brouard 610: Revision 1.137 2010/04/29 18:11:38 brouard
611: (Module): Checking covariates for more complex models
612: than V1+V2. A lot of change to be done. Unstable.
613:
1.137 brouard 614: Revision 1.136 2010/04/26 20:30:53 brouard
615: (Module): merging some libgsl code. Fixing computation
616: of likelione (using inter/intrapolation if mle = 0) in order to
617: get same likelihood as if mle=1.
618: Some cleaning of code and comments added.
619:
1.136 brouard 620: Revision 1.135 2009/10/29 15:33:14 brouard
621: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
622:
1.135 brouard 623: Revision 1.134 2009/10/29 13:18:53 brouard
624: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
625:
1.134 brouard 626: Revision 1.133 2009/07/06 10:21:25 brouard
627: just nforces
628:
1.133 brouard 629: Revision 1.132 2009/07/06 08:22:05 brouard
630: Many tings
631:
1.132 brouard 632: Revision 1.131 2009/06/20 16:22:47 brouard
633: Some dimensions resccaled
634:
1.131 brouard 635: Revision 1.130 2009/05/26 06:44:34 brouard
636: (Module): Max Covariate is now set to 20 instead of 8. A
637: lot of cleaning with variables initialized to 0. Trying to make
638: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
639:
1.130 brouard 640: Revision 1.129 2007/08/31 13:49:27 lievre
641: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
642:
1.129 lievre 643: Revision 1.128 2006/06/30 13:02:05 brouard
644: (Module): Clarifications on computing e.j
645:
1.128 brouard 646: Revision 1.127 2006/04/28 18:11:50 brouard
647: (Module): Yes the sum of survivors was wrong since
648: imach-114 because nhstepm was no more computed in the age
649: loop. Now we define nhstepma in the age loop.
650: (Module): In order to speed up (in case of numerous covariates) we
651: compute health expectancies (without variances) in a first step
652: and then all the health expectancies with variances or standard
653: deviation (needs data from the Hessian matrices) which slows the
654: computation.
655: In the future we should be able to stop the program is only health
656: expectancies and graph are needed without standard deviations.
657:
1.127 brouard 658: Revision 1.126 2006/04/28 17:23:28 brouard
659: (Module): Yes the sum of survivors was wrong since
660: imach-114 because nhstepm was no more computed in the age
661: loop. Now we define nhstepma in the age loop.
662: Version 0.98h
663:
1.126 brouard 664: Revision 1.125 2006/04/04 15:20:31 lievre
665: Errors in calculation of health expectancies. Age was not initialized.
666: Forecasting file added.
667:
668: Revision 1.124 2006/03/22 17:13:53 lievre
669: Parameters are printed with %lf instead of %f (more numbers after the comma).
670: The log-likelihood is printed in the log file
671:
672: Revision 1.123 2006/03/20 10:52:43 brouard
673: * imach.c (Module): <title> changed, corresponds to .htm file
674: name. <head> headers where missing.
675:
676: * imach.c (Module): Weights can have a decimal point as for
677: English (a comma might work with a correct LC_NUMERIC environment,
678: otherwise the weight is truncated).
679: Modification of warning when the covariates values are not 0 or
680: 1.
681: Version 0.98g
682:
683: Revision 1.122 2006/03/20 09:45:41 brouard
684: (Module): Weights can have a decimal point as for
685: English (a comma might work with a correct LC_NUMERIC environment,
686: otherwise the weight is truncated).
687: Modification of warning when the covariates values are not 0 or
688: 1.
689: Version 0.98g
690:
691: Revision 1.121 2006/03/16 17:45:01 lievre
692: * imach.c (Module): Comments concerning covariates added
693:
694: * imach.c (Module): refinements in the computation of lli if
695: status=-2 in order to have more reliable computation if stepm is
696: not 1 month. Version 0.98f
697:
698: Revision 1.120 2006/03/16 15:10:38 lievre
699: (Module): refinements in the computation of lli if
700: status=-2 in order to have more reliable computation if stepm is
701: not 1 month. Version 0.98f
702:
703: Revision 1.119 2006/03/15 17:42:26 brouard
704: (Module): Bug if status = -2, the loglikelihood was
705: computed as likelihood omitting the logarithm. Version O.98e
706:
707: Revision 1.118 2006/03/14 18:20:07 brouard
708: (Module): varevsij Comments added explaining the second
709: table of variances if popbased=1 .
710: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
711: (Module): Function pstamp added
712: (Module): Version 0.98d
713:
714: Revision 1.117 2006/03/14 17:16:22 brouard
715: (Module): varevsij Comments added explaining the second
716: table of variances if popbased=1 .
717: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
718: (Module): Function pstamp added
719: (Module): Version 0.98d
720:
721: Revision 1.116 2006/03/06 10:29:27 brouard
722: (Module): Variance-covariance wrong links and
723: varian-covariance of ej. is needed (Saito).
724:
725: Revision 1.115 2006/02/27 12:17:45 brouard
726: (Module): One freematrix added in mlikeli! 0.98c
727:
728: Revision 1.114 2006/02/26 12:57:58 brouard
729: (Module): Some improvements in processing parameter
730: filename with strsep.
731:
732: Revision 1.113 2006/02/24 14:20:24 brouard
733: (Module): Memory leaks checks with valgrind and:
734: datafile was not closed, some imatrix were not freed and on matrix
735: allocation too.
736:
737: Revision 1.112 2006/01/30 09:55:26 brouard
738: (Module): Back to gnuplot.exe instead of wgnuplot.exe
739:
740: Revision 1.111 2006/01/25 20:38:18 brouard
741: (Module): Lots of cleaning and bugs added (Gompertz)
742: (Module): Comments can be added in data file. Missing date values
743: can be a simple dot '.'.
744:
745: Revision 1.110 2006/01/25 00:51:50 brouard
746: (Module): Lots of cleaning and bugs added (Gompertz)
747:
748: Revision 1.109 2006/01/24 19:37:15 brouard
749: (Module): Comments (lines starting with a #) are allowed in data.
750:
751: Revision 1.108 2006/01/19 18:05:42 lievre
752: Gnuplot problem appeared...
753: To be fixed
754:
755: Revision 1.107 2006/01/19 16:20:37 brouard
756: Test existence of gnuplot in imach path
757:
758: Revision 1.106 2006/01/19 13:24:36 brouard
759: Some cleaning and links added in html output
760:
761: Revision 1.105 2006/01/05 20:23:19 lievre
762: *** empty log message ***
763:
764: Revision 1.104 2005/09/30 16:11:43 lievre
765: (Module): sump fixed, loop imx fixed, and simplifications.
766: (Module): If the status is missing at the last wave but we know
767: that the person is alive, then we can code his/her status as -2
768: (instead of missing=-1 in earlier versions) and his/her
769: contributions to the likelihood is 1 - Prob of dying from last
770: health status (= 1-p13= p11+p12 in the easiest case of somebody in
771: the healthy state at last known wave). Version is 0.98
772:
773: Revision 1.103 2005/09/30 15:54:49 lievre
774: (Module): sump fixed, loop imx fixed, and simplifications.
775:
776: Revision 1.102 2004/09/15 17:31:30 brouard
777: Add the possibility to read data file including tab characters.
778:
779: Revision 1.101 2004/09/15 10:38:38 brouard
780: Fix on curr_time
781:
782: Revision 1.100 2004/07/12 18:29:06 brouard
783: Add version for Mac OS X. Just define UNIX in Makefile
784:
785: Revision 1.99 2004/06/05 08:57:40 brouard
786: *** empty log message ***
787:
788: Revision 1.98 2004/05/16 15:05:56 brouard
789: New version 0.97 . First attempt to estimate force of mortality
790: directly from the data i.e. without the need of knowing the health
791: state at each age, but using a Gompertz model: log u =a + b*age .
792: This is the basic analysis of mortality and should be done before any
793: other analysis, in order to test if the mortality estimated from the
794: cross-longitudinal survey is different from the mortality estimated
795: from other sources like vital statistic data.
796:
797: The same imach parameter file can be used but the option for mle should be -3.
798:
1.133 brouard 799: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 800: former routines in order to include the new code within the former code.
801:
802: The output is very simple: only an estimate of the intercept and of
803: the slope with 95% confident intervals.
804:
805: Current limitations:
806: A) Even if you enter covariates, i.e. with the
807: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
808: B) There is no computation of Life Expectancy nor Life Table.
809:
810: Revision 1.97 2004/02/20 13:25:42 lievre
811: Version 0.96d. Population forecasting command line is (temporarily)
812: suppressed.
813:
814: Revision 1.96 2003/07/15 15:38:55 brouard
815: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
816: rewritten within the same printf. Workaround: many printfs.
817:
818: Revision 1.95 2003/07/08 07:54:34 brouard
819: * imach.c (Repository):
820: (Repository): Using imachwizard code to output a more meaningful covariance
821: matrix (cov(a12,c31) instead of numbers.
822:
823: Revision 1.94 2003/06/27 13:00:02 brouard
824: Just cleaning
825:
826: Revision 1.93 2003/06/25 16:33:55 brouard
827: (Module): On windows (cygwin) function asctime_r doesn't
828: exist so I changed back to asctime which exists.
829: (Module): Version 0.96b
830:
831: Revision 1.92 2003/06/25 16:30:45 brouard
832: (Module): On windows (cygwin) function asctime_r doesn't
833: exist so I changed back to asctime which exists.
834:
835: Revision 1.91 2003/06/25 15:30:29 brouard
836: * imach.c (Repository): Duplicated warning errors corrected.
837: (Repository): Elapsed time after each iteration is now output. It
838: helps to forecast when convergence will be reached. Elapsed time
839: is stamped in powell. We created a new html file for the graphs
840: concerning matrix of covariance. It has extension -cov.htm.
841:
842: Revision 1.90 2003/06/24 12:34:15 brouard
843: (Module): Some bugs corrected for windows. Also, when
844: mle=-1 a template is output in file "or"mypar.txt with the design
845: of the covariance matrix to be input.
846:
847: Revision 1.89 2003/06/24 12:30:52 brouard
848: (Module): Some bugs corrected for windows. Also, when
849: mle=-1 a template is output in file "or"mypar.txt with the design
850: of the covariance matrix to be input.
851:
852: Revision 1.88 2003/06/23 17:54:56 brouard
853: * 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.
854:
855: Revision 1.87 2003/06/18 12:26:01 brouard
856: Version 0.96
857:
858: Revision 1.86 2003/06/17 20:04:08 brouard
859: (Module): Change position of html and gnuplot routines and added
860: routine fileappend.
861:
862: Revision 1.85 2003/06/17 13:12:43 brouard
863: * imach.c (Repository): Check when date of death was earlier that
864: current date of interview. It may happen when the death was just
865: prior to the death. In this case, dh was negative and likelihood
866: was wrong (infinity). We still send an "Error" but patch by
867: assuming that the date of death was just one stepm after the
868: interview.
869: (Repository): Because some people have very long ID (first column)
870: we changed int to long in num[] and we added a new lvector for
871: memory allocation. But we also truncated to 8 characters (left
872: truncation)
873: (Repository): No more line truncation errors.
874:
875: Revision 1.84 2003/06/13 21:44:43 brouard
876: * imach.c (Repository): Replace "freqsummary" at a correct
877: place. It differs from routine "prevalence" which may be called
878: many times. Probs is memory consuming and must be used with
879: parcimony.
880: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
881:
882: Revision 1.83 2003/06/10 13:39:11 lievre
883: *** empty log message ***
884:
885: Revision 1.82 2003/06/05 15:57:20 brouard
886: Add log in imach.c and fullversion number is now printed.
887:
888: */
889: /*
890: Interpolated Markov Chain
891:
892: Short summary of the programme:
893:
1.227 brouard 894: This program computes Healthy Life Expectancies or State-specific
895: (if states aren't health statuses) Expectancies from
896: cross-longitudinal data. Cross-longitudinal data consist in:
897:
898: -1- a first survey ("cross") where individuals from different ages
899: are interviewed on their health status or degree of disability (in
900: the case of a health survey which is our main interest)
901:
902: -2- at least a second wave of interviews ("longitudinal") which
903: measure each change (if any) in individual health status. Health
904: expectancies are computed from the time spent in each health state
905: according to a model. More health states you consider, more time is
906: necessary to reach the Maximum Likelihood of the parameters involved
907: in the model. The simplest model is the multinomial logistic model
908: where pij is the probability to be observed in state j at the second
909: wave conditional to be observed in state i at the first
910: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
911: etc , where 'age' is age and 'sex' is a covariate. If you want to
912: have a more complex model than "constant and age", you should modify
913: the program where the markup *Covariates have to be included here
914: again* invites you to do it. More covariates you add, slower the
1.126 brouard 915: convergence.
916:
917: The advantage of this computer programme, compared to a simple
918: multinomial logistic model, is clear when the delay between waves is not
919: identical for each individual. Also, if a individual missed an
920: intermediate interview, the information is lost, but taken into
921: account using an interpolation or extrapolation.
922:
923: hPijx is the probability to be observed in state i at age x+h
924: conditional to the observed state i at age x. The delay 'h' can be
925: split into an exact number (nh*stepm) of unobserved intermediate
926: states. This elementary transition (by month, quarter,
927: semester or year) is modelled as a multinomial logistic. The hPx
928: matrix is simply the matrix product of nh*stepm elementary matrices
929: and the contribution of each individual to the likelihood is simply
930: hPijx.
931:
932: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 933: of the life expectancies. It also computes the period (stable) prevalence.
934:
935: Back prevalence and projections:
1.227 brouard 936:
937: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
938: double agemaxpar, double ftolpl, int *ncvyearp, double
939: dateprev1,double dateprev2, int firstpass, int lastpass, int
940: mobilavproj)
941:
942: Computes the back prevalence limit for any combination of
943: covariate values k at any age between ageminpar and agemaxpar and
944: returns it in **bprlim. In the loops,
945:
946: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
947: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
948:
949: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 950: Computes for any combination of covariates k and any age between bage and fage
951: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
952: oldm=oldms;savm=savms;
1.227 brouard 953:
1.267 brouard 954: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 955: Computes the transition matrix starting at age 'age' over
956: 'nhstepm*hstepm*stepm' months (i.e. until
957: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 958: nhstepm*hstepm matrices.
959:
960: Returns p3mat[i][j][h] after calling
961: p3mat[i][j][h]=matprod2(newm,
962: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
963: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
964: oldm);
1.226 brouard 965:
966: Important routines
967:
968: - func (or funcone), computes logit (pij) distinguishing
969: o fixed variables (single or product dummies or quantitative);
970: o varying variables by:
971: (1) wave (single, product dummies, quantitative),
972: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
973: % fixed dummy (treated) or quantitative (not done because time-consuming);
974: % varying dummy (not done) or quantitative (not done);
975: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
976: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
977: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
978: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
979: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 980:
1.226 brouard 981:
982:
1.133 brouard 983: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
984: Institut national d'études démographiques, Paris.
1.126 brouard 985: This software have been partly granted by Euro-REVES, a concerted action
986: from the European Union.
987: It is copyrighted identically to a GNU software product, ie programme and
988: software can be distributed freely for non commercial use. Latest version
989: can be accessed at http://euroreves.ined.fr/imach .
990:
991: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
992: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
993:
994: **********************************************************************/
995: /*
996: main
997: read parameterfile
998: read datafile
999: concatwav
1000: freqsummary
1001: if (mle >= 1)
1002: mlikeli
1003: print results files
1004: if mle==1
1005: computes hessian
1006: read end of parameter file: agemin, agemax, bage, fage, estepm
1007: begin-prev-date,...
1008: open gnuplot file
1009: open html file
1.145 brouard 1010: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
1011: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
1012: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
1013: freexexit2 possible for memory heap.
1014:
1015: h Pij x | pij_nom ficrestpij
1016: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
1017: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
1018: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
1019:
1020: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
1021: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
1022: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
1023: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
1024: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
1025:
1.126 brouard 1026: forecasting if prevfcast==1 prevforecast call prevalence()
1027: health expectancies
1028: Variance-covariance of DFLE
1029: prevalence()
1030: movingaverage()
1031: varevsij()
1032: if popbased==1 varevsij(,popbased)
1033: total life expectancies
1034: Variance of period (stable) prevalence
1035: end
1036: */
1037:
1.187 brouard 1038: /* #define DEBUG */
1039: /* #define DEBUGBRENT */
1.203 brouard 1040: /* #define DEBUGLINMIN */
1041: /* #define DEBUGHESS */
1042: #define DEBUGHESSIJ
1.224 brouard 1043: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 1044: #define POWELL /* Instead of NLOPT */
1.224 brouard 1045: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 1046: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
1047: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 1048:
1049: #include <math.h>
1050: #include <stdio.h>
1051: #include <stdlib.h>
1052: #include <string.h>
1.226 brouard 1053: #include <ctype.h>
1.159 brouard 1054:
1055: #ifdef _WIN32
1056: #include <io.h>
1.172 brouard 1057: #include <windows.h>
1058: #include <tchar.h>
1.159 brouard 1059: #else
1.126 brouard 1060: #include <unistd.h>
1.159 brouard 1061: #endif
1.126 brouard 1062:
1063: #include <limits.h>
1064: #include <sys/types.h>
1.171 brouard 1065:
1066: #if defined(__GNUC__)
1067: #include <sys/utsname.h> /* Doesn't work on Windows */
1068: #endif
1069:
1.126 brouard 1070: #include <sys/stat.h>
1071: #include <errno.h>
1.159 brouard 1072: /* extern int errno; */
1.126 brouard 1073:
1.157 brouard 1074: /* #ifdef LINUX */
1075: /* #include <time.h> */
1076: /* #include "timeval.h" */
1077: /* #else */
1078: /* #include <sys/time.h> */
1079: /* #endif */
1080:
1.126 brouard 1081: #include <time.h>
1082:
1.136 brouard 1083: #ifdef GSL
1084: #include <gsl/gsl_errno.h>
1085: #include <gsl/gsl_multimin.h>
1086: #endif
1087:
1.167 brouard 1088:
1.162 brouard 1089: #ifdef NLOPT
1090: #include <nlopt.h>
1091: typedef struct {
1092: double (* function)(double [] );
1093: } myfunc_data ;
1094: #endif
1095:
1.126 brouard 1096: /* #include <libintl.h> */
1097: /* #define _(String) gettext (String) */
1098:
1.251 brouard 1099: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1100:
1101: #define GNUPLOTPROGRAM "gnuplot"
1102: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1103: #define FILENAMELENGTH 132
1104:
1105: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1106: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1107:
1.144 brouard 1108: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1109: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1110:
1111: #define NINTERVMAX 8
1.144 brouard 1112: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1113: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1.291 brouard 1114: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1115: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1116: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1117: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.290 brouard 1118: /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
1.144 brouard 1119: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1120: /* #define AGESUP 130 */
1.288 brouard 1121: /* #define AGESUP 150 */
1122: #define AGESUP 200
1.268 brouard 1123: #define AGEINF 0
1.218 brouard 1124: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1125: #define AGEBASE 40
1.194 brouard 1126: #define AGEOVERFLOW 1.e20
1.164 brouard 1127: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1128: #ifdef _WIN32
1129: #define DIRSEPARATOR '\\'
1130: #define CHARSEPARATOR "\\"
1131: #define ODIRSEPARATOR '/'
1132: #else
1.126 brouard 1133: #define DIRSEPARATOR '/'
1134: #define CHARSEPARATOR "/"
1135: #define ODIRSEPARATOR '\\'
1136: #endif
1137:
1.306 ! brouard 1138: /* $Id: imach.c,v 1.305 2021/02/20 15:28:30 brouard Exp $ */
1.126 brouard 1139: /* $State: Exp $ */
1.196 brouard 1140: #include "version.h"
1141: char version[]=__IMACH_VERSION__;
1.306 ! brouard 1142: char copyright[]="Feb 2021,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, INED 2000-2021";
! 1143: char fullversion[]="$Revision: 1.305 $ $Date: 2021/02/20 15:28:30 $";
1.126 brouard 1144: char strstart[80];
1145: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1146: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1147: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1148: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1149: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1150: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1151: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1152: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1153: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1154: int cptcovprodnoage=0; /**< Number of covariate products without age */
1155: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1156: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1157: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1158: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1159: int nsd=0; /**< Total number of single dummy variables (output) */
1160: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1161: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1162: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1163: int ntveff=0; /**< ntveff number of effective time varying variables */
1164: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1165: int cptcov=0; /* Working variable */
1.290 brouard 1166: int nobs=10; /* Number of observations in the data lastobs-firstobs */
1.218 brouard 1167: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.302 brouard 1168: int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
1.126 brouard 1169: int nlstate=2; /* Number of live states */
1170: int ndeath=1; /* Number of dead states */
1.130 brouard 1171: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1172: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1173: int popbased=0;
1174:
1175: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1176: int maxwav=0; /* Maxim number of waves */
1177: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1178: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1179: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1180: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1181: int mle=1, weightopt=0;
1.126 brouard 1182: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1183: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1184: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1185: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1186: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1187: int selected(int kvar); /* Is covariate kvar selected for printing results */
1188:
1.130 brouard 1189: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1190: double **matprod2(); /* test */
1.126 brouard 1191: double **oldm, **newm, **savm; /* Working pointers to matrices */
1192: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1193: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1194:
1.136 brouard 1195: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1196: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1197: FILE *ficlog, *ficrespow;
1.130 brouard 1198: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1199: double fretone; /* Only one call to likelihood */
1.130 brouard 1200: long ipmx=0; /* Number of contributions */
1.126 brouard 1201: double sw; /* Sum of weights */
1202: char filerespow[FILENAMELENGTH];
1203: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1204: FILE *ficresilk;
1205: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1206: FILE *ficresprobmorprev;
1207: FILE *fichtm, *fichtmcov; /* Html File */
1208: FILE *ficreseij;
1209: char filerese[FILENAMELENGTH];
1210: FILE *ficresstdeij;
1211: char fileresstde[FILENAMELENGTH];
1212: FILE *ficrescveij;
1213: char filerescve[FILENAMELENGTH];
1214: FILE *ficresvij;
1215: char fileresv[FILENAMELENGTH];
1.269 brouard 1216:
1.126 brouard 1217: char title[MAXLINE];
1.234 brouard 1218: char model[MAXLINE]; /**< The model line */
1.217 brouard 1219: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1220: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1221: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1222: char command[FILENAMELENGTH];
1223: int outcmd=0;
1224:
1.217 brouard 1225: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1226: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1227: char filelog[FILENAMELENGTH]; /* Log file */
1228: char filerest[FILENAMELENGTH];
1229: char fileregp[FILENAMELENGTH];
1230: char popfile[FILENAMELENGTH];
1231:
1232: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1233:
1.157 brouard 1234: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1235: /* struct timezone tzp; */
1236: /* extern int gettimeofday(); */
1237: struct tm tml, *gmtime(), *localtime();
1238:
1239: extern time_t time();
1240:
1241: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1242: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1243: struct tm tm;
1244:
1.126 brouard 1245: char strcurr[80], strfor[80];
1246:
1247: char *endptr;
1248: long lval;
1249: double dval;
1250:
1251: #define NR_END 1
1252: #define FREE_ARG char*
1253: #define FTOL 1.0e-10
1254:
1255: #define NRANSI
1.240 brouard 1256: #define ITMAX 200
1257: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1258:
1259: #define TOL 2.0e-4
1260:
1261: #define CGOLD 0.3819660
1262: #define ZEPS 1.0e-10
1263: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1264:
1265: #define GOLD 1.618034
1266: #define GLIMIT 100.0
1267: #define TINY 1.0e-20
1268:
1269: static double maxarg1,maxarg2;
1270: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1271: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1272:
1273: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1274: #define rint(a) floor(a+0.5)
1.166 brouard 1275: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1276: #define mytinydouble 1.0e-16
1.166 brouard 1277: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1278: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1279: /* static double dsqrarg; */
1280: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1281: static double sqrarg;
1282: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1283: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1284: int agegomp= AGEGOMP;
1285:
1286: int imx;
1287: int stepm=1;
1288: /* Stepm, step in month: minimum step interpolation*/
1289:
1290: int estepm;
1291: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1292:
1293: int m,nb;
1294: long *num;
1.197 brouard 1295: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1296: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1297: covariate for which somebody answered excluding
1298: undefined. Usually 2: 0 and 1. */
1299: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1300: covariate for which somebody answered including
1301: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1302: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1303: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1304: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1305: double *ageexmed,*agecens;
1306: double dateintmean=0;
1.296 brouard 1307: double anprojd, mprojd, jprojd; /* For eventual projections */
1308: double anprojf, mprojf, jprojf;
1.126 brouard 1309:
1.296 brouard 1310: double anbackd, mbackd, jbackd; /* For eventual backprojections */
1311: double anbackf, mbackf, jbackf;
1312: double jintmean,mintmean,aintmean;
1.126 brouard 1313: double *weight;
1314: int **s; /* Status */
1.141 brouard 1315: double *agedc;
1.145 brouard 1316: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1317: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1318: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1319: double **coqvar; /* Fixed quantitative covariate nqv */
1320: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1321: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1322: double idx;
1323: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1324: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1325: /*k 1 2 3 4 5 6 7 8 9 */
1326: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1327: /* Tndvar[k] 1 2 3 4 5 */
1328: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1329: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1330: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1331: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1332: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1333: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1334: /* Tprod[i]=k 4 7 */
1335: /* Tage[i]=k 5 8 */
1336: /* */
1337: /* Type */
1338: /* V 1 2 3 4 5 */
1339: /* F F V V V */
1340: /* D Q D D Q */
1341: /* */
1342: int *TvarsD;
1343: int *TvarsDind;
1344: int *TvarsQ;
1345: int *TvarsQind;
1346:
1.235 brouard 1347: #define MAXRESULTLINES 10
1348: int nresult=0;
1.258 brouard 1349: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1350: int TKresult[MAXRESULTLINES];
1.237 brouard 1351: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1352: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1353: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1354: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1355: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1356: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1357:
1.234 brouard 1358: /* 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 1359: 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 */
1360: 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 */
1361: 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 */
1362: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1363: 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 */
1364: 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 1365: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1366: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1367: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1368: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1369: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1370: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1371: 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 */
1372: 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 */
1373:
1.230 brouard 1374: int *Tvarsel; /**< Selected covariates for output */
1375: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1376: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1377: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1378: 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 1379: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1380: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1381: int *Tage;
1.227 brouard 1382: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1383: 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 1384: 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*/
1385: 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 1386: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1387: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1388: int **Tvard;
1389: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1390: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1391: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1392: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1393: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1394: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1395: double *lsurv, *lpop, *tpop;
1396:
1.231 brouard 1397: #define FD 1; /* Fixed dummy covariate */
1398: #define FQ 2; /* Fixed quantitative covariate */
1399: #define FP 3; /* Fixed product covariate */
1400: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1401: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1402: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1403: #define VD 10; /* Varying dummy covariate */
1404: #define VQ 11; /* Varying quantitative covariate */
1405: #define VP 12; /* Varying product covariate */
1406: #define VPDD 13; /* Varying product dummy*dummy covariate */
1407: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1408: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1409: #define APFD 16; /* Age product * fixed dummy covariate */
1410: #define APFQ 17; /* Age product * fixed quantitative covariate */
1411: #define APVD 18; /* Age product * varying dummy covariate */
1412: #define APVQ 19; /* Age product * varying quantitative covariate */
1413:
1414: #define FTYPE 1; /* Fixed covariate */
1415: #define VTYPE 2; /* Varying covariate (loop in wave) */
1416: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1417:
1418: struct kmodel{
1419: int maintype; /* main type */
1420: int subtype; /* subtype */
1421: };
1422: struct kmodel modell[NCOVMAX];
1423:
1.143 brouard 1424: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1425: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1426:
1427: /**************** split *************************/
1428: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1429: {
1430: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1431: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1432: */
1433: char *ss; /* pointer */
1.186 brouard 1434: int l1=0, l2=0; /* length counters */
1.126 brouard 1435:
1436: l1 = strlen(path ); /* length of path */
1437: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1438: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1439: if ( ss == NULL ) { /* no directory, so determine current directory */
1440: strcpy( name, path ); /* we got the fullname name because no directory */
1441: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1442: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1443: /* get current working directory */
1444: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1445: #ifdef WIN32
1446: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1447: #else
1448: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1449: #endif
1.126 brouard 1450: return( GLOCK_ERROR_GETCWD );
1451: }
1452: /* got dirc from getcwd*/
1453: printf(" DIRC = %s \n",dirc);
1.205 brouard 1454: } else { /* strip directory from path */
1.126 brouard 1455: ss++; /* after this, the filename */
1456: l2 = strlen( ss ); /* length of filename */
1457: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1458: strcpy( name, ss ); /* save file name */
1459: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1460: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1461: printf(" DIRC2 = %s \n",dirc);
1462: }
1463: /* We add a separator at the end of dirc if not exists */
1464: l1 = strlen( dirc ); /* length of directory */
1465: if( dirc[l1-1] != DIRSEPARATOR ){
1466: dirc[l1] = DIRSEPARATOR;
1467: dirc[l1+1] = 0;
1468: printf(" DIRC3 = %s \n",dirc);
1469: }
1470: ss = strrchr( name, '.' ); /* find last / */
1471: if (ss >0){
1472: ss++;
1473: strcpy(ext,ss); /* save extension */
1474: l1= strlen( name);
1475: l2= strlen(ss)+1;
1476: strncpy( finame, name, l1-l2);
1477: finame[l1-l2]= 0;
1478: }
1479:
1480: return( 0 ); /* we're done */
1481: }
1482:
1483:
1484: /******************************************/
1485:
1486: void replace_back_to_slash(char *s, char*t)
1487: {
1488: int i;
1489: int lg=0;
1490: i=0;
1491: lg=strlen(t);
1492: for(i=0; i<= lg; i++) {
1493: (s[i] = t[i]);
1494: if (t[i]== '\\') s[i]='/';
1495: }
1496: }
1497:
1.132 brouard 1498: char *trimbb(char *out, char *in)
1.137 brouard 1499: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1500: char *s;
1501: s=out;
1502: while (*in != '\0'){
1.137 brouard 1503: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1504: in++;
1505: }
1506: *out++ = *in++;
1507: }
1508: *out='\0';
1509: return s;
1510: }
1511:
1.187 brouard 1512: /* char *substrchaine(char *out, char *in, char *chain) */
1513: /* { */
1514: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1515: /* char *s, *t; */
1516: /* t=in;s=out; */
1517: /* while ((*in != *chain) && (*in != '\0')){ */
1518: /* *out++ = *in++; */
1519: /* } */
1520:
1521: /* /\* *in matches *chain *\/ */
1522: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1523: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1524: /* } */
1525: /* in--; chain--; */
1526: /* while ( (*in != '\0')){ */
1527: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1528: /* *out++ = *in++; */
1529: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1530: /* } */
1531: /* *out='\0'; */
1532: /* out=s; */
1533: /* return out; */
1534: /* } */
1535: char *substrchaine(char *out, char *in, char *chain)
1536: {
1537: /* Substract chain 'chain' from 'in', return and output 'out' */
1538: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1539:
1540: char *strloc;
1541:
1542: strcpy (out, in);
1543: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1544: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1545: if(strloc != NULL){
1546: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1547: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1548: /* strcpy (strloc, strloc +strlen(chain));*/
1549: }
1550: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1551: return out;
1552: }
1553:
1554:
1.145 brouard 1555: char *cutl(char *blocc, char *alocc, char *in, char occ)
1556: {
1.187 brouard 1557: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1558: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1559: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1560: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1561: */
1.160 brouard 1562: char *s, *t;
1.145 brouard 1563: t=in;s=in;
1564: while ((*in != occ) && (*in != '\0')){
1565: *alocc++ = *in++;
1566: }
1567: if( *in == occ){
1568: *(alocc)='\0';
1569: s=++in;
1570: }
1571:
1572: if (s == t) {/* occ not found */
1573: *(alocc-(in-s))='\0';
1574: in=s;
1575: }
1576: while ( *in != '\0'){
1577: *blocc++ = *in++;
1578: }
1579:
1580: *blocc='\0';
1581: return t;
1582: }
1.137 brouard 1583: char *cutv(char *blocc, char *alocc, char *in, char occ)
1584: {
1.187 brouard 1585: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1586: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1587: gives blocc="abcdef2ghi" and alocc="j".
1588: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1589: */
1590: char *s, *t;
1591: t=in;s=in;
1592: while (*in != '\0'){
1593: while( *in == occ){
1594: *blocc++ = *in++;
1595: s=in;
1596: }
1597: *blocc++ = *in++;
1598: }
1599: if (s == t) /* occ not found */
1600: *(blocc-(in-s))='\0';
1601: else
1602: *(blocc-(in-s)-1)='\0';
1603: in=s;
1604: while ( *in != '\0'){
1605: *alocc++ = *in++;
1606: }
1607:
1608: *alocc='\0';
1609: return s;
1610: }
1611:
1.126 brouard 1612: int nbocc(char *s, char occ)
1613: {
1614: int i,j=0;
1615: int lg=20;
1616: i=0;
1617: lg=strlen(s);
1618: for(i=0; i<= lg; i++) {
1.234 brouard 1619: if (s[i] == occ ) j++;
1.126 brouard 1620: }
1621: return j;
1622: }
1623:
1.137 brouard 1624: /* void cutv(char *u,char *v, char*t, char occ) */
1625: /* { */
1626: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1627: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1628: /* gives u="abcdef2ghi" and v="j" *\/ */
1629: /* int i,lg,j,p=0; */
1630: /* i=0; */
1631: /* lg=strlen(t); */
1632: /* for(j=0; j<=lg-1; j++) { */
1633: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1634: /* } */
1.126 brouard 1635:
1.137 brouard 1636: /* for(j=0; j<p; j++) { */
1637: /* (u[j] = t[j]); */
1638: /* } */
1639: /* u[p]='\0'; */
1.126 brouard 1640:
1.137 brouard 1641: /* for(j=0; j<= lg; j++) { */
1642: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1643: /* } */
1644: /* } */
1.126 brouard 1645:
1.160 brouard 1646: #ifdef _WIN32
1647: char * strsep(char **pp, const char *delim)
1648: {
1649: char *p, *q;
1650:
1651: if ((p = *pp) == NULL)
1652: return 0;
1653: if ((q = strpbrk (p, delim)) != NULL)
1654: {
1655: *pp = q + 1;
1656: *q = '\0';
1657: }
1658: else
1659: *pp = 0;
1660: return p;
1661: }
1662: #endif
1663:
1.126 brouard 1664: /********************** nrerror ********************/
1665:
1666: void nrerror(char error_text[])
1667: {
1668: fprintf(stderr,"ERREUR ...\n");
1669: fprintf(stderr,"%s\n",error_text);
1670: exit(EXIT_FAILURE);
1671: }
1672: /*********************** vector *******************/
1673: double *vector(int nl, int nh)
1674: {
1675: double *v;
1676: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1677: if (!v) nrerror("allocation failure in vector");
1678: return v-nl+NR_END;
1679: }
1680:
1681: /************************ free vector ******************/
1682: void free_vector(double*v, int nl, int nh)
1683: {
1684: free((FREE_ARG)(v+nl-NR_END));
1685: }
1686:
1687: /************************ivector *******************************/
1688: int *ivector(long nl,long nh)
1689: {
1690: int *v;
1691: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1692: if (!v) nrerror("allocation failure in ivector");
1693: return v-nl+NR_END;
1694: }
1695:
1696: /******************free ivector **************************/
1697: void free_ivector(int *v, long nl, long nh)
1698: {
1699: free((FREE_ARG)(v+nl-NR_END));
1700: }
1701:
1702: /************************lvector *******************************/
1703: long *lvector(long nl,long nh)
1704: {
1705: long *v;
1706: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1707: if (!v) nrerror("allocation failure in ivector");
1708: return v-nl+NR_END;
1709: }
1710:
1711: /******************free lvector **************************/
1712: void free_lvector(long *v, long nl, long nh)
1713: {
1714: free((FREE_ARG)(v+nl-NR_END));
1715: }
1716:
1717: /******************* imatrix *******************************/
1718: int **imatrix(long nrl, long nrh, long ncl, long nch)
1719: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1720: {
1721: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1722: int **m;
1723:
1724: /* allocate pointers to rows */
1725: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1726: if (!m) nrerror("allocation failure 1 in matrix()");
1727: m += NR_END;
1728: m -= nrl;
1729:
1730:
1731: /* allocate rows and set pointers to them */
1732: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1733: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1734: m[nrl] += NR_END;
1735: m[nrl] -= ncl;
1736:
1737: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1738:
1739: /* return pointer to array of pointers to rows */
1740: return m;
1741: }
1742:
1743: /****************** free_imatrix *************************/
1744: void free_imatrix(m,nrl,nrh,ncl,nch)
1745: int **m;
1746: long nch,ncl,nrh,nrl;
1747: /* free an int matrix allocated by imatrix() */
1748: {
1749: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1750: free((FREE_ARG) (m+nrl-NR_END));
1751: }
1752:
1753: /******************* matrix *******************************/
1754: double **matrix(long nrl, long nrh, long ncl, long nch)
1755: {
1756: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1757: double **m;
1758:
1759: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1760: if (!m) nrerror("allocation failure 1 in matrix()");
1761: m += NR_END;
1762: m -= nrl;
1763:
1764: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1765: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1766: m[nrl] += NR_END;
1767: m[nrl] -= ncl;
1768:
1769: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1770: return m;
1.145 brouard 1771: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1772: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1773: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1774: */
1775: }
1776:
1777: /*************************free matrix ************************/
1778: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1779: {
1780: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1781: free((FREE_ARG)(m+nrl-NR_END));
1782: }
1783:
1784: /******************* ma3x *******************************/
1785: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1786: {
1787: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1788: double ***m;
1789:
1790: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1791: if (!m) nrerror("allocation failure 1 in matrix()");
1792: m += NR_END;
1793: m -= nrl;
1794:
1795: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1796: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1797: m[nrl] += NR_END;
1798: m[nrl] -= ncl;
1799:
1800: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1801:
1802: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1803: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1804: m[nrl][ncl] += NR_END;
1805: m[nrl][ncl] -= nll;
1806: for (j=ncl+1; j<=nch; j++)
1807: m[nrl][j]=m[nrl][j-1]+nlay;
1808:
1809: for (i=nrl+1; i<=nrh; i++) {
1810: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1811: for (j=ncl+1; j<=nch; j++)
1812: m[i][j]=m[i][j-1]+nlay;
1813: }
1814: return m;
1815: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1816: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1817: */
1818: }
1819:
1820: /*************************free ma3x ************************/
1821: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1822: {
1823: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1824: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1825: free((FREE_ARG)(m+nrl-NR_END));
1826: }
1827:
1828: /*************** function subdirf ***********/
1829: char *subdirf(char fileres[])
1830: {
1831: /* Caution optionfilefiname is hidden */
1832: strcpy(tmpout,optionfilefiname);
1833: strcat(tmpout,"/"); /* Add to the right */
1834: strcat(tmpout,fileres);
1835: return tmpout;
1836: }
1837:
1838: /*************** function subdirf2 ***********/
1839: char *subdirf2(char fileres[], char *preop)
1840: {
1841:
1842: /* Caution optionfilefiname is hidden */
1843: strcpy(tmpout,optionfilefiname);
1844: strcat(tmpout,"/");
1845: strcat(tmpout,preop);
1846: strcat(tmpout,fileres);
1847: return tmpout;
1848: }
1849:
1850: /*************** function subdirf3 ***********/
1851: char *subdirf3(char fileres[], char *preop, char *preop2)
1852: {
1853:
1854: /* Caution optionfilefiname is hidden */
1855: strcpy(tmpout,optionfilefiname);
1856: strcat(tmpout,"/");
1857: strcat(tmpout,preop);
1858: strcat(tmpout,preop2);
1859: strcat(tmpout,fileres);
1860: return tmpout;
1861: }
1.213 brouard 1862:
1863: /*************** function subdirfext ***********/
1864: char *subdirfext(char fileres[], char *preop, char *postop)
1865: {
1866:
1867: strcpy(tmpout,preop);
1868: strcat(tmpout,fileres);
1869: strcat(tmpout,postop);
1870: return tmpout;
1871: }
1.126 brouard 1872:
1.213 brouard 1873: /*************** function subdirfext3 ***********/
1874: char *subdirfext3(char fileres[], char *preop, char *postop)
1875: {
1876:
1877: /* Caution optionfilefiname is hidden */
1878: strcpy(tmpout,optionfilefiname);
1879: strcat(tmpout,"/");
1880: strcat(tmpout,preop);
1881: strcat(tmpout,fileres);
1882: strcat(tmpout,postop);
1883: return tmpout;
1884: }
1885:
1.162 brouard 1886: char *asc_diff_time(long time_sec, char ascdiff[])
1887: {
1888: long sec_left, days, hours, minutes;
1889: days = (time_sec) / (60*60*24);
1890: sec_left = (time_sec) % (60*60*24);
1891: hours = (sec_left) / (60*60) ;
1892: sec_left = (sec_left) %(60*60);
1893: minutes = (sec_left) /60;
1894: sec_left = (sec_left) % (60);
1895: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1896: return ascdiff;
1897: }
1898:
1.126 brouard 1899: /***************** f1dim *************************/
1900: extern int ncom;
1901: extern double *pcom,*xicom;
1902: extern double (*nrfunc)(double []);
1903:
1904: double f1dim(double x)
1905: {
1906: int j;
1907: double f;
1908: double *xt;
1909:
1910: xt=vector(1,ncom);
1911: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1912: f=(*nrfunc)(xt);
1913: free_vector(xt,1,ncom);
1914: return f;
1915: }
1916:
1917: /*****************brent *************************/
1918: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1919: {
1920: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1921: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1922: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1923: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1924: * returned function value.
1925: */
1.126 brouard 1926: int iter;
1927: double a,b,d,etemp;
1.159 brouard 1928: double fu=0,fv,fw,fx;
1.164 brouard 1929: double ftemp=0.;
1.126 brouard 1930: double p,q,r,tol1,tol2,u,v,w,x,xm;
1931: double e=0.0;
1932:
1933: a=(ax < cx ? ax : cx);
1934: b=(ax > cx ? ax : cx);
1935: x=w=v=bx;
1936: fw=fv=fx=(*f)(x);
1937: for (iter=1;iter<=ITMAX;iter++) {
1938: xm=0.5*(a+b);
1939: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1940: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1941: printf(".");fflush(stdout);
1942: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1943: #ifdef DEBUGBRENT
1.126 brouard 1944: 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);
1945: 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);
1946: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1947: #endif
1948: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1949: *xmin=x;
1950: return fx;
1951: }
1952: ftemp=fu;
1953: if (fabs(e) > tol1) {
1954: r=(x-w)*(fx-fv);
1955: q=(x-v)*(fx-fw);
1956: p=(x-v)*q-(x-w)*r;
1957: q=2.0*(q-r);
1958: if (q > 0.0) p = -p;
1959: q=fabs(q);
1960: etemp=e;
1961: e=d;
1962: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1963: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1964: else {
1.224 brouard 1965: d=p/q;
1966: u=x+d;
1967: if (u-a < tol2 || b-u < tol2)
1968: d=SIGN(tol1,xm-x);
1.126 brouard 1969: }
1970: } else {
1971: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1972: }
1973: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1974: fu=(*f)(u);
1975: if (fu <= fx) {
1976: if (u >= x) a=x; else b=x;
1977: SHFT(v,w,x,u)
1.183 brouard 1978: SHFT(fv,fw,fx,fu)
1979: } else {
1980: if (u < x) a=u; else b=u;
1981: if (fu <= fw || w == x) {
1.224 brouard 1982: v=w;
1983: w=u;
1984: fv=fw;
1985: fw=fu;
1.183 brouard 1986: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1987: v=u;
1988: fv=fu;
1.183 brouard 1989: }
1990: }
1.126 brouard 1991: }
1992: nrerror("Too many iterations in brent");
1993: *xmin=x;
1994: return fx;
1995: }
1996:
1997: /****************** mnbrak ***********************/
1998:
1999: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
2000: double (*func)(double))
1.183 brouard 2001: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
2002: the downhill direction (defined by the function as evaluated at the initial points) and returns
2003: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
2004: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
2005: */
1.126 brouard 2006: double ulim,u,r,q, dum;
2007: double fu;
1.187 brouard 2008:
2009: double scale=10.;
2010: int iterscale=0;
2011:
2012: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
2013: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
2014:
2015:
2016: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
2017: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
2018: /* *bx = *ax - (*ax - *bx)/scale; */
2019: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
2020: /* } */
2021:
1.126 brouard 2022: if (*fb > *fa) {
2023: SHFT(dum,*ax,*bx,dum)
1.183 brouard 2024: SHFT(dum,*fb,*fa,dum)
2025: }
1.126 brouard 2026: *cx=(*bx)+GOLD*(*bx-*ax);
2027: *fc=(*func)(*cx);
1.183 brouard 2028: #ifdef DEBUG
1.224 brouard 2029: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
2030: 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 2031: #endif
1.224 brouard 2032: 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 2033: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 2034: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 2035: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 2036: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
2037: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
2038: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 2039: fu=(*func)(u);
1.163 brouard 2040: #ifdef DEBUG
2041: /* f(x)=A(x-u)**2+f(u) */
2042: double A, fparabu;
2043: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2044: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 2045: 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);
2046: 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 2047: /* And thus,it can be that fu > *fc even if fparabu < *fc */
2048: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
2049: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
2050: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 2051: #endif
1.184 brouard 2052: #ifdef MNBRAKORIGINAL
1.183 brouard 2053: #else
1.191 brouard 2054: /* if (fu > *fc) { */
2055: /* #ifdef DEBUG */
2056: /* printf("mnbrak4 fu > fc \n"); */
2057: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
2058: /* #endif */
2059: /* /\* 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 *\\/ *\/ */
2060: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
2061: /* dum=u; /\* Shifting c and u *\/ */
2062: /* u = *cx; */
2063: /* *cx = dum; */
2064: /* dum = fu; */
2065: /* fu = *fc; */
2066: /* *fc =dum; */
2067: /* } else { /\* end *\/ */
2068: /* #ifdef DEBUG */
2069: /* printf("mnbrak3 fu < fc \n"); */
2070: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
2071: /* #endif */
2072: /* dum=u; /\* Shifting c and u *\/ */
2073: /* u = *cx; */
2074: /* *cx = dum; */
2075: /* dum = fu; */
2076: /* fu = *fc; */
2077: /* *fc =dum; */
2078: /* } */
1.224 brouard 2079: #ifdef DEBUGMNBRAK
2080: double A, fparabu;
2081: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2082: fparabu= *fa - A*(*ax-u)*(*ax-u);
2083: 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);
2084: 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 2085: #endif
1.191 brouard 2086: dum=u; /* Shifting c and u */
2087: u = *cx;
2088: *cx = dum;
2089: dum = fu;
2090: fu = *fc;
2091: *fc =dum;
1.183 brouard 2092: #endif
1.162 brouard 2093: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2094: #ifdef DEBUG
1.224 brouard 2095: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2096: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2097: #endif
1.126 brouard 2098: fu=(*func)(u);
2099: if (fu < *fc) {
1.183 brouard 2100: #ifdef DEBUG
1.224 brouard 2101: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2102: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2103: #endif
2104: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2105: SHFT(*fb,*fc,fu,(*func)(u))
2106: #ifdef DEBUG
2107: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2108: #endif
2109: }
1.162 brouard 2110: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2111: #ifdef DEBUG
1.224 brouard 2112: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2113: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2114: #endif
1.126 brouard 2115: u=ulim;
2116: fu=(*func)(u);
1.183 brouard 2117: } else { /* u could be left to b (if r > q parabola has a maximum) */
2118: #ifdef DEBUG
1.224 brouard 2119: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2120: 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 2121: #endif
1.126 brouard 2122: u=(*cx)+GOLD*(*cx-*bx);
2123: fu=(*func)(u);
1.224 brouard 2124: #ifdef DEBUG
2125: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2126: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2127: #endif
1.183 brouard 2128: } /* end tests */
1.126 brouard 2129: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2130: SHFT(*fa,*fb,*fc,fu)
2131: #ifdef DEBUG
1.224 brouard 2132: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2133: 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 2134: #endif
2135: } /* 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 2136: }
2137:
2138: /*************** linmin ************************/
1.162 brouard 2139: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2140: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2141: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2142: the value of func at the returned location p . This is actually all accomplished by calling the
2143: routines mnbrak and brent .*/
1.126 brouard 2144: int ncom;
2145: double *pcom,*xicom;
2146: double (*nrfunc)(double []);
2147:
1.224 brouard 2148: #ifdef LINMINORIGINAL
1.126 brouard 2149: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2150: #else
2151: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2152: #endif
1.126 brouard 2153: {
2154: double brent(double ax, double bx, double cx,
2155: double (*f)(double), double tol, double *xmin);
2156: double f1dim(double x);
2157: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2158: double *fc, double (*func)(double));
2159: int j;
2160: double xx,xmin,bx,ax;
2161: double fx,fb,fa;
1.187 brouard 2162:
1.203 brouard 2163: #ifdef LINMINORIGINAL
2164: #else
2165: double scale=10., axs, xxs; /* Scale added for infinity */
2166: #endif
2167:
1.126 brouard 2168: ncom=n;
2169: pcom=vector(1,n);
2170: xicom=vector(1,n);
2171: nrfunc=func;
2172: for (j=1;j<=n;j++) {
2173: pcom[j]=p[j];
1.202 brouard 2174: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2175: }
1.187 brouard 2176:
1.203 brouard 2177: #ifdef LINMINORIGINAL
2178: xx=1.;
2179: #else
2180: axs=0.0;
2181: xxs=1.;
2182: do{
2183: xx= xxs;
2184: #endif
1.187 brouard 2185: ax=0.;
2186: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2187: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2188: /* 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)) */
2189: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2190: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2191: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2192: /* 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 2193: #ifdef LINMINORIGINAL
2194: #else
2195: if (fx != fx){
1.224 brouard 2196: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2197: printf("|");
2198: fprintf(ficlog,"|");
1.203 brouard 2199: #ifdef DEBUGLINMIN
1.224 brouard 2200: 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 2201: #endif
2202: }
1.224 brouard 2203: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2204: #endif
2205:
1.191 brouard 2206: #ifdef DEBUGLINMIN
2207: 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 2208: 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 2209: #endif
1.224 brouard 2210: #ifdef LINMINORIGINAL
2211: #else
2212: if(fb == fx){ /* Flat function in the direction */
2213: xmin=xx;
2214: *flat=1;
2215: }else{
2216: *flat=0;
2217: #endif
2218: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2219: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2220: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2221: /* fmin = f(p[j] + xmin * xi[j]) */
2222: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2223: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2224: #ifdef DEBUG
1.224 brouard 2225: 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);
2226: 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);
2227: #endif
2228: #ifdef LINMINORIGINAL
2229: #else
2230: }
1.126 brouard 2231: #endif
1.191 brouard 2232: #ifdef DEBUGLINMIN
2233: printf("linmin end ");
1.202 brouard 2234: fprintf(ficlog,"linmin end ");
1.191 brouard 2235: #endif
1.126 brouard 2236: for (j=1;j<=n;j++) {
1.203 brouard 2237: #ifdef LINMINORIGINAL
2238: xi[j] *= xmin;
2239: #else
2240: #ifdef DEBUGLINMIN
2241: if(xxs <1.0)
2242: printf(" before xi[%d]=%12.8f", j,xi[j]);
2243: #endif
2244: 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) */
2245: #ifdef DEBUGLINMIN
2246: if(xxs <1.0)
2247: 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 );
2248: #endif
2249: #endif
1.187 brouard 2250: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2251: }
1.191 brouard 2252: #ifdef DEBUGLINMIN
1.203 brouard 2253: printf("\n");
1.191 brouard 2254: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2255: 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 2256: for (j=1;j<=n;j++) {
1.202 brouard 2257: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2258: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2259: if(j % ncovmodel == 0){
1.191 brouard 2260: printf("\n");
1.202 brouard 2261: fprintf(ficlog,"\n");
2262: }
1.191 brouard 2263: }
1.203 brouard 2264: #else
1.191 brouard 2265: #endif
1.126 brouard 2266: free_vector(xicom,1,n);
2267: free_vector(pcom,1,n);
2268: }
2269:
2270:
2271: /*************** powell ************************/
1.162 brouard 2272: /*
2273: Minimization of a function func of n variables. Input consists of an initial starting point
2274: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2275: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2276: such that failure to decrease by more than this amount on one iteration signals doneness. On
2277: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2278: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2279: */
1.224 brouard 2280: #ifdef LINMINORIGINAL
2281: #else
2282: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2283: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2284: #endif
1.126 brouard 2285: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2286: double (*func)(double []))
2287: {
1.224 brouard 2288: #ifdef LINMINORIGINAL
2289: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2290: double (*func)(double []));
1.224 brouard 2291: #else
1.241 brouard 2292: void linmin(double p[], double xi[], int n, double *fret,
2293: double (*func)(double []),int *flat);
1.224 brouard 2294: #endif
1.239 brouard 2295: int i,ibig,j,jk,k;
1.126 brouard 2296: double del,t,*pt,*ptt,*xit;
1.181 brouard 2297: double directest;
1.126 brouard 2298: double fp,fptt;
2299: double *xits;
2300: int niterf, itmp;
1.224 brouard 2301: #ifdef LINMINORIGINAL
2302: #else
2303:
2304: flatdir=ivector(1,n);
2305: for (j=1;j<=n;j++) flatdir[j]=0;
2306: #endif
1.126 brouard 2307:
2308: pt=vector(1,n);
2309: ptt=vector(1,n);
2310: xit=vector(1,n);
2311: xits=vector(1,n);
2312: *fret=(*func)(p);
2313: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2314: rcurr_time = time(NULL);
1.126 brouard 2315: for (*iter=1;;++(*iter)) {
1.187 brouard 2316: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2317: ibig=0;
2318: del=0.0;
1.157 brouard 2319: rlast_time=rcurr_time;
2320: /* (void) gettimeofday(&curr_time,&tzp); */
2321: rcurr_time = time(NULL);
2322: curr_time = *localtime(&rcurr_time);
2323: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2324: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2325: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2326: for (i=1;i<=n;i++) {
1.126 brouard 2327: fprintf(ficrespow," %.12lf", p[i]);
2328: }
1.239 brouard 2329: fprintf(ficrespow,"\n");fflush(ficrespow);
2330: printf("\n#model= 1 + age ");
2331: fprintf(ficlog,"\n#model= 1 + age ");
2332: if(nagesqr==1){
1.241 brouard 2333: printf(" + age*age ");
2334: fprintf(ficlog," + age*age ");
1.239 brouard 2335: }
2336: for(j=1;j <=ncovmodel-2;j++){
2337: if(Typevar[j]==0) {
2338: printf(" + V%d ",Tvar[j]);
2339: fprintf(ficlog," + V%d ",Tvar[j]);
2340: }else if(Typevar[j]==1) {
2341: printf(" + V%d*age ",Tvar[j]);
2342: fprintf(ficlog," + V%d*age ",Tvar[j]);
2343: }else if(Typevar[j]==2) {
2344: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2345: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2346: }
2347: }
1.126 brouard 2348: printf("\n");
1.239 brouard 2349: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2350: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2351: fprintf(ficlog,"\n");
1.239 brouard 2352: for(i=1,jk=1; i <=nlstate; i++){
2353: for(k=1; k <=(nlstate+ndeath); k++){
2354: if (k != i) {
2355: printf("%d%d ",i,k);
2356: fprintf(ficlog,"%d%d ",i,k);
2357: for(j=1; j <=ncovmodel; j++){
2358: printf("%12.7f ",p[jk]);
2359: fprintf(ficlog,"%12.7f ",p[jk]);
2360: jk++;
2361: }
2362: printf("\n");
2363: fprintf(ficlog,"\n");
2364: }
2365: }
2366: }
1.241 brouard 2367: if(*iter <=3 && *iter >1){
1.157 brouard 2368: tml = *localtime(&rcurr_time);
2369: strcpy(strcurr,asctime(&tml));
2370: rforecast_time=rcurr_time;
1.126 brouard 2371: itmp = strlen(strcurr);
2372: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2373: strcurr[itmp-1]='\0';
1.162 brouard 2374: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2375: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2376: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2377: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2378: forecast_time = *localtime(&rforecast_time);
2379: strcpy(strfor,asctime(&forecast_time));
2380: itmp = strlen(strfor);
2381: if(strfor[itmp-1]=='\n')
2382: strfor[itmp-1]='\0';
2383: 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);
2384: 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 2385: }
2386: }
1.187 brouard 2387: for (i=1;i<=n;i++) { /* For each direction i */
2388: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2389: fptt=(*fret);
2390: #ifdef DEBUG
1.203 brouard 2391: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2392: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2393: #endif
1.203 brouard 2394: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2395: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2396: #ifdef LINMINORIGINAL
1.188 brouard 2397: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2398: #else
2399: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2400: flatdir[i]=flat; /* Function is vanishing in that direction i */
2401: #endif
2402: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2403: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2404: /* because that direction will be replaced unless the gain del is small */
2405: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2406: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2407: /* with the new direction. */
2408: del=fabs(fptt-(*fret));
2409: ibig=i;
1.126 brouard 2410: }
2411: #ifdef DEBUG
2412: printf("%d %.12e",i,(*fret));
2413: fprintf(ficlog,"%d %.12e",i,(*fret));
2414: for (j=1;j<=n;j++) {
1.224 brouard 2415: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2416: printf(" x(%d)=%.12e",j,xit[j]);
2417: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2418: }
2419: for(j=1;j<=n;j++) {
1.225 brouard 2420: printf(" p(%d)=%.12e",j,p[j]);
2421: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2422: }
2423: printf("\n");
2424: fprintf(ficlog,"\n");
2425: #endif
1.187 brouard 2426: } /* end loop on each direction i */
2427: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2428: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2429: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2430: for(j=1;j<=n;j++) {
1.302 brouard 2431: if(flatdir[j] >0){
2432: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2433: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2434: }
2435: /* printf("\n"); */
2436: /* fprintf(ficlog,"\n"); */
2437: }
1.243 brouard 2438: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2439: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2440: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2441: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2442: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2443: /* decreased of more than 3.84 */
2444: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2445: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2446: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2447:
1.188 brouard 2448: /* Starting the program with initial values given by a former maximization will simply change */
2449: /* the scales of the directions and the directions, because the are reset to canonical directions */
2450: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2451: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2452: #ifdef DEBUG
2453: int k[2],l;
2454: k[0]=1;
2455: k[1]=-1;
2456: printf("Max: %.12e",(*func)(p));
2457: fprintf(ficlog,"Max: %.12e",(*func)(p));
2458: for (j=1;j<=n;j++) {
2459: printf(" %.12e",p[j]);
2460: fprintf(ficlog," %.12e",p[j]);
2461: }
2462: printf("\n");
2463: fprintf(ficlog,"\n");
2464: for(l=0;l<=1;l++) {
2465: for (j=1;j<=n;j++) {
2466: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2467: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2468: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2469: }
2470: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2471: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2472: }
2473: #endif
2474:
1.224 brouard 2475: #ifdef LINMINORIGINAL
2476: #else
2477: free_ivector(flatdir,1,n);
2478: #endif
1.126 brouard 2479: free_vector(xit,1,n);
2480: free_vector(xits,1,n);
2481: free_vector(ptt,1,n);
2482: free_vector(pt,1,n);
2483: return;
1.192 brouard 2484: } /* enough precision */
1.240 brouard 2485: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2486: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2487: ptt[j]=2.0*p[j]-pt[j];
2488: xit[j]=p[j]-pt[j];
2489: pt[j]=p[j];
2490: }
1.181 brouard 2491: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2492: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2493: if (*iter <=4) {
1.225 brouard 2494: #else
2495: #endif
1.224 brouard 2496: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2497: #else
1.161 brouard 2498: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2499: #endif
1.162 brouard 2500: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2501: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2502: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2503: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2504: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2505: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2506: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2507: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2508: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2509: /* Even if f3 <f1, directest can be negative and t >0 */
2510: /* mu² and del² are equal when f3=f1 */
2511: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2512: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2513: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2514: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2515: #ifdef NRCORIGINAL
2516: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2517: #else
2518: 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 2519: t= t- del*SQR(fp-fptt);
1.183 brouard 2520: #endif
1.202 brouard 2521: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2522: #ifdef DEBUG
1.181 brouard 2523: 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);
2524: 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 2525: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2526: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2527: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2528: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2529: 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);
2530: 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);
2531: #endif
1.183 brouard 2532: #ifdef POWELLORIGINAL
2533: if (t < 0.0) { /* Then we use it for new direction */
2534: #else
1.182 brouard 2535: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2536: 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 2537: 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 2538: 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 2539: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2540: }
1.181 brouard 2541: if (directest < 0.0) { /* Then we use it for new direction */
2542: #endif
1.191 brouard 2543: #ifdef DEBUGLINMIN
1.234 brouard 2544: printf("Before linmin in direction P%d-P0\n",n);
2545: for (j=1;j<=n;j++) {
2546: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2547: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2548: if(j % ncovmodel == 0){
2549: printf("\n");
2550: fprintf(ficlog,"\n");
2551: }
2552: }
1.224 brouard 2553: #endif
2554: #ifdef LINMINORIGINAL
1.234 brouard 2555: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2556: #else
1.234 brouard 2557: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2558: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2559: #endif
1.234 brouard 2560:
1.191 brouard 2561: #ifdef DEBUGLINMIN
1.234 brouard 2562: for (j=1;j<=n;j++) {
2563: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2564: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2565: if(j % ncovmodel == 0){
2566: printf("\n");
2567: fprintf(ficlog,"\n");
2568: }
2569: }
1.224 brouard 2570: #endif
1.234 brouard 2571: for (j=1;j<=n;j++) {
2572: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2573: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2574: }
1.224 brouard 2575: #ifdef LINMINORIGINAL
2576: #else
1.234 brouard 2577: for (j=1, flatd=0;j<=n;j++) {
2578: if(flatdir[j]>0)
2579: flatd++;
2580: }
2581: if(flatd >0){
1.255 brouard 2582: printf("%d flat directions: ",flatd);
2583: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2584: for (j=1;j<=n;j++) {
2585: if(flatdir[j]>0){
2586: printf("%d ",j);
2587: fprintf(ficlog,"%d ",j);
2588: }
2589: }
2590: printf("\n");
2591: fprintf(ficlog,"\n");
2592: }
1.191 brouard 2593: #endif
1.234 brouard 2594: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2595: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2596:
1.126 brouard 2597: #ifdef DEBUG
1.234 brouard 2598: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2599: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2600: for(j=1;j<=n;j++){
2601: printf(" %lf",xit[j]);
2602: fprintf(ficlog," %lf",xit[j]);
2603: }
2604: printf("\n");
2605: fprintf(ficlog,"\n");
1.126 brouard 2606: #endif
1.192 brouard 2607: } /* end of t or directest negative */
1.224 brouard 2608: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2609: #else
1.234 brouard 2610: } /* end if (fptt < fp) */
1.192 brouard 2611: #endif
1.225 brouard 2612: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2613: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2614: #else
1.224 brouard 2615: #endif
1.234 brouard 2616: } /* loop iteration */
1.126 brouard 2617: }
1.234 brouard 2618:
1.126 brouard 2619: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2620:
1.235 brouard 2621: 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 2622: {
1.279 brouard 2623: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2624: * (and selected quantitative values in nres)
2625: * by left multiplying the unit
2626: * matrix by transitions matrix until convergence is reached with precision ftolpl
2627: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2628: * Wx is row vector: population in state 1, population in state 2, population dead
2629: * or prevalence in state 1, prevalence in state 2, 0
2630: * newm is the matrix after multiplications, its rows are identical at a factor.
2631: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2632: * Output is prlim.
2633: * Initial matrix pimij
2634: */
1.206 brouard 2635: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2636: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2637: /* 0, 0 , 1} */
2638: /*
2639: * and after some iteration: */
2640: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2641: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2642: /* 0, 0 , 1} */
2643: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2644: /* {0.51571254859325999, 0.4842874514067399, */
2645: /* 0.51326036147820708, 0.48673963852179264} */
2646: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2647:
1.126 brouard 2648: int i, ii,j,k;
1.209 brouard 2649: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2650: /* double **matprod2(); */ /* test */
1.218 brouard 2651: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2652: double **newm;
1.209 brouard 2653: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2654: int ncvloop=0;
1.288 brouard 2655: int first=0;
1.169 brouard 2656:
1.209 brouard 2657: min=vector(1,nlstate);
2658: max=vector(1,nlstate);
2659: meandiff=vector(1,nlstate);
2660:
1.218 brouard 2661: /* Starting with matrix unity */
1.126 brouard 2662: for (ii=1;ii<=nlstate+ndeath;ii++)
2663: for (j=1;j<=nlstate+ndeath;j++){
2664: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2665: }
1.169 brouard 2666:
2667: cov[1]=1.;
2668:
2669: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2670: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2671: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2672: ncvloop++;
1.126 brouard 2673: newm=savm;
2674: /* Covariates have to be included here again */
1.138 brouard 2675: cov[2]=agefin;
1.187 brouard 2676: if(nagesqr==1)
2677: cov[3]= agefin*agefin;;
1.234 brouard 2678: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2679: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2680: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2681: /* 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 2682: }
2683: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2684: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2685: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2686: /* 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 2687: }
1.237 brouard 2688: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2689: if(Dummy[Tvar[Tage[k]]]){
2690: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2691: } else{
1.235 brouard 2692: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2693: }
1.235 brouard 2694: /* 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 2695: }
1.237 brouard 2696: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2697: /* 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 2698: if(Dummy[Tvard[k][1]==0]){
2699: if(Dummy[Tvard[k][2]==0]){
2700: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2701: }else{
2702: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2703: }
2704: }else{
2705: if(Dummy[Tvard[k][2]==0]){
2706: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2707: }else{
2708: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2709: }
2710: }
1.234 brouard 2711: }
1.138 brouard 2712: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2713: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2714: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2715: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2716: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2717: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2718: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2719:
1.126 brouard 2720: savm=oldm;
2721: oldm=newm;
1.209 brouard 2722:
2723: for(j=1; j<=nlstate; j++){
2724: max[j]=0.;
2725: min[j]=1.;
2726: }
2727: for(i=1;i<=nlstate;i++){
2728: sumnew=0;
2729: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2730: for(j=1; j<=nlstate; j++){
2731: prlim[i][j]= newm[i][j]/(1-sumnew);
2732: max[j]=FMAX(max[j],prlim[i][j]);
2733: min[j]=FMIN(min[j],prlim[i][j]);
2734: }
2735: }
2736:
1.126 brouard 2737: maxmax=0.;
1.209 brouard 2738: for(j=1; j<=nlstate; j++){
2739: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2740: maxmax=FMAX(maxmax,meandiff[j]);
2741: /* 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 2742: } /* j loop */
1.203 brouard 2743: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2744: /* 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 2745: if(maxmax < ftolpl){
1.209 brouard 2746: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2747: free_vector(min,1,nlstate);
2748: free_vector(max,1,nlstate);
2749: free_vector(meandiff,1,nlstate);
1.126 brouard 2750: return prlim;
2751: }
1.288 brouard 2752: } /* agefin loop */
1.208 brouard 2753: /* After some age loop it doesn't converge */
1.288 brouard 2754: if(!first){
2755: first=1;
2756: 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);
2757: }
2758: 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);
2759:
1.209 brouard 2760: /* 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); */
2761: free_vector(min,1,nlstate);
2762: free_vector(max,1,nlstate);
2763: free_vector(meandiff,1,nlstate);
1.208 brouard 2764:
1.169 brouard 2765: return prlim; /* should not reach here */
1.126 brouard 2766: }
2767:
1.217 brouard 2768:
2769: /**** Back Prevalence limit (stable or period prevalence) ****************/
2770:
1.218 brouard 2771: /* 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) */
2772: /* 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 2773: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2774: {
1.264 brouard 2775: /* 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 2776: matrix by transitions matrix until convergence is reached with precision ftolpl */
2777: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2778: /* Wx is row vector: population in state 1, population in state 2, population dead */
2779: /* or prevalence in state 1, prevalence in state 2, 0 */
2780: /* newm is the matrix after multiplications, its rows are identical at a factor */
2781: /* Initial matrix pimij */
2782: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2783: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2784: /* 0, 0 , 1} */
2785: /*
2786: * and after some iteration: */
2787: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2788: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2789: /* 0, 0 , 1} */
2790: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2791: /* {0.51571254859325999, 0.4842874514067399, */
2792: /* 0.51326036147820708, 0.48673963852179264} */
2793: /* If we start from prlim again, prlim tends to a constant matrix */
2794:
2795: int i, ii,j,k;
1.247 brouard 2796: int first=0;
1.217 brouard 2797: double *min, *max, *meandiff, maxmax,sumnew=0.;
2798: /* double **matprod2(); */ /* test */
2799: double **out, cov[NCOVMAX+1], **bmij();
2800: double **newm;
1.218 brouard 2801: double **dnewm, **doldm, **dsavm; /* for use */
2802: double **oldm, **savm; /* for use */
2803:
1.217 brouard 2804: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2805: int ncvloop=0;
2806:
2807: min=vector(1,nlstate);
2808: max=vector(1,nlstate);
2809: meandiff=vector(1,nlstate);
2810:
1.266 brouard 2811: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2812: oldm=oldms; savm=savms;
2813:
2814: /* Starting with matrix unity */
2815: for (ii=1;ii<=nlstate+ndeath;ii++)
2816: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2817: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2818: }
2819:
2820: cov[1]=1.;
2821:
2822: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2823: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2824: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
1.288 brouard 2825: /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2826: for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2827: ncvloop++;
1.218 brouard 2828: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2829: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2830: /* Covariates have to be included here again */
2831: cov[2]=agefin;
2832: if(nagesqr==1)
2833: cov[3]= agefin*agefin;;
1.242 brouard 2834: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2835: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2836: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2837: /* 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 2838: }
2839: /* for (k=1; k<=cptcovn;k++) { */
2840: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2841: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2842: /* /\* 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])]); *\/ */
2843: /* } */
2844: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2845: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2846: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2847: /* 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]); */
2848: }
2849: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2850: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2851: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2852: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2853: for (k=1; k<=cptcovage;k++){ /* For product with age */
2854: if(Dummy[Tvar[Tage[k]]]){
2855: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2856: } else{
2857: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2858: }
2859: /* 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]); */
2860: }
2861: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2862: /* 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]); */
2863: if(Dummy[Tvard[k][1]==0]){
2864: if(Dummy[Tvard[k][2]==0]){
2865: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2866: }else{
2867: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2868: }
2869: }else{
2870: if(Dummy[Tvard[k][2]==0]){
2871: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2872: }else{
2873: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2874: }
2875: }
1.217 brouard 2876: }
2877:
2878: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2879: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2880: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2881: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2882: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2883: /* ij should be linked to the correct index of cov */
2884: /* age and covariate values ij are in 'cov', but we need to pass
2885: * ij for the observed prevalence at age and status and covariate
2886: * number: prevacurrent[(int)agefin][ii][ij]
2887: */
2888: /* 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 *\/ */
2889: /* 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 *\/ */
2890: 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 2891: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2892: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2893: /* for(i=1; i<=nlstate+ndeath; i++) { */
2894: /* printf("%d newm= ",i); */
2895: /* for(j=1;j<=nlstate+ndeath;j++) { */
2896: /* printf("%f ",newm[i][j]); */
2897: /* } */
2898: /* printf("oldm * "); */
2899: /* for(j=1;j<=nlstate+ndeath;j++) { */
2900: /* printf("%f ",oldm[i][j]); */
2901: /* } */
1.268 brouard 2902: /* printf(" bmmij "); */
1.266 brouard 2903: /* for(j=1;j<=nlstate+ndeath;j++) { */
2904: /* printf("%f ",pmmij[i][j]); */
2905: /* } */
2906: /* printf("\n"); */
2907: /* } */
2908: /* } */
1.217 brouard 2909: savm=oldm;
2910: oldm=newm;
1.266 brouard 2911:
1.217 brouard 2912: for(j=1; j<=nlstate; j++){
2913: max[j]=0.;
2914: min[j]=1.;
2915: }
2916: for(j=1; j<=nlstate; j++){
2917: for(i=1;i<=nlstate;i++){
1.234 brouard 2918: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2919: bprlim[i][j]= newm[i][j];
2920: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2921: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2922: }
2923: }
1.218 brouard 2924:
1.217 brouard 2925: maxmax=0.;
2926: for(i=1; i<=nlstate; i++){
2927: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2928: maxmax=FMAX(maxmax,meandiff[i]);
2929: /* 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 2930: } /* i loop */
1.217 brouard 2931: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2932: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2933: if(maxmax < ftolpl){
1.220 brouard 2934: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2935: free_vector(min,1,nlstate);
2936: free_vector(max,1,nlstate);
2937: free_vector(meandiff,1,nlstate);
2938: return bprlim;
2939: }
1.288 brouard 2940: } /* agefin loop */
1.217 brouard 2941: /* After some age loop it doesn't converge */
1.288 brouard 2942: if(!first){
1.247 brouard 2943: first=1;
2944: 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\
2945: Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
2946: }
2947: 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 2948: 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);
2949: /* 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); */
2950: free_vector(min,1,nlstate);
2951: free_vector(max,1,nlstate);
2952: free_vector(meandiff,1,nlstate);
2953:
2954: return bprlim; /* should not reach here */
2955: }
2956:
1.126 brouard 2957: /*************** transition probabilities ***************/
2958:
2959: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2960: {
1.138 brouard 2961: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2962: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2963: model to the ncovmodel covariates (including constant and age).
2964: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2965: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2966: ncth covariate in the global vector x is given by the formula:
2967: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2968: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2969: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2970: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2971: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2972: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2973: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2974: */
2975: double s1, lnpijopii;
1.126 brouard 2976: /*double t34;*/
1.164 brouard 2977: int i,j, nc, ii, jj;
1.126 brouard 2978:
1.223 brouard 2979: for(i=1; i<= nlstate; i++){
2980: for(j=1; j<i;j++){
2981: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2982: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2983: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2984: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2985: }
2986: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2987: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2988: }
2989: for(j=i+1; j<=nlstate+ndeath;j++){
2990: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2991: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2992: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2993: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2994: }
2995: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2996: }
2997: }
1.218 brouard 2998:
1.223 brouard 2999: for(i=1; i<= nlstate; i++){
3000: s1=0;
3001: for(j=1; j<i; j++){
3002: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3003: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3004: }
3005: for(j=i+1; j<=nlstate+ndeath; j++){
3006: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3007: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3008: }
3009: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3010: ps[i][i]=1./(s1+1.);
3011: /* Computing other pijs */
3012: for(j=1; j<i; j++)
3013: ps[i][j]= exp(ps[i][j])*ps[i][i];
3014: for(j=i+1; j<=nlstate+ndeath; j++)
3015: ps[i][j]= exp(ps[i][j])*ps[i][i];
3016: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3017: } /* end i */
1.218 brouard 3018:
1.223 brouard 3019: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3020: for(jj=1; jj<= nlstate+ndeath; jj++){
3021: ps[ii][jj]=0;
3022: ps[ii][ii]=1;
3023: }
3024: }
1.294 brouard 3025:
3026:
1.223 brouard 3027: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3028: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3029: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3030: /* } */
3031: /* printf("\n "); */
3032: /* } */
3033: /* printf("\n ");printf("%lf ",cov[2]);*/
3034: /*
3035: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 3036: goto end;*/
1.266 brouard 3037: return ps; /* Pointer is unchanged since its call */
1.126 brouard 3038: }
3039:
1.218 brouard 3040: /*************** backward transition probabilities ***************/
3041:
3042: /* 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 ) */
3043: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
3044: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
3045: {
1.302 brouard 3046: /* 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 3047: * 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 3048: */
1.218 brouard 3049: int i, ii, j,k;
1.222 brouard 3050:
3051: double **out, **pmij();
3052: double sumnew=0.;
1.218 brouard 3053: double agefin;
1.292 brouard 3054: 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 3055: double **dnewm, **dsavm, **doldm;
3056: double **bbmij;
3057:
1.218 brouard 3058: doldm=ddoldms; /* global pointers */
1.222 brouard 3059: dnewm=ddnewms;
3060: dsavm=ddsavms;
3061:
3062: agefin=cov[2];
1.268 brouard 3063: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 3064: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 3065: the observed prevalence (with this covariate ij) at beginning of transition */
3066: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 3067:
3068: /* P_x */
1.266 brouard 3069: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 3070: /* outputs pmmij which is a stochastic matrix in row */
3071:
3072: /* Diag(w_x) */
1.292 brouard 3073: /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
1.268 brouard 3074: sumnew=0.;
1.269 brouard 3075: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 3076: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.297 brouard 3077: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 3078: sumnew+=prevacurrent[(int)agefin][ii][ij];
3079: }
3080: if(sumnew >0.01){ /* At least some value in the prevalence */
3081: for (ii=1;ii<=nlstate+ndeath;ii++){
3082: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 3083: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3084: }
3085: }else{
3086: for (ii=1;ii<=nlstate+ndeath;ii++){
3087: for (j=1;j<=nlstate+ndeath;j++)
3088: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3089: }
3090: /* if(sumnew <0.9){ */
3091: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3092: /* } */
3093: }
3094: k3=0.0; /* We put the last diagonal to 0 */
3095: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3096: doldm[ii][ii]= k3;
3097: }
3098: /* End doldm, At the end doldm is diag[(w_i)] */
3099:
1.292 brouard 3100: /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
3101: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
1.268 brouard 3102:
1.292 brouard 3103: /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
1.268 brouard 3104: /* 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 3105: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3106: sumnew=0.;
1.222 brouard 3107: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3108: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3109: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3110: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3111: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3112: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3113: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3114: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3115: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3116: /* }else */
1.268 brouard 3117: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3118: } /*End ii */
3119: } /* 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 */
3120:
1.292 brouard 3121: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
1.268 brouard 3122: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3123: /* end bmij */
1.266 brouard 3124: return ps; /*pointer is unchanged */
1.218 brouard 3125: }
1.217 brouard 3126: /*************** transition probabilities ***************/
3127:
1.218 brouard 3128: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3129: {
3130: /* According to parameters values stored in x and the covariate's values stored in cov,
3131: computes the probability to be observed in state j being in state i by appying the
3132: model to the ncovmodel covariates (including constant and age).
3133: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3134: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3135: ncth covariate in the global vector x is given by the formula:
3136: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3137: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3138: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3139: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3140: Outputs ps[i][j] the probability to be observed in j being in j according to
3141: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3142: */
3143: double s1, lnpijopii;
3144: /*double t34;*/
3145: int i,j, nc, ii, jj;
3146:
1.234 brouard 3147: for(i=1; i<= nlstate; i++){
3148: for(j=1; j<i;j++){
3149: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3150: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3151: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3152: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3153: }
3154: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3155: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3156: }
3157: for(j=i+1; j<=nlstate+ndeath;j++){
3158: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3159: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3160: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3161: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3162: }
3163: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3164: }
3165: }
3166:
3167: for(i=1; i<= nlstate; i++){
3168: s1=0;
3169: for(j=1; j<i; j++){
3170: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3171: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3172: }
3173: for(j=i+1; j<=nlstate+ndeath; j++){
3174: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3175: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3176: }
3177: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3178: ps[i][i]=1./(s1+1.);
3179: /* Computing other pijs */
3180: for(j=1; j<i; j++)
3181: ps[i][j]= exp(ps[i][j])*ps[i][i];
3182: for(j=i+1; j<=nlstate+ndeath; j++)
3183: ps[i][j]= exp(ps[i][j])*ps[i][i];
3184: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3185: } /* end i */
3186:
3187: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3188: for(jj=1; jj<= nlstate+ndeath; jj++){
3189: ps[ii][jj]=0;
3190: ps[ii][ii]=1;
3191: }
3192: }
1.296 brouard 3193: /* Added for prevbcast */ /* Transposed matrix too */
1.234 brouard 3194: for(jj=1; jj<= nlstate+ndeath; jj++){
3195: s1=0.;
3196: for(ii=1; ii<= nlstate+ndeath; ii++){
3197: s1+=ps[ii][jj];
3198: }
3199: for(ii=1; ii<= nlstate; ii++){
3200: ps[ii][jj]=ps[ii][jj]/s1;
3201: }
3202: }
3203: /* Transposition */
3204: for(jj=1; jj<= nlstate+ndeath; jj++){
3205: for(ii=jj; ii<= nlstate+ndeath; ii++){
3206: s1=ps[ii][jj];
3207: ps[ii][jj]=ps[jj][ii];
3208: ps[jj][ii]=s1;
3209: }
3210: }
3211: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3212: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3213: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3214: /* } */
3215: /* printf("\n "); */
3216: /* } */
3217: /* printf("\n ");printf("%lf ",cov[2]);*/
3218: /*
3219: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3220: goto end;*/
3221: return ps;
1.217 brouard 3222: }
3223:
3224:
1.126 brouard 3225: /**************** Product of 2 matrices ******************/
3226:
1.145 brouard 3227: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3228: {
3229: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3230: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3231: /* in, b, out are matrice of pointers which should have been initialized
3232: before: only the contents of out is modified. The function returns
3233: a pointer to pointers identical to out */
1.145 brouard 3234: int i, j, k;
1.126 brouard 3235: for(i=nrl; i<= nrh; i++)
1.145 brouard 3236: for(k=ncolol; k<=ncoloh; k++){
3237: out[i][k]=0.;
3238: for(j=ncl; j<=nch; j++)
3239: out[i][k] +=in[i][j]*b[j][k];
3240: }
1.126 brouard 3241: return out;
3242: }
3243:
3244:
3245: /************* Higher Matrix Product ***************/
3246:
1.235 brouard 3247: 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 3248: {
1.218 brouard 3249: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3250: 'nhstepm*hstepm*stepm' months (i.e. until
3251: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3252: nhstepm*hstepm matrices.
3253: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3254: (typically every 2 years instead of every month which is too big
3255: for the memory).
3256: Model is determined by parameters x and covariates have to be
3257: included manually here.
3258:
3259: */
3260:
3261: int i, j, d, h, k;
1.131 brouard 3262: double **out, cov[NCOVMAX+1];
1.126 brouard 3263: double **newm;
1.187 brouard 3264: double agexact;
1.214 brouard 3265: double agebegin, ageend;
1.126 brouard 3266:
3267: /* Hstepm could be zero and should return the unit matrix */
3268: for (i=1;i<=nlstate+ndeath;i++)
3269: for (j=1;j<=nlstate+ndeath;j++){
3270: oldm[i][j]=(i==j ? 1.0 : 0.0);
3271: po[i][j][0]=(i==j ? 1.0 : 0.0);
3272: }
3273: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3274: for(h=1; h <=nhstepm; h++){
3275: for(d=1; d <=hstepm; d++){
3276: newm=savm;
3277: /* Covariates have to be included here again */
3278: cov[1]=1.;
1.214 brouard 3279: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3280: cov[2]=agexact;
3281: if(nagesqr==1)
1.227 brouard 3282: cov[3]= agexact*agexact;
1.235 brouard 3283: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3284: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3285: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3286: /* 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)); */
3287: }
3288: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3289: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3290: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3291: /* 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]); */
3292: }
3293: for (k=1; k<=cptcovage;k++){
3294: if(Dummy[Tvar[Tage[k]]]){
3295: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3296: } else{
3297: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3298: }
3299: /* 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]); */
3300: }
3301: for (k=1; k<=cptcovprod;k++){ /* */
3302: /* 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]); */
3303: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3304: }
3305: /* for (k=1; k<=cptcovn;k++) */
3306: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3307: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3308: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3309: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3310: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3311:
3312:
1.126 brouard 3313: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3314: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3315: /* right multiplication of oldm by the current matrix */
1.126 brouard 3316: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3317: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3318: /* if((int)age == 70){ */
3319: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3320: /* for(i=1; i<=nlstate+ndeath; i++) { */
3321: /* printf("%d pmmij ",i); */
3322: /* for(j=1;j<=nlstate+ndeath;j++) { */
3323: /* printf("%f ",pmmij[i][j]); */
3324: /* } */
3325: /* printf(" oldm "); */
3326: /* for(j=1;j<=nlstate+ndeath;j++) { */
3327: /* printf("%f ",oldm[i][j]); */
3328: /* } */
3329: /* printf("\n"); */
3330: /* } */
3331: /* } */
1.126 brouard 3332: savm=oldm;
3333: oldm=newm;
3334: }
3335: for(i=1; i<=nlstate+ndeath; i++)
3336: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3337: po[i][j][h]=newm[i][j];
3338: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3339: }
1.128 brouard 3340: /*printf("h=%d ",h);*/
1.126 brouard 3341: } /* end h */
1.267 brouard 3342: /* printf("\n H=%d \n",h); */
1.126 brouard 3343: return po;
3344: }
3345:
1.217 brouard 3346: /************* Higher Back Matrix Product ***************/
1.218 brouard 3347: /* 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 3348: 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 3349: {
1.266 brouard 3350: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3351: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3352: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3353: nhstepm*hstepm matrices.
3354: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3355: (typically every 2 years instead of every month which is too big
1.217 brouard 3356: for the memory).
1.218 brouard 3357: Model is determined by parameters x and covariates have to be
1.266 brouard 3358: included manually here. Then we use a call to bmij(x and cov)
3359: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3360: */
1.217 brouard 3361:
3362: int i, j, d, h, k;
1.266 brouard 3363: double **out, cov[NCOVMAX+1], **bmij();
3364: double **newm, ***newmm;
1.217 brouard 3365: double agexact;
3366: double agebegin, ageend;
1.222 brouard 3367: double **oldm, **savm;
1.217 brouard 3368:
1.266 brouard 3369: newmm=po; /* To be saved */
3370: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3371: /* Hstepm could be zero and should return the unit matrix */
3372: for (i=1;i<=nlstate+ndeath;i++)
3373: for (j=1;j<=nlstate+ndeath;j++){
3374: oldm[i][j]=(i==j ? 1.0 : 0.0);
3375: po[i][j][0]=(i==j ? 1.0 : 0.0);
3376: }
3377: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3378: for(h=1; h <=nhstepm; h++){
3379: for(d=1; d <=hstepm; d++){
3380: newm=savm;
3381: /* Covariates have to be included here again */
3382: cov[1]=1.;
1.271 brouard 3383: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3384: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3385: cov[2]=agexact;
3386: if(nagesqr==1)
1.222 brouard 3387: cov[3]= agexact*agexact;
1.266 brouard 3388: for (k=1; k<=cptcovn;k++){
3389: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3390: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3391: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3392: /* 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)); */
3393: }
1.267 brouard 3394: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3395: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3396: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3397: /* 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]); */
3398: }
3399: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3400: if(Dummy[Tvar[Tage[k]]]){
3401: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3402: } else{
3403: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3404: }
3405: /* 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]); */
3406: }
3407: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3408: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3409: }
1.217 brouard 3410: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3411: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3412:
1.218 brouard 3413: /* Careful transposed matrix */
1.266 brouard 3414: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3415: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3416: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3417: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3418: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3419: /* if((int)age == 70){ */
3420: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3421: /* for(i=1; i<=nlstate+ndeath; i++) { */
3422: /* printf("%d pmmij ",i); */
3423: /* for(j=1;j<=nlstate+ndeath;j++) { */
3424: /* printf("%f ",pmmij[i][j]); */
3425: /* } */
3426: /* printf(" oldm "); */
3427: /* for(j=1;j<=nlstate+ndeath;j++) { */
3428: /* printf("%f ",oldm[i][j]); */
3429: /* } */
3430: /* printf("\n"); */
3431: /* } */
3432: /* } */
3433: savm=oldm;
3434: oldm=newm;
3435: }
3436: for(i=1; i<=nlstate+ndeath; i++)
3437: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3438: po[i][j][h]=newm[i][j];
1.268 brouard 3439: /* if(h==nhstepm) */
3440: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3441: }
1.268 brouard 3442: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3443: } /* end h */
1.268 brouard 3444: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3445: return po;
3446: }
3447:
3448:
1.162 brouard 3449: #ifdef NLOPT
3450: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3451: double fret;
3452: double *xt;
3453: int j;
3454: myfunc_data *d2 = (myfunc_data *) pd;
3455: /* xt = (p1-1); */
3456: xt=vector(1,n);
3457: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3458:
3459: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3460: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3461: printf("Function = %.12lf ",fret);
3462: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3463: printf("\n");
3464: free_vector(xt,1,n);
3465: return fret;
3466: }
3467: #endif
1.126 brouard 3468:
3469: /*************** log-likelihood *************/
3470: double func( double *x)
3471: {
1.226 brouard 3472: int i, ii, j, k, mi, d, kk;
3473: int ioffset=0;
3474: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3475: double **out;
3476: double lli; /* Individual log likelihood */
3477: int s1, s2;
1.228 brouard 3478: 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 3479: double bbh, survp;
3480: long ipmx;
3481: double agexact;
3482: /*extern weight */
3483: /* We are differentiating ll according to initial status */
3484: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3485: /*for(i=1;i<imx;i++)
3486: printf(" %d\n",s[4][i]);
3487: */
1.162 brouard 3488:
1.226 brouard 3489: ++countcallfunc;
1.162 brouard 3490:
1.226 brouard 3491: cov[1]=1.;
1.126 brouard 3492:
1.226 brouard 3493: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3494: ioffset=0;
1.226 brouard 3495: if(mle==1){
3496: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3497: /* Computes the values of the ncovmodel covariates of the model
3498: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3499: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3500: to be observed in j being in i according to the model.
3501: */
1.243 brouard 3502: ioffset=2+nagesqr ;
1.233 brouard 3503: /* Fixed */
1.234 brouard 3504: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3505: 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)*/
3506: }
1.226 brouard 3507: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3508: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3509: has been calculated etc */
3510: /* For an individual i, wav[i] gives the number of effective waves */
3511: /* We compute the contribution to Likelihood of each effective transition
3512: mw[mi][i] is real wave of the mi th effectve wave */
3513: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3514: s2=s[mw[mi+1][i]][i];
3515: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3516: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3517: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3518: */
3519: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3520: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3521: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3522: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3523: }
3524: for (ii=1;ii<=nlstate+ndeath;ii++)
3525: for (j=1;j<=nlstate+ndeath;j++){
3526: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3527: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3528: }
3529: for(d=0; d<dh[mi][i]; d++){
3530: newm=savm;
3531: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3532: cov[2]=agexact;
3533: if(nagesqr==1)
3534: cov[3]= agexact*agexact; /* Should be changed here */
3535: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3536: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3537: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3538: else
3539: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3540: }
3541: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3542: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3543: savm=oldm;
3544: oldm=newm;
3545: } /* end mult */
3546:
3547: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3548: /* But now since version 0.9 we anticipate for bias at large stepm.
3549: * If stepm is larger than one month (smallest stepm) and if the exact delay
3550: * (in months) between two waves is not a multiple of stepm, we rounded to
3551: * the nearest (and in case of equal distance, to the lowest) interval but now
3552: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3553: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3554: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3555: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3556: * -stepm/2 to stepm/2 .
3557: * For stepm=1 the results are the same as for previous versions of Imach.
3558: * For stepm > 1 the results are less biased than in previous versions.
3559: */
1.234 brouard 3560: s1=s[mw[mi][i]][i];
3561: s2=s[mw[mi+1][i]][i];
3562: bbh=(double)bh[mi][i]/(double)stepm;
3563: /* bias bh is positive if real duration
3564: * is higher than the multiple of stepm and negative otherwise.
3565: */
3566: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3567: if( s2 > nlstate){
3568: /* i.e. if s2 is a death state and if the date of death is known
3569: then the contribution to the likelihood is the probability to
3570: die between last step unit time and current step unit time,
3571: which is also equal to probability to die before dh
3572: minus probability to die before dh-stepm .
3573: In version up to 0.92 likelihood was computed
3574: as if date of death was unknown. Death was treated as any other
3575: health state: the date of the interview describes the actual state
3576: and not the date of a change in health state. The former idea was
3577: to consider that at each interview the state was recorded
3578: (healthy, disable or death) and IMaCh was corrected; but when we
3579: introduced the exact date of death then we should have modified
3580: the contribution of an exact death to the likelihood. This new
3581: contribution is smaller and very dependent of the step unit
3582: stepm. It is no more the probability to die between last interview
3583: and month of death but the probability to survive from last
3584: interview up to one month before death multiplied by the
3585: probability to die within a month. Thanks to Chris
3586: Jackson for correcting this bug. Former versions increased
3587: mortality artificially. The bad side is that we add another loop
3588: which slows down the processing. The difference can be up to 10%
3589: lower mortality.
3590: */
3591: /* If, at the beginning of the maximization mostly, the
3592: cumulative probability or probability to be dead is
3593: constant (ie = 1) over time d, the difference is equal to
3594: 0. out[s1][3] = savm[s1][3]: probability, being at state
3595: s1 at precedent wave, to be dead a month before current
3596: wave is equal to probability, being at state s1 at
3597: precedent wave, to be dead at mont of the current
3598: wave. Then the observed probability (that this person died)
3599: is null according to current estimated parameter. In fact,
3600: it should be very low but not zero otherwise the log go to
3601: infinity.
3602: */
1.183 brouard 3603: /* #ifdef INFINITYORIGINAL */
3604: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3605: /* #else */
3606: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3607: /* lli=log(mytinydouble); */
3608: /* else */
3609: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3610: /* #endif */
1.226 brouard 3611: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3612:
1.226 brouard 3613: } else if ( s2==-1 ) { /* alive */
3614: for (j=1,survp=0. ; j<=nlstate; j++)
3615: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3616: /*survp += out[s1][j]; */
3617: lli= log(survp);
3618: }
3619: else if (s2==-4) {
3620: for (j=3,survp=0. ; j<=nlstate; j++)
3621: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3622: lli= log(survp);
3623: }
3624: else if (s2==-5) {
3625: for (j=1,survp=0. ; j<=2; j++)
3626: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3627: lli= log(survp);
3628: }
3629: else{
3630: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3631: /* 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 */
3632: }
3633: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3634: /*if(lli ==000.0)*/
3635: /*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); */
3636: ipmx +=1;
3637: sw += weight[i];
3638: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3639: /* if (lli < log(mytinydouble)){ */
3640: /* 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); */
3641: /* 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]); */
3642: /* } */
3643: } /* end of wave */
3644: } /* end of individual */
3645: } else if(mle==2){
3646: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3647: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3648: for(mi=1; mi<= wav[i]-1; mi++){
3649: for (ii=1;ii<=nlstate+ndeath;ii++)
3650: for (j=1;j<=nlstate+ndeath;j++){
3651: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3652: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3653: }
3654: for(d=0; d<=dh[mi][i]; d++){
3655: newm=savm;
3656: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3657: cov[2]=agexact;
3658: if(nagesqr==1)
3659: cov[3]= agexact*agexact;
3660: for (kk=1; kk<=cptcovage;kk++) {
3661: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3662: }
3663: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3664: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3665: savm=oldm;
3666: oldm=newm;
3667: } /* end mult */
3668:
3669: s1=s[mw[mi][i]][i];
3670: s2=s[mw[mi+1][i]][i];
3671: bbh=(double)bh[mi][i]/(double)stepm;
3672: 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 */
3673: ipmx +=1;
3674: sw += weight[i];
3675: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3676: } /* end of wave */
3677: } /* end of individual */
3678: } else if(mle==3){ /* exponential inter-extrapolation */
3679: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3680: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3681: for(mi=1; mi<= wav[i]-1; mi++){
3682: for (ii=1;ii<=nlstate+ndeath;ii++)
3683: for (j=1;j<=nlstate+ndeath;j++){
3684: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3685: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3686: }
3687: for(d=0; d<dh[mi][i]; d++){
3688: newm=savm;
3689: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3690: cov[2]=agexact;
3691: if(nagesqr==1)
3692: cov[3]= agexact*agexact;
3693: for (kk=1; kk<=cptcovage;kk++) {
3694: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3695: }
3696: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3697: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3698: savm=oldm;
3699: oldm=newm;
3700: } /* end mult */
3701:
3702: s1=s[mw[mi][i]][i];
3703: s2=s[mw[mi+1][i]][i];
3704: bbh=(double)bh[mi][i]/(double)stepm;
3705: 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 */
3706: ipmx +=1;
3707: sw += weight[i];
3708: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3709: } /* end of wave */
3710: } /* end of individual */
3711: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3712: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3713: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3714: for(mi=1; mi<= wav[i]-1; mi++){
3715: for (ii=1;ii<=nlstate+ndeath;ii++)
3716: for (j=1;j<=nlstate+ndeath;j++){
3717: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3718: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3719: }
3720: for(d=0; d<dh[mi][i]; d++){
3721: newm=savm;
3722: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3723: cov[2]=agexact;
3724: if(nagesqr==1)
3725: cov[3]= agexact*agexact;
3726: for (kk=1; kk<=cptcovage;kk++) {
3727: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3728: }
1.126 brouard 3729:
1.226 brouard 3730: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3731: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3732: savm=oldm;
3733: oldm=newm;
3734: } /* end mult */
3735:
3736: s1=s[mw[mi][i]][i];
3737: s2=s[mw[mi+1][i]][i];
3738: if( s2 > nlstate){
3739: lli=log(out[s1][s2] - savm[s1][s2]);
3740: } else if ( s2==-1 ) { /* alive */
3741: for (j=1,survp=0. ; j<=nlstate; j++)
3742: survp += out[s1][j];
3743: lli= log(survp);
3744: }else{
3745: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3746: }
3747: ipmx +=1;
3748: sw += weight[i];
3749: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3750: /* 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 3751: } /* end of wave */
3752: } /* end of individual */
3753: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3754: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3755: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3756: for(mi=1; mi<= wav[i]-1; mi++){
3757: for (ii=1;ii<=nlstate+ndeath;ii++)
3758: for (j=1;j<=nlstate+ndeath;j++){
3759: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3760: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3761: }
3762: for(d=0; d<dh[mi][i]; d++){
3763: newm=savm;
3764: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3765: cov[2]=agexact;
3766: if(nagesqr==1)
3767: cov[3]= agexact*agexact;
3768: for (kk=1; kk<=cptcovage;kk++) {
3769: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3770: }
1.126 brouard 3771:
1.226 brouard 3772: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3773: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3774: savm=oldm;
3775: oldm=newm;
3776: } /* end mult */
3777:
3778: s1=s[mw[mi][i]][i];
3779: s2=s[mw[mi+1][i]][i];
3780: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3781: ipmx +=1;
3782: sw += weight[i];
3783: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3784: /*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]);*/
3785: } /* end of wave */
3786: } /* end of individual */
3787: } /* End of if */
3788: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3789: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3790: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3791: return -l;
1.126 brouard 3792: }
3793:
3794: /*************** log-likelihood *************/
3795: double funcone( double *x)
3796: {
1.228 brouard 3797: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3798: int i, ii, j, k, mi, d, kk;
1.228 brouard 3799: int ioffset=0;
1.131 brouard 3800: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3801: double **out;
3802: double lli; /* Individual log likelihood */
3803: double llt;
3804: int s1, s2;
1.228 brouard 3805: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3806:
1.126 brouard 3807: double bbh, survp;
1.187 brouard 3808: double agexact;
1.214 brouard 3809: double agebegin, ageend;
1.126 brouard 3810: /*extern weight */
3811: /* We are differentiating ll according to initial status */
3812: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3813: /*for(i=1;i<imx;i++)
3814: printf(" %d\n",s[4][i]);
3815: */
3816: cov[1]=1.;
3817:
3818: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3819: ioffset=0;
3820: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3821: /* ioffset=2+nagesqr+cptcovage; */
3822: ioffset=2+nagesqr;
1.232 brouard 3823: /* Fixed */
1.224 brouard 3824: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3825: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3826: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3827: 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)*/
3828: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3829: /* cov[2+6]=covar[Tvar[6]][i]; */
3830: /* cov[2+6]=covar[2][i]; V2 */
3831: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3832: /* cov[2+7]=covar[Tvar[7]][i]; */
3833: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3834: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3835: /* cov[2+9]=covar[Tvar[9]][i]; */
3836: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3837: }
1.232 brouard 3838: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3839: /* 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?)*\/ */
3840: /* } */
1.231 brouard 3841: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3842: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3843: /* } */
1.225 brouard 3844:
1.233 brouard 3845:
3846: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3847: /* Wave varying (but not age varying) */
3848: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3849: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3850: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3851: }
1.232 brouard 3852: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3853: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3854: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3855: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3856: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3857: /* 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 3858: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3859: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3860: /* /\* 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]); *\/ */
3861: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3862: /* } */
1.126 brouard 3863: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3864: for (j=1;j<=nlstate+ndeath;j++){
3865: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3866: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3867: }
1.214 brouard 3868:
3869: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3870: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3871: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3872: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3873: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3874: and mw[mi+1][i]. dh depends on stepm.*/
3875: newm=savm;
1.247 brouard 3876: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3877: cov[2]=agexact;
3878: if(nagesqr==1)
3879: cov[3]= agexact*agexact;
3880: for (kk=1; kk<=cptcovage;kk++) {
3881: if(!FixedV[Tvar[Tage[kk]]])
3882: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3883: else
3884: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3885: }
3886: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3887: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3888: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3889: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3890: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3891: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3892: savm=oldm;
3893: oldm=newm;
1.126 brouard 3894: } /* end mult */
3895:
3896: s1=s[mw[mi][i]][i];
3897: s2=s[mw[mi+1][i]][i];
1.217 brouard 3898: /* if(s2==-1){ */
1.268 brouard 3899: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3900: /* /\* exit(1); *\/ */
3901: /* } */
1.126 brouard 3902: bbh=(double)bh[mi][i]/(double)stepm;
3903: /* bias is positive if real duration
3904: * is higher than the multiple of stepm and negative otherwise.
3905: */
3906: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3907: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3908: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3909: for (j=1,survp=0. ; j<=nlstate; j++)
3910: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3911: lli= log(survp);
1.126 brouard 3912: }else if (mle==1){
1.242 brouard 3913: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3914: } else if(mle==2){
1.242 brouard 3915: 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 3916: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3917: 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 3918: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3919: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3920: } else{ /* mle=0 back to 1 */
1.242 brouard 3921: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3922: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3923: } /* End of if */
3924: ipmx +=1;
3925: sw += weight[i];
3926: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3927: /*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 3928: if(globpr){
1.246 brouard 3929: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3930: %11.6f %11.6f %11.6f ", \
1.242 brouard 3931: 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 3932: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3933: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3934: llt +=ll[k]*gipmx/gsw;
3935: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3936: }
3937: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3938: }
1.232 brouard 3939: } /* end of wave */
3940: } /* end of individual */
3941: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3942: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3943: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3944: if(globpr==0){ /* First time we count the contributions and weights */
3945: gipmx=ipmx;
3946: gsw=sw;
3947: }
3948: return -l;
1.126 brouard 3949: }
3950:
3951:
3952: /*************** function likelione ***********/
1.292 brouard 3953: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
1.126 brouard 3954: {
3955: /* This routine should help understanding what is done with
3956: the selection of individuals/waves and
3957: to check the exact contribution to the likelihood.
3958: Plotting could be done.
3959: */
3960: int k;
3961:
3962: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3963: strcpy(fileresilk,"ILK_");
1.202 brouard 3964: strcat(fileresilk,fileresu);
1.126 brouard 3965: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3966: printf("Problem with resultfile: %s\n", fileresilk);
3967: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3968: }
1.214 brouard 3969: 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");
3970: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3971: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3972: for(k=1; k<=nlstate; k++)
3973: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3974: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3975: }
3976:
1.292 brouard 3977: *fretone=(*func)(p);
1.126 brouard 3978: if(*globpri !=0){
3979: fclose(ficresilk);
1.205 brouard 3980: if (mle ==0)
3981: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3982: else if(mle >=1)
3983: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3984: 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 3985: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3986:
3987: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3988: 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 3989: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3990: }
1.207 brouard 3991: 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 3992: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3993: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3994: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3995: fflush(fichtm);
1.205 brouard 3996: }
1.126 brouard 3997: return;
3998: }
3999:
4000:
4001: /*********** Maximum Likelihood Estimation ***************/
4002:
4003: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
4004: {
1.165 brouard 4005: int i,j, iter=0;
1.126 brouard 4006: double **xi;
4007: double fret;
4008: double fretone; /* Only one call to likelihood */
4009: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 4010:
4011: #ifdef NLOPT
4012: int creturn;
4013: nlopt_opt opt;
4014: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
4015: double *lb;
4016: double minf; /* the minimum objective value, upon return */
4017: double * p1; /* Shifted parameters from 0 instead of 1 */
4018: myfunc_data dinst, *d = &dinst;
4019: #endif
4020:
4021:
1.126 brouard 4022: xi=matrix(1,npar,1,npar);
4023: for (i=1;i<=npar;i++)
4024: for (j=1;j<=npar;j++)
4025: xi[i][j]=(i==j ? 1.0 : 0.0);
4026: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 4027: strcpy(filerespow,"POW_");
1.126 brouard 4028: strcat(filerespow,fileres);
4029: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4030: printf("Problem with resultfile: %s\n", filerespow);
4031: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4032: }
4033: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4034: for (i=1;i<=nlstate;i++)
4035: for(j=1;j<=nlstate+ndeath;j++)
4036: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4037: fprintf(ficrespow,"\n");
1.162 brouard 4038: #ifdef POWELL
1.126 brouard 4039: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 4040: #endif
1.126 brouard 4041:
1.162 brouard 4042: #ifdef NLOPT
4043: #ifdef NEWUOA
4044: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
4045: #else
4046: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
4047: #endif
4048: lb=vector(0,npar-1);
4049: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
4050: nlopt_set_lower_bounds(opt, lb);
4051: nlopt_set_initial_step1(opt, 0.1);
4052:
4053: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
4054: d->function = func;
4055: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
4056: nlopt_set_min_objective(opt, myfunc, d);
4057: nlopt_set_xtol_rel(opt, ftol);
4058: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
4059: printf("nlopt failed! %d\n",creturn);
4060: }
4061: else {
4062: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
4063: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
4064: iter=1; /* not equal */
4065: }
4066: nlopt_destroy(opt);
4067: #endif
1.126 brouard 4068: free_matrix(xi,1,npar,1,npar);
4069: fclose(ficrespow);
1.203 brouard 4070: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
4071: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 4072: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 4073:
4074: }
4075:
4076: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 4077: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 4078: {
4079: double **a,**y,*x,pd;
1.203 brouard 4080: /* double **hess; */
1.164 brouard 4081: int i, j;
1.126 brouard 4082: int *indx;
4083:
4084: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4085: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4086: void lubksb(double **a, int npar, int *indx, double b[]) ;
4087: void ludcmp(double **a, int npar, int *indx, double *d) ;
4088: double gompertz(double p[]);
1.203 brouard 4089: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4090:
4091: printf("\nCalculation of the hessian matrix. Wait...\n");
4092: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4093: for (i=1;i<=npar;i++){
1.203 brouard 4094: printf("%d-",i);fflush(stdout);
4095: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4096:
4097: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4098:
4099: /* printf(" %f ",p[i]);
4100: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4101: }
4102:
4103: for (i=1;i<=npar;i++) {
4104: for (j=1;j<=npar;j++) {
4105: if (j>i) {
1.203 brouard 4106: printf(".%d-%d",i,j);fflush(stdout);
4107: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4108: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4109:
4110: hess[j][i]=hess[i][j];
4111: /*printf(" %lf ",hess[i][j]);*/
4112: }
4113: }
4114: }
4115: printf("\n");
4116: fprintf(ficlog,"\n");
4117:
4118: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4119: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4120:
4121: a=matrix(1,npar,1,npar);
4122: y=matrix(1,npar,1,npar);
4123: x=vector(1,npar);
4124: indx=ivector(1,npar);
4125: for (i=1;i<=npar;i++)
4126: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4127: ludcmp(a,npar,indx,&pd);
4128:
4129: for (j=1;j<=npar;j++) {
4130: for (i=1;i<=npar;i++) x[i]=0;
4131: x[j]=1;
4132: lubksb(a,npar,indx,x);
4133: for (i=1;i<=npar;i++){
4134: matcov[i][j]=x[i];
4135: }
4136: }
4137:
4138: printf("\n#Hessian matrix#\n");
4139: fprintf(ficlog,"\n#Hessian matrix#\n");
4140: for (i=1;i<=npar;i++) {
4141: for (j=1;j<=npar;j++) {
1.203 brouard 4142: printf("%.6e ",hess[i][j]);
4143: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4144: }
4145: printf("\n");
4146: fprintf(ficlog,"\n");
4147: }
4148:
1.203 brouard 4149: /* printf("\n#Covariance matrix#\n"); */
4150: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4151: /* for (i=1;i<=npar;i++) { */
4152: /* for (j=1;j<=npar;j++) { */
4153: /* printf("%.6e ",matcov[i][j]); */
4154: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4155: /* } */
4156: /* printf("\n"); */
4157: /* fprintf(ficlog,"\n"); */
4158: /* } */
4159:
1.126 brouard 4160: /* Recompute Inverse */
1.203 brouard 4161: /* for (i=1;i<=npar;i++) */
4162: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4163: /* ludcmp(a,npar,indx,&pd); */
4164:
4165: /* printf("\n#Hessian matrix recomputed#\n"); */
4166:
4167: /* for (j=1;j<=npar;j++) { */
4168: /* for (i=1;i<=npar;i++) x[i]=0; */
4169: /* x[j]=1; */
4170: /* lubksb(a,npar,indx,x); */
4171: /* for (i=1;i<=npar;i++){ */
4172: /* y[i][j]=x[i]; */
4173: /* printf("%.3e ",y[i][j]); */
4174: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4175: /* } */
4176: /* printf("\n"); */
4177: /* fprintf(ficlog,"\n"); */
4178: /* } */
4179:
4180: /* Verifying the inverse matrix */
4181: #ifdef DEBUGHESS
4182: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4183:
1.203 brouard 4184: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4185: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4186:
4187: for (j=1;j<=npar;j++) {
4188: for (i=1;i<=npar;i++){
1.203 brouard 4189: printf("%.2f ",y[i][j]);
4190: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4191: }
4192: printf("\n");
4193: fprintf(ficlog,"\n");
4194: }
1.203 brouard 4195: #endif
1.126 brouard 4196:
4197: free_matrix(a,1,npar,1,npar);
4198: free_matrix(y,1,npar,1,npar);
4199: free_vector(x,1,npar);
4200: free_ivector(indx,1,npar);
1.203 brouard 4201: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4202:
4203:
4204: }
4205:
4206: /*************** hessian matrix ****************/
4207: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4208: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4209: int i;
4210: int l=1, lmax=20;
1.203 brouard 4211: double k1,k2, res, fx;
1.132 brouard 4212: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4213: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4214: int k=0,kmax=10;
4215: double l1;
4216:
4217: fx=func(x);
4218: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4219: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4220: l1=pow(10,l);
4221: delts=delt;
4222: for(k=1 ; k <kmax; k=k+1){
4223: delt = delta*(l1*k);
4224: p2[theta]=x[theta] +delt;
1.145 brouard 4225: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4226: p2[theta]=x[theta]-delt;
4227: k2=func(p2)-fx;
4228: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4229: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4230:
1.203 brouard 4231: #ifdef DEBUGHESSII
1.126 brouard 4232: 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);
4233: 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);
4234: #endif
4235: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4236: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4237: k=kmax;
4238: }
4239: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4240: k=kmax; l=lmax*10;
1.126 brouard 4241: }
4242: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4243: delts=delt;
4244: }
1.203 brouard 4245: } /* End loop k */
1.126 brouard 4246: }
4247: delti[theta]=delts;
4248: return res;
4249:
4250: }
4251:
1.203 brouard 4252: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4253: {
4254: int i;
1.164 brouard 4255: int l=1, lmax=20;
1.126 brouard 4256: double k1,k2,k3,k4,res,fx;
1.132 brouard 4257: double p2[MAXPARM+1];
1.203 brouard 4258: int k, kmax=1;
4259: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4260:
4261: int firstime=0;
1.203 brouard 4262:
1.126 brouard 4263: fx=func(x);
1.203 brouard 4264: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4265: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4266: p2[thetai]=x[thetai]+delti[thetai]*k;
4267: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4268: k1=func(p2)-fx;
4269:
1.203 brouard 4270: p2[thetai]=x[thetai]+delti[thetai]*k;
4271: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4272: k2=func(p2)-fx;
4273:
1.203 brouard 4274: p2[thetai]=x[thetai]-delti[thetai]*k;
4275: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4276: k3=func(p2)-fx;
4277:
1.203 brouard 4278: p2[thetai]=x[thetai]-delti[thetai]*k;
4279: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4280: k4=func(p2)-fx;
1.203 brouard 4281: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4282: if(k1*k2*k3*k4 <0.){
1.208 brouard 4283: firstime=1;
1.203 brouard 4284: kmax=kmax+10;
1.208 brouard 4285: }
4286: if(kmax >=10 || firstime ==1){
1.246 brouard 4287: 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);
4288: 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 4289: 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);
4290: 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);
4291: }
4292: #ifdef DEBUGHESSIJ
4293: v1=hess[thetai][thetai];
4294: v2=hess[thetaj][thetaj];
4295: cv12=res;
4296: /* Computing eigen value of Hessian matrix */
4297: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4298: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4299: if ((lc2 <0) || (lc1 <0) ){
4300: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4301: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4302: 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);
4303: 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);
4304: }
1.126 brouard 4305: #endif
4306: }
4307: return res;
4308: }
4309:
1.203 brouard 4310: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4311: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4312: /* { */
4313: /* int i; */
4314: /* int l=1, lmax=20; */
4315: /* double k1,k2,k3,k4,res,fx; */
4316: /* double p2[MAXPARM+1]; */
4317: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4318: /* int k=0,kmax=10; */
4319: /* double l1; */
4320:
4321: /* fx=func(x); */
4322: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4323: /* l1=pow(10,l); */
4324: /* delts=delt; */
4325: /* for(k=1 ; k <kmax; k=k+1){ */
4326: /* delt = delti*(l1*k); */
4327: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4328: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4329: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4330: /* k1=func(p2)-fx; */
4331:
4332: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4333: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4334: /* k2=func(p2)-fx; */
4335:
4336: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4337: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4338: /* k3=func(p2)-fx; */
4339:
4340: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4341: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4342: /* k4=func(p2)-fx; */
4343: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4344: /* #ifdef DEBUGHESSIJ */
4345: /* 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); */
4346: /* 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); */
4347: /* #endif */
4348: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4349: /* k=kmax; */
4350: /* } */
4351: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4352: /* k=kmax; l=lmax*10; */
4353: /* } */
4354: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4355: /* delts=delt; */
4356: /* } */
4357: /* } /\* End loop k *\/ */
4358: /* } */
4359: /* delti[theta]=delts; */
4360: /* return res; */
4361: /* } */
4362:
4363:
1.126 brouard 4364: /************** Inverse of matrix **************/
4365: void ludcmp(double **a, int n, int *indx, double *d)
4366: {
4367: int i,imax,j,k;
4368: double big,dum,sum,temp;
4369: double *vv;
4370:
4371: vv=vector(1,n);
4372: *d=1.0;
4373: for (i=1;i<=n;i++) {
4374: big=0.0;
4375: for (j=1;j<=n;j++)
4376: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4377: if (big == 0.0){
4378: printf(" Singular Hessian matrix at row %d:\n",i);
4379: for (j=1;j<=n;j++) {
4380: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4381: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4382: }
4383: fflush(ficlog);
4384: fclose(ficlog);
4385: nrerror("Singular matrix in routine ludcmp");
4386: }
1.126 brouard 4387: vv[i]=1.0/big;
4388: }
4389: for (j=1;j<=n;j++) {
4390: for (i=1;i<j;i++) {
4391: sum=a[i][j];
4392: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4393: a[i][j]=sum;
4394: }
4395: big=0.0;
4396: for (i=j;i<=n;i++) {
4397: sum=a[i][j];
4398: for (k=1;k<j;k++)
4399: sum -= a[i][k]*a[k][j];
4400: a[i][j]=sum;
4401: if ( (dum=vv[i]*fabs(sum)) >= big) {
4402: big=dum;
4403: imax=i;
4404: }
4405: }
4406: if (j != imax) {
4407: for (k=1;k<=n;k++) {
4408: dum=a[imax][k];
4409: a[imax][k]=a[j][k];
4410: a[j][k]=dum;
4411: }
4412: *d = -(*d);
4413: vv[imax]=vv[j];
4414: }
4415: indx[j]=imax;
4416: if (a[j][j] == 0.0) a[j][j]=TINY;
4417: if (j != n) {
4418: dum=1.0/(a[j][j]);
4419: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4420: }
4421: }
4422: free_vector(vv,1,n); /* Doesn't work */
4423: ;
4424: }
4425:
4426: void lubksb(double **a, int n, int *indx, double b[])
4427: {
4428: int i,ii=0,ip,j;
4429: double sum;
4430:
4431: for (i=1;i<=n;i++) {
4432: ip=indx[i];
4433: sum=b[ip];
4434: b[ip]=b[i];
4435: if (ii)
4436: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4437: else if (sum) ii=i;
4438: b[i]=sum;
4439: }
4440: for (i=n;i>=1;i--) {
4441: sum=b[i];
4442: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4443: b[i]=sum/a[i][i];
4444: }
4445: }
4446:
4447: void pstamp(FILE *fichier)
4448: {
1.196 brouard 4449: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4450: }
4451:
1.297 brouard 4452: void date2dmy(double date,double *day, double *month, double *year){
4453: double yp=0., yp1=0., yp2=0.;
4454:
4455: yp1=modf(date,&yp);/* extracts integral of date in yp and
4456: fractional in yp1 */
4457: *year=yp;
4458: yp2=modf((yp1*12),&yp);
4459: *month=yp;
4460: yp1=modf((yp2*30.5),&yp);
4461: *day=yp;
4462: if(*day==0) *day=1;
4463: if(*month==0) *month=1;
4464: }
4465:
1.253 brouard 4466:
4467:
1.126 brouard 4468: /************ Frequencies ********************/
1.251 brouard 4469: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4470: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4471: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4472: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4473:
1.265 brouard 4474: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4475: int iind=0, iage=0;
4476: int mi; /* Effective wave */
4477: int first;
4478: double ***freq; /* Frequencies */
1.268 brouard 4479: 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 */
4480: 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 4481: double *meanq, *stdq, *idq;
1.226 brouard 4482: double **meanqt;
4483: double *pp, **prop, *posprop, *pospropt;
4484: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4485: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4486: double agebegin, ageend;
4487:
4488: pp=vector(1,nlstate);
1.251 brouard 4489: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4490: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4491: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4492: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4493: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4494: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4495: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4496: meanqt=matrix(1,lastpass,1,nqtveff);
4497: strcpy(fileresp,"P_");
4498: strcat(fileresp,fileresu);
4499: /*strcat(fileresphtm,fileresu);*/
4500: if((ficresp=fopen(fileresp,"w"))==NULL) {
4501: printf("Problem with prevalence resultfile: %s\n", fileresp);
4502: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4503: exit(0);
4504: }
1.240 brouard 4505:
1.226 brouard 4506: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4507: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4508: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4509: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4510: fflush(ficlog);
4511: exit(70);
4512: }
4513: else{
4514: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4515: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4516: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4517: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4518: }
1.237 brouard 4519: 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 4520:
1.226 brouard 4521: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4522: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4523: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4524: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4525: fflush(ficlog);
4526: exit(70);
1.240 brouard 4527: } else{
1.226 brouard 4528: 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 4529: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4530: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4531: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4532: }
1.240 brouard 4533: 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);
4534:
1.253 brouard 4535: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4536: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4537: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4538: j1=0;
1.126 brouard 4539:
1.227 brouard 4540: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4541: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4542: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4543:
4544:
1.226 brouard 4545: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4546: reference=low_education V1=0,V2=0
4547: med_educ V1=1 V2=0,
4548: high_educ V1=0 V2=1
4549: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4550: */
1.249 brouard 4551: dateintsum=0;
4552: k2cpt=0;
4553:
1.253 brouard 4554: if(cptcoveff == 0 )
1.265 brouard 4555: nl=1; /* Constant and age model only */
1.253 brouard 4556: else
4557: nl=2;
1.265 brouard 4558:
4559: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4560: /* Loop on nj=1 or 2 if dummy covariates j!=0
4561: * Loop on j1(1 to 2**cptcoveff) covariate combination
4562: * freq[s1][s2][iage] =0.
4563: * Loop on iind
4564: * ++freq[s1][s2][iage] weighted
4565: * end iind
4566: * if covariate and j!0
4567: * headers Variable on one line
4568: * endif cov j!=0
4569: * header of frequency table by age
4570: * Loop on age
4571: * pp[s1]+=freq[s1][s2][iage] weighted
4572: * pos+=freq[s1][s2][iage] weighted
4573: * Loop on s1 initial state
4574: * fprintf(ficresp
4575: * end s1
4576: * end age
4577: * if j!=0 computes starting values
4578: * end compute starting values
4579: * end j1
4580: * end nl
4581: */
1.253 brouard 4582: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4583: if(nj==1)
4584: j=0; /* First pass for the constant */
1.265 brouard 4585: else{
1.253 brouard 4586: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4587: }
1.251 brouard 4588: first=1;
1.265 brouard 4589: 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 4590: posproptt=0.;
4591: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4592: scanf("%d", i);*/
4593: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4594: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4595: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4596: freq[i][s2][m]=0;
1.251 brouard 4597:
4598: for (i=1; i<=nlstate; i++) {
1.240 brouard 4599: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4600: prop[i][m]=0;
4601: posprop[i]=0;
4602: pospropt[i]=0;
4603: }
1.283 brouard 4604: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4605: idq[z1]=0.;
4606: meanq[z1]=0.;
4607: stdq[z1]=0.;
1.283 brouard 4608: }
4609: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4610: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4611: /* meanqt[m][z1]=0.; */
4612: /* } */
4613: /* } */
1.251 brouard 4614: /* dateintsum=0; */
4615: /* k2cpt=0; */
4616:
1.265 brouard 4617: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4618: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4619: bool=1;
4620: if(j !=0){
4621: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4622: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4623: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4624: /* if(Tvaraff[z1] ==-20){ */
4625: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4626: /* }else if(Tvaraff[z1] ==-10){ */
4627: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4628: /* }else */
4629: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4630: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4631: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4632: /* 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",
4633: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4634: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4635: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4636: } /* Onlyf fixed */
4637: } /* end z1 */
4638: } /* cptcovn > 0 */
4639: } /* end any */
4640: }/* end j==0 */
1.265 brouard 4641: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4642: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4643: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4644: m=mw[mi][iind];
4645: if(j!=0){
4646: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4647: for (z1=1; z1<=cptcoveff; z1++) {
4648: if( Fixed[Tmodelind[z1]]==1){
4649: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4650: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4651: value is -1, we don't select. It differs from the
4652: constant and age model which counts them. */
4653: bool=0; /* not selected */
4654: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4655: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4656: bool=0;
4657: }
4658: }
4659: }
4660: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4661: } /* end j==0 */
4662: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4663: if(bool==1){ /*Selected */
1.251 brouard 4664: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4665: and mw[mi+1][iind]. dh depends on stepm. */
4666: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4667: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4668: if(m >=firstpass && m <=lastpass){
4669: k2=anint[m][iind]+(mint[m][iind]/12.);
4670: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4671: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4672: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4673: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4674: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4675: if (m<lastpass) {
4676: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4677: /* 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]); */
4678: if(s[m][iind]==-1)
4679: 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.));
4680: 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 4681: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4682: idq[z1]=idq[z1]+weight[iind];
4683: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4684: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4685: }
1.251 brouard 4686: /* if((int)agev[m][iind] == 55) */
4687: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4688: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4689: 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 4690: }
1.251 brouard 4691: } /* end if between passes */
4692: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4693: dateintsum=dateintsum+k2; /* on all covariates ?*/
4694: k2cpt++;
4695: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4696: }
1.251 brouard 4697: }else{
4698: bool=1;
4699: }/* end bool 2 */
4700: } /* end m */
1.284 brouard 4701: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4702: /* idq[z1]=idq[z1]+weight[iind]; */
4703: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4704: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4705: /* } */
1.251 brouard 4706: } /* end bool */
4707: } /* end iind = 1 to imx */
4708: /* prop[s][age] is feeded for any initial and valid live state as well as
4709: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4710:
4711:
4712: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4713: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4714: pstamp(ficresp);
1.251 brouard 4715: if (cptcoveff>0 && j!=0){
1.265 brouard 4716: pstamp(ficresp);
1.251 brouard 4717: printf( "\n#********** Variable ");
4718: fprintf(ficresp, "\n#********** Variable ");
4719: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4720: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4721: fprintf(ficlog, "\n#********** Variable ");
4722: for (z1=1; z1<=cptcoveff; z1++){
4723: if(!FixedV[Tvaraff[z1]]){
4724: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4725: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4726: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4727: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4728: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4729: }else{
1.251 brouard 4730: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4731: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4732: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4733: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4734: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4735: }
4736: }
4737: printf( "**********\n#");
4738: fprintf(ficresp, "**********\n#");
4739: fprintf(ficresphtm, "**********</h3>\n");
4740: fprintf(ficresphtmfr, "**********</h3>\n");
4741: fprintf(ficlog, "**********\n");
4742: }
1.284 brouard 4743: /*
4744: Printing means of quantitative variables if any
4745: */
4746: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4747: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4748: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4749: if(weightopt==1){
4750: printf(" Weighted mean and standard deviation of");
4751: fprintf(ficlog," Weighted mean and standard deviation of");
4752: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4753: }
1.285 brouard 4754: 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]));
4755: 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]));
4756: 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 4757: }
4758: /* for (z1=1; z1<= nqtveff; z1++) { */
4759: /* for(m=1;m<=lastpass;m++){ */
4760: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4761: /* } */
4762: /* } */
1.283 brouard 4763:
1.251 brouard 4764: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4765: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4766: fprintf(ficresp, " Age");
4767: 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 4768: for(i=1; i<=nlstate;i++) {
1.265 brouard 4769: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4770: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4771: }
1.265 brouard 4772: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4773: fprintf(ficresphtm, "\n");
4774:
4775: /* Header of frequency table by age */
4776: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4777: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4778: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4779: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4780: if(s2!=0 && m!=0)
4781: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4782: }
1.226 brouard 4783: }
1.251 brouard 4784: fprintf(ficresphtmfr, "\n");
4785:
4786: /* For each age */
4787: for(iage=iagemin; iage <= iagemax+3; iage++){
4788: fprintf(ficresphtm,"<tr>");
4789: if(iage==iagemax+1){
4790: fprintf(ficlog,"1");
4791: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4792: }else if(iage==iagemax+2){
4793: fprintf(ficlog,"0");
4794: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4795: }else if(iage==iagemax+3){
4796: fprintf(ficlog,"Total");
4797: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4798: }else{
1.240 brouard 4799: if(first==1){
1.251 brouard 4800: first=0;
4801: printf("See log file for details...\n");
4802: }
4803: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4804: fprintf(ficlog,"Age %d", iage);
4805: }
1.265 brouard 4806: for(s1=1; s1 <=nlstate ; s1++){
4807: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4808: pp[s1] += freq[s1][m][iage];
1.251 brouard 4809: }
1.265 brouard 4810: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4811: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4812: pos += freq[s1][m][iage];
4813: if(pp[s1]>=1.e-10){
1.251 brouard 4814: if(first==1){
1.265 brouard 4815: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4816: }
1.265 brouard 4817: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4818: }else{
4819: if(first==1)
1.265 brouard 4820: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4821: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4822: }
4823: }
4824:
1.265 brouard 4825: for(s1=1; s1 <=nlstate ; s1++){
4826: /* posprop[s1]=0; */
4827: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4828: pp[s1] += freq[s1][m][iage];
4829: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4830:
4831: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4832: pos += pp[s1]; /* pos is the total number of transitions until this age */
4833: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4834: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4835: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4836: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4837: }
4838:
4839: /* Writing ficresp */
4840: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4841: if( iage <= iagemax){
4842: fprintf(ficresp," %d",iage);
4843: }
4844: }else if( nj==2){
4845: if( iage <= iagemax){
4846: fprintf(ficresp," %d",iage);
4847: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4848: }
1.240 brouard 4849: }
1.265 brouard 4850: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4851: if(pos>=1.e-5){
1.251 brouard 4852: if(first==1)
1.265 brouard 4853: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4854: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4855: }else{
4856: if(first==1)
1.265 brouard 4857: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4858: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4859: }
4860: if( iage <= iagemax){
4861: if(pos>=1.e-5){
1.265 brouard 4862: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4863: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4864: }else if( nj==2){
4865: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4866: }
4867: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4868: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4869: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4870: } else{
4871: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4872: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4873: }
1.240 brouard 4874: }
1.265 brouard 4875: pospropt[s1] +=posprop[s1];
4876: } /* end loop s1 */
1.251 brouard 4877: /* pospropt=0.; */
1.265 brouard 4878: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4879: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4880: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4881: if(first==1){
1.265 brouard 4882: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4883: }
1.265 brouard 4884: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4885: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4886: }
1.265 brouard 4887: if(s1!=0 && m!=0)
4888: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4889: }
1.265 brouard 4890: } /* end loop s1 */
1.251 brouard 4891: posproptt=0.;
1.265 brouard 4892: for(s1=1; s1 <=nlstate; s1++){
4893: posproptt += pospropt[s1];
1.251 brouard 4894: }
4895: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4896: fprintf(ficresphtm,"</tr>\n");
4897: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4898: if(iage <= iagemax)
4899: fprintf(ficresp,"\n");
1.240 brouard 4900: }
1.251 brouard 4901: if(first==1)
4902: printf("Others in log...\n");
4903: fprintf(ficlog,"\n");
4904: } /* end loop age iage */
1.265 brouard 4905:
1.251 brouard 4906: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4907: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4908: if(posproptt < 1.e-5){
1.265 brouard 4909: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4910: }else{
1.265 brouard 4911: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4912: }
1.226 brouard 4913: }
1.251 brouard 4914: fprintf(ficresphtm,"</tr>\n");
4915: fprintf(ficresphtm,"</table>\n");
4916: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4917: if(posproptt < 1.e-5){
1.251 brouard 4918: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4919: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4920: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4921: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4922: invalidvarcomb[j1]=1;
1.226 brouard 4923: }else{
1.251 brouard 4924: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4925: invalidvarcomb[j1]=0;
1.226 brouard 4926: }
1.251 brouard 4927: fprintf(ficresphtmfr,"</table>\n");
4928: fprintf(ficlog,"\n");
4929: if(j!=0){
4930: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4931: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4932: for(k=1; k <=(nlstate+ndeath); k++){
4933: if (k != i) {
1.265 brouard 4934: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4935: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4936: if(j1==1){ /* All dummy covariates to zero */
4937: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4938: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4939: printf("%d%d ",i,k);
4940: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4941: 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]));
4942: 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]));
4943: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4944: }
1.253 brouard 4945: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4946: for(iage=iagemin; iage <= iagemax+3; iage++){
4947: x[iage]= (double)iage;
4948: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4949: /* 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 4950: }
1.268 brouard 4951: /* Some are not finite, but linreg will ignore these ages */
4952: no=0;
1.253 brouard 4953: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4954: pstart[s1]=b;
4955: pstart[s1-1]=a;
1.252 brouard 4956: }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 */
4957: 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]);
4958: 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 4959: 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 4960: printf("%d%d ",i,k);
4961: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4962: 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 4963: }else{ /* Other cases, like quantitative fixed or varying covariates */
4964: ;
4965: }
4966: /* printf("%12.7f )", param[i][jj][k]); */
4967: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4968: s1++;
1.251 brouard 4969: } /* end jj */
4970: } /* end k!= i */
4971: } /* end k */
1.265 brouard 4972: } /* end i, s1 */
1.251 brouard 4973: } /* end j !=0 */
4974: } /* end selected combination of covariate j1 */
4975: if(j==0){ /* We can estimate starting values from the occurences in each case */
4976: printf("#Freqsummary: Starting values for the constants:\n");
4977: fprintf(ficlog,"\n");
1.265 brouard 4978: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4979: for(k=1; k <=(nlstate+ndeath); k++){
4980: if (k != i) {
4981: printf("%d%d ",i,k);
4982: fprintf(ficlog,"%d%d ",i,k);
4983: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4984: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4985: if(jj==1){ /* Age has to be done */
1.265 brouard 4986: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4987: 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]));
4988: 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 4989: }
4990: /* printf("%12.7f )", param[i][jj][k]); */
4991: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4992: s1++;
1.250 brouard 4993: }
1.251 brouard 4994: printf("\n");
4995: fprintf(ficlog,"\n");
1.250 brouard 4996: }
4997: }
1.284 brouard 4998: } /* end of state i */
1.251 brouard 4999: printf("#Freqsummary\n");
5000: fprintf(ficlog,"\n");
1.265 brouard 5001: for(s1=-1; s1 <=nlstate+ndeath; s1++){
5002: for(s2=-1; s2 <=nlstate+ndeath; s2++){
5003: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
5004: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5005: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
5006: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
5007: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
5008: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 5009: /* } */
5010: }
1.265 brouard 5011: } /* end loop s1 */
1.251 brouard 5012:
5013: printf("\n");
5014: fprintf(ficlog,"\n");
5015: } /* end j=0 */
1.249 brouard 5016: } /* end j */
1.252 brouard 5017:
1.253 brouard 5018: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 5019: for(i=1, jk=1; i <=nlstate; i++){
5020: for(j=1; j <=nlstate+ndeath; j++){
5021: if(j!=i){
5022: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5023: printf("%1d%1d",i,j);
5024: fprintf(ficparo,"%1d%1d",i,j);
5025: for(k=1; k<=ncovmodel;k++){
5026: /* printf(" %lf",param[i][j][k]); */
5027: /* fprintf(ficparo," %lf",param[i][j][k]); */
5028: p[jk]=pstart[jk];
5029: printf(" %f ",pstart[jk]);
5030: fprintf(ficparo," %f ",pstart[jk]);
5031: jk++;
5032: }
5033: printf("\n");
5034: fprintf(ficparo,"\n");
5035: }
5036: }
5037: }
5038: } /* end mle=-2 */
1.226 brouard 5039: dateintmean=dateintsum/k2cpt;
1.296 brouard 5040: date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);
1.240 brouard 5041:
1.226 brouard 5042: fclose(ficresp);
5043: fclose(ficresphtm);
5044: fclose(ficresphtmfr);
1.283 brouard 5045: free_vector(idq,1,nqfveff);
1.226 brouard 5046: free_vector(meanq,1,nqfveff);
1.284 brouard 5047: free_vector(stdq,1,nqfveff);
1.226 brouard 5048: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 5049: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
5050: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 5051: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5052: free_vector(pospropt,1,nlstate);
5053: free_vector(posprop,1,nlstate);
1.251 brouard 5054: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 5055: free_vector(pp,1,nlstate);
5056: /* End of freqsummary */
5057: }
1.126 brouard 5058:
1.268 brouard 5059: /* Simple linear regression */
5060: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
5061:
5062: /* y=a+bx regression */
5063: double sumx = 0.0; /* sum of x */
5064: double sumx2 = 0.0; /* sum of x**2 */
5065: double sumxy = 0.0; /* sum of x * y */
5066: double sumy = 0.0; /* sum of y */
5067: double sumy2 = 0.0; /* sum of y**2 */
5068: double sume2 = 0.0; /* sum of square or residuals */
5069: double yhat;
5070:
5071: double denom=0;
5072: int i;
5073: int ne=*no;
5074:
5075: for ( i=ifi, ne=0;i<=ila;i++) {
5076: if(!isfinite(x[i]) || !isfinite(y[i])){
5077: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5078: continue;
5079: }
5080: ne=ne+1;
5081: sumx += x[i];
5082: sumx2 += x[i]*x[i];
5083: sumxy += x[i] * y[i];
5084: sumy += y[i];
5085: sumy2 += y[i]*y[i];
5086: denom = (ne * sumx2 - sumx*sumx);
5087: /* 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); */
5088: }
5089:
5090: denom = (ne * sumx2 - sumx*sumx);
5091: if (denom == 0) {
5092: // vertical, slope m is infinity
5093: *b = INFINITY;
5094: *a = 0;
5095: if (r) *r = 0;
5096: return 1;
5097: }
5098:
5099: *b = (ne * sumxy - sumx * sumy) / denom;
5100: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5101: if (r!=NULL) {
5102: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5103: sqrt((sumx2 - sumx*sumx/ne) *
5104: (sumy2 - sumy*sumy/ne));
5105: }
5106: *no=ne;
5107: for ( i=ifi, ne=0;i<=ila;i++) {
5108: if(!isfinite(x[i]) || !isfinite(y[i])){
5109: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5110: continue;
5111: }
5112: ne=ne+1;
5113: yhat = y[i] - *a -*b* x[i];
5114: sume2 += yhat * yhat ;
5115:
5116: denom = (ne * sumx2 - sumx*sumx);
5117: /* 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); */
5118: }
5119: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5120: *sa= *sb * sqrt(sumx2/ne);
5121:
5122: return 0;
5123: }
5124:
1.126 brouard 5125: /************ Prevalence ********************/
1.227 brouard 5126: 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)
5127: {
5128: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5129: in each health status at the date of interview (if between dateprev1 and dateprev2).
5130: We still use firstpass and lastpass as another selection.
5131: */
1.126 brouard 5132:
1.227 brouard 5133: int i, m, jk, j1, bool, z1,j, iv;
5134: int mi; /* Effective wave */
5135: int iage;
5136: double agebegin, ageend;
5137:
5138: double **prop;
5139: double posprop;
5140: double y2; /* in fractional years */
5141: int iagemin, iagemax;
5142: int first; /** to stop verbosity which is redirected to log file */
5143:
5144: iagemin= (int) agemin;
5145: iagemax= (int) agemax;
5146: /*pp=vector(1,nlstate);*/
1.251 brouard 5147: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5148: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5149: j1=0;
1.222 brouard 5150:
1.227 brouard 5151: /*j=cptcoveff;*/
5152: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5153:
1.288 brouard 5154: first=0;
1.227 brouard 5155: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5156: for (i=1; i<=nlstate; i++)
1.251 brouard 5157: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5158: prop[i][iage]=0.0;
5159: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5160: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5161: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5162:
5163: for (i=1; i<=imx; i++) { /* Each individual */
5164: bool=1;
5165: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5166: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5167: m=mw[mi][i];
5168: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5169: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5170: for (z1=1; z1<=cptcoveff; z1++){
5171: if( Fixed[Tmodelind[z1]]==1){
5172: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5173: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5174: bool=0;
5175: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5176: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5177: bool=0;
5178: }
5179: }
5180: if(bool==1){ /* Otherwise we skip that wave/person */
5181: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5182: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5183: if(m >=firstpass && m <=lastpass){
5184: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5185: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5186: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5187: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5188: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5189: 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);
5190: exit(1);
5191: }
5192: if (s[m][i]>0 && s[m][i]<=nlstate) {
5193: /*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]]);*/
5194: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5195: prop[s[m][i]][iagemax+3] += weight[i];
5196: } /* end valid statuses */
5197: } /* end selection of dates */
5198: } /* end selection of waves */
5199: } /* end bool */
5200: } /* end wave */
5201: } /* end individual */
5202: for(i=iagemin; i <= iagemax+3; i++){
5203: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5204: posprop += prop[jk][i];
5205: }
5206:
5207: for(jk=1; jk <=nlstate ; jk++){
5208: if( i <= iagemax){
5209: if(posprop>=1.e-5){
5210: probs[i][jk][j1]= prop[jk][i]/posprop;
5211: } else{
1.288 brouard 5212: if(!first){
5213: first=1;
1.266 brouard 5214: 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]);
5215: }else{
1.288 brouard 5216: 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 5217: }
5218: }
5219: }
5220: }/* end jk */
5221: }/* end i */
1.222 brouard 5222: /*} *//* end i1 */
1.227 brouard 5223: } /* end j1 */
1.222 brouard 5224:
1.227 brouard 5225: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5226: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5227: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5228: } /* End of prevalence */
1.126 brouard 5229:
5230: /************* Waves Concatenation ***************/
5231:
5232: 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)
5233: {
1.298 brouard 5234: /* 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 5235: Death is a valid wave (if date is known).
5236: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5237: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1.298 brouard 5238: and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
1.227 brouard 5239: */
1.126 brouard 5240:
1.224 brouard 5241: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5242: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5243: double sum=0., jmean=0.;*/
1.224 brouard 5244: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5245: int j, k=0,jk, ju, jl;
5246: double sum=0.;
5247: first=0;
1.214 brouard 5248: firstwo=0;
1.217 brouard 5249: firsthree=0;
1.218 brouard 5250: firstfour=0;
1.164 brouard 5251: jmin=100000;
1.126 brouard 5252: jmax=-1;
5253: jmean=0.;
1.224 brouard 5254:
5255: /* Treating live states */
1.214 brouard 5256: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5257: mi=0; /* First valid wave */
1.227 brouard 5258: mli=0; /* Last valid wave */
1.126 brouard 5259: m=firstpass;
1.214 brouard 5260: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5261: 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 */
5262: mli=m-1;/* mw[++mi][i]=m-1; */
5263: }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 */
5264: mw[++mi][i]=m;
5265: mli=m;
1.224 brouard 5266: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5267: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5268: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5269: }
1.227 brouard 5270: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5271: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5272: break;
1.224 brouard 5273: #else
1.227 brouard 5274: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5275: if(firsthree == 0){
1.302 brouard 5276: 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 5277: firsthree=1;
5278: }
1.302 brouard 5279: 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 5280: mw[++mi][i]=m;
5281: mli=m;
5282: }
5283: if(s[m][i]==-2){ /* Vital status is really unknown */
5284: nbwarn++;
5285: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5286: 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);
5287: 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);
5288: }
5289: break;
5290: }
5291: break;
1.224 brouard 5292: #endif
1.227 brouard 5293: }/* End m >= lastpass */
1.126 brouard 5294: }/* end while */
1.224 brouard 5295:
1.227 brouard 5296: /* 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 5297: /* After last pass */
1.224 brouard 5298: /* Treating death states */
1.214 brouard 5299: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5300: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5301: /* } */
1.126 brouard 5302: mi++; /* Death is another wave */
5303: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5304: /* Only death is a correct wave */
1.126 brouard 5305: mw[mi][i]=m;
1.257 brouard 5306: } /* else not in a death state */
1.224 brouard 5307: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5308: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5309: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5310: 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 */
5311: nbwarn++;
5312: if(firstfiv==0){
5313: 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 );
5314: firstfiv=1;
5315: }else{
5316: 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 );
5317: }
5318: }else{ /* Death occured afer last wave potential bias */
5319: nberr++;
5320: if(firstwo==0){
1.257 brouard 5321: 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 5322: firstwo=1;
5323: }
1.257 brouard 5324: 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 5325: }
1.257 brouard 5326: }else{ /* if date of interview is unknown */
1.227 brouard 5327: /* death is known but not confirmed by death status at any wave */
5328: if(firstfour==0){
5329: 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 );
5330: firstfour=1;
5331: }
5332: 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 5333: }
1.224 brouard 5334: } /* end if date of death is known */
5335: #endif
5336: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5337: /* wav[i]=mw[mi][i]; */
1.126 brouard 5338: if(mi==0){
5339: nbwarn++;
5340: if(first==0){
1.227 brouard 5341: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5342: first=1;
1.126 brouard 5343: }
5344: if(first==1){
1.227 brouard 5345: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5346: }
5347: } /* end mi==0 */
5348: } /* End individuals */
1.214 brouard 5349: /* wav and mw are no more changed */
1.223 brouard 5350:
1.214 brouard 5351:
1.126 brouard 5352: for(i=1; i<=imx; i++){
5353: for(mi=1; mi<wav[i];mi++){
5354: if (stepm <=0)
1.227 brouard 5355: dh[mi][i]=1;
1.126 brouard 5356: else{
1.260 brouard 5357: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5358: if (agedc[i] < 2*AGESUP) {
5359: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5360: if(j==0) j=1; /* Survives at least one month after exam */
5361: else if(j<0){
5362: nberr++;
5363: 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]);
5364: j=1; /* Temporary Dangerous patch */
5365: 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);
5366: 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]);
5367: 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);
5368: }
5369: k=k+1;
5370: if (j >= jmax){
5371: jmax=j;
5372: ijmax=i;
5373: }
5374: if (j <= jmin){
5375: jmin=j;
5376: ijmin=i;
5377: }
5378: sum=sum+j;
5379: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5380: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5381: }
5382: }
5383: else{
5384: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5385: /* 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 5386:
1.227 brouard 5387: k=k+1;
5388: if (j >= jmax) {
5389: jmax=j;
5390: ijmax=i;
5391: }
5392: else if (j <= jmin){
5393: jmin=j;
5394: ijmin=i;
5395: }
5396: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5397: /*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]);*/
5398: if(j<0){
5399: nberr++;
5400: 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]);
5401: 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]);
5402: }
5403: sum=sum+j;
5404: }
5405: jk= j/stepm;
5406: jl= j -jk*stepm;
5407: ju= j -(jk+1)*stepm;
5408: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5409: if(jl==0){
5410: dh[mi][i]=jk;
5411: bh[mi][i]=0;
5412: }else{ /* We want a negative bias in order to only have interpolation ie
5413: * to avoid the price of an extra matrix product in likelihood */
5414: dh[mi][i]=jk+1;
5415: bh[mi][i]=ju;
5416: }
5417: }else{
5418: if(jl <= -ju){
5419: dh[mi][i]=jk;
5420: bh[mi][i]=jl; /* bias is positive if real duration
5421: * is higher than the multiple of stepm and negative otherwise.
5422: */
5423: }
5424: else{
5425: dh[mi][i]=jk+1;
5426: bh[mi][i]=ju;
5427: }
5428: if(dh[mi][i]==0){
5429: dh[mi][i]=1; /* At least one step */
5430: bh[mi][i]=ju; /* At least one step */
5431: /* 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);*/
5432: }
5433: } /* end if mle */
1.126 brouard 5434: }
5435: } /* end wave */
5436: }
5437: jmean=sum/k;
5438: 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 5439: 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 5440: }
1.126 brouard 5441:
5442: /*********** Tricode ****************************/
1.220 brouard 5443: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5444: {
5445: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5446: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5447: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5448: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5449: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5450: */
1.130 brouard 5451:
1.242 brouard 5452: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5453: int modmaxcovj=0; /* Modality max of covariates j */
5454: int cptcode=0; /* Modality max of covariates j */
5455: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5456:
5457:
1.242 brouard 5458: /* cptcoveff=0; */
5459: /* *cptcov=0; */
1.126 brouard 5460:
1.242 brouard 5461: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5462: for (k=1; k <= maxncov; k++)
5463: for(j=1; j<=2; j++)
5464: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5465:
1.242 brouard 5466: /* Loop on covariates without age and products and no quantitative variable */
5467: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5468: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5469: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5470: switch(Fixed[k]) {
5471: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5472: 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*/
5473: ij=(int)(covar[Tvar[k]][i]);
5474: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5475: * If product of Vn*Vm, still boolean *:
5476: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5477: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5478: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5479: modality of the nth covariate of individual i. */
5480: if (ij > modmaxcovj)
5481: modmaxcovj=ij;
5482: else if (ij < modmincovj)
5483: modmincovj=ij;
1.287 brouard 5484: if (ij <0 || ij >1 ){
5485: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5486: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
5487: }
5488: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5489: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5490: exit(1);
5491: }else
5492: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5493: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5494: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5495: /* getting the maximum value of the modality of the covariate
5496: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5497: female ies 1, then modmaxcovj=1.
5498: */
5499: } /* end for loop on individuals i */
5500: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5501: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5502: cptcode=modmaxcovj;
5503: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5504: /*for (i=0; i<=cptcode; i++) {*/
5505: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5506: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5507: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5508: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5509: if( j != -1){
5510: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5511: covariate for which somebody answered excluding
5512: undefined. Usually 2: 0 and 1. */
5513: }
5514: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5515: covariate for which somebody answered including
5516: undefined. Usually 3: -1, 0 and 1. */
5517: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5518: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5519: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5520:
1.242 brouard 5521: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5522: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5523: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5524: /* modmincovj=3; modmaxcovj = 7; */
5525: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5526: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5527: /* defining two dummy variables: variables V1_1 and V1_2.*/
5528: /* nbcode[Tvar[j]][ij]=k; */
5529: /* nbcode[Tvar[j]][1]=0; */
5530: /* nbcode[Tvar[j]][2]=1; */
5531: /* nbcode[Tvar[j]][3]=2; */
5532: /* To be continued (not working yet). */
5533: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 brouard 5534:
5535: /* 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*/
5536: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
5537: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
5538: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
5539: /*, could be restored in the future */
5540: 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 5541: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5542: break;
5543: }
5544: ij++;
1.287 brouard 5545: 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 5546: cptcode = ij; /* New max modality for covar j */
5547: } /* end of loop on modality i=-1 to 1 or more */
5548: break;
5549: case 1: /* Testing on varying covariate, could be simple and
5550: * should look at waves or product of fixed *
5551: * varying. No time to test -1, assuming 0 and 1 only */
5552: ij=0;
5553: for(i=0; i<=1;i++){
5554: nbcode[Tvar[k]][++ij]=i;
5555: }
5556: break;
5557: default:
5558: break;
5559: } /* end switch */
5560: } /* end dummy test */
1.287 brouard 5561: } /* 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 5562:
5563: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5564: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5565: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5566: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5567: 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 */
5568: 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 */
5569: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5570: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5571:
5572: ij=0;
5573: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5574: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5575: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5576: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5577: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5578: /* If product not in single variable we don't print results */
5579: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5580: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5581: 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*/
5582: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5583: 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 */
5584: if(Fixed[k]!=0)
5585: anyvaryingduminmodel=1;
5586: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5587: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5588: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5589: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5590: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5591: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5592: }
5593: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5594: /* ij--; */
5595: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5596: *cptcov=ij; /*Number of total real effective covariates: effective
5597: * because they can be excluded from the model and real
5598: * if in the model but excluded because missing values, but how to get k from ij?*/
5599: for(j=ij+1; j<= cptcovt; j++){
5600: Tvaraff[j]=0;
5601: Tmodelind[j]=0;
5602: }
5603: for(j=ntveff+1; j<= cptcovt; j++){
5604: TmodelInvind[j]=0;
5605: }
5606: /* To be sorted */
5607: ;
5608: }
1.126 brouard 5609:
1.145 brouard 5610:
1.126 brouard 5611: /*********** Health Expectancies ****************/
5612:
1.235 brouard 5613: 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 5614:
5615: {
5616: /* Health expectancies, no variances */
1.164 brouard 5617: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5618: int nhstepma, nstepma; /* Decreasing with age */
5619: double age, agelim, hf;
5620: double ***p3mat;
5621: double eip;
5622:
1.238 brouard 5623: /* pstamp(ficreseij); */
1.126 brouard 5624: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5625: fprintf(ficreseij,"# Age");
5626: for(i=1; i<=nlstate;i++){
5627: for(j=1; j<=nlstate;j++){
5628: fprintf(ficreseij," e%1d%1d ",i,j);
5629: }
5630: fprintf(ficreseij," e%1d. ",i);
5631: }
5632: fprintf(ficreseij,"\n");
5633:
5634:
5635: if(estepm < stepm){
5636: printf ("Problem %d lower than %d\n",estepm, stepm);
5637: }
5638: else hstepm=estepm;
5639: /* We compute the life expectancy from trapezoids spaced every estepm months
5640: * This is mainly to measure the difference between two models: for example
5641: * if stepm=24 months pijx are given only every 2 years and by summing them
5642: * we are calculating an estimate of the Life Expectancy assuming a linear
5643: * progression in between and thus overestimating or underestimating according
5644: * to the curvature of the survival function. If, for the same date, we
5645: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5646: * to compare the new estimate of Life expectancy with the same linear
5647: * hypothesis. A more precise result, taking into account a more precise
5648: * curvature will be obtained if estepm is as small as stepm. */
5649:
5650: /* For example we decided to compute the life expectancy with the smallest unit */
5651: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5652: nhstepm is the number of hstepm from age to agelim
5653: nstepm is the number of stepm from age to agelin.
1.270 brouard 5654: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5655: and note for a fixed period like estepm months */
5656: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5657: survival function given by stepm (the optimization length). Unfortunately it
5658: means that if the survival funtion is printed only each two years of age and if
5659: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5660: results. So we changed our mind and took the option of the best precision.
5661: */
5662: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5663:
5664: agelim=AGESUP;
5665: /* If stepm=6 months */
5666: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5667: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5668:
5669: /* nhstepm age range expressed in number of stepm */
5670: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5671: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5672: /* if (stepm >= YEARM) hstepm=1;*/
5673: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5674: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5675:
5676: for (age=bage; age<=fage; age ++){
5677: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5678: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5679: /* if (stepm >= YEARM) hstepm=1;*/
5680: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5681:
5682: /* If stepm=6 months */
5683: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5684: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5685:
1.235 brouard 5686: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5687:
5688: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5689:
5690: printf("%d|",(int)age);fflush(stdout);
5691: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5692:
5693: /* Computing expectancies */
5694: for(i=1; i<=nlstate;i++)
5695: for(j=1; j<=nlstate;j++)
5696: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5697: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5698:
5699: /* 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]);*/
5700:
5701: }
5702:
5703: fprintf(ficreseij,"%3.0f",age );
5704: for(i=1; i<=nlstate;i++){
5705: eip=0;
5706: for(j=1; j<=nlstate;j++){
5707: eip +=eij[i][j][(int)age];
5708: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5709: }
5710: fprintf(ficreseij,"%9.4f", eip );
5711: }
5712: fprintf(ficreseij,"\n");
5713:
5714: }
5715: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5716: printf("\n");
5717: fprintf(ficlog,"\n");
5718:
5719: }
5720:
1.235 brouard 5721: 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 5722:
5723: {
5724: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5725: to initial status i, ei. .
1.126 brouard 5726: */
5727: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5728: int nhstepma, nstepma; /* Decreasing with age */
5729: double age, agelim, hf;
5730: double ***p3matp, ***p3matm, ***varhe;
5731: double **dnewm,**doldm;
5732: double *xp, *xm;
5733: double **gp, **gm;
5734: double ***gradg, ***trgradg;
5735: int theta;
5736:
5737: double eip, vip;
5738:
5739: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5740: xp=vector(1,npar);
5741: xm=vector(1,npar);
5742: dnewm=matrix(1,nlstate*nlstate,1,npar);
5743: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5744:
5745: pstamp(ficresstdeij);
5746: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5747: fprintf(ficresstdeij,"# Age");
5748: for(i=1; i<=nlstate;i++){
5749: for(j=1; j<=nlstate;j++)
5750: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5751: fprintf(ficresstdeij," e%1d. ",i);
5752: }
5753: fprintf(ficresstdeij,"\n");
5754:
5755: pstamp(ficrescveij);
5756: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5757: fprintf(ficrescveij,"# Age");
5758: for(i=1; i<=nlstate;i++)
5759: for(j=1; j<=nlstate;j++){
5760: cptj= (j-1)*nlstate+i;
5761: for(i2=1; i2<=nlstate;i2++)
5762: for(j2=1; j2<=nlstate;j2++){
5763: cptj2= (j2-1)*nlstate+i2;
5764: if(cptj2 <= cptj)
5765: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5766: }
5767: }
5768: fprintf(ficrescveij,"\n");
5769:
5770: if(estepm < stepm){
5771: printf ("Problem %d lower than %d\n",estepm, stepm);
5772: }
5773: else hstepm=estepm;
5774: /* We compute the life expectancy from trapezoids spaced every estepm months
5775: * This is mainly to measure the difference between two models: for example
5776: * if stepm=24 months pijx are given only every 2 years and by summing them
5777: * we are calculating an estimate of the Life Expectancy assuming a linear
5778: * progression in between and thus overestimating or underestimating according
5779: * to the curvature of the survival function. If, for the same date, we
5780: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5781: * to compare the new estimate of Life expectancy with the same linear
5782: * hypothesis. A more precise result, taking into account a more precise
5783: * curvature will be obtained if estepm is as small as stepm. */
5784:
5785: /* For example we decided to compute the life expectancy with the smallest unit */
5786: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5787: nhstepm is the number of hstepm from age to agelim
5788: nstepm is the number of stepm from age to agelin.
5789: Look at hpijx to understand the reason of that which relies in memory size
5790: and note for a fixed period like estepm months */
5791: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5792: survival function given by stepm (the optimization length). Unfortunately it
5793: means that if the survival funtion is printed only each two years of age and if
5794: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5795: results. So we changed our mind and took the option of the best precision.
5796: */
5797: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5798:
5799: /* If stepm=6 months */
5800: /* nhstepm age range expressed in number of stepm */
5801: agelim=AGESUP;
5802: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5803: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5804: /* if (stepm >= YEARM) hstepm=1;*/
5805: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5806:
5807: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5808: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5809: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5810: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5811: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5812: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5813:
5814: for (age=bage; age<=fage; age ++){
5815: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5816: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5817: /* if (stepm >= YEARM) hstepm=1;*/
5818: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5819:
1.126 brouard 5820: /* If stepm=6 months */
5821: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5822: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5823:
5824: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5825:
1.126 brouard 5826: /* Computing Variances of health expectancies */
5827: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5828: decrease memory allocation */
5829: for(theta=1; theta <=npar; theta++){
5830: for(i=1; i<=npar; i++){
1.222 brouard 5831: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5832: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5833: }
1.235 brouard 5834: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5835: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5836:
1.126 brouard 5837: for(j=1; j<= nlstate; j++){
1.222 brouard 5838: for(i=1; i<=nlstate; i++){
5839: for(h=0; h<=nhstepm-1; h++){
5840: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5841: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5842: }
5843: }
1.126 brouard 5844: }
1.218 brouard 5845:
1.126 brouard 5846: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5847: for(h=0; h<=nhstepm-1; h++){
5848: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5849: }
1.126 brouard 5850: }/* End theta */
5851:
5852:
5853: for(h=0; h<=nhstepm-1; h++)
5854: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5855: for(theta=1; theta <=npar; theta++)
5856: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5857:
1.218 brouard 5858:
1.222 brouard 5859: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5860: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5861: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5862:
1.222 brouard 5863: printf("%d|",(int)age);fflush(stdout);
5864: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5865: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5866: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5867: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5868: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5869: for(ij=1;ij<=nlstate*nlstate;ij++)
5870: for(ji=1;ji<=nlstate*nlstate;ji++)
5871: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5872: }
5873: }
1.218 brouard 5874:
1.126 brouard 5875: /* Computing expectancies */
1.235 brouard 5876: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5877: for(i=1; i<=nlstate;i++)
5878: for(j=1; j<=nlstate;j++)
1.222 brouard 5879: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5880: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5881:
1.222 brouard 5882: /* 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 5883:
1.222 brouard 5884: }
1.269 brouard 5885:
5886: /* Standard deviation of expectancies ij */
1.126 brouard 5887: fprintf(ficresstdeij,"%3.0f",age );
5888: for(i=1; i<=nlstate;i++){
5889: eip=0.;
5890: vip=0.;
5891: for(j=1; j<=nlstate;j++){
1.222 brouard 5892: eip += eij[i][j][(int)age];
5893: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5894: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5895: 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 5896: }
5897: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5898: }
5899: fprintf(ficresstdeij,"\n");
1.218 brouard 5900:
1.269 brouard 5901: /* Variance of expectancies ij */
1.126 brouard 5902: fprintf(ficrescveij,"%3.0f",age );
5903: for(i=1; i<=nlstate;i++)
5904: for(j=1; j<=nlstate;j++){
1.222 brouard 5905: cptj= (j-1)*nlstate+i;
5906: for(i2=1; i2<=nlstate;i2++)
5907: for(j2=1; j2<=nlstate;j2++){
5908: cptj2= (j2-1)*nlstate+i2;
5909: if(cptj2 <= cptj)
5910: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5911: }
1.126 brouard 5912: }
5913: fprintf(ficrescveij,"\n");
1.218 brouard 5914:
1.126 brouard 5915: }
5916: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5917: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5918: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5919: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5920: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5921: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5922: printf("\n");
5923: fprintf(ficlog,"\n");
1.218 brouard 5924:
1.126 brouard 5925: free_vector(xm,1,npar);
5926: free_vector(xp,1,npar);
5927: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5928: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5929: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5930: }
1.218 brouard 5931:
1.126 brouard 5932: /************ Variance ******************/
1.235 brouard 5933: 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 5934: {
1.279 brouard 5935: /** Variance of health expectancies
5936: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5937: * double **newm;
5938: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5939: */
1.218 brouard 5940:
5941: /* int movingaverage(); */
5942: double **dnewm,**doldm;
5943: double **dnewmp,**doldmp;
5944: int i, j, nhstepm, hstepm, h, nstepm ;
1.288 brouard 5945: int first=0;
1.218 brouard 5946: int k;
5947: double *xp;
1.279 brouard 5948: double **gp, **gm; /**< for var eij */
5949: double ***gradg, ***trgradg; /**< for var eij */
5950: double **gradgp, **trgradgp; /**< for var p point j */
5951: double *gpp, *gmp; /**< for var p point j */
5952: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5953: double ***p3mat;
5954: double age,agelim, hf;
5955: /* double ***mobaverage; */
5956: int theta;
5957: char digit[4];
5958: char digitp[25];
5959:
5960: char fileresprobmorprev[FILENAMELENGTH];
5961:
5962: if(popbased==1){
5963: if(mobilav!=0)
5964: strcpy(digitp,"-POPULBASED-MOBILAV_");
5965: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5966: }
5967: else
5968: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5969:
1.218 brouard 5970: /* if (mobilav!=0) { */
5971: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5972: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5973: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5974: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5975: /* } */
5976: /* } */
5977:
5978: strcpy(fileresprobmorprev,"PRMORPREV-");
5979: sprintf(digit,"%-d",ij);
5980: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5981: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5982: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5983: strcat(fileresprobmorprev,fileresu);
5984: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5985: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5986: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5987: }
5988: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5989: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5990: pstamp(ficresprobmorprev);
5991: 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 5992: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5993: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5994: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5995: }
5996: for(j=1;j<=cptcoveff;j++)
5997: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5998: fprintf(ficresprobmorprev,"\n");
5999:
1.218 brouard 6000: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
6001: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6002: fprintf(ficresprobmorprev," p.%-d SE",j);
6003: for(i=1; i<=nlstate;i++)
6004: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
6005: }
6006: fprintf(ficresprobmorprev,"\n");
6007:
6008: fprintf(ficgp,"\n# Routine varevsij");
6009: fprintf(ficgp,"\nunset title \n");
6010: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
6011: 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");
6012: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 6013:
1.218 brouard 6014: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6015: pstamp(ficresvij);
6016: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
6017: if(popbased==1)
6018: 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);
6019: else
6020: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
6021: fprintf(ficresvij,"# Age");
6022: for(i=1; i<=nlstate;i++)
6023: for(j=1; j<=nlstate;j++)
6024: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
6025: fprintf(ficresvij,"\n");
6026:
6027: xp=vector(1,npar);
6028: dnewm=matrix(1,nlstate,1,npar);
6029: doldm=matrix(1,nlstate,1,nlstate);
6030: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
6031: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6032:
6033: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
6034: gpp=vector(nlstate+1,nlstate+ndeath);
6035: gmp=vector(nlstate+1,nlstate+ndeath);
6036: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 6037:
1.218 brouard 6038: if(estepm < stepm){
6039: printf ("Problem %d lower than %d\n",estepm, stepm);
6040: }
6041: else hstepm=estepm;
6042: /* For example we decided to compute the life expectancy with the smallest unit */
6043: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
6044: nhstepm is the number of hstepm from age to agelim
6045: nstepm is the number of stepm from age to agelim.
6046: Look at function hpijx to understand why because of memory size limitations,
6047: we decided (b) to get a life expectancy respecting the most precise curvature of the
6048: survival function given by stepm (the optimization length). Unfortunately it
6049: means that if the survival funtion is printed every two years of age and if
6050: you sum them up and add 1 year (area under the trapezoids) you won't get the same
6051: results. So we changed our mind and took the option of the best precision.
6052: */
6053: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
6054: agelim = AGESUP;
6055: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6056: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6057: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
6058: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6059: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
6060: gp=matrix(0,nhstepm,1,nlstate);
6061: gm=matrix(0,nhstepm,1,nlstate);
6062:
6063:
6064: for(theta=1; theta <=npar; theta++){
6065: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
6066: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6067: }
1.279 brouard 6068: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
6069: * returns into prlim .
1.288 brouard 6070: */
1.242 brouard 6071: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 6072:
6073: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 6074: if (popbased==1) {
6075: if(mobilav ==0){
6076: for(i=1; i<=nlstate;i++)
6077: prlim[i][i]=probs[(int)age][i][ij];
6078: }else{ /* mobilav */
6079: for(i=1; i<=nlstate;i++)
6080: prlim[i][i]=mobaverage[(int)age][i][ij];
6081: }
6082: }
1.295 brouard 6083: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
1.279 brouard 6084: */
6085: 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 6086: /**< 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 6087: * at horizon h in state j including mortality.
6088: */
1.218 brouard 6089: for(j=1; j<= nlstate; j++){
6090: for(h=0; h<=nhstepm; h++){
6091: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
6092: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
6093: }
6094: }
1.279 brouard 6095: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 6096: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 6097: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 6098: */
6099: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6100: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6101: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6102: }
6103:
6104: /* Again with minus shift */
1.218 brouard 6105:
6106: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6107: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6108:
1.242 brouard 6109: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6110:
6111: if (popbased==1) {
6112: if(mobilav ==0){
6113: for(i=1; i<=nlstate;i++)
6114: prlim[i][i]=probs[(int)age][i][ij];
6115: }else{ /* mobilav */
6116: for(i=1; i<=nlstate;i++)
6117: prlim[i][i]=mobaverage[(int)age][i][ij];
6118: }
6119: }
6120:
1.235 brouard 6121: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6122:
6123: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6124: for(h=0; h<=nhstepm; h++){
6125: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6126: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6127: }
6128: }
6129: /* This for computing probability of death (h=1 means
6130: computed over hstepm matrices product = hstepm*stepm months)
6131: as a weighted average of prlim.
6132: */
6133: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6134: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6135: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6136: }
1.279 brouard 6137: /* end shifting computations */
6138:
6139: /**< Computing gradient matrix at horizon h
6140: */
1.218 brouard 6141: for(j=1; j<= nlstate; j++) /* vareij */
6142: for(h=0; h<=nhstepm; h++){
6143: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6144: }
1.279 brouard 6145: /**< Gradient of overall mortality p.3 (or p.j)
6146: */
6147: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6148: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6149: }
6150:
6151: } /* End theta */
1.279 brouard 6152:
6153: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6154: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6155:
6156: for(h=0; h<=nhstepm; h++) /* veij */
6157: for(j=1; j<=nlstate;j++)
6158: for(theta=1; theta <=npar; theta++)
6159: trgradg[h][j][theta]=gradg[h][theta][j];
6160:
6161: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6162: for(theta=1; theta <=npar; theta++)
6163: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6164: /**< as well as its transposed matrix
6165: */
1.218 brouard 6166:
6167: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6168: for(i=1;i<=nlstate;i++)
6169: for(j=1;j<=nlstate;j++)
6170: vareij[i][j][(int)age] =0.;
1.279 brouard 6171:
6172: /* Computing trgradg by matcov by gradg at age and summing over h
6173: * and k (nhstepm) formula 15 of article
6174: * Lievre-Brouard-Heathcote
6175: */
6176:
1.218 brouard 6177: for(h=0;h<=nhstepm;h++){
6178: for(k=0;k<=nhstepm;k++){
6179: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6180: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6181: for(i=1;i<=nlstate;i++)
6182: for(j=1;j<=nlstate;j++)
6183: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6184: }
6185: }
6186:
1.279 brouard 6187: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6188: * p.j overall mortality formula 49 but computed directly because
6189: * we compute the grad (wix pijx) instead of grad (pijx),even if
6190: * wix is independent of theta.
6191: */
1.218 brouard 6192: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6193: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6194: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6195: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6196: varppt[j][i]=doldmp[j][i];
6197: /* end ppptj */
6198: /* x centered again */
6199:
1.242 brouard 6200: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6201:
6202: if (popbased==1) {
6203: if(mobilav ==0){
6204: for(i=1; i<=nlstate;i++)
6205: prlim[i][i]=probs[(int)age][i][ij];
6206: }else{ /* mobilav */
6207: for(i=1; i<=nlstate;i++)
6208: prlim[i][i]=mobaverage[(int)age][i][ij];
6209: }
6210: }
6211:
6212: /* This for computing probability of death (h=1 means
6213: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6214: as a weighted average of prlim.
6215: */
1.235 brouard 6216: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6217: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6218: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6219: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6220: }
6221: /* end probability of death */
6222:
6223: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6224: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6225: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6226: for(i=1; i<=nlstate;i++){
6227: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6228: }
6229: }
6230: fprintf(ficresprobmorprev,"\n");
6231:
6232: fprintf(ficresvij,"%.0f ",age );
6233: for(i=1; i<=nlstate;i++)
6234: for(j=1; j<=nlstate;j++){
6235: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6236: }
6237: fprintf(ficresvij,"\n");
6238: free_matrix(gp,0,nhstepm,1,nlstate);
6239: free_matrix(gm,0,nhstepm,1,nlstate);
6240: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6241: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6242: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6243: } /* End age */
6244: free_vector(gpp,nlstate+1,nlstate+ndeath);
6245: free_vector(gmp,nlstate+1,nlstate+ndeath);
6246: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6247: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6248: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6249: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6250: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6251: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6252: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6253: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6254: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6255: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6256: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6257: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6258: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6259: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6260: 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);
6261: /* 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 6262: */
1.218 brouard 6263: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6264: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6265:
1.218 brouard 6266: free_vector(xp,1,npar);
6267: free_matrix(doldm,1,nlstate,1,nlstate);
6268: free_matrix(dnewm,1,nlstate,1,npar);
6269: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6270: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6271: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6272: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6273: fclose(ficresprobmorprev);
6274: fflush(ficgp);
6275: fflush(fichtm);
6276: } /* end varevsij */
1.126 brouard 6277:
6278: /************ Variance of prevlim ******************/
1.269 brouard 6279: 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 6280: {
1.205 brouard 6281: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6282: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6283:
1.268 brouard 6284: double **dnewmpar,**doldm;
1.126 brouard 6285: int i, j, nhstepm, hstepm;
6286: double *xp;
6287: double *gp, *gm;
6288: double **gradg, **trgradg;
1.208 brouard 6289: double **mgm, **mgp;
1.126 brouard 6290: double age,agelim;
6291: int theta;
6292:
6293: pstamp(ficresvpl);
1.288 brouard 6294: fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
1.241 brouard 6295: fprintf(ficresvpl,"# Age ");
6296: if(nresult >=1)
6297: fprintf(ficresvpl," Result# ");
1.126 brouard 6298: for(i=1; i<=nlstate;i++)
6299: fprintf(ficresvpl," %1d-%1d",i,i);
6300: fprintf(ficresvpl,"\n");
6301:
6302: xp=vector(1,npar);
1.268 brouard 6303: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6304: doldm=matrix(1,nlstate,1,nlstate);
6305:
6306: hstepm=1*YEARM; /* Every year of age */
6307: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6308: agelim = AGESUP;
6309: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6310: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6311: if (stepm >= YEARM) hstepm=1;
6312: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6313: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6314: mgp=matrix(1,npar,1,nlstate);
6315: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6316: gp=vector(1,nlstate);
6317: gm=vector(1,nlstate);
6318:
6319: for(theta=1; theta <=npar; theta++){
6320: for(i=1; i<=npar; i++){ /* Computes gradient */
6321: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6322: }
1.288 brouard 6323: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6324: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6325: /* else */
6326: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6327: for(i=1;i<=nlstate;i++){
1.126 brouard 6328: gp[i] = prlim[i][i];
1.208 brouard 6329: mgp[theta][i] = prlim[i][i];
6330: }
1.126 brouard 6331: for(i=1; i<=npar; i++) /* Computes gradient */
6332: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.288 brouard 6333: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
6334: /* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
6335: /* else */
6336: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6337: for(i=1;i<=nlstate;i++){
1.126 brouard 6338: gm[i] = prlim[i][i];
1.208 brouard 6339: mgm[theta][i] = prlim[i][i];
6340: }
1.126 brouard 6341: for(i=1;i<=nlstate;i++)
6342: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6343: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6344: } /* End theta */
6345:
6346: trgradg =matrix(1,nlstate,1,npar);
6347:
6348: for(j=1; j<=nlstate;j++)
6349: for(theta=1; theta <=npar; theta++)
6350: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6351: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6352: /* printf("\nmgm mgp %d ",(int)age); */
6353: /* for(j=1; j<=nlstate;j++){ */
6354: /* printf(" %d ",j); */
6355: /* for(theta=1; theta <=npar; theta++) */
6356: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6357: /* printf("\n "); */
6358: /* } */
6359: /* } */
6360: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6361: /* printf("\n gradg %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 ",theta,gradg[theta][j]); */
6366: /* printf("\n "); */
6367: /* } */
6368: /* } */
1.126 brouard 6369:
6370: for(i=1;i<=nlstate;i++)
6371: varpl[i][(int)age] =0.;
1.209 brouard 6372: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6373: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6374: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6375: }else{
1.268 brouard 6376: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6377: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6378: }
1.126 brouard 6379: for(i=1;i<=nlstate;i++)
6380: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6381:
6382: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6383: if(nresult >=1)
6384: fprintf(ficresvpl,"%d ",nres );
1.288 brouard 6385: for(i=1; i<=nlstate;i++){
1.126 brouard 6386: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
1.288 brouard 6387: /* for(j=1;j<=nlstate;j++) */
6388: /* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
6389: }
1.126 brouard 6390: fprintf(ficresvpl,"\n");
6391: free_vector(gp,1,nlstate);
6392: free_vector(gm,1,nlstate);
1.208 brouard 6393: free_matrix(mgm,1,npar,1,nlstate);
6394: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6395: free_matrix(gradg,1,npar,1,nlstate);
6396: free_matrix(trgradg,1,nlstate,1,npar);
6397: } /* End age */
6398:
6399: free_vector(xp,1,npar);
6400: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6401: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6402:
6403: }
6404:
6405:
6406: /************ Variance of backprevalence limit ******************/
1.269 brouard 6407: 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 6408: {
6409: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6410: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6411:
6412: double **dnewmpar,**doldm;
6413: int i, j, nhstepm, hstepm;
6414: double *xp;
6415: double *gp, *gm;
6416: double **gradg, **trgradg;
6417: double **mgm, **mgp;
6418: double age,agelim;
6419: int theta;
6420:
6421: pstamp(ficresvbl);
6422: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6423: fprintf(ficresvbl,"# Age ");
6424: if(nresult >=1)
6425: fprintf(ficresvbl," Result# ");
6426: for(i=1; i<=nlstate;i++)
6427: fprintf(ficresvbl," %1d-%1d",i,i);
6428: fprintf(ficresvbl,"\n");
6429:
6430: xp=vector(1,npar);
6431: dnewmpar=matrix(1,nlstate,1,npar);
6432: doldm=matrix(1,nlstate,1,nlstate);
6433:
6434: hstepm=1*YEARM; /* Every year of age */
6435: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6436: agelim = AGEINF;
6437: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6438: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6439: if (stepm >= YEARM) hstepm=1;
6440: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6441: gradg=matrix(1,npar,1,nlstate);
6442: mgp=matrix(1,npar,1,nlstate);
6443: mgm=matrix(1,npar,1,nlstate);
6444: gp=vector(1,nlstate);
6445: gm=vector(1,nlstate);
6446:
6447: for(theta=1; theta <=npar; theta++){
6448: for(i=1; i<=npar; i++){ /* Computes gradient */
6449: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6450: }
6451: if(mobilavproj > 0 )
6452: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6453: else
6454: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6455: for(i=1;i<=nlstate;i++){
6456: gp[i] = bprlim[i][i];
6457: mgp[theta][i] = bprlim[i][i];
6458: }
6459: for(i=1; i<=npar; i++) /* Computes gradient */
6460: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6461: if(mobilavproj > 0 )
6462: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6463: else
6464: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6465: for(i=1;i<=nlstate;i++){
6466: gm[i] = bprlim[i][i];
6467: mgm[theta][i] = bprlim[i][i];
6468: }
6469: for(i=1;i<=nlstate;i++)
6470: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6471: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6472: } /* End theta */
6473:
6474: trgradg =matrix(1,nlstate,1,npar);
6475:
6476: for(j=1; j<=nlstate;j++)
6477: for(theta=1; theta <=npar; theta++)
6478: trgradg[j][theta]=gradg[theta][j];
6479: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6480: /* printf("\nmgm mgp %d ",(int)age); */
6481: /* for(j=1; j<=nlstate;j++){ */
6482: /* printf(" %d ",j); */
6483: /* for(theta=1; theta <=npar; theta++) */
6484: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6485: /* printf("\n "); */
6486: /* } */
6487: /* } */
6488: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6489: /* printf("\n gradg %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 ",theta,gradg[theta][j]); */
6494: /* printf("\n "); */
6495: /* } */
6496: /* } */
6497:
6498: for(i=1;i<=nlstate;i++)
6499: varbpl[i][(int)age] =0.;
6500: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6501: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6502: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6503: }else{
6504: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6505: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6506: }
6507: for(i=1;i<=nlstate;i++)
6508: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6509:
6510: fprintf(ficresvbl,"%.0f ",age );
6511: if(nresult >=1)
6512: fprintf(ficresvbl,"%d ",nres );
6513: for(i=1; i<=nlstate;i++)
6514: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6515: fprintf(ficresvbl,"\n");
6516: free_vector(gp,1,nlstate);
6517: free_vector(gm,1,nlstate);
6518: free_matrix(mgm,1,npar,1,nlstate);
6519: free_matrix(mgp,1,npar,1,nlstate);
6520: free_matrix(gradg,1,npar,1,nlstate);
6521: free_matrix(trgradg,1,nlstate,1,npar);
6522: } /* End age */
6523:
6524: free_vector(xp,1,npar);
6525: free_matrix(doldm,1,nlstate,1,npar);
6526: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6527:
6528: }
6529:
6530: /************ Variance of one-step probabilities ******************/
6531: 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 6532: {
6533: int i, j=0, k1, l1, tj;
6534: int k2, l2, j1, z1;
6535: int k=0, l;
6536: int first=1, first1, first2;
6537: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6538: double **dnewm,**doldm;
6539: double *xp;
6540: double *gp, *gm;
6541: double **gradg, **trgradg;
6542: double **mu;
6543: double age, cov[NCOVMAX+1];
6544: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6545: int theta;
6546: char fileresprob[FILENAMELENGTH];
6547: char fileresprobcov[FILENAMELENGTH];
6548: char fileresprobcor[FILENAMELENGTH];
6549: double ***varpij;
6550:
6551: strcpy(fileresprob,"PROB_");
6552: strcat(fileresprob,fileres);
6553: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6554: printf("Problem with resultfile: %s\n", fileresprob);
6555: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6556: }
6557: strcpy(fileresprobcov,"PROBCOV_");
6558: strcat(fileresprobcov,fileresu);
6559: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6560: printf("Problem with resultfile: %s\n", fileresprobcov);
6561: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6562: }
6563: strcpy(fileresprobcor,"PROBCOR_");
6564: strcat(fileresprobcor,fileresu);
6565: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6566: printf("Problem with resultfile: %s\n", fileresprobcor);
6567: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6568: }
6569: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6570: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6571: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6572: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6573: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6574: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6575: pstamp(ficresprob);
6576: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6577: fprintf(ficresprob,"# Age");
6578: pstamp(ficresprobcov);
6579: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6580: fprintf(ficresprobcov,"# Age");
6581: pstamp(ficresprobcor);
6582: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6583: fprintf(ficresprobcor,"# Age");
1.126 brouard 6584:
6585:
1.222 brouard 6586: for(i=1; i<=nlstate;i++)
6587: for(j=1; j<=(nlstate+ndeath);j++){
6588: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6589: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6590: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6591: }
6592: /* fprintf(ficresprob,"\n");
6593: fprintf(ficresprobcov,"\n");
6594: fprintf(ficresprobcor,"\n");
6595: */
6596: xp=vector(1,npar);
6597: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6598: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6599: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6600: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6601: first=1;
6602: fprintf(ficgp,"\n# Routine varprob");
6603: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6604: fprintf(fichtm,"\n");
6605:
1.288 brouard 6606: 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 6607: 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);
6608: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6609: and drawn. It helps understanding how is the covariance between two incidences.\
6610: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6611: 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 6612: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6613: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6614: standard deviations wide on each axis. <br>\
6615: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6616: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6617: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6618:
1.222 brouard 6619: cov[1]=1;
6620: /* tj=cptcoveff; */
1.225 brouard 6621: tj = (int) pow(2,cptcoveff);
1.222 brouard 6622: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6623: j1=0;
1.224 brouard 6624: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6625: if (cptcovn>0) {
6626: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6627: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6628: fprintf(ficresprob, "**********\n#\n");
6629: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6630: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6631: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6632:
1.222 brouard 6633: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6634: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6635: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6636:
6637:
1.222 brouard 6638: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6639: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6640: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6641:
1.222 brouard 6642: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6643: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6644: fprintf(ficresprobcor, "**********\n#");
6645: if(invalidvarcomb[j1]){
6646: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6647: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6648: continue;
6649: }
6650: }
6651: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6652: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6653: gp=vector(1,(nlstate)*(nlstate+ndeath));
6654: gm=vector(1,(nlstate)*(nlstate+ndeath));
6655: for (age=bage; age<=fage; age ++){
6656: cov[2]=age;
6657: if(nagesqr==1)
6658: cov[3]= age*age;
6659: for (k=1; k<=cptcovn;k++) {
6660: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6661: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6662: * 1 1 1 1 1
6663: * 2 2 1 1 1
6664: * 3 1 2 1 1
6665: */
6666: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6667: }
6668: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6669: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6670: for (k=1; k<=cptcovprod;k++)
6671: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6672:
6673:
1.222 brouard 6674: for(theta=1; theta <=npar; theta++){
6675: for(i=1; i<=npar; i++)
6676: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6677:
1.222 brouard 6678: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6679:
1.222 brouard 6680: k=0;
6681: for(i=1; i<= (nlstate); i++){
6682: for(j=1; j<=(nlstate+ndeath);j++){
6683: k=k+1;
6684: gp[k]=pmmij[i][j];
6685: }
6686: }
1.220 brouard 6687:
1.222 brouard 6688: for(i=1; i<=npar; i++)
6689: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6690:
1.222 brouard 6691: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6692: k=0;
6693: for(i=1; i<=(nlstate); i++){
6694: for(j=1; j<=(nlstate+ndeath);j++){
6695: k=k+1;
6696: gm[k]=pmmij[i][j];
6697: }
6698: }
1.220 brouard 6699:
1.222 brouard 6700: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6701: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6702: }
1.126 brouard 6703:
1.222 brouard 6704: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6705: for(theta=1; theta <=npar; theta++)
6706: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6707:
1.222 brouard 6708: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6709: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6710:
1.222 brouard 6711: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6712:
1.222 brouard 6713: k=0;
6714: for(i=1; i<=(nlstate); i++){
6715: for(j=1; j<=(nlstate+ndeath);j++){
6716: k=k+1;
6717: mu[k][(int) age]=pmmij[i][j];
6718: }
6719: }
6720: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6721: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6722: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6723:
1.222 brouard 6724: /*printf("\n%d ",(int)age);
6725: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6726: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6727: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6728: }*/
1.220 brouard 6729:
1.222 brouard 6730: fprintf(ficresprob,"\n%d ",(int)age);
6731: fprintf(ficresprobcov,"\n%d ",(int)age);
6732: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6733:
1.222 brouard 6734: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6735: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6736: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6737: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6738: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6739: }
6740: i=0;
6741: for (k=1; k<=(nlstate);k++){
6742: for (l=1; l<=(nlstate+ndeath);l++){
6743: i++;
6744: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6745: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6746: for (j=1; j<=i;j++){
6747: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6748: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6749: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6750: }
6751: }
6752: }/* end of loop for state */
6753: } /* end of loop for age */
6754: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6755: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6756: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6757: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6758:
6759: /* Confidence intervalle of pij */
6760: /*
6761: fprintf(ficgp,"\nunset parametric;unset label");
6762: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6763: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6764: 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);
6765: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6766: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6767: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6768: */
6769:
6770: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6771: first1=1;first2=2;
6772: for (k2=1; k2<=(nlstate);k2++){
6773: for (l2=1; l2<=(nlstate+ndeath);l2++){
6774: if(l2==k2) continue;
6775: j=(k2-1)*(nlstate+ndeath)+l2;
6776: for (k1=1; k1<=(nlstate);k1++){
6777: for (l1=1; l1<=(nlstate+ndeath);l1++){
6778: if(l1==k1) continue;
6779: i=(k1-1)*(nlstate+ndeath)+l1;
6780: if(i<=j) continue;
6781: for (age=bage; age<=fage; age ++){
6782: if ((int)age %5==0){
6783: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6784: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6785: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6786: mu1=mu[i][(int) age]/stepm*YEARM ;
6787: mu2=mu[j][(int) age]/stepm*YEARM;
6788: c12=cv12/sqrt(v1*v2);
6789: /* Computing eigen value of matrix of covariance */
6790: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6791: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6792: if ((lc2 <0) || (lc1 <0) ){
6793: if(first2==1){
6794: first1=0;
6795: 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);
6796: }
6797: 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);
6798: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6799: /* lc2=fabs(lc2); */
6800: }
1.220 brouard 6801:
1.222 brouard 6802: /* Eigen vectors */
1.280 brouard 6803: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6804: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6805: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6806: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6807: }else
6808: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6809: /*v21=sqrt(1.-v11*v11); *//* error */
6810: v21=(lc1-v1)/cv12*v11;
6811: v12=-v21;
6812: v22=v11;
6813: tnalp=v21/v11;
6814: if(first1==1){
6815: first1=0;
6816: 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);
6817: }
6818: 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);
6819: /*printf(fignu*/
6820: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6821: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6822: if(first==1){
6823: first=0;
6824: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6825: fprintf(ficgp,"\nset parametric;unset label");
6826: 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);
6827: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6828: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6829: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6830: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6831: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6832: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6833: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6834: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6835: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6836: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6837: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6838: 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 6839: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6840: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6841: }else{
6842: first=0;
6843: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6844: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6845: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6846: 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 6847: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6848: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6849: }/* if first */
6850: } /* age mod 5 */
6851: } /* end loop age */
6852: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6853: first=1;
6854: } /*l12 */
6855: } /* k12 */
6856: } /*l1 */
6857: }/* k1 */
6858: } /* loop on combination of covariates j1 */
6859: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6860: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6861: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6862: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6863: free_vector(xp,1,npar);
6864: fclose(ficresprob);
6865: fclose(ficresprobcov);
6866: fclose(ficresprobcor);
6867: fflush(ficgp);
6868: fflush(fichtmcov);
6869: }
1.126 brouard 6870:
6871:
6872: /******************* Printing html file ***********/
1.201 brouard 6873: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6874: int lastpass, int stepm, int weightopt, char model[],\
6875: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.296 brouard 6876: int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
6877: double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
6878: double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
1.237 brouard 6879: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6880:
6881: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6882: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6883: </ul>");
1.237 brouard 6884: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6885: </ul>", model);
1.214 brouard 6886: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6887: 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",
6888: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6889: 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 6890: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6891: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6892: fprintf(fichtm,"\
6893: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6894: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6895: fprintf(fichtm,"\
1.217 brouard 6896: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6897: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6898: fprintf(fichtm,"\
1.288 brouard 6899: - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6900: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6901: fprintf(fichtm,"\
1.288 brouard 6902: - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.217 brouard 6903: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6904: fprintf(fichtm,"\
1.211 brouard 6905: - (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 6906: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6907: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6908: if(prevfcast==1){
6909: fprintf(fichtm,"\
6910: - Prevalence projections by age and states: \
1.201 brouard 6911: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6912: }
1.126 brouard 6913:
6914:
1.225 brouard 6915: m=pow(2,cptcoveff);
1.222 brouard 6916: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6917:
1.264 brouard 6918: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6919:
6920: jj1=0;
6921:
6922: fprintf(fichtm," \n<ul>");
6923: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6924: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6925: if(m != 1 && TKresult[nres]!= k1)
6926: continue;
6927: jj1++;
6928: if (cptcovn > 0) {
6929: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6930: for (cpt=1; cpt<=cptcoveff;cpt++){
6931: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6932: }
6933: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6934: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6935: }
6936: fprintf(fichtm,"\">");
6937:
6938: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6939: fprintf(fichtm,"************ Results for covariates");
6940: for (cpt=1; cpt<=cptcoveff;cpt++){
6941: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6942: }
6943: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6944: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6945: }
6946: if(invalidvarcomb[k1]){
6947: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6948: continue;
6949: }
6950: fprintf(fichtm,"</a></li>");
6951: } /* cptcovn >0 */
6952: }
6953: fprintf(fichtm," \n</ul>");
6954:
1.222 brouard 6955: jj1=0;
1.237 brouard 6956:
6957: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6958: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6959: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6960: continue;
1.220 brouard 6961:
1.222 brouard 6962: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6963: jj1++;
6964: if (cptcovn > 0) {
1.264 brouard 6965: fprintf(fichtm,"\n<p><a name=\"rescov");
6966: for (cpt=1; cpt<=cptcoveff;cpt++){
6967: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6968: }
6969: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6970: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6971: }
6972: fprintf(fichtm,"\"</a>");
6973:
1.222 brouard 6974: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6975: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6976: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6977: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6978: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6979: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6980: }
1.237 brouard 6981: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6982: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6983: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6984: }
6985:
1.230 brouard 6986: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6987: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6988: if(invalidvarcomb[k1]){
6989: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6990: printf("\nCombination (%d) ignored because no cases \n",k1);
6991: continue;
6992: }
6993: }
6994: /* aij, bij */
1.259 brouard 6995: 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 6996: <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 6997: /* Pij */
1.241 brouard 6998: 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> \
6999: <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 7000: /* Quasi-incidences */
7001: 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 7002: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 7003: 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 7004: 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> \
7005: <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 7006: /* Survival functions (period) in state j */
7007: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7008: 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 7009: <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 7010: }
7011: /* State specific survival functions (period) */
7012: for(cpt=1; cpt<=nlstate;cpt++){
1.292 brouard 7013: fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
7014: And probability to be observed in various states (up to %d) being in state %d at different ages. \
1.283 brouard 7015: <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 7016: }
1.288 brouard 7017: /* Period (forward stable) prevalence in each health state */
1.222 brouard 7018: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7019: 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> \
7020: <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 7021: }
1.296 brouard 7022: if(prevbcast==1){
1.288 brouard 7023: /* Backward prevalence in each health state */
1.222 brouard 7024: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 7025: fprintf(fichtm,"<br>\n- Convergence to 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 7026: <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 7027: }
1.217 brouard 7028: }
1.222 brouard 7029: if(prevfcast==1){
1.288 brouard 7030: /* Projection of prevalence up to period (forward stable) prevalence in each health state */
1.222 brouard 7031: for(cpt=1; cpt<=nlstate;cpt++){
1.288 brouard 7032: 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 7033: <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 7034: }
7035: }
1.296 brouard 7036: if(prevbcast==1){
1.268 brouard 7037: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
7038: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 7039: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
7040: 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 \
7041: 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) \
7042: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
7043: <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 7044: }
7045: }
1.220 brouard 7046:
1.222 brouard 7047: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 7048: 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> \
7049: <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 7050: }
7051: /* } /\* end i1 *\/ */
7052: }/* End k1 */
7053: fprintf(fichtm,"</ul>");
1.126 brouard 7054:
1.222 brouard 7055: fprintf(fichtm,"\
1.126 brouard 7056: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 7057: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 7058: - 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 7059: But because parameters are usually highly correlated (a higher incidence of disability \
7060: and a higher incidence of recovery can give very close observed transition) it might \
7061: be very useful to look not only at linear confidence intervals estimated from the \
7062: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
7063: (parameters) of the logistic regression, it might be more meaningful to visualize the \
7064: covariance matrix of the one-step probabilities. \
7065: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 7066:
1.222 brouard 7067: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
7068: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
7069: fprintf(fichtm,"\
1.126 brouard 7070: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7071: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 7072:
1.222 brouard 7073: fprintf(fichtm,"\
1.126 brouard 7074: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 7075: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
7076: fprintf(fichtm,"\
1.126 brouard 7077: - 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): \
7078: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7079: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 7080: fprintf(fichtm,"\
1.126 brouard 7081: - (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): \
7082: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 7083: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 7084: fprintf(fichtm,"\
1.288 brouard 7085: - 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 7086: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
7087: fprintf(fichtm,"\
1.128 brouard 7088: - 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 7089: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
7090: fprintf(fichtm,"\
1.288 brouard 7091: - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 7092: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 7093:
7094: /* if(popforecast==1) fprintf(fichtm,"\n */
7095: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
7096: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
7097: /* <br>",fileres,fileres,fileres,fileres); */
7098: /* else */
7099: /* 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 7100: fflush(fichtm);
7101: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7102:
1.225 brouard 7103: m=pow(2,cptcoveff);
1.222 brouard 7104: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7105:
1.222 brouard 7106: jj1=0;
1.237 brouard 7107:
1.241 brouard 7108: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7109: for(k1=1; k1<=m;k1++){
1.253 brouard 7110: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7111: continue;
1.222 brouard 7112: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7113: jj1++;
1.126 brouard 7114: if (cptcovn > 0) {
7115: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7116: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7117: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7118: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7119: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7120: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7121: }
7122:
1.126 brouard 7123: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7124:
1.222 brouard 7125: if(invalidvarcomb[k1]){
7126: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7127: continue;
7128: }
1.126 brouard 7129: }
7130: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7131: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7132: 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 7133: <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 7134: }
7135: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7136: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7137: true period expectancies (those weighted with period prevalences are also\
7138: drawn in addition to the population based expectancies computed using\
1.241 brouard 7139: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7140: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7141: /* } /\* end i1 *\/ */
7142: }/* End k1 */
1.241 brouard 7143: }/* End nres */
1.222 brouard 7144: fprintf(fichtm,"</ul>");
7145: fflush(fichtm);
1.126 brouard 7146: }
7147:
7148: /******************* Gnuplot file **************/
1.296 brouard 7149: 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 7150:
7151: char dirfileres[132],optfileres[132];
1.264 brouard 7152: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7153: 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 7154: int lv=0, vlv=0, kl=0;
1.130 brouard 7155: int ng=0;
1.201 brouard 7156: int vpopbased;
1.223 brouard 7157: int ioffset; /* variable offset for columns */
1.270 brouard 7158: int iyearc=1; /* variable column for year of projection */
7159: int iagec=1; /* variable column for age of projection */
1.235 brouard 7160: int nres=0; /* Index of resultline */
1.266 brouard 7161: int istart=1; /* For starting graphs in projections */
1.219 brouard 7162:
1.126 brouard 7163: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7164: /* printf("Problem with file %s",optionfilegnuplot); */
7165: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7166: /* } */
7167:
7168: /*#ifdef windows */
7169: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7170: /*#endif */
1.225 brouard 7171: m=pow(2,cptcoveff);
1.126 brouard 7172:
1.274 brouard 7173: /* diagram of the model */
7174: fprintf(ficgp,"\n#Diagram of the model \n");
7175: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7176: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7177: 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);
7178:
7179: 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);
7180: fprintf(ficgp,"\n#show arrow\nunset label\n");
7181: 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);
7182: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7183: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7184: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7185: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7186:
1.202 brouard 7187: /* Contribution to likelihood */
7188: /* Plot the probability implied in the likelihood */
1.223 brouard 7189: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7190: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7191: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7192: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7193: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7194: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7195: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7196: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7197: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7198: 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));
7199: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7200: 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));
7201: for (i=1; i<= nlstate ; i ++) {
7202: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7203: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7204: 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);
7205: for (j=2; j<= nlstate+ndeath ; j ++) {
7206: 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);
7207: }
7208: fprintf(ficgp,";\nset out; unset ylabel;\n");
7209: }
7210: /* 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 */
7211: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7212: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7213: fprintf(ficgp,"\nset out;unset log\n");
7214: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7215:
1.126 brouard 7216: strcpy(dirfileres,optionfilefiname);
7217: strcpy(optfileres,"vpl");
1.223 brouard 7218: /* 1eme*/
1.238 brouard 7219: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7220: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7221: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7222: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7223: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7224: continue;
7225: /* We are interested in selected combination by the resultline */
1.246 brouard 7226: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.288 brouard 7227: fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7228: strcpy(gplotlabel,"(");
1.238 brouard 7229: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7230: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7231: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7232: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7233: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7234: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7235: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7236: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7237: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7238: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7239: }
7240: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7241: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7242: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7243: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7244: }
7245: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7246: /* printf("\n#\n"); */
1.238 brouard 7247: fprintf(ficgp,"\n#\n");
7248: if(invalidvarcomb[k1]){
1.260 brouard 7249: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7250: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7251: continue;
7252: }
1.235 brouard 7253:
1.241 brouard 7254: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7255: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7256: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7257: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7258: 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);
7259: /* 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); */
7260: /* k1-1 error should be nres-1*/
1.238 brouard 7261: for (i=1; i<= nlstate ; i ++) {
7262: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7263: else fprintf(ficgp," %%*lf (%%*lf)");
7264: }
1.288 brouard 7265: 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 7266: for (i=1; i<= nlstate ; i ++) {
7267: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7268: else fprintf(ficgp," %%*lf (%%*lf)");
7269: }
1.260 brouard 7270: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7271: for (i=1; i<= nlstate ; i ++) {
7272: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7273: else fprintf(ficgp," %%*lf (%%*lf)");
7274: }
1.265 brouard 7275: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7276:
7277: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7278: if(cptcoveff ==0){
1.271 brouard 7279: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7280: }else{
7281: kl=0;
7282: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7283: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7284: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7285: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7286: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7287: vlv= nbcode[Tvaraff[k]][lv];
7288: kl++;
7289: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
7290: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7291: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7292: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7293: if(k==cptcoveff){
7294: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7295: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7296: }else{
7297: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7298: kl++;
7299: }
7300: } /* end covariate */
7301: } /* end if no covariate */
7302:
1.296 brouard 7303: if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
1.238 brouard 7304: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7305: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7306: if(cptcoveff ==0){
1.245 brouard 7307: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7308: }else{
7309: kl=0;
7310: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7311: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7312: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7313: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7314: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7315: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7316: kl++;
1.238 brouard 7317: /* 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 *\/ */
7318: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7319: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7320: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7321: if(k==cptcoveff){
1.245 brouard 7322: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7323: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7324: }else{
7325: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7326: kl++;
7327: }
7328: } /* end covariate */
7329: } /* end if no covariate */
1.296 brouard 7330: if(prevbcast == 1){
1.268 brouard 7331: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7332: /* k1-1 error should be nres-1*/
7333: for (i=1; i<= nlstate ; i ++) {
7334: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7335: else fprintf(ficgp," %%*lf (%%*lf)");
7336: }
1.271 brouard 7337: 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 7338: for (i=1; i<= nlstate ; i ++) {
7339: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7340: else fprintf(ficgp," %%*lf (%%*lf)");
7341: }
1.276 brouard 7342: 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 7343: for (i=1; i<= nlstate ; i ++) {
7344: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7345: else fprintf(ficgp," %%*lf (%%*lf)");
7346: }
1.274 brouard 7347: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7348: } /* end if backprojcast */
1.296 brouard 7349: } /* end if prevbcast */
1.276 brouard 7350: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7351: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7352: } /* nres */
1.201 brouard 7353: } /* k1 */
7354: } /* cpt */
1.235 brouard 7355:
7356:
1.126 brouard 7357: /*2 eme*/
1.238 brouard 7358: for (k1=1; k1<= m ; k1 ++){
7359: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7360: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7361: continue;
7362: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7363: strcpy(gplotlabel,"(");
1.238 brouard 7364: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7365: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7366: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7367: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7368: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7369: vlv= nbcode[Tvaraff[k]][lv];
7370: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7371: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7372: }
1.237 brouard 7373: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7374: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7375: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7376: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7377: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7378: }
1.264 brouard 7379: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7380: fprintf(ficgp,"\n#\n");
1.223 brouard 7381: if(invalidvarcomb[k1]){
7382: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7383: continue;
7384: }
1.219 brouard 7385:
1.241 brouard 7386: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7387: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7388: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7389: if(vpopbased==0){
1.238 brouard 7390: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7391: }else
1.238 brouard 7392: fprintf(ficgp,"\nreplot ");
7393: for (i=1; i<= nlstate+1 ; i ++) {
7394: k=2*i;
1.261 brouard 7395: 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 7396: for (j=1; j<= nlstate+1 ; j ++) {
7397: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7398: else fprintf(ficgp," %%*lf (%%*lf)");
7399: }
7400: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7401: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7402: 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 7403: for (j=1; j<= nlstate+1 ; j ++) {
7404: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7405: else fprintf(ficgp," %%*lf (%%*lf)");
7406: }
7407: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7408: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
1.238 brouard 7409: for (j=1; j<= nlstate+1 ; j ++) {
7410: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7411: else fprintf(ficgp," %%*lf (%%*lf)");
7412: }
7413: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7414: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7415: } /* state */
7416: } /* vpopbased */
1.264 brouard 7417: 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 7418: } /* end nres */
7419: } /* k1 end 2 eme*/
7420:
7421:
7422: /*3eme*/
7423: for (k1=1; k1<= m ; k1 ++){
7424: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7425: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7426: continue;
7427:
7428: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7429: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7430: strcpy(gplotlabel,"(");
1.238 brouard 7431: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7432: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7433: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7434: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7435: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7436: vlv= nbcode[Tvaraff[k]][lv];
7437: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7438: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7439: }
7440: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7441: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7442: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7443: }
1.264 brouard 7444: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7445: fprintf(ficgp,"\n#\n");
7446: if(invalidvarcomb[k1]){
7447: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7448: continue;
7449: }
7450:
7451: /* k=2+nlstate*(2*cpt-2); */
7452: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7453: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7454: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7455: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7456: 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 7457: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7458: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7459: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7460: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7461: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7462: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7463:
1.238 brouard 7464: */
7465: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7466: 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 7467: /* 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 7468:
1.238 brouard 7469: }
1.261 brouard 7470: 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 7471: }
1.264 brouard 7472: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7473: } /* end nres */
7474: } /* end kl 3eme */
1.126 brouard 7475:
1.223 brouard 7476: /* 4eme */
1.201 brouard 7477: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7478: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7479: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7480: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7481: continue;
1.238 brouard 7482: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7483: strcpy(gplotlabel,"(");
1.238 brouard 7484: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7485: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7486: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7487: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7488: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7489: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7490: vlv= nbcode[Tvaraff[k]][lv];
7491: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7492: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7493: }
7494: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7495: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7496: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7497: }
1.264 brouard 7498: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7499: fprintf(ficgp,"\n#\n");
7500: if(invalidvarcomb[k1]){
7501: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7502: continue;
1.223 brouard 7503: }
1.238 brouard 7504:
1.241 brouard 7505: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7506: 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 7507: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7508: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7509: k=3;
7510: for (i=1; i<= nlstate ; i ++){
7511: if(i==1){
7512: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7513: }else{
7514: fprintf(ficgp,", '' ");
7515: }
7516: l=(nlstate+ndeath)*(i-1)+1;
7517: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7518: for (j=2; j<= nlstate+ndeath ; j ++)
7519: fprintf(ficgp,"+$%d",k+l+j-1);
7520: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7521: } /* nlstate */
1.264 brouard 7522: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7523: } /* end cpt state*/
7524: } /* end nres */
7525: } /* end covariate k1 */
7526:
1.220 brouard 7527: /* 5eme */
1.201 brouard 7528: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7529: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7530: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7531: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7532: continue;
1.238 brouard 7533: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7534: strcpy(gplotlabel,"(");
1.238 brouard 7535: 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);
7536: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7537: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7538: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7539: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7540: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7541: vlv= nbcode[Tvaraff[k]][lv];
7542: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7543: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7544: }
7545: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7546: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7547: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7548: }
1.264 brouard 7549: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7550: fprintf(ficgp,"\n#\n");
7551: if(invalidvarcomb[k1]){
7552: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7553: continue;
7554: }
1.227 brouard 7555:
1.241 brouard 7556: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7557: 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 7558: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7559: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7560: k=3;
7561: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7562: if(j==1)
7563: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7564: else
7565: fprintf(ficgp,", '' ");
7566: l=(nlstate+ndeath)*(cpt-1) +j;
7567: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7568: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7569: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7570: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7571: } /* nlstate */
7572: fprintf(ficgp,", '' ");
7573: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7574: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7575: l=(nlstate+ndeath)*(cpt-1) +j;
7576: if(j < nlstate)
7577: fprintf(ficgp,"$%d +",k+l);
7578: else
7579: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7580: }
1.264 brouard 7581: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7582: } /* end cpt state*/
7583: } /* end covariate */
7584: } /* end nres */
1.227 brouard 7585:
1.220 brouard 7586: /* 6eme */
1.202 brouard 7587: /* CV preval stable (period) for each covariate */
1.237 brouard 7588: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7589: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7590: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7591: continue;
1.255 brouard 7592: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7593: strcpy(gplotlabel,"(");
1.288 brouard 7594: fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7595: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7596: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7597: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7598: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7599: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7600: vlv= nbcode[Tvaraff[k]][lv];
7601: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7602: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7603: }
1.237 brouard 7604: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7605: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7606: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7607: }
1.264 brouard 7608: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7609: fprintf(ficgp,"\n#\n");
1.223 brouard 7610: if(invalidvarcomb[k1]){
1.227 brouard 7611: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7612: continue;
1.223 brouard 7613: }
1.227 brouard 7614:
1.241 brouard 7615: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7616: 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 7617: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7618: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7619: k=3; /* Offset */
1.255 brouard 7620: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7621: if(i==1)
7622: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7623: else
7624: fprintf(ficgp,", '' ");
1.255 brouard 7625: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7626: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7627: for (j=2; j<= nlstate ; j ++)
7628: fprintf(ficgp,"+$%d",k+l+j-1);
7629: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7630: } /* nlstate */
1.264 brouard 7631: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7632: } /* end cpt state*/
7633: } /* end covariate */
1.227 brouard 7634:
7635:
1.220 brouard 7636: /* 7eme */
1.296 brouard 7637: if(prevbcast == 1){
1.288 brouard 7638: /* CV backward prevalence for each covariate */
1.237 brouard 7639: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7640: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7641: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7642: continue;
1.268 brouard 7643: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7644: strcpy(gplotlabel,"(");
1.288 brouard 7645: fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7646: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7647: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7648: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7649: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7650: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7651: vlv= nbcode[Tvaraff[k]][lv];
7652: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7653: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7654: }
1.237 brouard 7655: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7656: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7657: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7658: }
1.264 brouard 7659: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7660: fprintf(ficgp,"\n#\n");
7661: if(invalidvarcomb[k1]){
7662: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7663: continue;
7664: }
7665:
1.241 brouard 7666: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7667: 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 7668: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7669: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7670: k=3; /* Offset */
1.268 brouard 7671: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7672: if(i==1)
7673: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7674: else
7675: fprintf(ficgp,", '' ");
7676: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7677: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7678: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7679: /* 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 7680: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7681: /* for (j=2; j<= nlstate ; j ++) */
7682: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7683: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7684: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7685: } /* nlstate */
1.264 brouard 7686: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7687: } /* end cpt state*/
7688: } /* end covariate */
1.296 brouard 7689: } /* End if prevbcast */
1.218 brouard 7690:
1.223 brouard 7691: /* 8eme */
1.218 brouard 7692: if(prevfcast==1){
1.288 brouard 7693: /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
1.218 brouard 7694:
1.237 brouard 7695: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7696: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7697: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7698: continue;
1.211 brouard 7699: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7700: strcpy(gplotlabel,"(");
1.288 brouard 7701: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7702: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7703: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7704: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7705: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7706: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7707: vlv= nbcode[Tvaraff[k]][lv];
7708: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7709: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7710: }
1.237 brouard 7711: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7712: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7713: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7714: }
1.264 brouard 7715: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7716: fprintf(ficgp,"\n#\n");
7717: if(invalidvarcomb[k1]){
7718: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7719: continue;
7720: }
7721:
7722: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7723: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7724: 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 7725: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7726: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7727:
7728: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7729: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7730: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7731: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7732: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7733: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7734: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7735: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7736: if(i==istart){
1.227 brouard 7737: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7738: }else{
7739: fprintf(ficgp,",\\\n '' ");
7740: }
7741: if(cptcoveff ==0){ /* No covariate */
7742: ioffset=2; /* Age is in 2 */
7743: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7744: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7745: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7746: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7747: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7748: if(i==nlstate+1){
1.270 brouard 7749: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7750: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7751: fprintf(ficgp,",\\\n '' ");
7752: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7753: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7754: offyear, \
1.268 brouard 7755: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7756: }else
1.227 brouard 7757: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7758: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7759: }else{ /* more than 2 covariates */
1.270 brouard 7760: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7761: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7762: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7763: iyearc=ioffset-1;
7764: iagec=ioffset;
1.227 brouard 7765: fprintf(ficgp," u %d:(",ioffset);
7766: kl=0;
7767: strcpy(gplotcondition,"(");
7768: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7769: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7770: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7771: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7772: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7773: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7774: kl++;
7775: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7776: kl++;
7777: if(k <cptcoveff && cptcoveff>1)
7778: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7779: }
7780: strcpy(gplotcondition+strlen(gplotcondition),")");
7781: /* 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 *\/ */
7782: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7783: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7784: /* '' 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*/
7785: if(i==nlstate+1){
1.270 brouard 7786: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7787: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7788: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7789: fprintf(ficgp," u %d:(",iagec);
7790: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7791: iyearc, iagec, offyear, \
7792: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7793: /* '' 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 7794: }else{
7795: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7796: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7797: }
7798: } /* end if covariate */
7799: } /* nlstate */
1.264 brouard 7800: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7801: } /* end cpt state*/
7802: } /* end covariate */
7803: } /* End if prevfcast */
1.227 brouard 7804:
1.296 brouard 7805: if(prevbcast==1){
1.268 brouard 7806: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7807:
7808: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7809: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7810: if(m != 1 && TKresult[nres]!= k1)
7811: continue;
7812: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7813: strcpy(gplotlabel,"(");
7814: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7815: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7816: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7817: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7818: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7819: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7820: vlv= nbcode[Tvaraff[k]][lv];
7821: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7822: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7823: }
7824: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7825: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7826: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7827: }
7828: strcpy(gplotlabel+strlen(gplotlabel),")");
7829: fprintf(ficgp,"\n#\n");
7830: if(invalidvarcomb[k1]){
7831: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7832: continue;
7833: }
7834:
7835: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7836: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7837: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7838: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7839: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7840:
7841: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7842: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7843: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7844: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7845: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7846: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7847: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7848: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7849: if(i==istart){
7850: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7851: }else{
7852: fprintf(ficgp,",\\\n '' ");
7853: }
7854: if(cptcoveff ==0){ /* No covariate */
7855: ioffset=2; /* Age is in 2 */
7856: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7857: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7858: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7859: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7860: fprintf(ficgp," u %d:(", ioffset);
7861: if(i==nlstate+1){
1.270 brouard 7862: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7863: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7864: fprintf(ficgp,",\\\n '' ");
7865: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7866: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7867: offbyear, \
7868: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7869: }else
7870: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7871: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7872: }else{ /* more than 2 covariates */
1.270 brouard 7873: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7874: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7875: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7876: iyearc=ioffset-1;
7877: iagec=ioffset;
1.268 brouard 7878: fprintf(ficgp," u %d:(",ioffset);
7879: kl=0;
7880: strcpy(gplotcondition,"(");
7881: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7882: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7883: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7884: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7885: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7886: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7887: kl++;
7888: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7889: kl++;
7890: if(k <cptcoveff && cptcoveff>1)
7891: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7892: }
7893: strcpy(gplotcondition+strlen(gplotcondition),")");
7894: /* 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 *\/ */
7895: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7896: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7897: /* '' 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*/
7898: if(i==nlstate+1){
1.270 brouard 7899: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7900: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7901: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7902: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7903: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7904: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7905: iyearc,iagec,offbyear, \
7906: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7907: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7908: }else{
7909: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7910: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7911: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7912: }
7913: } /* end if covariate */
7914: } /* nlstate */
7915: fprintf(ficgp,"\nset out; unset label;\n");
7916: } /* end cpt state*/
7917: } /* end covariate */
1.296 brouard 7918: } /* End if prevbcast */
1.268 brouard 7919:
1.227 brouard 7920:
1.238 brouard 7921: /* 9eme writing MLE parameters */
7922: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7923: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7924: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7925: for(k=1; k <=(nlstate+ndeath); k++){
7926: if (k != i) {
1.227 brouard 7927: fprintf(ficgp,"# current state %d\n",k);
7928: for(j=1; j <=ncovmodel; j++){
7929: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7930: jk++;
7931: }
7932: fprintf(ficgp,"\n");
1.126 brouard 7933: }
7934: }
1.223 brouard 7935: }
1.187 brouard 7936: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7937:
1.145 brouard 7938: /*goto avoid;*/
1.238 brouard 7939: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7940: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7941: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7942: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7943: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7944: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7945: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7946: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7947: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7948: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7949: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7950: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7951: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7952: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7953: fprintf(ficgp,"#\n");
1.223 brouard 7954: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7955: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7956: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7957: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7958: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7959: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7960: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7961: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7962: continue;
1.264 brouard 7963: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7964: strcpy(gplotlabel,"(");
1.276 brouard 7965: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7966: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7967: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7968: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7969: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7970: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7971: vlv= nbcode[Tvaraff[k]][lv];
7972: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7973: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7974: }
1.237 brouard 7975: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7976: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7977: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7978: }
1.264 brouard 7979: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7980: fprintf(ficgp,"\n#\n");
1.264 brouard 7981: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7982: fprintf(ficgp,"\nset key outside ");
7983: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7984: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7985: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7986: if (ng==1){
7987: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7988: fprintf(ficgp,"\nunset log y");
7989: }else if (ng==2){
7990: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7991: fprintf(ficgp,"\nset log y");
7992: }else if (ng==3){
7993: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7994: fprintf(ficgp,"\nset log y");
7995: }else
7996: fprintf(ficgp,"\nunset title ");
7997: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7998: i=1;
7999: for(k2=1; k2<=nlstate; k2++) {
8000: k3=i;
8001: for(k=1; k<=(nlstate+ndeath); k++) {
8002: if (k != k2){
8003: switch( ng) {
8004: case 1:
8005: if(nagesqr==0)
8006: fprintf(ficgp," p%d+p%d*x",i,i+1);
8007: else /* nagesqr =1 */
8008: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8009: break;
8010: case 2: /* ng=2 */
8011: if(nagesqr==0)
8012: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
8013: else /* nagesqr =1 */
8014: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
8015: break;
8016: case 3:
8017: if(nagesqr==0)
8018: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
8019: else /* nagesqr =1 */
8020: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
8021: break;
8022: }
8023: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 8024: ijp=1; /* product no age */
8025: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
8026: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 8027: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 8028: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8029: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
8030: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
8031: if(DummyV[j]==0){
8032: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
8033: }else{ /* quantitative */
8034: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
8035: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8036: }
8037: ij++;
1.237 brouard 8038: }
1.268 brouard 8039: }
8040: }else if(cptcovprod >0){
8041: if(j==Tprod[ijp]) { /* */
8042: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
8043: if(ijp <=cptcovprod) { /* Product */
8044: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
8045: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
8046: /* 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)]); */
8047: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
8048: }else{ /* Vn is dummy and Vm is quanti */
8049: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
8050: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8051: }
8052: }else{ /* Vn*Vm Vn is quanti */
8053: if(DummyV[Tvard[ijp][2]]==0){
8054: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
8055: }else{ /* Both quanti */
8056: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
8057: }
1.237 brouard 8058: }
1.268 brouard 8059: ijp++;
1.237 brouard 8060: }
1.268 brouard 8061: } /* end Tprod */
1.237 brouard 8062: } else{ /* simple covariate */
1.264 brouard 8063: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 8064: if(Dummy[j]==0){
8065: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
8066: }else{ /* quantitative */
8067: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 8068: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 8069: }
1.237 brouard 8070: } /* end simple */
8071: } /* end j */
1.223 brouard 8072: }else{
8073: i=i-ncovmodel;
8074: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
8075: fprintf(ficgp," (1.");
8076: }
1.227 brouard 8077:
1.223 brouard 8078: if(ng != 1){
8079: fprintf(ficgp,")/(1");
1.227 brouard 8080:
1.264 brouard 8081: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 8082: if(nagesqr==0)
1.264 brouard 8083: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 8084: else /* nagesqr =1 */
1.264 brouard 8085: 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 8086:
1.223 brouard 8087: ij=1;
8088: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 8089: if(cptcovage >0){
8090: if((j-2)==Tage[ij]) { /* Bug valgrind */
8091: if(ij <=cptcovage) { /* Bug valgrind */
8092: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
8093: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
8094: ij++;
8095: }
8096: }
8097: }else
8098: 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 8099: }
8100: fprintf(ficgp,")");
8101: }
8102: fprintf(ficgp,")");
8103: if(ng ==2)
1.276 brouard 8104: 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 8105: else /* ng= 3 */
1.276 brouard 8106: 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 8107: }else{ /* end ng <> 1 */
8108: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8109: 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 8110: }
8111: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8112: fprintf(ficgp,",");
8113: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8114: fprintf(ficgp,",");
8115: i=i+ncovmodel;
8116: } /* end k */
8117: } /* end k2 */
1.276 brouard 8118: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8119: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8120: } /* end k1 */
1.223 brouard 8121: } /* end ng */
8122: /* avoid: */
8123: fflush(ficgp);
1.126 brouard 8124: } /* end gnuplot */
8125:
8126:
8127: /*************** Moving average **************/
1.219 brouard 8128: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8129: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8130:
1.222 brouard 8131: int i, cpt, cptcod;
8132: int modcovmax =1;
8133: int mobilavrange, mob;
8134: int iage=0;
1.288 brouard 8135: int firstA1=0, firstA2=0;
1.222 brouard 8136:
1.266 brouard 8137: double sum=0., sumr=0.;
1.222 brouard 8138: double age;
1.266 brouard 8139: double *sumnewp, *sumnewm, *sumnewmr;
8140: double *agemingood, *agemaxgood;
8141: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8142:
8143:
1.278 brouard 8144: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8145: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8146:
8147: sumnewp = vector(1,ncovcombmax);
8148: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8149: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8150: agemingood = vector(1,ncovcombmax);
1.266 brouard 8151: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8152: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8153: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8154:
8155: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8156: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8157: sumnewp[cptcod]=0.;
1.266 brouard 8158: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8159: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8160: }
8161: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8162:
1.266 brouard 8163: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8164: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8165: else mobilavrange=mobilav;
8166: for (age=bage; age<=fage; age++)
8167: for (i=1; i<=nlstate;i++)
8168: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8169: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8170: /* We keep the original values on the extreme ages bage, fage and for
8171: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8172: we use a 5 terms etc. until the borders are no more concerned.
8173: */
8174: for (mob=3;mob <=mobilavrange;mob=mob+2){
8175: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8176: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8177: sumnewm[cptcod]=0.;
8178: for (i=1; i<=nlstate;i++){
1.222 brouard 8179: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8180: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8181: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8182: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8183: }
8184: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8185: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8186: } /* end i */
8187: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8188: } /* end cptcod */
1.222 brouard 8189: }/* end age */
8190: }/* end mob */
1.266 brouard 8191: }else{
8192: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8193: return -1;
1.266 brouard 8194: }
8195:
8196: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8197: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8198: if(invalidvarcomb[cptcod]){
8199: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8200: continue;
8201: }
1.219 brouard 8202:
1.266 brouard 8203: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8204: sumnewm[cptcod]=0.;
8205: sumnewmr[cptcod]=0.;
8206: for (i=1; i<=nlstate;i++){
8207: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8208: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8209: }
8210: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8211: agemingoodr[cptcod]=age;
8212: }
8213: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8214: agemingood[cptcod]=age;
8215: }
8216: } /* age */
8217: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8218: sumnewm[cptcod]=0.;
1.266 brouard 8219: sumnewmr[cptcod]=0.;
1.222 brouard 8220: for (i=1; i<=nlstate;i++){
8221: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8222: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8223: }
8224: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8225: agemaxgoodr[cptcod]=age;
1.222 brouard 8226: }
8227: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8228: agemaxgood[cptcod]=age;
8229: }
8230: } /* age */
8231: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8232: /* but they will change */
1.288 brouard 8233: firstA1=0;firstA2=0;
1.266 brouard 8234: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8235: sumnewm[cptcod]=0.;
8236: sumnewmr[cptcod]=0.;
8237: for (i=1; i<=nlstate;i++){
8238: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8239: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8240: }
8241: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8242: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8243: agemaxgoodr[cptcod]=age; /* age min */
8244: for (i=1; i<=nlstate;i++)
8245: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8246: }else{ /* bad we change the value with the values of good ages */
8247: for (i=1; i<=nlstate;i++){
8248: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8249: } /* i */
8250: } /* end bad */
8251: }else{
8252: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8253: agemaxgood[cptcod]=age;
8254: }else{ /* bad we change the value with the values of good ages */
8255: for (i=1; i<=nlstate;i++){
8256: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8257: } /* i */
8258: } /* end bad */
8259: }/* end else */
8260: sum=0.;sumr=0.;
8261: for (i=1; i<=nlstate;i++){
8262: sum+=mobaverage[(int)age][i][cptcod];
8263: sumr+=probs[(int)age][i][cptcod];
8264: }
8265: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.288 brouard 8266: if(!firstA1){
8267: firstA1=1;
8268: 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);
8269: }
8270: 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 8271: } /* end bad */
8272: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8273: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.288 brouard 8274: if(!firstA2){
8275: firstA2=1;
8276: 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);
8277: }
8278: 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 8279: } /* end bad */
8280: }/* age */
1.266 brouard 8281:
8282: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8283: sumnewm[cptcod]=0.;
1.266 brouard 8284: sumnewmr[cptcod]=0.;
1.222 brouard 8285: for (i=1; i<=nlstate;i++){
8286: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8287: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8288: }
8289: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8290: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8291: agemingoodr[cptcod]=age;
8292: for (i=1; i<=nlstate;i++)
8293: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8294: }else{ /* bad we change the value with the values of good ages */
8295: for (i=1; i<=nlstate;i++){
8296: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8297: } /* i */
8298: } /* end bad */
8299: }else{
8300: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8301: agemingood[cptcod]=age;
8302: }else{ /* bad */
8303: for (i=1; i<=nlstate;i++){
8304: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8305: } /* i */
8306: } /* end bad */
8307: }/* end else */
8308: sum=0.;sumr=0.;
8309: for (i=1; i<=nlstate;i++){
8310: sum+=mobaverage[(int)age][i][cptcod];
8311: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8312: }
1.266 brouard 8313: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8314: 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 8315: } /* end bad */
8316: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8317: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8318: 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 8319: } /* end bad */
8320: }/* age */
1.266 brouard 8321:
1.222 brouard 8322:
8323: for (age=bage; age<=fage; age++){
1.235 brouard 8324: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8325: sumnewp[cptcod]=0.;
8326: sumnewm[cptcod]=0.;
8327: for (i=1; i<=nlstate;i++){
8328: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8329: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8330: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8331: }
8332: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8333: }
8334: /* printf("\n"); */
8335: /* } */
1.266 brouard 8336:
1.222 brouard 8337: /* brutal averaging */
1.266 brouard 8338: /* for (i=1; i<=nlstate;i++){ */
8339: /* for (age=1; age<=bage; age++){ */
8340: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8341: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8342: /* } */
8343: /* for (age=fage; age<=AGESUP; age++){ */
8344: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8345: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8346: /* } */
8347: /* } /\* end i status *\/ */
8348: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8349: /* for (age=1; age<=AGESUP; age++){ */
8350: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8351: /* mobaverage[(int)age][i][cptcod]=0.; */
8352: /* } */
8353: /* } */
1.222 brouard 8354: }/* end cptcod */
1.266 brouard 8355: free_vector(agemaxgoodr,1, ncovcombmax);
8356: free_vector(agemaxgood,1, ncovcombmax);
8357: free_vector(agemingood,1, ncovcombmax);
8358: free_vector(agemingoodr,1, ncovcombmax);
8359: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8360: free_vector(sumnewm,1, ncovcombmax);
8361: free_vector(sumnewp,1, ncovcombmax);
8362: return 0;
8363: }/* End movingaverage */
1.218 brouard 8364:
1.126 brouard 8365:
1.296 brouard 8366:
1.126 brouard 8367: /************** Forecasting ******************/
1.296 brouard 8368: /* 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)*/
8369: 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){
8370: /* dateintemean, mean date of interviews
8371: dateprojd, year, month, day of starting projection
8372: dateprojf date of end of projection;year of end of projection (same day and month as proj1).
1.126 brouard 8373: agemin, agemax range of age
8374: dateprev1 dateprev2 range of dates during which prevalence is computed
8375: */
1.296 brouard 8376: /* double anprojd, mprojd, jprojd; */
8377: /* double anprojf, mprojf, jprojf; */
1.267 brouard 8378: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8379: double agec; /* generic age */
1.296 brouard 8380: double agelim, ppij, yp,yp1,yp2;
1.126 brouard 8381: double *popeffectif,*popcount;
8382: double ***p3mat;
1.218 brouard 8383: /* double ***mobaverage; */
1.126 brouard 8384: char fileresf[FILENAMELENGTH];
8385:
8386: agelim=AGESUP;
1.211 brouard 8387: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8388: in each health status at the date of interview (if between dateprev1 and dateprev2).
8389: We still use firstpass and lastpass as another selection.
8390: */
1.214 brouard 8391: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8392: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8393:
1.201 brouard 8394: strcpy(fileresf,"F_");
8395: strcat(fileresf,fileresu);
1.126 brouard 8396: if((ficresf=fopen(fileresf,"w"))==NULL) {
8397: printf("Problem with forecast resultfile: %s\n", fileresf);
8398: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8399: }
1.235 brouard 8400: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8401: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8402:
1.225 brouard 8403: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8404:
8405:
8406: stepsize=(int) (stepm+YEARM-1)/YEARM;
8407: if (stepm<=12) stepsize=1;
8408: if(estepm < stepm){
8409: printf ("Problem %d lower than %d\n",estepm, stepm);
8410: }
1.270 brouard 8411: else{
8412: hstepm=estepm;
8413: }
8414: if(estepm > stepm){ /* Yes every two year */
8415: stepsize=2;
8416: }
1.296 brouard 8417: hstepm=hstepm/stepm;
1.126 brouard 8418:
1.296 brouard 8419:
8420: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8421: /* fractional in yp1 *\/ */
8422: /* aintmean=yp; */
8423: /* yp2=modf((yp1*12),&yp); */
8424: /* mintmean=yp; */
8425: /* yp1=modf((yp2*30.5),&yp); */
8426: /* jintmean=yp; */
8427: /* if(jintmean==0) jintmean=1; */
8428: /* if(mintmean==0) mintmean=1; */
1.126 brouard 8429:
1.296 brouard 8430:
8431: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
8432: /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
8433: /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
1.227 brouard 8434: i1=pow(2,cptcoveff);
1.126 brouard 8435: if (cptcovn < 1){i1=1;}
8436:
1.296 brouard 8437: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.126 brouard 8438:
8439: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8440:
1.126 brouard 8441: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8442: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8443: for(k=1; k<=i1;k++){
1.253 brouard 8444: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8445: continue;
1.227 brouard 8446: if(invalidvarcomb[k]){
8447: printf("\nCombination (%d) projection ignored because no cases \n",k);
8448: continue;
8449: }
8450: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8451: for(j=1;j<=cptcoveff;j++) {
8452: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8453: }
1.235 brouard 8454: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8455: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8456: }
1.227 brouard 8457: fprintf(ficresf," yearproj age");
8458: for(j=1; j<=nlstate+ndeath;j++){
8459: for(i=1; i<=nlstate;i++)
8460: fprintf(ficresf," p%d%d",i,j);
8461: fprintf(ficresf," wp.%d",j);
8462: }
1.296 brouard 8463: for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
1.227 brouard 8464: fprintf(ficresf,"\n");
1.296 brouard 8465: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
1.270 brouard 8466: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8467: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8468: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8469: nhstepm = nhstepm/hstepm;
8470: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8471: oldm=oldms;savm=savms;
1.268 brouard 8472: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8473: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8474: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8475: for (h=0; h<=nhstepm; h++){
8476: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8477: break;
8478: }
8479: }
8480: fprintf(ficresf,"\n");
8481: for(j=1;j<=cptcoveff;j++)
8482: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8483: fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
1.268 brouard 8484:
8485: for(j=1; j<=nlstate+ndeath;j++) {
8486: ppij=0.;
8487: for(i=1; i<=nlstate;i++) {
1.278 brouard 8488: if (mobilav>=1)
8489: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8490: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8491: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8492: }
1.268 brouard 8493: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8494: } /* end i */
8495: fprintf(ficresf," %.3f", ppij);
8496: }/* end j */
1.227 brouard 8497: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8498: } /* end agec */
1.266 brouard 8499: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8500: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8501: } /* end yearp */
8502: } /* end k */
1.219 brouard 8503:
1.126 brouard 8504: fclose(ficresf);
1.215 brouard 8505: printf("End of Computing forecasting \n");
8506: fprintf(ficlog,"End of Computing forecasting\n");
8507:
1.126 brouard 8508: }
8509:
1.269 brouard 8510: /************** Back Forecasting ******************/
1.296 brouard 8511: /* 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){ */
8512: 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){
8513: /* back1, year, month, day of starting backprojection
1.267 brouard 8514: agemin, agemax range of age
8515: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8516: anback2 year of end of backprojection (same day and month as back1).
8517: prevacurrent and prev are prevalences.
1.267 brouard 8518: */
8519: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8520: double agec; /* generic age */
1.302 brouard 8521: double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
1.267 brouard 8522: double *popeffectif,*popcount;
8523: double ***p3mat;
8524: /* double ***mobaverage; */
8525: char fileresfb[FILENAMELENGTH];
8526:
1.268 brouard 8527: agelim=AGEINF;
1.267 brouard 8528: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8529: in each health status at the date of interview (if between dateprev1 and dateprev2).
8530: We still use firstpass and lastpass as another selection.
8531: */
8532: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8533: /* firstpass, lastpass, stepm, weightopt, model); */
8534:
8535: /*Do we need to compute prevalence again?*/
8536:
8537: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8538:
8539: strcpy(fileresfb,"FB_");
8540: strcat(fileresfb,fileresu);
8541: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8542: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8543: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8544: }
8545: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8546: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8547:
8548: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8549:
8550:
8551: stepsize=(int) (stepm+YEARM-1)/YEARM;
8552: if (stepm<=12) stepsize=1;
8553: if(estepm < stepm){
8554: printf ("Problem %d lower than %d\n",estepm, stepm);
8555: }
1.270 brouard 8556: else{
8557: hstepm=estepm;
8558: }
8559: if(estepm >= stepm){ /* Yes every two year */
8560: stepsize=2;
8561: }
1.267 brouard 8562:
8563: hstepm=hstepm/stepm;
1.296 brouard 8564: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
8565: /* fractional in yp1 *\/ */
8566: /* aintmean=yp; */
8567: /* yp2=modf((yp1*12),&yp); */
8568: /* mintmean=yp; */
8569: /* yp1=modf((yp2*30.5),&yp); */
8570: /* jintmean=yp; */
8571: /* if(jintmean==0) jintmean=1; */
8572: /* if(mintmean==0) jintmean=1; */
1.267 brouard 8573:
8574: i1=pow(2,cptcoveff);
8575: if (cptcovn < 1){i1=1;}
8576:
1.296 brouard 8577: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
8578: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8579:
8580: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8581:
8582: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8583: for(k=1; k<=i1;k++){
8584: if(i1 != 1 && TKresult[nres]!= k)
8585: continue;
8586: if(invalidvarcomb[k]){
8587: printf("\nCombination (%d) projection ignored because no cases \n",k);
8588: continue;
8589: }
1.268 brouard 8590: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8591: for(j=1;j<=cptcoveff;j++) {
8592: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8593: }
8594: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8595: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8596: }
8597: fprintf(ficresfb," yearbproj age");
8598: for(j=1; j<=nlstate+ndeath;j++){
8599: for(i=1; i<=nlstate;i++)
1.268 brouard 8600: fprintf(ficresfb," b%d%d",i,j);
8601: fprintf(ficresfb," b.%d",j);
1.267 brouard 8602: }
1.296 brouard 8603: for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
1.267 brouard 8604: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8605: fprintf(ficresfb,"\n");
1.296 brouard 8606: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
1.273 brouard 8607: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8608: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8609: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8610: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8611: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8612: nhstepm = nhstepm/hstepm;
8613: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8614: oldm=oldms;savm=savms;
1.268 brouard 8615: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8616: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8617: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8618: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8619: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8620: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8621: for (h=0; h<=nhstepm; h++){
1.268 brouard 8622: if (h*hstepm/YEARM*stepm ==-yearp) {
8623: break;
8624: }
8625: }
8626: fprintf(ficresfb,"\n");
8627: for(j=1;j<=cptcoveff;j++)
8628: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.296 brouard 8629: fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
1.268 brouard 8630: for(i=1; i<=nlstate+ndeath;i++) {
8631: ppij=0.;ppi=0.;
8632: for(j=1; j<=nlstate;j++) {
8633: /* if (mobilav==1) */
1.269 brouard 8634: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8635: ppi=ppi+prevacurrent[(int)agec][j][k];
8636: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8637: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8638: /* else { */
8639: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8640: /* } */
1.268 brouard 8641: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8642: } /* end j */
8643: if(ppi <0.99){
8644: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8645: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8646: }
8647: fprintf(ficresfb," %.3f", ppij);
8648: }/* end j */
1.267 brouard 8649: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8650: } /* end agec */
8651: } /* end yearp */
8652: } /* end k */
1.217 brouard 8653:
1.267 brouard 8654: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8655:
1.267 brouard 8656: fclose(ficresfb);
8657: printf("End of Computing Back forecasting \n");
8658: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8659:
1.267 brouard 8660: }
1.217 brouard 8661:
1.269 brouard 8662: /* Variance of prevalence limit: varprlim */
8663: 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 8664: /*------- Variance of forward period (stable) prevalence------*/
1.269 brouard 8665:
8666: char fileresvpl[FILENAMELENGTH];
8667: FILE *ficresvpl;
8668: double **oldm, **savm;
8669: double **varpl; /* Variances of prevalence limits by age */
8670: int i1, k, nres, j ;
8671:
8672: strcpy(fileresvpl,"VPL_");
8673: strcat(fileresvpl,fileresu);
8674: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
1.288 brouard 8675: printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
1.269 brouard 8676: exit(0);
8677: }
1.288 brouard 8678: printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8679: fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.269 brouard 8680:
8681: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8682: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8683:
8684: i1=pow(2,cptcoveff);
8685: if (cptcovn < 1){i1=1;}
8686:
8687: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8688: for(k=1; k<=i1;k++){
8689: if(i1 != 1 && TKresult[nres]!= k)
8690: continue;
8691: fprintf(ficresvpl,"\n#****** ");
8692: printf("\n#****** ");
8693: fprintf(ficlog,"\n#****** ");
8694: for(j=1;j<=cptcoveff;j++) {
8695: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8696: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8697: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8698: }
8699: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8700: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8701: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8702: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8703: }
8704: fprintf(ficresvpl,"******\n");
8705: printf("******\n");
8706: fprintf(ficlog,"******\n");
8707:
8708: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8709: oldm=oldms;savm=savms;
8710: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8711: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8712: /*}*/
8713: }
8714:
8715: fclose(ficresvpl);
1.288 brouard 8716: printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
8717: fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
1.269 brouard 8718:
8719: }
8720: /* Variance of back prevalence: varbprlim */
8721: 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){
8722: /*------- Variance of back (stable) prevalence------*/
8723:
8724: char fileresvbl[FILENAMELENGTH];
8725: FILE *ficresvbl;
8726:
8727: double **oldm, **savm;
8728: double **varbpl; /* Variances of back prevalence limits by age */
8729: int i1, k, nres, j ;
8730:
8731: strcpy(fileresvbl,"VBL_");
8732: strcat(fileresvbl,fileresu);
8733: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8734: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8735: exit(0);
8736: }
8737: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8738: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8739:
8740:
8741: i1=pow(2,cptcoveff);
8742: if (cptcovn < 1){i1=1;}
8743:
8744: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8745: for(k=1; k<=i1;k++){
8746: if(i1 != 1 && TKresult[nres]!= k)
8747: continue;
8748: fprintf(ficresvbl,"\n#****** ");
8749: printf("\n#****** ");
8750: fprintf(ficlog,"\n#****** ");
8751: for(j=1;j<=cptcoveff;j++) {
8752: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8753: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8754: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8755: }
8756: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8757: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8758: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8759: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8760: }
8761: fprintf(ficresvbl,"******\n");
8762: printf("******\n");
8763: fprintf(ficlog,"******\n");
8764:
8765: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8766: oldm=oldms;savm=savms;
8767:
8768: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8769: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8770: /*}*/
8771: }
8772:
8773: fclose(ficresvbl);
8774: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8775: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8776:
8777: } /* End of varbprlim */
8778:
1.126 brouard 8779: /************** Forecasting *****not tested NB*************/
1.227 brouard 8780: /* 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 8781:
1.227 brouard 8782: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8783: /* int *popage; */
8784: /* double calagedatem, agelim, kk1, kk2; */
8785: /* double *popeffectif,*popcount; */
8786: /* double ***p3mat,***tabpop,***tabpopprev; */
8787: /* /\* double ***mobaverage; *\/ */
8788: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8789:
1.227 brouard 8790: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8791: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8792: /* agelim=AGESUP; */
8793: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8794:
1.227 brouard 8795: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8796:
8797:
1.227 brouard 8798: /* strcpy(filerespop,"POP_"); */
8799: /* strcat(filerespop,fileresu); */
8800: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8801: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8802: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8803: /* } */
8804: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8805: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8806:
1.227 brouard 8807: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8808:
1.227 brouard 8809: /* /\* if (mobilav!=0) { *\/ */
8810: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8811: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8812: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8813: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8814: /* /\* } *\/ */
8815: /* /\* } *\/ */
1.126 brouard 8816:
1.227 brouard 8817: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8818: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8819:
1.227 brouard 8820: /* agelim=AGESUP; */
1.126 brouard 8821:
1.227 brouard 8822: /* hstepm=1; */
8823: /* hstepm=hstepm/stepm; */
1.218 brouard 8824:
1.227 brouard 8825: /* if (popforecast==1) { */
8826: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8827: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8828: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8829: /* } */
8830: /* popage=ivector(0,AGESUP); */
8831: /* popeffectif=vector(0,AGESUP); */
8832: /* popcount=vector(0,AGESUP); */
1.126 brouard 8833:
1.227 brouard 8834: /* i=1; */
8835: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8836:
1.227 brouard 8837: /* imx=i; */
8838: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8839: /* } */
1.218 brouard 8840:
1.227 brouard 8841: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8842: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8843: /* k=k+1; */
8844: /* fprintf(ficrespop,"\n#******"); */
8845: /* for(j=1;j<=cptcoveff;j++) { */
8846: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8847: /* } */
8848: /* fprintf(ficrespop,"******\n"); */
8849: /* fprintf(ficrespop,"# Age"); */
8850: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8851: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8852:
1.227 brouard 8853: /* for (cpt=0; cpt<=0;cpt++) { */
8854: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8855:
1.227 brouard 8856: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8857: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8858: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8859:
1.227 brouard 8860: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8861: /* oldm=oldms;savm=savms; */
8862: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8863:
1.227 brouard 8864: /* for (h=0; h<=nhstepm; h++){ */
8865: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8866: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8867: /* } */
8868: /* for(j=1; j<=nlstate+ndeath;j++) { */
8869: /* kk1=0.;kk2=0; */
8870: /* for(i=1; i<=nlstate;i++) { */
8871: /* if (mobilav==1) */
8872: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8873: /* else { */
8874: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8875: /* } */
8876: /* } */
8877: /* if (h==(int)(calagedatem+12*cpt)){ */
8878: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8879: /* /\*fprintf(ficrespop," %.3f", kk1); */
8880: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8881: /* } */
8882: /* } */
8883: /* for(i=1; i<=nlstate;i++){ */
8884: /* kk1=0.; */
8885: /* for(j=1; j<=nlstate;j++){ */
8886: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8887: /* } */
8888: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8889: /* } */
1.218 brouard 8890:
1.227 brouard 8891: /* if (h==(int)(calagedatem+12*cpt)) */
8892: /* for(j=1; j<=nlstate;j++) */
8893: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8894: /* } */
8895: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8896: /* } */
8897: /* } */
1.218 brouard 8898:
1.227 brouard 8899: /* /\******\/ */
1.218 brouard 8900:
1.227 brouard 8901: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8902: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8903: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8904: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8905: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8906:
1.227 brouard 8907: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8908: /* oldm=oldms;savm=savms; */
8909: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8910: /* for (h=0; h<=nhstepm; h++){ */
8911: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8912: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8913: /* } */
8914: /* for(j=1; j<=nlstate+ndeath;j++) { */
8915: /* kk1=0.;kk2=0; */
8916: /* for(i=1; i<=nlstate;i++) { */
8917: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8918: /* } */
8919: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8920: /* } */
8921: /* } */
8922: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8923: /* } */
8924: /* } */
8925: /* } */
8926: /* } */
1.218 brouard 8927:
1.227 brouard 8928: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8929:
1.227 brouard 8930: /* if (popforecast==1) { */
8931: /* free_ivector(popage,0,AGESUP); */
8932: /* free_vector(popeffectif,0,AGESUP); */
8933: /* free_vector(popcount,0,AGESUP); */
8934: /* } */
8935: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8936: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8937: /* fclose(ficrespop); */
8938: /* } /\* End of popforecast *\/ */
1.218 brouard 8939:
1.126 brouard 8940: int fileappend(FILE *fichier, char *optionfich)
8941: {
8942: if((fichier=fopen(optionfich,"a"))==NULL) {
8943: printf("Problem with file: %s\n", optionfich);
8944: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8945: return (0);
8946: }
8947: fflush(fichier);
8948: return (1);
8949: }
8950:
8951:
8952: /**************** function prwizard **********************/
8953: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8954: {
8955:
8956: /* Wizard to print covariance matrix template */
8957:
1.164 brouard 8958: char ca[32], cb[32];
8959: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8960: int numlinepar;
8961:
8962: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8963: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8964: for(i=1; i <=nlstate; i++){
8965: jj=0;
8966: for(j=1; j <=nlstate+ndeath; j++){
8967: if(j==i) continue;
8968: jj++;
8969: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8970: printf("%1d%1d",i,j);
8971: fprintf(ficparo,"%1d%1d",i,j);
8972: for(k=1; k<=ncovmodel;k++){
8973: /* printf(" %lf",param[i][j][k]); */
8974: /* fprintf(ficparo," %lf",param[i][j][k]); */
8975: printf(" 0.");
8976: fprintf(ficparo," 0.");
8977: }
8978: printf("\n");
8979: fprintf(ficparo,"\n");
8980: }
8981: }
8982: printf("# Scales (for hessian or gradient estimation)\n");
8983: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8984: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8985: for(i=1; i <=nlstate; i++){
8986: jj=0;
8987: for(j=1; j <=nlstate+ndeath; j++){
8988: if(j==i) continue;
8989: jj++;
8990: fprintf(ficparo,"%1d%1d",i,j);
8991: printf("%1d%1d",i,j);
8992: fflush(stdout);
8993: for(k=1; k<=ncovmodel;k++){
8994: /* printf(" %le",delti3[i][j][k]); */
8995: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8996: printf(" 0.");
8997: fprintf(ficparo," 0.");
8998: }
8999: numlinepar++;
9000: printf("\n");
9001: fprintf(ficparo,"\n");
9002: }
9003: }
9004: printf("# Covariance matrix\n");
9005: /* # 121 Var(a12)\n\ */
9006: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9007: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9008: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9009: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9010: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9011: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9012: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9013: fflush(stdout);
9014: fprintf(ficparo,"# Covariance matrix\n");
9015: /* # 121 Var(a12)\n\ */
9016: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9017: /* # ...\n\ */
9018: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9019:
9020: for(itimes=1;itimes<=2;itimes++){
9021: jj=0;
9022: for(i=1; i <=nlstate; i++){
9023: for(j=1; j <=nlstate+ndeath; j++){
9024: if(j==i) continue;
9025: for(k=1; k<=ncovmodel;k++){
9026: jj++;
9027: ca[0]= k+'a'-1;ca[1]='\0';
9028: if(itimes==1){
9029: printf("#%1d%1d%d",i,j,k);
9030: fprintf(ficparo,"#%1d%1d%d",i,j,k);
9031: }else{
9032: printf("%1d%1d%d",i,j,k);
9033: fprintf(ficparo,"%1d%1d%d",i,j,k);
9034: /* printf(" %.5le",matcov[i][j]); */
9035: }
9036: ll=0;
9037: for(li=1;li <=nlstate; li++){
9038: for(lj=1;lj <=nlstate+ndeath; lj++){
9039: if(lj==li) continue;
9040: for(lk=1;lk<=ncovmodel;lk++){
9041: ll++;
9042: if(ll<=jj){
9043: cb[0]= lk +'a'-1;cb[1]='\0';
9044: if(ll<jj){
9045: if(itimes==1){
9046: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9047: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9048: }else{
9049: printf(" 0.");
9050: fprintf(ficparo," 0.");
9051: }
9052: }else{
9053: if(itimes==1){
9054: printf(" Var(%s%1d%1d)",ca,i,j);
9055: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
9056: }else{
9057: printf(" 0.");
9058: fprintf(ficparo," 0.");
9059: }
9060: }
9061: }
9062: } /* end lk */
9063: } /* end lj */
9064: } /* end li */
9065: printf("\n");
9066: fprintf(ficparo,"\n");
9067: numlinepar++;
9068: } /* end k*/
9069: } /*end j */
9070: } /* end i */
9071: } /* end itimes */
9072:
9073: } /* end of prwizard */
9074: /******************* Gompertz Likelihood ******************************/
9075: double gompertz(double x[])
9076: {
1.302 brouard 9077: double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
1.126 brouard 9078: int i,n=0; /* n is the size of the sample */
9079:
1.220 brouard 9080: for (i=1;i<=imx ; i++) {
1.126 brouard 9081: sump=sump+weight[i];
9082: /* sump=sump+1;*/
9083: num=num+1;
9084: }
1.302 brouard 9085: L=0.0;
9086: /* agegomp=AGEGOMP; */
1.126 brouard 9087: /* for (i=0; i<=imx; i++)
9088: 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]);*/
9089:
1.302 brouard 9090: for (i=1;i<=imx ; i++) {
9091: /* mu(a)=mu(agecomp)*exp(teta*(age-agegomp))
9092: mu(a)=x[1]*exp(x[2]*(age-agegomp)); x[1] and x[2] are per year.
9093: * L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
9094: * and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
9095: * +
9096: * exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
9097: */
9098: if (wav[i] > 1 || agedc[i] < AGESUP) {
9099: if (cens[i] == 1){
9100: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
9101: } else if (cens[i] == 0){
1.126 brouard 9102: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
1.302 brouard 9103: +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
9104: } else
9105: printf("Gompertz cens[%d] neither 1 nor 0\n",i);
1.126 brouard 9106: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
1.302 brouard 9107: L=L+A*weight[i];
1.126 brouard 9108: /* 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 9109: }
9110: }
1.126 brouard 9111:
1.302 brouard 9112: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
1.126 brouard 9113:
9114: return -2*L*num/sump;
9115: }
9116:
1.136 brouard 9117: #ifdef GSL
9118: /******************* Gompertz_f Likelihood ******************************/
9119: double gompertz_f(const gsl_vector *v, void *params)
9120: {
1.302 brouard 9121: double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
1.136 brouard 9122: double *x= (double *) v->data;
9123: int i,n=0; /* n is the size of the sample */
9124:
9125: for (i=0;i<=imx-1 ; i++) {
9126: sump=sump+weight[i];
9127: /* sump=sump+1;*/
9128: num=num+1;
9129: }
9130:
9131:
9132: /* for (i=0; i<=imx; i++)
9133: 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]);*/
9134: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9135: for (i=1;i<=imx ; i++)
9136: {
9137: if (cens[i] == 1 && wav[i]>1)
9138: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9139:
9140: if (cens[i] == 0 && wav[i]>1)
9141: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9142: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9143:
9144: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9145: if (wav[i] > 1 ) { /* ??? */
9146: LL=LL+A*weight[i];
9147: /* 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]);*/
9148: }
9149: }
9150:
9151: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9152: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9153:
9154: return -2*LL*num/sump;
9155: }
9156: #endif
9157:
1.126 brouard 9158: /******************* Printing html file ***********/
1.201 brouard 9159: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9160: int lastpass, int stepm, int weightopt, char model[],\
9161: int imx, double p[],double **matcov,double agemortsup){
9162: int i,k;
9163:
9164: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9165: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9166: for (i=1;i<=2;i++)
9167: 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 9168: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9169: fprintf(fichtm,"</ul>");
9170:
9171: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9172:
9173: 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>");
9174:
9175: for (k=agegomp;k<(agemortsup-2);k++)
9176: 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]);
9177:
9178:
9179: fflush(fichtm);
9180: }
9181:
9182: /******************* Gnuplot file **************/
1.201 brouard 9183: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9184:
9185: char dirfileres[132],optfileres[132];
1.164 brouard 9186:
1.126 brouard 9187: int ng;
9188:
9189:
9190: /*#ifdef windows */
9191: fprintf(ficgp,"cd \"%s\" \n",pathc);
9192: /*#endif */
9193:
9194:
9195: strcpy(dirfileres,optionfilefiname);
9196: strcpy(optfileres,"vpl");
1.199 brouard 9197: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9198: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9199: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9200: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9201: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9202:
9203: }
9204:
1.136 brouard 9205: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9206: {
1.126 brouard 9207:
1.136 brouard 9208: /*-------- data file ----------*/
9209: FILE *fic;
9210: char dummy[]=" ";
1.240 brouard 9211: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9212: int lstra;
1.136 brouard 9213: int linei, month, year,iout;
1.302 brouard 9214: int noffset=0; /* This is the offset if BOM data file */
1.136 brouard 9215: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9216: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9217: char *stratrunc;
1.223 brouard 9218:
1.240 brouard 9219: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9220: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9221:
1.240 brouard 9222: for(v=1; v <=ncovcol;v++){
9223: DummyV[v]=0;
9224: FixedV[v]=0;
9225: }
9226: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9227: DummyV[v]=1;
9228: FixedV[v]=0;
9229: }
9230: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9231: DummyV[v]=0;
9232: FixedV[v]=1;
9233: }
9234: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9235: DummyV[v]=1;
9236: FixedV[v]=1;
9237: }
9238: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9239: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9240: 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]);
9241: }
1.126 brouard 9242:
1.136 brouard 9243: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9244: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9245: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9246: }
1.126 brouard 9247:
1.302 brouard 9248: /* Is it a BOM UTF-8 Windows file? */
9249: /* First data line */
9250: linei=0;
9251: while(fgets(line, MAXLINE, fic)) {
9252: noffset=0;
9253: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
9254: {
9255: noffset=noffset+3;
9256: printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
9257: fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
9258: fflush(ficlog); return 1;
9259: }
9260: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
9261: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
9262: {
9263: noffset=noffset+2;
1.304 brouard 9264: 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);
9265: 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 9266: fflush(ficlog); return 1;
9267: }
9268: else if( line[0] == 0 && line[1] == 0)
9269: {
9270: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
9271: noffset=noffset+4;
1.304 brouard 9272: 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);
9273: 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 9274: fflush(ficlog); return 1;
9275: }
9276: } else{
9277: ;/*printf(" Not a BOM file\n");*/
9278: }
9279: /* If line starts with a # it is a comment */
9280: if (line[noffset] == '#') {
9281: linei=linei+1;
9282: break;
9283: }else{
9284: break;
9285: }
9286: }
9287: fclose(fic);
9288: if((fic=fopen(datafile,"r"))==NULL) {
9289: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9290: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
9291: }
9292: /* Not a Bom file */
9293:
1.136 brouard 9294: i=1;
9295: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9296: linei=linei+1;
9297: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9298: if(line[j] == '\t')
9299: line[j] = ' ';
9300: }
9301: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9302: ;
9303: };
9304: line[j+1]=0; /* Trims blanks at end of line */
9305: if(line[0]=='#'){
9306: fprintf(ficlog,"Comment line\n%s\n",line);
9307: printf("Comment line\n%s\n",line);
9308: continue;
9309: }
9310: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9311: strcpy(line, linetmp);
1.223 brouard 9312:
9313: /* Loops on waves */
9314: for (j=maxwav;j>=1;j--){
9315: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9316: cutv(stra, strb, line, ' ');
9317: if(strb[0]=='.') { /* Missing value */
9318: lval=-1;
9319: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9320: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9321: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9322: 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);
9323: 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);
9324: return 1;
9325: }
9326: }else{
9327: errno=0;
9328: /* what_kind_of_number(strb); */
9329: dval=strtod(strb,&endptr);
9330: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9331: /* if(strb != endptr && *endptr == '\0') */
9332: /* dval=dlval; */
9333: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9334: if( strb[0]=='\0' || (*endptr != '\0')){
9335: 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);
9336: 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);
9337: return 1;
9338: }
9339: cotqvar[j][iv][i]=dval;
9340: cotvar[j][ntv+iv][i]=dval;
9341: }
9342: strcpy(line,stra);
1.223 brouard 9343: }/* end loop ntqv */
1.225 brouard 9344:
1.223 brouard 9345: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9346: cutv(stra, strb, line, ' ');
9347: if(strb[0]=='.') { /* Missing value */
9348: lval=-1;
9349: }else{
9350: errno=0;
9351: lval=strtol(strb,&endptr,10);
9352: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9353: if( strb[0]=='\0' || (*endptr != '\0')){
9354: 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);
9355: 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);
9356: return 1;
9357: }
9358: }
9359: if(lval <-1 || lval >1){
9360: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9361: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9362: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9363: For example, for multinomial values like 1, 2 and 3,\n \
9364: build V1=0 V2=0 for the reference value (1),\n \
9365: V1=1 V2=0 for (2) \n \
1.223 brouard 9366: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9367: output of IMaCh is often meaningless.\n \
1.223 brouard 9368: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9369: fprintf(ficlog,"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);fflush(ficlog);
1.238 brouard 9378: return 1;
9379: }
9380: cotvar[j][iv][i]=(double)(lval);
9381: strcpy(line,stra);
1.223 brouard 9382: }/* end loop ntv */
1.225 brouard 9383:
1.223 brouard 9384: /* Statuses at wave */
1.137 brouard 9385: cutv(stra, strb, line, ' ');
1.223 brouard 9386: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9387: lval=-1;
1.136 brouard 9388: }else{
1.238 brouard 9389: errno=0;
9390: lval=strtol(strb,&endptr,10);
9391: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9392: if( strb[0]=='\0' || (*endptr != '\0')){
9393: 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);
9394: 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);
9395: return 1;
9396: }
1.136 brouard 9397: }
1.225 brouard 9398:
1.136 brouard 9399: s[j][i]=lval;
1.225 brouard 9400:
1.223 brouard 9401: /* Date of Interview */
1.136 brouard 9402: strcpy(line,stra);
9403: cutv(stra, strb,line,' ');
1.169 brouard 9404: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9405: }
1.169 brouard 9406: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9407: month=99;
9408: year=9999;
1.136 brouard 9409: }else{
1.225 brouard 9410: 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);
9411: 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);
9412: return 1;
1.136 brouard 9413: }
9414: anint[j][i]= (double) year;
1.302 brouard 9415: mint[j][i]= (double)month;
9416: /* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
9417: /* 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]); */
9418: /* 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]); */
9419: /* } */
1.136 brouard 9420: strcpy(line,stra);
1.223 brouard 9421: } /* End loop on waves */
1.225 brouard 9422:
1.223 brouard 9423: /* Date of death */
1.136 brouard 9424: cutv(stra, strb,line,' ');
1.169 brouard 9425: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9426: }
1.169 brouard 9427: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9428: month=99;
9429: year=9999;
9430: }else{
1.141 brouard 9431: 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 9432: 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);
9433: return 1;
1.136 brouard 9434: }
9435: andc[i]=(double) year;
9436: moisdc[i]=(double) month;
9437: strcpy(line,stra);
9438:
1.223 brouard 9439: /* Date of birth */
1.136 brouard 9440: cutv(stra, strb,line,' ');
1.169 brouard 9441: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9442: }
1.169 brouard 9443: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9444: month=99;
9445: year=9999;
9446: }else{
1.141 brouard 9447: 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);
9448: 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 9449: return 1;
1.136 brouard 9450: }
9451: if (year==9999) {
1.141 brouard 9452: 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);
9453: 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 9454: return 1;
9455:
1.136 brouard 9456: }
9457: annais[i]=(double)(year);
1.302 brouard 9458: moisnais[i]=(double)(month);
9459: for (j=1;j<=maxwav;j++){
9460: if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
9461: 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]);
9462: 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]);
9463: }
9464: }
9465:
1.136 brouard 9466: strcpy(line,stra);
1.225 brouard 9467:
1.223 brouard 9468: /* Sample weight */
1.136 brouard 9469: cutv(stra, strb,line,' ');
9470: errno=0;
9471: dval=strtod(strb,&endptr);
9472: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9473: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9474: 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 9475: fflush(ficlog);
9476: return 1;
9477: }
9478: weight[i]=dval;
9479: strcpy(line,stra);
1.225 brouard 9480:
1.223 brouard 9481: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9482: cutv(stra, strb, line, ' ');
9483: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9484: lval=-1;
1.223 brouard 9485: }else{
1.225 brouard 9486: errno=0;
9487: /* what_kind_of_number(strb); */
9488: dval=strtod(strb,&endptr);
9489: /* if(strb != endptr && *endptr == '\0') */
9490: /* dval=dlval; */
9491: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9492: if( strb[0]=='\0' || (*endptr != '\0')){
9493: 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);
9494: 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);
9495: return 1;
9496: }
9497: coqvar[iv][i]=dval;
1.226 brouard 9498: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9499: }
9500: strcpy(line,stra);
9501: }/* end loop nqv */
1.136 brouard 9502:
1.223 brouard 9503: /* Covariate values */
1.136 brouard 9504: for (j=ncovcol;j>=1;j--){
9505: cutv(stra, strb,line,' ');
1.223 brouard 9506: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9507: lval=-1;
1.136 brouard 9508: }else{
1.225 brouard 9509: errno=0;
9510: lval=strtol(strb,&endptr,10);
9511: if( strb[0]=='\0' || (*endptr != '\0')){
9512: 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);
9513: 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);
9514: return 1;
9515: }
1.136 brouard 9516: }
9517: if(lval <-1 || lval >1){
1.225 brouard 9518: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9519: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9520: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9521: For example, for multinomial values like 1, 2 and 3,\n \
9522: build V1=0 V2=0 for the reference value (1),\n \
9523: V1=1 V2=0 for (2) \n \
1.136 brouard 9524: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9525: output of IMaCh is often meaningless.\n \
1.136 brouard 9526: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9527: fprintf(ficlog,"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);fflush(ficlog);
1.225 brouard 9536: return 1;
1.136 brouard 9537: }
9538: covar[j][i]=(double)(lval);
9539: strcpy(line,stra);
9540: }
9541: lstra=strlen(stra);
1.225 brouard 9542:
1.136 brouard 9543: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9544: stratrunc = &(stra[lstra-9]);
9545: num[i]=atol(stratrunc);
9546: }
9547: else
9548: num[i]=atol(stra);
9549: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9550: 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;}*/
9551:
9552: i=i+1;
9553: } /* End loop reading data */
1.225 brouard 9554:
1.136 brouard 9555: *imax=i-1; /* Number of individuals */
9556: fclose(fic);
1.225 brouard 9557:
1.136 brouard 9558: return (0);
1.164 brouard 9559: /* endread: */
1.225 brouard 9560: printf("Exiting readdata: ");
9561: fclose(fic);
9562: return (1);
1.223 brouard 9563: }
1.126 brouard 9564:
1.234 brouard 9565: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9566: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9567: while (*p2 == ' ')
1.234 brouard 9568: p2++;
9569: /* while ((*p1++ = *p2++) !=0) */
9570: /* ; */
9571: /* do */
9572: /* while (*p2 == ' ') */
9573: /* p2++; */
9574: /* while (*p1++ == *p2++); */
9575: *stri=p2;
1.145 brouard 9576: }
9577:
1.235 brouard 9578: int decoderesult ( char resultline[], int nres)
1.230 brouard 9579: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9580: {
1.235 brouard 9581: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9582: char resultsav[MAXLINE];
1.234 brouard 9583: int resultmodel[MAXLINE];
9584: int modelresult[MAXLINE];
1.230 brouard 9585: char stra[80], strb[80], strc[80], strd[80],stre[80];
9586:
1.234 brouard 9587: removefirstspace(&resultline);
1.233 brouard 9588: printf("decoderesult:%s\n",resultline);
1.230 brouard 9589:
9590: if (strstr(resultline,"v") !=0){
9591: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9592: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9593: return 1;
9594: }
9595: trimbb(resultsav, resultline);
9596: if (strlen(resultsav) >1){
9597: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9598: }
1.253 brouard 9599: if(j == 0){ /* Resultline but no = */
9600: TKresult[nres]=0; /* Combination for the nresult and the model */
9601: return (0);
9602: }
9603:
1.234 brouard 9604: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9605: 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);
9606: 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);
9607: }
9608: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9609: if(nbocc(resultsav,'=') >1){
9610: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9611: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9612: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9613: }else
9614: cutl(strc,strd,resultsav,'=');
1.230 brouard 9615: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9616:
1.230 brouard 9617: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9618: Tvarsel[k]=atoi(strc);
9619: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9620: /* cptcovsel++; */
9621: if (nbocc(stra,'=') >0)
9622: strcpy(resultsav,stra); /* and analyzes it */
9623: }
1.235 brouard 9624: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9625: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9626: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9627: match=0;
1.236 brouard 9628: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9629: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9630: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9631: match=1;
9632: break;
9633: }
9634: }
9635: if(match == 0){
9636: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9637: }
9638: }
9639: }
1.235 brouard 9640: /* Checking for missing or useless values in comparison of current model needs */
9641: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9642: match=0;
1.235 brouard 9643: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9644: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9645: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9646: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9647: ++match;
9648: }
9649: }
9650: }
9651: if(match == 0){
9652: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9653: }else if(match > 1){
9654: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9655: }
9656: }
1.235 brouard 9657:
1.234 brouard 9658: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9659: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9660: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9661: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9662: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9663: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9664: /* 1 0 0 0 */
9665: /* 2 1 0 0 */
9666: /* 3 0 1 0 */
9667: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9668: /* 5 0 0 1 */
9669: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9670: /* 7 0 1 1 */
9671: /* 8 1 1 1 */
1.237 brouard 9672: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9673: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9674: /* V5*age V5 known which value for nres? */
9675: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9676: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9677: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9678: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9679: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9680: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9681: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9682: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9683: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9684: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9685: k4++;;
9686: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9687: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9688: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9689: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9690: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9691: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9692: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9693: k4q++;;
9694: }
9695: }
1.234 brouard 9696:
1.235 brouard 9697: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9698: return (0);
9699: }
1.235 brouard 9700:
1.230 brouard 9701: int decodemodel( char model[], int lastobs)
9702: /**< This routine decodes the model and returns:
1.224 brouard 9703: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9704: * - nagesqr = 1 if age*age in the model, otherwise 0.
9705: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9706: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9707: * - cptcovage number of covariates with age*products =2
9708: * - cptcovs number of simple covariates
9709: * - 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
9710: * which is a new column after the 9 (ncovcol) variables.
9711: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9712: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9713: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9714: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9715: */
1.136 brouard 9716: {
1.238 brouard 9717: int i, j, k, ks, v;
1.227 brouard 9718: int j1, k1, k2, k3, k4;
1.136 brouard 9719: char modelsav[80];
1.145 brouard 9720: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9721: char *strpt;
1.136 brouard 9722:
1.145 brouard 9723: /*removespace(model);*/
1.136 brouard 9724: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9725: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9726: if (strstr(model,"AGE") !=0){
1.192 brouard 9727: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9728: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9729: return 1;
9730: }
1.141 brouard 9731: if (strstr(model,"v") !=0){
9732: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9733: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9734: return 1;
9735: }
1.187 brouard 9736: strcpy(modelsav,model);
9737: if ((strpt=strstr(model,"age*age")) !=0){
9738: printf(" strpt=%s, model=%s\n",strpt, model);
9739: if(strpt != model){
1.234 brouard 9740: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9741: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9742: corresponding column of parameters.\n",model);
1.234 brouard 9743: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9744: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9745: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9746: return 1;
1.225 brouard 9747: }
1.187 brouard 9748: nagesqr=1;
9749: if (strstr(model,"+age*age") !=0)
1.234 brouard 9750: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9751: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9752: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9753: else
1.234 brouard 9754: substrchaine(modelsav, model, "age*age");
1.187 brouard 9755: }else
9756: nagesqr=0;
9757: if (strlen(modelsav) >1){
9758: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9759: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9760: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9761: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9762: * cst, age and age*age
9763: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9764: /* including age products which are counted in cptcovage.
9765: * but the covariates which are products must be treated
9766: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9767: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9768: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9769:
9770:
1.187 brouard 9771: /* Design
9772: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9773: * < ncovcol=8 >
9774: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9775: * k= 1 2 3 4 5 6 7 8
9776: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9777: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9778: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9779: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9780: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9781: * Tage[++cptcovage]=k
9782: * if products, new covar are created after ncovcol with k1
9783: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9784: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9785: * 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
9786: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9787: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9788: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9789: * < ncovcol=8 >
9790: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9791: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9792: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9793: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9794: * p Tprod[1]@2={ 6, 5}
9795: *p Tvard[1][1]@4= {7, 8, 5, 6}
9796: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9797: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9798: *How to reorganize?
9799: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9800: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9801: * {2, 1, 4, 8, 5, 6, 3, 7}
9802: * Struct []
9803: */
1.225 brouard 9804:
1.187 brouard 9805: /* This loop fills the array Tvar from the string 'model'.*/
9806: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9807: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9808: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9809: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9810: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9811: /* k=1 Tvar[1]=2 (from V2) */
9812: /* k=5 Tvar[5] */
9813: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9814: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9815: /* } */
1.198 brouard 9816: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9817: /*
9818: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9819: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9820: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9821: }
1.187 brouard 9822: cptcovage=0;
9823: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9824: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9825: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9826: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9827: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9828: /*scanf("%d",i);*/
9829: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9830: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9831: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9832: /* covar is not filled and then is empty */
9833: cptcovprod--;
9834: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9835: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9836: Typevar[k]=1; /* 1 for age product */
9837: cptcovage++; /* Sums the number of covariates which include age as a product */
9838: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9839: /*printf("stre=%s ", stre);*/
9840: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9841: cptcovprod--;
9842: cutl(stre,strb,strc,'V');
9843: Tvar[k]=atoi(stre);
9844: Typevar[k]=1; /* 1 for age product */
9845: cptcovage++;
9846: Tage[cptcovage]=k;
9847: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9848: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9849: cptcovn++;
9850: cptcovprodnoage++;k1++;
9851: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9852: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9853: because this model-covariate is a construction we invent a new column
9854: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9855: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9856: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9857: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9858: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9859: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9860: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9861: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9862: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9863: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9864: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9865: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9866: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9867: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9868: for (i=1; i<=lastobs;i++){
9869: /* Computes the new covariate which is a product of
9870: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9871: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9872: }
9873: } /* End age is not in the model */
9874: } /* End if model includes a product */
9875: else { /* no more sum */
9876: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9877: /* scanf("%d",i);*/
9878: cutl(strd,strc,strb,'V');
9879: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9880: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9881: Tvar[k]=atoi(strd);
9882: Typevar[k]=0; /* 0 for simple covariates */
9883: }
9884: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9885: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9886: scanf("%d",i);*/
1.187 brouard 9887: } /* end of loop + on total covariates */
9888: } /* end if strlen(modelsave == 0) age*age might exist */
9889: } /* end if strlen(model == 0) */
1.136 brouard 9890:
9891: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9892: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9893:
1.136 brouard 9894: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9895: printf("cptcovprod=%d ", cptcovprod);
9896: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9897: scanf("%d ",i);*/
9898:
9899:
1.230 brouard 9900: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9901: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9902: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9903: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9904: k = 1 2 3 4 5 6 7 8 9
9905: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9906: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9907: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9908: Dummy[k] 1 0 0 0 3 1 1 2 3
9909: Tmodelind[combination of covar]=k;
1.225 brouard 9910: */
9911: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9912: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9913: /* 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 9914: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9915: printf("Model=%s\n\
9916: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9917: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9918: 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);
9919: fprintf(ficlog,"Model=%s\n\
9920: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9921: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9922: Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
1.285 brouard 9923: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9924: 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 */
9925: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9926: Fixed[k]= 0;
9927: Dummy[k]= 0;
1.225 brouard 9928: ncoveff++;
1.232 brouard 9929: ncovf++;
1.234 brouard 9930: nsd++;
9931: modell[k].maintype= FTYPE;
9932: TvarsD[nsd]=Tvar[k];
9933: TvarsDind[nsd]=k;
9934: TvarF[ncovf]=Tvar[k];
9935: TvarFind[ncovf]=k;
9936: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9937: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9938: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9939: Fixed[k]= 0;
9940: Dummy[k]= 0;
9941: ncoveff++;
9942: ncovf++;
9943: modell[k].maintype= FTYPE;
9944: TvarF[ncovf]=Tvar[k];
9945: TvarFind[ncovf]=k;
1.230 brouard 9946: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9947: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9948: }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 9949: Fixed[k]= 0;
9950: Dummy[k]= 1;
1.230 brouard 9951: nqfveff++;
1.234 brouard 9952: modell[k].maintype= FTYPE;
9953: modell[k].subtype= FQ;
9954: nsq++;
9955: TvarsQ[nsq]=Tvar[k];
9956: TvarsQind[nsq]=k;
1.232 brouard 9957: ncovf++;
1.234 brouard 9958: TvarF[ncovf]=Tvar[k];
9959: TvarFind[ncovf]=k;
1.231 brouard 9960: 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 9961: 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 9962: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9963: Fixed[k]= 1;
9964: Dummy[k]= 0;
1.225 brouard 9965: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9966: modell[k].maintype= VTYPE;
9967: modell[k].subtype= VD;
9968: nsd++;
9969: TvarsD[nsd]=Tvar[k];
9970: TvarsDind[nsd]=k;
9971: ncovv++; /* Only simple time varying variables */
9972: TvarV[ncovv]=Tvar[k];
1.242 brouard 9973: 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 9974: 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 */
9975: 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 9976: 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);
9977: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9978: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9979: Fixed[k]= 1;
9980: Dummy[k]= 1;
9981: nqtveff++;
9982: modell[k].maintype= VTYPE;
9983: modell[k].subtype= VQ;
9984: ncovv++; /* Only simple time varying variables */
9985: nsq++;
9986: TvarsQ[nsq]=Tvar[k];
9987: TvarsQind[nsq]=k;
9988: TvarV[ncovv]=Tvar[k];
1.242 brouard 9989: 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 9990: 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 */
9991: 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 9992: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9993: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9994: 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 9995: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9996: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9997: ncova++;
9998: TvarA[ncova]=Tvar[k];
9999: TvarAind[ncova]=k;
1.231 brouard 10000: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 10001: Fixed[k]= 2;
10002: Dummy[k]= 2;
10003: modell[k].maintype= ATYPE;
10004: modell[k].subtype= APFD;
10005: /* ncoveff++; */
1.227 brouard 10006: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 10007: Fixed[k]= 2;
10008: Dummy[k]= 3;
10009: modell[k].maintype= ATYPE;
10010: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
10011: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 10012: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 10013: Fixed[k]= 3;
10014: Dummy[k]= 2;
10015: modell[k].maintype= ATYPE;
10016: modell[k].subtype= APVD; /* Product age * varying dummy */
10017: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 10018: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10019: Fixed[k]= 3;
10020: Dummy[k]= 3;
10021: modell[k].maintype= ATYPE;
10022: modell[k].subtype= APVQ; /* Product age * varying quantitative */
10023: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 10024: }
10025: }else if (Typevar[k] == 2) { /* product without age */
10026: k1=Tposprod[k];
10027: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 10028: if(Tvard[k1][2] <=ncovcol){
10029: Fixed[k]= 1;
10030: Dummy[k]= 0;
10031: modell[k].maintype= FTYPE;
10032: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
10033: ncovf++; /* Fixed variables without age */
10034: TvarF[ncovf]=Tvar[k];
10035: TvarFind[ncovf]=k;
10036: }else if(Tvard[k1][2] <=ncovcol+nqv){
10037: Fixed[k]= 0; /* or 2 ?*/
10038: Dummy[k]= 1;
10039: modell[k].maintype= FTYPE;
10040: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
10041: ncovf++; /* Varying variables without age */
10042: TvarF[ncovf]=Tvar[k];
10043: TvarFind[ncovf]=k;
10044: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10045: Fixed[k]= 1;
10046: Dummy[k]= 0;
10047: modell[k].maintype= VTYPE;
10048: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
10049: ncovv++; /* Varying variables without age */
10050: TvarV[ncovv]=Tvar[k];
10051: TvarVind[ncovv]=k;
10052: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10053: Fixed[k]= 1;
10054: Dummy[k]= 1;
10055: modell[k].maintype= VTYPE;
10056: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
10057: ncovv++; /* Varying variables without age */
10058: TvarV[ncovv]=Tvar[k];
10059: TvarVind[ncovv]=k;
10060: }
1.227 brouard 10061: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 10062: if(Tvard[k1][2] <=ncovcol){
10063: Fixed[k]= 0; /* or 2 ?*/
10064: Dummy[k]= 1;
10065: modell[k].maintype= FTYPE;
10066: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
10067: ncovf++; /* Fixed variables without age */
10068: TvarF[ncovf]=Tvar[k];
10069: TvarFind[ncovf]=k;
10070: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10071: Fixed[k]= 1;
10072: Dummy[k]= 1;
10073: modell[k].maintype= VTYPE;
10074: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
10075: ncovv++; /* Varying variables without age */
10076: TvarV[ncovv]=Tvar[k];
10077: TvarVind[ncovv]=k;
10078: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10079: Fixed[k]= 1;
10080: Dummy[k]= 1;
10081: modell[k].maintype= VTYPE;
10082: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
10083: ncovv++; /* Varying variables without age */
10084: TvarV[ncovv]=Tvar[k];
10085: TvarVind[ncovv]=k;
10086: ncovv++; /* Varying variables without age */
10087: TvarV[ncovv]=Tvar[k];
10088: TvarVind[ncovv]=k;
10089: }
1.227 brouard 10090: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 10091: if(Tvard[k1][2] <=ncovcol){
10092: Fixed[k]= 1;
10093: Dummy[k]= 1;
10094: modell[k].maintype= VTYPE;
10095: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
10096: ncovv++; /* Varying variables without age */
10097: TvarV[ncovv]=Tvar[k];
10098: TvarVind[ncovv]=k;
10099: }else if(Tvard[k1][2] <=ncovcol+nqv){
10100: Fixed[k]= 1;
10101: Dummy[k]= 1;
10102: modell[k].maintype= VTYPE;
10103: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
10104: ncovv++; /* Varying variables without age */
10105: TvarV[ncovv]=Tvar[k];
10106: TvarVind[ncovv]=k;
10107: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10108: Fixed[k]= 1;
10109: Dummy[k]= 0;
10110: modell[k].maintype= VTYPE;
10111: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
10112: ncovv++; /* Varying variables without age */
10113: TvarV[ncovv]=Tvar[k];
10114: TvarVind[ncovv]=k;
10115: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10116: Fixed[k]= 1;
10117: Dummy[k]= 1;
10118: modell[k].maintype= VTYPE;
10119: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
10120: ncovv++; /* Varying variables without age */
10121: TvarV[ncovv]=Tvar[k];
10122: TvarVind[ncovv]=k;
10123: }
1.227 brouard 10124: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 10125: if(Tvard[k1][2] <=ncovcol){
10126: Fixed[k]= 1;
10127: Dummy[k]= 1;
10128: modell[k].maintype= VTYPE;
10129: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
10130: ncovv++; /* Varying variables without age */
10131: TvarV[ncovv]=Tvar[k];
10132: TvarVind[ncovv]=k;
10133: }else if(Tvard[k1][2] <=ncovcol+nqv){
10134: Fixed[k]= 1;
10135: Dummy[k]= 1;
10136: modell[k].maintype= VTYPE;
10137: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
10138: ncovv++; /* Varying variables without age */
10139: TvarV[ncovv]=Tvar[k];
10140: TvarVind[ncovv]=k;
10141: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
10142: Fixed[k]= 1;
10143: Dummy[k]= 1;
10144: modell[k].maintype= VTYPE;
10145: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
10146: ncovv++; /* Varying variables without age */
10147: TvarV[ncovv]=Tvar[k];
10148: TvarVind[ncovv]=k;
10149: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
10150: Fixed[k]= 1;
10151: Dummy[k]= 1;
10152: modell[k].maintype= VTYPE;
10153: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
10154: ncovv++; /* Varying variables without age */
10155: TvarV[ncovv]=Tvar[k];
10156: TvarVind[ncovv]=k;
10157: }
1.227 brouard 10158: }else{
1.240 brouard 10159: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10160: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
10161: } /*end k1*/
1.225 brouard 10162: }else{
1.226 brouard 10163: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
10164: 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 10165: }
1.227 brouard 10166: 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 10167: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 10168: 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]);
10169: }
10170: /* Searching for doublons in the model */
10171: for(k1=1; k1<= cptcovt;k1++){
10172: for(k2=1; k2 <k1;k2++){
1.285 brouard 10173: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
10174: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 10175: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
10176: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 10177: 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]);
10178: 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 10179: return(1);
10180: }
10181: }else if (Typevar[k1] ==2){
10182: k3=Tposprod[k1];
10183: k4=Tposprod[k2];
10184: 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])) ){
10185: 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]]);
10186: 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);
10187: return(1);
10188: }
10189: }
1.227 brouard 10190: }
10191: }
1.225 brouard 10192: }
10193: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10194: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10195: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10196: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10197: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10198: /*endread:*/
1.225 brouard 10199: printf("Exiting decodemodel: ");
10200: return (1);
1.136 brouard 10201: }
10202:
1.169 brouard 10203: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10204: {/* Check ages at death */
1.136 brouard 10205: int i, m;
1.218 brouard 10206: int firstone=0;
10207:
1.136 brouard 10208: for (i=1; i<=imx; i++) {
10209: for(m=2; (m<= maxwav); m++) {
10210: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10211: anint[m][i]=9999;
1.216 brouard 10212: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10213: s[m][i]=-1;
1.136 brouard 10214: }
10215: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10216: *nberr = *nberr + 1;
1.218 brouard 10217: if(firstone == 0){
10218: firstone=1;
1.260 brouard 10219: 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 10220: }
1.262 brouard 10221: 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 10222: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10223: }
10224: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10225: (*nberr)++;
1.259 brouard 10226: 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 10227: 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 10228: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10229: }
10230: }
10231: }
10232:
10233: for (i=1; i<=imx; i++) {
10234: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10235: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10236: 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 10237: if (s[m][i] >= nlstate+1) {
1.169 brouard 10238: if(agedc[i]>0){
10239: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10240: agev[m][i]=agedc[i];
1.214 brouard 10241: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10242: }else {
1.136 brouard 10243: if ((int)andc[i]!=9999){
10244: nbwarn++;
10245: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10246: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10247: agev[m][i]=-1;
10248: }
10249: }
1.169 brouard 10250: } /* agedc > 0 */
1.214 brouard 10251: } /* end if */
1.136 brouard 10252: else if(s[m][i] !=9){ /* Standard case, age in fractional
10253: years but with the precision of a month */
10254: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10255: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10256: agev[m][i]=1;
10257: else if(agev[m][i] < *agemin){
10258: *agemin=agev[m][i];
10259: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10260: }
10261: else if(agev[m][i] >*agemax){
10262: *agemax=agev[m][i];
1.156 brouard 10263: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10264: }
10265: /*agev[m][i]=anint[m][i]-annais[i];*/
10266: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10267: } /* en if 9*/
1.136 brouard 10268: else { /* =9 */
1.214 brouard 10269: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10270: agev[m][i]=1;
10271: s[m][i]=-1;
10272: }
10273: }
1.214 brouard 10274: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10275: agev[m][i]=1;
1.214 brouard 10276: else{
10277: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10278: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10279: agev[m][i]=0;
10280: }
10281: } /* End for lastpass */
10282: }
1.136 brouard 10283:
10284: for (i=1; i<=imx; i++) {
10285: for(m=firstpass; (m<=lastpass); m++){
10286: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10287: (*nberr)++;
1.136 brouard 10288: 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);
10289: 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);
10290: return 1;
10291: }
10292: }
10293: }
10294:
10295: /*for (i=1; i<=imx; i++){
10296: for (m=firstpass; (m<lastpass); m++){
10297: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10298: }
10299:
10300: }*/
10301:
10302:
1.139 brouard 10303: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10304: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10305:
10306: return (0);
1.164 brouard 10307: /* endread:*/
1.136 brouard 10308: printf("Exiting calandcheckages: ");
10309: return (1);
10310: }
10311:
1.172 brouard 10312: #if defined(_MSC_VER)
10313: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10314: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10315: //#include "stdafx.h"
10316: //#include <stdio.h>
10317: //#include <tchar.h>
10318: //#include <windows.h>
10319: //#include <iostream>
10320: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10321:
10322: LPFN_ISWOW64PROCESS fnIsWow64Process;
10323:
10324: BOOL IsWow64()
10325: {
10326: BOOL bIsWow64 = FALSE;
10327:
10328: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10329: // (HANDLE, PBOOL);
10330:
10331: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10332:
10333: HMODULE module = GetModuleHandle(_T("kernel32"));
10334: const char funcName[] = "IsWow64Process";
10335: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10336: GetProcAddress(module, funcName);
10337:
10338: if (NULL != fnIsWow64Process)
10339: {
10340: if (!fnIsWow64Process(GetCurrentProcess(),
10341: &bIsWow64))
10342: //throw std::exception("Unknown error");
10343: printf("Unknown error\n");
10344: }
10345: return bIsWow64 != FALSE;
10346: }
10347: #endif
1.177 brouard 10348:
1.191 brouard 10349: void syscompilerinfo(int logged)
1.292 brouard 10350: {
10351: #include <stdint.h>
10352:
10353: /* #include "syscompilerinfo.h"*/
1.185 brouard 10354: /* command line Intel compiler 32bit windows, XP compatible:*/
10355: /* /GS /W3 /Gy
10356: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10357: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10358: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10359: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10360: */
10361: /* 64 bits */
1.185 brouard 10362: /*
10363: /GS /W3 /Gy
10364: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10365: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10366: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10367: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10368: /* Optimization are useless and O3 is slower than O2 */
10369: /*
10370: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10371: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10372: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10373: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10374: */
1.186 brouard 10375: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10376: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10377: /PDB:"visual studio
10378: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10379: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10380: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10381: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10382: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10383: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10384: uiAccess='false'"
10385: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10386: /NOLOGO /TLBID:1
10387: */
1.292 brouard 10388:
10389:
1.177 brouard 10390: #if defined __INTEL_COMPILER
1.178 brouard 10391: #if defined(__GNUC__)
10392: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10393: #endif
1.177 brouard 10394: #elif defined(__GNUC__)
1.179 brouard 10395: #ifndef __APPLE__
1.174 brouard 10396: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10397: #endif
1.177 brouard 10398: struct utsname sysInfo;
1.178 brouard 10399: int cross = CROSS;
10400: if (cross){
10401: printf("Cross-");
1.191 brouard 10402: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10403: }
1.174 brouard 10404: #endif
10405:
1.191 brouard 10406: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10407: #if defined(__clang__)
1.191 brouard 10408: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10409: #endif
10410: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10411: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10412: #endif
10413: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10414: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10415: #endif
10416: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10417: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10418: #endif
10419: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10420: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10421: #endif
10422: #if defined(_MSC_VER)
1.191 brouard 10423: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10424: #endif
10425: #if defined(__PGI)
1.191 brouard 10426: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10427: #endif
10428: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10429: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10430: #endif
1.191 brouard 10431: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10432:
1.167 brouard 10433: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10434: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10435: // Windows (x64 and x86)
1.191 brouard 10436: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10437: #elif __unix__ // all unices, not all compilers
10438: // Unix
1.191 brouard 10439: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10440: #elif __linux__
10441: // linux
1.191 brouard 10442: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10443: #elif __APPLE__
1.174 brouard 10444: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10445: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10446: #endif
10447:
10448: /* __MINGW32__ */
10449: /* __CYGWIN__ */
10450: /* __MINGW64__ */
10451: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10452: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10453: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10454: /* _WIN64 // Defined for applications for Win64. */
10455: /* _M_X64 // Defined for compilations that target x64 processors. */
10456: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10457:
1.167 brouard 10458: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10459: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10460: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10461: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10462: #else
1.191 brouard 10463: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10464: #endif
10465:
1.169 brouard 10466: #if defined(__GNUC__)
10467: # if defined(__GNUC_PATCHLEVEL__)
10468: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10469: + __GNUC_MINOR__ * 100 \
10470: + __GNUC_PATCHLEVEL__)
10471: # else
10472: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10473: + __GNUC_MINOR__ * 100)
10474: # endif
1.174 brouard 10475: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10476: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10477:
10478: if (uname(&sysInfo) != -1) {
10479: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10480: 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 10481: }
10482: else
10483: perror("uname() error");
1.179 brouard 10484: //#ifndef __INTEL_COMPILER
10485: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10486: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10487: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10488: #endif
1.169 brouard 10489: #endif
1.172 brouard 10490:
1.286 brouard 10491: // void main ()
1.172 brouard 10492: // {
1.169 brouard 10493: #if defined(_MSC_VER)
1.174 brouard 10494: if (IsWow64()){
1.191 brouard 10495: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10496: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10497: }
10498: else{
1.191 brouard 10499: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10500: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10501: }
1.172 brouard 10502: // printf("\nPress Enter to continue...");
10503: // getchar();
10504: // }
10505:
1.169 brouard 10506: #endif
10507:
1.167 brouard 10508:
1.219 brouard 10509: }
1.136 brouard 10510:
1.219 brouard 10511: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.288 brouard 10512: /*--------------- Prevalence limit (forward period or forward stable prevalence) --------------*/
1.235 brouard 10513: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10514: /* double ftolpl = 1.e-10; */
1.180 brouard 10515: double age, agebase, agelim;
1.203 brouard 10516: double tot;
1.180 brouard 10517:
1.202 brouard 10518: strcpy(filerespl,"PL_");
10519: strcat(filerespl,fileresu);
10520: if((ficrespl=fopen(filerespl,"w"))==NULL) {
1.288 brouard 10521: printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10522: fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
1.202 brouard 10523: }
1.288 brouard 10524: printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
10525: fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10526: pstamp(ficrespl);
1.288 brouard 10527: fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10528: fprintf(ficrespl,"#Age ");
10529: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10530: fprintf(ficrespl,"\n");
1.180 brouard 10531:
1.219 brouard 10532: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10533:
1.219 brouard 10534: agebase=ageminpar;
10535: agelim=agemaxpar;
1.180 brouard 10536:
1.227 brouard 10537: /* i1=pow(2,ncoveff); */
1.234 brouard 10538: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10539: if (cptcovn < 1){i1=1;}
1.180 brouard 10540:
1.238 brouard 10541: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10542: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10543: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10544: continue;
1.235 brouard 10545:
1.238 brouard 10546: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10547: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10548: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10549: /* k=k+1; */
10550: /* to clean */
10551: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10552: fprintf(ficrespl,"#******");
10553: printf("#******");
10554: fprintf(ficlog,"#******");
10555: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10556: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10557: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10558: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10559: }
10560: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10561: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10562: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10563: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10564: }
10565: fprintf(ficrespl,"******\n");
10566: printf("******\n");
10567: fprintf(ficlog,"******\n");
10568: if(invalidvarcomb[k]){
10569: printf("\nCombination (%d) ignored because no case \n",k);
10570: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10571: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10572: continue;
10573: }
1.219 brouard 10574:
1.238 brouard 10575: fprintf(ficrespl,"#Age ");
10576: for(j=1;j<=cptcoveff;j++) {
10577: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10578: }
10579: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10580: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10581:
1.238 brouard 10582: for (age=agebase; age<=agelim; age++){
10583: /* for (age=agebase; age<=agebase; age++){ */
10584: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10585: fprintf(ficrespl,"%.0f ",age );
10586: for(j=1;j<=cptcoveff;j++)
10587: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10588: tot=0.;
10589: for(i=1; i<=nlstate;i++){
10590: tot += prlim[i][i];
10591: fprintf(ficrespl," %.5f", prlim[i][i]);
10592: }
10593: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10594: } /* Age */
10595: /* was end of cptcod */
10596: } /* cptcov */
10597: } /* nres */
1.219 brouard 10598: return 0;
1.180 brouard 10599: }
10600:
1.218 brouard 10601: 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 10602: /*--------------- Back Prevalence limit (backward stable prevalence) --------------*/
1.218 brouard 10603:
10604: /* Computes the back prevalence limit for any combination of covariate values
10605: * at any age between ageminpar and agemaxpar
10606: */
1.235 brouard 10607: int i, j, k, i1, nres=0 ;
1.217 brouard 10608: /* double ftolpl = 1.e-10; */
10609: double age, agebase, agelim;
10610: double tot;
1.218 brouard 10611: /* double ***mobaverage; */
10612: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10613:
10614: strcpy(fileresplb,"PLB_");
10615: strcat(fileresplb,fileresu);
10616: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
1.288 brouard 10617: printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
10618: fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
1.217 brouard 10619: }
1.288 brouard 10620: printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
10621: fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
1.217 brouard 10622: pstamp(ficresplb);
1.288 brouard 10623: fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.217 brouard 10624: fprintf(ficresplb,"#Age ");
10625: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10626: fprintf(ficresplb,"\n");
10627:
1.218 brouard 10628:
10629: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10630:
10631: agebase=ageminpar;
10632: agelim=agemaxpar;
10633:
10634:
1.227 brouard 10635: i1=pow(2,cptcoveff);
1.218 brouard 10636: if (cptcovn < 1){i1=1;}
1.227 brouard 10637:
1.238 brouard 10638: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10639: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10640: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10641: continue;
10642: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10643: fprintf(ficresplb,"#******");
10644: printf("#******");
10645: fprintf(ficlog,"#******");
10646: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10647: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10648: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10649: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10650: }
10651: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10652: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10653: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10654: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10655: }
10656: fprintf(ficresplb,"******\n");
10657: printf("******\n");
10658: fprintf(ficlog,"******\n");
10659: if(invalidvarcomb[k]){
10660: printf("\nCombination (%d) ignored because no cases \n",k);
10661: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10662: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10663: continue;
10664: }
1.218 brouard 10665:
1.238 brouard 10666: fprintf(ficresplb,"#Age ");
10667: for(j=1;j<=cptcoveff;j++) {
10668: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10669: }
10670: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10671: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10672:
10673:
1.238 brouard 10674: for (age=agebase; age<=agelim; age++){
10675: /* for (age=agebase; age<=agebase; age++){ */
10676: if(mobilavproj > 0){
10677: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10678: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10679: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10680: }else if (mobilavproj == 0){
10681: 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);
10682: 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);
10683: exit(1);
10684: }else{
10685: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10686: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10687: /* printf("TOTOT\n"); */
10688: /* exit(1); */
1.238 brouard 10689: }
10690: fprintf(ficresplb,"%.0f ",age );
10691: for(j=1;j<=cptcoveff;j++)
10692: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10693: tot=0.;
10694: for(i=1; i<=nlstate;i++){
10695: tot += bprlim[i][i];
10696: fprintf(ficresplb," %.5f", bprlim[i][i]);
10697: }
10698: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10699: } /* Age */
10700: /* was end of cptcod */
1.255 brouard 10701: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10702: } /* end of any combination */
10703: } /* end of nres */
1.218 brouard 10704: /* hBijx(p, bage, fage); */
10705: /* fclose(ficrespijb); */
10706:
10707: return 0;
1.217 brouard 10708: }
1.218 brouard 10709:
1.180 brouard 10710: int hPijx(double *p, int bage, int fage){
10711: /*------------- h Pij x at various ages ------------*/
10712:
10713: int stepsize;
10714: int agelim;
10715: int hstepm;
10716: int nhstepm;
1.235 brouard 10717: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10718:
10719: double agedeb;
10720: double ***p3mat;
10721:
1.201 brouard 10722: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10723: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10724: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10725: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10726: }
10727: printf("Computing pij: result on file '%s' \n", filerespij);
10728: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10729:
10730: stepsize=(int) (stepm+YEARM-1)/YEARM;
10731: /*if (stepm<=24) stepsize=2;*/
10732:
10733: agelim=AGESUP;
10734: hstepm=stepsize*YEARM; /* Every year of age */
10735: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10736:
1.180 brouard 10737: /* hstepm=1; aff par mois*/
10738: pstamp(ficrespij);
10739: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10740: i1= pow(2,cptcoveff);
1.218 brouard 10741: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10742: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10743: /* k=k+1; */
1.235 brouard 10744: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10745: for(k=1; k<=i1;k++){
1.253 brouard 10746: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10747: continue;
1.183 brouard 10748: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10749: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10750: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10751: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10752: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10753: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10754: }
1.183 brouard 10755: fprintf(ficrespij,"******\n");
10756:
10757: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10758: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10759: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10760:
10761: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10762:
1.183 brouard 10763: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10764: oldm=oldms;savm=savms;
1.235 brouard 10765: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10766: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10767: for(i=1; i<=nlstate;i++)
10768: for(j=1; j<=nlstate+ndeath;j++)
10769: fprintf(ficrespij," %1d-%1d",i,j);
10770: fprintf(ficrespij,"\n");
10771: for (h=0; h<=nhstepm; h++){
10772: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10773: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10774: for(i=1; i<=nlstate;i++)
10775: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10776: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10777: fprintf(ficrespij,"\n");
10778: }
1.183 brouard 10779: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10780: fprintf(ficrespij,"\n");
10781: }
1.180 brouard 10782: /*}*/
10783: }
1.218 brouard 10784: return 0;
1.180 brouard 10785: }
1.218 brouard 10786:
10787: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10788: /*------------- h Bij x at various ages ------------*/
10789:
10790: int stepsize;
1.218 brouard 10791: /* int agelim; */
10792: int ageminl;
1.217 brouard 10793: int hstepm;
10794: int nhstepm;
1.238 brouard 10795: int h, i, i1, j, k, nres;
1.218 brouard 10796:
1.217 brouard 10797: double agedeb;
10798: double ***p3mat;
1.218 brouard 10799:
10800: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10801: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10802: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10803: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10804: }
10805: printf("Computing pij back: result on file '%s' \n", filerespijb);
10806: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10807:
10808: stepsize=(int) (stepm+YEARM-1)/YEARM;
10809: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10810:
1.218 brouard 10811: /* agelim=AGESUP; */
1.289 brouard 10812: ageminl=AGEINF; /* was 30 */
1.218 brouard 10813: hstepm=stepsize*YEARM; /* Every year of age */
10814: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10815:
10816: /* hstepm=1; aff par mois*/
10817: pstamp(ficrespijb);
1.255 brouard 10818: 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 10819: i1= pow(2,cptcoveff);
1.218 brouard 10820: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10821: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10822: /* k=k+1; */
1.238 brouard 10823: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10824: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10825: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10826: continue;
10827: fprintf(ficrespijb,"\n#****** ");
10828: for(j=1;j<=cptcoveff;j++)
10829: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10830: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10831: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10832: }
10833: fprintf(ficrespijb,"******\n");
1.264 brouard 10834: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10835: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10836: continue;
10837: }
10838:
10839: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10840: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10841: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
1.297 brouard 10842: 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 */
10843: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
1.238 brouard 10844:
10845: /* nhstepm=nhstepm*YEARM; aff par mois*/
10846:
1.266 brouard 10847: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10848: /* and memory limitations if stepm is small */
10849:
1.238 brouard 10850: /* oldm=oldms;savm=savms; */
10851: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10852: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10853: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10854: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10855: for(i=1; i<=nlstate;i++)
10856: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10857: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10858: fprintf(ficrespijb,"\n");
1.238 brouard 10859: for (h=0; h<=nhstepm; h++){
10860: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10861: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10862: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10863: for(i=1; i<=nlstate;i++)
10864: for(j=1; j<=nlstate+ndeath;j++)
10865: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10866: fprintf(ficrespijb,"\n");
10867: }
10868: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10869: fprintf(ficrespijb,"\n");
10870: } /* end age deb */
10871: } /* end combination */
10872: } /* end nres */
1.218 brouard 10873: return 0;
10874: } /* hBijx */
1.217 brouard 10875:
1.180 brouard 10876:
1.136 brouard 10877: /***********************************************/
10878: /**************** Main Program *****************/
10879: /***********************************************/
10880:
10881: int main(int argc, char *argv[])
10882: {
10883: #ifdef GSL
10884: const gsl_multimin_fminimizer_type *T;
10885: size_t iteri = 0, it;
10886: int rval = GSL_CONTINUE;
10887: int status = GSL_SUCCESS;
10888: double ssval;
10889: #endif
10890: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.290 brouard 10891: int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
10892: /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
1.209 brouard 10893: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10894: int jj, ll, li, lj, lk;
1.136 brouard 10895: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10896: int num_filled;
1.136 brouard 10897: int itimes;
10898: int NDIM=2;
10899: int vpopbased=0;
1.235 brouard 10900: int nres=0;
1.258 brouard 10901: int endishere=0;
1.277 brouard 10902: int noffset=0;
1.274 brouard 10903: int ncurrv=0; /* Temporary variable */
10904:
1.164 brouard 10905: char ca[32], cb[32];
1.136 brouard 10906: /* FILE *fichtm; *//* Html File */
10907: /* FILE *ficgp;*/ /*Gnuplot File */
10908: struct stat info;
1.191 brouard 10909: double agedeb=0.;
1.194 brouard 10910:
10911: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10912: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10913:
1.165 brouard 10914: double fret;
1.191 brouard 10915: double dum=0.; /* Dummy variable */
1.136 brouard 10916: double ***p3mat;
1.218 brouard 10917: /* double ***mobaverage; */
1.164 brouard 10918:
10919: char line[MAXLINE];
1.197 brouard 10920: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10921:
1.234 brouard 10922: char modeltemp[MAXLINE];
1.230 brouard 10923: char resultline[MAXLINE];
10924:
1.136 brouard 10925: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10926: char *tok, *val; /* pathtot */
1.290 brouard 10927: int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
1.195 brouard 10928: int c, h , cpt, c2;
1.191 brouard 10929: int jl=0;
10930: int i1, j1, jk, stepsize=0;
1.194 brouard 10931: int count=0;
10932:
1.164 brouard 10933: int *tab;
1.136 brouard 10934: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.296 brouard 10935: /* double anprojd, mprojd, jprojd; /\* For eventual projections *\/ */
10936: /* double anprojf, mprojf, jprojf; */
10937: /* double jintmean,mintmean,aintmean; */
10938: int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10939: int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
10940: double yrfproj= 10.0; /* Number of years of forward projections */
10941: double yrbproj= 10.0; /* Number of years of backward projections */
10942: int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
1.136 brouard 10943: int mobilav=0,popforecast=0;
1.191 brouard 10944: int hstepm=0, nhstepm=0;
1.136 brouard 10945: int agemortsup;
10946: float sumlpop=0.;
10947: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10948: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10949:
1.191 brouard 10950: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10951: double ftolpl=FTOL;
10952: double **prlim;
1.217 brouard 10953: double **bprlim;
1.136 brouard 10954: double ***param; /* Matrix of parameters */
1.251 brouard 10955: double ***paramstart; /* Matrix of starting parameter values */
10956: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10957: double **matcov; /* Matrix of covariance */
1.203 brouard 10958: double **hess; /* Hessian matrix */
1.136 brouard 10959: double ***delti3; /* Scale */
10960: double *delti; /* Scale */
10961: double ***eij, ***vareij;
10962: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10963:
1.136 brouard 10964: double *epj, vepp;
1.164 brouard 10965:
1.273 brouard 10966: double dateprev1, dateprev2;
1.296 brouard 10967: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
10968: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;
10969:
1.217 brouard 10970:
1.136 brouard 10971: double **ximort;
1.145 brouard 10972: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10973: int *dcwave;
10974:
1.164 brouard 10975: char z[1]="c";
1.136 brouard 10976:
10977: /*char *strt;*/
10978: char strtend[80];
1.126 brouard 10979:
1.164 brouard 10980:
1.126 brouard 10981: /* setlocale (LC_ALL, ""); */
10982: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10983: /* textdomain (PACKAGE); */
10984: /* setlocale (LC_CTYPE, ""); */
10985: /* setlocale (LC_MESSAGES, ""); */
10986:
10987: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10988: rstart_time = time(NULL);
10989: /* (void) gettimeofday(&start_time,&tzp);*/
10990: start_time = *localtime(&rstart_time);
1.126 brouard 10991: curr_time=start_time;
1.157 brouard 10992: /*tml = *localtime(&start_time.tm_sec);*/
10993: /* strcpy(strstart,asctime(&tml)); */
10994: strcpy(strstart,asctime(&start_time));
1.126 brouard 10995:
10996: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10997: /* tp.tm_sec = tp.tm_sec +86400; */
10998: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10999: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
11000: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
11001: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 11002: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 11003: /* strt=asctime(&tmg); */
11004: /* printf("Time(after) =%s",strstart); */
11005: /* (void) time (&time_value);
11006: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
11007: * tm = *localtime(&time_value);
11008: * strstart=asctime(&tm);
11009: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
11010: */
11011:
11012: nberr=0; /* Number of errors and warnings */
11013: nbwarn=0;
1.184 brouard 11014: #ifdef WIN32
11015: _getcwd(pathcd, size);
11016: #else
1.126 brouard 11017: getcwd(pathcd, size);
1.184 brouard 11018: #endif
1.191 brouard 11019: syscompilerinfo(0);
1.196 brouard 11020: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 11021: if(argc <=1){
11022: printf("\nEnter the parameter file name: ");
1.205 brouard 11023: if(!fgets(pathr,FILENAMELENGTH,stdin)){
11024: printf("ERROR Empty parameter file name\n");
11025: goto end;
11026: }
1.126 brouard 11027: i=strlen(pathr);
11028: if(pathr[i-1]=='\n')
11029: pathr[i-1]='\0';
1.156 brouard 11030: i=strlen(pathr);
1.205 brouard 11031: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 11032: pathr[i-1]='\0';
1.205 brouard 11033: }
11034: i=strlen(pathr);
11035: if( i==0 ){
11036: printf("ERROR Empty parameter file name\n");
11037: goto end;
11038: }
11039: for (tok = pathr; tok != NULL; ){
1.126 brouard 11040: printf("Pathr |%s|\n",pathr);
11041: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
11042: printf("val= |%s| pathr=%s\n",val,pathr);
11043: strcpy (pathtot, val);
11044: if(pathr[0] == '\0') break; /* Dirty */
11045: }
11046: }
1.281 brouard 11047: else if (argc<=2){
11048: strcpy(pathtot,argv[1]);
11049: }
1.126 brouard 11050: else{
11051: strcpy(pathtot,argv[1]);
1.281 brouard 11052: strcpy(z,argv[2]);
11053: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 11054: }
11055: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
11056: /*cygwin_split_path(pathtot,path,optionfile);
11057: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
11058: /* cutv(path,optionfile,pathtot,'\\');*/
11059:
11060: /* Split argv[0], imach program to get pathimach */
11061: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
11062: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11063: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
11064: /* strcpy(pathimach,argv[0]); */
11065: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
11066: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
11067: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 11068: #ifdef WIN32
11069: _chdir(path); /* Can be a relative path */
11070: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
11071: #else
1.126 brouard 11072: chdir(path); /* Can be a relative path */
1.184 brouard 11073: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
11074: #endif
11075: printf("Current directory %s!\n",pathcd);
1.126 brouard 11076: strcpy(command,"mkdir ");
11077: strcat(command,optionfilefiname);
11078: if((outcmd=system(command)) != 0){
1.169 brouard 11079: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 11080: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
11081: /* fclose(ficlog); */
11082: /* exit(1); */
11083: }
11084: /* if((imk=mkdir(optionfilefiname))<0){ */
11085: /* perror("mkdir"); */
11086: /* } */
11087:
11088: /*-------- arguments in the command line --------*/
11089:
1.186 brouard 11090: /* Main Log file */
1.126 brouard 11091: strcat(filelog, optionfilefiname);
11092: strcat(filelog,".log"); /* */
11093: if((ficlog=fopen(filelog,"w"))==NULL) {
11094: printf("Problem with logfile %s\n",filelog);
11095: goto end;
11096: }
11097: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 11098: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 11099: fprintf(ficlog,"\nEnter the parameter file name: \n");
11100: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
11101: path=%s \n\
11102: optionfile=%s\n\
11103: optionfilext=%s\n\
1.156 brouard 11104: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 11105:
1.197 brouard 11106: syscompilerinfo(1);
1.167 brouard 11107:
1.126 brouard 11108: printf("Local time (at start):%s",strstart);
11109: fprintf(ficlog,"Local time (at start): %s",strstart);
11110: fflush(ficlog);
11111: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 11112: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 11113:
11114: /* */
11115: strcpy(fileres,"r");
11116: strcat(fileres, optionfilefiname);
1.201 brouard 11117: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 11118: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 11119: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 11120:
1.186 brouard 11121: /* Main ---------arguments file --------*/
1.126 brouard 11122:
11123: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 11124: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
11125: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 11126: fflush(ficlog);
1.149 brouard 11127: /* goto end; */
11128: exit(70);
1.126 brouard 11129: }
11130:
11131: strcpy(filereso,"o");
1.201 brouard 11132: strcat(filereso,fileresu);
1.126 brouard 11133: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
11134: printf("Problem with Output resultfile: %s\n", filereso);
11135: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
11136: fflush(ficlog);
11137: goto end;
11138: }
1.278 brouard 11139: /*-------- Rewriting parameter file ----------*/
11140: strcpy(rfileres,"r"); /* "Rparameterfile */
11141: strcat(rfileres,optionfilefiname); /* Parameter file first name */
11142: strcat(rfileres,"."); /* */
11143: strcat(rfileres,optionfilext); /* Other files have txt extension */
11144: if((ficres =fopen(rfileres,"w"))==NULL) {
11145: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
11146: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
11147: fflush(ficlog);
11148: goto end;
11149: }
11150: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 11151:
1.278 brouard 11152:
1.126 brouard 11153: /* Reads comments: lines beginning with '#' */
11154: numlinepar=0;
1.277 brouard 11155: /* Is it a BOM UTF-8 Windows file? */
11156: /* First parameter line */
1.197 brouard 11157: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 11158: noffset=0;
11159: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
11160: {
11161: noffset=noffset+3;
11162: printf("# File is an UTF8 Bom.\n"); // 0xBF
11163: }
1.302 brouard 11164: /* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
11165: else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
1.277 brouard 11166: {
11167: noffset=noffset+2;
11168: printf("# File is an UTF16BE BOM file\n");
11169: }
11170: else if( line[0] == 0 && line[1] == 0)
11171: {
11172: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
11173: noffset=noffset+4;
11174: printf("# File is an UTF16BE BOM file\n");
11175: }
11176: } else{
11177: ;/*printf(" Not a BOM file\n");*/
11178: }
11179:
1.197 brouard 11180: /* If line starts with a # it is a comment */
1.277 brouard 11181: if (line[noffset] == '#') {
1.197 brouard 11182: numlinepar++;
11183: fputs(line,stdout);
11184: fputs(line,ficparo);
1.278 brouard 11185: fputs(line,ficres);
1.197 brouard 11186: fputs(line,ficlog);
11187: continue;
11188: }else
11189: break;
11190: }
11191: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
11192: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
11193: if (num_filled != 5) {
11194: printf("Should be 5 parameters\n");
1.283 brouard 11195: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 11196: }
1.126 brouard 11197: numlinepar++;
1.197 brouard 11198: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11199: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11200: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11201: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11202: }
11203: /* Second parameter line */
11204: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11205: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11206: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11207: if (line[0] == '#') {
11208: numlinepar++;
1.283 brouard 11209: printf("%s",line);
11210: fprintf(ficres,"%s",line);
11211: fprintf(ficparo,"%s",line);
11212: fprintf(ficlog,"%s",line);
1.197 brouard 11213: continue;
11214: }else
11215: break;
11216: }
1.223 brouard 11217: 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", \
11218: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11219: if (num_filled != 11) {
11220: 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 11221: printf("but line=%s\n",line);
1.283 brouard 11222: 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");
11223: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11224: }
1.286 brouard 11225: if( lastpass > maxwav){
11226: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11227: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11228: fflush(ficlog);
11229: goto end;
11230: }
11231: 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 11232: 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 11233: 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 11234: 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 11235: }
1.203 brouard 11236: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11237: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11238: /* Third parameter line */
11239: while(fgets(line, MAXLINE, ficpar)) {
11240: /* If line starts with a # it is a comment */
11241: if (line[0] == '#') {
11242: numlinepar++;
1.283 brouard 11243: printf("%s",line);
11244: fprintf(ficres,"%s",line);
11245: fprintf(ficparo,"%s",line);
11246: fprintf(ficlog,"%s",line);
1.197 brouard 11247: continue;
11248: }else
11249: break;
11250: }
1.201 brouard 11251: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11252: if (num_filled != 1){
1.302 brouard 11253: printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
11254: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
1.197 brouard 11255: model[0]='\0';
11256: goto end;
11257: }
11258: else{
11259: if (model[0]=='+'){
11260: for(i=1; i<=strlen(model);i++)
11261: modeltemp[i-1]=model[i];
1.201 brouard 11262: strcpy(model,modeltemp);
1.197 brouard 11263: }
11264: }
1.199 brouard 11265: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11266: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11267: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11268: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11269: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11270: }
11271: /* 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); */
11272: /* numlinepar=numlinepar+3; /\* In general *\/ */
11273: /* 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 11274: /* 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); */
11275: /* 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 11276: fflush(ficlog);
1.190 brouard 11277: /* if(model[0]=='#'|| model[0]== '\0'){ */
11278: if(model[0]=='#'){
1.279 brouard 11279: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11280: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11281: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11282: if(mle != -1){
1.279 brouard 11283: 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 11284: exit(1);
11285: }
11286: }
1.126 brouard 11287: while((c=getc(ficpar))=='#' && c!= EOF){
11288: ungetc(c,ficpar);
11289: fgets(line, MAXLINE, ficpar);
11290: numlinepar++;
1.195 brouard 11291: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11292: z[0]=line[1];
11293: }
11294: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11295: fputs(line, stdout);
11296: //puts(line);
1.126 brouard 11297: fputs(line,ficparo);
11298: fputs(line,ficlog);
11299: }
11300: ungetc(c,ficpar);
11301:
11302:
1.290 brouard 11303: covar=matrix(0,NCOVMAX,firstobs,lastobs); /**< used in readdata */
11304: if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /**< Fixed quantitative covariate */
11305: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /**< Time varying quantitative covariate */
11306: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11307: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11308: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11309: v1+v2*age+v2*v3 makes cptcovn = 3
11310: */
11311: if (strlen(model)>1)
1.187 brouard 11312: 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 11313: else
1.187 brouard 11314: ncovmodel=2; /* Constant and age */
1.133 brouard 11315: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11316: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11317: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11318: 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);
11319: 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);
11320: fflush(stdout);
11321: fclose (ficlog);
11322: goto end;
11323: }
1.126 brouard 11324: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11325: delti=delti3[1][1];
11326: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11327: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11328: /* We could also provide initial parameters values giving by simple logistic regression
11329: * only one way, that is without matrix product. We will have nlstate maximizations */
11330: /* for(i=1;i<nlstate;i++){ */
11331: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11332: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11333: /* } */
1.126 brouard 11334: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11335: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11336: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11337: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11338: fclose (ficparo);
11339: fclose (ficlog);
11340: goto end;
11341: exit(0);
1.220 brouard 11342: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11343: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11344: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11345: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11346: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11347: matcov=matrix(1,npar,1,npar);
1.203 brouard 11348: hess=matrix(1,npar,1,npar);
1.220 brouard 11349: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11350: /* Read guessed parameters */
1.126 brouard 11351: /* Reads comments: lines beginning with '#' */
11352: while((c=getc(ficpar))=='#' && c!= EOF){
11353: ungetc(c,ficpar);
11354: fgets(line, MAXLINE, ficpar);
11355: numlinepar++;
1.141 brouard 11356: fputs(line,stdout);
1.126 brouard 11357: fputs(line,ficparo);
11358: fputs(line,ficlog);
11359: }
11360: ungetc(c,ficpar);
11361:
11362: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11363: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11364: for(i=1; i <=nlstate; i++){
1.234 brouard 11365: j=0;
1.126 brouard 11366: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11367: if(jj==i) continue;
11368: j++;
1.292 brouard 11369: while((c=getc(ficpar))=='#' && c!= EOF){
11370: ungetc(c,ficpar);
11371: fgets(line, MAXLINE, ficpar);
11372: numlinepar++;
11373: fputs(line,stdout);
11374: fputs(line,ficparo);
11375: fputs(line,ficlog);
11376: }
11377: ungetc(c,ficpar);
1.234 brouard 11378: fscanf(ficpar,"%1d%1d",&i1,&j1);
11379: if ((i1 != i) || (j1 != jj)){
11380: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11381: It might be a problem of design; if ncovcol and the model are correct\n \
11382: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11383: exit(1);
11384: }
11385: fprintf(ficparo,"%1d%1d",i1,j1);
11386: if(mle==1)
11387: printf("%1d%1d",i,jj);
11388: fprintf(ficlog,"%1d%1d",i,jj);
11389: for(k=1; k<=ncovmodel;k++){
11390: fscanf(ficpar," %lf",¶m[i][j][k]);
11391: if(mle==1){
11392: printf(" %lf",param[i][j][k]);
11393: fprintf(ficlog," %lf",param[i][j][k]);
11394: }
11395: else
11396: fprintf(ficlog," %lf",param[i][j][k]);
11397: fprintf(ficparo," %lf",param[i][j][k]);
11398: }
11399: fscanf(ficpar,"\n");
11400: numlinepar++;
11401: if(mle==1)
11402: printf("\n");
11403: fprintf(ficlog,"\n");
11404: fprintf(ficparo,"\n");
1.126 brouard 11405: }
11406: }
11407: fflush(ficlog);
1.234 brouard 11408:
1.251 brouard 11409: /* Reads parameters values */
1.126 brouard 11410: p=param[1][1];
1.251 brouard 11411: pstart=paramstart[1][1];
1.126 brouard 11412:
11413: /* Reads comments: lines beginning with '#' */
11414: while((c=getc(ficpar))=='#' && c!= EOF){
11415: ungetc(c,ficpar);
11416: fgets(line, MAXLINE, ficpar);
11417: numlinepar++;
1.141 brouard 11418: fputs(line,stdout);
1.126 brouard 11419: fputs(line,ficparo);
11420: fputs(line,ficlog);
11421: }
11422: ungetc(c,ficpar);
11423:
11424: for(i=1; i <=nlstate; i++){
11425: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11426: fscanf(ficpar,"%1d%1d",&i1,&j1);
11427: if ( (i1-i) * (j1-j) != 0){
11428: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11429: exit(1);
11430: }
11431: printf("%1d%1d",i,j);
11432: fprintf(ficparo,"%1d%1d",i1,j1);
11433: fprintf(ficlog,"%1d%1d",i1,j1);
11434: for(k=1; k<=ncovmodel;k++){
11435: fscanf(ficpar,"%le",&delti3[i][j][k]);
11436: printf(" %le",delti3[i][j][k]);
11437: fprintf(ficparo," %le",delti3[i][j][k]);
11438: fprintf(ficlog," %le",delti3[i][j][k]);
11439: }
11440: fscanf(ficpar,"\n");
11441: numlinepar++;
11442: printf("\n");
11443: fprintf(ficparo,"\n");
11444: fprintf(ficlog,"\n");
1.126 brouard 11445: }
11446: }
11447: fflush(ficlog);
1.234 brouard 11448:
1.145 brouard 11449: /* Reads covariance matrix */
1.126 brouard 11450: delti=delti3[1][1];
1.220 brouard 11451:
11452:
1.126 brouard 11453: /* 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 11454:
1.126 brouard 11455: /* Reads comments: lines beginning with '#' */
11456: while((c=getc(ficpar))=='#' && c!= EOF){
11457: ungetc(c,ficpar);
11458: fgets(line, MAXLINE, ficpar);
11459: numlinepar++;
1.141 brouard 11460: fputs(line,stdout);
1.126 brouard 11461: fputs(line,ficparo);
11462: fputs(line,ficlog);
11463: }
11464: ungetc(c,ficpar);
1.220 brouard 11465:
1.126 brouard 11466: matcov=matrix(1,npar,1,npar);
1.203 brouard 11467: hess=matrix(1,npar,1,npar);
1.131 brouard 11468: for(i=1; i <=npar; i++)
11469: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11470:
1.194 brouard 11471: /* Scans npar lines */
1.126 brouard 11472: for(i=1; i <=npar; i++){
1.226 brouard 11473: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11474: if(count != 3){
1.226 brouard 11475: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11476: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11477: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11478: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11479: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11480: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11481: exit(1);
1.220 brouard 11482: }else{
1.226 brouard 11483: if(mle==1)
11484: printf("%1d%1d%d",i1,j1,jk);
11485: }
11486: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11487: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11488: for(j=1; j <=i; j++){
1.226 brouard 11489: fscanf(ficpar," %le",&matcov[i][j]);
11490: if(mle==1){
11491: printf(" %.5le",matcov[i][j]);
11492: }
11493: fprintf(ficlog," %.5le",matcov[i][j]);
11494: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11495: }
11496: fscanf(ficpar,"\n");
11497: numlinepar++;
11498: if(mle==1)
1.220 brouard 11499: printf("\n");
1.126 brouard 11500: fprintf(ficlog,"\n");
11501: fprintf(ficparo,"\n");
11502: }
1.194 brouard 11503: /* End of read covariance matrix npar lines */
1.126 brouard 11504: for(i=1; i <=npar; i++)
11505: for(j=i+1;j<=npar;j++)
1.226 brouard 11506: matcov[i][j]=matcov[j][i];
1.126 brouard 11507:
11508: if(mle==1)
11509: printf("\n");
11510: fprintf(ficlog,"\n");
11511:
11512: fflush(ficlog);
11513:
11514: } /* End of mle != -3 */
1.218 brouard 11515:
1.186 brouard 11516: /* Main data
11517: */
1.290 brouard 11518: nobs=lastobs-firstobs+1; /* was = lastobs;*/
11519: /* num=lvector(1,n); */
11520: /* moisnais=vector(1,n); */
11521: /* annais=vector(1,n); */
11522: /* moisdc=vector(1,n); */
11523: /* andc=vector(1,n); */
11524: /* weight=vector(1,n); */
11525: /* agedc=vector(1,n); */
11526: /* cod=ivector(1,n); */
11527: /* for(i=1;i<=n;i++){ */
11528: num=lvector(firstobs,lastobs);
11529: moisnais=vector(firstobs,lastobs);
11530: annais=vector(firstobs,lastobs);
11531: moisdc=vector(firstobs,lastobs);
11532: andc=vector(firstobs,lastobs);
11533: weight=vector(firstobs,lastobs);
11534: agedc=vector(firstobs,lastobs);
11535: cod=ivector(firstobs,lastobs);
11536: for(i=firstobs;i<=lastobs;i++){
1.234 brouard 11537: num[i]=0;
11538: moisnais[i]=0;
11539: annais[i]=0;
11540: moisdc[i]=0;
11541: andc[i]=0;
11542: agedc[i]=0;
11543: cod[i]=0;
11544: weight[i]=1.0; /* Equal weights, 1 by default */
11545: }
1.290 brouard 11546: mint=matrix(1,maxwav,firstobs,lastobs);
11547: anint=matrix(1,maxwav,firstobs,lastobs);
11548: s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11549: tab=ivector(1,NCOVMAX);
1.144 brouard 11550: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11551: 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 11552:
1.136 brouard 11553: /* Reads data from file datafile */
11554: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11555: goto end;
11556:
11557: /* Calculation of the number of parameters from char model */
1.234 brouard 11558: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11559: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11560: k=3 V4 Tvar[k=3]= 4 (from V4)
11561: k=2 V1 Tvar[k=2]= 1 (from V1)
11562: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11563: */
11564:
11565: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11566: TvarsDind=ivector(1,NCOVMAX); /* */
11567: TvarsD=ivector(1,NCOVMAX); /* */
11568: TvarsQind=ivector(1,NCOVMAX); /* */
11569: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11570: TvarF=ivector(1,NCOVMAX); /* */
11571: TvarFind=ivector(1,NCOVMAX); /* */
11572: TvarV=ivector(1,NCOVMAX); /* */
11573: TvarVind=ivector(1,NCOVMAX); /* */
11574: TvarA=ivector(1,NCOVMAX); /* */
11575: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11576: TvarFD=ivector(1,NCOVMAX); /* */
11577: TvarFDind=ivector(1,NCOVMAX); /* */
11578: TvarFQ=ivector(1,NCOVMAX); /* */
11579: TvarFQind=ivector(1,NCOVMAX); /* */
11580: TvarVD=ivector(1,NCOVMAX); /* */
11581: TvarVDind=ivector(1,NCOVMAX); /* */
11582: TvarVQ=ivector(1,NCOVMAX); /* */
11583: TvarVQind=ivector(1,NCOVMAX); /* */
11584:
1.230 brouard 11585: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11586: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11587: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11588: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11589: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11590: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11591: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11592: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11593: */
11594: /* For model-covariate k tells which data-covariate to use but
11595: because this model-covariate is a construction we invent a new column
11596: ncovcol + k1
11597: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11598: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11599: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11600: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11601: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11602: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11603: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11604: */
1.145 brouard 11605: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11606: 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 11607: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11608: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11609: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11610: 4 covariates (3 plus signs)
11611: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11612: */
1.230 brouard 11613: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11614: * individual dummy, fixed or varying:
11615: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11616: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11617: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11618: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11619: * Tmodelind[1]@9={9,0,3,2,}*/
11620: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11621: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11622: * individual quantitative, fixed or varying:
11623: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11624: * 3, 1, 0, 0, 0, 0, 0, 0},
11625: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11626: /* Main decodemodel */
11627:
1.187 brouard 11628:
1.223 brouard 11629: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11630: goto end;
11631:
1.137 brouard 11632: if((double)(lastobs-imx)/(double)imx > 1.10){
11633: nbwarn++;
11634: 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);
11635: 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);
11636: }
1.136 brouard 11637: /* if(mle==1){*/
1.137 brouard 11638: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11639: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11640: }
11641:
11642: /*-calculation of age at interview from date of interview and age at death -*/
11643: agev=matrix(1,maxwav,1,imx);
11644:
11645: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11646: goto end;
11647:
1.126 brouard 11648:
1.136 brouard 11649: agegomp=(int)agemin;
1.290 brouard 11650: free_vector(moisnais,firstobs,lastobs);
11651: free_vector(annais,firstobs,lastobs);
1.126 brouard 11652: /* free_matrix(mint,1,maxwav,1,n);
11653: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11654: /* free_vector(moisdc,1,n); */
11655: /* free_vector(andc,1,n); */
1.145 brouard 11656: /* */
11657:
1.126 brouard 11658: wav=ivector(1,imx);
1.214 brouard 11659: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11660: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11661: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11662: 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.*/
11663: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11664: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11665:
11666: /* Concatenates waves */
1.214 brouard 11667: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11668: Death is a valid wave (if date is known).
11669: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11670: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11671: and mw[mi+1][i]. dh depends on stepm.
11672: */
11673:
1.126 brouard 11674: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11675: /* Concatenates waves */
1.145 brouard 11676:
1.290 brouard 11677: free_vector(moisdc,firstobs,lastobs);
11678: free_vector(andc,firstobs,lastobs);
1.215 brouard 11679:
1.126 brouard 11680: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11681: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11682: ncodemax[1]=1;
1.145 brouard 11683: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11684: cptcoveff=0;
1.220 brouard 11685: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11686: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11687: }
11688:
11689: ncovcombmax=pow(2,cptcoveff);
11690: invalidvarcomb=ivector(1, ncovcombmax);
11691: for(i=1;i<ncovcombmax;i++)
11692: invalidvarcomb[i]=0;
11693:
1.211 brouard 11694: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11695: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11696: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11697:
1.200 brouard 11698: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11699: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11700: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11701: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11702: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11703: * (currently 0 or 1) in the data.
11704: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11705: * corresponding modality (h,j).
11706: */
11707:
1.145 brouard 11708: h=0;
11709: /*if (cptcovn > 0) */
1.126 brouard 11710: m=pow(2,cptcoveff);
11711:
1.144 brouard 11712: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11713: * For k=4 covariates, h goes from 1 to m=2**k
11714: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11715: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11716: * h\k 1 2 3 4
1.143 brouard 11717: *______________________________
11718: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11719: * 2 2 1 1 1
11720: * 3 i=2 1 2 1 1
11721: * 4 2 2 1 1
11722: * 5 i=3 1 i=2 1 2 1
11723: * 6 2 1 2 1
11724: * 7 i=4 1 2 2 1
11725: * 8 2 2 2 1
1.197 brouard 11726: * 9 i=5 1 i=3 1 i=2 1 2
11727: * 10 2 1 1 2
11728: * 11 i=6 1 2 1 2
11729: * 12 2 2 1 2
11730: * 13 i=7 1 i=4 1 2 2
11731: * 14 2 1 2 2
11732: * 15 i=8 1 2 2 2
11733: * 16 2 2 2 2
1.143 brouard 11734: */
1.212 brouard 11735: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11736: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11737: * and the value of each covariate?
11738: * V1=1, V2=1, V3=2, V4=1 ?
11739: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11740: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11741: * In order to get the real value in the data, we use nbcode
11742: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11743: * We are keeping this crazy system in order to be able (in the future?)
11744: * to have more than 2 values (0 or 1) for a covariate.
11745: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11746: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11747: * bbbbbbbb
11748: * 76543210
11749: * h-1 00000101 (6-1=5)
1.219 brouard 11750: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11751: * &
11752: * 1 00000001 (1)
1.219 brouard 11753: * 00000000 = 1 & ((h-1) >> (k-1))
11754: * +1= 00000001 =1
1.211 brouard 11755: *
11756: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11757: * h' 1101 =2^3+2^2+0x2^1+2^0
11758: * >>k' 11
11759: * & 00000001
11760: * = 00000001
11761: * +1 = 00000010=2 = codtabm(14,3)
11762: * Reverse h=6 and m=16?
11763: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11764: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11765: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11766: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11767: * V3=decodtabm(14,3,2**4)=2
11768: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11769: *(h-1) >> (j-1) 0011 =13 >> 2
11770: * &1 000000001
11771: * = 000000001
11772: * +1= 000000010 =2
11773: * 2211
11774: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11775: * V3=2
1.220 brouard 11776: * codtabm and decodtabm are identical
1.211 brouard 11777: */
11778:
1.145 brouard 11779:
11780: free_ivector(Ndum,-1,NCOVMAX);
11781:
11782:
1.126 brouard 11783:
1.186 brouard 11784: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11785: strcpy(optionfilegnuplot,optionfilefiname);
11786: if(mle==-3)
1.201 brouard 11787: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11788: strcat(optionfilegnuplot,".gp");
11789:
11790: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11791: printf("Problem with file %s",optionfilegnuplot);
11792: }
11793: else{
1.204 brouard 11794: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11795: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11796: //fprintf(ficgp,"set missing 'NaNq'\n");
11797: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11798: }
11799: /* fclose(ficgp);*/
1.186 brouard 11800:
11801:
11802: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11803:
11804: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11805: if(mle==-3)
1.201 brouard 11806: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11807: strcat(optionfilehtm,".htm");
11808: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11809: printf("Problem with %s \n",optionfilehtm);
11810: exit(0);
1.126 brouard 11811: }
11812:
11813: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11814: strcat(optionfilehtmcov,"-cov.htm");
11815: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11816: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11817: }
11818: else{
11819: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11820: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11821: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11822: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11823: }
11824:
1.213 brouard 11825: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
1.204 brouard 11826: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11827: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11828: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11829: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11830: \n\
11831: <hr size=\"2\" color=\"#EC5E5E\">\
11832: <ul><li><h4>Parameter files</h4>\n\
11833: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11834: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11835: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11836: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11837: - Date and time at start: %s</ul>\n",\
11838: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11839: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11840: fileres,fileres,\
11841: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11842: fflush(fichtm);
11843:
11844: strcpy(pathr,path);
11845: strcat(pathr,optionfilefiname);
1.184 brouard 11846: #ifdef WIN32
11847: _chdir(optionfilefiname); /* Move to directory named optionfile */
11848: #else
1.126 brouard 11849: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11850: #endif
11851:
1.126 brouard 11852:
1.220 brouard 11853: /* Calculates basic frequencies. Computes observed prevalence at single age
11854: and for any valid combination of covariates
1.126 brouard 11855: and prints on file fileres'p'. */
1.251 brouard 11856: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11857: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11858:
11859: fprintf(fichtm,"\n");
1.286 brouard 11860: 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 11861: ftol, stepm);
11862: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11863: ncurrv=1;
11864: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11865: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11866: ncurrv=i;
11867: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11868: fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
1.274 brouard 11869: ncurrv=i;
11870: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
1.290 brouard 11871: fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
1.274 brouard 11872: ncurrv=i;
11873: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11874: 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", \
11875: nlstate, ndeath, maxwav, mle, weightopt);
11876:
11877: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11878: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11879:
11880:
11881: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11882: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11883: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11884: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11885: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11886: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11887: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11888: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11889: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11890:
1.126 brouard 11891: /* For Powell, parameters are in a vector p[] starting at p[1]
11892: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11893: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11894:
11895: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11896: /* For mortality only */
1.126 brouard 11897: if (mle==-3){
1.136 brouard 11898: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11899: for(i=1;i<=NDIM;i++)
11900: for(j=1;j<=NDIM;j++)
11901: ximort[i][j]=0.;
1.186 brouard 11902: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.290 brouard 11903: cens=ivector(firstobs,lastobs);
11904: ageexmed=vector(firstobs,lastobs);
11905: agecens=vector(firstobs,lastobs);
11906: dcwave=ivector(firstobs,lastobs);
1.223 brouard 11907:
1.126 brouard 11908: for (i=1; i<=imx; i++){
11909: dcwave[i]=-1;
11910: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11911: if (s[m][i]>nlstate) {
11912: dcwave[i]=m;
11913: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11914: break;
11915: }
1.126 brouard 11916: }
1.226 brouard 11917:
1.126 brouard 11918: for (i=1; i<=imx; i++) {
11919: if (wav[i]>0){
1.226 brouard 11920: ageexmed[i]=agev[mw[1][i]][i];
11921: j=wav[i];
11922: agecens[i]=1.;
11923:
11924: if (ageexmed[i]> 1 && wav[i] > 0){
11925: agecens[i]=agev[mw[j][i]][i];
11926: cens[i]= 1;
11927: }else if (ageexmed[i]< 1)
11928: cens[i]= -1;
11929: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11930: cens[i]=0 ;
1.126 brouard 11931: }
11932: else cens[i]=-1;
11933: }
11934:
11935: for (i=1;i<=NDIM;i++) {
11936: for (j=1;j<=NDIM;j++)
1.226 brouard 11937: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11938: }
11939:
1.302 brouard 11940: p[1]=0.0268; p[NDIM]=0.083;
11941: /* printf("%lf %lf", p[1], p[2]); */
1.126 brouard 11942:
11943:
1.136 brouard 11944: #ifdef GSL
11945: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11946: #else
1.126 brouard 11947: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11948: #endif
1.201 brouard 11949: strcpy(filerespow,"POW-MORT_");
11950: strcat(filerespow,fileresu);
1.126 brouard 11951: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11952: printf("Problem with resultfile: %s\n", filerespow);
11953: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11954: }
1.136 brouard 11955: #ifdef GSL
11956: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11957: #else
1.126 brouard 11958: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11959: #endif
1.126 brouard 11960: /* for (i=1;i<=nlstate;i++)
11961: for(j=1;j<=nlstate+ndeath;j++)
11962: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11963: */
11964: fprintf(ficrespow,"\n");
1.136 brouard 11965: #ifdef GSL
11966: /* gsl starts here */
11967: T = gsl_multimin_fminimizer_nmsimplex;
11968: gsl_multimin_fminimizer *sfm = NULL;
11969: gsl_vector *ss, *x;
11970: gsl_multimin_function minex_func;
11971:
11972: /* Initial vertex size vector */
11973: ss = gsl_vector_alloc (NDIM);
11974:
11975: if (ss == NULL){
11976: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11977: }
11978: /* Set all step sizes to 1 */
11979: gsl_vector_set_all (ss, 0.001);
11980:
11981: /* Starting point */
1.126 brouard 11982:
1.136 brouard 11983: x = gsl_vector_alloc (NDIM);
11984:
11985: if (x == NULL){
11986: gsl_vector_free(ss);
11987: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11988: }
11989:
11990: /* Initialize method and iterate */
11991: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11992: /* gsl_vector_set(x, 0, 0.0268); */
11993: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11994: gsl_vector_set(x, 0, p[1]);
11995: gsl_vector_set(x, 1, p[2]);
11996:
11997: minex_func.f = &gompertz_f;
11998: minex_func.n = NDIM;
11999: minex_func.params = (void *)&p; /* ??? */
12000:
12001: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
12002: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
12003:
12004: printf("Iterations beginning .....\n\n");
12005: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
12006:
12007: iteri=0;
12008: while (rval == GSL_CONTINUE){
12009: iteri++;
12010: status = gsl_multimin_fminimizer_iterate(sfm);
12011:
12012: if (status) printf("error: %s\n", gsl_strerror (status));
12013: fflush(0);
12014:
12015: if (status)
12016: break;
12017:
12018: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
12019: ssval = gsl_multimin_fminimizer_size (sfm);
12020:
12021: if (rval == GSL_SUCCESS)
12022: printf ("converged to a local maximum at\n");
12023:
12024: printf("%5d ", iteri);
12025: for (it = 0; it < NDIM; it++){
12026: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
12027: }
12028: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
12029: }
12030:
12031: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
12032:
12033: gsl_vector_free(x); /* initial values */
12034: gsl_vector_free(ss); /* inital step size */
12035: for (it=0; it<NDIM; it++){
12036: p[it+1]=gsl_vector_get(sfm->x,it);
12037: fprintf(ficrespow," %.12lf", p[it]);
12038: }
12039: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
12040: #endif
12041: #ifdef POWELL
12042: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
12043: #endif
1.126 brouard 12044: fclose(ficrespow);
12045:
1.203 brouard 12046: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 12047:
12048: for(i=1; i <=NDIM; i++)
12049: for(j=i+1;j<=NDIM;j++)
1.220 brouard 12050: matcov[i][j]=matcov[j][i];
1.126 brouard 12051:
12052: printf("\nCovariance matrix\n ");
1.203 brouard 12053: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 12054: for(i=1; i <=NDIM; i++) {
12055: for(j=1;j<=NDIM;j++){
1.220 brouard 12056: printf("%f ",matcov[i][j]);
12057: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 12058: }
1.203 brouard 12059: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 12060: }
12061:
12062: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 12063: for (i=1;i<=NDIM;i++) {
1.126 brouard 12064: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 12065: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
12066: }
1.302 brouard 12067: lsurv=vector(agegomp,AGESUP);
12068: lpop=vector(agegomp,AGESUP);
12069: tpop=vector(agegomp,AGESUP);
1.126 brouard 12070: lsurv[agegomp]=100000;
12071:
12072: for (k=agegomp;k<=AGESUP;k++) {
12073: agemortsup=k;
12074: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
12075: }
12076:
12077: for (k=agegomp;k<agemortsup;k++)
12078: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
12079:
12080: for (k=agegomp;k<agemortsup;k++){
12081: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
12082: sumlpop=sumlpop+lpop[k];
12083: }
12084:
12085: tpop[agegomp]=sumlpop;
12086: for (k=agegomp;k<(agemortsup-3);k++){
12087: /* tpop[k+1]=2;*/
12088: tpop[k+1]=tpop[k]-lpop[k];
12089: }
12090:
12091:
12092: printf("\nAge lx qx dx Lx Tx e(x)\n");
12093: for (k=agegomp;k<(agemortsup-2);k++)
12094: 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]);
12095:
12096:
12097: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 12098: ageminpar=50;
12099: agemaxpar=100;
1.194 brouard 12100: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
12101: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12102: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12103: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
12104: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
12105: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12106: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12107: }else{
12108: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
12109: 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 12110: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 12111: }
1.201 brouard 12112: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 12113: stepm, weightopt,\
12114: model,imx,p,matcov,agemortsup);
12115:
1.302 brouard 12116: free_vector(lsurv,agegomp,AGESUP);
12117: free_vector(lpop,agegomp,AGESUP);
12118: free_vector(tpop,agegomp,AGESUP);
1.220 brouard 12119: free_matrix(ximort,1,NDIM,1,NDIM);
1.290 brouard 12120: free_ivector(dcwave,firstobs,lastobs);
12121: free_vector(agecens,firstobs,lastobs);
12122: free_vector(ageexmed,firstobs,lastobs);
12123: free_ivector(cens,firstobs,lastobs);
1.220 brouard 12124: #ifdef GSL
1.136 brouard 12125: #endif
1.186 brouard 12126: } /* Endof if mle==-3 mortality only */
1.205 brouard 12127: /* Standard */
12128: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
12129: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12130: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 12131: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 12132: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12133: for (k=1; k<=npar;k++)
12134: printf(" %d %8.5f",k,p[k]);
12135: printf("\n");
1.205 brouard 12136: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
12137: /* mlikeli uses func not funcone */
1.247 brouard 12138: /* for(i=1;i<nlstate;i++){ */
12139: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
12140: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
12141: /* } */
1.205 brouard 12142: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
12143: }
12144: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
12145: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
12146: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
12147: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12148: }
12149: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 12150: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
12151: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
12152: for (k=1; k<=npar;k++)
12153: printf(" %d %8.5f",k,p[k]);
12154: printf("\n");
12155:
12156: /*--------- results files --------------*/
1.283 brouard 12157: /* 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 12158:
12159:
12160: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12161: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12162: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
12163: for(i=1,jk=1; i <=nlstate; i++){
12164: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 12165: if (k != i) {
12166: printf("%d%d ",i,k);
12167: fprintf(ficlog,"%d%d ",i,k);
12168: fprintf(ficres,"%1d%1d ",i,k);
12169: for(j=1; j <=ncovmodel; j++){
12170: printf("%12.7f ",p[jk]);
12171: fprintf(ficlog,"%12.7f ",p[jk]);
12172: fprintf(ficres,"%12.7f ",p[jk]);
12173: jk++;
12174: }
12175: printf("\n");
12176: fprintf(ficlog,"\n");
12177: fprintf(ficres,"\n");
12178: }
1.126 brouard 12179: }
12180: }
1.203 brouard 12181: if(mle != 0){
12182: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 12183: ftolhess=ftol; /* Usually correct */
1.203 brouard 12184: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
12185: 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");
12186: 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");
12187: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 12188: for(k=1; k <=(nlstate+ndeath); k++){
12189: if (k != i) {
12190: printf("%d%d ",i,k);
12191: fprintf(ficlog,"%d%d ",i,k);
12192: for(j=1; j <=ncovmodel; j++){
12193: 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]));
12194: 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]));
12195: jk++;
12196: }
12197: printf("\n");
12198: fprintf(ficlog,"\n");
12199: }
12200: }
1.193 brouard 12201: }
1.203 brouard 12202: } /* end of hesscov and Wald tests */
1.225 brouard 12203:
1.203 brouard 12204: /* */
1.126 brouard 12205: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
12206: printf("# Scales (for hessian or gradient estimation)\n");
12207: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
12208: for(i=1,jk=1; i <=nlstate; i++){
12209: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 12210: if (j!=i) {
12211: fprintf(ficres,"%1d%1d",i,j);
12212: printf("%1d%1d",i,j);
12213: fprintf(ficlog,"%1d%1d",i,j);
12214: for(k=1; k<=ncovmodel;k++){
12215: printf(" %.5e",delti[jk]);
12216: fprintf(ficlog," %.5e",delti[jk]);
12217: fprintf(ficres," %.5e",delti[jk]);
12218: jk++;
12219: }
12220: printf("\n");
12221: fprintf(ficlog,"\n");
12222: fprintf(ficres,"\n");
12223: }
1.126 brouard 12224: }
12225: }
12226:
12227: 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 12228: if(mle >= 1) /* To big for the screen */
1.126 brouard 12229: 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");
12230: 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");
12231: /* # 121 Var(a12)\n\ */
12232: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12233: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12234: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12235: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12236: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12237: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12238: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12239:
12240:
12241: /* Just to have a covariance matrix which will be more understandable
12242: even is we still don't want to manage dictionary of variables
12243: */
12244: for(itimes=1;itimes<=2;itimes++){
12245: jj=0;
12246: for(i=1; i <=nlstate; i++){
1.225 brouard 12247: for(j=1; j <=nlstate+ndeath; j++){
12248: if(j==i) continue;
12249: for(k=1; k<=ncovmodel;k++){
12250: jj++;
12251: ca[0]= k+'a'-1;ca[1]='\0';
12252: if(itimes==1){
12253: if(mle>=1)
12254: printf("#%1d%1d%d",i,j,k);
12255: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12256: fprintf(ficres,"#%1d%1d%d",i,j,k);
12257: }else{
12258: if(mle>=1)
12259: printf("%1d%1d%d",i,j,k);
12260: fprintf(ficlog,"%1d%1d%d",i,j,k);
12261: fprintf(ficres,"%1d%1d%d",i,j,k);
12262: }
12263: ll=0;
12264: for(li=1;li <=nlstate; li++){
12265: for(lj=1;lj <=nlstate+ndeath; lj++){
12266: if(lj==li) continue;
12267: for(lk=1;lk<=ncovmodel;lk++){
12268: ll++;
12269: if(ll<=jj){
12270: cb[0]= lk +'a'-1;cb[1]='\0';
12271: if(ll<jj){
12272: if(itimes==1){
12273: if(mle>=1)
12274: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12275: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12276: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12277: }else{
12278: if(mle>=1)
12279: printf(" %.5e",matcov[jj][ll]);
12280: fprintf(ficlog," %.5e",matcov[jj][ll]);
12281: fprintf(ficres," %.5e",matcov[jj][ll]);
12282: }
12283: }else{
12284: if(itimes==1){
12285: if(mle>=1)
12286: printf(" Var(%s%1d%1d)",ca,i,j);
12287: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12288: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12289: }else{
12290: if(mle>=1)
12291: printf(" %.7e",matcov[jj][ll]);
12292: fprintf(ficlog," %.7e",matcov[jj][ll]);
12293: fprintf(ficres," %.7e",matcov[jj][ll]);
12294: }
12295: }
12296: }
12297: } /* end lk */
12298: } /* end lj */
12299: } /* end li */
12300: if(mle>=1)
12301: printf("\n");
12302: fprintf(ficlog,"\n");
12303: fprintf(ficres,"\n");
12304: numlinepar++;
12305: } /* end k*/
12306: } /*end j */
1.126 brouard 12307: } /* end i */
12308: } /* end itimes */
12309:
12310: fflush(ficlog);
12311: fflush(ficres);
1.225 brouard 12312: while(fgets(line, MAXLINE, ficpar)) {
12313: /* If line starts with a # it is a comment */
12314: if (line[0] == '#') {
12315: numlinepar++;
12316: fputs(line,stdout);
12317: fputs(line,ficparo);
12318: fputs(line,ficlog);
1.299 brouard 12319: fputs(line,ficres);
1.225 brouard 12320: continue;
12321: }else
12322: break;
12323: }
12324:
1.209 brouard 12325: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12326: /* ungetc(c,ficpar); */
12327: /* fgets(line, MAXLINE, ficpar); */
12328: /* fputs(line,stdout); */
12329: /* fputs(line,ficparo); */
12330: /* } */
12331: /* ungetc(c,ficpar); */
1.126 brouard 12332:
12333: estepm=0;
1.209 brouard 12334: 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 12335:
12336: if (num_filled != 6) {
12337: 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);
12338: 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);
12339: goto end;
12340: }
12341: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12342: }
12343: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12344: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12345:
1.209 brouard 12346: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12347: if (estepm==0 || estepm < stepm) estepm=stepm;
12348: if (fage <= 2) {
12349: bage = ageminpar;
12350: fage = agemaxpar;
12351: }
12352:
12353: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12354: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12355: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12356:
1.186 brouard 12357: /* Other stuffs, more or less useful */
1.254 brouard 12358: while(fgets(line, MAXLINE, ficpar)) {
12359: /* If line starts with a # it is a comment */
12360: if (line[0] == '#') {
12361: numlinepar++;
12362: fputs(line,stdout);
12363: fputs(line,ficparo);
12364: fputs(line,ficlog);
1.299 brouard 12365: fputs(line,ficres);
1.254 brouard 12366: continue;
12367: }else
12368: break;
12369: }
12370:
12371: 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){
12372:
12373: if (num_filled != 7) {
12374: 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);
12375: 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);
12376: goto end;
12377: }
12378: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12379: 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);
12380: 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);
12381: 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 12382: }
1.254 brouard 12383:
12384: while(fgets(line, MAXLINE, ficpar)) {
12385: /* If line starts with a # it is a comment */
12386: if (line[0] == '#') {
12387: numlinepar++;
12388: fputs(line,stdout);
12389: fputs(line,ficparo);
12390: fputs(line,ficlog);
1.299 brouard 12391: fputs(line,ficres);
1.254 brouard 12392: continue;
12393: }else
12394: break;
1.126 brouard 12395: }
12396:
12397:
12398: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12399: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12400:
1.254 brouard 12401: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12402: if (num_filled != 1) {
12403: 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);
12404: 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);
12405: goto end;
12406: }
12407: printf("pop_based=%d\n",popbased);
12408: fprintf(ficlog,"pop_based=%d\n",popbased);
12409: fprintf(ficparo,"pop_based=%d\n",popbased);
12410: fprintf(ficres,"pop_based=%d\n",popbased);
12411: }
12412:
1.258 brouard 12413: /* Results */
12414: nresult=0;
12415: do{
12416: if(!fgets(line, MAXLINE, ficpar)){
12417: endishere=1;
12418: parameterline=14;
12419: }else if (line[0] == '#') {
12420: /* If line starts with a # it is a comment */
1.254 brouard 12421: numlinepar++;
12422: fputs(line,stdout);
12423: fputs(line,ficparo);
12424: fputs(line,ficlog);
1.299 brouard 12425: fputs(line,ficres);
1.254 brouard 12426: continue;
1.258 brouard 12427: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12428: parameterline=11;
1.296 brouard 12429: else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
1.258 brouard 12430: parameterline=12;
12431: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12432: parameterline=13;
12433: else{
12434: parameterline=14;
1.254 brouard 12435: }
1.258 brouard 12436: switch (parameterline){
12437: case 11:
1.296 brouard 12438: 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)){
12439: 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 12440: 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);
12441: 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);
12442: 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);
12443: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12444: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12445: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
1.296 brouard 12446: prvforecast = 1;
12447: }
12448: else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
1.302 brouard 12449: printf("prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12450: fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
12451: fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
1.296 brouard 12452: prvforecast = 2;
12453: }
12454: else {
12455: 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);
12456: 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);
12457: goto end;
1.258 brouard 12458: }
1.254 brouard 12459: break;
1.258 brouard 12460: case 12:
1.296 brouard 12461: 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)){
12462: 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);
12463: 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);
12464: 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);
12465: 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);
12466: /* day and month of back2 are not used but only year anback2.*/
1.273 brouard 12467: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12468: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.296 brouard 12469: prvbackcast = 1;
12470: }
12471: else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
1.302 brouard 12472: printf("prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12473: fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
12474: fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
1.296 brouard 12475: prvbackcast = 2;
12476: }
12477: else {
12478: 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);
12479: 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);
12480: goto end;
1.258 brouard 12481: }
1.230 brouard 12482: break;
1.258 brouard 12483: case 13:
12484: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12485: if (num_filled == 0){
12486: resultline[0]='\0';
12487: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12488: fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12489: break;
12490: } else if (num_filled != 1){
12491: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12492: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12493: }
12494: nresult++; /* Sum of resultlines */
12495: printf("Result %d: result=%s\n",nresult, resultline);
12496: if(nresult > MAXRESULTLINES){
12497: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12498: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12499: goto end;
12500: }
12501: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12502: fprintf(ficparo,"result: %s\n",resultline);
12503: fprintf(ficres,"result: %s\n",resultline);
12504: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12505: break;
1.303 brouard 12506: case 14:
12507: printf("Error: Unknown command '%s'\n",line);
12508: fprintf(ficlog,"Error: Unknown command '%s'\n",line);
12509: if(ncovmodel >=2 && nresult==0 ){
1.259 brouard 12510: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.303 brouard 12511: fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12512: }
1.305 brouard 12513: /* goto end; */
1.259 brouard 12514: break;
1.258 brouard 12515: default:
12516: nresult=1;
12517: decoderesult(".",nresult ); /* No covariate */
12518: }
12519: } /* End switch parameterline */
12520: }while(endishere==0); /* End do */
1.126 brouard 12521:
1.230 brouard 12522: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12523: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12524:
12525: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12526: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12527: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12528: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12529: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12530: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12531: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12532: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12533: }else{
1.270 brouard 12534: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
1.296 brouard 12535: /* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
12536: /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */ /* Done in freqsummary */
12537: if(prvforecast==1){
12538: dateprojd=(jproj1+12*mproj1+365*anproj1)/365;
12539: jprojd=jproj1;
12540: mprojd=mproj1;
12541: anprojd=anproj1;
12542: dateprojf=(jproj2+12*mproj2+365*anproj2)/365;
12543: jprojf=jproj2;
12544: mprojf=mproj2;
12545: anprojf=anproj2;
12546: } else if(prvforecast == 2){
12547: dateprojd=dateintmean;
12548: date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
12549: dateprojf=dateintmean+yrfproj;
12550: date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
12551: }
12552: if(prvbackcast==1){
12553: datebackd=(jback1+12*mback1+365*anback1)/365;
12554: jbackd=jback1;
12555: mbackd=mback1;
12556: anbackd=anback1;
12557: datebackf=(jback2+12*mback2+365*anback2)/365;
12558: jbackf=jback2;
12559: mbackf=mback2;
12560: anbackf=anback2;
12561: } else if(prvbackcast == 2){
12562: datebackd=dateintmean;
12563: date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
12564: datebackf=dateintmean-yrbproj;
12565: date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
12566: }
12567:
12568: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
1.220 brouard 12569: }
12570: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.296 brouard 12571: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
12572: jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);
1.220 brouard 12573:
1.225 brouard 12574: /*------------ free_vector -------------*/
12575: /* chdir(path); */
1.220 brouard 12576:
1.215 brouard 12577: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12578: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12579: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12580: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.290 brouard 12581: free_lvector(num,firstobs,lastobs);
12582: free_vector(agedc,firstobs,lastobs);
1.126 brouard 12583: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12584: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12585: fclose(ficparo);
12586: fclose(ficres);
1.220 brouard 12587:
12588:
1.186 brouard 12589: /* Other results (useful)*/
1.220 brouard 12590:
12591:
1.126 brouard 12592: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12593: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12594: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12595: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12596: fclose(ficrespl);
12597:
12598: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12599: /*#include "hpijx.h"*/
12600: hPijx(p, bage, fage);
1.145 brouard 12601: fclose(ficrespij);
1.227 brouard 12602:
1.220 brouard 12603: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12604: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12605: k=1;
1.126 brouard 12606: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12607:
1.269 brouard 12608: /* Prevalence for each covariate combination in probs[age][status][cov] */
12609: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12610: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12611: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12612: for(k=1;k<=ncovcombmax;k++)
12613: probs[i][j][k]=0.;
1.269 brouard 12614: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12615: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12616: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12617: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12618: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12619: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12620: for(k=1;k<=ncovcombmax;k++)
12621: mobaverages[i][j][k]=0.;
1.219 brouard 12622: mobaverage=mobaverages;
12623: if (mobilav!=0) {
1.235 brouard 12624: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12625: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12626: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12627: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12628: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12629: }
1.269 brouard 12630: } else if (mobilavproj !=0) {
1.235 brouard 12631: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12632: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12633: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12634: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12635: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12636: }
1.269 brouard 12637: }else{
12638: printf("Internal error moving average\n");
12639: fflush(stdout);
12640: exit(1);
1.219 brouard 12641: }
12642: }/* end if moving average */
1.227 brouard 12643:
1.126 brouard 12644: /*---------- Forecasting ------------------*/
1.296 brouard 12645: if(prevfcast==1){
12646: /* /\* if(stepm ==1){*\/ */
12647: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12648: /*This done previously after freqsummary.*/
12649: /* dateprojd=(jproj1+12*mproj1+365*anproj1)/365; */
12650: /* dateprojf=(jproj2+12*mproj2+365*anproj2)/365; */
12651:
12652: /* } else if (prvforecast==2){ */
12653: /* /\* if(stepm ==1){*\/ */
12654: /* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj *\/ */
12655: /* } */
12656: /*prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);*/
12657: prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
1.126 brouard 12658: }
1.269 brouard 12659:
1.296 brouard 12660: /* Prevbcasting */
12661: if(prevbcast==1){
1.219 brouard 12662: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12663: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12664: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12665:
12666: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12667:
12668: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12669:
1.219 brouard 12670: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12671: fclose(ficresplb);
12672:
1.222 brouard 12673: hBijx(p, bage, fage, mobaverage);
12674: fclose(ficrespijb);
1.219 brouard 12675:
1.296 brouard 12676: /* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, *\/ */
12677: /* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); *\/ */
12678: /* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
12679: /* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
12680: prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
12681: mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);
12682:
12683:
1.269 brouard 12684: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12685:
12686:
1.269 brouard 12687: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12688: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12689: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12690: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.296 brouard 12691: } /* end Prevbcasting */
1.268 brouard 12692:
1.186 brouard 12693:
12694: /* ------ Other prevalence ratios------------ */
1.126 brouard 12695:
1.215 brouard 12696: free_ivector(wav,1,imx);
12697: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12698: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12699: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12700:
12701:
1.127 brouard 12702: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12703:
1.201 brouard 12704: strcpy(filerese,"E_");
12705: strcat(filerese,fileresu);
1.126 brouard 12706: if((ficreseij=fopen(filerese,"w"))==NULL) {
12707: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12708: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12709: }
1.208 brouard 12710: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12711: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12712:
12713: pstamp(ficreseij);
1.219 brouard 12714:
1.235 brouard 12715: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12716: if (cptcovn < 1){i1=1;}
12717:
12718: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12719: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12720: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12721: continue;
1.219 brouard 12722: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12723: printf("\n#****** ");
1.225 brouard 12724: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12725: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12726: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12727: }
12728: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12729: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12730: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12731: }
12732: fprintf(ficreseij,"******\n");
1.235 brouard 12733: printf("******\n");
1.219 brouard 12734:
12735: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12736: oldm=oldms;savm=savms;
1.235 brouard 12737: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12738:
1.219 brouard 12739: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12740: }
12741: fclose(ficreseij);
1.208 brouard 12742: printf("done evsij\n");fflush(stdout);
12743: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12744:
1.218 brouard 12745:
1.227 brouard 12746: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12747:
1.201 brouard 12748: strcpy(filerest,"T_");
12749: strcat(filerest,fileresu);
1.127 brouard 12750: if((ficrest=fopen(filerest,"w"))==NULL) {
12751: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12752: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12753: }
1.208 brouard 12754: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12755: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12756: strcpy(fileresstde,"STDE_");
12757: strcat(fileresstde,fileresu);
1.126 brouard 12758: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12759: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12760: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12761: }
1.227 brouard 12762: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12763: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12764:
1.201 brouard 12765: strcpy(filerescve,"CVE_");
12766: strcat(filerescve,fileresu);
1.126 brouard 12767: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12768: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12769: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12770: }
1.227 brouard 12771: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12772: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12773:
1.201 brouard 12774: strcpy(fileresv,"V_");
12775: strcat(fileresv,fileresu);
1.126 brouard 12776: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12777: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12778: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12779: }
1.227 brouard 12780: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12781: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12782:
1.235 brouard 12783: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12784: if (cptcovn < 1){i1=1;}
12785:
12786: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12787: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12788: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12789: continue;
1.242 brouard 12790: printf("\n#****** Result for:");
12791: fprintf(ficrest,"\n#****** Result for:");
12792: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12793: for(j=1;j<=cptcoveff;j++){
12794: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12795: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12796: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12797: }
1.235 brouard 12798: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12799: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12800: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12801: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12802: }
1.208 brouard 12803: fprintf(ficrest,"******\n");
1.227 brouard 12804: fprintf(ficlog,"******\n");
12805: printf("******\n");
1.208 brouard 12806:
12807: fprintf(ficresstdeij,"\n#****** ");
12808: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12809: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12810: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12811: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12812: }
1.235 brouard 12813: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12814: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12815: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12816: }
1.208 brouard 12817: fprintf(ficresstdeij,"******\n");
12818: fprintf(ficrescveij,"******\n");
12819:
12820: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12821: /* pstamp(ficresvij); */
1.225 brouard 12822: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12823: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12824: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12825: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12826: }
1.208 brouard 12827: fprintf(ficresvij,"******\n");
12828:
12829: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12830: oldm=oldms;savm=savms;
1.235 brouard 12831: printf(" cvevsij ");
12832: fprintf(ficlog, " cvevsij ");
12833: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12834: printf(" end cvevsij \n ");
12835: fprintf(ficlog, " end cvevsij \n ");
12836:
12837: /*
12838: */
12839: /* goto endfree; */
12840:
12841: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12842: pstamp(ficrest);
12843:
1.269 brouard 12844: epj=vector(1,nlstate+1);
1.208 brouard 12845: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12846: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12847: cptcod= 0; /* To be deleted */
12848: printf("varevsij vpopbased=%d \n",vpopbased);
12849: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12850: 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 12851: 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 ");
12852: if(vpopbased==1)
12853: 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);
12854: else
1.288 brouard 12855: fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12856: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12857: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12858: fprintf(ficrest,"\n");
12859: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.288 brouard 12860: printf("Computing age specific forward period (stable) prevalences in each health state \n");
12861: fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
1.227 brouard 12862: for(age=bage; age <=fage ;age++){
1.235 brouard 12863: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12864: if (vpopbased==1) {
12865: if(mobilav ==0){
12866: for(i=1; i<=nlstate;i++)
12867: prlim[i][i]=probs[(int)age][i][k];
12868: }else{ /* mobilav */
12869: for(i=1; i<=nlstate;i++)
12870: prlim[i][i]=mobaverage[(int)age][i][k];
12871: }
12872: }
1.219 brouard 12873:
1.227 brouard 12874: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12875: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12876: /* printf(" age %4.0f ",age); */
12877: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12878: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12879: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12880: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12881: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12882: }
12883: epj[nlstate+1] +=epj[j];
12884: }
12885: /* printf(" age %4.0f \n",age); */
1.219 brouard 12886:
1.227 brouard 12887: for(i=1, vepp=0.;i <=nlstate;i++)
12888: for(j=1;j <=nlstate;j++)
12889: vepp += vareij[i][j][(int)age];
12890: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12891: for(j=1;j <=nlstate;j++){
12892: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12893: }
12894: fprintf(ficrest,"\n");
12895: }
1.208 brouard 12896: } /* End vpopbased */
1.269 brouard 12897: free_vector(epj,1,nlstate+1);
1.208 brouard 12898: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12899: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12900: printf("done selection\n");fflush(stdout);
12901: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12902:
1.235 brouard 12903: } /* End k selection */
1.227 brouard 12904:
12905: printf("done State-specific expectancies\n");fflush(stdout);
12906: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12907:
1.288 brouard 12908: /* variance-covariance of forward period prevalence*/
1.269 brouard 12909: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12910:
1.227 brouard 12911:
1.290 brouard 12912: free_vector(weight,firstobs,lastobs);
1.227 brouard 12913: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.290 brouard 12914: free_imatrix(s,1,maxwav+1,firstobs,lastobs);
12915: free_matrix(anint,1,maxwav,firstobs,lastobs);
12916: free_matrix(mint,1,maxwav,firstobs,lastobs);
12917: free_ivector(cod,firstobs,lastobs);
1.227 brouard 12918: free_ivector(tab,1,NCOVMAX);
12919: fclose(ficresstdeij);
12920: fclose(ficrescveij);
12921: fclose(ficresvij);
12922: fclose(ficrest);
12923: fclose(ficpar);
12924:
12925:
1.126 brouard 12926: /*---------- End : free ----------------*/
1.219 brouard 12927: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12928: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12929: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12930: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12931: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12932: } /* mle==-3 arrives here for freeing */
1.227 brouard 12933: /* endfree:*/
12934: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12935: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12936: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.290 brouard 12937: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
12938: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
12939: if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
12940: free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
1.227 brouard 12941: free_matrix(matcov,1,npar,1,npar);
12942: free_matrix(hess,1,npar,1,npar);
12943: /*free_vector(delti,1,npar);*/
12944: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12945: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12946: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12947: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12948:
12949: free_ivector(ncodemax,1,NCOVMAX);
12950: free_ivector(ncodemaxwundef,1,NCOVMAX);
12951: free_ivector(Dummy,-1,NCOVMAX);
12952: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12953: free_ivector(DummyV,1,NCOVMAX);
12954: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12955: free_ivector(Typevar,-1,NCOVMAX);
12956: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12957: free_ivector(TvarsQ,1,NCOVMAX);
12958: free_ivector(TvarsQind,1,NCOVMAX);
12959: free_ivector(TvarsD,1,NCOVMAX);
12960: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12961: free_ivector(TvarFD,1,NCOVMAX);
12962: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12963: free_ivector(TvarF,1,NCOVMAX);
12964: free_ivector(TvarFind,1,NCOVMAX);
12965: free_ivector(TvarV,1,NCOVMAX);
12966: free_ivector(TvarVind,1,NCOVMAX);
12967: free_ivector(TvarA,1,NCOVMAX);
12968: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12969: free_ivector(TvarFQ,1,NCOVMAX);
12970: free_ivector(TvarFQind,1,NCOVMAX);
12971: free_ivector(TvarVD,1,NCOVMAX);
12972: free_ivector(TvarVDind,1,NCOVMAX);
12973: free_ivector(TvarVQ,1,NCOVMAX);
12974: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12975: free_ivector(Tvarsel,1,NCOVMAX);
12976: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12977: free_ivector(Tposprod,1,NCOVMAX);
12978: free_ivector(Tprod,1,NCOVMAX);
12979: free_ivector(Tvaraff,1,NCOVMAX);
12980: free_ivector(invalidvarcomb,1,ncovcombmax);
12981: free_ivector(Tage,1,NCOVMAX);
12982: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12983: free_ivector(TmodelInvind,1,NCOVMAX);
12984: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12985:
12986: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12987: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12988: fflush(fichtm);
12989: fflush(ficgp);
12990:
1.227 brouard 12991:
1.126 brouard 12992: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12993: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12994: 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 12995: }else{
12996: printf("End of Imach\n");
12997: fprintf(ficlog,"End of Imach\n");
12998: }
12999: printf("See log file on %s\n",filelog);
13000: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 13001: /*(void) gettimeofday(&end_time,&tzp);*/
13002: rend_time = time(NULL);
13003: end_time = *localtime(&rend_time);
13004: /* tml = *localtime(&end_time.tm_sec); */
13005: strcpy(strtend,asctime(&end_time));
1.126 brouard 13006: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
13007: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 13008: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 13009:
1.157 brouard 13010: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
13011: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
13012: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 13013: /* printf("Total time was %d uSec.\n", total_usecs);*/
13014: /* if(fileappend(fichtm,optionfilehtm)){ */
13015: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13016: fclose(fichtm);
13017: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
13018: fclose(fichtmcov);
13019: fclose(ficgp);
13020: fclose(ficlog);
13021: /*------ End -----------*/
1.227 brouard 13022:
1.281 brouard 13023:
13024: /* Executes gnuplot */
1.227 brouard 13025:
13026: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 13027: #ifdef WIN32
1.227 brouard 13028: if (_chdir(pathcd) != 0)
13029: printf("Can't move to directory %s!\n",path);
13030: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 13031: #else
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: #endif
1.126 brouard 13036: printf("Current directory %s!\n",pathcd);
13037: /*strcat(plotcmd,CHARSEPARATOR);*/
13038: sprintf(plotcmd,"gnuplot");
1.157 brouard 13039: #ifdef _WIN32
1.126 brouard 13040: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
13041: #endif
13042: if(!stat(plotcmd,&info)){
1.158 brouard 13043: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13044: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 13045: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 13046: }else
13047: strcpy(pplotcmd,plotcmd);
1.157 brouard 13048: #ifdef __unix
1.126 brouard 13049: strcpy(plotcmd,GNUPLOTPROGRAM);
13050: if(!stat(plotcmd,&info)){
1.158 brouard 13051: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 13052: }else
13053: strcpy(pplotcmd,plotcmd);
13054: #endif
13055: }else
13056: strcpy(pplotcmd,plotcmd);
13057:
13058: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 13059: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.292 brouard 13060: strcpy(pplotcmd,plotcmd);
1.227 brouard 13061:
1.126 brouard 13062: if((outcmd=system(plotcmd)) != 0){
1.292 brouard 13063: printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 13064: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 13065: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.292 brouard 13066: if((outcmd=system(plotcmd)) != 0){
1.153 brouard 13067: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.292 brouard 13068: strcpy(plotcmd,pplotcmd);
13069: }
1.126 brouard 13070: }
1.158 brouard 13071: printf(" Successful, please wait...");
1.126 brouard 13072: while (z[0] != 'q') {
13073: /* chdir(path); */
1.154 brouard 13074: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 13075: scanf("%s",z);
13076: /* if (z[0] == 'c') system("./imach"); */
13077: if (z[0] == 'e') {
1.158 brouard 13078: #ifdef __APPLE__
1.152 brouard 13079: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 13080: #elif __linux
13081: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 13082: #else
1.152 brouard 13083: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 13084: #endif
13085: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
13086: system(pplotcmd);
1.126 brouard 13087: }
13088: else if (z[0] == 'g') system(plotcmd);
13089: else if (z[0] == 'q') exit(0);
13090: }
1.227 brouard 13091: end:
1.126 brouard 13092: while (z[0] != 'q') {
1.195 brouard 13093: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 13094: scanf("%s",z);
13095: }
1.283 brouard 13096: printf("End\n");
1.282 brouard 13097: exit(0);
1.126 brouard 13098: }
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