Annotation of imach/src/imach.c, revision 1.287
1.287 ! brouard 1: /* $Id: imach.c,v 1.286 2018/04/27 14:27:04 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.287 ! brouard 4: Revision 1.286 2018/04/27 14:27:04 brouard
! 5: Summary: some minor bugs
! 6:
1.286 brouard 7: Revision 1.285 2018/04/21 21:02:16 brouard
8: Summary: Some bugs fixed, valgrind tested
9:
1.285 brouard 10: Revision 1.284 2018/04/20 05:22:13 brouard
11: Summary: Computing mean and stdeviation of fixed quantitative variables
12:
1.284 brouard 13: Revision 1.283 2018/04/19 14:49:16 brouard
14: Summary: Some minor bugs fixed
15:
1.283 brouard 16: Revision 1.282 2018/02/27 22:50:02 brouard
17: *** empty log message ***
18:
1.282 brouard 19: Revision 1.281 2018/02/27 19:25:23 brouard
20: Summary: Adding second argument for quitting
21:
1.281 brouard 22: Revision 1.280 2018/02/21 07:58:13 brouard
23: Summary: 0.99r15
24:
25: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
26:
1.280 brouard 27: Revision 1.279 2017/07/20 13:35:01 brouard
28: Summary: temporary working
29:
1.279 brouard 30: Revision 1.278 2017/07/19 14:09:02 brouard
31: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
32:
1.278 brouard 33: Revision 1.277 2017/07/17 08:53:49 brouard
34: Summary: BOM files can be read now
35:
1.277 brouard 36: Revision 1.276 2017/06/30 15:48:31 brouard
37: Summary: Graphs improvements
38:
1.276 brouard 39: Revision 1.275 2017/06/30 13:39:33 brouard
40: Summary: Saito's color
41:
1.275 brouard 42: Revision 1.274 2017/06/29 09:47:08 brouard
43: Summary: Version 0.99r14
44:
1.274 brouard 45: Revision 1.273 2017/06/27 11:06:02 brouard
46: Summary: More documentation on projections
47:
1.273 brouard 48: Revision 1.272 2017/06/27 10:22:40 brouard
49: Summary: Color of backprojection changed from 6 to 5(yellow)
50:
1.272 brouard 51: Revision 1.271 2017/06/27 10:17:50 brouard
52: Summary: Some bug with rint
53:
1.271 brouard 54: Revision 1.270 2017/05/24 05:45:29 brouard
55: *** empty log message ***
56:
1.270 brouard 57: Revision 1.269 2017/05/23 08:39:25 brouard
58: Summary: Code into subroutine, cleanings
59:
1.269 brouard 60: Revision 1.268 2017/05/18 20:09:32 brouard
61: Summary: backprojection and confidence intervals of backprevalence
62:
1.268 brouard 63: Revision 1.267 2017/05/13 10:25:05 brouard
64: Summary: temporary save for backprojection
65:
1.267 brouard 66: Revision 1.266 2017/05/13 07:26:12 brouard
67: Summary: Version 0.99r13 (improvements and bugs fixed)
68:
1.266 brouard 69: Revision 1.265 2017/04/26 16:22:11 brouard
70: Summary: imach 0.99r13 Some bugs fixed
71:
1.265 brouard 72: Revision 1.264 2017/04/26 06:01:29 brouard
73: Summary: Labels in graphs
74:
1.264 brouard 75: Revision 1.263 2017/04/24 15:23:15 brouard
76: Summary: to save
77:
1.263 brouard 78: Revision 1.262 2017/04/18 16:48:12 brouard
79: *** empty log message ***
80:
1.262 brouard 81: Revision 1.261 2017/04/05 10:14:09 brouard
82: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
83:
1.261 brouard 84: Revision 1.260 2017/04/04 17:46:59 brouard
85: Summary: Gnuplot indexations fixed (humm)
86:
1.260 brouard 87: Revision 1.259 2017/04/04 13:01:16 brouard
88: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
89:
1.259 brouard 90: Revision 1.258 2017/04/03 10:17:47 brouard
91: Summary: Version 0.99r12
92:
93: Some cleanings, conformed with updated documentation.
94:
1.258 brouard 95: Revision 1.257 2017/03/29 16:53:30 brouard
96: Summary: Temp
97:
1.257 brouard 98: Revision 1.256 2017/03/27 05:50:23 brouard
99: Summary: Temporary
100:
1.256 brouard 101: Revision 1.255 2017/03/08 16:02:28 brouard
102: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
103:
1.255 brouard 104: Revision 1.254 2017/03/08 07:13:00 brouard
105: Summary: Fixing data parameter line
106:
1.254 brouard 107: Revision 1.253 2016/12/15 11:59:41 brouard
108: Summary: 0.99 in progress
109:
1.253 brouard 110: Revision 1.252 2016/09/15 21:15:37 brouard
111: *** empty log message ***
112:
1.252 brouard 113: Revision 1.251 2016/09/15 15:01:13 brouard
114: Summary: not working
115:
1.251 brouard 116: Revision 1.250 2016/09/08 16:07:27 brouard
117: Summary: continue
118:
1.250 brouard 119: Revision 1.249 2016/09/07 17:14:18 brouard
120: Summary: Starting values from frequencies
121:
1.249 brouard 122: Revision 1.248 2016/09/07 14:10:18 brouard
123: *** empty log message ***
124:
1.248 brouard 125: Revision 1.247 2016/09/02 11:11:21 brouard
126: *** empty log message ***
127:
1.247 brouard 128: Revision 1.246 2016/09/02 08:49:22 brouard
129: *** empty log message ***
130:
1.246 brouard 131: Revision 1.245 2016/09/02 07:25:01 brouard
132: *** empty log message ***
133:
1.245 brouard 134: Revision 1.244 2016/09/02 07:17:34 brouard
135: *** empty log message ***
136:
1.244 brouard 137: Revision 1.243 2016/09/02 06:45:35 brouard
138: *** empty log message ***
139:
1.243 brouard 140: Revision 1.242 2016/08/30 15:01:20 brouard
141: Summary: Fixing a lots
142:
1.242 brouard 143: Revision 1.241 2016/08/29 17:17:25 brouard
144: Summary: gnuplot problem in Back projection to fix
145:
1.241 brouard 146: Revision 1.240 2016/08/29 07:53:18 brouard
147: Summary: Better
148:
1.240 brouard 149: Revision 1.239 2016/08/26 15:51:03 brouard
150: Summary: Improvement in Powell output in order to copy and paste
151:
152: Author:
153:
1.239 brouard 154: Revision 1.238 2016/08/26 14:23:35 brouard
155: Summary: Starting tests of 0.99
156:
1.238 brouard 157: Revision 1.237 2016/08/26 09:20:19 brouard
158: Summary: to valgrind
159:
1.237 brouard 160: Revision 1.236 2016/08/25 10:50:18 brouard
161: *** empty log message ***
162:
1.236 brouard 163: Revision 1.235 2016/08/25 06:59:23 brouard
164: *** empty log message ***
165:
1.235 brouard 166: Revision 1.234 2016/08/23 16:51:20 brouard
167: *** empty log message ***
168:
1.234 brouard 169: Revision 1.233 2016/08/23 07:40:50 brouard
170: Summary: not working
171:
1.233 brouard 172: Revision 1.232 2016/08/22 14:20:21 brouard
173: Summary: not working
174:
1.232 brouard 175: Revision 1.231 2016/08/22 07:17:15 brouard
176: Summary: not working
177:
1.231 brouard 178: Revision 1.230 2016/08/22 06:55:53 brouard
179: Summary: Not working
180:
1.230 brouard 181: Revision 1.229 2016/07/23 09:45:53 brouard
182: Summary: Completing for func too
183:
1.229 brouard 184: Revision 1.228 2016/07/22 17:45:30 brouard
185: Summary: Fixing some arrays, still debugging
186:
1.227 brouard 187: Revision 1.226 2016/07/12 18:42:34 brouard
188: Summary: temp
189:
1.226 brouard 190: Revision 1.225 2016/07/12 08:40:03 brouard
191: Summary: saving but not running
192:
1.225 brouard 193: Revision 1.224 2016/07/01 13:16:01 brouard
194: Summary: Fixes
195:
1.224 brouard 196: Revision 1.223 2016/02/19 09:23:35 brouard
197: Summary: temporary
198:
1.223 brouard 199: Revision 1.222 2016/02/17 08:14:50 brouard
200: Summary: Probably last 0.98 stable version 0.98r6
201:
1.222 brouard 202: Revision 1.221 2016/02/15 23:35:36 brouard
203: Summary: minor bug
204:
1.220 brouard 205: Revision 1.219 2016/02/15 00:48:12 brouard
206: *** empty log message ***
207:
1.219 brouard 208: Revision 1.218 2016/02/12 11:29:23 brouard
209: Summary: 0.99 Back projections
210:
1.218 brouard 211: Revision 1.217 2015/12/23 17:18:31 brouard
212: Summary: Experimental backcast
213:
1.217 brouard 214: Revision 1.216 2015/12/18 17:32:11 brouard
215: Summary: 0.98r4 Warning and status=-2
216:
217: Version 0.98r4 is now:
218: - displaying an error when status is -1, date of interview unknown and date of death known;
219: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
220: Older changes concerning s=-2, dating from 2005 have been supersed.
221:
1.216 brouard 222: Revision 1.215 2015/12/16 08:52:24 brouard
223: Summary: 0.98r4 working
224:
1.215 brouard 225: Revision 1.214 2015/12/16 06:57:54 brouard
226: Summary: temporary not working
227:
1.214 brouard 228: Revision 1.213 2015/12/11 18:22:17 brouard
229: Summary: 0.98r4
230:
1.213 brouard 231: Revision 1.212 2015/11/21 12:47:24 brouard
232: Summary: minor typo
233:
1.212 brouard 234: Revision 1.211 2015/11/21 12:41:11 brouard
235: Summary: 0.98r3 with some graph of projected cross-sectional
236:
237: Author: Nicolas Brouard
238:
1.211 brouard 239: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 240: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 241: Summary: Adding ftolpl parameter
242: Author: N Brouard
243:
244: We had difficulties to get smoothed confidence intervals. It was due
245: to the period prevalence which wasn't computed accurately. The inner
246: parameter ftolpl is now an outer parameter of the .imach parameter
247: file after estepm. If ftolpl is small 1.e-4 and estepm too,
248: computation are long.
249:
1.209 brouard 250: Revision 1.208 2015/11/17 14:31:57 brouard
251: Summary: temporary
252:
1.208 brouard 253: Revision 1.207 2015/10/27 17:36:57 brouard
254: *** empty log message ***
255:
1.207 brouard 256: Revision 1.206 2015/10/24 07:14:11 brouard
257: *** empty log message ***
258:
1.206 brouard 259: Revision 1.205 2015/10/23 15:50:53 brouard
260: Summary: 0.98r3 some clarification for graphs on likelihood contributions
261:
1.205 brouard 262: Revision 1.204 2015/10/01 16:20:26 brouard
263: Summary: Some new graphs of contribution to likelihood
264:
1.204 brouard 265: Revision 1.203 2015/09/30 17:45:14 brouard
266: Summary: looking at better estimation of the hessian
267:
268: Also a better criteria for convergence to the period prevalence And
269: therefore adding the number of years needed to converge. (The
270: prevalence in any alive state shold sum to one
271:
1.203 brouard 272: Revision 1.202 2015/09/22 19:45:16 brouard
273: Summary: Adding some overall graph on contribution to likelihood. Might change
274:
1.202 brouard 275: Revision 1.201 2015/09/15 17:34:58 brouard
276: Summary: 0.98r0
277:
278: - Some new graphs like suvival functions
279: - Some bugs fixed like model=1+age+V2.
280:
1.201 brouard 281: Revision 1.200 2015/09/09 16:53:55 brouard
282: Summary: Big bug thanks to Flavia
283:
284: Even model=1+age+V2. did not work anymore
285:
1.200 brouard 286: Revision 1.199 2015/09/07 14:09:23 brouard
287: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
288:
1.199 brouard 289: Revision 1.198 2015/09/03 07:14:39 brouard
290: Summary: 0.98q5 Flavia
291:
1.198 brouard 292: Revision 1.197 2015/09/01 18:24:39 brouard
293: *** empty log message ***
294:
1.197 brouard 295: Revision 1.196 2015/08/18 23:17:52 brouard
296: Summary: 0.98q5
297:
1.196 brouard 298: Revision 1.195 2015/08/18 16:28:39 brouard
299: Summary: Adding a hack for testing purpose
300:
301: After reading the title, ftol and model lines, if the comment line has
302: a q, starting with #q, the answer at the end of the run is quit. It
303: permits to run test files in batch with ctest. The former workaround was
304: $ echo q | imach foo.imach
305:
1.195 brouard 306: Revision 1.194 2015/08/18 13:32:00 brouard
307: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
308:
1.194 brouard 309: Revision 1.193 2015/08/04 07:17:42 brouard
310: Summary: 0.98q4
311:
1.193 brouard 312: Revision 1.192 2015/07/16 16:49:02 brouard
313: Summary: Fixing some outputs
314:
1.192 brouard 315: Revision 1.191 2015/07/14 10:00:33 brouard
316: Summary: Some fixes
317:
1.191 brouard 318: Revision 1.190 2015/05/05 08:51:13 brouard
319: Summary: Adding digits in output parameters (7 digits instead of 6)
320:
321: Fix 1+age+.
322:
1.190 brouard 323: Revision 1.189 2015/04/30 14:45:16 brouard
324: Summary: 0.98q2
325:
1.189 brouard 326: Revision 1.188 2015/04/30 08:27:53 brouard
327: *** empty log message ***
328:
1.188 brouard 329: Revision 1.187 2015/04/29 09:11:15 brouard
330: *** empty log message ***
331:
1.187 brouard 332: Revision 1.186 2015/04/23 12:01:52 brouard
333: Summary: V1*age is working now, version 0.98q1
334:
335: Some codes had been disabled in order to simplify and Vn*age was
336: working in the optimization phase, ie, giving correct MLE parameters,
337: but, as usual, outputs were not correct and program core dumped.
338:
1.186 brouard 339: Revision 1.185 2015/03/11 13:26:42 brouard
340: Summary: Inclusion of compile and links command line for Intel Compiler
341:
1.185 brouard 342: Revision 1.184 2015/03/11 11:52:39 brouard
343: Summary: Back from Windows 8. Intel Compiler
344:
1.184 brouard 345: Revision 1.183 2015/03/10 20:34:32 brouard
346: Summary: 0.98q0, trying with directest, mnbrak fixed
347:
348: We use directest instead of original Powell test; probably no
349: incidence on the results, but better justifications;
350: We fixed Numerical Recipes mnbrak routine which was wrong and gave
351: wrong results.
352:
1.183 brouard 353: Revision 1.182 2015/02/12 08:19:57 brouard
354: Summary: Trying to keep directest which seems simpler and more general
355: Author: Nicolas Brouard
356:
1.182 brouard 357: Revision 1.181 2015/02/11 23:22:24 brouard
358: Summary: Comments on Powell added
359:
360: Author:
361:
1.181 brouard 362: Revision 1.180 2015/02/11 17:33:45 brouard
363: Summary: Finishing move from main to function (hpijx and prevalence_limit)
364:
1.180 brouard 365: Revision 1.179 2015/01/04 09:57:06 brouard
366: Summary: back to OS/X
367:
1.179 brouard 368: Revision 1.178 2015/01/04 09:35:48 brouard
369: *** empty log message ***
370:
1.178 brouard 371: Revision 1.177 2015/01/03 18:40:56 brouard
372: Summary: Still testing ilc32 on OSX
373:
1.177 brouard 374: Revision 1.176 2015/01/03 16:45:04 brouard
375: *** empty log message ***
376:
1.176 brouard 377: Revision 1.175 2015/01/03 16:33:42 brouard
378: *** empty log message ***
379:
1.175 brouard 380: Revision 1.174 2015/01/03 16:15:49 brouard
381: Summary: Still in cross-compilation
382:
1.174 brouard 383: Revision 1.173 2015/01/03 12:06:26 brouard
384: Summary: trying to detect cross-compilation
385:
1.173 brouard 386: Revision 1.172 2014/12/27 12:07:47 brouard
387: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
388:
1.172 brouard 389: Revision 1.171 2014/12/23 13:26:59 brouard
390: Summary: Back from Visual C
391:
392: Still problem with utsname.h on Windows
393:
1.171 brouard 394: Revision 1.170 2014/12/23 11:17:12 brouard
395: Summary: Cleaning some \%% back to %%
396:
397: The escape was mandatory for a specific compiler (which one?), but too many warnings.
398:
1.170 brouard 399: Revision 1.169 2014/12/22 23:08:31 brouard
400: Summary: 0.98p
401:
402: Outputs some informations on compiler used, OS etc. Testing on different platforms.
403:
1.169 brouard 404: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 405: Summary: update
1.169 brouard 406:
1.168 brouard 407: Revision 1.167 2014/12/22 13:50:56 brouard
408: Summary: Testing uname and compiler version and if compiled 32 or 64
409:
410: Testing on Linux 64
411:
1.167 brouard 412: Revision 1.166 2014/12/22 11:40:47 brouard
413: *** empty log message ***
414:
1.166 brouard 415: Revision 1.165 2014/12/16 11:20:36 brouard
416: Summary: After compiling on Visual C
417:
418: * imach.c (Module): Merging 1.61 to 1.162
419:
1.165 brouard 420: Revision 1.164 2014/12/16 10:52:11 brouard
421: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
422:
423: * imach.c (Module): Merging 1.61 to 1.162
424:
1.164 brouard 425: Revision 1.163 2014/12/16 10:30:11 brouard
426: * imach.c (Module): Merging 1.61 to 1.162
427:
1.163 brouard 428: Revision 1.162 2014/09/25 11:43:39 brouard
429: Summary: temporary backup 0.99!
430:
1.162 brouard 431: Revision 1.1 2014/09/16 11:06:58 brouard
432: Summary: With some code (wrong) for nlopt
433:
434: Author:
435:
436: Revision 1.161 2014/09/15 20:41:41 brouard
437: Summary: Problem with macro SQR on Intel compiler
438:
1.161 brouard 439: Revision 1.160 2014/09/02 09:24:05 brouard
440: *** empty log message ***
441:
1.160 brouard 442: Revision 1.159 2014/09/01 10:34:10 brouard
443: Summary: WIN32
444: Author: Brouard
445:
1.159 brouard 446: Revision 1.158 2014/08/27 17:11:51 brouard
447: *** empty log message ***
448:
1.158 brouard 449: Revision 1.157 2014/08/27 16:26:55 brouard
450: Summary: Preparing windows Visual studio version
451: Author: Brouard
452:
453: In order to compile on Visual studio, time.h is now correct and time_t
454: and tm struct should be used. difftime should be used but sometimes I
455: just make the differences in raw time format (time(&now).
456: Trying to suppress #ifdef LINUX
457: Add xdg-open for __linux in order to open default browser.
458:
1.157 brouard 459: Revision 1.156 2014/08/25 20:10:10 brouard
460: *** empty log message ***
461:
1.156 brouard 462: Revision 1.155 2014/08/25 18:32:34 brouard
463: Summary: New compile, minor changes
464: Author: Brouard
465:
1.155 brouard 466: Revision 1.154 2014/06/20 17:32:08 brouard
467: Summary: Outputs now all graphs of convergence to period prevalence
468:
1.154 brouard 469: Revision 1.153 2014/06/20 16:45:46 brouard
470: Summary: If 3 live state, convergence to period prevalence on same graph
471: Author: Brouard
472:
1.153 brouard 473: Revision 1.152 2014/06/18 17:54:09 brouard
474: Summary: open browser, use gnuplot on same dir than imach if not found in the path
475:
1.152 brouard 476: Revision 1.151 2014/06/18 16:43:30 brouard
477: *** empty log message ***
478:
1.151 brouard 479: Revision 1.150 2014/06/18 16:42:35 brouard
480: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
481: Author: brouard
482:
1.150 brouard 483: Revision 1.149 2014/06/18 15:51:14 brouard
484: Summary: Some fixes in parameter files errors
485: Author: Nicolas Brouard
486:
1.149 brouard 487: Revision 1.148 2014/06/17 17:38:48 brouard
488: Summary: Nothing new
489: Author: Brouard
490:
491: Just a new packaging for OS/X version 0.98nS
492:
1.148 brouard 493: Revision 1.147 2014/06/16 10:33:11 brouard
494: *** empty log message ***
495:
1.147 brouard 496: Revision 1.146 2014/06/16 10:20:28 brouard
497: Summary: Merge
498: Author: Brouard
499:
500: Merge, before building revised version.
501:
1.146 brouard 502: Revision 1.145 2014/06/10 21:23:15 brouard
503: Summary: Debugging with valgrind
504: Author: Nicolas Brouard
505:
506: Lot of changes in order to output the results with some covariates
507: After the Edimburgh REVES conference 2014, it seems mandatory to
508: improve the code.
509: No more memory valgrind error but a lot has to be done in order to
510: continue the work of splitting the code into subroutines.
511: Also, decodemodel has been improved. Tricode is still not
512: optimal. nbcode should be improved. Documentation has been added in
513: the source code.
514:
1.144 brouard 515: Revision 1.143 2014/01/26 09:45:38 brouard
516: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
517:
518: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
519: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
520:
1.143 brouard 521: Revision 1.142 2014/01/26 03:57:36 brouard
522: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
523:
524: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
525:
1.142 brouard 526: Revision 1.141 2014/01/26 02:42:01 brouard
527: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
528:
1.141 brouard 529: Revision 1.140 2011/09/02 10:37:54 brouard
530: Summary: times.h is ok with mingw32 now.
531:
1.140 brouard 532: Revision 1.139 2010/06/14 07:50:17 brouard
533: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
534: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
535:
1.139 brouard 536: Revision 1.138 2010/04/30 18:19:40 brouard
537: *** empty log message ***
538:
1.138 brouard 539: Revision 1.137 2010/04/29 18:11:38 brouard
540: (Module): Checking covariates for more complex models
541: than V1+V2. A lot of change to be done. Unstable.
542:
1.137 brouard 543: Revision 1.136 2010/04/26 20:30:53 brouard
544: (Module): merging some libgsl code. Fixing computation
545: of likelione (using inter/intrapolation if mle = 0) in order to
546: get same likelihood as if mle=1.
547: Some cleaning of code and comments added.
548:
1.136 brouard 549: Revision 1.135 2009/10/29 15:33:14 brouard
550: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
551:
1.135 brouard 552: Revision 1.134 2009/10/29 13:18:53 brouard
553: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
554:
1.134 brouard 555: Revision 1.133 2009/07/06 10:21:25 brouard
556: just nforces
557:
1.133 brouard 558: Revision 1.132 2009/07/06 08:22:05 brouard
559: Many tings
560:
1.132 brouard 561: Revision 1.131 2009/06/20 16:22:47 brouard
562: Some dimensions resccaled
563:
1.131 brouard 564: Revision 1.130 2009/05/26 06:44:34 brouard
565: (Module): Max Covariate is now set to 20 instead of 8. A
566: lot of cleaning with variables initialized to 0. Trying to make
567: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
568:
1.130 brouard 569: Revision 1.129 2007/08/31 13:49:27 lievre
570: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
571:
1.129 lievre 572: Revision 1.128 2006/06/30 13:02:05 brouard
573: (Module): Clarifications on computing e.j
574:
1.128 brouard 575: Revision 1.127 2006/04/28 18:11:50 brouard
576: (Module): Yes the sum of survivors was wrong since
577: imach-114 because nhstepm was no more computed in the age
578: loop. Now we define nhstepma in the age loop.
579: (Module): In order to speed up (in case of numerous covariates) we
580: compute health expectancies (without variances) in a first step
581: and then all the health expectancies with variances or standard
582: deviation (needs data from the Hessian matrices) which slows the
583: computation.
584: In the future we should be able to stop the program is only health
585: expectancies and graph are needed without standard deviations.
586:
1.127 brouard 587: Revision 1.126 2006/04/28 17:23:28 brouard
588: (Module): Yes the sum of survivors was wrong since
589: imach-114 because nhstepm was no more computed in the age
590: loop. Now we define nhstepma in the age loop.
591: Version 0.98h
592:
1.126 brouard 593: Revision 1.125 2006/04/04 15:20:31 lievre
594: Errors in calculation of health expectancies. Age was not initialized.
595: Forecasting file added.
596:
597: Revision 1.124 2006/03/22 17:13:53 lievre
598: Parameters are printed with %lf instead of %f (more numbers after the comma).
599: The log-likelihood is printed in the log file
600:
601: Revision 1.123 2006/03/20 10:52:43 brouard
602: * imach.c (Module): <title> changed, corresponds to .htm file
603: name. <head> headers where missing.
604:
605: * imach.c (Module): Weights can have a decimal point as for
606: English (a comma might work with a correct LC_NUMERIC environment,
607: otherwise the weight is truncated).
608: Modification of warning when the covariates values are not 0 or
609: 1.
610: Version 0.98g
611:
612: Revision 1.122 2006/03/20 09:45:41 brouard
613: (Module): Weights can have a decimal point as for
614: English (a comma might work with a correct LC_NUMERIC environment,
615: otherwise the weight is truncated).
616: Modification of warning when the covariates values are not 0 or
617: 1.
618: Version 0.98g
619:
620: Revision 1.121 2006/03/16 17:45:01 lievre
621: * imach.c (Module): Comments concerning covariates added
622:
623: * imach.c (Module): refinements in the computation of lli if
624: status=-2 in order to have more reliable computation if stepm is
625: not 1 month. Version 0.98f
626:
627: Revision 1.120 2006/03/16 15:10:38 lievre
628: (Module): refinements in the computation of lli if
629: status=-2 in order to have more reliable computation if stepm is
630: not 1 month. Version 0.98f
631:
632: Revision 1.119 2006/03/15 17:42:26 brouard
633: (Module): Bug if status = -2, the loglikelihood was
634: computed as likelihood omitting the logarithm. Version O.98e
635:
636: Revision 1.118 2006/03/14 18:20:07 brouard
637: (Module): varevsij Comments added explaining the second
638: table of variances if popbased=1 .
639: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
640: (Module): Function pstamp added
641: (Module): Version 0.98d
642:
643: Revision 1.117 2006/03/14 17:16:22 brouard
644: (Module): varevsij Comments added explaining the second
645: table of variances if popbased=1 .
646: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
647: (Module): Function pstamp added
648: (Module): Version 0.98d
649:
650: Revision 1.116 2006/03/06 10:29:27 brouard
651: (Module): Variance-covariance wrong links and
652: varian-covariance of ej. is needed (Saito).
653:
654: Revision 1.115 2006/02/27 12:17:45 brouard
655: (Module): One freematrix added in mlikeli! 0.98c
656:
657: Revision 1.114 2006/02/26 12:57:58 brouard
658: (Module): Some improvements in processing parameter
659: filename with strsep.
660:
661: Revision 1.113 2006/02/24 14:20:24 brouard
662: (Module): Memory leaks checks with valgrind and:
663: datafile was not closed, some imatrix were not freed and on matrix
664: allocation too.
665:
666: Revision 1.112 2006/01/30 09:55:26 brouard
667: (Module): Back to gnuplot.exe instead of wgnuplot.exe
668:
669: Revision 1.111 2006/01/25 20:38:18 brouard
670: (Module): Lots of cleaning and bugs added (Gompertz)
671: (Module): Comments can be added in data file. Missing date values
672: can be a simple dot '.'.
673:
674: Revision 1.110 2006/01/25 00:51:50 brouard
675: (Module): Lots of cleaning and bugs added (Gompertz)
676:
677: Revision 1.109 2006/01/24 19:37:15 brouard
678: (Module): Comments (lines starting with a #) are allowed in data.
679:
680: Revision 1.108 2006/01/19 18:05:42 lievre
681: Gnuplot problem appeared...
682: To be fixed
683:
684: Revision 1.107 2006/01/19 16:20:37 brouard
685: Test existence of gnuplot in imach path
686:
687: Revision 1.106 2006/01/19 13:24:36 brouard
688: Some cleaning and links added in html output
689:
690: Revision 1.105 2006/01/05 20:23:19 lievre
691: *** empty log message ***
692:
693: Revision 1.104 2005/09/30 16:11:43 lievre
694: (Module): sump fixed, loop imx fixed, and simplifications.
695: (Module): If the status is missing at the last wave but we know
696: that the person is alive, then we can code his/her status as -2
697: (instead of missing=-1 in earlier versions) and his/her
698: contributions to the likelihood is 1 - Prob of dying from last
699: health status (= 1-p13= p11+p12 in the easiest case of somebody in
700: the healthy state at last known wave). Version is 0.98
701:
702: Revision 1.103 2005/09/30 15:54:49 lievre
703: (Module): sump fixed, loop imx fixed, and simplifications.
704:
705: Revision 1.102 2004/09/15 17:31:30 brouard
706: Add the possibility to read data file including tab characters.
707:
708: Revision 1.101 2004/09/15 10:38:38 brouard
709: Fix on curr_time
710:
711: Revision 1.100 2004/07/12 18:29:06 brouard
712: Add version for Mac OS X. Just define UNIX in Makefile
713:
714: Revision 1.99 2004/06/05 08:57:40 brouard
715: *** empty log message ***
716:
717: Revision 1.98 2004/05/16 15:05:56 brouard
718: New version 0.97 . First attempt to estimate force of mortality
719: directly from the data i.e. without the need of knowing the health
720: state at each age, but using a Gompertz model: log u =a + b*age .
721: This is the basic analysis of mortality and should be done before any
722: other analysis, in order to test if the mortality estimated from the
723: cross-longitudinal survey is different from the mortality estimated
724: from other sources like vital statistic data.
725:
726: The same imach parameter file can be used but the option for mle should be -3.
727:
1.133 brouard 728: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 729: former routines in order to include the new code within the former code.
730:
731: The output is very simple: only an estimate of the intercept and of
732: the slope with 95% confident intervals.
733:
734: Current limitations:
735: A) Even if you enter covariates, i.e. with the
736: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
737: B) There is no computation of Life Expectancy nor Life Table.
738:
739: Revision 1.97 2004/02/20 13:25:42 lievre
740: Version 0.96d. Population forecasting command line is (temporarily)
741: suppressed.
742:
743: Revision 1.96 2003/07/15 15:38:55 brouard
744: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
745: rewritten within the same printf. Workaround: many printfs.
746:
747: Revision 1.95 2003/07/08 07:54:34 brouard
748: * imach.c (Repository):
749: (Repository): Using imachwizard code to output a more meaningful covariance
750: matrix (cov(a12,c31) instead of numbers.
751:
752: Revision 1.94 2003/06/27 13:00:02 brouard
753: Just cleaning
754:
755: Revision 1.93 2003/06/25 16:33:55 brouard
756: (Module): On windows (cygwin) function asctime_r doesn't
757: exist so I changed back to asctime which exists.
758: (Module): Version 0.96b
759:
760: Revision 1.92 2003/06/25 16:30:45 brouard
761: (Module): On windows (cygwin) function asctime_r doesn't
762: exist so I changed back to asctime which exists.
763:
764: Revision 1.91 2003/06/25 15:30:29 brouard
765: * imach.c (Repository): Duplicated warning errors corrected.
766: (Repository): Elapsed time after each iteration is now output. It
767: helps to forecast when convergence will be reached. Elapsed time
768: is stamped in powell. We created a new html file for the graphs
769: concerning matrix of covariance. It has extension -cov.htm.
770:
771: Revision 1.90 2003/06/24 12:34:15 brouard
772: (Module): Some bugs corrected for windows. Also, when
773: mle=-1 a template is output in file "or"mypar.txt with the design
774: of the covariance matrix to be input.
775:
776: Revision 1.89 2003/06/24 12:30:52 brouard
777: (Module): Some bugs corrected for windows. Also, when
778: mle=-1 a template is output in file "or"mypar.txt with the design
779: of the covariance matrix to be input.
780:
781: Revision 1.88 2003/06/23 17:54:56 brouard
782: * 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.
783:
784: Revision 1.87 2003/06/18 12:26:01 brouard
785: Version 0.96
786:
787: Revision 1.86 2003/06/17 20:04:08 brouard
788: (Module): Change position of html and gnuplot routines and added
789: routine fileappend.
790:
791: Revision 1.85 2003/06/17 13:12:43 brouard
792: * imach.c (Repository): Check when date of death was earlier that
793: current date of interview. It may happen when the death was just
794: prior to the death. In this case, dh was negative and likelihood
795: was wrong (infinity). We still send an "Error" but patch by
796: assuming that the date of death was just one stepm after the
797: interview.
798: (Repository): Because some people have very long ID (first column)
799: we changed int to long in num[] and we added a new lvector for
800: memory allocation. But we also truncated to 8 characters (left
801: truncation)
802: (Repository): No more line truncation errors.
803:
804: Revision 1.84 2003/06/13 21:44:43 brouard
805: * imach.c (Repository): Replace "freqsummary" at a correct
806: place. It differs from routine "prevalence" which may be called
807: many times. Probs is memory consuming and must be used with
808: parcimony.
809: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
810:
811: Revision 1.83 2003/06/10 13:39:11 lievre
812: *** empty log message ***
813:
814: Revision 1.82 2003/06/05 15:57:20 brouard
815: Add log in imach.c and fullversion number is now printed.
816:
817: */
818: /*
819: Interpolated Markov Chain
820:
821: Short summary of the programme:
822:
1.227 brouard 823: This program computes Healthy Life Expectancies or State-specific
824: (if states aren't health statuses) Expectancies from
825: cross-longitudinal data. Cross-longitudinal data consist in:
826:
827: -1- a first survey ("cross") where individuals from different ages
828: are interviewed on their health status or degree of disability (in
829: the case of a health survey which is our main interest)
830:
831: -2- at least a second wave of interviews ("longitudinal") which
832: measure each change (if any) in individual health status. Health
833: expectancies are computed from the time spent in each health state
834: according to a model. More health states you consider, more time is
835: necessary to reach the Maximum Likelihood of the parameters involved
836: in the model. The simplest model is the multinomial logistic model
837: where pij is the probability to be observed in state j at the second
838: wave conditional to be observed in state i at the first
839: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
840: etc , where 'age' is age and 'sex' is a covariate. If you want to
841: have a more complex model than "constant and age", you should modify
842: the program where the markup *Covariates have to be included here
843: again* invites you to do it. More covariates you add, slower the
1.126 brouard 844: convergence.
845:
846: The advantage of this computer programme, compared to a simple
847: multinomial logistic model, is clear when the delay between waves is not
848: identical for each individual. Also, if a individual missed an
849: intermediate interview, the information is lost, but taken into
850: account using an interpolation or extrapolation.
851:
852: hPijx is the probability to be observed in state i at age x+h
853: conditional to the observed state i at age x. The delay 'h' can be
854: split into an exact number (nh*stepm) of unobserved intermediate
855: states. This elementary transition (by month, quarter,
856: semester or year) is modelled as a multinomial logistic. The hPx
857: matrix is simply the matrix product of nh*stepm elementary matrices
858: and the contribution of each individual to the likelihood is simply
859: hPijx.
860:
861: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 862: of the life expectancies. It also computes the period (stable) prevalence.
863:
864: Back prevalence and projections:
1.227 brouard 865:
866: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
867: double agemaxpar, double ftolpl, int *ncvyearp, double
868: dateprev1,double dateprev2, int firstpass, int lastpass, int
869: mobilavproj)
870:
871: Computes the back prevalence limit for any combination of
872: covariate values k at any age between ageminpar and agemaxpar and
873: returns it in **bprlim. In the loops,
874:
875: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
876: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
877:
878: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 879: Computes for any combination of covariates k and any age between bage and fage
880: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
881: oldm=oldms;savm=savms;
1.227 brouard 882:
1.267 brouard 883: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 884: Computes the transition matrix starting at age 'age' over
885: 'nhstepm*hstepm*stepm' months (i.e. until
886: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 887: nhstepm*hstepm matrices.
888:
889: Returns p3mat[i][j][h] after calling
890: p3mat[i][j][h]=matprod2(newm,
891: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
892: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
893: oldm);
1.226 brouard 894:
895: Important routines
896:
897: - func (or funcone), computes logit (pij) distinguishing
898: o fixed variables (single or product dummies or quantitative);
899: o varying variables by:
900: (1) wave (single, product dummies, quantitative),
901: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
902: % fixed dummy (treated) or quantitative (not done because time-consuming);
903: % varying dummy (not done) or quantitative (not done);
904: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
905: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
906: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
907: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
908: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 909:
1.226 brouard 910:
911:
1.133 brouard 912: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
913: Institut national d'études démographiques, Paris.
1.126 brouard 914: This software have been partly granted by Euro-REVES, a concerted action
915: from the European Union.
916: It is copyrighted identically to a GNU software product, ie programme and
917: software can be distributed freely for non commercial use. Latest version
918: can be accessed at http://euroreves.ined.fr/imach .
919:
920: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
921: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
922:
923: **********************************************************************/
924: /*
925: main
926: read parameterfile
927: read datafile
928: concatwav
929: freqsummary
930: if (mle >= 1)
931: mlikeli
932: print results files
933: if mle==1
934: computes hessian
935: read end of parameter file: agemin, agemax, bage, fage, estepm
936: begin-prev-date,...
937: open gnuplot file
938: open html file
1.145 brouard 939: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
940: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
941: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
942: freexexit2 possible for memory heap.
943:
944: h Pij x | pij_nom ficrestpij
945: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
946: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
947: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
948:
949: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
950: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
951: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
952: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
953: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
954:
1.126 brouard 955: forecasting if prevfcast==1 prevforecast call prevalence()
956: health expectancies
957: Variance-covariance of DFLE
958: prevalence()
959: movingaverage()
960: varevsij()
961: if popbased==1 varevsij(,popbased)
962: total life expectancies
963: Variance of period (stable) prevalence
964: end
965: */
966:
1.187 brouard 967: /* #define DEBUG */
968: /* #define DEBUGBRENT */
1.203 brouard 969: /* #define DEBUGLINMIN */
970: /* #define DEBUGHESS */
971: #define DEBUGHESSIJ
1.224 brouard 972: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 973: #define POWELL /* Instead of NLOPT */
1.224 brouard 974: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 975: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
976: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 977:
978: #include <math.h>
979: #include <stdio.h>
980: #include <stdlib.h>
981: #include <string.h>
1.226 brouard 982: #include <ctype.h>
1.159 brouard 983:
984: #ifdef _WIN32
985: #include <io.h>
1.172 brouard 986: #include <windows.h>
987: #include <tchar.h>
1.159 brouard 988: #else
1.126 brouard 989: #include <unistd.h>
1.159 brouard 990: #endif
1.126 brouard 991:
992: #include <limits.h>
993: #include <sys/types.h>
1.171 brouard 994:
995: #if defined(__GNUC__)
996: #include <sys/utsname.h> /* Doesn't work on Windows */
997: #endif
998:
1.126 brouard 999: #include <sys/stat.h>
1000: #include <errno.h>
1.159 brouard 1001: /* extern int errno; */
1.126 brouard 1002:
1.157 brouard 1003: /* #ifdef LINUX */
1004: /* #include <time.h> */
1005: /* #include "timeval.h" */
1006: /* #else */
1007: /* #include <sys/time.h> */
1008: /* #endif */
1009:
1.126 brouard 1010: #include <time.h>
1011:
1.136 brouard 1012: #ifdef GSL
1013: #include <gsl/gsl_errno.h>
1014: #include <gsl/gsl_multimin.h>
1015: #endif
1016:
1.167 brouard 1017:
1.162 brouard 1018: #ifdef NLOPT
1019: #include <nlopt.h>
1020: typedef struct {
1021: double (* function)(double [] );
1022: } myfunc_data ;
1023: #endif
1024:
1.126 brouard 1025: /* #include <libintl.h> */
1026: /* #define _(String) gettext (String) */
1027:
1.251 brouard 1028: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1029:
1030: #define GNUPLOTPROGRAM "gnuplot"
1031: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1032: #define FILENAMELENGTH 132
1033:
1034: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1035: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1036:
1.144 brouard 1037: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1038: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1039:
1040: #define NINTERVMAX 8
1.144 brouard 1041: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1042: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1043: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1044: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1045: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1046: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 1047: #define MAXN 20000
1.144 brouard 1048: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1049: /* #define AGESUP 130 */
1050: #define AGESUP 150
1.268 brouard 1051: #define AGEINF 0
1.218 brouard 1052: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1053: #define AGEBASE 40
1.194 brouard 1054: #define AGEOVERFLOW 1.e20
1.164 brouard 1055: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1056: #ifdef _WIN32
1057: #define DIRSEPARATOR '\\'
1058: #define CHARSEPARATOR "\\"
1059: #define ODIRSEPARATOR '/'
1060: #else
1.126 brouard 1061: #define DIRSEPARATOR '/'
1062: #define CHARSEPARATOR "/"
1063: #define ODIRSEPARATOR '\\'
1064: #endif
1065:
1.287 ! brouard 1066: /* $Id: imach.c,v 1.286 2018/04/27 14:27:04 brouard Exp $ */
1.126 brouard 1067: /* $State: Exp $ */
1.196 brouard 1068: #include "version.h"
1069: char version[]=__IMACH_VERSION__;
1.283 brouard 1070: char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.287 ! brouard 1071: char fullversion[]="$Revision: 1.286 $ $Date: 2018/04/27 14:27:04 $";
1.126 brouard 1072: char strstart[80];
1073: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1074: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1075: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1076: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1077: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1078: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1079: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1080: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1081: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1082: int cptcovprodnoage=0; /**< Number of covariate products without age */
1083: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1084: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1085: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1086: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1087: int nsd=0; /**< Total number of single dummy variables (output) */
1088: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1089: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1090: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1091: int ntveff=0; /**< ntveff number of effective time varying variables */
1092: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1093: int cptcov=0; /* Working variable */
1.218 brouard 1094: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 1095: int npar=NPARMAX;
1096: int nlstate=2; /* Number of live states */
1097: int ndeath=1; /* Number of dead states */
1.130 brouard 1098: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1099: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1100: int popbased=0;
1101:
1102: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1103: int maxwav=0; /* Maxim number of waves */
1104: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1105: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1106: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1107: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1108: int mle=1, weightopt=0;
1.126 brouard 1109: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1110: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1111: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1112: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1113: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1114: int selected(int kvar); /* Is covariate kvar selected for printing results */
1115:
1.130 brouard 1116: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1117: double **matprod2(); /* test */
1.126 brouard 1118: double **oldm, **newm, **savm; /* Working pointers to matrices */
1119: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1120: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1121:
1.136 brouard 1122: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1123: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1124: FILE *ficlog, *ficrespow;
1.130 brouard 1125: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1126: double fretone; /* Only one call to likelihood */
1.130 brouard 1127: long ipmx=0; /* Number of contributions */
1.126 brouard 1128: double sw; /* Sum of weights */
1129: char filerespow[FILENAMELENGTH];
1130: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1131: FILE *ficresilk;
1132: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1133: FILE *ficresprobmorprev;
1134: FILE *fichtm, *fichtmcov; /* Html File */
1135: FILE *ficreseij;
1136: char filerese[FILENAMELENGTH];
1137: FILE *ficresstdeij;
1138: char fileresstde[FILENAMELENGTH];
1139: FILE *ficrescveij;
1140: char filerescve[FILENAMELENGTH];
1141: FILE *ficresvij;
1142: char fileresv[FILENAMELENGTH];
1.269 brouard 1143:
1.126 brouard 1144: char title[MAXLINE];
1.234 brouard 1145: char model[MAXLINE]; /**< The model line */
1.217 brouard 1146: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1147: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1148: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1149: char command[FILENAMELENGTH];
1150: int outcmd=0;
1151:
1.217 brouard 1152: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1153: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1154: char filelog[FILENAMELENGTH]; /* Log file */
1155: char filerest[FILENAMELENGTH];
1156: char fileregp[FILENAMELENGTH];
1157: char popfile[FILENAMELENGTH];
1158:
1159: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1160:
1.157 brouard 1161: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1162: /* struct timezone tzp; */
1163: /* extern int gettimeofday(); */
1164: struct tm tml, *gmtime(), *localtime();
1165:
1166: extern time_t time();
1167:
1168: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1169: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1170: struct tm tm;
1171:
1.126 brouard 1172: char strcurr[80], strfor[80];
1173:
1174: char *endptr;
1175: long lval;
1176: double dval;
1177:
1178: #define NR_END 1
1179: #define FREE_ARG char*
1180: #define FTOL 1.0e-10
1181:
1182: #define NRANSI
1.240 brouard 1183: #define ITMAX 200
1184: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1185:
1186: #define TOL 2.0e-4
1187:
1188: #define CGOLD 0.3819660
1189: #define ZEPS 1.0e-10
1190: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1191:
1192: #define GOLD 1.618034
1193: #define GLIMIT 100.0
1194: #define TINY 1.0e-20
1195:
1196: static double maxarg1,maxarg2;
1197: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1198: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1199:
1200: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1201: #define rint(a) floor(a+0.5)
1.166 brouard 1202: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1203: #define mytinydouble 1.0e-16
1.166 brouard 1204: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1205: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1206: /* static double dsqrarg; */
1207: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1208: static double sqrarg;
1209: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1210: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1211: int agegomp= AGEGOMP;
1212:
1213: int imx;
1214: int stepm=1;
1215: /* Stepm, step in month: minimum step interpolation*/
1216:
1217: int estepm;
1218: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1219:
1220: int m,nb;
1221: long *num;
1.197 brouard 1222: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1223: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1224: covariate for which somebody answered excluding
1225: undefined. Usually 2: 0 and 1. */
1226: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1227: covariate for which somebody answered including
1228: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1229: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1230: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1231: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1232: double *ageexmed,*agecens;
1233: double dateintmean=0;
1234:
1235: double *weight;
1236: int **s; /* Status */
1.141 brouard 1237: double *agedc;
1.145 brouard 1238: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1239: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1240: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1241: double **coqvar; /* Fixed quantitative covariate nqv */
1242: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1243: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1244: double idx;
1245: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1246: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1247: /*k 1 2 3 4 5 6 7 8 9 */
1248: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1249: /* Tndvar[k] 1 2 3 4 5 */
1250: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1251: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1252: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1253: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1254: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1255: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1256: /* Tprod[i]=k 4 7 */
1257: /* Tage[i]=k 5 8 */
1258: /* */
1259: /* Type */
1260: /* V 1 2 3 4 5 */
1261: /* F F V V V */
1262: /* D Q D D Q */
1263: /* */
1264: int *TvarsD;
1265: int *TvarsDind;
1266: int *TvarsQ;
1267: int *TvarsQind;
1268:
1.235 brouard 1269: #define MAXRESULTLINES 10
1270: int nresult=0;
1.258 brouard 1271: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1272: int TKresult[MAXRESULTLINES];
1.237 brouard 1273: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1274: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1275: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1276: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1277: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1278: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1279:
1.234 brouard 1280: /* 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 1281: 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 */
1282: 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 */
1283: 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 */
1284: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1285: 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 */
1286: 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 1287: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1288: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1289: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1290: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1291: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1292: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1293: 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 */
1294: 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 */
1295:
1.230 brouard 1296: int *Tvarsel; /**< Selected covariates for output */
1297: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1298: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1299: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1300: 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 1301: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1302: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1303: int *Tage;
1.227 brouard 1304: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1305: 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 1306: 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*/
1307: 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 1308: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1309: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1310: int **Tvard;
1311: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1312: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1313: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1314: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1315: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1316: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1317: double *lsurv, *lpop, *tpop;
1318:
1.231 brouard 1319: #define FD 1; /* Fixed dummy covariate */
1320: #define FQ 2; /* Fixed quantitative covariate */
1321: #define FP 3; /* Fixed product covariate */
1322: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1323: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1324: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1325: #define VD 10; /* Varying dummy covariate */
1326: #define VQ 11; /* Varying quantitative covariate */
1327: #define VP 12; /* Varying product covariate */
1328: #define VPDD 13; /* Varying product dummy*dummy covariate */
1329: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1330: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1331: #define APFD 16; /* Age product * fixed dummy covariate */
1332: #define APFQ 17; /* Age product * fixed quantitative covariate */
1333: #define APVD 18; /* Age product * varying dummy covariate */
1334: #define APVQ 19; /* Age product * varying quantitative covariate */
1335:
1336: #define FTYPE 1; /* Fixed covariate */
1337: #define VTYPE 2; /* Varying covariate (loop in wave) */
1338: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1339:
1340: struct kmodel{
1341: int maintype; /* main type */
1342: int subtype; /* subtype */
1343: };
1344: struct kmodel modell[NCOVMAX];
1345:
1.143 brouard 1346: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1347: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1348:
1349: /**************** split *************************/
1350: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1351: {
1352: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1353: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1354: */
1355: char *ss; /* pointer */
1.186 brouard 1356: int l1=0, l2=0; /* length counters */
1.126 brouard 1357:
1358: l1 = strlen(path ); /* length of path */
1359: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1360: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1361: if ( ss == NULL ) { /* no directory, so determine current directory */
1362: strcpy( name, path ); /* we got the fullname name because no directory */
1363: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1364: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1365: /* get current working directory */
1366: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1367: #ifdef WIN32
1368: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1369: #else
1370: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1371: #endif
1.126 brouard 1372: return( GLOCK_ERROR_GETCWD );
1373: }
1374: /* got dirc from getcwd*/
1375: printf(" DIRC = %s \n",dirc);
1.205 brouard 1376: } else { /* strip directory from path */
1.126 brouard 1377: ss++; /* after this, the filename */
1378: l2 = strlen( ss ); /* length of filename */
1379: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1380: strcpy( name, ss ); /* save file name */
1381: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1382: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1383: printf(" DIRC2 = %s \n",dirc);
1384: }
1385: /* We add a separator at the end of dirc if not exists */
1386: l1 = strlen( dirc ); /* length of directory */
1387: if( dirc[l1-1] != DIRSEPARATOR ){
1388: dirc[l1] = DIRSEPARATOR;
1389: dirc[l1+1] = 0;
1390: printf(" DIRC3 = %s \n",dirc);
1391: }
1392: ss = strrchr( name, '.' ); /* find last / */
1393: if (ss >0){
1394: ss++;
1395: strcpy(ext,ss); /* save extension */
1396: l1= strlen( name);
1397: l2= strlen(ss)+1;
1398: strncpy( finame, name, l1-l2);
1399: finame[l1-l2]= 0;
1400: }
1401:
1402: return( 0 ); /* we're done */
1403: }
1404:
1405:
1406: /******************************************/
1407:
1408: void replace_back_to_slash(char *s, char*t)
1409: {
1410: int i;
1411: int lg=0;
1412: i=0;
1413: lg=strlen(t);
1414: for(i=0; i<= lg; i++) {
1415: (s[i] = t[i]);
1416: if (t[i]== '\\') s[i]='/';
1417: }
1418: }
1419:
1.132 brouard 1420: char *trimbb(char *out, char *in)
1.137 brouard 1421: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1422: char *s;
1423: s=out;
1424: while (*in != '\0'){
1.137 brouard 1425: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1426: in++;
1427: }
1428: *out++ = *in++;
1429: }
1430: *out='\0';
1431: return s;
1432: }
1433:
1.187 brouard 1434: /* char *substrchaine(char *out, char *in, char *chain) */
1435: /* { */
1436: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1437: /* char *s, *t; */
1438: /* t=in;s=out; */
1439: /* while ((*in != *chain) && (*in != '\0')){ */
1440: /* *out++ = *in++; */
1441: /* } */
1442:
1443: /* /\* *in matches *chain *\/ */
1444: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1445: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1446: /* } */
1447: /* in--; chain--; */
1448: /* while ( (*in != '\0')){ */
1449: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1450: /* *out++ = *in++; */
1451: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1452: /* } */
1453: /* *out='\0'; */
1454: /* out=s; */
1455: /* return out; */
1456: /* } */
1457: char *substrchaine(char *out, char *in, char *chain)
1458: {
1459: /* Substract chain 'chain' from 'in', return and output 'out' */
1460: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1461:
1462: char *strloc;
1463:
1464: strcpy (out, in);
1465: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1466: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1467: if(strloc != NULL){
1468: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1469: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1470: /* strcpy (strloc, strloc +strlen(chain));*/
1471: }
1472: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1473: return out;
1474: }
1475:
1476:
1.145 brouard 1477: char *cutl(char *blocc, char *alocc, char *in, char occ)
1478: {
1.187 brouard 1479: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1480: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1481: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1482: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1483: */
1.160 brouard 1484: char *s, *t;
1.145 brouard 1485: t=in;s=in;
1486: while ((*in != occ) && (*in != '\0')){
1487: *alocc++ = *in++;
1488: }
1489: if( *in == occ){
1490: *(alocc)='\0';
1491: s=++in;
1492: }
1493:
1494: if (s == t) {/* occ not found */
1495: *(alocc-(in-s))='\0';
1496: in=s;
1497: }
1498: while ( *in != '\0'){
1499: *blocc++ = *in++;
1500: }
1501:
1502: *blocc='\0';
1503: return t;
1504: }
1.137 brouard 1505: char *cutv(char *blocc, char *alocc, char *in, char occ)
1506: {
1.187 brouard 1507: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1508: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1509: gives blocc="abcdef2ghi" and alocc="j".
1510: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1511: */
1512: char *s, *t;
1513: t=in;s=in;
1514: while (*in != '\0'){
1515: while( *in == occ){
1516: *blocc++ = *in++;
1517: s=in;
1518: }
1519: *blocc++ = *in++;
1520: }
1521: if (s == t) /* occ not found */
1522: *(blocc-(in-s))='\0';
1523: else
1524: *(blocc-(in-s)-1)='\0';
1525: in=s;
1526: while ( *in != '\0'){
1527: *alocc++ = *in++;
1528: }
1529:
1530: *alocc='\0';
1531: return s;
1532: }
1533:
1.126 brouard 1534: int nbocc(char *s, char occ)
1535: {
1536: int i,j=0;
1537: int lg=20;
1538: i=0;
1539: lg=strlen(s);
1540: for(i=0; i<= lg; i++) {
1.234 brouard 1541: if (s[i] == occ ) j++;
1.126 brouard 1542: }
1543: return j;
1544: }
1545:
1.137 brouard 1546: /* void cutv(char *u,char *v, char*t, char occ) */
1547: /* { */
1548: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1549: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1550: /* gives u="abcdef2ghi" and v="j" *\/ */
1551: /* int i,lg,j,p=0; */
1552: /* i=0; */
1553: /* lg=strlen(t); */
1554: /* for(j=0; j<=lg-1; j++) { */
1555: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1556: /* } */
1.126 brouard 1557:
1.137 brouard 1558: /* for(j=0; j<p; j++) { */
1559: /* (u[j] = t[j]); */
1560: /* } */
1561: /* u[p]='\0'; */
1.126 brouard 1562:
1.137 brouard 1563: /* for(j=0; j<= lg; j++) { */
1564: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1565: /* } */
1566: /* } */
1.126 brouard 1567:
1.160 brouard 1568: #ifdef _WIN32
1569: char * strsep(char **pp, const char *delim)
1570: {
1571: char *p, *q;
1572:
1573: if ((p = *pp) == NULL)
1574: return 0;
1575: if ((q = strpbrk (p, delim)) != NULL)
1576: {
1577: *pp = q + 1;
1578: *q = '\0';
1579: }
1580: else
1581: *pp = 0;
1582: return p;
1583: }
1584: #endif
1585:
1.126 brouard 1586: /********************** nrerror ********************/
1587:
1588: void nrerror(char error_text[])
1589: {
1590: fprintf(stderr,"ERREUR ...\n");
1591: fprintf(stderr,"%s\n",error_text);
1592: exit(EXIT_FAILURE);
1593: }
1594: /*********************** vector *******************/
1595: double *vector(int nl, int nh)
1596: {
1597: double *v;
1598: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1599: if (!v) nrerror("allocation failure in vector");
1600: return v-nl+NR_END;
1601: }
1602:
1603: /************************ free vector ******************/
1604: void free_vector(double*v, int nl, int nh)
1605: {
1606: free((FREE_ARG)(v+nl-NR_END));
1607: }
1608:
1609: /************************ivector *******************************/
1610: int *ivector(long nl,long nh)
1611: {
1612: int *v;
1613: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1614: if (!v) nrerror("allocation failure in ivector");
1615: return v-nl+NR_END;
1616: }
1617:
1618: /******************free ivector **************************/
1619: void free_ivector(int *v, long nl, long nh)
1620: {
1621: free((FREE_ARG)(v+nl-NR_END));
1622: }
1623:
1624: /************************lvector *******************************/
1625: long *lvector(long nl,long nh)
1626: {
1627: long *v;
1628: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1629: if (!v) nrerror("allocation failure in ivector");
1630: return v-nl+NR_END;
1631: }
1632:
1633: /******************free lvector **************************/
1634: void free_lvector(long *v, long nl, long nh)
1635: {
1636: free((FREE_ARG)(v+nl-NR_END));
1637: }
1638:
1639: /******************* imatrix *******************************/
1640: int **imatrix(long nrl, long nrh, long ncl, long nch)
1641: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1642: {
1643: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1644: int **m;
1645:
1646: /* allocate pointers to rows */
1647: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1648: if (!m) nrerror("allocation failure 1 in matrix()");
1649: m += NR_END;
1650: m -= nrl;
1651:
1652:
1653: /* allocate rows and set pointers to them */
1654: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1655: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1656: m[nrl] += NR_END;
1657: m[nrl] -= ncl;
1658:
1659: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1660:
1661: /* return pointer to array of pointers to rows */
1662: return m;
1663: }
1664:
1665: /****************** free_imatrix *************************/
1666: void free_imatrix(m,nrl,nrh,ncl,nch)
1667: int **m;
1668: long nch,ncl,nrh,nrl;
1669: /* free an int matrix allocated by imatrix() */
1670: {
1671: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1672: free((FREE_ARG) (m+nrl-NR_END));
1673: }
1674:
1675: /******************* matrix *******************************/
1676: double **matrix(long nrl, long nrh, long ncl, long nch)
1677: {
1678: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1679: double **m;
1680:
1681: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1682: if (!m) nrerror("allocation failure 1 in matrix()");
1683: m += NR_END;
1684: m -= nrl;
1685:
1686: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1687: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1688: m[nrl] += NR_END;
1689: m[nrl] -= ncl;
1690:
1691: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1692: return m;
1.145 brouard 1693: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1694: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1695: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1696: */
1697: }
1698:
1699: /*************************free matrix ************************/
1700: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1701: {
1702: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1703: free((FREE_ARG)(m+nrl-NR_END));
1704: }
1705:
1706: /******************* ma3x *******************************/
1707: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1708: {
1709: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1710: double ***m;
1711:
1712: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1713: if (!m) nrerror("allocation failure 1 in matrix()");
1714: m += NR_END;
1715: m -= nrl;
1716:
1717: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1718: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1719: m[nrl] += NR_END;
1720: m[nrl] -= ncl;
1721:
1722: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1723:
1724: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1725: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1726: m[nrl][ncl] += NR_END;
1727: m[nrl][ncl] -= nll;
1728: for (j=ncl+1; j<=nch; j++)
1729: m[nrl][j]=m[nrl][j-1]+nlay;
1730:
1731: for (i=nrl+1; i<=nrh; i++) {
1732: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1733: for (j=ncl+1; j<=nch; j++)
1734: m[i][j]=m[i][j-1]+nlay;
1735: }
1736: return m;
1737: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1738: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1739: */
1740: }
1741:
1742: /*************************free ma3x ************************/
1743: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1744: {
1745: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1746: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1747: free((FREE_ARG)(m+nrl-NR_END));
1748: }
1749:
1750: /*************** function subdirf ***********/
1751: char *subdirf(char fileres[])
1752: {
1753: /* Caution optionfilefiname is hidden */
1754: strcpy(tmpout,optionfilefiname);
1755: strcat(tmpout,"/"); /* Add to the right */
1756: strcat(tmpout,fileres);
1757: return tmpout;
1758: }
1759:
1760: /*************** function subdirf2 ***********/
1761: char *subdirf2(char fileres[], char *preop)
1762: {
1763:
1764: /* Caution optionfilefiname is hidden */
1765: strcpy(tmpout,optionfilefiname);
1766: strcat(tmpout,"/");
1767: strcat(tmpout,preop);
1768: strcat(tmpout,fileres);
1769: return tmpout;
1770: }
1771:
1772: /*************** function subdirf3 ***********/
1773: char *subdirf3(char fileres[], char *preop, char *preop2)
1774: {
1775:
1776: /* Caution optionfilefiname is hidden */
1777: strcpy(tmpout,optionfilefiname);
1778: strcat(tmpout,"/");
1779: strcat(tmpout,preop);
1780: strcat(tmpout,preop2);
1781: strcat(tmpout,fileres);
1782: return tmpout;
1783: }
1.213 brouard 1784:
1785: /*************** function subdirfext ***********/
1786: char *subdirfext(char fileres[], char *preop, char *postop)
1787: {
1788:
1789: strcpy(tmpout,preop);
1790: strcat(tmpout,fileres);
1791: strcat(tmpout,postop);
1792: return tmpout;
1793: }
1.126 brouard 1794:
1.213 brouard 1795: /*************** function subdirfext3 ***********/
1796: char *subdirfext3(char fileres[], char *preop, char *postop)
1797: {
1798:
1799: /* Caution optionfilefiname is hidden */
1800: strcpy(tmpout,optionfilefiname);
1801: strcat(tmpout,"/");
1802: strcat(tmpout,preop);
1803: strcat(tmpout,fileres);
1804: strcat(tmpout,postop);
1805: return tmpout;
1806: }
1807:
1.162 brouard 1808: char *asc_diff_time(long time_sec, char ascdiff[])
1809: {
1810: long sec_left, days, hours, minutes;
1811: days = (time_sec) / (60*60*24);
1812: sec_left = (time_sec) % (60*60*24);
1813: hours = (sec_left) / (60*60) ;
1814: sec_left = (sec_left) %(60*60);
1815: minutes = (sec_left) /60;
1816: sec_left = (sec_left) % (60);
1817: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1818: return ascdiff;
1819: }
1820:
1.126 brouard 1821: /***************** f1dim *************************/
1822: extern int ncom;
1823: extern double *pcom,*xicom;
1824: extern double (*nrfunc)(double []);
1825:
1826: double f1dim(double x)
1827: {
1828: int j;
1829: double f;
1830: double *xt;
1831:
1832: xt=vector(1,ncom);
1833: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1834: f=(*nrfunc)(xt);
1835: free_vector(xt,1,ncom);
1836: return f;
1837: }
1838:
1839: /*****************brent *************************/
1840: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1841: {
1842: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1843: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1844: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1845: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1846: * returned function value.
1847: */
1.126 brouard 1848: int iter;
1849: double a,b,d,etemp;
1.159 brouard 1850: double fu=0,fv,fw,fx;
1.164 brouard 1851: double ftemp=0.;
1.126 brouard 1852: double p,q,r,tol1,tol2,u,v,w,x,xm;
1853: double e=0.0;
1854:
1855: a=(ax < cx ? ax : cx);
1856: b=(ax > cx ? ax : cx);
1857: x=w=v=bx;
1858: fw=fv=fx=(*f)(x);
1859: for (iter=1;iter<=ITMAX;iter++) {
1860: xm=0.5*(a+b);
1861: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1862: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1863: printf(".");fflush(stdout);
1864: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1865: #ifdef DEBUGBRENT
1.126 brouard 1866: 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);
1867: 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);
1868: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1869: #endif
1870: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1871: *xmin=x;
1872: return fx;
1873: }
1874: ftemp=fu;
1875: if (fabs(e) > tol1) {
1876: r=(x-w)*(fx-fv);
1877: q=(x-v)*(fx-fw);
1878: p=(x-v)*q-(x-w)*r;
1879: q=2.0*(q-r);
1880: if (q > 0.0) p = -p;
1881: q=fabs(q);
1882: etemp=e;
1883: e=d;
1884: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1885: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1886: else {
1.224 brouard 1887: d=p/q;
1888: u=x+d;
1889: if (u-a < tol2 || b-u < tol2)
1890: d=SIGN(tol1,xm-x);
1.126 brouard 1891: }
1892: } else {
1893: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1894: }
1895: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1896: fu=(*f)(u);
1897: if (fu <= fx) {
1898: if (u >= x) a=x; else b=x;
1899: SHFT(v,w,x,u)
1.183 brouard 1900: SHFT(fv,fw,fx,fu)
1901: } else {
1902: if (u < x) a=u; else b=u;
1903: if (fu <= fw || w == x) {
1.224 brouard 1904: v=w;
1905: w=u;
1906: fv=fw;
1907: fw=fu;
1.183 brouard 1908: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1909: v=u;
1910: fv=fu;
1.183 brouard 1911: }
1912: }
1.126 brouard 1913: }
1914: nrerror("Too many iterations in brent");
1915: *xmin=x;
1916: return fx;
1917: }
1918:
1919: /****************** mnbrak ***********************/
1920:
1921: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1922: double (*func)(double))
1.183 brouard 1923: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1924: the downhill direction (defined by the function as evaluated at the initial points) and returns
1925: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1926: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1927: */
1.126 brouard 1928: double ulim,u,r,q, dum;
1929: double fu;
1.187 brouard 1930:
1931: double scale=10.;
1932: int iterscale=0;
1933:
1934: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1935: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1936:
1937:
1938: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1939: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1940: /* *bx = *ax - (*ax - *bx)/scale; */
1941: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1942: /* } */
1943:
1.126 brouard 1944: if (*fb > *fa) {
1945: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1946: SHFT(dum,*fb,*fa,dum)
1947: }
1.126 brouard 1948: *cx=(*bx)+GOLD*(*bx-*ax);
1949: *fc=(*func)(*cx);
1.183 brouard 1950: #ifdef DEBUG
1.224 brouard 1951: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1952: 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 1953: #endif
1.224 brouard 1954: 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 1955: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1956: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1957: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1958: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1959: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1960: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1961: fu=(*func)(u);
1.163 brouard 1962: #ifdef DEBUG
1963: /* f(x)=A(x-u)**2+f(u) */
1964: double A, fparabu;
1965: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1966: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1967: 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);
1968: 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 1969: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1970: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1971: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1972: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1973: #endif
1.184 brouard 1974: #ifdef MNBRAKORIGINAL
1.183 brouard 1975: #else
1.191 brouard 1976: /* if (fu > *fc) { */
1977: /* #ifdef DEBUG */
1978: /* printf("mnbrak4 fu > fc \n"); */
1979: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1980: /* #endif */
1981: /* /\* 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 *\\/ *\/ */
1982: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1983: /* dum=u; /\* Shifting c and u *\/ */
1984: /* u = *cx; */
1985: /* *cx = dum; */
1986: /* dum = fu; */
1987: /* fu = *fc; */
1988: /* *fc =dum; */
1989: /* } else { /\* end *\/ */
1990: /* #ifdef DEBUG */
1991: /* printf("mnbrak3 fu < fc \n"); */
1992: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1993: /* #endif */
1994: /* dum=u; /\* Shifting c and u *\/ */
1995: /* u = *cx; */
1996: /* *cx = dum; */
1997: /* dum = fu; */
1998: /* fu = *fc; */
1999: /* *fc =dum; */
2000: /* } */
1.224 brouard 2001: #ifdef DEBUGMNBRAK
2002: double A, fparabu;
2003: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
2004: fparabu= *fa - A*(*ax-u)*(*ax-u);
2005: 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);
2006: 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 2007: #endif
1.191 brouard 2008: dum=u; /* Shifting c and u */
2009: u = *cx;
2010: *cx = dum;
2011: dum = fu;
2012: fu = *fc;
2013: *fc =dum;
1.183 brouard 2014: #endif
1.162 brouard 2015: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2016: #ifdef DEBUG
1.224 brouard 2017: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2018: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2019: #endif
1.126 brouard 2020: fu=(*func)(u);
2021: if (fu < *fc) {
1.183 brouard 2022: #ifdef DEBUG
1.224 brouard 2023: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2024: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2025: #endif
2026: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2027: SHFT(*fb,*fc,fu,(*func)(u))
2028: #ifdef DEBUG
2029: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2030: #endif
2031: }
1.162 brouard 2032: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2033: #ifdef DEBUG
1.224 brouard 2034: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2035: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2036: #endif
1.126 brouard 2037: u=ulim;
2038: fu=(*func)(u);
1.183 brouard 2039: } else { /* u could be left to b (if r > q parabola has a maximum) */
2040: #ifdef DEBUG
1.224 brouard 2041: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2042: 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 2043: #endif
1.126 brouard 2044: u=(*cx)+GOLD*(*cx-*bx);
2045: fu=(*func)(u);
1.224 brouard 2046: #ifdef DEBUG
2047: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2048: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2049: #endif
1.183 brouard 2050: } /* end tests */
1.126 brouard 2051: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2052: SHFT(*fa,*fb,*fc,fu)
2053: #ifdef DEBUG
1.224 brouard 2054: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2055: 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 2056: #endif
2057: } /* 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 2058: }
2059:
2060: /*************** linmin ************************/
1.162 brouard 2061: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2062: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2063: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2064: the value of func at the returned location p . This is actually all accomplished by calling the
2065: routines mnbrak and brent .*/
1.126 brouard 2066: int ncom;
2067: double *pcom,*xicom;
2068: double (*nrfunc)(double []);
2069:
1.224 brouard 2070: #ifdef LINMINORIGINAL
1.126 brouard 2071: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2072: #else
2073: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2074: #endif
1.126 brouard 2075: {
2076: double brent(double ax, double bx, double cx,
2077: double (*f)(double), double tol, double *xmin);
2078: double f1dim(double x);
2079: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2080: double *fc, double (*func)(double));
2081: int j;
2082: double xx,xmin,bx,ax;
2083: double fx,fb,fa;
1.187 brouard 2084:
1.203 brouard 2085: #ifdef LINMINORIGINAL
2086: #else
2087: double scale=10., axs, xxs; /* Scale added for infinity */
2088: #endif
2089:
1.126 brouard 2090: ncom=n;
2091: pcom=vector(1,n);
2092: xicom=vector(1,n);
2093: nrfunc=func;
2094: for (j=1;j<=n;j++) {
2095: pcom[j]=p[j];
1.202 brouard 2096: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2097: }
1.187 brouard 2098:
1.203 brouard 2099: #ifdef LINMINORIGINAL
2100: xx=1.;
2101: #else
2102: axs=0.0;
2103: xxs=1.;
2104: do{
2105: xx= xxs;
2106: #endif
1.187 brouard 2107: ax=0.;
2108: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2109: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2110: /* 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)) */
2111: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2112: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2113: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2114: /* 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 2115: #ifdef LINMINORIGINAL
2116: #else
2117: if (fx != fx){
1.224 brouard 2118: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2119: printf("|");
2120: fprintf(ficlog,"|");
1.203 brouard 2121: #ifdef DEBUGLINMIN
1.224 brouard 2122: 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 2123: #endif
2124: }
1.224 brouard 2125: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2126: #endif
2127:
1.191 brouard 2128: #ifdef DEBUGLINMIN
2129: 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 2130: 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 2131: #endif
1.224 brouard 2132: #ifdef LINMINORIGINAL
2133: #else
2134: if(fb == fx){ /* Flat function in the direction */
2135: xmin=xx;
2136: *flat=1;
2137: }else{
2138: *flat=0;
2139: #endif
2140: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2141: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2142: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2143: /* fmin = f(p[j] + xmin * xi[j]) */
2144: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2145: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2146: #ifdef DEBUG
1.224 brouard 2147: 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);
2148: 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);
2149: #endif
2150: #ifdef LINMINORIGINAL
2151: #else
2152: }
1.126 brouard 2153: #endif
1.191 brouard 2154: #ifdef DEBUGLINMIN
2155: printf("linmin end ");
1.202 brouard 2156: fprintf(ficlog,"linmin end ");
1.191 brouard 2157: #endif
1.126 brouard 2158: for (j=1;j<=n;j++) {
1.203 brouard 2159: #ifdef LINMINORIGINAL
2160: xi[j] *= xmin;
2161: #else
2162: #ifdef DEBUGLINMIN
2163: if(xxs <1.0)
2164: printf(" before xi[%d]=%12.8f", j,xi[j]);
2165: #endif
2166: 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) */
2167: #ifdef DEBUGLINMIN
2168: if(xxs <1.0)
2169: 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 );
2170: #endif
2171: #endif
1.187 brouard 2172: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2173: }
1.191 brouard 2174: #ifdef DEBUGLINMIN
1.203 brouard 2175: printf("\n");
1.191 brouard 2176: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2177: 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 2178: for (j=1;j<=n;j++) {
1.202 brouard 2179: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2180: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2181: if(j % ncovmodel == 0){
1.191 brouard 2182: printf("\n");
1.202 brouard 2183: fprintf(ficlog,"\n");
2184: }
1.191 brouard 2185: }
1.203 brouard 2186: #else
1.191 brouard 2187: #endif
1.126 brouard 2188: free_vector(xicom,1,n);
2189: free_vector(pcom,1,n);
2190: }
2191:
2192:
2193: /*************** powell ************************/
1.162 brouard 2194: /*
2195: Minimization of a function func of n variables. Input consists of an initial starting point
2196: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2197: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2198: such that failure to decrease by more than this amount on one iteration signals doneness. On
2199: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2200: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2201: */
1.224 brouard 2202: #ifdef LINMINORIGINAL
2203: #else
2204: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2205: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2206: #endif
1.126 brouard 2207: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2208: double (*func)(double []))
2209: {
1.224 brouard 2210: #ifdef LINMINORIGINAL
2211: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2212: double (*func)(double []));
1.224 brouard 2213: #else
1.241 brouard 2214: void linmin(double p[], double xi[], int n, double *fret,
2215: double (*func)(double []),int *flat);
1.224 brouard 2216: #endif
1.239 brouard 2217: int i,ibig,j,jk,k;
1.126 brouard 2218: double del,t,*pt,*ptt,*xit;
1.181 brouard 2219: double directest;
1.126 brouard 2220: double fp,fptt;
2221: double *xits;
2222: int niterf, itmp;
1.224 brouard 2223: #ifdef LINMINORIGINAL
2224: #else
2225:
2226: flatdir=ivector(1,n);
2227: for (j=1;j<=n;j++) flatdir[j]=0;
2228: #endif
1.126 brouard 2229:
2230: pt=vector(1,n);
2231: ptt=vector(1,n);
2232: xit=vector(1,n);
2233: xits=vector(1,n);
2234: *fret=(*func)(p);
2235: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2236: rcurr_time = time(NULL);
1.126 brouard 2237: for (*iter=1;;++(*iter)) {
1.187 brouard 2238: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2239: ibig=0;
2240: del=0.0;
1.157 brouard 2241: rlast_time=rcurr_time;
2242: /* (void) gettimeofday(&curr_time,&tzp); */
2243: rcurr_time = time(NULL);
2244: curr_time = *localtime(&rcurr_time);
2245: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2246: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2247: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2248: for (i=1;i<=n;i++) {
1.126 brouard 2249: fprintf(ficrespow," %.12lf", p[i]);
2250: }
1.239 brouard 2251: fprintf(ficrespow,"\n");fflush(ficrespow);
2252: printf("\n#model= 1 + age ");
2253: fprintf(ficlog,"\n#model= 1 + age ");
2254: if(nagesqr==1){
1.241 brouard 2255: printf(" + age*age ");
2256: fprintf(ficlog," + age*age ");
1.239 brouard 2257: }
2258: for(j=1;j <=ncovmodel-2;j++){
2259: if(Typevar[j]==0) {
2260: printf(" + V%d ",Tvar[j]);
2261: fprintf(ficlog," + V%d ",Tvar[j]);
2262: }else if(Typevar[j]==1) {
2263: printf(" + V%d*age ",Tvar[j]);
2264: fprintf(ficlog," + V%d*age ",Tvar[j]);
2265: }else if(Typevar[j]==2) {
2266: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2267: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2268: }
2269: }
1.126 brouard 2270: printf("\n");
1.239 brouard 2271: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2272: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2273: fprintf(ficlog,"\n");
1.239 brouard 2274: for(i=1,jk=1; i <=nlstate; i++){
2275: for(k=1; k <=(nlstate+ndeath); k++){
2276: if (k != i) {
2277: printf("%d%d ",i,k);
2278: fprintf(ficlog,"%d%d ",i,k);
2279: for(j=1; j <=ncovmodel; j++){
2280: printf("%12.7f ",p[jk]);
2281: fprintf(ficlog,"%12.7f ",p[jk]);
2282: jk++;
2283: }
2284: printf("\n");
2285: fprintf(ficlog,"\n");
2286: }
2287: }
2288: }
1.241 brouard 2289: if(*iter <=3 && *iter >1){
1.157 brouard 2290: tml = *localtime(&rcurr_time);
2291: strcpy(strcurr,asctime(&tml));
2292: rforecast_time=rcurr_time;
1.126 brouard 2293: itmp = strlen(strcurr);
2294: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2295: strcurr[itmp-1]='\0';
1.162 brouard 2296: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2297: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2298: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2299: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2300: forecast_time = *localtime(&rforecast_time);
2301: strcpy(strfor,asctime(&forecast_time));
2302: itmp = strlen(strfor);
2303: if(strfor[itmp-1]=='\n')
2304: strfor[itmp-1]='\0';
2305: 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);
2306: 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 2307: }
2308: }
1.187 brouard 2309: for (i=1;i<=n;i++) { /* For each direction i */
2310: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2311: fptt=(*fret);
2312: #ifdef DEBUG
1.203 brouard 2313: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2314: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2315: #endif
1.203 brouard 2316: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2317: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2318: #ifdef LINMINORIGINAL
1.188 brouard 2319: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2320: #else
2321: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2322: flatdir[i]=flat; /* Function is vanishing in that direction i */
2323: #endif
2324: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2325: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2326: /* because that direction will be replaced unless the gain del is small */
2327: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2328: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2329: /* with the new direction. */
2330: del=fabs(fptt-(*fret));
2331: ibig=i;
1.126 brouard 2332: }
2333: #ifdef DEBUG
2334: printf("%d %.12e",i,(*fret));
2335: fprintf(ficlog,"%d %.12e",i,(*fret));
2336: for (j=1;j<=n;j++) {
1.224 brouard 2337: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2338: printf(" x(%d)=%.12e",j,xit[j]);
2339: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2340: }
2341: for(j=1;j<=n;j++) {
1.225 brouard 2342: printf(" p(%d)=%.12e",j,p[j]);
2343: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2344: }
2345: printf("\n");
2346: fprintf(ficlog,"\n");
2347: #endif
1.187 brouard 2348: } /* end loop on each direction i */
2349: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2350: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2351: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2352: for(j=1;j<=n;j++) {
1.225 brouard 2353: if(flatdir[j] >0){
2354: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2355: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2356: }
2357: /* printf("\n"); */
2358: /* fprintf(ficlog,"\n"); */
2359: }
1.243 brouard 2360: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2361: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2362: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2363: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2364: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2365: /* decreased of more than 3.84 */
2366: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2367: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2368: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2369:
1.188 brouard 2370: /* Starting the program with initial values given by a former maximization will simply change */
2371: /* the scales of the directions and the directions, because the are reset to canonical directions */
2372: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2373: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2374: #ifdef DEBUG
2375: int k[2],l;
2376: k[0]=1;
2377: k[1]=-1;
2378: printf("Max: %.12e",(*func)(p));
2379: fprintf(ficlog,"Max: %.12e",(*func)(p));
2380: for (j=1;j<=n;j++) {
2381: printf(" %.12e",p[j]);
2382: fprintf(ficlog," %.12e",p[j]);
2383: }
2384: printf("\n");
2385: fprintf(ficlog,"\n");
2386: for(l=0;l<=1;l++) {
2387: for (j=1;j<=n;j++) {
2388: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2389: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2390: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2391: }
2392: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2393: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2394: }
2395: #endif
2396:
1.224 brouard 2397: #ifdef LINMINORIGINAL
2398: #else
2399: free_ivector(flatdir,1,n);
2400: #endif
1.126 brouard 2401: free_vector(xit,1,n);
2402: free_vector(xits,1,n);
2403: free_vector(ptt,1,n);
2404: free_vector(pt,1,n);
2405: return;
1.192 brouard 2406: } /* enough precision */
1.240 brouard 2407: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2408: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2409: ptt[j]=2.0*p[j]-pt[j];
2410: xit[j]=p[j]-pt[j];
2411: pt[j]=p[j];
2412: }
1.181 brouard 2413: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2414: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2415: if (*iter <=4) {
1.225 brouard 2416: #else
2417: #endif
1.224 brouard 2418: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2419: #else
1.161 brouard 2420: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2421: #endif
1.162 brouard 2422: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2423: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2424: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2425: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2426: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2427: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2428: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2429: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2430: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2431: /* Even if f3 <f1, directest can be negative and t >0 */
2432: /* mu² and del² are equal when f3=f1 */
2433: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2434: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2435: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2436: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2437: #ifdef NRCORIGINAL
2438: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2439: #else
2440: 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 2441: t= t- del*SQR(fp-fptt);
1.183 brouard 2442: #endif
1.202 brouard 2443: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2444: #ifdef DEBUG
1.181 brouard 2445: 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);
2446: 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 2447: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2448: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2449: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2450: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2451: 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);
2452: 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);
2453: #endif
1.183 brouard 2454: #ifdef POWELLORIGINAL
2455: if (t < 0.0) { /* Then we use it for new direction */
2456: #else
1.182 brouard 2457: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2458: 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 2459: 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 2460: 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 2461: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2462: }
1.181 brouard 2463: if (directest < 0.0) { /* Then we use it for new direction */
2464: #endif
1.191 brouard 2465: #ifdef DEBUGLINMIN
1.234 brouard 2466: printf("Before linmin in direction P%d-P0\n",n);
2467: for (j=1;j<=n;j++) {
2468: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2469: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2470: if(j % ncovmodel == 0){
2471: printf("\n");
2472: fprintf(ficlog,"\n");
2473: }
2474: }
1.224 brouard 2475: #endif
2476: #ifdef LINMINORIGINAL
1.234 brouard 2477: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2478: #else
1.234 brouard 2479: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2480: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2481: #endif
1.234 brouard 2482:
1.191 brouard 2483: #ifdef DEBUGLINMIN
1.234 brouard 2484: for (j=1;j<=n;j++) {
2485: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2486: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2487: if(j % ncovmodel == 0){
2488: printf("\n");
2489: fprintf(ficlog,"\n");
2490: }
2491: }
1.224 brouard 2492: #endif
1.234 brouard 2493: for (j=1;j<=n;j++) {
2494: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2495: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2496: }
1.224 brouard 2497: #ifdef LINMINORIGINAL
2498: #else
1.234 brouard 2499: for (j=1, flatd=0;j<=n;j++) {
2500: if(flatdir[j]>0)
2501: flatd++;
2502: }
2503: if(flatd >0){
1.255 brouard 2504: printf("%d flat directions: ",flatd);
2505: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2506: for (j=1;j<=n;j++) {
2507: if(flatdir[j]>0){
2508: printf("%d ",j);
2509: fprintf(ficlog,"%d ",j);
2510: }
2511: }
2512: printf("\n");
2513: fprintf(ficlog,"\n");
2514: }
1.191 brouard 2515: #endif
1.234 brouard 2516: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2517: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2518:
1.126 brouard 2519: #ifdef DEBUG
1.234 brouard 2520: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2521: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2522: for(j=1;j<=n;j++){
2523: printf(" %lf",xit[j]);
2524: fprintf(ficlog," %lf",xit[j]);
2525: }
2526: printf("\n");
2527: fprintf(ficlog,"\n");
1.126 brouard 2528: #endif
1.192 brouard 2529: } /* end of t or directest negative */
1.224 brouard 2530: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2531: #else
1.234 brouard 2532: } /* end if (fptt < fp) */
1.192 brouard 2533: #endif
1.225 brouard 2534: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2535: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2536: #else
1.224 brouard 2537: #endif
1.234 brouard 2538: } /* loop iteration */
1.126 brouard 2539: }
1.234 brouard 2540:
1.126 brouard 2541: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2542:
1.235 brouard 2543: 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 2544: {
1.279 brouard 2545: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2546: * (and selected quantitative values in nres)
2547: * by left multiplying the unit
2548: * matrix by transitions matrix until convergence is reached with precision ftolpl
2549: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2550: * Wx is row vector: population in state 1, population in state 2, population dead
2551: * or prevalence in state 1, prevalence in state 2, 0
2552: * newm is the matrix after multiplications, its rows are identical at a factor.
2553: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2554: * Output is prlim.
2555: * Initial matrix pimij
2556: */
1.206 brouard 2557: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2558: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2559: /* 0, 0 , 1} */
2560: /*
2561: * and after some iteration: */
2562: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2563: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2564: /* 0, 0 , 1} */
2565: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2566: /* {0.51571254859325999, 0.4842874514067399, */
2567: /* 0.51326036147820708, 0.48673963852179264} */
2568: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2569:
1.126 brouard 2570: int i, ii,j,k;
1.209 brouard 2571: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2572: /* double **matprod2(); */ /* test */
1.218 brouard 2573: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2574: double **newm;
1.209 brouard 2575: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2576: int ncvloop=0;
1.169 brouard 2577:
1.209 brouard 2578: min=vector(1,nlstate);
2579: max=vector(1,nlstate);
2580: meandiff=vector(1,nlstate);
2581:
1.218 brouard 2582: /* Starting with matrix unity */
1.126 brouard 2583: for (ii=1;ii<=nlstate+ndeath;ii++)
2584: for (j=1;j<=nlstate+ndeath;j++){
2585: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2586: }
1.169 brouard 2587:
2588: cov[1]=1.;
2589:
2590: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2591: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2592: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2593: ncvloop++;
1.126 brouard 2594: newm=savm;
2595: /* Covariates have to be included here again */
1.138 brouard 2596: cov[2]=agefin;
1.187 brouard 2597: if(nagesqr==1)
2598: cov[3]= agefin*agefin;;
1.234 brouard 2599: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2600: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2601: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2602: /* 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 2603: }
2604: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2605: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2606: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2607: /* 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 2608: }
1.237 brouard 2609: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2610: if(Dummy[Tvar[Tage[k]]]){
2611: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2612: } else{
1.235 brouard 2613: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2614: }
1.235 brouard 2615: /* 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 2616: }
1.237 brouard 2617: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2618: /* 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 2619: if(Dummy[Tvard[k][1]==0]){
2620: if(Dummy[Tvard[k][2]==0]){
2621: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2622: }else{
2623: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2624: }
2625: }else{
2626: if(Dummy[Tvard[k][2]==0]){
2627: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2628: }else{
2629: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2630: }
2631: }
1.234 brouard 2632: }
1.138 brouard 2633: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2634: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2635: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2636: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2637: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2638: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2639: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2640:
1.126 brouard 2641: savm=oldm;
2642: oldm=newm;
1.209 brouard 2643:
2644: for(j=1; j<=nlstate; j++){
2645: max[j]=0.;
2646: min[j]=1.;
2647: }
2648: for(i=1;i<=nlstate;i++){
2649: sumnew=0;
2650: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2651: for(j=1; j<=nlstate; j++){
2652: prlim[i][j]= newm[i][j]/(1-sumnew);
2653: max[j]=FMAX(max[j],prlim[i][j]);
2654: min[j]=FMIN(min[j],prlim[i][j]);
2655: }
2656: }
2657:
1.126 brouard 2658: maxmax=0.;
1.209 brouard 2659: for(j=1; j<=nlstate; j++){
2660: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2661: maxmax=FMAX(maxmax,meandiff[j]);
2662: /* 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 2663: } /* j loop */
1.203 brouard 2664: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2665: /* 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 2666: if(maxmax < ftolpl){
1.209 brouard 2667: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2668: free_vector(min,1,nlstate);
2669: free_vector(max,1,nlstate);
2670: free_vector(meandiff,1,nlstate);
1.126 brouard 2671: return prlim;
2672: }
1.169 brouard 2673: } /* age loop */
1.208 brouard 2674: /* After some age loop it doesn't converge */
1.209 brouard 2675: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208 brouard 2676: Earliest 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);
1.209 brouard 2677: /* 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); */
2678: free_vector(min,1,nlstate);
2679: free_vector(max,1,nlstate);
2680: free_vector(meandiff,1,nlstate);
1.208 brouard 2681:
1.169 brouard 2682: return prlim; /* should not reach here */
1.126 brouard 2683: }
2684:
1.217 brouard 2685:
2686: /**** Back Prevalence limit (stable or period prevalence) ****************/
2687:
1.218 brouard 2688: /* 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) */
2689: /* 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 2690: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2691: {
1.264 brouard 2692: /* 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 2693: matrix by transitions matrix until convergence is reached with precision ftolpl */
2694: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2695: /* Wx is row vector: population in state 1, population in state 2, population dead */
2696: /* or prevalence in state 1, prevalence in state 2, 0 */
2697: /* newm is the matrix after multiplications, its rows are identical at a factor */
2698: /* Initial matrix pimij */
2699: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2700: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2701: /* 0, 0 , 1} */
2702: /*
2703: * and after some iteration: */
2704: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2705: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2706: /* 0, 0 , 1} */
2707: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2708: /* {0.51571254859325999, 0.4842874514067399, */
2709: /* 0.51326036147820708, 0.48673963852179264} */
2710: /* If we start from prlim again, prlim tends to a constant matrix */
2711:
2712: int i, ii,j,k;
1.247 brouard 2713: int first=0;
1.217 brouard 2714: double *min, *max, *meandiff, maxmax,sumnew=0.;
2715: /* double **matprod2(); */ /* test */
2716: double **out, cov[NCOVMAX+1], **bmij();
2717: double **newm;
1.218 brouard 2718: double **dnewm, **doldm, **dsavm; /* for use */
2719: double **oldm, **savm; /* for use */
2720:
1.217 brouard 2721: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2722: int ncvloop=0;
2723:
2724: min=vector(1,nlstate);
2725: max=vector(1,nlstate);
2726: meandiff=vector(1,nlstate);
2727:
1.266 brouard 2728: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2729: oldm=oldms; savm=savms;
2730:
2731: /* Starting with matrix unity */
2732: for (ii=1;ii<=nlstate+ndeath;ii++)
2733: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2734: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2735: }
2736:
2737: cov[1]=1.;
2738:
2739: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2740: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2741: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2742: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2743: ncvloop++;
1.218 brouard 2744: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2745: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2746: /* Covariates have to be included here again */
2747: cov[2]=agefin;
2748: if(nagesqr==1)
2749: cov[3]= agefin*agefin;;
1.242 brouard 2750: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2751: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2752: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2753: /* 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 2754: }
2755: /* for (k=1; k<=cptcovn;k++) { */
2756: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2757: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2758: /* /\* 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])]); *\/ */
2759: /* } */
2760: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2761: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2762: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2763: /* 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]); */
2764: }
2765: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2766: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2767: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2768: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2769: for (k=1; k<=cptcovage;k++){ /* For product with age */
2770: if(Dummy[Tvar[Tage[k]]]){
2771: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2772: } else{
2773: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2774: }
2775: /* 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]); */
2776: }
2777: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2778: /* 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]); */
2779: if(Dummy[Tvard[k][1]==0]){
2780: if(Dummy[Tvard[k][2]==0]){
2781: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2782: }else{
2783: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2784: }
2785: }else{
2786: if(Dummy[Tvard[k][2]==0]){
2787: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2788: }else{
2789: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2790: }
2791: }
1.217 brouard 2792: }
2793:
2794: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2795: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2796: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2797: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2798: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2799: /* ij should be linked to the correct index of cov */
2800: /* age and covariate values ij are in 'cov', but we need to pass
2801: * ij for the observed prevalence at age and status and covariate
2802: * number: prevacurrent[(int)agefin][ii][ij]
2803: */
2804: /* 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 *\/ */
2805: /* 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 *\/ */
2806: 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 2807: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2808: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2809: /* for(i=1; i<=nlstate+ndeath; i++) { */
2810: /* printf("%d newm= ",i); */
2811: /* for(j=1;j<=nlstate+ndeath;j++) { */
2812: /* printf("%f ",newm[i][j]); */
2813: /* } */
2814: /* printf("oldm * "); */
2815: /* for(j=1;j<=nlstate+ndeath;j++) { */
2816: /* printf("%f ",oldm[i][j]); */
2817: /* } */
1.268 brouard 2818: /* printf(" bmmij "); */
1.266 brouard 2819: /* for(j=1;j<=nlstate+ndeath;j++) { */
2820: /* printf("%f ",pmmij[i][j]); */
2821: /* } */
2822: /* printf("\n"); */
2823: /* } */
2824: /* } */
1.217 brouard 2825: savm=oldm;
2826: oldm=newm;
1.266 brouard 2827:
1.217 brouard 2828: for(j=1; j<=nlstate; j++){
2829: max[j]=0.;
2830: min[j]=1.;
2831: }
2832: for(j=1; j<=nlstate; j++){
2833: for(i=1;i<=nlstate;i++){
1.234 brouard 2834: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2835: bprlim[i][j]= newm[i][j];
2836: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2837: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2838: }
2839: }
1.218 brouard 2840:
1.217 brouard 2841: maxmax=0.;
2842: for(i=1; i<=nlstate; i++){
2843: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2844: maxmax=FMAX(maxmax,meandiff[i]);
2845: /* 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 2846: } /* i loop */
1.217 brouard 2847: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2848: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2849: if(maxmax < ftolpl){
1.220 brouard 2850: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2851: free_vector(min,1,nlstate);
2852: free_vector(max,1,nlstate);
2853: free_vector(meandiff,1,nlstate);
2854: return bprlim;
2855: }
2856: } /* age loop */
2857: /* After some age loop it doesn't converge */
1.247 brouard 2858: if(first){
2859: first=1;
2860: 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\
2861: 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);
2862: }
2863: 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 2864: 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);
2865: /* 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); */
2866: free_vector(min,1,nlstate);
2867: free_vector(max,1,nlstate);
2868: free_vector(meandiff,1,nlstate);
2869:
2870: return bprlim; /* should not reach here */
2871: }
2872:
1.126 brouard 2873: /*************** transition probabilities ***************/
2874:
2875: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2876: {
1.138 brouard 2877: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2878: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2879: model to the ncovmodel covariates (including constant and age).
2880: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2881: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2882: ncth covariate in the global vector x is given by the formula:
2883: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2884: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2885: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2886: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2887: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2888: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2889: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2890: */
2891: double s1, lnpijopii;
1.126 brouard 2892: /*double t34;*/
1.164 brouard 2893: int i,j, nc, ii, jj;
1.126 brouard 2894:
1.223 brouard 2895: for(i=1; i<= nlstate; i++){
2896: for(j=1; j<i;j++){
2897: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2898: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2899: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2900: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2901: }
2902: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2903: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2904: }
2905: for(j=i+1; j<=nlstate+ndeath;j++){
2906: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2907: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2908: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2909: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2910: }
2911: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2912: }
2913: }
1.218 brouard 2914:
1.223 brouard 2915: for(i=1; i<= nlstate; i++){
2916: s1=0;
2917: for(j=1; j<i; j++){
2918: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2919: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2920: }
2921: for(j=i+1; j<=nlstate+ndeath; j++){
2922: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2923: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2924: }
2925: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2926: ps[i][i]=1./(s1+1.);
2927: /* Computing other pijs */
2928: for(j=1; j<i; j++)
2929: ps[i][j]= exp(ps[i][j])*ps[i][i];
2930: for(j=i+1; j<=nlstate+ndeath; j++)
2931: ps[i][j]= exp(ps[i][j])*ps[i][i];
2932: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2933: } /* end i */
1.218 brouard 2934:
1.223 brouard 2935: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2936: for(jj=1; jj<= nlstate+ndeath; jj++){
2937: ps[ii][jj]=0;
2938: ps[ii][ii]=1;
2939: }
2940: }
1.218 brouard 2941:
2942:
1.223 brouard 2943: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2944: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2945: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2946: /* } */
2947: /* printf("\n "); */
2948: /* } */
2949: /* printf("\n ");printf("%lf ",cov[2]);*/
2950: /*
2951: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2952: goto end;*/
1.266 brouard 2953: return ps; /* Pointer is unchanged since its call */
1.126 brouard 2954: }
2955:
1.218 brouard 2956: /*************** backward transition probabilities ***************/
2957:
2958: /* 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 ) */
2959: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2960: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2961: {
1.266 brouard 2962: /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
2963: * 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 2964: */
1.218 brouard 2965: int i, ii, j,k;
1.222 brouard 2966:
2967: double **out, **pmij();
2968: double sumnew=0.;
1.218 brouard 2969: double agefin;
1.268 brouard 2970: double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
1.222 brouard 2971: double **dnewm, **dsavm, **doldm;
2972: double **bbmij;
2973:
1.218 brouard 2974: doldm=ddoldms; /* global pointers */
1.222 brouard 2975: dnewm=ddnewms;
2976: dsavm=ddsavms;
2977:
2978: agefin=cov[2];
1.268 brouard 2979: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 2980: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 2981: the observed prevalence (with this covariate ij) at beginning of transition */
2982: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 2983:
2984: /* P_x */
1.266 brouard 2985: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 2986: /* outputs pmmij which is a stochastic matrix in row */
2987:
2988: /* Diag(w_x) */
2989: /* Problem with prevacurrent which can be zero */
2990: sumnew=0.;
1.269 brouard 2991: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 2992: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.269 brouard 2993: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 2994: sumnew+=prevacurrent[(int)agefin][ii][ij];
2995: }
2996: if(sumnew >0.01){ /* At least some value in the prevalence */
2997: for (ii=1;ii<=nlstate+ndeath;ii++){
2998: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 2999: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 3000: }
3001: }else{
3002: for (ii=1;ii<=nlstate+ndeath;ii++){
3003: for (j=1;j<=nlstate+ndeath;j++)
3004: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
3005: }
3006: /* if(sumnew <0.9){ */
3007: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
3008: /* } */
3009: }
3010: k3=0.0; /* We put the last diagonal to 0 */
3011: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3012: doldm[ii][ii]= k3;
3013: }
3014: /* End doldm, At the end doldm is diag[(w_i)] */
3015:
3016: /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
3017: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
3018:
3019: /* Diag(Sum_i w^i_x p^ij_x */
3020: /* 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 3021: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3022: sumnew=0.;
1.222 brouard 3023: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3024: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3025: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3026: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3027: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3028: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3029: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3030: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3031: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3032: /* }else */
1.268 brouard 3033: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3034: } /*End ii */
3035: } /* 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 */
3036:
3037: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
3038: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3039: /* end bmij */
1.266 brouard 3040: return ps; /*pointer is unchanged */
1.218 brouard 3041: }
1.217 brouard 3042: /*************** transition probabilities ***************/
3043:
1.218 brouard 3044: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3045: {
3046: /* According to parameters values stored in x and the covariate's values stored in cov,
3047: computes the probability to be observed in state j being in state i by appying the
3048: model to the ncovmodel covariates (including constant and age).
3049: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3050: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3051: ncth covariate in the global vector x is given by the formula:
3052: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3053: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3054: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3055: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3056: Outputs ps[i][j] the probability to be observed in j being in j according to
3057: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3058: */
3059: double s1, lnpijopii;
3060: /*double t34;*/
3061: int i,j, nc, ii, jj;
3062:
1.234 brouard 3063: for(i=1; i<= nlstate; i++){
3064: for(j=1; j<i;j++){
3065: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3066: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3067: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3068: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3069: }
3070: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3071: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3072: }
3073: for(j=i+1; j<=nlstate+ndeath;j++){
3074: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3075: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3076: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3077: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3078: }
3079: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3080: }
3081: }
3082:
3083: for(i=1; i<= nlstate; i++){
3084: s1=0;
3085: for(j=1; j<i; j++){
3086: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3087: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3088: }
3089: for(j=i+1; j<=nlstate+ndeath; j++){
3090: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3091: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3092: }
3093: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3094: ps[i][i]=1./(s1+1.);
3095: /* Computing other pijs */
3096: for(j=1; j<i; j++)
3097: ps[i][j]= exp(ps[i][j])*ps[i][i];
3098: for(j=i+1; j<=nlstate+ndeath; j++)
3099: ps[i][j]= exp(ps[i][j])*ps[i][i];
3100: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3101: } /* end i */
3102:
3103: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3104: for(jj=1; jj<= nlstate+ndeath; jj++){
3105: ps[ii][jj]=0;
3106: ps[ii][ii]=1;
3107: }
3108: }
3109: /* Added for backcast */ /* Transposed matrix too */
3110: for(jj=1; jj<= nlstate+ndeath; jj++){
3111: s1=0.;
3112: for(ii=1; ii<= nlstate+ndeath; ii++){
3113: s1+=ps[ii][jj];
3114: }
3115: for(ii=1; ii<= nlstate; ii++){
3116: ps[ii][jj]=ps[ii][jj]/s1;
3117: }
3118: }
3119: /* Transposition */
3120: for(jj=1; jj<= nlstate+ndeath; jj++){
3121: for(ii=jj; ii<= nlstate+ndeath; ii++){
3122: s1=ps[ii][jj];
3123: ps[ii][jj]=ps[jj][ii];
3124: ps[jj][ii]=s1;
3125: }
3126: }
3127: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3128: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3129: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3130: /* } */
3131: /* printf("\n "); */
3132: /* } */
3133: /* printf("\n ");printf("%lf ",cov[2]);*/
3134: /*
3135: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3136: goto end;*/
3137: return ps;
1.217 brouard 3138: }
3139:
3140:
1.126 brouard 3141: /**************** Product of 2 matrices ******************/
3142:
1.145 brouard 3143: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3144: {
3145: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3146: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3147: /* in, b, out are matrice of pointers which should have been initialized
3148: before: only the contents of out is modified. The function returns
3149: a pointer to pointers identical to out */
1.145 brouard 3150: int i, j, k;
1.126 brouard 3151: for(i=nrl; i<= nrh; i++)
1.145 brouard 3152: for(k=ncolol; k<=ncoloh; k++){
3153: out[i][k]=0.;
3154: for(j=ncl; j<=nch; j++)
3155: out[i][k] +=in[i][j]*b[j][k];
3156: }
1.126 brouard 3157: return out;
3158: }
3159:
3160:
3161: /************* Higher Matrix Product ***************/
3162:
1.235 brouard 3163: 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 3164: {
1.218 brouard 3165: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3166: 'nhstepm*hstepm*stepm' months (i.e. until
3167: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3168: nhstepm*hstepm matrices.
3169: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3170: (typically every 2 years instead of every month which is too big
3171: for the memory).
3172: Model is determined by parameters x and covariates have to be
3173: included manually here.
3174:
3175: */
3176:
3177: int i, j, d, h, k;
1.131 brouard 3178: double **out, cov[NCOVMAX+1];
1.126 brouard 3179: double **newm;
1.187 brouard 3180: double agexact;
1.214 brouard 3181: double agebegin, ageend;
1.126 brouard 3182:
3183: /* Hstepm could be zero and should return the unit matrix */
3184: for (i=1;i<=nlstate+ndeath;i++)
3185: for (j=1;j<=nlstate+ndeath;j++){
3186: oldm[i][j]=(i==j ? 1.0 : 0.0);
3187: po[i][j][0]=(i==j ? 1.0 : 0.0);
3188: }
3189: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3190: for(h=1; h <=nhstepm; h++){
3191: for(d=1; d <=hstepm; d++){
3192: newm=savm;
3193: /* Covariates have to be included here again */
3194: cov[1]=1.;
1.214 brouard 3195: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3196: cov[2]=agexact;
3197: if(nagesqr==1)
1.227 brouard 3198: cov[3]= agexact*agexact;
1.235 brouard 3199: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3200: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3201: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3202: /* 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)); */
3203: }
3204: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3205: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3206: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3207: /* 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]); */
3208: }
3209: for (k=1; k<=cptcovage;k++){
3210: if(Dummy[Tvar[Tage[k]]]){
3211: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3212: } else{
3213: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3214: }
3215: /* 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]); */
3216: }
3217: for (k=1; k<=cptcovprod;k++){ /* */
3218: /* 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]); */
3219: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3220: }
3221: /* for (k=1; k<=cptcovn;k++) */
3222: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3223: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3224: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3225: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3226: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3227:
3228:
1.126 brouard 3229: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3230: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3231: /* right multiplication of oldm by the current matrix */
1.126 brouard 3232: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3233: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3234: /* if((int)age == 70){ */
3235: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3236: /* for(i=1; i<=nlstate+ndeath; i++) { */
3237: /* printf("%d pmmij ",i); */
3238: /* for(j=1;j<=nlstate+ndeath;j++) { */
3239: /* printf("%f ",pmmij[i][j]); */
3240: /* } */
3241: /* printf(" oldm "); */
3242: /* for(j=1;j<=nlstate+ndeath;j++) { */
3243: /* printf("%f ",oldm[i][j]); */
3244: /* } */
3245: /* printf("\n"); */
3246: /* } */
3247: /* } */
1.126 brouard 3248: savm=oldm;
3249: oldm=newm;
3250: }
3251: for(i=1; i<=nlstate+ndeath; i++)
3252: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3253: po[i][j][h]=newm[i][j];
3254: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3255: }
1.128 brouard 3256: /*printf("h=%d ",h);*/
1.126 brouard 3257: } /* end h */
1.267 brouard 3258: /* printf("\n H=%d \n",h); */
1.126 brouard 3259: return po;
3260: }
3261:
1.217 brouard 3262: /************* Higher Back Matrix Product ***************/
1.218 brouard 3263: /* 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 3264: 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 3265: {
1.266 brouard 3266: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3267: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3268: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3269: nhstepm*hstepm matrices.
3270: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3271: (typically every 2 years instead of every month which is too big
1.217 brouard 3272: for the memory).
1.218 brouard 3273: Model is determined by parameters x and covariates have to be
1.266 brouard 3274: included manually here. Then we use a call to bmij(x and cov)
3275: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3276: */
1.217 brouard 3277:
3278: int i, j, d, h, k;
1.266 brouard 3279: double **out, cov[NCOVMAX+1], **bmij();
3280: double **newm, ***newmm;
1.217 brouard 3281: double agexact;
3282: double agebegin, ageend;
1.222 brouard 3283: double **oldm, **savm;
1.217 brouard 3284:
1.266 brouard 3285: newmm=po; /* To be saved */
3286: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3287: /* Hstepm could be zero and should return the unit matrix */
3288: for (i=1;i<=nlstate+ndeath;i++)
3289: for (j=1;j<=nlstate+ndeath;j++){
3290: oldm[i][j]=(i==j ? 1.0 : 0.0);
3291: po[i][j][0]=(i==j ? 1.0 : 0.0);
3292: }
3293: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3294: for(h=1; h <=nhstepm; h++){
3295: for(d=1; d <=hstepm; d++){
3296: newm=savm;
3297: /* Covariates have to be included here again */
3298: cov[1]=1.;
1.271 brouard 3299: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3300: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3301: cov[2]=agexact;
3302: if(nagesqr==1)
1.222 brouard 3303: cov[3]= agexact*agexact;
1.266 brouard 3304: for (k=1; k<=cptcovn;k++){
3305: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3306: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3307: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3308: /* 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)); */
3309: }
1.267 brouard 3310: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3311: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3312: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3313: /* 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]); */
3314: }
3315: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3316: if(Dummy[Tvar[Tage[k]]]){
3317: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3318: } else{
3319: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3320: }
3321: /* 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]); */
3322: }
3323: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3324: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3325: }
1.217 brouard 3326: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3327: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3328:
1.218 brouard 3329: /* Careful transposed matrix */
1.266 brouard 3330: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3331: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3332: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3333: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3334: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3335: /* if((int)age == 70){ */
3336: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3337: /* for(i=1; i<=nlstate+ndeath; i++) { */
3338: /* printf("%d pmmij ",i); */
3339: /* for(j=1;j<=nlstate+ndeath;j++) { */
3340: /* printf("%f ",pmmij[i][j]); */
3341: /* } */
3342: /* printf(" oldm "); */
3343: /* for(j=1;j<=nlstate+ndeath;j++) { */
3344: /* printf("%f ",oldm[i][j]); */
3345: /* } */
3346: /* printf("\n"); */
3347: /* } */
3348: /* } */
3349: savm=oldm;
3350: oldm=newm;
3351: }
3352: for(i=1; i<=nlstate+ndeath; i++)
3353: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3354: po[i][j][h]=newm[i][j];
1.268 brouard 3355: /* if(h==nhstepm) */
3356: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3357: }
1.268 brouard 3358: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3359: } /* end h */
1.268 brouard 3360: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3361: return po;
3362: }
3363:
3364:
1.162 brouard 3365: #ifdef NLOPT
3366: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3367: double fret;
3368: double *xt;
3369: int j;
3370: myfunc_data *d2 = (myfunc_data *) pd;
3371: /* xt = (p1-1); */
3372: xt=vector(1,n);
3373: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3374:
3375: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3376: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3377: printf("Function = %.12lf ",fret);
3378: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3379: printf("\n");
3380: free_vector(xt,1,n);
3381: return fret;
3382: }
3383: #endif
1.126 brouard 3384:
3385: /*************** log-likelihood *************/
3386: double func( double *x)
3387: {
1.226 brouard 3388: int i, ii, j, k, mi, d, kk;
3389: int ioffset=0;
3390: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3391: double **out;
3392: double lli; /* Individual log likelihood */
3393: int s1, s2;
1.228 brouard 3394: 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 3395: double bbh, survp;
3396: long ipmx;
3397: double agexact;
3398: /*extern weight */
3399: /* We are differentiating ll according to initial status */
3400: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3401: /*for(i=1;i<imx;i++)
3402: printf(" %d\n",s[4][i]);
3403: */
1.162 brouard 3404:
1.226 brouard 3405: ++countcallfunc;
1.162 brouard 3406:
1.226 brouard 3407: cov[1]=1.;
1.126 brouard 3408:
1.226 brouard 3409: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3410: ioffset=0;
1.226 brouard 3411: if(mle==1){
3412: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3413: /* Computes the values of the ncovmodel covariates of the model
3414: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3415: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3416: to be observed in j being in i according to the model.
3417: */
1.243 brouard 3418: ioffset=2+nagesqr ;
1.233 brouard 3419: /* Fixed */
1.234 brouard 3420: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3421: 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)*/
3422: }
1.226 brouard 3423: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3424: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3425: has been calculated etc */
3426: /* For an individual i, wav[i] gives the number of effective waves */
3427: /* We compute the contribution to Likelihood of each effective transition
3428: mw[mi][i] is real wave of the mi th effectve wave */
3429: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3430: s2=s[mw[mi+1][i]][i];
3431: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3432: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3433: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3434: */
3435: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3436: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3437: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3438: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3439: }
3440: for (ii=1;ii<=nlstate+ndeath;ii++)
3441: for (j=1;j<=nlstate+ndeath;j++){
3442: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3443: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3444: }
3445: for(d=0; d<dh[mi][i]; d++){
3446: newm=savm;
3447: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3448: cov[2]=agexact;
3449: if(nagesqr==1)
3450: cov[3]= agexact*agexact; /* Should be changed here */
3451: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3452: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3453: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3454: else
3455: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3456: }
3457: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3458: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3459: savm=oldm;
3460: oldm=newm;
3461: } /* end mult */
3462:
3463: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3464: /* But now since version 0.9 we anticipate for bias at large stepm.
3465: * If stepm is larger than one month (smallest stepm) and if the exact delay
3466: * (in months) between two waves is not a multiple of stepm, we rounded to
3467: * the nearest (and in case of equal distance, to the lowest) interval but now
3468: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3469: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3470: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3471: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3472: * -stepm/2 to stepm/2 .
3473: * For stepm=1 the results are the same as for previous versions of Imach.
3474: * For stepm > 1 the results are less biased than in previous versions.
3475: */
1.234 brouard 3476: s1=s[mw[mi][i]][i];
3477: s2=s[mw[mi+1][i]][i];
3478: bbh=(double)bh[mi][i]/(double)stepm;
3479: /* bias bh is positive if real duration
3480: * is higher than the multiple of stepm and negative otherwise.
3481: */
3482: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3483: if( s2 > nlstate){
3484: /* i.e. if s2 is a death state and if the date of death is known
3485: then the contribution to the likelihood is the probability to
3486: die between last step unit time and current step unit time,
3487: which is also equal to probability to die before dh
3488: minus probability to die before dh-stepm .
3489: In version up to 0.92 likelihood was computed
3490: as if date of death was unknown. Death was treated as any other
3491: health state: the date of the interview describes the actual state
3492: and not the date of a change in health state. The former idea was
3493: to consider that at each interview the state was recorded
3494: (healthy, disable or death) and IMaCh was corrected; but when we
3495: introduced the exact date of death then we should have modified
3496: the contribution of an exact death to the likelihood. This new
3497: contribution is smaller and very dependent of the step unit
3498: stepm. It is no more the probability to die between last interview
3499: and month of death but the probability to survive from last
3500: interview up to one month before death multiplied by the
3501: probability to die within a month. Thanks to Chris
3502: Jackson for correcting this bug. Former versions increased
3503: mortality artificially. The bad side is that we add another loop
3504: which slows down the processing. The difference can be up to 10%
3505: lower mortality.
3506: */
3507: /* If, at the beginning of the maximization mostly, the
3508: cumulative probability or probability to be dead is
3509: constant (ie = 1) over time d, the difference is equal to
3510: 0. out[s1][3] = savm[s1][3]: probability, being at state
3511: s1 at precedent wave, to be dead a month before current
3512: wave is equal to probability, being at state s1 at
3513: precedent wave, to be dead at mont of the current
3514: wave. Then the observed probability (that this person died)
3515: is null according to current estimated parameter. In fact,
3516: it should be very low but not zero otherwise the log go to
3517: infinity.
3518: */
1.183 brouard 3519: /* #ifdef INFINITYORIGINAL */
3520: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3521: /* #else */
3522: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3523: /* lli=log(mytinydouble); */
3524: /* else */
3525: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3526: /* #endif */
1.226 brouard 3527: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3528:
1.226 brouard 3529: } else if ( s2==-1 ) { /* alive */
3530: for (j=1,survp=0. ; j<=nlstate; j++)
3531: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3532: /*survp += out[s1][j]; */
3533: lli= log(survp);
3534: }
3535: else if (s2==-4) {
3536: for (j=3,survp=0. ; j<=nlstate; j++)
3537: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3538: lli= log(survp);
3539: }
3540: else if (s2==-5) {
3541: for (j=1,survp=0. ; j<=2; j++)
3542: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3543: lli= log(survp);
3544: }
3545: else{
3546: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3547: /* 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 */
3548: }
3549: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3550: /*if(lli ==000.0)*/
3551: /*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); */
3552: ipmx +=1;
3553: sw += weight[i];
3554: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3555: /* if (lli < log(mytinydouble)){ */
3556: /* 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); */
3557: /* 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]); */
3558: /* } */
3559: } /* end of wave */
3560: } /* end of individual */
3561: } else if(mle==2){
3562: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3563: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3564: for(mi=1; mi<= wav[i]-1; mi++){
3565: for (ii=1;ii<=nlstate+ndeath;ii++)
3566: for (j=1;j<=nlstate+ndeath;j++){
3567: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3568: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3569: }
3570: for(d=0; d<=dh[mi][i]; d++){
3571: newm=savm;
3572: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3573: cov[2]=agexact;
3574: if(nagesqr==1)
3575: cov[3]= agexact*agexact;
3576: for (kk=1; kk<=cptcovage;kk++) {
3577: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3578: }
3579: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3580: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3581: savm=oldm;
3582: oldm=newm;
3583: } /* end mult */
3584:
3585: s1=s[mw[mi][i]][i];
3586: s2=s[mw[mi+1][i]][i];
3587: bbh=(double)bh[mi][i]/(double)stepm;
3588: 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 */
3589: ipmx +=1;
3590: sw += weight[i];
3591: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3592: } /* end of wave */
3593: } /* end of individual */
3594: } else if(mle==3){ /* exponential inter-extrapolation */
3595: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3596: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3597: for(mi=1; mi<= wav[i]-1; mi++){
3598: for (ii=1;ii<=nlstate+ndeath;ii++)
3599: for (j=1;j<=nlstate+ndeath;j++){
3600: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3601: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3602: }
3603: for(d=0; d<dh[mi][i]; d++){
3604: newm=savm;
3605: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3606: cov[2]=agexact;
3607: if(nagesqr==1)
3608: cov[3]= agexact*agexact;
3609: for (kk=1; kk<=cptcovage;kk++) {
3610: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3611: }
3612: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3613: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3614: savm=oldm;
3615: oldm=newm;
3616: } /* end mult */
3617:
3618: s1=s[mw[mi][i]][i];
3619: s2=s[mw[mi+1][i]][i];
3620: bbh=(double)bh[mi][i]/(double)stepm;
3621: 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 */
3622: ipmx +=1;
3623: sw += weight[i];
3624: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3625: } /* end of wave */
3626: } /* end of individual */
3627: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3628: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3629: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3630: for(mi=1; mi<= wav[i]-1; mi++){
3631: for (ii=1;ii<=nlstate+ndeath;ii++)
3632: for (j=1;j<=nlstate+ndeath;j++){
3633: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3634: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3635: }
3636: for(d=0; d<dh[mi][i]; d++){
3637: newm=savm;
3638: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3639: cov[2]=agexact;
3640: if(nagesqr==1)
3641: cov[3]= agexact*agexact;
3642: for (kk=1; kk<=cptcovage;kk++) {
3643: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3644: }
1.126 brouard 3645:
1.226 brouard 3646: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3647: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3648: savm=oldm;
3649: oldm=newm;
3650: } /* end mult */
3651:
3652: s1=s[mw[mi][i]][i];
3653: s2=s[mw[mi+1][i]][i];
3654: if( s2 > nlstate){
3655: lli=log(out[s1][s2] - savm[s1][s2]);
3656: } else if ( s2==-1 ) { /* alive */
3657: for (j=1,survp=0. ; j<=nlstate; j++)
3658: survp += out[s1][j];
3659: lli= log(survp);
3660: }else{
3661: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3662: }
3663: ipmx +=1;
3664: sw += weight[i];
3665: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3666: /* 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 3667: } /* end of wave */
3668: } /* end of individual */
3669: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3670: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3671: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3672: for(mi=1; mi<= wav[i]-1; mi++){
3673: for (ii=1;ii<=nlstate+ndeath;ii++)
3674: for (j=1;j<=nlstate+ndeath;j++){
3675: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3676: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3677: }
3678: for(d=0; d<dh[mi][i]; d++){
3679: newm=savm;
3680: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3681: cov[2]=agexact;
3682: if(nagesqr==1)
3683: cov[3]= agexact*agexact;
3684: for (kk=1; kk<=cptcovage;kk++) {
3685: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3686: }
1.126 brouard 3687:
1.226 brouard 3688: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3689: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3690: savm=oldm;
3691: oldm=newm;
3692: } /* end mult */
3693:
3694: s1=s[mw[mi][i]][i];
3695: s2=s[mw[mi+1][i]][i];
3696: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3697: ipmx +=1;
3698: sw += weight[i];
3699: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3700: /*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]);*/
3701: } /* end of wave */
3702: } /* end of individual */
3703: } /* End of if */
3704: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3705: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3706: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3707: return -l;
1.126 brouard 3708: }
3709:
3710: /*************** log-likelihood *************/
3711: double funcone( double *x)
3712: {
1.228 brouard 3713: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3714: int i, ii, j, k, mi, d, kk;
1.228 brouard 3715: int ioffset=0;
1.131 brouard 3716: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3717: double **out;
3718: double lli; /* Individual log likelihood */
3719: double llt;
3720: int s1, s2;
1.228 brouard 3721: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3722:
1.126 brouard 3723: double bbh, survp;
1.187 brouard 3724: double agexact;
1.214 brouard 3725: double agebegin, ageend;
1.126 brouard 3726: /*extern weight */
3727: /* We are differentiating ll according to initial status */
3728: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3729: /*for(i=1;i<imx;i++)
3730: printf(" %d\n",s[4][i]);
3731: */
3732: cov[1]=1.;
3733:
3734: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3735: ioffset=0;
3736: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3737: /* ioffset=2+nagesqr+cptcovage; */
3738: ioffset=2+nagesqr;
1.232 brouard 3739: /* Fixed */
1.224 brouard 3740: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3741: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3742: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3743: 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)*/
3744: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3745: /* cov[2+6]=covar[Tvar[6]][i]; */
3746: /* cov[2+6]=covar[2][i]; V2 */
3747: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3748: /* cov[2+7]=covar[Tvar[7]][i]; */
3749: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3750: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3751: /* cov[2+9]=covar[Tvar[9]][i]; */
3752: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3753: }
1.232 brouard 3754: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3755: /* 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?)*\/ */
3756: /* } */
1.231 brouard 3757: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3758: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3759: /* } */
1.225 brouard 3760:
1.233 brouard 3761:
3762: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3763: /* Wave varying (but not age varying) */
3764: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3765: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3766: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3767: }
1.232 brouard 3768: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3769: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3770: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3771: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3772: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3773: /* 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 3774: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3775: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3776: /* /\* 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]); *\/ */
3777: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3778: /* } */
1.126 brouard 3779: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3780: for (j=1;j<=nlstate+ndeath;j++){
3781: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3782: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3783: }
1.214 brouard 3784:
3785: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3786: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3787: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3788: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3789: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3790: and mw[mi+1][i]. dh depends on stepm.*/
3791: newm=savm;
1.247 brouard 3792: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3793: cov[2]=agexact;
3794: if(nagesqr==1)
3795: cov[3]= agexact*agexact;
3796: for (kk=1; kk<=cptcovage;kk++) {
3797: if(!FixedV[Tvar[Tage[kk]]])
3798: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3799: else
3800: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3801: }
3802: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3803: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3804: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3805: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3806: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3807: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3808: savm=oldm;
3809: oldm=newm;
1.126 brouard 3810: } /* end mult */
3811:
3812: s1=s[mw[mi][i]][i];
3813: s2=s[mw[mi+1][i]][i];
1.217 brouard 3814: /* if(s2==-1){ */
1.268 brouard 3815: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3816: /* /\* exit(1); *\/ */
3817: /* } */
1.126 brouard 3818: bbh=(double)bh[mi][i]/(double)stepm;
3819: /* bias is positive if real duration
3820: * is higher than the multiple of stepm and negative otherwise.
3821: */
3822: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3823: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3824: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3825: for (j=1,survp=0. ; j<=nlstate; j++)
3826: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3827: lli= log(survp);
1.126 brouard 3828: }else if (mle==1){
1.242 brouard 3829: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3830: } else if(mle==2){
1.242 brouard 3831: 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 3832: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3833: 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 3834: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3835: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3836: } else{ /* mle=0 back to 1 */
1.242 brouard 3837: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3838: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3839: } /* End of if */
3840: ipmx +=1;
3841: sw += weight[i];
3842: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3843: /*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 3844: if(globpr){
1.246 brouard 3845: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3846: %11.6f %11.6f %11.6f ", \
1.242 brouard 3847: 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 3848: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3849: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3850: llt +=ll[k]*gipmx/gsw;
3851: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3852: }
3853: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3854: }
1.232 brouard 3855: } /* end of wave */
3856: } /* end of individual */
3857: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3858: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3859: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3860: if(globpr==0){ /* First time we count the contributions and weights */
3861: gipmx=ipmx;
3862: gsw=sw;
3863: }
3864: return -l;
1.126 brouard 3865: }
3866:
3867:
3868: /*************** function likelione ***********/
3869: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3870: {
3871: /* This routine should help understanding what is done with
3872: the selection of individuals/waves and
3873: to check the exact contribution to the likelihood.
3874: Plotting could be done.
3875: */
3876: int k;
3877:
3878: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3879: strcpy(fileresilk,"ILK_");
1.202 brouard 3880: strcat(fileresilk,fileresu);
1.126 brouard 3881: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3882: printf("Problem with resultfile: %s\n", fileresilk);
3883: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3884: }
1.214 brouard 3885: 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");
3886: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3887: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3888: for(k=1; k<=nlstate; k++)
3889: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3890: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3891: }
3892:
3893: *fretone=(*funcone)(p);
3894: if(*globpri !=0){
3895: fclose(ficresilk);
1.205 brouard 3896: if (mle ==0)
3897: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3898: else if(mle >=1)
3899: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3900: 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 3901: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3902:
3903: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3904: 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 3905: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3906: }
1.207 brouard 3907: 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 3908: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3909: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3910: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3911: fflush(fichtm);
1.205 brouard 3912: }
1.126 brouard 3913: return;
3914: }
3915:
3916:
3917: /*********** Maximum Likelihood Estimation ***************/
3918:
3919: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3920: {
1.165 brouard 3921: int i,j, iter=0;
1.126 brouard 3922: double **xi;
3923: double fret;
3924: double fretone; /* Only one call to likelihood */
3925: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3926:
3927: #ifdef NLOPT
3928: int creturn;
3929: nlopt_opt opt;
3930: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3931: double *lb;
3932: double minf; /* the minimum objective value, upon return */
3933: double * p1; /* Shifted parameters from 0 instead of 1 */
3934: myfunc_data dinst, *d = &dinst;
3935: #endif
3936:
3937:
1.126 brouard 3938: xi=matrix(1,npar,1,npar);
3939: for (i=1;i<=npar;i++)
3940: for (j=1;j<=npar;j++)
3941: xi[i][j]=(i==j ? 1.0 : 0.0);
3942: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3943: strcpy(filerespow,"POW_");
1.126 brouard 3944: strcat(filerespow,fileres);
3945: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3946: printf("Problem with resultfile: %s\n", filerespow);
3947: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3948: }
3949: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3950: for (i=1;i<=nlstate;i++)
3951: for(j=1;j<=nlstate+ndeath;j++)
3952: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3953: fprintf(ficrespow,"\n");
1.162 brouard 3954: #ifdef POWELL
1.126 brouard 3955: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3956: #endif
1.126 brouard 3957:
1.162 brouard 3958: #ifdef NLOPT
3959: #ifdef NEWUOA
3960: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3961: #else
3962: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3963: #endif
3964: lb=vector(0,npar-1);
3965: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3966: nlopt_set_lower_bounds(opt, lb);
3967: nlopt_set_initial_step1(opt, 0.1);
3968:
3969: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3970: d->function = func;
3971: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3972: nlopt_set_min_objective(opt, myfunc, d);
3973: nlopt_set_xtol_rel(opt, ftol);
3974: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3975: printf("nlopt failed! %d\n",creturn);
3976: }
3977: else {
3978: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3979: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3980: iter=1; /* not equal */
3981: }
3982: nlopt_destroy(opt);
3983: #endif
1.126 brouard 3984: free_matrix(xi,1,npar,1,npar);
3985: fclose(ficrespow);
1.203 brouard 3986: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3987: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3988: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3989:
3990: }
3991:
3992: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3993: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3994: {
3995: double **a,**y,*x,pd;
1.203 brouard 3996: /* double **hess; */
1.164 brouard 3997: int i, j;
1.126 brouard 3998: int *indx;
3999:
4000: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 4001: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 4002: void lubksb(double **a, int npar, int *indx, double b[]) ;
4003: void ludcmp(double **a, int npar, int *indx, double *d) ;
4004: double gompertz(double p[]);
1.203 brouard 4005: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 4006:
4007: printf("\nCalculation of the hessian matrix. Wait...\n");
4008: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
4009: for (i=1;i<=npar;i++){
1.203 brouard 4010: printf("%d-",i);fflush(stdout);
4011: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4012:
4013: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4014:
4015: /* printf(" %f ",p[i]);
4016: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4017: }
4018:
4019: for (i=1;i<=npar;i++) {
4020: for (j=1;j<=npar;j++) {
4021: if (j>i) {
1.203 brouard 4022: printf(".%d-%d",i,j);fflush(stdout);
4023: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4024: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4025:
4026: hess[j][i]=hess[i][j];
4027: /*printf(" %lf ",hess[i][j]);*/
4028: }
4029: }
4030: }
4031: printf("\n");
4032: fprintf(ficlog,"\n");
4033:
4034: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4035: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4036:
4037: a=matrix(1,npar,1,npar);
4038: y=matrix(1,npar,1,npar);
4039: x=vector(1,npar);
4040: indx=ivector(1,npar);
4041: for (i=1;i<=npar;i++)
4042: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4043: ludcmp(a,npar,indx,&pd);
4044:
4045: for (j=1;j<=npar;j++) {
4046: for (i=1;i<=npar;i++) x[i]=0;
4047: x[j]=1;
4048: lubksb(a,npar,indx,x);
4049: for (i=1;i<=npar;i++){
4050: matcov[i][j]=x[i];
4051: }
4052: }
4053:
4054: printf("\n#Hessian matrix#\n");
4055: fprintf(ficlog,"\n#Hessian matrix#\n");
4056: for (i=1;i<=npar;i++) {
4057: for (j=1;j<=npar;j++) {
1.203 brouard 4058: printf("%.6e ",hess[i][j]);
4059: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4060: }
4061: printf("\n");
4062: fprintf(ficlog,"\n");
4063: }
4064:
1.203 brouard 4065: /* printf("\n#Covariance matrix#\n"); */
4066: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4067: /* for (i=1;i<=npar;i++) { */
4068: /* for (j=1;j<=npar;j++) { */
4069: /* printf("%.6e ",matcov[i][j]); */
4070: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4071: /* } */
4072: /* printf("\n"); */
4073: /* fprintf(ficlog,"\n"); */
4074: /* } */
4075:
1.126 brouard 4076: /* Recompute Inverse */
1.203 brouard 4077: /* for (i=1;i<=npar;i++) */
4078: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4079: /* ludcmp(a,npar,indx,&pd); */
4080:
4081: /* printf("\n#Hessian matrix recomputed#\n"); */
4082:
4083: /* for (j=1;j<=npar;j++) { */
4084: /* for (i=1;i<=npar;i++) x[i]=0; */
4085: /* x[j]=1; */
4086: /* lubksb(a,npar,indx,x); */
4087: /* for (i=1;i<=npar;i++){ */
4088: /* y[i][j]=x[i]; */
4089: /* printf("%.3e ",y[i][j]); */
4090: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4091: /* } */
4092: /* printf("\n"); */
4093: /* fprintf(ficlog,"\n"); */
4094: /* } */
4095:
4096: /* Verifying the inverse matrix */
4097: #ifdef DEBUGHESS
4098: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4099:
1.203 brouard 4100: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4101: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4102:
4103: for (j=1;j<=npar;j++) {
4104: for (i=1;i<=npar;i++){
1.203 brouard 4105: printf("%.2f ",y[i][j]);
4106: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4107: }
4108: printf("\n");
4109: fprintf(ficlog,"\n");
4110: }
1.203 brouard 4111: #endif
1.126 brouard 4112:
4113: free_matrix(a,1,npar,1,npar);
4114: free_matrix(y,1,npar,1,npar);
4115: free_vector(x,1,npar);
4116: free_ivector(indx,1,npar);
1.203 brouard 4117: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4118:
4119:
4120: }
4121:
4122: /*************** hessian matrix ****************/
4123: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4124: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4125: int i;
4126: int l=1, lmax=20;
1.203 brouard 4127: double k1,k2, res, fx;
1.132 brouard 4128: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4129: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4130: int k=0,kmax=10;
4131: double l1;
4132:
4133: fx=func(x);
4134: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4135: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4136: l1=pow(10,l);
4137: delts=delt;
4138: for(k=1 ; k <kmax; k=k+1){
4139: delt = delta*(l1*k);
4140: p2[theta]=x[theta] +delt;
1.145 brouard 4141: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4142: p2[theta]=x[theta]-delt;
4143: k2=func(p2)-fx;
4144: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4145: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4146:
1.203 brouard 4147: #ifdef DEBUGHESSII
1.126 brouard 4148: 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);
4149: 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);
4150: #endif
4151: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4152: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4153: k=kmax;
4154: }
4155: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4156: k=kmax; l=lmax*10;
1.126 brouard 4157: }
4158: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4159: delts=delt;
4160: }
1.203 brouard 4161: } /* End loop k */
1.126 brouard 4162: }
4163: delti[theta]=delts;
4164: return res;
4165:
4166: }
4167:
1.203 brouard 4168: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4169: {
4170: int i;
1.164 brouard 4171: int l=1, lmax=20;
1.126 brouard 4172: double k1,k2,k3,k4,res,fx;
1.132 brouard 4173: double p2[MAXPARM+1];
1.203 brouard 4174: int k, kmax=1;
4175: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4176:
4177: int firstime=0;
1.203 brouard 4178:
1.126 brouard 4179: fx=func(x);
1.203 brouard 4180: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4181: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4182: p2[thetai]=x[thetai]+delti[thetai]*k;
4183: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4184: k1=func(p2)-fx;
4185:
1.203 brouard 4186: p2[thetai]=x[thetai]+delti[thetai]*k;
4187: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4188: k2=func(p2)-fx;
4189:
1.203 brouard 4190: p2[thetai]=x[thetai]-delti[thetai]*k;
4191: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4192: k3=func(p2)-fx;
4193:
1.203 brouard 4194: p2[thetai]=x[thetai]-delti[thetai]*k;
4195: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4196: k4=func(p2)-fx;
1.203 brouard 4197: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4198: if(k1*k2*k3*k4 <0.){
1.208 brouard 4199: firstime=1;
1.203 brouard 4200: kmax=kmax+10;
1.208 brouard 4201: }
4202: if(kmax >=10 || firstime ==1){
1.246 brouard 4203: 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);
4204: 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 4205: 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);
4206: 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);
4207: }
4208: #ifdef DEBUGHESSIJ
4209: v1=hess[thetai][thetai];
4210: v2=hess[thetaj][thetaj];
4211: cv12=res;
4212: /* Computing eigen value of Hessian matrix */
4213: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4214: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4215: if ((lc2 <0) || (lc1 <0) ){
4216: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4217: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4218: 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);
4219: 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);
4220: }
1.126 brouard 4221: #endif
4222: }
4223: return res;
4224: }
4225:
1.203 brouard 4226: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4227: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4228: /* { */
4229: /* int i; */
4230: /* int l=1, lmax=20; */
4231: /* double k1,k2,k3,k4,res,fx; */
4232: /* double p2[MAXPARM+1]; */
4233: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4234: /* int k=0,kmax=10; */
4235: /* double l1; */
4236:
4237: /* fx=func(x); */
4238: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4239: /* l1=pow(10,l); */
4240: /* delts=delt; */
4241: /* for(k=1 ; k <kmax; k=k+1){ */
4242: /* delt = delti*(l1*k); */
4243: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4244: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4245: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4246: /* k1=func(p2)-fx; */
4247:
4248: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4249: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4250: /* k2=func(p2)-fx; */
4251:
4252: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4253: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4254: /* k3=func(p2)-fx; */
4255:
4256: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4257: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4258: /* k4=func(p2)-fx; */
4259: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4260: /* #ifdef DEBUGHESSIJ */
4261: /* printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
4262: /* fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4); */
4263: /* #endif */
4264: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4265: /* k=kmax; */
4266: /* } */
4267: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4268: /* k=kmax; l=lmax*10; */
4269: /* } */
4270: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4271: /* delts=delt; */
4272: /* } */
4273: /* } /\* End loop k *\/ */
4274: /* } */
4275: /* delti[theta]=delts; */
4276: /* return res; */
4277: /* } */
4278:
4279:
1.126 brouard 4280: /************** Inverse of matrix **************/
4281: void ludcmp(double **a, int n, int *indx, double *d)
4282: {
4283: int i,imax,j,k;
4284: double big,dum,sum,temp;
4285: double *vv;
4286:
4287: vv=vector(1,n);
4288: *d=1.0;
4289: for (i=1;i<=n;i++) {
4290: big=0.0;
4291: for (j=1;j<=n;j++)
4292: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4293: if (big == 0.0){
4294: printf(" Singular Hessian matrix at row %d:\n",i);
4295: for (j=1;j<=n;j++) {
4296: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4297: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4298: }
4299: fflush(ficlog);
4300: fclose(ficlog);
4301: nrerror("Singular matrix in routine ludcmp");
4302: }
1.126 brouard 4303: vv[i]=1.0/big;
4304: }
4305: for (j=1;j<=n;j++) {
4306: for (i=1;i<j;i++) {
4307: sum=a[i][j];
4308: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4309: a[i][j]=sum;
4310: }
4311: big=0.0;
4312: for (i=j;i<=n;i++) {
4313: sum=a[i][j];
4314: for (k=1;k<j;k++)
4315: sum -= a[i][k]*a[k][j];
4316: a[i][j]=sum;
4317: if ( (dum=vv[i]*fabs(sum)) >= big) {
4318: big=dum;
4319: imax=i;
4320: }
4321: }
4322: if (j != imax) {
4323: for (k=1;k<=n;k++) {
4324: dum=a[imax][k];
4325: a[imax][k]=a[j][k];
4326: a[j][k]=dum;
4327: }
4328: *d = -(*d);
4329: vv[imax]=vv[j];
4330: }
4331: indx[j]=imax;
4332: if (a[j][j] == 0.0) a[j][j]=TINY;
4333: if (j != n) {
4334: dum=1.0/(a[j][j]);
4335: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4336: }
4337: }
4338: free_vector(vv,1,n); /* Doesn't work */
4339: ;
4340: }
4341:
4342: void lubksb(double **a, int n, int *indx, double b[])
4343: {
4344: int i,ii=0,ip,j;
4345: double sum;
4346:
4347: for (i=1;i<=n;i++) {
4348: ip=indx[i];
4349: sum=b[ip];
4350: b[ip]=b[i];
4351: if (ii)
4352: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4353: else if (sum) ii=i;
4354: b[i]=sum;
4355: }
4356: for (i=n;i>=1;i--) {
4357: sum=b[i];
4358: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4359: b[i]=sum/a[i][i];
4360: }
4361: }
4362:
4363: void pstamp(FILE *fichier)
4364: {
1.196 brouard 4365: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4366: }
4367:
1.253 brouard 4368:
4369:
1.126 brouard 4370: /************ Frequencies ********************/
1.251 brouard 4371: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4372: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4373: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4374: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4375:
1.265 brouard 4376: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4377: int iind=0, iage=0;
4378: int mi; /* Effective wave */
4379: int first;
4380: double ***freq; /* Frequencies */
1.268 brouard 4381: 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 */
4382: 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 4383: double *meanq, *stdq, *idq;
1.226 brouard 4384: double **meanqt;
4385: double *pp, **prop, *posprop, *pospropt;
4386: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4387: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4388: double agebegin, ageend;
4389:
4390: pp=vector(1,nlstate);
1.251 brouard 4391: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4392: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4393: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4394: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4395: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.284 brouard 4396: stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 brouard 4397: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4398: meanqt=matrix(1,lastpass,1,nqtveff);
4399: strcpy(fileresp,"P_");
4400: strcat(fileresp,fileresu);
4401: /*strcat(fileresphtm,fileresu);*/
4402: if((ficresp=fopen(fileresp,"w"))==NULL) {
4403: printf("Problem with prevalence resultfile: %s\n", fileresp);
4404: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4405: exit(0);
4406: }
1.240 brouard 4407:
1.226 brouard 4408: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4409: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4410: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4411: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4412: fflush(ficlog);
4413: exit(70);
4414: }
4415: else{
4416: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4417: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4418: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4419: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4420: }
1.237 brouard 4421: 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 4422:
1.226 brouard 4423: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4424: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4425: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4426: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4427: fflush(ficlog);
4428: exit(70);
1.240 brouard 4429: } else{
1.226 brouard 4430: 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 4431: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4432: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4433: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4434: }
1.240 brouard 4435: 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);
4436:
1.253 brouard 4437: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4438: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4439: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4440: j1=0;
1.126 brouard 4441:
1.227 brouard 4442: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4443: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4444: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4445:
4446:
1.226 brouard 4447: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4448: reference=low_education V1=0,V2=0
4449: med_educ V1=1 V2=0,
4450: high_educ V1=0 V2=1
4451: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4452: */
1.249 brouard 4453: dateintsum=0;
4454: k2cpt=0;
4455:
1.253 brouard 4456: if(cptcoveff == 0 )
1.265 brouard 4457: nl=1; /* Constant and age model only */
1.253 brouard 4458: else
4459: nl=2;
1.265 brouard 4460:
4461: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4462: /* Loop on nj=1 or 2 if dummy covariates j!=0
4463: * Loop on j1(1 to 2**cptcoveff) covariate combination
4464: * freq[s1][s2][iage] =0.
4465: * Loop on iind
4466: * ++freq[s1][s2][iage] weighted
4467: * end iind
4468: * if covariate and j!0
4469: * headers Variable on one line
4470: * endif cov j!=0
4471: * header of frequency table by age
4472: * Loop on age
4473: * pp[s1]+=freq[s1][s2][iage] weighted
4474: * pos+=freq[s1][s2][iage] weighted
4475: * Loop on s1 initial state
4476: * fprintf(ficresp
4477: * end s1
4478: * end age
4479: * if j!=0 computes starting values
4480: * end compute starting values
4481: * end j1
4482: * end nl
4483: */
1.253 brouard 4484: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4485: if(nj==1)
4486: j=0; /* First pass for the constant */
1.265 brouard 4487: else{
1.253 brouard 4488: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4489: }
1.251 brouard 4490: first=1;
1.265 brouard 4491: 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 4492: posproptt=0.;
4493: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4494: scanf("%d", i);*/
4495: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4496: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4497: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4498: freq[i][s2][m]=0;
1.251 brouard 4499:
4500: for (i=1; i<=nlstate; i++) {
1.240 brouard 4501: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4502: prop[i][m]=0;
4503: posprop[i]=0;
4504: pospropt[i]=0;
4505: }
1.283 brouard 4506: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
1.284 brouard 4507: idq[z1]=0.;
4508: meanq[z1]=0.;
4509: stdq[z1]=0.;
1.283 brouard 4510: }
4511: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4512: /* for(m=1;m<=lastpass;m++){ */
1.283 brouard 4513: /* meanqt[m][z1]=0.; */
4514: /* } */
4515: /* } */
1.251 brouard 4516: /* dateintsum=0; */
4517: /* k2cpt=0; */
4518:
1.265 brouard 4519: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4520: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4521: bool=1;
4522: if(j !=0){
4523: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4524: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4525: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4526: /* if(Tvaraff[z1] ==-20){ */
4527: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4528: /* }else if(Tvaraff[z1] ==-10){ */
4529: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4530: /* }else */
4531: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4532: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4533: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4534: /* 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",
4535: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4536: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4537: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4538: } /* Onlyf fixed */
4539: } /* end z1 */
4540: } /* cptcovn > 0 */
4541: } /* end any */
4542: }/* end j==0 */
1.265 brouard 4543: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4544: /* for(m=firstpass; m<=lastpass; m++){ */
1.284 brouard 4545: for(mi=1; mi<wav[iind];mi++){ /* For each wave */
1.251 brouard 4546: m=mw[mi][iind];
4547: if(j!=0){
4548: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4549: for (z1=1; z1<=cptcoveff; z1++) {
4550: if( Fixed[Tmodelind[z1]]==1){
4551: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4552: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4553: value is -1, we don't select. It differs from the
4554: constant and age model which counts them. */
4555: bool=0; /* not selected */
4556: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4557: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4558: bool=0;
4559: }
4560: }
4561: }
4562: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4563: } /* end j==0 */
4564: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
1.284 brouard 4565: if(bool==1){ /*Selected */
1.251 brouard 4566: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4567: and mw[mi+1][iind]. dh depends on stepm. */
4568: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4569: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4570: if(m >=firstpass && m <=lastpass){
4571: k2=anint[m][iind]+(mint[m][iind]/12.);
4572: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4573: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4574: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4575: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4576: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4577: if (m<lastpass) {
4578: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4579: /* 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]); */
4580: if(s[m][iind]==-1)
4581: 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.));
4582: 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 4583: for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
4584: idq[z1]=idq[z1]+weight[iind];
4585: meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
4586: stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
4587: }
1.251 brouard 4588: /* if((int)agev[m][iind] == 55) */
4589: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4590: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4591: 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 4592: }
1.251 brouard 4593: } /* end if between passes */
4594: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4595: dateintsum=dateintsum+k2; /* on all covariates ?*/
4596: k2cpt++;
4597: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4598: }
1.251 brouard 4599: }else{
4600: bool=1;
4601: }/* end bool 2 */
4602: } /* end m */
1.284 brouard 4603: /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
4604: /* idq[z1]=idq[z1]+weight[iind]; */
4605: /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
4606: /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
4607: /* } */
1.251 brouard 4608: } /* end bool */
4609: } /* end iind = 1 to imx */
4610: /* prop[s][age] is feeded for any initial and valid live state as well as
4611: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4612:
4613:
4614: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4615: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4616: pstamp(ficresp);
1.251 brouard 4617: if (cptcoveff>0 && j!=0){
1.265 brouard 4618: pstamp(ficresp);
1.251 brouard 4619: printf( "\n#********** Variable ");
4620: fprintf(ficresp, "\n#********** Variable ");
4621: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4622: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4623: fprintf(ficlog, "\n#********** Variable ");
4624: for (z1=1; z1<=cptcoveff; z1++){
4625: if(!FixedV[Tvaraff[z1]]){
4626: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4627: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4628: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4629: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4630: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4631: }else{
1.251 brouard 4632: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4633: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4634: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4635: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4636: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4637: }
4638: }
4639: printf( "**********\n#");
4640: fprintf(ficresp, "**********\n#");
4641: fprintf(ficresphtm, "**********</h3>\n");
4642: fprintf(ficresphtmfr, "**********</h3>\n");
4643: fprintf(ficlog, "**********\n");
4644: }
1.284 brouard 4645: /*
4646: Printing means of quantitative variables if any
4647: */
4648: for (z1=1; z1<= nqfveff; z1++) {
1.285 brouard 4649: fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
1.284 brouard 4650: fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
4651: if(weightopt==1){
4652: printf(" Weighted mean and standard deviation of");
4653: fprintf(ficlog," Weighted mean and standard deviation of");
4654: fprintf(ficresphtmfr," Weighted mean and standard deviation of");
4655: }
1.285 brouard 4656: 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]));
4657: 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]));
4658: 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 4659: }
4660: /* for (z1=1; z1<= nqtveff; z1++) { */
4661: /* for(m=1;m<=lastpass;m++){ */
4662: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
4663: /* } */
4664: /* } */
1.283 brouard 4665:
1.251 brouard 4666: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4667: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4668: fprintf(ficresp, " Age");
4669: 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 4670: for(i=1; i<=nlstate;i++) {
1.265 brouard 4671: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4672: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4673: }
1.265 brouard 4674: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4675: fprintf(ficresphtm, "\n");
4676:
4677: /* Header of frequency table by age */
4678: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4679: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4680: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4681: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4682: if(s2!=0 && m!=0)
4683: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4684: }
1.226 brouard 4685: }
1.251 brouard 4686: fprintf(ficresphtmfr, "\n");
4687:
4688: /* For each age */
4689: for(iage=iagemin; iage <= iagemax+3; iage++){
4690: fprintf(ficresphtm,"<tr>");
4691: if(iage==iagemax+1){
4692: fprintf(ficlog,"1");
4693: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4694: }else if(iage==iagemax+2){
4695: fprintf(ficlog,"0");
4696: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4697: }else if(iage==iagemax+3){
4698: fprintf(ficlog,"Total");
4699: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4700: }else{
1.240 brouard 4701: if(first==1){
1.251 brouard 4702: first=0;
4703: printf("See log file for details...\n");
4704: }
4705: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4706: fprintf(ficlog,"Age %d", iage);
4707: }
1.265 brouard 4708: for(s1=1; s1 <=nlstate ; s1++){
4709: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4710: pp[s1] += freq[s1][m][iage];
1.251 brouard 4711: }
1.265 brouard 4712: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4713: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4714: pos += freq[s1][m][iage];
4715: if(pp[s1]>=1.e-10){
1.251 brouard 4716: if(first==1){
1.265 brouard 4717: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4718: }
1.265 brouard 4719: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4720: }else{
4721: if(first==1)
1.265 brouard 4722: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4723: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4724: }
4725: }
4726:
1.265 brouard 4727: for(s1=1; s1 <=nlstate ; s1++){
4728: /* posprop[s1]=0; */
4729: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4730: pp[s1] += freq[s1][m][iage];
4731: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4732:
4733: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4734: pos += pp[s1]; /* pos is the total number of transitions until this age */
4735: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4736: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4737: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4738: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4739: }
4740:
4741: /* Writing ficresp */
4742: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4743: if( iage <= iagemax){
4744: fprintf(ficresp," %d",iage);
4745: }
4746: }else if( nj==2){
4747: if( iage <= iagemax){
4748: fprintf(ficresp," %d",iage);
4749: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4750: }
1.240 brouard 4751: }
1.265 brouard 4752: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4753: if(pos>=1.e-5){
1.251 brouard 4754: if(first==1)
1.265 brouard 4755: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4756: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4757: }else{
4758: if(first==1)
1.265 brouard 4759: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4760: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4761: }
4762: if( iage <= iagemax){
4763: if(pos>=1.e-5){
1.265 brouard 4764: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4765: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4766: }else if( nj==2){
4767: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4768: }
4769: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4770: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4771: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4772: } else{
4773: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4774: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4775: }
1.240 brouard 4776: }
1.265 brouard 4777: pospropt[s1] +=posprop[s1];
4778: } /* end loop s1 */
1.251 brouard 4779: /* pospropt=0.; */
1.265 brouard 4780: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4781: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4782: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4783: if(first==1){
1.265 brouard 4784: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4785: }
1.265 brouard 4786: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4787: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4788: }
1.265 brouard 4789: if(s1!=0 && m!=0)
4790: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4791: }
1.265 brouard 4792: } /* end loop s1 */
1.251 brouard 4793: posproptt=0.;
1.265 brouard 4794: for(s1=1; s1 <=nlstate; s1++){
4795: posproptt += pospropt[s1];
1.251 brouard 4796: }
4797: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4798: fprintf(ficresphtm,"</tr>\n");
4799: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4800: if(iage <= iagemax)
4801: fprintf(ficresp,"\n");
1.240 brouard 4802: }
1.251 brouard 4803: if(first==1)
4804: printf("Others in log...\n");
4805: fprintf(ficlog,"\n");
4806: } /* end loop age iage */
1.265 brouard 4807:
1.251 brouard 4808: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4809: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4810: if(posproptt < 1.e-5){
1.265 brouard 4811: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4812: }else{
1.265 brouard 4813: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4814: }
1.226 brouard 4815: }
1.251 brouard 4816: fprintf(ficresphtm,"</tr>\n");
4817: fprintf(ficresphtm,"</table>\n");
4818: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4819: if(posproptt < 1.e-5){
1.251 brouard 4820: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4821: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4822: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4823: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4824: invalidvarcomb[j1]=1;
1.226 brouard 4825: }else{
1.251 brouard 4826: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4827: invalidvarcomb[j1]=0;
1.226 brouard 4828: }
1.251 brouard 4829: fprintf(ficresphtmfr,"</table>\n");
4830: fprintf(ficlog,"\n");
4831: if(j!=0){
4832: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4833: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4834: for(k=1; k <=(nlstate+ndeath); k++){
4835: if (k != i) {
1.265 brouard 4836: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4837: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4838: if(j1==1){ /* All dummy covariates to zero */
4839: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4840: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4841: printf("%d%d ",i,k);
4842: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4843: 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]));
4844: 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]));
4845: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4846: }
1.253 brouard 4847: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4848: for(iage=iagemin; iage <= iagemax+3; iage++){
4849: x[iage]= (double)iage;
4850: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4851: /* 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 4852: }
1.268 brouard 4853: /* Some are not finite, but linreg will ignore these ages */
4854: no=0;
1.253 brouard 4855: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4856: pstart[s1]=b;
4857: pstart[s1-1]=a;
1.252 brouard 4858: }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 */
4859: 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]);
4860: 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 4861: 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 4862: printf("%d%d ",i,k);
4863: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4864: 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 4865: }else{ /* Other cases, like quantitative fixed or varying covariates */
4866: ;
4867: }
4868: /* printf("%12.7f )", param[i][jj][k]); */
4869: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4870: s1++;
1.251 brouard 4871: } /* end jj */
4872: } /* end k!= i */
4873: } /* end k */
1.265 brouard 4874: } /* end i, s1 */
1.251 brouard 4875: } /* end j !=0 */
4876: } /* end selected combination of covariate j1 */
4877: if(j==0){ /* We can estimate starting values from the occurences in each case */
4878: printf("#Freqsummary: Starting values for the constants:\n");
4879: fprintf(ficlog,"\n");
1.265 brouard 4880: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4881: for(k=1; k <=(nlstate+ndeath); k++){
4882: if (k != i) {
4883: printf("%d%d ",i,k);
4884: fprintf(ficlog,"%d%d ",i,k);
4885: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4886: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4887: if(jj==1){ /* Age has to be done */
1.265 brouard 4888: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4889: 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]));
4890: 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 4891: }
4892: /* printf("%12.7f )", param[i][jj][k]); */
4893: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4894: s1++;
1.250 brouard 4895: }
1.251 brouard 4896: printf("\n");
4897: fprintf(ficlog,"\n");
1.250 brouard 4898: }
4899: }
1.284 brouard 4900: } /* end of state i */
1.251 brouard 4901: printf("#Freqsummary\n");
4902: fprintf(ficlog,"\n");
1.265 brouard 4903: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4904: for(s2=-1; s2 <=nlstate+ndeath; s2++){
4905: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
4906: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4907: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4908: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
4909: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
4910: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 4911: /* } */
4912: }
1.265 brouard 4913: } /* end loop s1 */
1.251 brouard 4914:
4915: printf("\n");
4916: fprintf(ficlog,"\n");
4917: } /* end j=0 */
1.249 brouard 4918: } /* end j */
1.252 brouard 4919:
1.253 brouard 4920: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4921: for(i=1, jk=1; i <=nlstate; i++){
4922: for(j=1; j <=nlstate+ndeath; j++){
4923: if(j!=i){
4924: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4925: printf("%1d%1d",i,j);
4926: fprintf(ficparo,"%1d%1d",i,j);
4927: for(k=1; k<=ncovmodel;k++){
4928: /* printf(" %lf",param[i][j][k]); */
4929: /* fprintf(ficparo," %lf",param[i][j][k]); */
4930: p[jk]=pstart[jk];
4931: printf(" %f ",pstart[jk]);
4932: fprintf(ficparo," %f ",pstart[jk]);
4933: jk++;
4934: }
4935: printf("\n");
4936: fprintf(ficparo,"\n");
4937: }
4938: }
4939: }
4940: } /* end mle=-2 */
1.226 brouard 4941: dateintmean=dateintsum/k2cpt;
1.240 brouard 4942:
1.226 brouard 4943: fclose(ficresp);
4944: fclose(ficresphtm);
4945: fclose(ficresphtmfr);
1.283 brouard 4946: free_vector(idq,1,nqfveff);
1.226 brouard 4947: free_vector(meanq,1,nqfveff);
1.284 brouard 4948: free_vector(stdq,1,nqfveff);
1.226 brouard 4949: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 4950: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
4951: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 4952: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4953: free_vector(pospropt,1,nlstate);
4954: free_vector(posprop,1,nlstate);
1.251 brouard 4955: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4956: free_vector(pp,1,nlstate);
4957: /* End of freqsummary */
4958: }
1.126 brouard 4959:
1.268 brouard 4960: /* Simple linear regression */
4961: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
4962:
4963: /* y=a+bx regression */
4964: double sumx = 0.0; /* sum of x */
4965: double sumx2 = 0.0; /* sum of x**2 */
4966: double sumxy = 0.0; /* sum of x * y */
4967: double sumy = 0.0; /* sum of y */
4968: double sumy2 = 0.0; /* sum of y**2 */
4969: double sume2 = 0.0; /* sum of square or residuals */
4970: double yhat;
4971:
4972: double denom=0;
4973: int i;
4974: int ne=*no;
4975:
4976: for ( i=ifi, ne=0;i<=ila;i++) {
4977: if(!isfinite(x[i]) || !isfinite(y[i])){
4978: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4979: continue;
4980: }
4981: ne=ne+1;
4982: sumx += x[i];
4983: sumx2 += x[i]*x[i];
4984: sumxy += x[i] * y[i];
4985: sumy += y[i];
4986: sumy2 += y[i]*y[i];
4987: denom = (ne * sumx2 - sumx*sumx);
4988: /* 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); */
4989: }
4990:
4991: denom = (ne * sumx2 - sumx*sumx);
4992: if (denom == 0) {
4993: // vertical, slope m is infinity
4994: *b = INFINITY;
4995: *a = 0;
4996: if (r) *r = 0;
4997: return 1;
4998: }
4999:
5000: *b = (ne * sumxy - sumx * sumy) / denom;
5001: *a = (sumy * sumx2 - sumx * sumxy) / denom;
5002: if (r!=NULL) {
5003: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
5004: sqrt((sumx2 - sumx*sumx/ne) *
5005: (sumy2 - sumy*sumy/ne));
5006: }
5007: *no=ne;
5008: for ( i=ifi, ne=0;i<=ila;i++) {
5009: if(!isfinite(x[i]) || !isfinite(y[i])){
5010: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
5011: continue;
5012: }
5013: ne=ne+1;
5014: yhat = y[i] - *a -*b* x[i];
5015: sume2 += yhat * yhat ;
5016:
5017: denom = (ne * sumx2 - sumx*sumx);
5018: /* 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); */
5019: }
5020: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
5021: *sa= *sb * sqrt(sumx2/ne);
5022:
5023: return 0;
5024: }
5025:
1.126 brouard 5026: /************ Prevalence ********************/
1.227 brouard 5027: 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)
5028: {
5029: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5030: in each health status at the date of interview (if between dateprev1 and dateprev2).
5031: We still use firstpass and lastpass as another selection.
5032: */
1.126 brouard 5033:
1.227 brouard 5034: int i, m, jk, j1, bool, z1,j, iv;
5035: int mi; /* Effective wave */
5036: int iage;
5037: double agebegin, ageend;
5038:
5039: double **prop;
5040: double posprop;
5041: double y2; /* in fractional years */
5042: int iagemin, iagemax;
5043: int first; /** to stop verbosity which is redirected to log file */
5044:
5045: iagemin= (int) agemin;
5046: iagemax= (int) agemax;
5047: /*pp=vector(1,nlstate);*/
1.251 brouard 5048: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5049: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5050: j1=0;
1.222 brouard 5051:
1.227 brouard 5052: /*j=cptcoveff;*/
5053: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5054:
1.227 brouard 5055: first=1;
5056: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5057: for (i=1; i<=nlstate; i++)
1.251 brouard 5058: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5059: prop[i][iage]=0.0;
5060: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5061: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5062: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5063:
5064: for (i=1; i<=imx; i++) { /* Each individual */
5065: bool=1;
5066: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5067: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5068: m=mw[mi][i];
5069: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5070: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5071: for (z1=1; z1<=cptcoveff; z1++){
5072: if( Fixed[Tmodelind[z1]]==1){
5073: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5074: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5075: bool=0;
5076: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5077: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5078: bool=0;
5079: }
5080: }
5081: if(bool==1){ /* Otherwise we skip that wave/person */
5082: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5083: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5084: if(m >=firstpass && m <=lastpass){
5085: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5086: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5087: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5088: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5089: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5090: 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);
5091: exit(1);
5092: }
5093: if (s[m][i]>0 && s[m][i]<=nlstate) {
5094: /*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]]);*/
5095: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5096: prop[s[m][i]][iagemax+3] += weight[i];
5097: } /* end valid statuses */
5098: } /* end selection of dates */
5099: } /* end selection of waves */
5100: } /* end bool */
5101: } /* end wave */
5102: } /* end individual */
5103: for(i=iagemin; i <= iagemax+3; i++){
5104: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5105: posprop += prop[jk][i];
5106: }
5107:
5108: for(jk=1; jk <=nlstate ; jk++){
5109: if( i <= iagemax){
5110: if(posprop>=1.e-5){
5111: probs[i][jk][j1]= prop[jk][i]/posprop;
5112: } else{
5113: if(first==1){
5114: first=0;
1.266 brouard 5115: 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]);
5116: fprintf(ficlog,"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]);
5117: }else{
5118: fprintf(ficlog,"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]);
1.227 brouard 5119: }
5120: }
5121: }
5122: }/* end jk */
5123: }/* end i */
1.222 brouard 5124: /*} *//* end i1 */
1.227 brouard 5125: } /* end j1 */
1.222 brouard 5126:
1.227 brouard 5127: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5128: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5129: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5130: } /* End of prevalence */
1.126 brouard 5131:
5132: /************* Waves Concatenation ***************/
5133:
5134: 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)
5135: {
5136: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
5137: Death is a valid wave (if date is known).
5138: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5139: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
5140: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 5141: */
1.126 brouard 5142:
1.224 brouard 5143: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5144: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5145: double sum=0., jmean=0.;*/
1.224 brouard 5146: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5147: int j, k=0,jk, ju, jl;
5148: double sum=0.;
5149: first=0;
1.214 brouard 5150: firstwo=0;
1.217 brouard 5151: firsthree=0;
1.218 brouard 5152: firstfour=0;
1.164 brouard 5153: jmin=100000;
1.126 brouard 5154: jmax=-1;
5155: jmean=0.;
1.224 brouard 5156:
5157: /* Treating live states */
1.214 brouard 5158: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5159: mi=0; /* First valid wave */
1.227 brouard 5160: mli=0; /* Last valid wave */
1.126 brouard 5161: m=firstpass;
1.214 brouard 5162: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5163: 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 */
5164: mli=m-1;/* mw[++mi][i]=m-1; */
5165: }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 */
5166: mw[++mi][i]=m;
5167: mli=m;
1.224 brouard 5168: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5169: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5170: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5171: }
1.227 brouard 5172: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5173: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5174: break;
1.224 brouard 5175: #else
1.227 brouard 5176: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5177: if(firsthree == 0){
1.262 brouard 5178: 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 5179: firsthree=1;
5180: }
1.262 brouard 5181: 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 5182: mw[++mi][i]=m;
5183: mli=m;
5184: }
5185: if(s[m][i]==-2){ /* Vital status is really unknown */
5186: nbwarn++;
5187: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5188: 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);
5189: 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);
5190: }
5191: break;
5192: }
5193: break;
1.224 brouard 5194: #endif
1.227 brouard 5195: }/* End m >= lastpass */
1.126 brouard 5196: }/* end while */
1.224 brouard 5197:
1.227 brouard 5198: /* 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 5199: /* After last pass */
1.224 brouard 5200: /* Treating death states */
1.214 brouard 5201: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5202: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5203: /* } */
1.126 brouard 5204: mi++; /* Death is another wave */
5205: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5206: /* Only death is a correct wave */
1.126 brouard 5207: mw[mi][i]=m;
1.257 brouard 5208: } /* else not in a death state */
1.224 brouard 5209: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5210: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5211: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5212: 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 */
5213: nbwarn++;
5214: if(firstfiv==0){
5215: 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 );
5216: firstfiv=1;
5217: }else{
5218: 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 );
5219: }
5220: }else{ /* Death occured afer last wave potential bias */
5221: nberr++;
5222: if(firstwo==0){
1.257 brouard 5223: 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 5224: firstwo=1;
5225: }
1.257 brouard 5226: 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 5227: }
1.257 brouard 5228: }else{ /* if date of interview is unknown */
1.227 brouard 5229: /* death is known but not confirmed by death status at any wave */
5230: if(firstfour==0){
5231: 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 );
5232: firstfour=1;
5233: }
5234: 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 5235: }
1.224 brouard 5236: } /* end if date of death is known */
5237: #endif
5238: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5239: /* wav[i]=mw[mi][i]; */
1.126 brouard 5240: if(mi==0){
5241: nbwarn++;
5242: if(first==0){
1.227 brouard 5243: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5244: first=1;
1.126 brouard 5245: }
5246: if(first==1){
1.227 brouard 5247: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5248: }
5249: } /* end mi==0 */
5250: } /* End individuals */
1.214 brouard 5251: /* wav and mw are no more changed */
1.223 brouard 5252:
1.214 brouard 5253:
1.126 brouard 5254: for(i=1; i<=imx; i++){
5255: for(mi=1; mi<wav[i];mi++){
5256: if (stepm <=0)
1.227 brouard 5257: dh[mi][i]=1;
1.126 brouard 5258: else{
1.260 brouard 5259: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5260: if (agedc[i] < 2*AGESUP) {
5261: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5262: if(j==0) j=1; /* Survives at least one month after exam */
5263: else if(j<0){
5264: nberr++;
5265: 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]);
5266: j=1; /* Temporary Dangerous patch */
5267: 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);
5268: 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]);
5269: 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);
5270: }
5271: k=k+1;
5272: if (j >= jmax){
5273: jmax=j;
5274: ijmax=i;
5275: }
5276: if (j <= jmin){
5277: jmin=j;
5278: ijmin=i;
5279: }
5280: sum=sum+j;
5281: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5282: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5283: }
5284: }
5285: else{
5286: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5287: /* 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 5288:
1.227 brouard 5289: k=k+1;
5290: if (j >= jmax) {
5291: jmax=j;
5292: ijmax=i;
5293: }
5294: else if (j <= jmin){
5295: jmin=j;
5296: ijmin=i;
5297: }
5298: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5299: /*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]);*/
5300: if(j<0){
5301: nberr++;
5302: 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]);
5303: 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]);
5304: }
5305: sum=sum+j;
5306: }
5307: jk= j/stepm;
5308: jl= j -jk*stepm;
5309: ju= j -(jk+1)*stepm;
5310: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5311: if(jl==0){
5312: dh[mi][i]=jk;
5313: bh[mi][i]=0;
5314: }else{ /* We want a negative bias in order to only have interpolation ie
5315: * to avoid the price of an extra matrix product in likelihood */
5316: dh[mi][i]=jk+1;
5317: bh[mi][i]=ju;
5318: }
5319: }else{
5320: if(jl <= -ju){
5321: dh[mi][i]=jk;
5322: bh[mi][i]=jl; /* bias is positive if real duration
5323: * is higher than the multiple of stepm and negative otherwise.
5324: */
5325: }
5326: else{
5327: dh[mi][i]=jk+1;
5328: bh[mi][i]=ju;
5329: }
5330: if(dh[mi][i]==0){
5331: dh[mi][i]=1; /* At least one step */
5332: bh[mi][i]=ju; /* At least one step */
5333: /* 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);*/
5334: }
5335: } /* end if mle */
1.126 brouard 5336: }
5337: } /* end wave */
5338: }
5339: jmean=sum/k;
5340: 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 5341: 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 5342: }
1.126 brouard 5343:
5344: /*********** Tricode ****************************/
1.220 brouard 5345: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5346: {
5347: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5348: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5349: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5350: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5351: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5352: */
1.130 brouard 5353:
1.242 brouard 5354: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5355: int modmaxcovj=0; /* Modality max of covariates j */
5356: int cptcode=0; /* Modality max of covariates j */
5357: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5358:
5359:
1.242 brouard 5360: /* cptcoveff=0; */
5361: /* *cptcov=0; */
1.126 brouard 5362:
1.242 brouard 5363: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.285 brouard 5364: for (k=1; k <= maxncov; k++)
5365: for(j=1; j<=2; j++)
5366: nbcode[k][j]=0; /* Valgrind */
1.126 brouard 5367:
1.242 brouard 5368: /* Loop on covariates without age and products and no quantitative variable */
5369: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5370: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5371: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5372: switch(Fixed[k]) {
5373: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5374: 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*/
5375: ij=(int)(covar[Tvar[k]][i]);
5376: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5377: * If product of Vn*Vm, still boolean *:
5378: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5379: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5380: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5381: modality of the nth covariate of individual i. */
5382: if (ij > modmaxcovj)
5383: modmaxcovj=ij;
5384: else if (ij < modmincovj)
5385: modmincovj=ij;
1.287 ! brouard 5386: if (ij <0 || ij >1 ){
! 5387: printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
! 5388: fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
! 5389: }
! 5390: if ((ij < -1) || (ij > NCOVMAX)){
1.242 brouard 5391: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5392: exit(1);
5393: }else
5394: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5395: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5396: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5397: /* getting the maximum value of the modality of the covariate
5398: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5399: female ies 1, then modmaxcovj=1.
5400: */
5401: } /* end for loop on individuals i */
5402: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5403: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5404: cptcode=modmaxcovj;
5405: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5406: /*for (i=0; i<=cptcode; i++) {*/
5407: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5408: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5409: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5410: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5411: if( j != -1){
5412: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5413: covariate for which somebody answered excluding
5414: undefined. Usually 2: 0 and 1. */
5415: }
5416: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5417: covariate for which somebody answered including
5418: undefined. Usually 3: -1, 0 and 1. */
5419: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5420: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5421: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5422:
1.242 brouard 5423: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5424: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5425: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5426: /* modmincovj=3; modmaxcovj = 7; */
5427: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5428: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5429: /* defining two dummy variables: variables V1_1 and V1_2.*/
5430: /* nbcode[Tvar[j]][ij]=k; */
5431: /* nbcode[Tvar[j]][1]=0; */
5432: /* nbcode[Tvar[j]][2]=1; */
5433: /* nbcode[Tvar[j]][3]=2; */
5434: /* To be continued (not working yet). */
5435: ij=0; /* ij is similar to i but can jump over null modalities */
1.287 ! brouard 5436:
! 5437: /* 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*/
! 5438: /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
! 5439: /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
! 5440: * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
! 5441: /*, could be restored in the future */
! 5442: 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 5443: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5444: break;
5445: }
5446: ij++;
1.287 ! brouard 5447: 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 5448: cptcode = ij; /* New max modality for covar j */
5449: } /* end of loop on modality i=-1 to 1 or more */
5450: break;
5451: case 1: /* Testing on varying covariate, could be simple and
5452: * should look at waves or product of fixed *
5453: * varying. No time to test -1, assuming 0 and 1 only */
5454: ij=0;
5455: for(i=0; i<=1;i++){
5456: nbcode[Tvar[k]][++ij]=i;
5457: }
5458: break;
5459: default:
5460: break;
5461: } /* end switch */
5462: } /* end dummy test */
1.287 ! brouard 5463: } /* 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 5464:
5465: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5466: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5467: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5468: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5469: 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 */
5470: 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 */
5471: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5472: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5473:
5474: ij=0;
5475: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5476: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5477: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5478: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5479: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5480: /* If product not in single variable we don't print results */
5481: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5482: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5483: 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*/
5484: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5485: 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 */
5486: if(Fixed[k]!=0)
5487: anyvaryingduminmodel=1;
5488: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5489: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5490: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5491: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5492: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5493: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5494: }
5495: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5496: /* ij--; */
5497: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5498: *cptcov=ij; /*Number of total real effective covariates: effective
5499: * because they can be excluded from the model and real
5500: * if in the model but excluded because missing values, but how to get k from ij?*/
5501: for(j=ij+1; j<= cptcovt; j++){
5502: Tvaraff[j]=0;
5503: Tmodelind[j]=0;
5504: }
5505: for(j=ntveff+1; j<= cptcovt; j++){
5506: TmodelInvind[j]=0;
5507: }
5508: /* To be sorted */
5509: ;
5510: }
1.126 brouard 5511:
1.145 brouard 5512:
1.126 brouard 5513: /*********** Health Expectancies ****************/
5514:
1.235 brouard 5515: 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 5516:
5517: {
5518: /* Health expectancies, no variances */
1.164 brouard 5519: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5520: int nhstepma, nstepma; /* Decreasing with age */
5521: double age, agelim, hf;
5522: double ***p3mat;
5523: double eip;
5524:
1.238 brouard 5525: /* pstamp(ficreseij); */
1.126 brouard 5526: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5527: fprintf(ficreseij,"# Age");
5528: for(i=1; i<=nlstate;i++){
5529: for(j=1; j<=nlstate;j++){
5530: fprintf(ficreseij," e%1d%1d ",i,j);
5531: }
5532: fprintf(ficreseij," e%1d. ",i);
5533: }
5534: fprintf(ficreseij,"\n");
5535:
5536:
5537: if(estepm < stepm){
5538: printf ("Problem %d lower than %d\n",estepm, stepm);
5539: }
5540: else hstepm=estepm;
5541: /* We compute the life expectancy from trapezoids spaced every estepm months
5542: * This is mainly to measure the difference between two models: for example
5543: * if stepm=24 months pijx are given only every 2 years and by summing them
5544: * we are calculating an estimate of the Life Expectancy assuming a linear
5545: * progression in between and thus overestimating or underestimating according
5546: * to the curvature of the survival function. If, for the same date, we
5547: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5548: * to compare the new estimate of Life expectancy with the same linear
5549: * hypothesis. A more precise result, taking into account a more precise
5550: * curvature will be obtained if estepm is as small as stepm. */
5551:
5552: /* For example we decided to compute the life expectancy with the smallest unit */
5553: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5554: nhstepm is the number of hstepm from age to agelim
5555: nstepm is the number of stepm from age to agelin.
1.270 brouard 5556: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5557: and note for a fixed period like estepm months */
5558: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5559: survival function given by stepm (the optimization length). Unfortunately it
5560: means that if the survival funtion is printed only each two years of age and if
5561: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5562: results. So we changed our mind and took the option of the best precision.
5563: */
5564: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5565:
5566: agelim=AGESUP;
5567: /* If stepm=6 months */
5568: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5569: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5570:
5571: /* nhstepm age range expressed in number of stepm */
5572: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5573: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5574: /* if (stepm >= YEARM) hstepm=1;*/
5575: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5576: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5577:
5578: for (age=bage; age<=fage; age ++){
5579: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5580: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5581: /* if (stepm >= YEARM) hstepm=1;*/
5582: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5583:
5584: /* If stepm=6 months */
5585: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5586: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5587:
1.235 brouard 5588: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5589:
5590: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5591:
5592: printf("%d|",(int)age);fflush(stdout);
5593: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5594:
5595: /* Computing expectancies */
5596: for(i=1; i<=nlstate;i++)
5597: for(j=1; j<=nlstate;j++)
5598: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5599: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5600:
5601: /* 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]);*/
5602:
5603: }
5604:
5605: fprintf(ficreseij,"%3.0f",age );
5606: for(i=1; i<=nlstate;i++){
5607: eip=0;
5608: for(j=1; j<=nlstate;j++){
5609: eip +=eij[i][j][(int)age];
5610: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5611: }
5612: fprintf(ficreseij,"%9.4f", eip );
5613: }
5614: fprintf(ficreseij,"\n");
5615:
5616: }
5617: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5618: printf("\n");
5619: fprintf(ficlog,"\n");
5620:
5621: }
5622:
1.235 brouard 5623: 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 5624:
5625: {
5626: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5627: to initial status i, ei. .
1.126 brouard 5628: */
5629: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5630: int nhstepma, nstepma; /* Decreasing with age */
5631: double age, agelim, hf;
5632: double ***p3matp, ***p3matm, ***varhe;
5633: double **dnewm,**doldm;
5634: double *xp, *xm;
5635: double **gp, **gm;
5636: double ***gradg, ***trgradg;
5637: int theta;
5638:
5639: double eip, vip;
5640:
5641: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5642: xp=vector(1,npar);
5643: xm=vector(1,npar);
5644: dnewm=matrix(1,nlstate*nlstate,1,npar);
5645: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5646:
5647: pstamp(ficresstdeij);
5648: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5649: fprintf(ficresstdeij,"# Age");
5650: for(i=1; i<=nlstate;i++){
5651: for(j=1; j<=nlstate;j++)
5652: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5653: fprintf(ficresstdeij," e%1d. ",i);
5654: }
5655: fprintf(ficresstdeij,"\n");
5656:
5657: pstamp(ficrescveij);
5658: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5659: fprintf(ficrescveij,"# Age");
5660: for(i=1; i<=nlstate;i++)
5661: for(j=1; j<=nlstate;j++){
5662: cptj= (j-1)*nlstate+i;
5663: for(i2=1; i2<=nlstate;i2++)
5664: for(j2=1; j2<=nlstate;j2++){
5665: cptj2= (j2-1)*nlstate+i2;
5666: if(cptj2 <= cptj)
5667: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5668: }
5669: }
5670: fprintf(ficrescveij,"\n");
5671:
5672: if(estepm < stepm){
5673: printf ("Problem %d lower than %d\n",estepm, stepm);
5674: }
5675: else hstepm=estepm;
5676: /* We compute the life expectancy from trapezoids spaced every estepm months
5677: * This is mainly to measure the difference between two models: for example
5678: * if stepm=24 months pijx are given only every 2 years and by summing them
5679: * we are calculating an estimate of the Life Expectancy assuming a linear
5680: * progression in between and thus overestimating or underestimating according
5681: * to the curvature of the survival function. If, for the same date, we
5682: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5683: * to compare the new estimate of Life expectancy with the same linear
5684: * hypothesis. A more precise result, taking into account a more precise
5685: * curvature will be obtained if estepm is as small as stepm. */
5686:
5687: /* For example we decided to compute the life expectancy with the smallest unit */
5688: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5689: nhstepm is the number of hstepm from age to agelim
5690: nstepm is the number of stepm from age to agelin.
5691: Look at hpijx to understand the reason of that which relies in memory size
5692: and note for a fixed period like estepm months */
5693: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5694: survival function given by stepm (the optimization length). Unfortunately it
5695: means that if the survival funtion is printed only each two years of age and if
5696: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5697: results. So we changed our mind and took the option of the best precision.
5698: */
5699: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5700:
5701: /* If stepm=6 months */
5702: /* nhstepm age range expressed in number of stepm */
5703: agelim=AGESUP;
5704: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5705: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5706: /* if (stepm >= YEARM) hstepm=1;*/
5707: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5708:
5709: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5710: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5711: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5712: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5713: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5714: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5715:
5716: for (age=bage; age<=fage; age ++){
5717: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5718: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5719: /* if (stepm >= YEARM) hstepm=1;*/
5720: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5721:
1.126 brouard 5722: /* If stepm=6 months */
5723: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5724: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5725:
5726: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5727:
1.126 brouard 5728: /* Computing Variances of health expectancies */
5729: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5730: decrease memory allocation */
5731: for(theta=1; theta <=npar; theta++){
5732: for(i=1; i<=npar; i++){
1.222 brouard 5733: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5734: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5735: }
1.235 brouard 5736: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5737: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5738:
1.126 brouard 5739: for(j=1; j<= nlstate; j++){
1.222 brouard 5740: for(i=1; i<=nlstate; i++){
5741: for(h=0; h<=nhstepm-1; h++){
5742: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5743: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5744: }
5745: }
1.126 brouard 5746: }
1.218 brouard 5747:
1.126 brouard 5748: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5749: for(h=0; h<=nhstepm-1; h++){
5750: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5751: }
1.126 brouard 5752: }/* End theta */
5753:
5754:
5755: for(h=0; h<=nhstepm-1; h++)
5756: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5757: for(theta=1; theta <=npar; theta++)
5758: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5759:
1.218 brouard 5760:
1.222 brouard 5761: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5762: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5763: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5764:
1.222 brouard 5765: printf("%d|",(int)age);fflush(stdout);
5766: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5767: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5768: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5769: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5770: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5771: for(ij=1;ij<=nlstate*nlstate;ij++)
5772: for(ji=1;ji<=nlstate*nlstate;ji++)
5773: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5774: }
5775: }
1.218 brouard 5776:
1.126 brouard 5777: /* Computing expectancies */
1.235 brouard 5778: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5779: for(i=1; i<=nlstate;i++)
5780: for(j=1; j<=nlstate;j++)
1.222 brouard 5781: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5782: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5783:
1.222 brouard 5784: /* 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 5785:
1.222 brouard 5786: }
1.269 brouard 5787:
5788: /* Standard deviation of expectancies ij */
1.126 brouard 5789: fprintf(ficresstdeij,"%3.0f",age );
5790: for(i=1; i<=nlstate;i++){
5791: eip=0.;
5792: vip=0.;
5793: for(j=1; j<=nlstate;j++){
1.222 brouard 5794: eip += eij[i][j][(int)age];
5795: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5796: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5797: 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 5798: }
5799: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5800: }
5801: fprintf(ficresstdeij,"\n");
1.218 brouard 5802:
1.269 brouard 5803: /* Variance of expectancies ij */
1.126 brouard 5804: fprintf(ficrescveij,"%3.0f",age );
5805: for(i=1; i<=nlstate;i++)
5806: for(j=1; j<=nlstate;j++){
1.222 brouard 5807: cptj= (j-1)*nlstate+i;
5808: for(i2=1; i2<=nlstate;i2++)
5809: for(j2=1; j2<=nlstate;j2++){
5810: cptj2= (j2-1)*nlstate+i2;
5811: if(cptj2 <= cptj)
5812: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5813: }
1.126 brouard 5814: }
5815: fprintf(ficrescveij,"\n");
1.218 brouard 5816:
1.126 brouard 5817: }
5818: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5819: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5820: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5821: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5822: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5823: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5824: printf("\n");
5825: fprintf(ficlog,"\n");
1.218 brouard 5826:
1.126 brouard 5827: free_vector(xm,1,npar);
5828: free_vector(xp,1,npar);
5829: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5830: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5831: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5832: }
1.218 brouard 5833:
1.126 brouard 5834: /************ Variance ******************/
1.235 brouard 5835: 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 5836: {
1.279 brouard 5837: /** Variance of health expectancies
5838: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5839: * double **newm;
5840: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5841: */
1.218 brouard 5842:
5843: /* int movingaverage(); */
5844: double **dnewm,**doldm;
5845: double **dnewmp,**doldmp;
5846: int i, j, nhstepm, hstepm, h, nstepm ;
5847: int k;
5848: double *xp;
1.279 brouard 5849: double **gp, **gm; /**< for var eij */
5850: double ***gradg, ***trgradg; /**< for var eij */
5851: double **gradgp, **trgradgp; /**< for var p point j */
5852: double *gpp, *gmp; /**< for var p point j */
5853: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5854: double ***p3mat;
5855: double age,agelim, hf;
5856: /* double ***mobaverage; */
5857: int theta;
5858: char digit[4];
5859: char digitp[25];
5860:
5861: char fileresprobmorprev[FILENAMELENGTH];
5862:
5863: if(popbased==1){
5864: if(mobilav!=0)
5865: strcpy(digitp,"-POPULBASED-MOBILAV_");
5866: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5867: }
5868: else
5869: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5870:
1.218 brouard 5871: /* if (mobilav!=0) { */
5872: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5873: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5874: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5875: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5876: /* } */
5877: /* } */
5878:
5879: strcpy(fileresprobmorprev,"PRMORPREV-");
5880: sprintf(digit,"%-d",ij);
5881: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5882: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5883: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5884: strcat(fileresprobmorprev,fileresu);
5885: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5886: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5887: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5888: }
5889: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5890: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5891: pstamp(ficresprobmorprev);
5892: 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 5893: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5894: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5895: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5896: }
5897: for(j=1;j<=cptcoveff;j++)
5898: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5899: fprintf(ficresprobmorprev,"\n");
5900:
1.218 brouard 5901: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5902: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5903: fprintf(ficresprobmorprev," p.%-d SE",j);
5904: for(i=1; i<=nlstate;i++)
5905: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5906: }
5907: fprintf(ficresprobmorprev,"\n");
5908:
5909: fprintf(ficgp,"\n# Routine varevsij");
5910: fprintf(ficgp,"\nunset title \n");
5911: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5912: 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");
5913: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 5914:
1.218 brouard 5915: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5916: pstamp(ficresvij);
5917: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5918: if(popbased==1)
5919: 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);
5920: else
5921: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5922: fprintf(ficresvij,"# Age");
5923: for(i=1; i<=nlstate;i++)
5924: for(j=1; j<=nlstate;j++)
5925: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5926: fprintf(ficresvij,"\n");
5927:
5928: xp=vector(1,npar);
5929: dnewm=matrix(1,nlstate,1,npar);
5930: doldm=matrix(1,nlstate,1,nlstate);
5931: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5932: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5933:
5934: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5935: gpp=vector(nlstate+1,nlstate+ndeath);
5936: gmp=vector(nlstate+1,nlstate+ndeath);
5937: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5938:
1.218 brouard 5939: if(estepm < stepm){
5940: printf ("Problem %d lower than %d\n",estepm, stepm);
5941: }
5942: else hstepm=estepm;
5943: /* For example we decided to compute the life expectancy with the smallest unit */
5944: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5945: nhstepm is the number of hstepm from age to agelim
5946: nstepm is the number of stepm from age to agelim.
5947: Look at function hpijx to understand why because of memory size limitations,
5948: we decided (b) to get a life expectancy respecting the most precise curvature of the
5949: survival function given by stepm (the optimization length). Unfortunately it
5950: means that if the survival funtion is printed every two years of age and if
5951: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5952: results. So we changed our mind and took the option of the best precision.
5953: */
5954: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5955: agelim = AGESUP;
5956: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5957: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5958: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5959: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5960: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5961: gp=matrix(0,nhstepm,1,nlstate);
5962: gm=matrix(0,nhstepm,1,nlstate);
5963:
5964:
5965: for(theta=1; theta <=npar; theta++){
5966: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5967: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5968: }
1.279 brouard 5969: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
5970: * returns into prlim .
5971: */
1.242 brouard 5972: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 5973:
5974: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 5975: if (popbased==1) {
5976: if(mobilav ==0){
5977: for(i=1; i<=nlstate;i++)
5978: prlim[i][i]=probs[(int)age][i][ij];
5979: }else{ /* mobilav */
5980: for(i=1; i<=nlstate;i++)
5981: prlim[i][i]=mobaverage[(int)age][i][ij];
5982: }
5983: }
1.279 brouard 5984: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
5985: */
5986: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
5987: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
5988: * at horizon h in state j including mortality.
5989: */
1.218 brouard 5990: for(j=1; j<= nlstate; j++){
5991: for(h=0; h<=nhstepm; h++){
5992: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5993: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5994: }
5995: }
1.279 brouard 5996: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 5997: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 5998: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 5999: */
6000: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6001: for(i=1,gpp[j]=0.; i<= nlstate; i++)
6002: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 6003: }
6004:
6005: /* Again with minus shift */
1.218 brouard 6006:
6007: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
6008: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6009:
1.242 brouard 6010: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 6011:
6012: if (popbased==1) {
6013: if(mobilav ==0){
6014: for(i=1; i<=nlstate;i++)
6015: prlim[i][i]=probs[(int)age][i][ij];
6016: }else{ /* mobilav */
6017: for(i=1; i<=nlstate;i++)
6018: prlim[i][i]=mobaverage[(int)age][i][ij];
6019: }
6020: }
6021:
1.235 brouard 6022: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6023:
6024: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6025: for(h=0; h<=nhstepm; h++){
6026: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6027: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6028: }
6029: }
6030: /* This for computing probability of death (h=1 means
6031: computed over hstepm matrices product = hstepm*stepm months)
6032: as a weighted average of prlim.
6033: */
6034: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6035: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6036: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6037: }
1.279 brouard 6038: /* end shifting computations */
6039:
6040: /**< Computing gradient matrix at horizon h
6041: */
1.218 brouard 6042: for(j=1; j<= nlstate; j++) /* vareij */
6043: for(h=0; h<=nhstepm; h++){
6044: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6045: }
1.279 brouard 6046: /**< Gradient of overall mortality p.3 (or p.j)
6047: */
6048: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6049: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6050: }
6051:
6052: } /* End theta */
1.279 brouard 6053:
6054: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6055: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6056:
6057: for(h=0; h<=nhstepm; h++) /* veij */
6058: for(j=1; j<=nlstate;j++)
6059: for(theta=1; theta <=npar; theta++)
6060: trgradg[h][j][theta]=gradg[h][theta][j];
6061:
6062: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6063: for(theta=1; theta <=npar; theta++)
6064: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6065: /**< as well as its transposed matrix
6066: */
1.218 brouard 6067:
6068: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6069: for(i=1;i<=nlstate;i++)
6070: for(j=1;j<=nlstate;j++)
6071: vareij[i][j][(int)age] =0.;
1.279 brouard 6072:
6073: /* Computing trgradg by matcov by gradg at age and summing over h
6074: * and k (nhstepm) formula 15 of article
6075: * Lievre-Brouard-Heathcote
6076: */
6077:
1.218 brouard 6078: for(h=0;h<=nhstepm;h++){
6079: for(k=0;k<=nhstepm;k++){
6080: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6081: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6082: for(i=1;i<=nlstate;i++)
6083: for(j=1;j<=nlstate;j++)
6084: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6085: }
6086: }
6087:
1.279 brouard 6088: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6089: * p.j overall mortality formula 49 but computed directly because
6090: * we compute the grad (wix pijx) instead of grad (pijx),even if
6091: * wix is independent of theta.
6092: */
1.218 brouard 6093: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6094: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6095: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6096: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6097: varppt[j][i]=doldmp[j][i];
6098: /* end ppptj */
6099: /* x centered again */
6100:
1.242 brouard 6101: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6102:
6103: if (popbased==1) {
6104: if(mobilav ==0){
6105: for(i=1; i<=nlstate;i++)
6106: prlim[i][i]=probs[(int)age][i][ij];
6107: }else{ /* mobilav */
6108: for(i=1; i<=nlstate;i++)
6109: prlim[i][i]=mobaverage[(int)age][i][ij];
6110: }
6111: }
6112:
6113: /* This for computing probability of death (h=1 means
6114: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6115: as a weighted average of prlim.
6116: */
1.235 brouard 6117: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6118: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6119: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6120: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6121: }
6122: /* end probability of death */
6123:
6124: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6125: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6126: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6127: for(i=1; i<=nlstate;i++){
6128: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6129: }
6130: }
6131: fprintf(ficresprobmorprev,"\n");
6132:
6133: fprintf(ficresvij,"%.0f ",age );
6134: for(i=1; i<=nlstate;i++)
6135: for(j=1; j<=nlstate;j++){
6136: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6137: }
6138: fprintf(ficresvij,"\n");
6139: free_matrix(gp,0,nhstepm,1,nlstate);
6140: free_matrix(gm,0,nhstepm,1,nlstate);
6141: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6142: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6143: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6144: } /* End age */
6145: free_vector(gpp,nlstate+1,nlstate+ndeath);
6146: free_vector(gmp,nlstate+1,nlstate+ndeath);
6147: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6148: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6149: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6150: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6151: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6152: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6153: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6154: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6155: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6156: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6157: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6158: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6159: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6160: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6161: 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);
6162: /* 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 6163: */
1.218 brouard 6164: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6165: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6166:
1.218 brouard 6167: free_vector(xp,1,npar);
6168: free_matrix(doldm,1,nlstate,1,nlstate);
6169: free_matrix(dnewm,1,nlstate,1,npar);
6170: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6171: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6172: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6173: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6174: fclose(ficresprobmorprev);
6175: fflush(ficgp);
6176: fflush(fichtm);
6177: } /* end varevsij */
1.126 brouard 6178:
6179: /************ Variance of prevlim ******************/
1.269 brouard 6180: 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 6181: {
1.205 brouard 6182: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6183: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6184:
1.268 brouard 6185: double **dnewmpar,**doldm;
1.126 brouard 6186: int i, j, nhstepm, hstepm;
6187: double *xp;
6188: double *gp, *gm;
6189: double **gradg, **trgradg;
1.208 brouard 6190: double **mgm, **mgp;
1.126 brouard 6191: double age,agelim;
6192: int theta;
6193:
6194: pstamp(ficresvpl);
6195: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.241 brouard 6196: fprintf(ficresvpl,"# Age ");
6197: if(nresult >=1)
6198: fprintf(ficresvpl," Result# ");
1.126 brouard 6199: for(i=1; i<=nlstate;i++)
6200: fprintf(ficresvpl," %1d-%1d",i,i);
6201: fprintf(ficresvpl,"\n");
6202:
6203: xp=vector(1,npar);
1.268 brouard 6204: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6205: doldm=matrix(1,nlstate,1,nlstate);
6206:
6207: hstepm=1*YEARM; /* Every year of age */
6208: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6209: agelim = AGESUP;
6210: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6211: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6212: if (stepm >= YEARM) hstepm=1;
6213: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6214: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6215: mgp=matrix(1,npar,1,nlstate);
6216: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6217: gp=vector(1,nlstate);
6218: gm=vector(1,nlstate);
6219:
6220: for(theta=1; theta <=npar; theta++){
6221: for(i=1; i<=npar; i++){ /* Computes gradient */
6222: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6223: }
1.209 brouard 6224: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6225: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6226: else
1.235 brouard 6227: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6228: for(i=1;i<=nlstate;i++){
1.126 brouard 6229: gp[i] = prlim[i][i];
1.208 brouard 6230: mgp[theta][i] = prlim[i][i];
6231: }
1.126 brouard 6232: for(i=1; i<=npar; i++) /* Computes gradient */
6233: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 6234: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6235: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6236: else
1.235 brouard 6237: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6238: for(i=1;i<=nlstate;i++){
1.126 brouard 6239: gm[i] = prlim[i][i];
1.208 brouard 6240: mgm[theta][i] = prlim[i][i];
6241: }
1.126 brouard 6242: for(i=1;i<=nlstate;i++)
6243: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6244: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6245: } /* End theta */
6246:
6247: trgradg =matrix(1,nlstate,1,npar);
6248:
6249: for(j=1; j<=nlstate;j++)
6250: for(theta=1; theta <=npar; theta++)
6251: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6252: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6253: /* printf("\nmgm mgp %d ",(int)age); */
6254: /* for(j=1; j<=nlstate;j++){ */
6255: /* printf(" %d ",j); */
6256: /* for(theta=1; theta <=npar; theta++) */
6257: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6258: /* printf("\n "); */
6259: /* } */
6260: /* } */
6261: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6262: /* printf("\n gradg %d ",(int)age); */
6263: /* for(j=1; j<=nlstate;j++){ */
6264: /* printf("%d ",j); */
6265: /* for(theta=1; theta <=npar; theta++) */
6266: /* printf("%d %lf ",theta,gradg[theta][j]); */
6267: /* printf("\n "); */
6268: /* } */
6269: /* } */
1.126 brouard 6270:
6271: for(i=1;i<=nlstate;i++)
6272: varpl[i][(int)age] =0.;
1.209 brouard 6273: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6274: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6275: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6276: }else{
1.268 brouard 6277: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6278: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6279: }
1.126 brouard 6280: for(i=1;i<=nlstate;i++)
6281: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6282:
6283: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6284: if(nresult >=1)
6285: fprintf(ficresvpl,"%d ",nres );
1.126 brouard 6286: for(i=1; i<=nlstate;i++)
6287: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
6288: fprintf(ficresvpl,"\n");
6289: free_vector(gp,1,nlstate);
6290: free_vector(gm,1,nlstate);
1.208 brouard 6291: free_matrix(mgm,1,npar,1,nlstate);
6292: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6293: free_matrix(gradg,1,npar,1,nlstate);
6294: free_matrix(trgradg,1,nlstate,1,npar);
6295: } /* End age */
6296:
6297: free_vector(xp,1,npar);
6298: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6299: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6300:
6301: }
6302:
6303:
6304: /************ Variance of backprevalence limit ******************/
1.269 brouard 6305: 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 6306: {
6307: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6308: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6309:
6310: double **dnewmpar,**doldm;
6311: int i, j, nhstepm, hstepm;
6312: double *xp;
6313: double *gp, *gm;
6314: double **gradg, **trgradg;
6315: double **mgm, **mgp;
6316: double age,agelim;
6317: int theta;
6318:
6319: pstamp(ficresvbl);
6320: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6321: fprintf(ficresvbl,"# Age ");
6322: if(nresult >=1)
6323: fprintf(ficresvbl," Result# ");
6324: for(i=1; i<=nlstate;i++)
6325: fprintf(ficresvbl," %1d-%1d",i,i);
6326: fprintf(ficresvbl,"\n");
6327:
6328: xp=vector(1,npar);
6329: dnewmpar=matrix(1,nlstate,1,npar);
6330: doldm=matrix(1,nlstate,1,nlstate);
6331:
6332: hstepm=1*YEARM; /* Every year of age */
6333: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6334: agelim = AGEINF;
6335: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6336: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6337: if (stepm >= YEARM) hstepm=1;
6338: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6339: gradg=matrix(1,npar,1,nlstate);
6340: mgp=matrix(1,npar,1,nlstate);
6341: mgm=matrix(1,npar,1,nlstate);
6342: gp=vector(1,nlstate);
6343: gm=vector(1,nlstate);
6344:
6345: for(theta=1; theta <=npar; theta++){
6346: for(i=1; i<=npar; i++){ /* Computes gradient */
6347: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6348: }
6349: if(mobilavproj > 0 )
6350: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6351: else
6352: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6353: for(i=1;i<=nlstate;i++){
6354: gp[i] = bprlim[i][i];
6355: mgp[theta][i] = bprlim[i][i];
6356: }
6357: for(i=1; i<=npar; i++) /* Computes gradient */
6358: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6359: if(mobilavproj > 0 )
6360: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6361: else
6362: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6363: for(i=1;i<=nlstate;i++){
6364: gm[i] = bprlim[i][i];
6365: mgm[theta][i] = bprlim[i][i];
6366: }
6367: for(i=1;i<=nlstate;i++)
6368: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6369: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6370: } /* End theta */
6371:
6372: trgradg =matrix(1,nlstate,1,npar);
6373:
6374: for(j=1; j<=nlstate;j++)
6375: for(theta=1; theta <=npar; theta++)
6376: trgradg[j][theta]=gradg[theta][j];
6377: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6378: /* printf("\nmgm mgp %d ",(int)age); */
6379: /* for(j=1; j<=nlstate;j++){ */
6380: /* printf(" %d ",j); */
6381: /* for(theta=1; theta <=npar; theta++) */
6382: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6383: /* printf("\n "); */
6384: /* } */
6385: /* } */
6386: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6387: /* printf("\n gradg %d ",(int)age); */
6388: /* for(j=1; j<=nlstate;j++){ */
6389: /* printf("%d ",j); */
6390: /* for(theta=1; theta <=npar; theta++) */
6391: /* printf("%d %lf ",theta,gradg[theta][j]); */
6392: /* printf("\n "); */
6393: /* } */
6394: /* } */
6395:
6396: for(i=1;i<=nlstate;i++)
6397: varbpl[i][(int)age] =0.;
6398: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6399: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6400: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6401: }else{
6402: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6403: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6404: }
6405: for(i=1;i<=nlstate;i++)
6406: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6407:
6408: fprintf(ficresvbl,"%.0f ",age );
6409: if(nresult >=1)
6410: fprintf(ficresvbl,"%d ",nres );
6411: for(i=1; i<=nlstate;i++)
6412: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6413: fprintf(ficresvbl,"\n");
6414: free_vector(gp,1,nlstate);
6415: free_vector(gm,1,nlstate);
6416: free_matrix(mgm,1,npar,1,nlstate);
6417: free_matrix(mgp,1,npar,1,nlstate);
6418: free_matrix(gradg,1,npar,1,nlstate);
6419: free_matrix(trgradg,1,nlstate,1,npar);
6420: } /* End age */
6421:
6422: free_vector(xp,1,npar);
6423: free_matrix(doldm,1,nlstate,1,npar);
6424: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6425:
6426: }
6427:
6428: /************ Variance of one-step probabilities ******************/
6429: 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 6430: {
6431: int i, j=0, k1, l1, tj;
6432: int k2, l2, j1, z1;
6433: int k=0, l;
6434: int first=1, first1, first2;
6435: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6436: double **dnewm,**doldm;
6437: double *xp;
6438: double *gp, *gm;
6439: double **gradg, **trgradg;
6440: double **mu;
6441: double age, cov[NCOVMAX+1];
6442: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6443: int theta;
6444: char fileresprob[FILENAMELENGTH];
6445: char fileresprobcov[FILENAMELENGTH];
6446: char fileresprobcor[FILENAMELENGTH];
6447: double ***varpij;
6448:
6449: strcpy(fileresprob,"PROB_");
6450: strcat(fileresprob,fileres);
6451: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6452: printf("Problem with resultfile: %s\n", fileresprob);
6453: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6454: }
6455: strcpy(fileresprobcov,"PROBCOV_");
6456: strcat(fileresprobcov,fileresu);
6457: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6458: printf("Problem with resultfile: %s\n", fileresprobcov);
6459: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6460: }
6461: strcpy(fileresprobcor,"PROBCOR_");
6462: strcat(fileresprobcor,fileresu);
6463: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6464: printf("Problem with resultfile: %s\n", fileresprobcor);
6465: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6466: }
6467: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6468: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6469: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6470: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6471: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6472: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6473: pstamp(ficresprob);
6474: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6475: fprintf(ficresprob,"# Age");
6476: pstamp(ficresprobcov);
6477: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6478: fprintf(ficresprobcov,"# Age");
6479: pstamp(ficresprobcor);
6480: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6481: fprintf(ficresprobcor,"# Age");
1.126 brouard 6482:
6483:
1.222 brouard 6484: for(i=1; i<=nlstate;i++)
6485: for(j=1; j<=(nlstate+ndeath);j++){
6486: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6487: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6488: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6489: }
6490: /* fprintf(ficresprob,"\n");
6491: fprintf(ficresprobcov,"\n");
6492: fprintf(ficresprobcor,"\n");
6493: */
6494: xp=vector(1,npar);
6495: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6496: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6497: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6498: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6499: first=1;
6500: fprintf(ficgp,"\n# Routine varprob");
6501: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6502: fprintf(fichtm,"\n");
6503:
1.266 brouard 6504: 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. %s</li>\n",optionfilehtmcov,optionfilehtmcov);
1.222 brouard 6505: 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);
6506: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6507: and drawn. It helps understanding how is the covariance between two incidences.\
6508: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6509: 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 6510: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6511: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6512: standard deviations wide on each axis. <br>\
6513: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6514: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6515: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6516:
1.222 brouard 6517: cov[1]=1;
6518: /* tj=cptcoveff; */
1.225 brouard 6519: tj = (int) pow(2,cptcoveff);
1.222 brouard 6520: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6521: j1=0;
1.224 brouard 6522: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6523: if (cptcovn>0) {
6524: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6525: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6526: fprintf(ficresprob, "**********\n#\n");
6527: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6528: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6529: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6530:
1.222 brouard 6531: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6532: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6533: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6534:
6535:
1.222 brouard 6536: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6537: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6538: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6539:
1.222 brouard 6540: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6541: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6542: fprintf(ficresprobcor, "**********\n#");
6543: if(invalidvarcomb[j1]){
6544: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6545: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6546: continue;
6547: }
6548: }
6549: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6550: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6551: gp=vector(1,(nlstate)*(nlstate+ndeath));
6552: gm=vector(1,(nlstate)*(nlstate+ndeath));
6553: for (age=bage; age<=fage; age ++){
6554: cov[2]=age;
6555: if(nagesqr==1)
6556: cov[3]= age*age;
6557: for (k=1; k<=cptcovn;k++) {
6558: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6559: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6560: * 1 1 1 1 1
6561: * 2 2 1 1 1
6562: * 3 1 2 1 1
6563: */
6564: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6565: }
6566: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6567: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6568: for (k=1; k<=cptcovprod;k++)
6569: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6570:
6571:
1.222 brouard 6572: for(theta=1; theta <=npar; theta++){
6573: for(i=1; i<=npar; i++)
6574: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6575:
1.222 brouard 6576: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6577:
1.222 brouard 6578: k=0;
6579: for(i=1; i<= (nlstate); i++){
6580: for(j=1; j<=(nlstate+ndeath);j++){
6581: k=k+1;
6582: gp[k]=pmmij[i][j];
6583: }
6584: }
1.220 brouard 6585:
1.222 brouard 6586: for(i=1; i<=npar; i++)
6587: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6588:
1.222 brouard 6589: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6590: k=0;
6591: for(i=1; i<=(nlstate); i++){
6592: for(j=1; j<=(nlstate+ndeath);j++){
6593: k=k+1;
6594: gm[k]=pmmij[i][j];
6595: }
6596: }
1.220 brouard 6597:
1.222 brouard 6598: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6599: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6600: }
1.126 brouard 6601:
1.222 brouard 6602: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6603: for(theta=1; theta <=npar; theta++)
6604: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6605:
1.222 brouard 6606: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6607: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6608:
1.222 brouard 6609: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6610:
1.222 brouard 6611: k=0;
6612: for(i=1; i<=(nlstate); i++){
6613: for(j=1; j<=(nlstate+ndeath);j++){
6614: k=k+1;
6615: mu[k][(int) age]=pmmij[i][j];
6616: }
6617: }
6618: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6619: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6620: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6621:
1.222 brouard 6622: /*printf("\n%d ",(int)age);
6623: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6624: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6625: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6626: }*/
1.220 brouard 6627:
1.222 brouard 6628: fprintf(ficresprob,"\n%d ",(int)age);
6629: fprintf(ficresprobcov,"\n%d ",(int)age);
6630: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6631:
1.222 brouard 6632: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6633: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6634: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6635: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6636: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6637: }
6638: i=0;
6639: for (k=1; k<=(nlstate);k++){
6640: for (l=1; l<=(nlstate+ndeath);l++){
6641: i++;
6642: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6643: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6644: for (j=1; j<=i;j++){
6645: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6646: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6647: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6648: }
6649: }
6650: }/* end of loop for state */
6651: } /* end of loop for age */
6652: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6653: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6654: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6655: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6656:
6657: /* Confidence intervalle of pij */
6658: /*
6659: fprintf(ficgp,"\nunset parametric;unset label");
6660: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6661: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6662: 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);
6663: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6664: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6665: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6666: */
6667:
6668: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6669: first1=1;first2=2;
6670: for (k2=1; k2<=(nlstate);k2++){
6671: for (l2=1; l2<=(nlstate+ndeath);l2++){
6672: if(l2==k2) continue;
6673: j=(k2-1)*(nlstate+ndeath)+l2;
6674: for (k1=1; k1<=(nlstate);k1++){
6675: for (l1=1; l1<=(nlstate+ndeath);l1++){
6676: if(l1==k1) continue;
6677: i=(k1-1)*(nlstate+ndeath)+l1;
6678: if(i<=j) continue;
6679: for (age=bage; age<=fage; age ++){
6680: if ((int)age %5==0){
6681: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6682: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6683: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6684: mu1=mu[i][(int) age]/stepm*YEARM ;
6685: mu2=mu[j][(int) age]/stepm*YEARM;
6686: c12=cv12/sqrt(v1*v2);
6687: /* Computing eigen value of matrix of covariance */
6688: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6689: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6690: if ((lc2 <0) || (lc1 <0) ){
6691: if(first2==1){
6692: first1=0;
6693: 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);
6694: }
6695: 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);
6696: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6697: /* lc2=fabs(lc2); */
6698: }
1.220 brouard 6699:
1.222 brouard 6700: /* Eigen vectors */
1.280 brouard 6701: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6702: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6703: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6704: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6705: }else
6706: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6707: /*v21=sqrt(1.-v11*v11); *//* error */
6708: v21=(lc1-v1)/cv12*v11;
6709: v12=-v21;
6710: v22=v11;
6711: tnalp=v21/v11;
6712: if(first1==1){
6713: first1=0;
6714: 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);
6715: }
6716: 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);
6717: /*printf(fignu*/
6718: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6719: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6720: if(first==1){
6721: first=0;
6722: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6723: fprintf(ficgp,"\nset parametric;unset label");
6724: 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);
6725: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6726: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6727: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6728: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6729: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6730: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6731: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6732: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6733: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6734: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6735: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6736: 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 6737: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6738: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6739: }else{
6740: first=0;
6741: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6742: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6743: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6744: 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 6745: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6746: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6747: }/* if first */
6748: } /* age mod 5 */
6749: } /* end loop age */
6750: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6751: first=1;
6752: } /*l12 */
6753: } /* k12 */
6754: } /*l1 */
6755: }/* k1 */
6756: } /* loop on combination of covariates j1 */
6757: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6758: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6759: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6760: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6761: free_vector(xp,1,npar);
6762: fclose(ficresprob);
6763: fclose(ficresprobcov);
6764: fclose(ficresprobcor);
6765: fflush(ficgp);
6766: fflush(fichtmcov);
6767: }
1.126 brouard 6768:
6769:
6770: /******************* Printing html file ***********/
1.201 brouard 6771: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6772: int lastpass, int stepm, int weightopt, char model[],\
6773: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.258 brouard 6774: int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
1.273 brouard 6775: double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
6776: double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
1.237 brouard 6777: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6778:
6779: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6780: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6781: </ul>");
1.237 brouard 6782: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6783: </ul>", model);
1.214 brouard 6784: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6785: 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",
6786: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6787: 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 6788: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6789: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6790: fprintf(fichtm,"\
6791: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6792: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6793: fprintf(fichtm,"\
1.217 brouard 6794: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6795: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6796: fprintf(fichtm,"\
1.126 brouard 6797: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6798: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6799: fprintf(fichtm,"\
1.217 brouard 6800: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6801: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6802: fprintf(fichtm,"\
1.211 brouard 6803: - (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 6804: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6805: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6806: if(prevfcast==1){
6807: fprintf(fichtm,"\
6808: - Prevalence projections by age and states: \
1.201 brouard 6809: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6810: }
1.126 brouard 6811:
6812:
1.225 brouard 6813: m=pow(2,cptcoveff);
1.222 brouard 6814: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6815:
1.264 brouard 6816: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6817:
6818: jj1=0;
6819:
6820: fprintf(fichtm," \n<ul>");
6821: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6822: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6823: if(m != 1 && TKresult[nres]!= k1)
6824: continue;
6825: jj1++;
6826: if (cptcovn > 0) {
6827: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6828: for (cpt=1; cpt<=cptcoveff;cpt++){
6829: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6830: }
6831: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6832: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6833: }
6834: fprintf(fichtm,"\">");
6835:
6836: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6837: fprintf(fichtm,"************ Results for covariates");
6838: for (cpt=1; cpt<=cptcoveff;cpt++){
6839: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6840: }
6841: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6842: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6843: }
6844: if(invalidvarcomb[k1]){
6845: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6846: continue;
6847: }
6848: fprintf(fichtm,"</a></li>");
6849: } /* cptcovn >0 */
6850: }
6851: fprintf(fichtm," \n</ul>");
6852:
1.222 brouard 6853: jj1=0;
1.237 brouard 6854:
6855: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6856: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6857: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6858: continue;
1.220 brouard 6859:
1.222 brouard 6860: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6861: jj1++;
6862: if (cptcovn > 0) {
1.264 brouard 6863: fprintf(fichtm,"\n<p><a name=\"rescov");
6864: for (cpt=1; cpt<=cptcoveff;cpt++){
6865: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6866: }
6867: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6868: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6869: }
6870: fprintf(fichtm,"\"</a>");
6871:
1.222 brouard 6872: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6873: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6874: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6875: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6876: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6877: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6878: }
1.237 brouard 6879: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6880: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6881: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6882: }
6883:
1.230 brouard 6884: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6885: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6886: if(invalidvarcomb[k1]){
6887: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6888: printf("\nCombination (%d) ignored because no cases \n",k1);
6889: continue;
6890: }
6891: }
6892: /* aij, bij */
1.259 brouard 6893: 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 6894: <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 6895: /* Pij */
1.241 brouard 6896: 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> \
6897: <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 6898: /* Quasi-incidences */
6899: 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 6900: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6901: 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 6902: 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> \
6903: <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 6904: /* Survival functions (period) in state j */
6905: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6906: fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
6907: <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 6908: }
6909: /* State specific survival functions (period) */
6910: for(cpt=1; cpt<=nlstate;cpt++){
6911: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6912: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.283 brouard 6913: <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 6914: }
6915: /* Period (stable) prevalence in each health state */
6916: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6917: 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> \
6918: <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 6919: }
6920: if(backcast==1){
6921: /* Period (stable) back prevalence in each health state */
6922: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6923: 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 6924: <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 6925: }
1.217 brouard 6926: }
1.222 brouard 6927: if(prevfcast==1){
6928: /* Projection of prevalence up to period (stable) prevalence in each health state */
6929: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6930: 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) 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> \
6931: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 6932: }
6933: }
1.268 brouard 6934: if(backcast==1){
6935: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
6936: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6937: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
6938: 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 \
6939: 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) \
6940: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
6941: <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 6942: }
6943: }
1.220 brouard 6944:
1.222 brouard 6945: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 6946: 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> \
6947: <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 6948: }
6949: /* } /\* end i1 *\/ */
6950: }/* End k1 */
6951: fprintf(fichtm,"</ul>");
1.126 brouard 6952:
1.222 brouard 6953: fprintf(fichtm,"\
1.126 brouard 6954: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6955: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6956: - 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 6957: But because parameters are usually highly correlated (a higher incidence of disability \
6958: and a higher incidence of recovery can give very close observed transition) it might \
6959: be very useful to look not only at linear confidence intervals estimated from the \
6960: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6961: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6962: covariance matrix of the one-step probabilities. \
6963: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6964:
1.222 brouard 6965: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6966: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6967: fprintf(fichtm,"\
1.126 brouard 6968: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6969: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6970:
1.222 brouard 6971: fprintf(fichtm,"\
1.126 brouard 6972: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6973: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6974: fprintf(fichtm,"\
1.126 brouard 6975: - 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): \
6976: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6977: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6978: fprintf(fichtm,"\
1.126 brouard 6979: - (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): \
6980: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6981: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6982: fprintf(fichtm,"\
1.128 brouard 6983: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the 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 6984: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6985: fprintf(fichtm,"\
1.128 brouard 6986: - 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 6987: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6988: fprintf(fichtm,"\
1.126 brouard 6989: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6990: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6991:
6992: /* if(popforecast==1) fprintf(fichtm,"\n */
6993: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6994: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6995: /* <br>",fileres,fileres,fileres,fileres); */
6996: /* else */
6997: /* 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 6998: fflush(fichtm);
6999: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 7000:
1.225 brouard 7001: m=pow(2,cptcoveff);
1.222 brouard 7002: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 7003:
1.222 brouard 7004: jj1=0;
1.237 brouard 7005:
1.241 brouard 7006: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 7007: for(k1=1; k1<=m;k1++){
1.253 brouard 7008: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7009: continue;
1.222 brouard 7010: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
7011: jj1++;
1.126 brouard 7012: if (cptcovn > 0) {
7013: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 7014: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 7015: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
7016: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
7017: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7018: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7019: }
7020:
1.126 brouard 7021: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 7022:
1.222 brouard 7023: if(invalidvarcomb[k1]){
7024: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7025: continue;
7026: }
1.126 brouard 7027: }
7028: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7029: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7030: 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 7031: <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 7032: }
7033: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7034: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7035: true period expectancies (those weighted with period prevalences are also\
7036: drawn in addition to the population based expectancies computed using\
1.241 brouard 7037: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7038: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7039: /* } /\* end i1 *\/ */
7040: }/* End k1 */
1.241 brouard 7041: }/* End nres */
1.222 brouard 7042: fprintf(fichtm,"</ul>");
7043: fflush(fichtm);
1.126 brouard 7044: }
7045:
7046: /******************* Gnuplot file **************/
1.270 brouard 7047: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
1.126 brouard 7048:
7049: char dirfileres[132],optfileres[132];
1.264 brouard 7050: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7051: 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 7052: int lv=0, vlv=0, kl=0;
1.130 brouard 7053: int ng=0;
1.201 brouard 7054: int vpopbased;
1.223 brouard 7055: int ioffset; /* variable offset for columns */
1.270 brouard 7056: int iyearc=1; /* variable column for year of projection */
7057: int iagec=1; /* variable column for age of projection */
1.235 brouard 7058: int nres=0; /* Index of resultline */
1.266 brouard 7059: int istart=1; /* For starting graphs in projections */
1.219 brouard 7060:
1.126 brouard 7061: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7062: /* printf("Problem with file %s",optionfilegnuplot); */
7063: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7064: /* } */
7065:
7066: /*#ifdef windows */
7067: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7068: /*#endif */
1.225 brouard 7069: m=pow(2,cptcoveff);
1.126 brouard 7070:
1.274 brouard 7071: /* diagram of the model */
7072: fprintf(ficgp,"\n#Diagram of the model \n");
7073: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7074: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7075: 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);
7076:
7077: 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);
7078: fprintf(ficgp,"\n#show arrow\nunset label\n");
7079: 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);
7080: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7081: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7082: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7083: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7084:
1.202 brouard 7085: /* Contribution to likelihood */
7086: /* Plot the probability implied in the likelihood */
1.223 brouard 7087: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7088: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7089: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7090: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7091: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7092: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7093: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7094: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7095: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7096: 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));
7097: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7098: 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));
7099: for (i=1; i<= nlstate ; i ++) {
7100: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7101: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7102: 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);
7103: for (j=2; j<= nlstate+ndeath ; j ++) {
7104: 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);
7105: }
7106: fprintf(ficgp,";\nset out; unset ylabel;\n");
7107: }
7108: /* 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 */
7109: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7110: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7111: fprintf(ficgp,"\nset out;unset log\n");
7112: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7113:
1.126 brouard 7114: strcpy(dirfileres,optionfilefiname);
7115: strcpy(optfileres,"vpl");
1.223 brouard 7116: /* 1eme*/
1.238 brouard 7117: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7118: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7119: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7120: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7121: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7122: continue;
7123: /* We are interested in selected combination by the resultline */
1.246 brouard 7124: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.238 brouard 7125: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7126: strcpy(gplotlabel,"(");
1.238 brouard 7127: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7128: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7129: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7130: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7131: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7132: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7133: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7134: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7135: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7136: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7137: }
7138: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7139: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7140: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7141: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7142: }
7143: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7144: /* printf("\n#\n"); */
1.238 brouard 7145: fprintf(ficgp,"\n#\n");
7146: if(invalidvarcomb[k1]){
1.260 brouard 7147: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7148: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7149: continue;
7150: }
1.235 brouard 7151:
1.241 brouard 7152: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7153: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7154: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7155: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7156: 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);
7157: /* 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); */
7158: /* k1-1 error should be nres-1*/
1.238 brouard 7159: for (i=1; i<= nlstate ; i ++) {
7160: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7161: else fprintf(ficgp," %%*lf (%%*lf)");
7162: }
1.260 brouard 7163: fprintf(ficgp,"\" t\"Period (stable) 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 7164: for (i=1; i<= nlstate ; i ++) {
7165: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7166: else fprintf(ficgp," %%*lf (%%*lf)");
7167: }
1.260 brouard 7168: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7169: for (i=1; i<= nlstate ; i ++) {
7170: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7171: else fprintf(ficgp," %%*lf (%%*lf)");
7172: }
1.265 brouard 7173: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7174:
7175: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7176: if(cptcoveff ==0){
1.271 brouard 7177: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7178: }else{
7179: kl=0;
7180: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7181: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7182: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7183: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7184: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7185: vlv= nbcode[Tvaraff[k]][lv];
7186: kl++;
7187: /* 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 *\/ */
7188: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7189: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7190: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7191: if(k==cptcoveff){
7192: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7193: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7194: }else{
7195: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7196: kl++;
7197: }
7198: } /* end covariate */
7199: } /* end if no covariate */
7200:
1.238 brouard 7201: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
7202: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7203: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7204: if(cptcoveff ==0){
1.245 brouard 7205: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7206: }else{
7207: kl=0;
7208: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7209: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7210: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7211: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7212: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7213: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7214: kl++;
1.238 brouard 7215: /* 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 *\/ */
7216: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7217: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7218: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7219: if(k==cptcoveff){
1.245 brouard 7220: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7221: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7222: }else{
7223: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7224: kl++;
7225: }
7226: } /* end covariate */
7227: } /* end if no covariate */
1.268 brouard 7228: if(backcast == 1){
7229: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7230: /* k1-1 error should be nres-1*/
7231: for (i=1; i<= nlstate ; i ++) {
7232: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7233: else fprintf(ficgp," %%*lf (%%*lf)");
7234: }
1.271 brouard 7235: 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 7236: for (i=1; i<= nlstate ; i ++) {
7237: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7238: else fprintf(ficgp," %%*lf (%%*lf)");
7239: }
1.276 brouard 7240: 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 7241: for (i=1; i<= nlstate ; i ++) {
7242: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7243: else fprintf(ficgp," %%*lf (%%*lf)");
7244: }
1.274 brouard 7245: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7246: } /* end if backprojcast */
1.238 brouard 7247: } /* end if backcast */
1.276 brouard 7248: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7249: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7250: } /* nres */
1.201 brouard 7251: } /* k1 */
7252: } /* cpt */
1.235 brouard 7253:
7254:
1.126 brouard 7255: /*2 eme*/
1.238 brouard 7256: for (k1=1; k1<= m ; k1 ++){
7257: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7258: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7259: continue;
7260: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7261: strcpy(gplotlabel,"(");
1.238 brouard 7262: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7263: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7264: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7265: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7266: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7267: vlv= nbcode[Tvaraff[k]][lv];
7268: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7269: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7270: }
1.237 brouard 7271: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7272: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7273: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7274: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7275: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7276: }
1.264 brouard 7277: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7278: fprintf(ficgp,"\n#\n");
1.223 brouard 7279: if(invalidvarcomb[k1]){
7280: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7281: continue;
7282: }
1.219 brouard 7283:
1.241 brouard 7284: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7285: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7286: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7287: if(vpopbased==0){
1.238 brouard 7288: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7289: }else
1.238 brouard 7290: fprintf(ficgp,"\nreplot ");
7291: for (i=1; i<= nlstate+1 ; i ++) {
7292: k=2*i;
1.261 brouard 7293: 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 7294: for (j=1; j<= nlstate+1 ; j ++) {
7295: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7296: else fprintf(ficgp," %%*lf (%%*lf)");
7297: }
7298: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7299: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7300: 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 7301: for (j=1; j<= nlstate+1 ; j ++) {
7302: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7303: else fprintf(ficgp," %%*lf (%%*lf)");
7304: }
7305: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7306: 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 7307: for (j=1; j<= nlstate+1 ; j ++) {
7308: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7309: else fprintf(ficgp," %%*lf (%%*lf)");
7310: }
7311: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7312: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7313: } /* state */
7314: } /* vpopbased */
1.264 brouard 7315: 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 7316: } /* end nres */
7317: } /* k1 end 2 eme*/
7318:
7319:
7320: /*3eme*/
7321: for (k1=1; k1<= m ; k1 ++){
7322: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7323: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7324: continue;
7325:
7326: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7327: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7328: strcpy(gplotlabel,"(");
1.238 brouard 7329: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7330: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7331: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7332: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7333: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7334: vlv= nbcode[Tvaraff[k]][lv];
7335: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7336: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7337: }
7338: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7339: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7340: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7341: }
1.264 brouard 7342: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7343: fprintf(ficgp,"\n#\n");
7344: if(invalidvarcomb[k1]){
7345: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7346: continue;
7347: }
7348:
7349: /* k=2+nlstate*(2*cpt-2); */
7350: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7351: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7352: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7353: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7354: 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 7355: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7356: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7357: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7358: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7359: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7360: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7361:
1.238 brouard 7362: */
7363: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7364: 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 7365: /* 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 7366:
1.238 brouard 7367: }
1.261 brouard 7368: 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 7369: }
1.264 brouard 7370: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7371: } /* end nres */
7372: } /* end kl 3eme */
1.126 brouard 7373:
1.223 brouard 7374: /* 4eme */
1.201 brouard 7375: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7376: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7377: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7378: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7379: continue;
1.238 brouard 7380: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7381: strcpy(gplotlabel,"(");
1.238 brouard 7382: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7383: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7384: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7385: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7386: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7387: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7388: vlv= nbcode[Tvaraff[k]][lv];
7389: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7390: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7391: }
7392: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7393: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7394: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7395: }
1.264 brouard 7396: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7397: fprintf(ficgp,"\n#\n");
7398: if(invalidvarcomb[k1]){
7399: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7400: continue;
1.223 brouard 7401: }
1.238 brouard 7402:
1.241 brouard 7403: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7404: 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 7405: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7406: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7407: k=3;
7408: for (i=1; i<= nlstate ; i ++){
7409: if(i==1){
7410: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7411: }else{
7412: fprintf(ficgp,", '' ");
7413: }
7414: l=(nlstate+ndeath)*(i-1)+1;
7415: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7416: for (j=2; j<= nlstate+ndeath ; j ++)
7417: fprintf(ficgp,"+$%d",k+l+j-1);
7418: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7419: } /* nlstate */
1.264 brouard 7420: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7421: } /* end cpt state*/
7422: } /* end nres */
7423: } /* end covariate k1 */
7424:
1.220 brouard 7425: /* 5eme */
1.201 brouard 7426: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7427: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7428: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7429: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7430: continue;
1.238 brouard 7431: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7432: strcpy(gplotlabel,"(");
1.238 brouard 7433: 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);
7434: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7435: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7436: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7437: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7438: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7439: vlv= nbcode[Tvaraff[k]][lv];
7440: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7441: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7442: }
7443: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7444: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7445: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7446: }
1.264 brouard 7447: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7448: fprintf(ficgp,"\n#\n");
7449: if(invalidvarcomb[k1]){
7450: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7451: continue;
7452: }
1.227 brouard 7453:
1.241 brouard 7454: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7455: 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 7456: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7457: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7458: k=3;
7459: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7460: if(j==1)
7461: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7462: else
7463: fprintf(ficgp,", '' ");
7464: l=(nlstate+ndeath)*(cpt-1) +j;
7465: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7466: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7467: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7468: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7469: } /* nlstate */
7470: fprintf(ficgp,", '' ");
7471: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7472: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7473: l=(nlstate+ndeath)*(cpt-1) +j;
7474: if(j < nlstate)
7475: fprintf(ficgp,"$%d +",k+l);
7476: else
7477: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7478: }
1.264 brouard 7479: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7480: } /* end cpt state*/
7481: } /* end covariate */
7482: } /* end nres */
1.227 brouard 7483:
1.220 brouard 7484: /* 6eme */
1.202 brouard 7485: /* CV preval stable (period) for each covariate */
1.237 brouard 7486: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7487: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7488: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7489: continue;
1.255 brouard 7490: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7491: strcpy(gplotlabel,"(");
1.211 brouard 7492: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7493: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7494: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7495: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7496: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7497: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7498: vlv= nbcode[Tvaraff[k]][lv];
7499: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7500: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7501: }
1.237 brouard 7502: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7503: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7504: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7505: }
1.264 brouard 7506: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7507: fprintf(ficgp,"\n#\n");
1.223 brouard 7508: if(invalidvarcomb[k1]){
1.227 brouard 7509: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7510: continue;
1.223 brouard 7511: }
1.227 brouard 7512:
1.241 brouard 7513: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7514: 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 7515: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7516: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7517: k=3; /* Offset */
1.255 brouard 7518: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7519: if(i==1)
7520: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7521: else
7522: fprintf(ficgp,", '' ");
1.255 brouard 7523: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7524: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7525: for (j=2; j<= nlstate ; j ++)
7526: fprintf(ficgp,"+$%d",k+l+j-1);
7527: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7528: } /* nlstate */
1.264 brouard 7529: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7530: } /* end cpt state*/
7531: } /* end covariate */
1.227 brouard 7532:
7533:
1.220 brouard 7534: /* 7eme */
1.218 brouard 7535: if(backcast == 1){
1.217 brouard 7536: /* CV back preval stable (period) for each covariate */
1.237 brouard 7537: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7538: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7539: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7540: continue;
1.268 brouard 7541: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7542: strcpy(gplotlabel,"(");
7543: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7544: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7545: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7546: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7547: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7548: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7549: vlv= nbcode[Tvaraff[k]][lv];
7550: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7551: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7552: }
1.237 brouard 7553: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7554: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7555: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7556: }
1.264 brouard 7557: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7558: fprintf(ficgp,"\n#\n");
7559: if(invalidvarcomb[k1]){
7560: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7561: continue;
7562: }
7563:
1.241 brouard 7564: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7565: 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 7566: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7567: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7568: k=3; /* Offset */
1.268 brouard 7569: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7570: if(i==1)
7571: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7572: else
7573: fprintf(ficgp,", '' ");
7574: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7575: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7576: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7577: /* 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 7578: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7579: /* for (j=2; j<= nlstate ; j ++) */
7580: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7581: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7582: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7583: } /* nlstate */
1.264 brouard 7584: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7585: } /* end cpt state*/
7586: } /* end covariate */
7587: } /* End if backcast */
7588:
1.223 brouard 7589: /* 8eme */
1.218 brouard 7590: if(prevfcast==1){
7591: /* Projection from cross-sectional to stable (period) for each covariate */
7592:
1.237 brouard 7593: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7594: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7595: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7596: continue;
1.211 brouard 7597: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7598: strcpy(gplotlabel,"(");
1.227 brouard 7599: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
7600: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7601: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7602: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7603: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7604: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7605: vlv= nbcode[Tvaraff[k]][lv];
7606: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7607: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7608: }
1.237 brouard 7609: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7610: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7611: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7612: }
1.264 brouard 7613: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7614: fprintf(ficgp,"\n#\n");
7615: if(invalidvarcomb[k1]){
7616: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7617: continue;
7618: }
7619:
7620: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7621: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7622: 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 7623: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7624: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7625:
7626: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7627: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7628: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7629: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7630: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7631: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7632: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7633: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7634: if(i==istart){
1.227 brouard 7635: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7636: }else{
7637: fprintf(ficgp,",\\\n '' ");
7638: }
7639: if(cptcoveff ==0){ /* No covariate */
7640: ioffset=2; /* Age is in 2 */
7641: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7642: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7643: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7644: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7645: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7646: if(i==nlstate+1){
1.270 brouard 7647: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7648: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7649: fprintf(ficgp,",\\\n '' ");
7650: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7651: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7652: offyear, \
1.268 brouard 7653: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7654: }else
1.227 brouard 7655: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7656: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7657: }else{ /* more than 2 covariates */
1.270 brouard 7658: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7659: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7660: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7661: iyearc=ioffset-1;
7662: iagec=ioffset;
1.227 brouard 7663: fprintf(ficgp," u %d:(",ioffset);
7664: kl=0;
7665: strcpy(gplotcondition,"(");
7666: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7667: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7668: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7669: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7670: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7671: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7672: kl++;
7673: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7674: kl++;
7675: if(k <cptcoveff && cptcoveff>1)
7676: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7677: }
7678: strcpy(gplotcondition+strlen(gplotcondition),")");
7679: /* 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 *\/ */
7680: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7681: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7682: /* '' 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*/
7683: if(i==nlstate+1){
1.270 brouard 7684: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7685: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7686: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7687: fprintf(ficgp," u %d:(",iagec);
7688: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7689: iyearc, iagec, offyear, \
7690: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7691: /* '' 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 7692: }else{
7693: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7694: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7695: }
7696: } /* end if covariate */
7697: } /* nlstate */
1.264 brouard 7698: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7699: } /* end cpt state*/
7700: } /* end covariate */
7701: } /* End if prevfcast */
1.227 brouard 7702:
1.268 brouard 7703: if(backcast==1){
7704: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7705:
7706: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7707: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7708: if(m != 1 && TKresult[nres]!= k1)
7709: continue;
7710: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7711: strcpy(gplotlabel,"(");
7712: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7713: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7714: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7715: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7716: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7717: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7718: vlv= nbcode[Tvaraff[k]][lv];
7719: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7720: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7721: }
7722: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7723: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7724: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7725: }
7726: strcpy(gplotlabel+strlen(gplotlabel),")");
7727: fprintf(ficgp,"\n#\n");
7728: if(invalidvarcomb[k1]){
7729: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7730: continue;
7731: }
7732:
7733: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7734: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7735: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7736: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7737: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7738:
7739: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7740: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7741: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7742: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7743: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7744: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7745: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7746: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7747: if(i==istart){
7748: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7749: }else{
7750: fprintf(ficgp,",\\\n '' ");
7751: }
7752: if(cptcoveff ==0){ /* No covariate */
7753: ioffset=2; /* Age is in 2 */
7754: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7755: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7756: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7757: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7758: fprintf(ficgp," u %d:(", ioffset);
7759: if(i==nlstate+1){
1.270 brouard 7760: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7761: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7762: fprintf(ficgp,",\\\n '' ");
7763: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7764: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7765: offbyear, \
7766: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7767: }else
7768: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7769: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7770: }else{ /* more than 2 covariates */
1.270 brouard 7771: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7772: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7773: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7774: iyearc=ioffset-1;
7775: iagec=ioffset;
1.268 brouard 7776: fprintf(ficgp," u %d:(",ioffset);
7777: kl=0;
7778: strcpy(gplotcondition,"(");
7779: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7780: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7781: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7782: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7783: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7784: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7785: kl++;
7786: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7787: kl++;
7788: if(k <cptcoveff && cptcoveff>1)
7789: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7790: }
7791: strcpy(gplotcondition+strlen(gplotcondition),")");
7792: /* 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 *\/ */
7793: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7794: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7795: /* '' 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*/
7796: if(i==nlstate+1){
1.270 brouard 7797: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7798: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7799: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7800: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7801: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7802: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7803: iyearc,iagec,offbyear, \
7804: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7805: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7806: }else{
7807: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7808: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7809: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7810: }
7811: } /* end if covariate */
7812: } /* nlstate */
7813: fprintf(ficgp,"\nset out; unset label;\n");
7814: } /* end cpt state*/
7815: } /* end covariate */
7816: } /* End if backcast */
7817:
1.227 brouard 7818:
1.238 brouard 7819: /* 9eme writing MLE parameters */
7820: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7821: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7822: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7823: for(k=1; k <=(nlstate+ndeath); k++){
7824: if (k != i) {
1.227 brouard 7825: fprintf(ficgp,"# current state %d\n",k);
7826: for(j=1; j <=ncovmodel; j++){
7827: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7828: jk++;
7829: }
7830: fprintf(ficgp,"\n");
1.126 brouard 7831: }
7832: }
1.223 brouard 7833: }
1.187 brouard 7834: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7835:
1.145 brouard 7836: /*goto avoid;*/
1.238 brouard 7837: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7838: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7839: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7840: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7841: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7842: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7843: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7844: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7845: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7846: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7847: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7848: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7849: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7850: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7851: fprintf(ficgp,"#\n");
1.223 brouard 7852: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7853: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7854: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7855: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7856: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7857: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7858: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7859: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7860: continue;
1.264 brouard 7861: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7862: strcpy(gplotlabel,"(");
1.276 brouard 7863: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7864: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7865: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7866: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7867: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7868: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7869: vlv= nbcode[Tvaraff[k]][lv];
7870: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7871: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7872: }
1.237 brouard 7873: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7874: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7875: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7876: }
1.264 brouard 7877: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7878: fprintf(ficgp,"\n#\n");
1.264 brouard 7879: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7880: fprintf(ficgp,"\nset key outside ");
7881: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7882: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7883: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7884: if (ng==1){
7885: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7886: fprintf(ficgp,"\nunset log y");
7887: }else if (ng==2){
7888: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7889: fprintf(ficgp,"\nset log y");
7890: }else if (ng==3){
7891: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7892: fprintf(ficgp,"\nset log y");
7893: }else
7894: fprintf(ficgp,"\nunset title ");
7895: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7896: i=1;
7897: for(k2=1; k2<=nlstate; k2++) {
7898: k3=i;
7899: for(k=1; k<=(nlstate+ndeath); k++) {
7900: if (k != k2){
7901: switch( ng) {
7902: case 1:
7903: if(nagesqr==0)
7904: fprintf(ficgp," p%d+p%d*x",i,i+1);
7905: else /* nagesqr =1 */
7906: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7907: break;
7908: case 2: /* ng=2 */
7909: if(nagesqr==0)
7910: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7911: else /* nagesqr =1 */
7912: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7913: break;
7914: case 3:
7915: if(nagesqr==0)
7916: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7917: else /* nagesqr =1 */
7918: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7919: break;
7920: }
7921: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7922: ijp=1; /* product no age */
7923: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7924: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7925: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 7926: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7927: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
7928: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7929: if(DummyV[j]==0){
7930: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
7931: }else{ /* quantitative */
7932: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
7933: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7934: }
7935: ij++;
1.237 brouard 7936: }
1.268 brouard 7937: }
7938: }else if(cptcovprod >0){
7939: if(j==Tprod[ijp]) { /* */
7940: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
7941: if(ijp <=cptcovprod) { /* Product */
7942: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
7943: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
7944: /* 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)]); */
7945: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
7946: }else{ /* Vn is dummy and Vm is quanti */
7947: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
7948: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7949: }
7950: }else{ /* Vn*Vm Vn is quanti */
7951: if(DummyV[Tvard[ijp][2]]==0){
7952: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
7953: }else{ /* Both quanti */
7954: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7955: }
1.237 brouard 7956: }
1.268 brouard 7957: ijp++;
1.237 brouard 7958: }
1.268 brouard 7959: } /* end Tprod */
1.237 brouard 7960: } else{ /* simple covariate */
1.264 brouard 7961: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 7962: if(Dummy[j]==0){
7963: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
7964: }else{ /* quantitative */
7965: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 7966: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 7967: }
1.237 brouard 7968: } /* end simple */
7969: } /* end j */
1.223 brouard 7970: }else{
7971: i=i-ncovmodel;
7972: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
7973: fprintf(ficgp," (1.");
7974: }
1.227 brouard 7975:
1.223 brouard 7976: if(ng != 1){
7977: fprintf(ficgp,")/(1");
1.227 brouard 7978:
1.264 brouard 7979: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 7980: if(nagesqr==0)
1.264 brouard 7981: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 7982: else /* nagesqr =1 */
1.264 brouard 7983: 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 7984:
1.223 brouard 7985: ij=1;
7986: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 7987: if(cptcovage >0){
7988: if((j-2)==Tage[ij]) { /* Bug valgrind */
7989: if(ij <=cptcovage) { /* Bug valgrind */
7990: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
7991: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7992: ij++;
7993: }
7994: }
7995: }else
7996: 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 7997: }
7998: fprintf(ficgp,")");
7999: }
8000: fprintf(ficgp,")");
8001: if(ng ==2)
1.276 brouard 8002: 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 8003: else /* ng= 3 */
1.276 brouard 8004: 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 8005: }else{ /* end ng <> 1 */
8006: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 8007: 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 8008: }
8009: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
8010: fprintf(ficgp,",");
8011: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
8012: fprintf(ficgp,",");
8013: i=i+ncovmodel;
8014: } /* end k */
8015: } /* end k2 */
1.276 brouard 8016: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
8017: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 8018: } /* end k1 */
1.223 brouard 8019: } /* end ng */
8020: /* avoid: */
8021: fflush(ficgp);
1.126 brouard 8022: } /* end gnuplot */
8023:
8024:
8025: /*************** Moving average **************/
1.219 brouard 8026: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8027: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8028:
1.222 brouard 8029: int i, cpt, cptcod;
8030: int modcovmax =1;
8031: int mobilavrange, mob;
8032: int iage=0;
8033:
1.266 brouard 8034: double sum=0., sumr=0.;
1.222 brouard 8035: double age;
1.266 brouard 8036: double *sumnewp, *sumnewm, *sumnewmr;
8037: double *agemingood, *agemaxgood;
8038: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8039:
8040:
1.278 brouard 8041: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8042: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8043:
8044: sumnewp = vector(1,ncovcombmax);
8045: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8046: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8047: agemingood = vector(1,ncovcombmax);
1.266 brouard 8048: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8049: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8050: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8051:
8052: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8053: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8054: sumnewp[cptcod]=0.;
1.266 brouard 8055: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8056: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8057: }
8058: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8059:
1.266 brouard 8060: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8061: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8062: else mobilavrange=mobilav;
8063: for (age=bage; age<=fage; age++)
8064: for (i=1; i<=nlstate;i++)
8065: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8066: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8067: /* We keep the original values on the extreme ages bage, fage and for
8068: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8069: we use a 5 terms etc. until the borders are no more concerned.
8070: */
8071: for (mob=3;mob <=mobilavrange;mob=mob+2){
8072: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8073: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8074: sumnewm[cptcod]=0.;
8075: for (i=1; i<=nlstate;i++){
1.222 brouard 8076: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8077: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8078: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8079: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8080: }
8081: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8082: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8083: } /* end i */
8084: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8085: } /* end cptcod */
1.222 brouard 8086: }/* end age */
8087: }/* end mob */
1.266 brouard 8088: }else{
8089: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8090: return -1;
1.266 brouard 8091: }
8092:
8093: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8094: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8095: if(invalidvarcomb[cptcod]){
8096: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8097: continue;
8098: }
1.219 brouard 8099:
1.266 brouard 8100: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8101: sumnewm[cptcod]=0.;
8102: sumnewmr[cptcod]=0.;
8103: for (i=1; i<=nlstate;i++){
8104: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8105: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8106: }
8107: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8108: agemingoodr[cptcod]=age;
8109: }
8110: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8111: agemingood[cptcod]=age;
8112: }
8113: } /* age */
8114: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8115: sumnewm[cptcod]=0.;
1.266 brouard 8116: sumnewmr[cptcod]=0.;
1.222 brouard 8117: for (i=1; i<=nlstate;i++){
8118: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8119: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8120: }
8121: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8122: agemaxgoodr[cptcod]=age;
1.222 brouard 8123: }
8124: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8125: agemaxgood[cptcod]=age;
8126: }
8127: } /* age */
8128: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8129: /* but they will change */
8130: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8131: sumnewm[cptcod]=0.;
8132: sumnewmr[cptcod]=0.;
8133: for (i=1; i<=nlstate;i++){
8134: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8135: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8136: }
8137: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8138: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8139: agemaxgoodr[cptcod]=age; /* age min */
8140: for (i=1; i<=nlstate;i++)
8141: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8142: }else{ /* bad we change the value with the values of good ages */
8143: for (i=1; i<=nlstate;i++){
8144: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8145: } /* i */
8146: } /* end bad */
8147: }else{
8148: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8149: agemaxgood[cptcod]=age;
8150: }else{ /* bad we change the value with the values of good ages */
8151: for (i=1; i<=nlstate;i++){
8152: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8153: } /* i */
8154: } /* end bad */
8155: }/* end else */
8156: sum=0.;sumr=0.;
8157: for (i=1; i<=nlstate;i++){
8158: sum+=mobaverage[(int)age][i][cptcod];
8159: sumr+=probs[(int)age][i][cptcod];
8160: }
8161: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8162: 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\n",cptcod,sumr, (int)age, (int)bage);
1.266 brouard 8163: } /* end bad */
8164: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8165: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8166: 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\n",cptcod,sumr, (int)age, (int)bage);
1.222 brouard 8167: } /* end bad */
8168: }/* age */
1.266 brouard 8169:
8170: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8171: sumnewm[cptcod]=0.;
1.266 brouard 8172: sumnewmr[cptcod]=0.;
1.222 brouard 8173: for (i=1; i<=nlstate;i++){
8174: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8175: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8176: }
8177: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8178: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8179: agemingoodr[cptcod]=age;
8180: for (i=1; i<=nlstate;i++)
8181: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8182: }else{ /* bad we change the value with the values of good ages */
8183: for (i=1; i<=nlstate;i++){
8184: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8185: } /* i */
8186: } /* end bad */
8187: }else{
8188: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8189: agemingood[cptcod]=age;
8190: }else{ /* bad */
8191: for (i=1; i<=nlstate;i++){
8192: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8193: } /* i */
8194: } /* end bad */
8195: }/* end else */
8196: sum=0.;sumr=0.;
8197: for (i=1; i<=nlstate;i++){
8198: sum+=mobaverage[(int)age][i][cptcod];
8199: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8200: }
1.266 brouard 8201: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8202: 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 8203: } /* end bad */
8204: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8205: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8206: 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 8207: } /* end bad */
8208: }/* age */
1.266 brouard 8209:
1.222 brouard 8210:
8211: for (age=bage; age<=fage; age++){
1.235 brouard 8212: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8213: sumnewp[cptcod]=0.;
8214: sumnewm[cptcod]=0.;
8215: for (i=1; i<=nlstate;i++){
8216: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8217: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8218: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8219: }
8220: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8221: }
8222: /* printf("\n"); */
8223: /* } */
1.266 brouard 8224:
1.222 brouard 8225: /* brutal averaging */
1.266 brouard 8226: /* for (i=1; i<=nlstate;i++){ */
8227: /* for (age=1; age<=bage; age++){ */
8228: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8229: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8230: /* } */
8231: /* for (age=fage; age<=AGESUP; age++){ */
8232: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8233: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8234: /* } */
8235: /* } /\* end i status *\/ */
8236: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8237: /* for (age=1; age<=AGESUP; age++){ */
8238: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8239: /* mobaverage[(int)age][i][cptcod]=0.; */
8240: /* } */
8241: /* } */
1.222 brouard 8242: }/* end cptcod */
1.266 brouard 8243: free_vector(agemaxgoodr,1, ncovcombmax);
8244: free_vector(agemaxgood,1, ncovcombmax);
8245: free_vector(agemingood,1, ncovcombmax);
8246: free_vector(agemingoodr,1, ncovcombmax);
8247: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8248: free_vector(sumnewm,1, ncovcombmax);
8249: free_vector(sumnewp,1, ncovcombmax);
8250: return 0;
8251: }/* End movingaverage */
1.218 brouard 8252:
1.126 brouard 8253:
8254: /************** Forecasting ******************/
1.269 brouard 8255: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 8256: /* proj1, year, month, day of starting projection
8257: agemin, agemax range of age
8258: dateprev1 dateprev2 range of dates during which prevalence is computed
8259: anproj2 year of en of projection (same day and month as proj1).
8260: */
1.267 brouard 8261: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8262: double agec; /* generic age */
8263: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
8264: double *popeffectif,*popcount;
8265: double ***p3mat;
1.218 brouard 8266: /* double ***mobaverage; */
1.126 brouard 8267: char fileresf[FILENAMELENGTH];
8268:
8269: agelim=AGESUP;
1.211 brouard 8270: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8271: in each health status at the date of interview (if between dateprev1 and dateprev2).
8272: We still use firstpass and lastpass as another selection.
8273: */
1.214 brouard 8274: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8275: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8276:
1.201 brouard 8277: strcpy(fileresf,"F_");
8278: strcat(fileresf,fileresu);
1.126 brouard 8279: if((ficresf=fopen(fileresf,"w"))==NULL) {
8280: printf("Problem with forecast resultfile: %s\n", fileresf);
8281: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8282: }
1.235 brouard 8283: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8284: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8285:
1.225 brouard 8286: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8287:
8288:
8289: stepsize=(int) (stepm+YEARM-1)/YEARM;
8290: if (stepm<=12) stepsize=1;
8291: if(estepm < stepm){
8292: printf ("Problem %d lower than %d\n",estepm, stepm);
8293: }
1.270 brouard 8294: else{
8295: hstepm=estepm;
8296: }
8297: if(estepm > stepm){ /* Yes every two year */
8298: stepsize=2;
8299: }
1.126 brouard 8300:
8301: hstepm=hstepm/stepm;
8302: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8303: fractional in yp1 */
8304: anprojmean=yp;
8305: yp2=modf((yp1*12),&yp);
8306: mprojmean=yp;
8307: yp1=modf((yp2*30.5),&yp);
8308: jprojmean=yp;
8309: if(jprojmean==0) jprojmean=1;
8310: if(mprojmean==0) jprojmean=1;
8311:
1.227 brouard 8312: i1=pow(2,cptcoveff);
1.126 brouard 8313: if (cptcovn < 1){i1=1;}
8314:
8315: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
8316:
8317: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8318:
1.126 brouard 8319: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8320: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8321: for(k=1; k<=i1;k++){
1.253 brouard 8322: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8323: continue;
1.227 brouard 8324: if(invalidvarcomb[k]){
8325: printf("\nCombination (%d) projection ignored because no cases \n",k);
8326: continue;
8327: }
8328: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8329: for(j=1;j<=cptcoveff;j++) {
8330: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8331: }
1.235 brouard 8332: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8333: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8334: }
1.227 brouard 8335: fprintf(ficresf," yearproj age");
8336: for(j=1; j<=nlstate+ndeath;j++){
8337: for(i=1; i<=nlstate;i++)
8338: fprintf(ficresf," p%d%d",i,j);
8339: fprintf(ficresf," wp.%d",j);
8340: }
8341: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
8342: fprintf(ficresf,"\n");
8343: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.270 brouard 8344: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8345: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8346: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8347: nhstepm = nhstepm/hstepm;
8348: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8349: oldm=oldms;savm=savms;
1.268 brouard 8350: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8351: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8352: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8353: for (h=0; h<=nhstepm; h++){
8354: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8355: break;
8356: }
8357: }
8358: fprintf(ficresf,"\n");
8359: for(j=1;j<=cptcoveff;j++)
8360: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8361: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
8362:
8363: for(j=1; j<=nlstate+ndeath;j++) {
8364: ppij=0.;
8365: for(i=1; i<=nlstate;i++) {
1.278 brouard 8366: if (mobilav>=1)
8367: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8368: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8369: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8370: }
1.268 brouard 8371: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8372: } /* end i */
8373: fprintf(ficresf," %.3f", ppij);
8374: }/* end j */
1.227 brouard 8375: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8376: } /* end agec */
1.266 brouard 8377: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8378: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8379: } /* end yearp */
8380: } /* end k */
1.219 brouard 8381:
1.126 brouard 8382: fclose(ficresf);
1.215 brouard 8383: printf("End of Computing forecasting \n");
8384: fprintf(ficlog,"End of Computing forecasting\n");
8385:
1.126 brouard 8386: }
8387:
1.269 brouard 8388: /************** Back Forecasting ******************/
8389: void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
1.267 brouard 8390: /* back1, year, month, day of starting backection
8391: agemin, agemax range of age
8392: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8393: anback2 year of end of backprojection (same day and month as back1).
8394: prevacurrent and prev are prevalences.
1.267 brouard 8395: */
8396: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8397: double agec; /* generic age */
1.268 brouard 8398: double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.267 brouard 8399: double *popeffectif,*popcount;
8400: double ***p3mat;
8401: /* double ***mobaverage; */
8402: char fileresfb[FILENAMELENGTH];
8403:
1.268 brouard 8404: agelim=AGEINF;
1.267 brouard 8405: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8406: in each health status at the date of interview (if between dateprev1 and dateprev2).
8407: We still use firstpass and lastpass as another selection.
8408: */
8409: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8410: /* firstpass, lastpass, stepm, weightopt, model); */
8411:
8412: /*Do we need to compute prevalence again?*/
8413:
8414: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8415:
8416: strcpy(fileresfb,"FB_");
8417: strcat(fileresfb,fileresu);
8418: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8419: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8420: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8421: }
8422: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8423: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8424:
8425: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8426:
8427:
8428: stepsize=(int) (stepm+YEARM-1)/YEARM;
8429: if (stepm<=12) stepsize=1;
8430: if(estepm < stepm){
8431: printf ("Problem %d lower than %d\n",estepm, stepm);
8432: }
1.270 brouard 8433: else{
8434: hstepm=estepm;
8435: }
8436: if(estepm >= stepm){ /* Yes every two year */
8437: stepsize=2;
8438: }
1.267 brouard 8439:
8440: hstepm=hstepm/stepm;
8441: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8442: fractional in yp1 */
8443: anprojmean=yp;
8444: yp2=modf((yp1*12),&yp);
8445: mprojmean=yp;
8446: yp1=modf((yp2*30.5),&yp);
8447: jprojmean=yp;
8448: if(jprojmean==0) jprojmean=1;
8449: if(mprojmean==0) jprojmean=1;
8450:
8451: i1=pow(2,cptcoveff);
8452: if (cptcovn < 1){i1=1;}
8453:
8454: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.268 brouard 8455: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8456:
8457: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8458:
8459: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8460: for(k=1; k<=i1;k++){
8461: if(i1 != 1 && TKresult[nres]!= k)
8462: continue;
8463: if(invalidvarcomb[k]){
8464: printf("\nCombination (%d) projection ignored because no cases \n",k);
8465: continue;
8466: }
1.268 brouard 8467: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8468: for(j=1;j<=cptcoveff;j++) {
8469: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8470: }
8471: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8472: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8473: }
8474: fprintf(ficresfb," yearbproj age");
8475: for(j=1; j<=nlstate+ndeath;j++){
8476: for(i=1; i<=nlstate;i++)
1.268 brouard 8477: fprintf(ficresfb," b%d%d",i,j);
8478: fprintf(ficresfb," b.%d",j);
1.267 brouard 8479: }
8480: for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
8481: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8482: fprintf(ficresfb,"\n");
8483: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
1.273 brouard 8484: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8485: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8486: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8487: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8488: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8489: nhstepm = nhstepm/hstepm;
8490: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8491: oldm=oldms;savm=savms;
1.268 brouard 8492: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8493: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8494: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8495: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8496: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8497: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8498: for (h=0; h<=nhstepm; h++){
1.268 brouard 8499: if (h*hstepm/YEARM*stepm ==-yearp) {
8500: break;
8501: }
8502: }
8503: fprintf(ficresfb,"\n");
8504: for(j=1;j<=cptcoveff;j++)
8505: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8506: fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
8507: for(i=1; i<=nlstate+ndeath;i++) {
8508: ppij=0.;ppi=0.;
8509: for(j=1; j<=nlstate;j++) {
8510: /* if (mobilav==1) */
1.269 brouard 8511: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8512: ppi=ppi+prevacurrent[(int)agec][j][k];
8513: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8514: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8515: /* else { */
8516: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8517: /* } */
1.268 brouard 8518: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8519: } /* end j */
8520: if(ppi <0.99){
8521: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8522: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8523: }
8524: fprintf(ficresfb," %.3f", ppij);
8525: }/* end j */
1.267 brouard 8526: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8527: } /* end agec */
8528: } /* end yearp */
8529: } /* end k */
1.217 brouard 8530:
1.267 brouard 8531: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8532:
1.267 brouard 8533: fclose(ficresfb);
8534: printf("End of Computing Back forecasting \n");
8535: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8536:
1.267 brouard 8537: }
1.217 brouard 8538:
1.269 brouard 8539: /* Variance of prevalence limit: varprlim */
8540: 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){
8541: /*------- Variance of period (stable) prevalence------*/
8542:
8543: char fileresvpl[FILENAMELENGTH];
8544: FILE *ficresvpl;
8545: double **oldm, **savm;
8546: double **varpl; /* Variances of prevalence limits by age */
8547: int i1, k, nres, j ;
8548:
8549: strcpy(fileresvpl,"VPL_");
8550: strcat(fileresvpl,fileresu);
8551: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8552: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8553: exit(0);
8554: }
8555: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8556: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
8557:
8558: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8559: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8560:
8561: i1=pow(2,cptcoveff);
8562: if (cptcovn < 1){i1=1;}
8563:
8564: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8565: for(k=1; k<=i1;k++){
8566: if(i1 != 1 && TKresult[nres]!= k)
8567: continue;
8568: fprintf(ficresvpl,"\n#****** ");
8569: printf("\n#****** ");
8570: fprintf(ficlog,"\n#****** ");
8571: for(j=1;j<=cptcoveff;j++) {
8572: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8573: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8574: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8575: }
8576: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8577: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8578: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8579: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8580: }
8581: fprintf(ficresvpl,"******\n");
8582: printf("******\n");
8583: fprintf(ficlog,"******\n");
8584:
8585: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8586: oldm=oldms;savm=savms;
8587: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8588: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8589: /*}*/
8590: }
8591:
8592: fclose(ficresvpl);
8593: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8594: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
8595:
8596: }
8597: /* Variance of back prevalence: varbprlim */
8598: 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){
8599: /*------- Variance of back (stable) prevalence------*/
8600:
8601: char fileresvbl[FILENAMELENGTH];
8602: FILE *ficresvbl;
8603:
8604: double **oldm, **savm;
8605: double **varbpl; /* Variances of back prevalence limits by age */
8606: int i1, k, nres, j ;
8607:
8608: strcpy(fileresvbl,"VBL_");
8609: strcat(fileresvbl,fileresu);
8610: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8611: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8612: exit(0);
8613: }
8614: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8615: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8616:
8617:
8618: i1=pow(2,cptcoveff);
8619: if (cptcovn < 1){i1=1;}
8620:
8621: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8622: for(k=1; k<=i1;k++){
8623: if(i1 != 1 && TKresult[nres]!= k)
8624: continue;
8625: fprintf(ficresvbl,"\n#****** ");
8626: printf("\n#****** ");
8627: fprintf(ficlog,"\n#****** ");
8628: for(j=1;j<=cptcoveff;j++) {
8629: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8630: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8631: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8632: }
8633: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8634: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8635: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8636: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8637: }
8638: fprintf(ficresvbl,"******\n");
8639: printf("******\n");
8640: fprintf(ficlog,"******\n");
8641:
8642: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8643: oldm=oldms;savm=savms;
8644:
8645: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8646: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8647: /*}*/
8648: }
8649:
8650: fclose(ficresvbl);
8651: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8652: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8653:
8654: } /* End of varbprlim */
8655:
1.126 brouard 8656: /************** Forecasting *****not tested NB*************/
1.227 brouard 8657: /* 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 8658:
1.227 brouard 8659: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8660: /* int *popage; */
8661: /* double calagedatem, agelim, kk1, kk2; */
8662: /* double *popeffectif,*popcount; */
8663: /* double ***p3mat,***tabpop,***tabpopprev; */
8664: /* /\* double ***mobaverage; *\/ */
8665: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8666:
1.227 brouard 8667: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8668: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8669: /* agelim=AGESUP; */
8670: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8671:
1.227 brouard 8672: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8673:
8674:
1.227 brouard 8675: /* strcpy(filerespop,"POP_"); */
8676: /* strcat(filerespop,fileresu); */
8677: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8678: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8679: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8680: /* } */
8681: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8682: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8683:
1.227 brouard 8684: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8685:
1.227 brouard 8686: /* /\* if (mobilav!=0) { *\/ */
8687: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8688: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8689: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8690: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8691: /* /\* } *\/ */
8692: /* /\* } *\/ */
1.126 brouard 8693:
1.227 brouard 8694: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8695: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8696:
1.227 brouard 8697: /* agelim=AGESUP; */
1.126 brouard 8698:
1.227 brouard 8699: /* hstepm=1; */
8700: /* hstepm=hstepm/stepm; */
1.218 brouard 8701:
1.227 brouard 8702: /* if (popforecast==1) { */
8703: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8704: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8705: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8706: /* } */
8707: /* popage=ivector(0,AGESUP); */
8708: /* popeffectif=vector(0,AGESUP); */
8709: /* popcount=vector(0,AGESUP); */
1.126 brouard 8710:
1.227 brouard 8711: /* i=1; */
8712: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8713:
1.227 brouard 8714: /* imx=i; */
8715: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8716: /* } */
1.218 brouard 8717:
1.227 brouard 8718: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8719: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8720: /* k=k+1; */
8721: /* fprintf(ficrespop,"\n#******"); */
8722: /* for(j=1;j<=cptcoveff;j++) { */
8723: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8724: /* } */
8725: /* fprintf(ficrespop,"******\n"); */
8726: /* fprintf(ficrespop,"# Age"); */
8727: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8728: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8729:
1.227 brouard 8730: /* for (cpt=0; cpt<=0;cpt++) { */
8731: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8732:
1.227 brouard 8733: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8734: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8735: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8736:
1.227 brouard 8737: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8738: /* oldm=oldms;savm=savms; */
8739: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8740:
1.227 brouard 8741: /* for (h=0; h<=nhstepm; h++){ */
8742: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8743: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8744: /* } */
8745: /* for(j=1; j<=nlstate+ndeath;j++) { */
8746: /* kk1=0.;kk2=0; */
8747: /* for(i=1; i<=nlstate;i++) { */
8748: /* if (mobilav==1) */
8749: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8750: /* else { */
8751: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8752: /* } */
8753: /* } */
8754: /* if (h==(int)(calagedatem+12*cpt)){ */
8755: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8756: /* /\*fprintf(ficrespop," %.3f", kk1); */
8757: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8758: /* } */
8759: /* } */
8760: /* for(i=1; i<=nlstate;i++){ */
8761: /* kk1=0.; */
8762: /* for(j=1; j<=nlstate;j++){ */
8763: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8764: /* } */
8765: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8766: /* } */
1.218 brouard 8767:
1.227 brouard 8768: /* if (h==(int)(calagedatem+12*cpt)) */
8769: /* for(j=1; j<=nlstate;j++) */
8770: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8771: /* } */
8772: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8773: /* } */
8774: /* } */
1.218 brouard 8775:
1.227 brouard 8776: /* /\******\/ */
1.218 brouard 8777:
1.227 brouard 8778: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8779: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8780: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8781: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8782: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8783:
1.227 brouard 8784: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8785: /* oldm=oldms;savm=savms; */
8786: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8787: /* for (h=0; h<=nhstepm; h++){ */
8788: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8789: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8790: /* } */
8791: /* for(j=1; j<=nlstate+ndeath;j++) { */
8792: /* kk1=0.;kk2=0; */
8793: /* for(i=1; i<=nlstate;i++) { */
8794: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8795: /* } */
8796: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8797: /* } */
8798: /* } */
8799: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8800: /* } */
8801: /* } */
8802: /* } */
8803: /* } */
1.218 brouard 8804:
1.227 brouard 8805: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8806:
1.227 brouard 8807: /* if (popforecast==1) { */
8808: /* free_ivector(popage,0,AGESUP); */
8809: /* free_vector(popeffectif,0,AGESUP); */
8810: /* free_vector(popcount,0,AGESUP); */
8811: /* } */
8812: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8813: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8814: /* fclose(ficrespop); */
8815: /* } /\* End of popforecast *\/ */
1.218 brouard 8816:
1.126 brouard 8817: int fileappend(FILE *fichier, char *optionfich)
8818: {
8819: if((fichier=fopen(optionfich,"a"))==NULL) {
8820: printf("Problem with file: %s\n", optionfich);
8821: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8822: return (0);
8823: }
8824: fflush(fichier);
8825: return (1);
8826: }
8827:
8828:
8829: /**************** function prwizard **********************/
8830: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8831: {
8832:
8833: /* Wizard to print covariance matrix template */
8834:
1.164 brouard 8835: char ca[32], cb[32];
8836: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8837: int numlinepar;
8838:
8839: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8840: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8841: for(i=1; i <=nlstate; i++){
8842: jj=0;
8843: for(j=1; j <=nlstate+ndeath; j++){
8844: if(j==i) continue;
8845: jj++;
8846: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8847: printf("%1d%1d",i,j);
8848: fprintf(ficparo,"%1d%1d",i,j);
8849: for(k=1; k<=ncovmodel;k++){
8850: /* printf(" %lf",param[i][j][k]); */
8851: /* fprintf(ficparo," %lf",param[i][j][k]); */
8852: printf(" 0.");
8853: fprintf(ficparo," 0.");
8854: }
8855: printf("\n");
8856: fprintf(ficparo,"\n");
8857: }
8858: }
8859: printf("# Scales (for hessian or gradient estimation)\n");
8860: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8861: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8862: for(i=1; i <=nlstate; i++){
8863: jj=0;
8864: for(j=1; j <=nlstate+ndeath; j++){
8865: if(j==i) continue;
8866: jj++;
8867: fprintf(ficparo,"%1d%1d",i,j);
8868: printf("%1d%1d",i,j);
8869: fflush(stdout);
8870: for(k=1; k<=ncovmodel;k++){
8871: /* printf(" %le",delti3[i][j][k]); */
8872: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8873: printf(" 0.");
8874: fprintf(ficparo," 0.");
8875: }
8876: numlinepar++;
8877: printf("\n");
8878: fprintf(ficparo,"\n");
8879: }
8880: }
8881: printf("# Covariance matrix\n");
8882: /* # 121 Var(a12)\n\ */
8883: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8884: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8885: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8886: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8887: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8888: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8889: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8890: fflush(stdout);
8891: fprintf(ficparo,"# Covariance matrix\n");
8892: /* # 121 Var(a12)\n\ */
8893: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8894: /* # ...\n\ */
8895: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8896:
8897: for(itimes=1;itimes<=2;itimes++){
8898: jj=0;
8899: for(i=1; i <=nlstate; i++){
8900: for(j=1; j <=nlstate+ndeath; j++){
8901: if(j==i) continue;
8902: for(k=1; k<=ncovmodel;k++){
8903: jj++;
8904: ca[0]= k+'a'-1;ca[1]='\0';
8905: if(itimes==1){
8906: printf("#%1d%1d%d",i,j,k);
8907: fprintf(ficparo,"#%1d%1d%d",i,j,k);
8908: }else{
8909: printf("%1d%1d%d",i,j,k);
8910: fprintf(ficparo,"%1d%1d%d",i,j,k);
8911: /* printf(" %.5le",matcov[i][j]); */
8912: }
8913: ll=0;
8914: for(li=1;li <=nlstate; li++){
8915: for(lj=1;lj <=nlstate+ndeath; lj++){
8916: if(lj==li) continue;
8917: for(lk=1;lk<=ncovmodel;lk++){
8918: ll++;
8919: if(ll<=jj){
8920: cb[0]= lk +'a'-1;cb[1]='\0';
8921: if(ll<jj){
8922: if(itimes==1){
8923: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8924: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8925: }else{
8926: printf(" 0.");
8927: fprintf(ficparo," 0.");
8928: }
8929: }else{
8930: if(itimes==1){
8931: printf(" Var(%s%1d%1d)",ca,i,j);
8932: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
8933: }else{
8934: printf(" 0.");
8935: fprintf(ficparo," 0.");
8936: }
8937: }
8938: }
8939: } /* end lk */
8940: } /* end lj */
8941: } /* end li */
8942: printf("\n");
8943: fprintf(ficparo,"\n");
8944: numlinepar++;
8945: } /* end k*/
8946: } /*end j */
8947: } /* end i */
8948: } /* end itimes */
8949:
8950: } /* end of prwizard */
8951: /******************* Gompertz Likelihood ******************************/
8952: double gompertz(double x[])
8953: {
8954: double A,B,L=0.0,sump=0.,num=0.;
8955: int i,n=0; /* n is the size of the sample */
8956:
1.220 brouard 8957: for (i=1;i<=imx ; i++) {
1.126 brouard 8958: sump=sump+weight[i];
8959: /* sump=sump+1;*/
8960: num=num+1;
8961: }
8962:
8963:
8964: /* for (i=0; i<=imx; i++)
8965: 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]);*/
8966:
8967: for (i=1;i<=imx ; i++)
8968: {
8969: if (cens[i] == 1 && wav[i]>1)
8970: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
8971:
8972: if (cens[i] == 0 && wav[i]>1)
8973: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
8974: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
8975:
8976: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8977: if (wav[i] > 1 ) { /* ??? */
8978: L=L+A*weight[i];
8979: /* 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]);*/
8980: }
8981: }
8982:
8983: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8984:
8985: return -2*L*num/sump;
8986: }
8987:
1.136 brouard 8988: #ifdef GSL
8989: /******************* Gompertz_f Likelihood ******************************/
8990: double gompertz_f(const gsl_vector *v, void *params)
8991: {
8992: double A,B,LL=0.0,sump=0.,num=0.;
8993: double *x= (double *) v->data;
8994: int i,n=0; /* n is the size of the sample */
8995:
8996: for (i=0;i<=imx-1 ; i++) {
8997: sump=sump+weight[i];
8998: /* sump=sump+1;*/
8999: num=num+1;
9000: }
9001:
9002:
9003: /* for (i=0; i<=imx; i++)
9004: 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]);*/
9005: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
9006: for (i=1;i<=imx ; i++)
9007: {
9008: if (cens[i] == 1 && wav[i]>1)
9009: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
9010:
9011: if (cens[i] == 0 && wav[i]>1)
9012: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
9013: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
9014:
9015: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
9016: if (wav[i] > 1 ) { /* ??? */
9017: LL=LL+A*weight[i];
9018: /* 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]);*/
9019: }
9020: }
9021:
9022: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9023: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9024:
9025: return -2*LL*num/sump;
9026: }
9027: #endif
9028:
1.126 brouard 9029: /******************* Printing html file ***********/
1.201 brouard 9030: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9031: int lastpass, int stepm, int weightopt, char model[],\
9032: int imx, double p[],double **matcov,double agemortsup){
9033: int i,k;
9034:
9035: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9036: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9037: for (i=1;i<=2;i++)
9038: 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 9039: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9040: fprintf(fichtm,"</ul>");
9041:
9042: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9043:
9044: 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>");
9045:
9046: for (k=agegomp;k<(agemortsup-2);k++)
9047: 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]);
9048:
9049:
9050: fflush(fichtm);
9051: }
9052:
9053: /******************* Gnuplot file **************/
1.201 brouard 9054: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9055:
9056: char dirfileres[132],optfileres[132];
1.164 brouard 9057:
1.126 brouard 9058: int ng;
9059:
9060:
9061: /*#ifdef windows */
9062: fprintf(ficgp,"cd \"%s\" \n",pathc);
9063: /*#endif */
9064:
9065:
9066: strcpy(dirfileres,optionfilefiname);
9067: strcpy(optfileres,"vpl");
1.199 brouard 9068: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9069: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9070: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9071: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9072: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9073:
9074: }
9075:
1.136 brouard 9076: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9077: {
1.126 brouard 9078:
1.136 brouard 9079: /*-------- data file ----------*/
9080: FILE *fic;
9081: char dummy[]=" ";
1.240 brouard 9082: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9083: int lstra;
1.136 brouard 9084: int linei, month, year,iout;
9085: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9086: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9087: char *stratrunc;
1.223 brouard 9088:
1.240 brouard 9089: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9090: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9091:
1.240 brouard 9092: for(v=1; v <=ncovcol;v++){
9093: DummyV[v]=0;
9094: FixedV[v]=0;
9095: }
9096: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9097: DummyV[v]=1;
9098: FixedV[v]=0;
9099: }
9100: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9101: DummyV[v]=0;
9102: FixedV[v]=1;
9103: }
9104: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9105: DummyV[v]=1;
9106: FixedV[v]=1;
9107: }
9108: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9109: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9110: 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]);
9111: }
1.126 brouard 9112:
1.136 brouard 9113: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9114: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9115: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9116: }
1.126 brouard 9117:
1.136 brouard 9118: i=1;
9119: linei=0;
9120: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9121: linei=linei+1;
9122: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9123: if(line[j] == '\t')
9124: line[j] = ' ';
9125: }
9126: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9127: ;
9128: };
9129: line[j+1]=0; /* Trims blanks at end of line */
9130: if(line[0]=='#'){
9131: fprintf(ficlog,"Comment line\n%s\n",line);
9132: printf("Comment line\n%s\n",line);
9133: continue;
9134: }
9135: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9136: strcpy(line, linetmp);
1.223 brouard 9137:
9138: /* Loops on waves */
9139: for (j=maxwav;j>=1;j--){
9140: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9141: cutv(stra, strb, line, ' ');
9142: if(strb[0]=='.') { /* Missing value */
9143: lval=-1;
9144: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9145: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9146: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9147: 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);
9148: 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);
9149: return 1;
9150: }
9151: }else{
9152: errno=0;
9153: /* what_kind_of_number(strb); */
9154: dval=strtod(strb,&endptr);
9155: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9156: /* if(strb != endptr && *endptr == '\0') */
9157: /* dval=dlval; */
9158: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9159: if( strb[0]=='\0' || (*endptr != '\0')){
9160: 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);
9161: 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);
9162: return 1;
9163: }
9164: cotqvar[j][iv][i]=dval;
9165: cotvar[j][ntv+iv][i]=dval;
9166: }
9167: strcpy(line,stra);
1.223 brouard 9168: }/* end loop ntqv */
1.225 brouard 9169:
1.223 brouard 9170: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9171: cutv(stra, strb, line, ' ');
9172: if(strb[0]=='.') { /* Missing value */
9173: lval=-1;
9174: }else{
9175: errno=0;
9176: lval=strtol(strb,&endptr,10);
9177: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9178: if( strb[0]=='\0' || (*endptr != '\0')){
9179: 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);
9180: 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);
9181: return 1;
9182: }
9183: }
9184: if(lval <-1 || lval >1){
9185: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9186: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9187: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9188: For example, for multinomial values like 1, 2 and 3,\n \
9189: build V1=0 V2=0 for the reference value (1),\n \
9190: V1=1 V2=0 for (2) \n \
1.223 brouard 9191: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9192: output of IMaCh is often meaningless.\n \
1.223 brouard 9193: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9194: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9195: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9196: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9197: For example, for multinomial values like 1, 2 and 3,\n \
9198: build V1=0 V2=0 for the reference value (1),\n \
9199: V1=1 V2=0 for (2) \n \
1.223 brouard 9200: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9201: output of IMaCh is often meaningless.\n \
1.223 brouard 9202: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9203: return 1;
9204: }
9205: cotvar[j][iv][i]=(double)(lval);
9206: strcpy(line,stra);
1.223 brouard 9207: }/* end loop ntv */
1.225 brouard 9208:
1.223 brouard 9209: /* Statuses at wave */
1.137 brouard 9210: cutv(stra, strb, line, ' ');
1.223 brouard 9211: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9212: lval=-1;
1.136 brouard 9213: }else{
1.238 brouard 9214: errno=0;
9215: lval=strtol(strb,&endptr,10);
9216: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9217: if( strb[0]=='\0' || (*endptr != '\0')){
9218: 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);
9219: 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);
9220: return 1;
9221: }
1.136 brouard 9222: }
1.225 brouard 9223:
1.136 brouard 9224: s[j][i]=lval;
1.225 brouard 9225:
1.223 brouard 9226: /* Date of Interview */
1.136 brouard 9227: strcpy(line,stra);
9228: cutv(stra, strb,line,' ');
1.169 brouard 9229: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9230: }
1.169 brouard 9231: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9232: month=99;
9233: year=9999;
1.136 brouard 9234: }else{
1.225 brouard 9235: 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);
9236: 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);
9237: return 1;
1.136 brouard 9238: }
9239: anint[j][i]= (double) year;
9240: mint[j][i]= (double)month;
9241: strcpy(line,stra);
1.223 brouard 9242: } /* End loop on waves */
1.225 brouard 9243:
1.223 brouard 9244: /* Date of death */
1.136 brouard 9245: cutv(stra, strb,line,' ');
1.169 brouard 9246: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9247: }
1.169 brouard 9248: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9249: month=99;
9250: year=9999;
9251: }else{
1.141 brouard 9252: 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 9253: 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);
9254: return 1;
1.136 brouard 9255: }
9256: andc[i]=(double) year;
9257: moisdc[i]=(double) month;
9258: strcpy(line,stra);
9259:
1.223 brouard 9260: /* Date of birth */
1.136 brouard 9261: cutv(stra, strb,line,' ');
1.169 brouard 9262: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9263: }
1.169 brouard 9264: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9265: month=99;
9266: year=9999;
9267: }else{
1.141 brouard 9268: 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);
9269: 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 9270: return 1;
1.136 brouard 9271: }
9272: if (year==9999) {
1.141 brouard 9273: 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);
9274: 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 9275: return 1;
9276:
1.136 brouard 9277: }
9278: annais[i]=(double)(year);
9279: moisnais[i]=(double)(month);
9280: strcpy(line,stra);
1.225 brouard 9281:
1.223 brouard 9282: /* Sample weight */
1.136 brouard 9283: cutv(stra, strb,line,' ');
9284: errno=0;
9285: dval=strtod(strb,&endptr);
9286: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9287: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9288: 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 9289: fflush(ficlog);
9290: return 1;
9291: }
9292: weight[i]=dval;
9293: strcpy(line,stra);
1.225 brouard 9294:
1.223 brouard 9295: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9296: cutv(stra, strb, line, ' ');
9297: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9298: lval=-1;
1.223 brouard 9299: }else{
1.225 brouard 9300: errno=0;
9301: /* what_kind_of_number(strb); */
9302: dval=strtod(strb,&endptr);
9303: /* if(strb != endptr && *endptr == '\0') */
9304: /* dval=dlval; */
9305: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9306: if( strb[0]=='\0' || (*endptr != '\0')){
9307: 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);
9308: 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);
9309: return 1;
9310: }
9311: coqvar[iv][i]=dval;
1.226 brouard 9312: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9313: }
9314: strcpy(line,stra);
9315: }/* end loop nqv */
1.136 brouard 9316:
1.223 brouard 9317: /* Covariate values */
1.136 brouard 9318: for (j=ncovcol;j>=1;j--){
9319: cutv(stra, strb,line,' ');
1.223 brouard 9320: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9321: lval=-1;
1.136 brouard 9322: }else{
1.225 brouard 9323: errno=0;
9324: lval=strtol(strb,&endptr,10);
9325: if( strb[0]=='\0' || (*endptr != '\0')){
9326: 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);
9327: 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);
9328: return 1;
9329: }
1.136 brouard 9330: }
9331: if(lval <-1 || lval >1){
1.225 brouard 9332: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9333: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9334: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9335: For example, for multinomial values like 1, 2 and 3,\n \
9336: build V1=0 V2=0 for the reference value (1),\n \
9337: V1=1 V2=0 for (2) \n \
1.136 brouard 9338: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9339: output of IMaCh is often meaningless.\n \
1.136 brouard 9340: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9341: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9342: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9343: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9344: For example, for multinomial values like 1, 2 and 3,\n \
9345: build V1=0 V2=0 for the reference value (1),\n \
9346: V1=1 V2=0 for (2) \n \
1.136 brouard 9347: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9348: output of IMaCh is often meaningless.\n \
1.136 brouard 9349: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9350: return 1;
1.136 brouard 9351: }
9352: covar[j][i]=(double)(lval);
9353: strcpy(line,stra);
9354: }
9355: lstra=strlen(stra);
1.225 brouard 9356:
1.136 brouard 9357: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9358: stratrunc = &(stra[lstra-9]);
9359: num[i]=atol(stratrunc);
9360: }
9361: else
9362: num[i]=atol(stra);
9363: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9364: 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;}*/
9365:
9366: i=i+1;
9367: } /* End loop reading data */
1.225 brouard 9368:
1.136 brouard 9369: *imax=i-1; /* Number of individuals */
9370: fclose(fic);
1.225 brouard 9371:
1.136 brouard 9372: return (0);
1.164 brouard 9373: /* endread: */
1.225 brouard 9374: printf("Exiting readdata: ");
9375: fclose(fic);
9376: return (1);
1.223 brouard 9377: }
1.126 brouard 9378:
1.234 brouard 9379: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9380: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9381: while (*p2 == ' ')
1.234 brouard 9382: p2++;
9383: /* while ((*p1++ = *p2++) !=0) */
9384: /* ; */
9385: /* do */
9386: /* while (*p2 == ' ') */
9387: /* p2++; */
9388: /* while (*p1++ == *p2++); */
9389: *stri=p2;
1.145 brouard 9390: }
9391:
1.235 brouard 9392: int decoderesult ( char resultline[], int nres)
1.230 brouard 9393: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9394: {
1.235 brouard 9395: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9396: char resultsav[MAXLINE];
1.234 brouard 9397: int resultmodel[MAXLINE];
9398: int modelresult[MAXLINE];
1.230 brouard 9399: char stra[80], strb[80], strc[80], strd[80],stre[80];
9400:
1.234 brouard 9401: removefirstspace(&resultline);
1.233 brouard 9402: printf("decoderesult:%s\n",resultline);
1.230 brouard 9403:
9404: if (strstr(resultline,"v") !=0){
9405: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9406: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9407: return 1;
9408: }
9409: trimbb(resultsav, resultline);
9410: if (strlen(resultsav) >1){
9411: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9412: }
1.253 brouard 9413: if(j == 0){ /* Resultline but no = */
9414: TKresult[nres]=0; /* Combination for the nresult and the model */
9415: return (0);
9416: }
9417:
1.234 brouard 9418: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9419: 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);
9420: 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);
9421: }
9422: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9423: if(nbocc(resultsav,'=') >1){
9424: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9425: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9426: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9427: }else
9428: cutl(strc,strd,resultsav,'=');
1.230 brouard 9429: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9430:
1.230 brouard 9431: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9432: Tvarsel[k]=atoi(strc);
9433: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9434: /* cptcovsel++; */
9435: if (nbocc(stra,'=') >0)
9436: strcpy(resultsav,stra); /* and analyzes it */
9437: }
1.235 brouard 9438: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9439: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9440: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9441: match=0;
1.236 brouard 9442: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9443: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9444: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9445: match=1;
9446: break;
9447: }
9448: }
9449: if(match == 0){
9450: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9451: }
9452: }
9453: }
1.235 brouard 9454: /* Checking for missing or useless values in comparison of current model needs */
9455: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9456: match=0;
1.235 brouard 9457: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9458: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9459: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9460: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9461: ++match;
9462: }
9463: }
9464: }
9465: if(match == 0){
9466: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9467: }else if(match > 1){
9468: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9469: }
9470: }
1.235 brouard 9471:
1.234 brouard 9472: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9473: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9474: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9475: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9476: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9477: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9478: /* 1 0 0 0 */
9479: /* 2 1 0 0 */
9480: /* 3 0 1 0 */
9481: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9482: /* 5 0 0 1 */
9483: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9484: /* 7 0 1 1 */
9485: /* 8 1 1 1 */
1.237 brouard 9486: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9487: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9488: /* V5*age V5 known which value for nres? */
9489: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9490: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9491: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9492: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9493: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9494: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9495: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9496: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9497: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9498: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9499: k4++;;
9500: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9501: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9502: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9503: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9504: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9505: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9506: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9507: k4q++;;
9508: }
9509: }
1.234 brouard 9510:
1.235 brouard 9511: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9512: return (0);
9513: }
1.235 brouard 9514:
1.230 brouard 9515: int decodemodel( char model[], int lastobs)
9516: /**< This routine decodes the model and returns:
1.224 brouard 9517: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9518: * - nagesqr = 1 if age*age in the model, otherwise 0.
9519: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9520: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9521: * - cptcovage number of covariates with age*products =2
9522: * - cptcovs number of simple covariates
9523: * - 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
9524: * which is a new column after the 9 (ncovcol) variables.
9525: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9526: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9527: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9528: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9529: */
1.136 brouard 9530: {
1.238 brouard 9531: int i, j, k, ks, v;
1.227 brouard 9532: int j1, k1, k2, k3, k4;
1.136 brouard 9533: char modelsav[80];
1.145 brouard 9534: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9535: char *strpt;
1.136 brouard 9536:
1.145 brouard 9537: /*removespace(model);*/
1.136 brouard 9538: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9539: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9540: if (strstr(model,"AGE") !=0){
1.192 brouard 9541: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9542: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9543: return 1;
9544: }
1.141 brouard 9545: if (strstr(model,"v") !=0){
9546: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9547: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9548: return 1;
9549: }
1.187 brouard 9550: strcpy(modelsav,model);
9551: if ((strpt=strstr(model,"age*age")) !=0){
9552: printf(" strpt=%s, model=%s\n",strpt, model);
9553: if(strpt != model){
1.234 brouard 9554: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9555: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9556: corresponding column of parameters.\n",model);
1.234 brouard 9557: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9558: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9559: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9560: return 1;
1.225 brouard 9561: }
1.187 brouard 9562: nagesqr=1;
9563: if (strstr(model,"+age*age") !=0)
1.234 brouard 9564: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9565: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9566: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9567: else
1.234 brouard 9568: substrchaine(modelsav, model, "age*age");
1.187 brouard 9569: }else
9570: nagesqr=0;
9571: if (strlen(modelsav) >1){
9572: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9573: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9574: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9575: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9576: * cst, age and age*age
9577: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9578: /* including age products which are counted in cptcovage.
9579: * but the covariates which are products must be treated
9580: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9581: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9582: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9583:
9584:
1.187 brouard 9585: /* Design
9586: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9587: * < ncovcol=8 >
9588: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9589: * k= 1 2 3 4 5 6 7 8
9590: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9591: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9592: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9593: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9594: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9595: * Tage[++cptcovage]=k
9596: * if products, new covar are created after ncovcol with k1
9597: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9598: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9599: * 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
9600: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9601: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9602: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9603: * < ncovcol=8 >
9604: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9605: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9606: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9607: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9608: * p Tprod[1]@2={ 6, 5}
9609: *p Tvard[1][1]@4= {7, 8, 5, 6}
9610: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9611: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9612: *How to reorganize?
9613: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9614: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9615: * {2, 1, 4, 8, 5, 6, 3, 7}
9616: * Struct []
9617: */
1.225 brouard 9618:
1.187 brouard 9619: /* This loop fills the array Tvar from the string 'model'.*/
9620: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9621: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9622: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9623: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9624: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9625: /* k=1 Tvar[1]=2 (from V2) */
9626: /* k=5 Tvar[5] */
9627: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9628: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9629: /* } */
1.198 brouard 9630: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9631: /*
9632: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9633: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9634: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9635: }
1.187 brouard 9636: cptcovage=0;
9637: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9638: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9639: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9640: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9641: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9642: /*scanf("%d",i);*/
9643: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9644: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9645: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9646: /* covar is not filled and then is empty */
9647: cptcovprod--;
9648: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9649: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9650: Typevar[k]=1; /* 1 for age product */
9651: cptcovage++; /* Sums the number of covariates which include age as a product */
9652: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9653: /*printf("stre=%s ", stre);*/
9654: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9655: cptcovprod--;
9656: cutl(stre,strb,strc,'V');
9657: Tvar[k]=atoi(stre);
9658: Typevar[k]=1; /* 1 for age product */
9659: cptcovage++;
9660: Tage[cptcovage]=k;
9661: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9662: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9663: cptcovn++;
9664: cptcovprodnoage++;k1++;
9665: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9666: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9667: because this model-covariate is a construction we invent a new column
9668: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9669: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9670: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9671: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9672: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9673: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9674: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9675: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9676: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9677: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9678: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9679: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9680: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9681: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9682: for (i=1; i<=lastobs;i++){
9683: /* Computes the new covariate which is a product of
9684: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9685: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9686: }
9687: } /* End age is not in the model */
9688: } /* End if model includes a product */
9689: else { /* no more sum */
9690: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9691: /* scanf("%d",i);*/
9692: cutl(strd,strc,strb,'V');
9693: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9694: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9695: Tvar[k]=atoi(strd);
9696: Typevar[k]=0; /* 0 for simple covariates */
9697: }
9698: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9699: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9700: scanf("%d",i);*/
1.187 brouard 9701: } /* end of loop + on total covariates */
9702: } /* end if strlen(modelsave == 0) age*age might exist */
9703: } /* end if strlen(model == 0) */
1.136 brouard 9704:
9705: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9706: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9707:
1.136 brouard 9708: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9709: printf("cptcovprod=%d ", cptcovprod);
9710: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9711: scanf("%d ",i);*/
9712:
9713:
1.230 brouard 9714: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9715: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9716: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9717: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9718: k = 1 2 3 4 5 6 7 8 9
9719: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9720: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9721: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9722: Dummy[k] 1 0 0 0 3 1 1 2 3
9723: Tmodelind[combination of covar]=k;
1.225 brouard 9724: */
9725: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9726: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9727: /* 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 9728: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9729: printf("Model=%s\n\
9730: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9731: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9732: 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);
9733: fprintf(ficlog,"Model=%s\n\
9734: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9735: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9736: 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 9737: for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9738: 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 */
9739: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9740: Fixed[k]= 0;
9741: Dummy[k]= 0;
1.225 brouard 9742: ncoveff++;
1.232 brouard 9743: ncovf++;
1.234 brouard 9744: nsd++;
9745: modell[k].maintype= FTYPE;
9746: TvarsD[nsd]=Tvar[k];
9747: TvarsDind[nsd]=k;
9748: TvarF[ncovf]=Tvar[k];
9749: TvarFind[ncovf]=k;
9750: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9751: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9752: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9753: Fixed[k]= 0;
9754: Dummy[k]= 0;
9755: ncoveff++;
9756: ncovf++;
9757: modell[k].maintype= FTYPE;
9758: TvarF[ncovf]=Tvar[k];
9759: TvarFind[ncovf]=k;
1.230 brouard 9760: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9761: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9762: }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 9763: Fixed[k]= 0;
9764: Dummy[k]= 1;
1.230 brouard 9765: nqfveff++;
1.234 brouard 9766: modell[k].maintype= FTYPE;
9767: modell[k].subtype= FQ;
9768: nsq++;
9769: TvarsQ[nsq]=Tvar[k];
9770: TvarsQind[nsq]=k;
1.232 brouard 9771: ncovf++;
1.234 brouard 9772: TvarF[ncovf]=Tvar[k];
9773: TvarFind[ncovf]=k;
1.231 brouard 9774: 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 9775: 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 9776: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9777: Fixed[k]= 1;
9778: Dummy[k]= 0;
1.225 brouard 9779: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9780: modell[k].maintype= VTYPE;
9781: modell[k].subtype= VD;
9782: nsd++;
9783: TvarsD[nsd]=Tvar[k];
9784: TvarsDind[nsd]=k;
9785: ncovv++; /* Only simple time varying variables */
9786: TvarV[ncovv]=Tvar[k];
1.242 brouard 9787: 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 9788: 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 */
9789: 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 9790: 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);
9791: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9792: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9793: Fixed[k]= 1;
9794: Dummy[k]= 1;
9795: nqtveff++;
9796: modell[k].maintype= VTYPE;
9797: modell[k].subtype= VQ;
9798: ncovv++; /* Only simple time varying variables */
9799: nsq++;
9800: TvarsQ[nsq]=Tvar[k];
9801: TvarsQind[nsq]=k;
9802: TvarV[ncovv]=Tvar[k];
1.242 brouard 9803: 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 9804: 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 */
9805: 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 9806: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9807: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9808: 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 9809: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9810: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9811: ncova++;
9812: TvarA[ncova]=Tvar[k];
9813: TvarAind[ncova]=k;
1.231 brouard 9814: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9815: Fixed[k]= 2;
9816: Dummy[k]= 2;
9817: modell[k].maintype= ATYPE;
9818: modell[k].subtype= APFD;
9819: /* ncoveff++; */
1.227 brouard 9820: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 9821: Fixed[k]= 2;
9822: Dummy[k]= 3;
9823: modell[k].maintype= ATYPE;
9824: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
9825: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 9826: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 9827: Fixed[k]= 3;
9828: Dummy[k]= 2;
9829: modell[k].maintype= ATYPE;
9830: modell[k].subtype= APVD; /* Product age * varying dummy */
9831: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 9832: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9833: Fixed[k]= 3;
9834: Dummy[k]= 3;
9835: modell[k].maintype= ATYPE;
9836: modell[k].subtype= APVQ; /* Product age * varying quantitative */
9837: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 9838: }
9839: }else if (Typevar[k] == 2) { /* product without age */
9840: k1=Tposprod[k];
9841: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 9842: if(Tvard[k1][2] <=ncovcol){
9843: Fixed[k]= 1;
9844: Dummy[k]= 0;
9845: modell[k].maintype= FTYPE;
9846: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
9847: ncovf++; /* Fixed variables without age */
9848: TvarF[ncovf]=Tvar[k];
9849: TvarFind[ncovf]=k;
9850: }else if(Tvard[k1][2] <=ncovcol+nqv){
9851: Fixed[k]= 0; /* or 2 ?*/
9852: Dummy[k]= 1;
9853: modell[k].maintype= FTYPE;
9854: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
9855: ncovf++; /* Varying variables without age */
9856: TvarF[ncovf]=Tvar[k];
9857: TvarFind[ncovf]=k;
9858: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9859: Fixed[k]= 1;
9860: Dummy[k]= 0;
9861: modell[k].maintype= VTYPE;
9862: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
9863: ncovv++; /* Varying variables without age */
9864: TvarV[ncovv]=Tvar[k];
9865: TvarVind[ncovv]=k;
9866: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9867: Fixed[k]= 1;
9868: Dummy[k]= 1;
9869: modell[k].maintype= VTYPE;
9870: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
9871: ncovv++; /* Varying variables without age */
9872: TvarV[ncovv]=Tvar[k];
9873: TvarVind[ncovv]=k;
9874: }
1.227 brouard 9875: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 9876: if(Tvard[k1][2] <=ncovcol){
9877: Fixed[k]= 0; /* or 2 ?*/
9878: Dummy[k]= 1;
9879: modell[k].maintype= FTYPE;
9880: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
9881: ncovf++; /* Fixed variables without age */
9882: TvarF[ncovf]=Tvar[k];
9883: TvarFind[ncovf]=k;
9884: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9885: Fixed[k]= 1;
9886: Dummy[k]= 1;
9887: modell[k].maintype= VTYPE;
9888: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
9889: ncovv++; /* Varying variables without age */
9890: TvarV[ncovv]=Tvar[k];
9891: TvarVind[ncovv]=k;
9892: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9893: Fixed[k]= 1;
9894: Dummy[k]= 1;
9895: modell[k].maintype= VTYPE;
9896: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
9897: ncovv++; /* Varying variables without age */
9898: TvarV[ncovv]=Tvar[k];
9899: TvarVind[ncovv]=k;
9900: ncovv++; /* Varying variables without age */
9901: TvarV[ncovv]=Tvar[k];
9902: TvarVind[ncovv]=k;
9903: }
1.227 brouard 9904: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 9905: if(Tvard[k1][2] <=ncovcol){
9906: Fixed[k]= 1;
9907: Dummy[k]= 1;
9908: modell[k].maintype= VTYPE;
9909: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
9910: ncovv++; /* Varying variables without age */
9911: TvarV[ncovv]=Tvar[k];
9912: TvarVind[ncovv]=k;
9913: }else if(Tvard[k1][2] <=ncovcol+nqv){
9914: Fixed[k]= 1;
9915: Dummy[k]= 1;
9916: modell[k].maintype= VTYPE;
9917: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
9918: ncovv++; /* Varying variables without age */
9919: TvarV[ncovv]=Tvar[k];
9920: TvarVind[ncovv]=k;
9921: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9922: Fixed[k]= 1;
9923: Dummy[k]= 0;
9924: modell[k].maintype= VTYPE;
9925: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
9926: ncovv++; /* Varying variables without age */
9927: TvarV[ncovv]=Tvar[k];
9928: TvarVind[ncovv]=k;
9929: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9930: Fixed[k]= 1;
9931: Dummy[k]= 1;
9932: modell[k].maintype= VTYPE;
9933: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
9934: ncovv++; /* Varying variables without age */
9935: TvarV[ncovv]=Tvar[k];
9936: TvarVind[ncovv]=k;
9937: }
1.227 brouard 9938: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9939: if(Tvard[k1][2] <=ncovcol){
9940: Fixed[k]= 1;
9941: Dummy[k]= 1;
9942: modell[k].maintype= VTYPE;
9943: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
9944: ncovv++; /* Varying variables without age */
9945: TvarV[ncovv]=Tvar[k];
9946: TvarVind[ncovv]=k;
9947: }else if(Tvard[k1][2] <=ncovcol+nqv){
9948: Fixed[k]= 1;
9949: Dummy[k]= 1;
9950: modell[k].maintype= VTYPE;
9951: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
9952: ncovv++; /* Varying variables without age */
9953: TvarV[ncovv]=Tvar[k];
9954: TvarVind[ncovv]=k;
9955: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9956: Fixed[k]= 1;
9957: Dummy[k]= 1;
9958: modell[k].maintype= VTYPE;
9959: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
9960: ncovv++; /* Varying variables without age */
9961: TvarV[ncovv]=Tvar[k];
9962: TvarVind[ncovv]=k;
9963: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9964: Fixed[k]= 1;
9965: Dummy[k]= 1;
9966: modell[k].maintype= VTYPE;
9967: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
9968: ncovv++; /* Varying variables without age */
9969: TvarV[ncovv]=Tvar[k];
9970: TvarVind[ncovv]=k;
9971: }
1.227 brouard 9972: }else{
1.240 brouard 9973: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9974: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9975: } /*end k1*/
1.225 brouard 9976: }else{
1.226 brouard 9977: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
9978: 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 9979: }
1.227 brouard 9980: 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 9981: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 9982: 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]);
9983: }
9984: /* Searching for doublons in the model */
9985: for(k1=1; k1<= cptcovt;k1++){
9986: for(k2=1; k2 <k1;k2++){
1.285 brouard 9987: /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){ */
9988: if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
1.234 brouard 9989: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
9990: if(Tvar[k1]==Tvar[k2]){
1.285 brouard 9991: 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]);
9992: 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 9993: return(1);
9994: }
9995: }else if (Typevar[k1] ==2){
9996: k3=Tposprod[k1];
9997: k4=Tposprod[k2];
9998: 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])) ){
9999: 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]]);
10000: 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);
10001: return(1);
10002: }
10003: }
1.227 brouard 10004: }
10005: }
1.225 brouard 10006: }
10007: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
10008: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 10009: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
10010: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 10011: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 10012: /*endread:*/
1.225 brouard 10013: printf("Exiting decodemodel: ");
10014: return (1);
1.136 brouard 10015: }
10016:
1.169 brouard 10017: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 10018: {/* Check ages at death */
1.136 brouard 10019: int i, m;
1.218 brouard 10020: int firstone=0;
10021:
1.136 brouard 10022: for (i=1; i<=imx; i++) {
10023: for(m=2; (m<= maxwav); m++) {
10024: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10025: anint[m][i]=9999;
1.216 brouard 10026: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10027: s[m][i]=-1;
1.136 brouard 10028: }
10029: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10030: *nberr = *nberr + 1;
1.218 brouard 10031: if(firstone == 0){
10032: firstone=1;
1.260 brouard 10033: 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 10034: }
1.262 brouard 10035: 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 10036: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10037: }
10038: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10039: (*nberr)++;
1.259 brouard 10040: 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 10041: 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 10042: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10043: }
10044: }
10045: }
10046:
10047: for (i=1; i<=imx; i++) {
10048: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10049: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10050: 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 10051: if (s[m][i] >= nlstate+1) {
1.169 brouard 10052: if(agedc[i]>0){
10053: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10054: agev[m][i]=agedc[i];
1.214 brouard 10055: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10056: }else {
1.136 brouard 10057: if ((int)andc[i]!=9999){
10058: nbwarn++;
10059: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10060: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10061: agev[m][i]=-1;
10062: }
10063: }
1.169 brouard 10064: } /* agedc > 0 */
1.214 brouard 10065: } /* end if */
1.136 brouard 10066: else if(s[m][i] !=9){ /* Standard case, age in fractional
10067: years but with the precision of a month */
10068: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10069: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10070: agev[m][i]=1;
10071: else if(agev[m][i] < *agemin){
10072: *agemin=agev[m][i];
10073: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10074: }
10075: else if(agev[m][i] >*agemax){
10076: *agemax=agev[m][i];
1.156 brouard 10077: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10078: }
10079: /*agev[m][i]=anint[m][i]-annais[i];*/
10080: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10081: } /* en if 9*/
1.136 brouard 10082: else { /* =9 */
1.214 brouard 10083: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10084: agev[m][i]=1;
10085: s[m][i]=-1;
10086: }
10087: }
1.214 brouard 10088: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10089: agev[m][i]=1;
1.214 brouard 10090: else{
10091: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10092: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10093: agev[m][i]=0;
10094: }
10095: } /* End for lastpass */
10096: }
1.136 brouard 10097:
10098: for (i=1; i<=imx; i++) {
10099: for(m=firstpass; (m<=lastpass); m++){
10100: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10101: (*nberr)++;
1.136 brouard 10102: 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);
10103: 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);
10104: return 1;
10105: }
10106: }
10107: }
10108:
10109: /*for (i=1; i<=imx; i++){
10110: for (m=firstpass; (m<lastpass); m++){
10111: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10112: }
10113:
10114: }*/
10115:
10116:
1.139 brouard 10117: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10118: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10119:
10120: return (0);
1.164 brouard 10121: /* endread:*/
1.136 brouard 10122: printf("Exiting calandcheckages: ");
10123: return (1);
10124: }
10125:
1.172 brouard 10126: #if defined(_MSC_VER)
10127: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10128: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10129: //#include "stdafx.h"
10130: //#include <stdio.h>
10131: //#include <tchar.h>
10132: //#include <windows.h>
10133: //#include <iostream>
10134: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10135:
10136: LPFN_ISWOW64PROCESS fnIsWow64Process;
10137:
10138: BOOL IsWow64()
10139: {
10140: BOOL bIsWow64 = FALSE;
10141:
10142: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10143: // (HANDLE, PBOOL);
10144:
10145: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10146:
10147: HMODULE module = GetModuleHandle(_T("kernel32"));
10148: const char funcName[] = "IsWow64Process";
10149: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10150: GetProcAddress(module, funcName);
10151:
10152: if (NULL != fnIsWow64Process)
10153: {
10154: if (!fnIsWow64Process(GetCurrentProcess(),
10155: &bIsWow64))
10156: //throw std::exception("Unknown error");
10157: printf("Unknown error\n");
10158: }
10159: return bIsWow64 != FALSE;
10160: }
10161: #endif
1.177 brouard 10162:
1.191 brouard 10163: void syscompilerinfo(int logged)
1.167 brouard 10164: {
10165: /* #include "syscompilerinfo.h"*/
1.185 brouard 10166: /* command line Intel compiler 32bit windows, XP compatible:*/
10167: /* /GS /W3 /Gy
10168: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10169: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10170: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10171: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10172: */
10173: /* 64 bits */
1.185 brouard 10174: /*
10175: /GS /W3 /Gy
10176: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10177: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10178: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10179: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10180: /* Optimization are useless and O3 is slower than O2 */
10181: /*
10182: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10183: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10184: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10185: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10186: */
1.186 brouard 10187: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10188: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10189: /PDB:"visual studio
10190: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10191: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10192: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10193: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10194: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10195: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10196: uiAccess='false'"
10197: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10198: /NOLOGO /TLBID:1
10199: */
1.177 brouard 10200: #if defined __INTEL_COMPILER
1.178 brouard 10201: #if defined(__GNUC__)
10202: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10203: #endif
1.177 brouard 10204: #elif defined(__GNUC__)
1.179 brouard 10205: #ifndef __APPLE__
1.174 brouard 10206: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10207: #endif
1.177 brouard 10208: struct utsname sysInfo;
1.178 brouard 10209: int cross = CROSS;
10210: if (cross){
10211: printf("Cross-");
1.191 brouard 10212: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10213: }
1.174 brouard 10214: #endif
10215:
1.171 brouard 10216: #include <stdint.h>
1.178 brouard 10217:
1.191 brouard 10218: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10219: #if defined(__clang__)
1.191 brouard 10220: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10221: #endif
10222: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10223: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10224: #endif
10225: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10226: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10227: #endif
10228: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10229: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10230: #endif
10231: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10232: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10233: #endif
10234: #if defined(_MSC_VER)
1.191 brouard 10235: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10236: #endif
10237: #if defined(__PGI)
1.191 brouard 10238: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10239: #endif
10240: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10241: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10242: #endif
1.191 brouard 10243: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10244:
1.167 brouard 10245: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10246: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10247: // Windows (x64 and x86)
1.191 brouard 10248: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10249: #elif __unix__ // all unices, not all compilers
10250: // Unix
1.191 brouard 10251: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10252: #elif __linux__
10253: // linux
1.191 brouard 10254: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10255: #elif __APPLE__
1.174 brouard 10256: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10257: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10258: #endif
10259:
10260: /* __MINGW32__ */
10261: /* __CYGWIN__ */
10262: /* __MINGW64__ */
10263: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10264: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10265: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10266: /* _WIN64 // Defined for applications for Win64. */
10267: /* _M_X64 // Defined for compilations that target x64 processors. */
10268: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10269:
1.167 brouard 10270: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10271: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10272: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10273: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10274: #else
1.191 brouard 10275: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10276: #endif
10277:
1.169 brouard 10278: #if defined(__GNUC__)
10279: # if defined(__GNUC_PATCHLEVEL__)
10280: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10281: + __GNUC_MINOR__ * 100 \
10282: + __GNUC_PATCHLEVEL__)
10283: # else
10284: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10285: + __GNUC_MINOR__ * 100)
10286: # endif
1.174 brouard 10287: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10288: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10289:
10290: if (uname(&sysInfo) != -1) {
10291: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10292: 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 10293: }
10294: else
10295: perror("uname() error");
1.179 brouard 10296: //#ifndef __INTEL_COMPILER
10297: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10298: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10299: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10300: #endif
1.169 brouard 10301: #endif
1.172 brouard 10302:
1.286 brouard 10303: // void main ()
1.172 brouard 10304: // {
1.169 brouard 10305: #if defined(_MSC_VER)
1.174 brouard 10306: if (IsWow64()){
1.191 brouard 10307: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10308: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10309: }
10310: else{
1.191 brouard 10311: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10312: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10313: }
1.172 brouard 10314: // printf("\nPress Enter to continue...");
10315: // getchar();
10316: // }
10317:
1.169 brouard 10318: #endif
10319:
1.167 brouard 10320:
1.219 brouard 10321: }
1.136 brouard 10322:
1.219 brouard 10323: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 10324: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 brouard 10325: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10326: /* double ftolpl = 1.e-10; */
1.180 brouard 10327: double age, agebase, agelim;
1.203 brouard 10328: double tot;
1.180 brouard 10329:
1.202 brouard 10330: strcpy(filerespl,"PL_");
10331: strcat(filerespl,fileresu);
10332: if((ficrespl=fopen(filerespl,"w"))==NULL) {
10333: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10334: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10335: }
1.227 brouard 10336: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
10337: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10338: pstamp(ficrespl);
1.203 brouard 10339: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10340: fprintf(ficrespl,"#Age ");
10341: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10342: fprintf(ficrespl,"\n");
1.180 brouard 10343:
1.219 brouard 10344: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10345:
1.219 brouard 10346: agebase=ageminpar;
10347: agelim=agemaxpar;
1.180 brouard 10348:
1.227 brouard 10349: /* i1=pow(2,ncoveff); */
1.234 brouard 10350: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10351: if (cptcovn < 1){i1=1;}
1.180 brouard 10352:
1.238 brouard 10353: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10354: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10355: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10356: continue;
1.235 brouard 10357:
1.238 brouard 10358: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10359: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10360: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10361: /* k=k+1; */
10362: /* to clean */
10363: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10364: fprintf(ficrespl,"#******");
10365: printf("#******");
10366: fprintf(ficlog,"#******");
10367: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10368: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10369: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10370: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10371: }
10372: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10373: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10374: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10375: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10376: }
10377: fprintf(ficrespl,"******\n");
10378: printf("******\n");
10379: fprintf(ficlog,"******\n");
10380: if(invalidvarcomb[k]){
10381: printf("\nCombination (%d) ignored because no case \n",k);
10382: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10383: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10384: continue;
10385: }
1.219 brouard 10386:
1.238 brouard 10387: fprintf(ficrespl,"#Age ");
10388: for(j=1;j<=cptcoveff;j++) {
10389: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10390: }
10391: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10392: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10393:
1.238 brouard 10394: for (age=agebase; age<=agelim; age++){
10395: /* for (age=agebase; age<=agebase; age++){ */
10396: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10397: fprintf(ficrespl,"%.0f ",age );
10398: for(j=1;j<=cptcoveff;j++)
10399: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10400: tot=0.;
10401: for(i=1; i<=nlstate;i++){
10402: tot += prlim[i][i];
10403: fprintf(ficrespl," %.5f", prlim[i][i]);
10404: }
10405: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10406: } /* Age */
10407: /* was end of cptcod */
10408: } /* cptcov */
10409: } /* nres */
1.219 brouard 10410: return 0;
1.180 brouard 10411: }
10412:
1.218 brouard 10413: 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){
10414: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10415:
10416: /* Computes the back prevalence limit for any combination of covariate values
10417: * at any age between ageminpar and agemaxpar
10418: */
1.235 brouard 10419: int i, j, k, i1, nres=0 ;
1.217 brouard 10420: /* double ftolpl = 1.e-10; */
10421: double age, agebase, agelim;
10422: double tot;
1.218 brouard 10423: /* double ***mobaverage; */
10424: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10425:
10426: strcpy(fileresplb,"PLB_");
10427: strcat(fileresplb,fileresu);
10428: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
10429: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10430: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10431: }
10432: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10433: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10434: pstamp(ficresplb);
10435: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
10436: fprintf(ficresplb,"#Age ");
10437: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10438: fprintf(ficresplb,"\n");
10439:
1.218 brouard 10440:
10441: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10442:
10443: agebase=ageminpar;
10444: agelim=agemaxpar;
10445:
10446:
1.227 brouard 10447: i1=pow(2,cptcoveff);
1.218 brouard 10448: if (cptcovn < 1){i1=1;}
1.227 brouard 10449:
1.238 brouard 10450: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10451: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10452: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10453: continue;
10454: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10455: fprintf(ficresplb,"#******");
10456: printf("#******");
10457: fprintf(ficlog,"#******");
10458: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10459: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10460: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10461: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10462: }
10463: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10464: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10465: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10466: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10467: }
10468: fprintf(ficresplb,"******\n");
10469: printf("******\n");
10470: fprintf(ficlog,"******\n");
10471: if(invalidvarcomb[k]){
10472: printf("\nCombination (%d) ignored because no cases \n",k);
10473: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10474: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10475: continue;
10476: }
1.218 brouard 10477:
1.238 brouard 10478: fprintf(ficresplb,"#Age ");
10479: for(j=1;j<=cptcoveff;j++) {
10480: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10481: }
10482: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10483: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10484:
10485:
1.238 brouard 10486: for (age=agebase; age<=agelim; age++){
10487: /* for (age=agebase; age<=agebase; age++){ */
10488: if(mobilavproj > 0){
10489: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10490: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10491: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10492: }else if (mobilavproj == 0){
10493: 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);
10494: 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);
10495: exit(1);
10496: }else{
10497: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10498: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10499: /* printf("TOTOT\n"); */
10500: /* exit(1); */
1.238 brouard 10501: }
10502: fprintf(ficresplb,"%.0f ",age );
10503: for(j=1;j<=cptcoveff;j++)
10504: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10505: tot=0.;
10506: for(i=1; i<=nlstate;i++){
10507: tot += bprlim[i][i];
10508: fprintf(ficresplb," %.5f", bprlim[i][i]);
10509: }
10510: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10511: } /* Age */
10512: /* was end of cptcod */
1.255 brouard 10513: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10514: } /* end of any combination */
10515: } /* end of nres */
1.218 brouard 10516: /* hBijx(p, bage, fage); */
10517: /* fclose(ficrespijb); */
10518:
10519: return 0;
1.217 brouard 10520: }
1.218 brouard 10521:
1.180 brouard 10522: int hPijx(double *p, int bage, int fage){
10523: /*------------- h Pij x at various ages ------------*/
10524:
10525: int stepsize;
10526: int agelim;
10527: int hstepm;
10528: int nhstepm;
1.235 brouard 10529: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10530:
10531: double agedeb;
10532: double ***p3mat;
10533:
1.201 brouard 10534: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10535: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10536: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10537: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10538: }
10539: printf("Computing pij: result on file '%s' \n", filerespij);
10540: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10541:
10542: stepsize=(int) (stepm+YEARM-1)/YEARM;
10543: /*if (stepm<=24) stepsize=2;*/
10544:
10545: agelim=AGESUP;
10546: hstepm=stepsize*YEARM; /* Every year of age */
10547: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10548:
1.180 brouard 10549: /* hstepm=1; aff par mois*/
10550: pstamp(ficrespij);
10551: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10552: i1= pow(2,cptcoveff);
1.218 brouard 10553: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10554: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10555: /* k=k+1; */
1.235 brouard 10556: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10557: for(k=1; k<=i1;k++){
1.253 brouard 10558: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10559: continue;
1.183 brouard 10560: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10561: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10562: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10563: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10564: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10565: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10566: }
1.183 brouard 10567: fprintf(ficrespij,"******\n");
10568:
10569: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10570: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10571: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10572:
10573: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10574:
1.183 brouard 10575: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10576: oldm=oldms;savm=savms;
1.235 brouard 10577: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10578: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10579: for(i=1; i<=nlstate;i++)
10580: for(j=1; j<=nlstate+ndeath;j++)
10581: fprintf(ficrespij," %1d-%1d",i,j);
10582: fprintf(ficrespij,"\n");
10583: for (h=0; h<=nhstepm; h++){
10584: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10585: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10586: for(i=1; i<=nlstate;i++)
10587: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10588: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10589: fprintf(ficrespij,"\n");
10590: }
1.183 brouard 10591: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10592: fprintf(ficrespij,"\n");
10593: }
1.180 brouard 10594: /*}*/
10595: }
1.218 brouard 10596: return 0;
1.180 brouard 10597: }
1.218 brouard 10598:
10599: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10600: /*------------- h Bij x at various ages ------------*/
10601:
10602: int stepsize;
1.218 brouard 10603: /* int agelim; */
10604: int ageminl;
1.217 brouard 10605: int hstepm;
10606: int nhstepm;
1.238 brouard 10607: int h, i, i1, j, k, nres;
1.218 brouard 10608:
1.217 brouard 10609: double agedeb;
10610: double ***p3mat;
1.218 brouard 10611:
10612: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10613: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10614: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10615: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10616: }
10617: printf("Computing pij back: result on file '%s' \n", filerespijb);
10618: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10619:
10620: stepsize=(int) (stepm+YEARM-1)/YEARM;
10621: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10622:
1.218 brouard 10623: /* agelim=AGESUP; */
10624: ageminl=30;
10625: hstepm=stepsize*YEARM; /* Every year of age */
10626: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10627:
10628: /* hstepm=1; aff par mois*/
10629: pstamp(ficrespijb);
1.255 brouard 10630: 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 10631: i1= pow(2,cptcoveff);
1.218 brouard 10632: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10633: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10634: /* k=k+1; */
1.238 brouard 10635: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10636: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10637: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10638: continue;
10639: fprintf(ficrespijb,"\n#****** ");
10640: for(j=1;j<=cptcoveff;j++)
10641: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10642: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10643: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10644: }
10645: fprintf(ficrespijb,"******\n");
1.264 brouard 10646: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10647: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10648: continue;
10649: }
10650:
10651: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10652: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10653: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
10654: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10655: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
10656:
10657: /* nhstepm=nhstepm*YEARM; aff par mois*/
10658:
1.266 brouard 10659: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10660: /* and memory limitations if stepm is small */
10661:
1.238 brouard 10662: /* oldm=oldms;savm=savms; */
10663: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10664: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10665: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10666: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10667: for(i=1; i<=nlstate;i++)
10668: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10669: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10670: fprintf(ficrespijb,"\n");
1.238 brouard 10671: for (h=0; h<=nhstepm; h++){
10672: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10673: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10674: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10675: for(i=1; i<=nlstate;i++)
10676: for(j=1; j<=nlstate+ndeath;j++)
10677: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10678: fprintf(ficrespijb,"\n");
10679: }
10680: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10681: fprintf(ficrespijb,"\n");
10682: } /* end age deb */
10683: } /* end combination */
10684: } /* end nres */
1.218 brouard 10685: return 0;
10686: } /* hBijx */
1.217 brouard 10687:
1.180 brouard 10688:
1.136 brouard 10689: /***********************************************/
10690: /**************** Main Program *****************/
10691: /***********************************************/
10692:
10693: int main(int argc, char *argv[])
10694: {
10695: #ifdef GSL
10696: const gsl_multimin_fminimizer_type *T;
10697: size_t iteri = 0, it;
10698: int rval = GSL_CONTINUE;
10699: int status = GSL_SUCCESS;
10700: double ssval;
10701: #endif
10702: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 10703: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 10704: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10705: int jj, ll, li, lj, lk;
1.136 brouard 10706: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10707: int num_filled;
1.136 brouard 10708: int itimes;
10709: int NDIM=2;
10710: int vpopbased=0;
1.235 brouard 10711: int nres=0;
1.258 brouard 10712: int endishere=0;
1.277 brouard 10713: int noffset=0;
1.274 brouard 10714: int ncurrv=0; /* Temporary variable */
10715:
1.164 brouard 10716: char ca[32], cb[32];
1.136 brouard 10717: /* FILE *fichtm; *//* Html File */
10718: /* FILE *ficgp;*/ /*Gnuplot File */
10719: struct stat info;
1.191 brouard 10720: double agedeb=0.;
1.194 brouard 10721:
10722: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10723: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10724:
1.165 brouard 10725: double fret;
1.191 brouard 10726: double dum=0.; /* Dummy variable */
1.136 brouard 10727: double ***p3mat;
1.218 brouard 10728: /* double ***mobaverage; */
1.164 brouard 10729:
10730: char line[MAXLINE];
1.197 brouard 10731: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10732:
1.234 brouard 10733: char modeltemp[MAXLINE];
1.230 brouard 10734: char resultline[MAXLINE];
10735:
1.136 brouard 10736: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10737: char *tok, *val; /* pathtot */
1.136 brouard 10738: int firstobs=1, lastobs=10;
1.195 brouard 10739: int c, h , cpt, c2;
1.191 brouard 10740: int jl=0;
10741: int i1, j1, jk, stepsize=0;
1.194 brouard 10742: int count=0;
10743:
1.164 brouard 10744: int *tab;
1.136 brouard 10745: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 10746: int backcast=0;
1.136 brouard 10747: int mobilav=0,popforecast=0;
1.191 brouard 10748: int hstepm=0, nhstepm=0;
1.136 brouard 10749: int agemortsup;
10750: float sumlpop=0.;
10751: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10752: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10753:
1.191 brouard 10754: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10755: double ftolpl=FTOL;
10756: double **prlim;
1.217 brouard 10757: double **bprlim;
1.136 brouard 10758: double ***param; /* Matrix of parameters */
1.251 brouard 10759: double ***paramstart; /* Matrix of starting parameter values */
10760: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10761: double **matcov; /* Matrix of covariance */
1.203 brouard 10762: double **hess; /* Hessian matrix */
1.136 brouard 10763: double ***delti3; /* Scale */
10764: double *delti; /* Scale */
10765: double ***eij, ***vareij;
10766: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10767:
1.136 brouard 10768: double *epj, vepp;
1.164 brouard 10769:
1.273 brouard 10770: double dateprev1, dateprev2;
10771: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
10772: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
1.217 brouard 10773:
1.136 brouard 10774: double **ximort;
1.145 brouard 10775: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10776: int *dcwave;
10777:
1.164 brouard 10778: char z[1]="c";
1.136 brouard 10779:
10780: /*char *strt;*/
10781: char strtend[80];
1.126 brouard 10782:
1.164 brouard 10783:
1.126 brouard 10784: /* setlocale (LC_ALL, ""); */
10785: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10786: /* textdomain (PACKAGE); */
10787: /* setlocale (LC_CTYPE, ""); */
10788: /* setlocale (LC_MESSAGES, ""); */
10789:
10790: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10791: rstart_time = time(NULL);
10792: /* (void) gettimeofday(&start_time,&tzp);*/
10793: start_time = *localtime(&rstart_time);
1.126 brouard 10794: curr_time=start_time;
1.157 brouard 10795: /*tml = *localtime(&start_time.tm_sec);*/
10796: /* strcpy(strstart,asctime(&tml)); */
10797: strcpy(strstart,asctime(&start_time));
1.126 brouard 10798:
10799: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10800: /* tp.tm_sec = tp.tm_sec +86400; */
10801: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10802: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10803: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10804: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10805: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 10806: /* strt=asctime(&tmg); */
10807: /* printf("Time(after) =%s",strstart); */
10808: /* (void) time (&time_value);
10809: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
10810: * tm = *localtime(&time_value);
10811: * strstart=asctime(&tm);
10812: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
10813: */
10814:
10815: nberr=0; /* Number of errors and warnings */
10816: nbwarn=0;
1.184 brouard 10817: #ifdef WIN32
10818: _getcwd(pathcd, size);
10819: #else
1.126 brouard 10820: getcwd(pathcd, size);
1.184 brouard 10821: #endif
1.191 brouard 10822: syscompilerinfo(0);
1.196 brouard 10823: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 10824: if(argc <=1){
10825: printf("\nEnter the parameter file name: ");
1.205 brouard 10826: if(!fgets(pathr,FILENAMELENGTH,stdin)){
10827: printf("ERROR Empty parameter file name\n");
10828: goto end;
10829: }
1.126 brouard 10830: i=strlen(pathr);
10831: if(pathr[i-1]=='\n')
10832: pathr[i-1]='\0';
1.156 brouard 10833: i=strlen(pathr);
1.205 brouard 10834: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 10835: pathr[i-1]='\0';
1.205 brouard 10836: }
10837: i=strlen(pathr);
10838: if( i==0 ){
10839: printf("ERROR Empty parameter file name\n");
10840: goto end;
10841: }
10842: for (tok = pathr; tok != NULL; ){
1.126 brouard 10843: printf("Pathr |%s|\n",pathr);
10844: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
10845: printf("val= |%s| pathr=%s\n",val,pathr);
10846: strcpy (pathtot, val);
10847: if(pathr[0] == '\0') break; /* Dirty */
10848: }
10849: }
1.281 brouard 10850: else if (argc<=2){
10851: strcpy(pathtot,argv[1]);
10852: }
1.126 brouard 10853: else{
10854: strcpy(pathtot,argv[1]);
1.281 brouard 10855: strcpy(z,argv[2]);
10856: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 10857: }
10858: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
10859: /*cygwin_split_path(pathtot,path,optionfile);
10860: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
10861: /* cutv(path,optionfile,pathtot,'\\');*/
10862:
10863: /* Split argv[0], imach program to get pathimach */
10864: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
10865: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10866: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10867: /* strcpy(pathimach,argv[0]); */
10868: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
10869: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
10870: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 10871: #ifdef WIN32
10872: _chdir(path); /* Can be a relative path */
10873: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
10874: #else
1.126 brouard 10875: chdir(path); /* Can be a relative path */
1.184 brouard 10876: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
10877: #endif
10878: printf("Current directory %s!\n",pathcd);
1.126 brouard 10879: strcpy(command,"mkdir ");
10880: strcat(command,optionfilefiname);
10881: if((outcmd=system(command)) != 0){
1.169 brouard 10882: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 10883: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
10884: /* fclose(ficlog); */
10885: /* exit(1); */
10886: }
10887: /* if((imk=mkdir(optionfilefiname))<0){ */
10888: /* perror("mkdir"); */
10889: /* } */
10890:
10891: /*-------- arguments in the command line --------*/
10892:
1.186 brouard 10893: /* Main Log file */
1.126 brouard 10894: strcat(filelog, optionfilefiname);
10895: strcat(filelog,".log"); /* */
10896: if((ficlog=fopen(filelog,"w"))==NULL) {
10897: printf("Problem with logfile %s\n",filelog);
10898: goto end;
10899: }
10900: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 10901: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 10902: fprintf(ficlog,"\nEnter the parameter file name: \n");
10903: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
10904: path=%s \n\
10905: optionfile=%s\n\
10906: optionfilext=%s\n\
1.156 brouard 10907: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 10908:
1.197 brouard 10909: syscompilerinfo(1);
1.167 brouard 10910:
1.126 brouard 10911: printf("Local time (at start):%s",strstart);
10912: fprintf(ficlog,"Local time (at start): %s",strstart);
10913: fflush(ficlog);
10914: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 10915: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 10916:
10917: /* */
10918: strcpy(fileres,"r");
10919: strcat(fileres, optionfilefiname);
1.201 brouard 10920: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 10921: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 10922: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 10923:
1.186 brouard 10924: /* Main ---------arguments file --------*/
1.126 brouard 10925:
10926: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 10927: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
10928: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 10929: fflush(ficlog);
1.149 brouard 10930: /* goto end; */
10931: exit(70);
1.126 brouard 10932: }
10933:
10934: strcpy(filereso,"o");
1.201 brouard 10935: strcat(filereso,fileresu);
1.126 brouard 10936: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
10937: printf("Problem with Output resultfile: %s\n", filereso);
10938: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
10939: fflush(ficlog);
10940: goto end;
10941: }
1.278 brouard 10942: /*-------- Rewriting parameter file ----------*/
10943: strcpy(rfileres,"r"); /* "Rparameterfile */
10944: strcat(rfileres,optionfilefiname); /* Parameter file first name */
10945: strcat(rfileres,"."); /* */
10946: strcat(rfileres,optionfilext); /* Other files have txt extension */
10947: if((ficres =fopen(rfileres,"w"))==NULL) {
10948: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
10949: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
10950: fflush(ficlog);
10951: goto end;
10952: }
10953: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 10954:
1.278 brouard 10955:
1.126 brouard 10956: /* Reads comments: lines beginning with '#' */
10957: numlinepar=0;
1.277 brouard 10958: /* Is it a BOM UTF-8 Windows file? */
10959: /* First parameter line */
1.197 brouard 10960: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 10961: noffset=0;
10962: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
10963: {
10964: noffset=noffset+3;
10965: printf("# File is an UTF8 Bom.\n"); // 0xBF
10966: }
10967: else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
10968: {
10969: noffset=noffset+2;
10970: printf("# File is an UTF16BE BOM file\n");
10971: }
10972: else if( line[0] == 0 && line[1] == 0)
10973: {
10974: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
10975: noffset=noffset+4;
10976: printf("# File is an UTF16BE BOM file\n");
10977: }
10978: } else{
10979: ;/*printf(" Not a BOM file\n");*/
10980: }
10981:
1.197 brouard 10982: /* If line starts with a # it is a comment */
1.277 brouard 10983: if (line[noffset] == '#') {
1.197 brouard 10984: numlinepar++;
10985: fputs(line,stdout);
10986: fputs(line,ficparo);
1.278 brouard 10987: fputs(line,ficres);
1.197 brouard 10988: fputs(line,ficlog);
10989: continue;
10990: }else
10991: break;
10992: }
10993: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
10994: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
10995: if (num_filled != 5) {
10996: printf("Should be 5 parameters\n");
1.283 brouard 10997: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 10998: }
1.126 brouard 10999: numlinepar++;
1.197 brouard 11000: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 brouard 11001: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11002: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
11003: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 11004: }
11005: /* Second parameter line */
11006: while(fgets(line, MAXLINE, ficpar)) {
1.283 brouard 11007: /* while(fscanf(ficpar,"%[^\n]", line)) { */
11008: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 11009: if (line[0] == '#') {
11010: numlinepar++;
1.283 brouard 11011: printf("%s",line);
11012: fprintf(ficres,"%s",line);
11013: fprintf(ficparo,"%s",line);
11014: fprintf(ficlog,"%s",line);
1.197 brouard 11015: continue;
11016: }else
11017: break;
11018: }
1.223 brouard 11019: 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", \
11020: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
11021: if (num_filled != 11) {
11022: 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 11023: printf("but line=%s\n",line);
1.283 brouard 11024: 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");
11025: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11026: }
1.286 brouard 11027: if( lastpass > maxwav){
11028: printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11029: fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
11030: fflush(ficlog);
11031: goto end;
11032: }
11033: 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 11034: 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 11035: 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 11036: 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 11037: }
1.203 brouard 11038: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11039: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11040: /* Third parameter line */
11041: while(fgets(line, MAXLINE, ficpar)) {
11042: /* If line starts with a # it is a comment */
11043: if (line[0] == '#') {
11044: numlinepar++;
1.283 brouard 11045: printf("%s",line);
11046: fprintf(ficres,"%s",line);
11047: fprintf(ficparo,"%s",line);
11048: fprintf(ficlog,"%s",line);
1.197 brouard 11049: continue;
11050: }else
11051: break;
11052: }
1.201 brouard 11053: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11054: if (num_filled != 1){
11055: printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
11056: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
1.197 brouard 11057: model[0]='\0';
11058: goto end;
11059: }
11060: else{
11061: if (model[0]=='+'){
11062: for(i=1; i<=strlen(model);i++)
11063: modeltemp[i-1]=model[i];
1.201 brouard 11064: strcpy(model,modeltemp);
1.197 brouard 11065: }
11066: }
1.199 brouard 11067: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11068: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 brouard 11069: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
11070: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
11071: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11072: }
11073: /* 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); */
11074: /* numlinepar=numlinepar+3; /\* In general *\/ */
11075: /* 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 11076: /* 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); */
11077: /* 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 11078: fflush(ficlog);
1.190 brouard 11079: /* if(model[0]=='#'|| model[0]== '\0'){ */
11080: if(model[0]=='#'){
1.279 brouard 11081: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11082: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11083: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11084: if(mle != -1){
1.279 brouard 11085: 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 11086: exit(1);
11087: }
11088: }
1.126 brouard 11089: while((c=getc(ficpar))=='#' && c!= EOF){
11090: ungetc(c,ficpar);
11091: fgets(line, MAXLINE, ficpar);
11092: numlinepar++;
1.195 brouard 11093: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11094: z[0]=line[1];
11095: }
11096: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11097: fputs(line, stdout);
11098: //puts(line);
1.126 brouard 11099: fputs(line,ficparo);
11100: fputs(line,ficlog);
11101: }
11102: ungetc(c,ficpar);
11103:
11104:
1.145 brouard 11105: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.268 brouard 11106: if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
11107: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
11108: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11109: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11110: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11111: v1+v2*age+v2*v3 makes cptcovn = 3
11112: */
11113: if (strlen(model)>1)
1.187 brouard 11114: 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 11115: else
1.187 brouard 11116: ncovmodel=2; /* Constant and age */
1.133 brouard 11117: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11118: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11119: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11120: 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);
11121: 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);
11122: fflush(stdout);
11123: fclose (ficlog);
11124: goto end;
11125: }
1.126 brouard 11126: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11127: delti=delti3[1][1];
11128: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11129: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11130: /* We could also provide initial parameters values giving by simple logistic regression
11131: * only one way, that is without matrix product. We will have nlstate maximizations */
11132: /* for(i=1;i<nlstate;i++){ */
11133: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11134: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11135: /* } */
1.126 brouard 11136: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11137: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11138: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11139: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11140: fclose (ficparo);
11141: fclose (ficlog);
11142: goto end;
11143: exit(0);
1.220 brouard 11144: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11145: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11146: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11147: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11148: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11149: matcov=matrix(1,npar,1,npar);
1.203 brouard 11150: hess=matrix(1,npar,1,npar);
1.220 brouard 11151: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11152: /* Read guessed parameters */
1.126 brouard 11153: /* Reads comments: lines beginning with '#' */
11154: while((c=getc(ficpar))=='#' && c!= EOF){
11155: ungetc(c,ficpar);
11156: fgets(line, MAXLINE, ficpar);
11157: numlinepar++;
1.141 brouard 11158: fputs(line,stdout);
1.126 brouard 11159: fputs(line,ficparo);
11160: fputs(line,ficlog);
11161: }
11162: ungetc(c,ficpar);
11163:
11164: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11165: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11166: for(i=1; i <=nlstate; i++){
1.234 brouard 11167: j=0;
1.126 brouard 11168: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11169: if(jj==i) continue;
11170: j++;
11171: fscanf(ficpar,"%1d%1d",&i1,&j1);
11172: if ((i1 != i) || (j1 != jj)){
11173: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11174: It might be a problem of design; if ncovcol and the model are correct\n \
11175: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11176: exit(1);
11177: }
11178: fprintf(ficparo,"%1d%1d",i1,j1);
11179: if(mle==1)
11180: printf("%1d%1d",i,jj);
11181: fprintf(ficlog,"%1d%1d",i,jj);
11182: for(k=1; k<=ncovmodel;k++){
11183: fscanf(ficpar," %lf",¶m[i][j][k]);
11184: if(mle==1){
11185: printf(" %lf",param[i][j][k]);
11186: fprintf(ficlog," %lf",param[i][j][k]);
11187: }
11188: else
11189: fprintf(ficlog," %lf",param[i][j][k]);
11190: fprintf(ficparo," %lf",param[i][j][k]);
11191: }
11192: fscanf(ficpar,"\n");
11193: numlinepar++;
11194: if(mle==1)
11195: printf("\n");
11196: fprintf(ficlog,"\n");
11197: fprintf(ficparo,"\n");
1.126 brouard 11198: }
11199: }
11200: fflush(ficlog);
1.234 brouard 11201:
1.251 brouard 11202: /* Reads parameters values */
1.126 brouard 11203: p=param[1][1];
1.251 brouard 11204: pstart=paramstart[1][1];
1.126 brouard 11205:
11206: /* Reads comments: lines beginning with '#' */
11207: while((c=getc(ficpar))=='#' && c!= EOF){
11208: ungetc(c,ficpar);
11209: fgets(line, MAXLINE, ficpar);
11210: numlinepar++;
1.141 brouard 11211: fputs(line,stdout);
1.126 brouard 11212: fputs(line,ficparo);
11213: fputs(line,ficlog);
11214: }
11215: ungetc(c,ficpar);
11216:
11217: for(i=1; i <=nlstate; i++){
11218: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11219: fscanf(ficpar,"%1d%1d",&i1,&j1);
11220: if ( (i1-i) * (j1-j) != 0){
11221: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11222: exit(1);
11223: }
11224: printf("%1d%1d",i,j);
11225: fprintf(ficparo,"%1d%1d",i1,j1);
11226: fprintf(ficlog,"%1d%1d",i1,j1);
11227: for(k=1; k<=ncovmodel;k++){
11228: fscanf(ficpar,"%le",&delti3[i][j][k]);
11229: printf(" %le",delti3[i][j][k]);
11230: fprintf(ficparo," %le",delti3[i][j][k]);
11231: fprintf(ficlog," %le",delti3[i][j][k]);
11232: }
11233: fscanf(ficpar,"\n");
11234: numlinepar++;
11235: printf("\n");
11236: fprintf(ficparo,"\n");
11237: fprintf(ficlog,"\n");
1.126 brouard 11238: }
11239: }
11240: fflush(ficlog);
1.234 brouard 11241:
1.145 brouard 11242: /* Reads covariance matrix */
1.126 brouard 11243: delti=delti3[1][1];
1.220 brouard 11244:
11245:
1.126 brouard 11246: /* 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 11247:
1.126 brouard 11248: /* Reads comments: lines beginning with '#' */
11249: while((c=getc(ficpar))=='#' && c!= EOF){
11250: ungetc(c,ficpar);
11251: fgets(line, MAXLINE, ficpar);
11252: numlinepar++;
1.141 brouard 11253: fputs(line,stdout);
1.126 brouard 11254: fputs(line,ficparo);
11255: fputs(line,ficlog);
11256: }
11257: ungetc(c,ficpar);
1.220 brouard 11258:
1.126 brouard 11259: matcov=matrix(1,npar,1,npar);
1.203 brouard 11260: hess=matrix(1,npar,1,npar);
1.131 brouard 11261: for(i=1; i <=npar; i++)
11262: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11263:
1.194 brouard 11264: /* Scans npar lines */
1.126 brouard 11265: for(i=1; i <=npar; i++){
1.226 brouard 11266: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11267: if(count != 3){
1.226 brouard 11268: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11269: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11270: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11271: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11272: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11273: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11274: exit(1);
1.220 brouard 11275: }else{
1.226 brouard 11276: if(mle==1)
11277: printf("%1d%1d%d",i1,j1,jk);
11278: }
11279: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11280: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11281: for(j=1; j <=i; j++){
1.226 brouard 11282: fscanf(ficpar," %le",&matcov[i][j]);
11283: if(mle==1){
11284: printf(" %.5le",matcov[i][j]);
11285: }
11286: fprintf(ficlog," %.5le",matcov[i][j]);
11287: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11288: }
11289: fscanf(ficpar,"\n");
11290: numlinepar++;
11291: if(mle==1)
1.220 brouard 11292: printf("\n");
1.126 brouard 11293: fprintf(ficlog,"\n");
11294: fprintf(ficparo,"\n");
11295: }
1.194 brouard 11296: /* End of read covariance matrix npar lines */
1.126 brouard 11297: for(i=1; i <=npar; i++)
11298: for(j=i+1;j<=npar;j++)
1.226 brouard 11299: matcov[i][j]=matcov[j][i];
1.126 brouard 11300:
11301: if(mle==1)
11302: printf("\n");
11303: fprintf(ficlog,"\n");
11304:
11305: fflush(ficlog);
11306:
11307: } /* End of mle != -3 */
1.218 brouard 11308:
1.186 brouard 11309: /* Main data
11310: */
1.126 brouard 11311: n= lastobs;
11312: num=lvector(1,n);
11313: moisnais=vector(1,n);
11314: annais=vector(1,n);
11315: moisdc=vector(1,n);
11316: andc=vector(1,n);
1.220 brouard 11317: weight=vector(1,n);
1.126 brouard 11318: agedc=vector(1,n);
11319: cod=ivector(1,n);
1.220 brouard 11320: for(i=1;i<=n;i++){
1.234 brouard 11321: num[i]=0;
11322: moisnais[i]=0;
11323: annais[i]=0;
11324: moisdc[i]=0;
11325: andc[i]=0;
11326: agedc[i]=0;
11327: cod[i]=0;
11328: weight[i]=1.0; /* Equal weights, 1 by default */
11329: }
1.126 brouard 11330: mint=matrix(1,maxwav,1,n);
11331: anint=matrix(1,maxwav,1,n);
1.131 brouard 11332: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11333: tab=ivector(1,NCOVMAX);
1.144 brouard 11334: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11335: 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 11336:
1.136 brouard 11337: /* Reads data from file datafile */
11338: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11339: goto end;
11340:
11341: /* Calculation of the number of parameters from char model */
1.234 brouard 11342: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11343: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11344: k=3 V4 Tvar[k=3]= 4 (from V4)
11345: k=2 V1 Tvar[k=2]= 1 (from V1)
11346: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11347: */
11348:
11349: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11350: TvarsDind=ivector(1,NCOVMAX); /* */
11351: TvarsD=ivector(1,NCOVMAX); /* */
11352: TvarsQind=ivector(1,NCOVMAX); /* */
11353: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11354: TvarF=ivector(1,NCOVMAX); /* */
11355: TvarFind=ivector(1,NCOVMAX); /* */
11356: TvarV=ivector(1,NCOVMAX); /* */
11357: TvarVind=ivector(1,NCOVMAX); /* */
11358: TvarA=ivector(1,NCOVMAX); /* */
11359: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11360: TvarFD=ivector(1,NCOVMAX); /* */
11361: TvarFDind=ivector(1,NCOVMAX); /* */
11362: TvarFQ=ivector(1,NCOVMAX); /* */
11363: TvarFQind=ivector(1,NCOVMAX); /* */
11364: TvarVD=ivector(1,NCOVMAX); /* */
11365: TvarVDind=ivector(1,NCOVMAX); /* */
11366: TvarVQ=ivector(1,NCOVMAX); /* */
11367: TvarVQind=ivector(1,NCOVMAX); /* */
11368:
1.230 brouard 11369: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11370: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11371: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11372: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11373: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11374: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11375: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11376: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11377: */
11378: /* For model-covariate k tells which data-covariate to use but
11379: because this model-covariate is a construction we invent a new column
11380: ncovcol + k1
11381: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11382: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11383: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11384: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11385: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11386: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11387: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11388: */
1.145 brouard 11389: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11390: 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 11391: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11392: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11393: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11394: 4 covariates (3 plus signs)
11395: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11396: */
1.230 brouard 11397: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11398: * individual dummy, fixed or varying:
11399: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11400: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11401: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11402: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11403: * Tmodelind[1]@9={9,0,3,2,}*/
11404: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11405: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11406: * individual quantitative, fixed or varying:
11407: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11408: * 3, 1, 0, 0, 0, 0, 0, 0},
11409: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11410: /* Main decodemodel */
11411:
1.187 brouard 11412:
1.223 brouard 11413: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11414: goto end;
11415:
1.137 brouard 11416: if((double)(lastobs-imx)/(double)imx > 1.10){
11417: nbwarn++;
11418: 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);
11419: 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);
11420: }
1.136 brouard 11421: /* if(mle==1){*/
1.137 brouard 11422: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11423: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11424: }
11425:
11426: /*-calculation of age at interview from date of interview and age at death -*/
11427: agev=matrix(1,maxwav,1,imx);
11428:
11429: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11430: goto end;
11431:
1.126 brouard 11432:
1.136 brouard 11433: agegomp=(int)agemin;
11434: free_vector(moisnais,1,n);
11435: free_vector(annais,1,n);
1.126 brouard 11436: /* free_matrix(mint,1,maxwav,1,n);
11437: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11438: /* free_vector(moisdc,1,n); */
11439: /* free_vector(andc,1,n); */
1.145 brouard 11440: /* */
11441:
1.126 brouard 11442: wav=ivector(1,imx);
1.214 brouard 11443: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11444: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11445: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11446: 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.*/
11447: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11448: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11449:
11450: /* Concatenates waves */
1.214 brouard 11451: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11452: Death is a valid wave (if date is known).
11453: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11454: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11455: and mw[mi+1][i]. dh depends on stepm.
11456: */
11457:
1.126 brouard 11458: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11459: /* Concatenates waves */
1.145 brouard 11460:
1.215 brouard 11461: free_vector(moisdc,1,n);
11462: free_vector(andc,1,n);
11463:
1.126 brouard 11464: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11465: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11466: ncodemax[1]=1;
1.145 brouard 11467: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11468: cptcoveff=0;
1.220 brouard 11469: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11470: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11471: }
11472:
11473: ncovcombmax=pow(2,cptcoveff);
11474: invalidvarcomb=ivector(1, ncovcombmax);
11475: for(i=1;i<ncovcombmax;i++)
11476: invalidvarcomb[i]=0;
11477:
1.211 brouard 11478: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11479: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11480: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11481:
1.200 brouard 11482: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11483: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11484: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11485: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11486: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11487: * (currently 0 or 1) in the data.
11488: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11489: * corresponding modality (h,j).
11490: */
11491:
1.145 brouard 11492: h=0;
11493: /*if (cptcovn > 0) */
1.126 brouard 11494: m=pow(2,cptcoveff);
11495:
1.144 brouard 11496: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11497: * For k=4 covariates, h goes from 1 to m=2**k
11498: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11499: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11500: * h\k 1 2 3 4
1.143 brouard 11501: *______________________________
11502: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11503: * 2 2 1 1 1
11504: * 3 i=2 1 2 1 1
11505: * 4 2 2 1 1
11506: * 5 i=3 1 i=2 1 2 1
11507: * 6 2 1 2 1
11508: * 7 i=4 1 2 2 1
11509: * 8 2 2 2 1
1.197 brouard 11510: * 9 i=5 1 i=3 1 i=2 1 2
11511: * 10 2 1 1 2
11512: * 11 i=6 1 2 1 2
11513: * 12 2 2 1 2
11514: * 13 i=7 1 i=4 1 2 2
11515: * 14 2 1 2 2
11516: * 15 i=8 1 2 2 2
11517: * 16 2 2 2 2
1.143 brouard 11518: */
1.212 brouard 11519: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11520: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11521: * and the value of each covariate?
11522: * V1=1, V2=1, V3=2, V4=1 ?
11523: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11524: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11525: * In order to get the real value in the data, we use nbcode
11526: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11527: * We are keeping this crazy system in order to be able (in the future?)
11528: * to have more than 2 values (0 or 1) for a covariate.
11529: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11530: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11531: * bbbbbbbb
11532: * 76543210
11533: * h-1 00000101 (6-1=5)
1.219 brouard 11534: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11535: * &
11536: * 1 00000001 (1)
1.219 brouard 11537: * 00000000 = 1 & ((h-1) >> (k-1))
11538: * +1= 00000001 =1
1.211 brouard 11539: *
11540: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11541: * h' 1101 =2^3+2^2+0x2^1+2^0
11542: * >>k' 11
11543: * & 00000001
11544: * = 00000001
11545: * +1 = 00000010=2 = codtabm(14,3)
11546: * Reverse h=6 and m=16?
11547: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11548: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11549: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11550: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11551: * V3=decodtabm(14,3,2**4)=2
11552: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11553: *(h-1) >> (j-1) 0011 =13 >> 2
11554: * &1 000000001
11555: * = 000000001
11556: * +1= 000000010 =2
11557: * 2211
11558: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11559: * V3=2
1.220 brouard 11560: * codtabm and decodtabm are identical
1.211 brouard 11561: */
11562:
1.145 brouard 11563:
11564: free_ivector(Ndum,-1,NCOVMAX);
11565:
11566:
1.126 brouard 11567:
1.186 brouard 11568: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11569: strcpy(optionfilegnuplot,optionfilefiname);
11570: if(mle==-3)
1.201 brouard 11571: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11572: strcat(optionfilegnuplot,".gp");
11573:
11574: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11575: printf("Problem with file %s",optionfilegnuplot);
11576: }
11577: else{
1.204 brouard 11578: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11579: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11580: //fprintf(ficgp,"set missing 'NaNq'\n");
11581: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11582: }
11583: /* fclose(ficgp);*/
1.186 brouard 11584:
11585:
11586: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11587:
11588: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11589: if(mle==-3)
1.201 brouard 11590: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11591: strcat(optionfilehtm,".htm");
11592: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11593: printf("Problem with %s \n",optionfilehtm);
11594: exit(0);
1.126 brouard 11595: }
11596:
11597: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11598: strcat(optionfilehtmcov,"-cov.htm");
11599: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11600: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11601: }
11602: else{
11603: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11604: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11605: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11606: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11607: }
11608:
1.213 brouard 11609: 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 11610: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11611: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11612: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11613: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11614: \n\
11615: <hr size=\"2\" color=\"#EC5E5E\">\
11616: <ul><li><h4>Parameter files</h4>\n\
11617: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11618: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11619: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11620: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11621: - Date and time at start: %s</ul>\n",\
11622: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11623: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11624: fileres,fileres,\
11625: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11626: fflush(fichtm);
11627:
11628: strcpy(pathr,path);
11629: strcat(pathr,optionfilefiname);
1.184 brouard 11630: #ifdef WIN32
11631: _chdir(optionfilefiname); /* Move to directory named optionfile */
11632: #else
1.126 brouard 11633: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11634: #endif
11635:
1.126 brouard 11636:
1.220 brouard 11637: /* Calculates basic frequencies. Computes observed prevalence at single age
11638: and for any valid combination of covariates
1.126 brouard 11639: and prints on file fileres'p'. */
1.251 brouard 11640: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11641: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11642:
11643: fprintf(fichtm,"\n");
1.286 brouard 11644: 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 11645: ftol, stepm);
11646: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11647: ncurrv=1;
11648: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11649: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11650: ncurrv=i;
11651: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
11652: fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);
11653: ncurrv=i;
11654: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
11655: fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);
11656: ncurrv=i;
11657: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11658: 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", \
11659: nlstate, ndeath, maxwav, mle, weightopt);
11660:
11661: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11662: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11663:
11664:
11665: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11666: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11667: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11668: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11669: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11670: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11671: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11672: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11673: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11674:
1.126 brouard 11675: /* For Powell, parameters are in a vector p[] starting at p[1]
11676: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11677: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11678:
11679: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11680: /* For mortality only */
1.126 brouard 11681: if (mle==-3){
1.136 brouard 11682: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11683: for(i=1;i<=NDIM;i++)
11684: for(j=1;j<=NDIM;j++)
11685: ximort[i][j]=0.;
1.186 brouard 11686: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 11687: cens=ivector(1,n);
11688: ageexmed=vector(1,n);
11689: agecens=vector(1,n);
11690: dcwave=ivector(1,n);
1.223 brouard 11691:
1.126 brouard 11692: for (i=1; i<=imx; i++){
11693: dcwave[i]=-1;
11694: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11695: if (s[m][i]>nlstate) {
11696: dcwave[i]=m;
11697: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11698: break;
11699: }
1.126 brouard 11700: }
1.226 brouard 11701:
1.126 brouard 11702: for (i=1; i<=imx; i++) {
11703: if (wav[i]>0){
1.226 brouard 11704: ageexmed[i]=agev[mw[1][i]][i];
11705: j=wav[i];
11706: agecens[i]=1.;
11707:
11708: if (ageexmed[i]> 1 && wav[i] > 0){
11709: agecens[i]=agev[mw[j][i]][i];
11710: cens[i]= 1;
11711: }else if (ageexmed[i]< 1)
11712: cens[i]= -1;
11713: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11714: cens[i]=0 ;
1.126 brouard 11715: }
11716: else cens[i]=-1;
11717: }
11718:
11719: for (i=1;i<=NDIM;i++) {
11720: for (j=1;j<=NDIM;j++)
1.226 brouard 11721: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11722: }
11723:
1.145 brouard 11724: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 11725: /*printf("%lf %lf", p[1], p[2]);*/
11726:
11727:
1.136 brouard 11728: #ifdef GSL
11729: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11730: #else
1.126 brouard 11731: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11732: #endif
1.201 brouard 11733: strcpy(filerespow,"POW-MORT_");
11734: strcat(filerespow,fileresu);
1.126 brouard 11735: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11736: printf("Problem with resultfile: %s\n", filerespow);
11737: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11738: }
1.136 brouard 11739: #ifdef GSL
11740: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11741: #else
1.126 brouard 11742: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11743: #endif
1.126 brouard 11744: /* for (i=1;i<=nlstate;i++)
11745: for(j=1;j<=nlstate+ndeath;j++)
11746: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11747: */
11748: fprintf(ficrespow,"\n");
1.136 brouard 11749: #ifdef GSL
11750: /* gsl starts here */
11751: T = gsl_multimin_fminimizer_nmsimplex;
11752: gsl_multimin_fminimizer *sfm = NULL;
11753: gsl_vector *ss, *x;
11754: gsl_multimin_function minex_func;
11755:
11756: /* Initial vertex size vector */
11757: ss = gsl_vector_alloc (NDIM);
11758:
11759: if (ss == NULL){
11760: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11761: }
11762: /* Set all step sizes to 1 */
11763: gsl_vector_set_all (ss, 0.001);
11764:
11765: /* Starting point */
1.126 brouard 11766:
1.136 brouard 11767: x = gsl_vector_alloc (NDIM);
11768:
11769: if (x == NULL){
11770: gsl_vector_free(ss);
11771: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11772: }
11773:
11774: /* Initialize method and iterate */
11775: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11776: /* gsl_vector_set(x, 0, 0.0268); */
11777: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11778: gsl_vector_set(x, 0, p[1]);
11779: gsl_vector_set(x, 1, p[2]);
11780:
11781: minex_func.f = &gompertz_f;
11782: minex_func.n = NDIM;
11783: minex_func.params = (void *)&p; /* ??? */
11784:
11785: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11786: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
11787:
11788: printf("Iterations beginning .....\n\n");
11789: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
11790:
11791: iteri=0;
11792: while (rval == GSL_CONTINUE){
11793: iteri++;
11794: status = gsl_multimin_fminimizer_iterate(sfm);
11795:
11796: if (status) printf("error: %s\n", gsl_strerror (status));
11797: fflush(0);
11798:
11799: if (status)
11800: break;
11801:
11802: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
11803: ssval = gsl_multimin_fminimizer_size (sfm);
11804:
11805: if (rval == GSL_SUCCESS)
11806: printf ("converged to a local maximum at\n");
11807:
11808: printf("%5d ", iteri);
11809: for (it = 0; it < NDIM; it++){
11810: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
11811: }
11812: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
11813: }
11814:
11815: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
11816:
11817: gsl_vector_free(x); /* initial values */
11818: gsl_vector_free(ss); /* inital step size */
11819: for (it=0; it<NDIM; it++){
11820: p[it+1]=gsl_vector_get(sfm->x,it);
11821: fprintf(ficrespow," %.12lf", p[it]);
11822: }
11823: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
11824: #endif
11825: #ifdef POWELL
11826: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
11827: #endif
1.126 brouard 11828: fclose(ficrespow);
11829:
1.203 brouard 11830: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 11831:
11832: for(i=1; i <=NDIM; i++)
11833: for(j=i+1;j<=NDIM;j++)
1.220 brouard 11834: matcov[i][j]=matcov[j][i];
1.126 brouard 11835:
11836: printf("\nCovariance matrix\n ");
1.203 brouard 11837: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 11838: for(i=1; i <=NDIM; i++) {
11839: for(j=1;j<=NDIM;j++){
1.220 brouard 11840: printf("%f ",matcov[i][j]);
11841: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 11842: }
1.203 brouard 11843: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 11844: }
11845:
11846: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 11847: for (i=1;i<=NDIM;i++) {
1.126 brouard 11848: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 11849: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
11850: }
1.126 brouard 11851: lsurv=vector(1,AGESUP);
11852: lpop=vector(1,AGESUP);
11853: tpop=vector(1,AGESUP);
11854: lsurv[agegomp]=100000;
11855:
11856: for (k=agegomp;k<=AGESUP;k++) {
11857: agemortsup=k;
11858: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
11859: }
11860:
11861: for (k=agegomp;k<agemortsup;k++)
11862: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
11863:
11864: for (k=agegomp;k<agemortsup;k++){
11865: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
11866: sumlpop=sumlpop+lpop[k];
11867: }
11868:
11869: tpop[agegomp]=sumlpop;
11870: for (k=agegomp;k<(agemortsup-3);k++){
11871: /* tpop[k+1]=2;*/
11872: tpop[k+1]=tpop[k]-lpop[k];
11873: }
11874:
11875:
11876: printf("\nAge lx qx dx Lx Tx e(x)\n");
11877: for (k=agegomp;k<(agemortsup-2);k++)
11878: 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]);
11879:
11880:
11881: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 11882: ageminpar=50;
11883: agemaxpar=100;
1.194 brouard 11884: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
11885: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11886: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11887: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
11888: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11889: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11890: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 11891: }else{
11892: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
11893: 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 11894: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 11895: }
1.201 brouard 11896: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 11897: stepm, weightopt,\
11898: model,imx,p,matcov,agemortsup);
11899:
11900: free_vector(lsurv,1,AGESUP);
11901: free_vector(lpop,1,AGESUP);
11902: free_vector(tpop,1,AGESUP);
1.220 brouard 11903: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 11904: free_ivector(cens,1,n);
11905: free_vector(agecens,1,n);
11906: free_ivector(dcwave,1,n);
1.220 brouard 11907: #ifdef GSL
1.136 brouard 11908: #endif
1.186 brouard 11909: } /* Endof if mle==-3 mortality only */
1.205 brouard 11910: /* Standard */
11911: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
11912: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11913: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 11914: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 11915: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11916: for (k=1; k<=npar;k++)
11917: printf(" %d %8.5f",k,p[k]);
11918: printf("\n");
1.205 brouard 11919: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
11920: /* mlikeli uses func not funcone */
1.247 brouard 11921: /* for(i=1;i<nlstate;i++){ */
11922: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11923: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11924: /* } */
1.205 brouard 11925: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
11926: }
11927: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
11928: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11929: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
11930: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11931: }
11932: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 11933: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11934: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11935: for (k=1; k<=npar;k++)
11936: printf(" %d %8.5f",k,p[k]);
11937: printf("\n");
11938:
11939: /*--------- results files --------------*/
1.283 brouard 11940: /* 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 11941:
11942:
11943: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11944: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11945: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11946: for(i=1,jk=1; i <=nlstate; i++){
11947: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 11948: if (k != i) {
11949: printf("%d%d ",i,k);
11950: fprintf(ficlog,"%d%d ",i,k);
11951: fprintf(ficres,"%1d%1d ",i,k);
11952: for(j=1; j <=ncovmodel; j++){
11953: printf("%12.7f ",p[jk]);
11954: fprintf(ficlog,"%12.7f ",p[jk]);
11955: fprintf(ficres,"%12.7f ",p[jk]);
11956: jk++;
11957: }
11958: printf("\n");
11959: fprintf(ficlog,"\n");
11960: fprintf(ficres,"\n");
11961: }
1.126 brouard 11962: }
11963: }
1.203 brouard 11964: if(mle != 0){
11965: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 11966: ftolhess=ftol; /* Usually correct */
1.203 brouard 11967: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
11968: 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");
11969: 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");
11970: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 11971: for(k=1; k <=(nlstate+ndeath); k++){
11972: if (k != i) {
11973: printf("%d%d ",i,k);
11974: fprintf(ficlog,"%d%d ",i,k);
11975: for(j=1; j <=ncovmodel; j++){
11976: 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]));
11977: 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]));
11978: jk++;
11979: }
11980: printf("\n");
11981: fprintf(ficlog,"\n");
11982: }
11983: }
1.193 brouard 11984: }
1.203 brouard 11985: } /* end of hesscov and Wald tests */
1.225 brouard 11986:
1.203 brouard 11987: /* */
1.126 brouard 11988: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
11989: printf("# Scales (for hessian or gradient estimation)\n");
11990: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
11991: for(i=1,jk=1; i <=nlstate; i++){
11992: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 11993: if (j!=i) {
11994: fprintf(ficres,"%1d%1d",i,j);
11995: printf("%1d%1d",i,j);
11996: fprintf(ficlog,"%1d%1d",i,j);
11997: for(k=1; k<=ncovmodel;k++){
11998: printf(" %.5e",delti[jk]);
11999: fprintf(ficlog," %.5e",delti[jk]);
12000: fprintf(ficres," %.5e",delti[jk]);
12001: jk++;
12002: }
12003: printf("\n");
12004: fprintf(ficlog,"\n");
12005: fprintf(ficres,"\n");
12006: }
1.126 brouard 12007: }
12008: }
12009:
12010: 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 12011: if(mle >= 1) /* To big for the screen */
1.126 brouard 12012: 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");
12013: 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");
12014: /* # 121 Var(a12)\n\ */
12015: /* # 122 Cov(b12,a12) Var(b12)\n\ */
12016: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
12017: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
12018: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
12019: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
12020: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
12021: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
12022:
12023:
12024: /* Just to have a covariance matrix which will be more understandable
12025: even is we still don't want to manage dictionary of variables
12026: */
12027: for(itimes=1;itimes<=2;itimes++){
12028: jj=0;
12029: for(i=1; i <=nlstate; i++){
1.225 brouard 12030: for(j=1; j <=nlstate+ndeath; j++){
12031: if(j==i) continue;
12032: for(k=1; k<=ncovmodel;k++){
12033: jj++;
12034: ca[0]= k+'a'-1;ca[1]='\0';
12035: if(itimes==1){
12036: if(mle>=1)
12037: printf("#%1d%1d%d",i,j,k);
12038: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12039: fprintf(ficres,"#%1d%1d%d",i,j,k);
12040: }else{
12041: if(mle>=1)
12042: printf("%1d%1d%d",i,j,k);
12043: fprintf(ficlog,"%1d%1d%d",i,j,k);
12044: fprintf(ficres,"%1d%1d%d",i,j,k);
12045: }
12046: ll=0;
12047: for(li=1;li <=nlstate; li++){
12048: for(lj=1;lj <=nlstate+ndeath; lj++){
12049: if(lj==li) continue;
12050: for(lk=1;lk<=ncovmodel;lk++){
12051: ll++;
12052: if(ll<=jj){
12053: cb[0]= lk +'a'-1;cb[1]='\0';
12054: if(ll<jj){
12055: if(itimes==1){
12056: if(mle>=1)
12057: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12058: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12059: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12060: }else{
12061: if(mle>=1)
12062: printf(" %.5e",matcov[jj][ll]);
12063: fprintf(ficlog," %.5e",matcov[jj][ll]);
12064: fprintf(ficres," %.5e",matcov[jj][ll]);
12065: }
12066: }else{
12067: if(itimes==1){
12068: if(mle>=1)
12069: printf(" Var(%s%1d%1d)",ca,i,j);
12070: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12071: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12072: }else{
12073: if(mle>=1)
12074: printf(" %.7e",matcov[jj][ll]);
12075: fprintf(ficlog," %.7e",matcov[jj][ll]);
12076: fprintf(ficres," %.7e",matcov[jj][ll]);
12077: }
12078: }
12079: }
12080: } /* end lk */
12081: } /* end lj */
12082: } /* end li */
12083: if(mle>=1)
12084: printf("\n");
12085: fprintf(ficlog,"\n");
12086: fprintf(ficres,"\n");
12087: numlinepar++;
12088: } /* end k*/
12089: } /*end j */
1.126 brouard 12090: } /* end i */
12091: } /* end itimes */
12092:
12093: fflush(ficlog);
12094: fflush(ficres);
1.225 brouard 12095: while(fgets(line, MAXLINE, ficpar)) {
12096: /* If line starts with a # it is a comment */
12097: if (line[0] == '#') {
12098: numlinepar++;
12099: fputs(line,stdout);
12100: fputs(line,ficparo);
12101: fputs(line,ficlog);
12102: continue;
12103: }else
12104: break;
12105: }
12106:
1.209 brouard 12107: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12108: /* ungetc(c,ficpar); */
12109: /* fgets(line, MAXLINE, ficpar); */
12110: /* fputs(line,stdout); */
12111: /* fputs(line,ficparo); */
12112: /* } */
12113: /* ungetc(c,ficpar); */
1.126 brouard 12114:
12115: estepm=0;
1.209 brouard 12116: 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 12117:
12118: if (num_filled != 6) {
12119: 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);
12120: 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);
12121: goto end;
12122: }
12123: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12124: }
12125: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12126: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12127:
1.209 brouard 12128: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12129: if (estepm==0 || estepm < stepm) estepm=stepm;
12130: if (fage <= 2) {
12131: bage = ageminpar;
12132: fage = agemaxpar;
12133: }
12134:
12135: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12136: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12137: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12138:
1.186 brouard 12139: /* Other stuffs, more or less useful */
1.254 brouard 12140: while(fgets(line, MAXLINE, ficpar)) {
12141: /* If line starts with a # it is a comment */
12142: if (line[0] == '#') {
12143: numlinepar++;
12144: fputs(line,stdout);
12145: fputs(line,ficparo);
12146: fputs(line,ficlog);
12147: continue;
12148: }else
12149: break;
12150: }
12151:
12152: 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){
12153:
12154: if (num_filled != 7) {
12155: 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);
12156: 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);
12157: goto end;
12158: }
12159: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12160: 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);
12161: 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);
12162: 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 12163: }
1.254 brouard 12164:
12165: while(fgets(line, MAXLINE, ficpar)) {
12166: /* If line starts with a # it is a comment */
12167: if (line[0] == '#') {
12168: numlinepar++;
12169: fputs(line,stdout);
12170: fputs(line,ficparo);
12171: fputs(line,ficlog);
12172: continue;
12173: }else
12174: break;
1.126 brouard 12175: }
12176:
12177:
12178: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12179: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12180:
1.254 brouard 12181: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12182: if (num_filled != 1) {
12183: 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);
12184: 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);
12185: goto end;
12186: }
12187: printf("pop_based=%d\n",popbased);
12188: fprintf(ficlog,"pop_based=%d\n",popbased);
12189: fprintf(ficparo,"pop_based=%d\n",popbased);
12190: fprintf(ficres,"pop_based=%d\n",popbased);
12191: }
12192:
1.258 brouard 12193: /* Results */
12194: nresult=0;
12195: do{
12196: if(!fgets(line, MAXLINE, ficpar)){
12197: endishere=1;
12198: parameterline=14;
12199: }else if (line[0] == '#') {
12200: /* If line starts with a # it is a comment */
1.254 brouard 12201: numlinepar++;
12202: fputs(line,stdout);
12203: fputs(line,ficparo);
12204: fputs(line,ficlog);
12205: continue;
1.258 brouard 12206: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12207: parameterline=11;
12208: else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
12209: parameterline=12;
12210: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12211: parameterline=13;
12212: else{
12213: parameterline=14;
1.254 brouard 12214: }
1.258 brouard 12215: switch (parameterline){
12216: case 11:
12217: 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){
12218: if (num_filled != 8) {
12219: printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12220: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12221: goto end;
12222: }
12223: 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);
12224: 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);
12225: 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);
12226: 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);
12227: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12228: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12229: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
12230:
1.258 brouard 12231: }
1.254 brouard 12232: break;
1.258 brouard 12233: case 12:
12234: /*fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);*/
12235: if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
12236: if (num_filled != 8) {
1.262 brouard 12237: printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
12238: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
1.258 brouard 12239: goto end;
12240: }
12241: printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12242: fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12243: fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12244: fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
12245: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12246: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12247: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.258 brouard 12248: }
1.230 brouard 12249: break;
1.258 brouard 12250: case 13:
12251: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12252: if (num_filled == 0){
12253: resultline[0]='\0';
12254: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12255: 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);
12256: break;
12257: } else if (num_filled != 1){
12258: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12259: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12260: }
12261: nresult++; /* Sum of resultlines */
12262: printf("Result %d: result=%s\n",nresult, resultline);
12263: if(nresult > MAXRESULTLINES){
12264: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12265: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12266: goto end;
12267: }
12268: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12269: fprintf(ficparo,"result: %s\n",resultline);
12270: fprintf(ficres,"result: %s\n",resultline);
12271: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12272: break;
1.258 brouard 12273: case 14:
1.259 brouard 12274: if(ncovmodel >2 && nresult==0 ){
12275: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12276: goto end;
12277: }
1.259 brouard 12278: break;
1.258 brouard 12279: default:
12280: nresult=1;
12281: decoderesult(".",nresult ); /* No covariate */
12282: }
12283: } /* End switch parameterline */
12284: }while(endishere==0); /* End do */
1.126 brouard 12285:
1.230 brouard 12286: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12287: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12288:
12289: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12290: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12291: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12292: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12293: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12294: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12295: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12296: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12297: }else{
1.270 brouard 12298: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
12299: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
1.220 brouard 12300: }
12301: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.258 brouard 12302: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
1.273 brouard 12303: jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
1.220 brouard 12304:
1.225 brouard 12305: /*------------ free_vector -------------*/
12306: /* chdir(path); */
1.220 brouard 12307:
1.215 brouard 12308: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12309: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12310: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12311: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 12312: free_lvector(num,1,n);
12313: free_vector(agedc,1,n);
12314: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12315: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12316: fclose(ficparo);
12317: fclose(ficres);
1.220 brouard 12318:
12319:
1.186 brouard 12320: /* Other results (useful)*/
1.220 brouard 12321:
12322:
1.126 brouard 12323: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12324: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12325: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12326: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12327: fclose(ficrespl);
12328:
12329: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12330: /*#include "hpijx.h"*/
12331: hPijx(p, bage, fage);
1.145 brouard 12332: fclose(ficrespij);
1.227 brouard 12333:
1.220 brouard 12334: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12335: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12336: k=1;
1.126 brouard 12337: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12338:
1.269 brouard 12339: /* Prevalence for each covariate combination in probs[age][status][cov] */
12340: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12341: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12342: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12343: for(k=1;k<=ncovcombmax;k++)
12344: probs[i][j][k]=0.;
1.269 brouard 12345: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12346: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12347: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12348: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12349: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12350: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12351: for(k=1;k<=ncovcombmax;k++)
12352: mobaverages[i][j][k]=0.;
1.219 brouard 12353: mobaverage=mobaverages;
12354: if (mobilav!=0) {
1.235 brouard 12355: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12356: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12357: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12358: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12359: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12360: }
1.269 brouard 12361: } else if (mobilavproj !=0) {
1.235 brouard 12362: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12363: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12364: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12365: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12366: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12367: }
1.269 brouard 12368: }else{
12369: printf("Internal error moving average\n");
12370: fflush(stdout);
12371: exit(1);
1.219 brouard 12372: }
12373: }/* end if moving average */
1.227 brouard 12374:
1.126 brouard 12375: /*---------- Forecasting ------------------*/
12376: if(prevfcast==1){
12377: /* if(stepm ==1){*/
1.269 brouard 12378: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 12379: }
1.269 brouard 12380:
12381: /* Backcasting */
1.217 brouard 12382: if(backcast==1){
1.219 brouard 12383: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12384: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12385: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12386:
12387: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12388:
12389: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12390:
1.219 brouard 12391: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12392: fclose(ficresplb);
12393:
1.222 brouard 12394: hBijx(p, bage, fage, mobaverage);
12395: fclose(ficrespijb);
1.219 brouard 12396:
1.269 brouard 12397: prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
12398: mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
12399: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12400:
12401:
1.269 brouard 12402: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12403: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12404: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12405: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.269 brouard 12406: } /* end Backcasting */
1.268 brouard 12407:
1.186 brouard 12408:
12409: /* ------ Other prevalence ratios------------ */
1.126 brouard 12410:
1.215 brouard 12411: free_ivector(wav,1,imx);
12412: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12413: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12414: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12415:
12416:
1.127 brouard 12417: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12418:
1.201 brouard 12419: strcpy(filerese,"E_");
12420: strcat(filerese,fileresu);
1.126 brouard 12421: if((ficreseij=fopen(filerese,"w"))==NULL) {
12422: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12423: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12424: }
1.208 brouard 12425: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12426: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12427:
12428: pstamp(ficreseij);
1.219 brouard 12429:
1.235 brouard 12430: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12431: if (cptcovn < 1){i1=1;}
12432:
12433: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12434: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12435: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12436: continue;
1.219 brouard 12437: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12438: printf("\n#****** ");
1.225 brouard 12439: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12440: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12441: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12442: }
12443: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12444: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12445: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12446: }
12447: fprintf(ficreseij,"******\n");
1.235 brouard 12448: printf("******\n");
1.219 brouard 12449:
12450: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12451: oldm=oldms;savm=savms;
1.235 brouard 12452: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12453:
1.219 brouard 12454: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12455: }
12456: fclose(ficreseij);
1.208 brouard 12457: printf("done evsij\n");fflush(stdout);
12458: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12459:
1.218 brouard 12460:
1.227 brouard 12461: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12462:
1.201 brouard 12463: strcpy(filerest,"T_");
12464: strcat(filerest,fileresu);
1.127 brouard 12465: if((ficrest=fopen(filerest,"w"))==NULL) {
12466: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12467: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12468: }
1.208 brouard 12469: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12470: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12471: strcpy(fileresstde,"STDE_");
12472: strcat(fileresstde,fileresu);
1.126 brouard 12473: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12474: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12475: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12476: }
1.227 brouard 12477: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12478: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12479:
1.201 brouard 12480: strcpy(filerescve,"CVE_");
12481: strcat(filerescve,fileresu);
1.126 brouard 12482: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12483: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12484: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12485: }
1.227 brouard 12486: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12487: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12488:
1.201 brouard 12489: strcpy(fileresv,"V_");
12490: strcat(fileresv,fileresu);
1.126 brouard 12491: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12492: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12493: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12494: }
1.227 brouard 12495: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12496: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12497:
1.235 brouard 12498: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12499: if (cptcovn < 1){i1=1;}
12500:
12501: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12502: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12503: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12504: continue;
1.242 brouard 12505: printf("\n#****** Result for:");
12506: fprintf(ficrest,"\n#****** Result for:");
12507: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12508: for(j=1;j<=cptcoveff;j++){
12509: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12510: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12511: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12512: }
1.235 brouard 12513: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12514: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12515: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12516: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12517: }
1.208 brouard 12518: fprintf(ficrest,"******\n");
1.227 brouard 12519: fprintf(ficlog,"******\n");
12520: printf("******\n");
1.208 brouard 12521:
12522: fprintf(ficresstdeij,"\n#****** ");
12523: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12524: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12525: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12526: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12527: }
1.235 brouard 12528: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12529: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12530: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12531: }
1.208 brouard 12532: fprintf(ficresstdeij,"******\n");
12533: fprintf(ficrescveij,"******\n");
12534:
12535: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12536: /* pstamp(ficresvij); */
1.225 brouard 12537: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12538: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12539: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12540: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12541: }
1.208 brouard 12542: fprintf(ficresvij,"******\n");
12543:
12544: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12545: oldm=oldms;savm=savms;
1.235 brouard 12546: printf(" cvevsij ");
12547: fprintf(ficlog, " cvevsij ");
12548: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12549: printf(" end cvevsij \n ");
12550: fprintf(ficlog, " end cvevsij \n ");
12551:
12552: /*
12553: */
12554: /* goto endfree; */
12555:
12556: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12557: pstamp(ficrest);
12558:
1.269 brouard 12559: epj=vector(1,nlstate+1);
1.208 brouard 12560: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12561: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12562: cptcod= 0; /* To be deleted */
12563: printf("varevsij vpopbased=%d \n",vpopbased);
12564: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12565: 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 12566: 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 ");
12567: if(vpopbased==1)
12568: 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);
12569: else
12570: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
12571: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12572: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12573: fprintf(ficrest,"\n");
12574: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
12575: printf("Computing age specific period (stable) prevalences in each health state \n");
12576: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
12577: for(age=bage; age <=fage ;age++){
1.235 brouard 12578: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12579: if (vpopbased==1) {
12580: if(mobilav ==0){
12581: for(i=1; i<=nlstate;i++)
12582: prlim[i][i]=probs[(int)age][i][k];
12583: }else{ /* mobilav */
12584: for(i=1; i<=nlstate;i++)
12585: prlim[i][i]=mobaverage[(int)age][i][k];
12586: }
12587: }
1.219 brouard 12588:
1.227 brouard 12589: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12590: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12591: /* printf(" age %4.0f ",age); */
12592: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12593: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12594: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12595: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12596: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12597: }
12598: epj[nlstate+1] +=epj[j];
12599: }
12600: /* printf(" age %4.0f \n",age); */
1.219 brouard 12601:
1.227 brouard 12602: for(i=1, vepp=0.;i <=nlstate;i++)
12603: for(j=1;j <=nlstate;j++)
12604: vepp += vareij[i][j][(int)age];
12605: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12606: for(j=1;j <=nlstate;j++){
12607: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12608: }
12609: fprintf(ficrest,"\n");
12610: }
1.208 brouard 12611: } /* End vpopbased */
1.269 brouard 12612: free_vector(epj,1,nlstate+1);
1.208 brouard 12613: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12614: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12615: printf("done selection\n");fflush(stdout);
12616: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12617:
1.235 brouard 12618: } /* End k selection */
1.227 brouard 12619:
12620: printf("done State-specific expectancies\n");fflush(stdout);
12621: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12622:
1.269 brouard 12623: /* variance-covariance of period prevalence*/
12624: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12625:
1.227 brouard 12626:
12627: free_vector(weight,1,n);
12628: free_imatrix(Tvard,1,NCOVMAX,1,2);
12629: free_imatrix(s,1,maxwav+1,1,n);
12630: free_matrix(anint,1,maxwav,1,n);
12631: free_matrix(mint,1,maxwav,1,n);
12632: free_ivector(cod,1,n);
12633: free_ivector(tab,1,NCOVMAX);
12634: fclose(ficresstdeij);
12635: fclose(ficrescveij);
12636: fclose(ficresvij);
12637: fclose(ficrest);
12638: fclose(ficpar);
12639:
12640:
1.126 brouard 12641: /*---------- End : free ----------------*/
1.219 brouard 12642: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12643: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12644: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12645: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12646: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12647: } /* mle==-3 arrives here for freeing */
1.227 brouard 12648: /* endfree:*/
12649: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12650: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12651: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.268 brouard 12652: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
12653: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
12654: if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
1.227 brouard 12655: free_matrix(covar,0,NCOVMAX,1,n);
12656: free_matrix(matcov,1,npar,1,npar);
12657: free_matrix(hess,1,npar,1,npar);
12658: /*free_vector(delti,1,npar);*/
12659: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12660: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12661: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12662: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12663:
12664: free_ivector(ncodemax,1,NCOVMAX);
12665: free_ivector(ncodemaxwundef,1,NCOVMAX);
12666: free_ivector(Dummy,-1,NCOVMAX);
12667: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12668: free_ivector(DummyV,1,NCOVMAX);
12669: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12670: free_ivector(Typevar,-1,NCOVMAX);
12671: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12672: free_ivector(TvarsQ,1,NCOVMAX);
12673: free_ivector(TvarsQind,1,NCOVMAX);
12674: free_ivector(TvarsD,1,NCOVMAX);
12675: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12676: free_ivector(TvarFD,1,NCOVMAX);
12677: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12678: free_ivector(TvarF,1,NCOVMAX);
12679: free_ivector(TvarFind,1,NCOVMAX);
12680: free_ivector(TvarV,1,NCOVMAX);
12681: free_ivector(TvarVind,1,NCOVMAX);
12682: free_ivector(TvarA,1,NCOVMAX);
12683: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12684: free_ivector(TvarFQ,1,NCOVMAX);
12685: free_ivector(TvarFQind,1,NCOVMAX);
12686: free_ivector(TvarVD,1,NCOVMAX);
12687: free_ivector(TvarVDind,1,NCOVMAX);
12688: free_ivector(TvarVQ,1,NCOVMAX);
12689: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12690: free_ivector(Tvarsel,1,NCOVMAX);
12691: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12692: free_ivector(Tposprod,1,NCOVMAX);
12693: free_ivector(Tprod,1,NCOVMAX);
12694: free_ivector(Tvaraff,1,NCOVMAX);
12695: free_ivector(invalidvarcomb,1,ncovcombmax);
12696: free_ivector(Tage,1,NCOVMAX);
12697: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12698: free_ivector(TmodelInvind,1,NCOVMAX);
12699: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12700:
12701: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12702: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12703: fflush(fichtm);
12704: fflush(ficgp);
12705:
1.227 brouard 12706:
1.126 brouard 12707: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12708: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12709: 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 12710: }else{
12711: printf("End of Imach\n");
12712: fprintf(ficlog,"End of Imach\n");
12713: }
12714: printf("See log file on %s\n",filelog);
12715: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12716: /*(void) gettimeofday(&end_time,&tzp);*/
12717: rend_time = time(NULL);
12718: end_time = *localtime(&rend_time);
12719: /* tml = *localtime(&end_time.tm_sec); */
12720: strcpy(strtend,asctime(&end_time));
1.126 brouard 12721: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
12722: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 12723: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 12724:
1.157 brouard 12725: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
12726: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
12727: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 12728: /* printf("Total time was %d uSec.\n", total_usecs);*/
12729: /* if(fileappend(fichtm,optionfilehtm)){ */
12730: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12731: fclose(fichtm);
12732: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12733: fclose(fichtmcov);
12734: fclose(ficgp);
12735: fclose(ficlog);
12736: /*------ End -----------*/
1.227 brouard 12737:
1.281 brouard 12738:
12739: /* Executes gnuplot */
1.227 brouard 12740:
12741: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 12742: #ifdef WIN32
1.227 brouard 12743: if (_chdir(pathcd) != 0)
12744: printf("Can't move to directory %s!\n",path);
12745: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 12746: #else
1.227 brouard 12747: if(chdir(pathcd) != 0)
12748: printf("Can't move to directory %s!\n", path);
12749: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 12750: #endif
1.126 brouard 12751: printf("Current directory %s!\n",pathcd);
12752: /*strcat(plotcmd,CHARSEPARATOR);*/
12753: sprintf(plotcmd,"gnuplot");
1.157 brouard 12754: #ifdef _WIN32
1.126 brouard 12755: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
12756: #endif
12757: if(!stat(plotcmd,&info)){
1.158 brouard 12758: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12759: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 12760: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 12761: }else
12762: strcpy(pplotcmd,plotcmd);
1.157 brouard 12763: #ifdef __unix
1.126 brouard 12764: strcpy(plotcmd,GNUPLOTPROGRAM);
12765: if(!stat(plotcmd,&info)){
1.158 brouard 12766: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12767: }else
12768: strcpy(pplotcmd,plotcmd);
12769: #endif
12770: }else
12771: strcpy(pplotcmd,plotcmd);
12772:
12773: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 12774: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 12775:
1.126 brouard 12776: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 12777: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 12778: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 12779: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 12780: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 12781: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 12782: }
1.158 brouard 12783: printf(" Successful, please wait...");
1.126 brouard 12784: while (z[0] != 'q') {
12785: /* chdir(path); */
1.154 brouard 12786: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 12787: scanf("%s",z);
12788: /* if (z[0] == 'c') system("./imach"); */
12789: if (z[0] == 'e') {
1.158 brouard 12790: #ifdef __APPLE__
1.152 brouard 12791: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 12792: #elif __linux
12793: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 12794: #else
1.152 brouard 12795: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 12796: #endif
12797: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
12798: system(pplotcmd);
1.126 brouard 12799: }
12800: else if (z[0] == 'g') system(plotcmd);
12801: else if (z[0] == 'q') exit(0);
12802: }
1.227 brouard 12803: end:
1.126 brouard 12804: while (z[0] != 'q') {
1.195 brouard 12805: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 12806: scanf("%s",z);
12807: }
1.283 brouard 12808: printf("End\n");
1.282 brouard 12809: exit(0);
1.126 brouard 12810: }
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