Annotation of imach/src/imach.c, revision 1.283
1.283 ! brouard 1: /* $Id: imach.c,v 1.282 2018/02/27 22:50:02 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.283 ! brouard 4: Revision 1.282 2018/02/27 22:50:02 brouard
! 5: *** empty log message ***
! 6:
1.282 brouard 7: Revision 1.281 2018/02/27 19:25:23 brouard
8: Summary: Adding second argument for quitting
9:
1.281 brouard 10: Revision 1.280 2018/02/21 07:58:13 brouard
11: Summary: 0.99r15
12:
13: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
14:
1.280 brouard 15: Revision 1.279 2017/07/20 13:35:01 brouard
16: Summary: temporary working
17:
1.279 brouard 18: Revision 1.278 2017/07/19 14:09:02 brouard
19: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
20:
1.278 brouard 21: Revision 1.277 2017/07/17 08:53:49 brouard
22: Summary: BOM files can be read now
23:
1.277 brouard 24: Revision 1.276 2017/06/30 15:48:31 brouard
25: Summary: Graphs improvements
26:
1.276 brouard 27: Revision 1.275 2017/06/30 13:39:33 brouard
28: Summary: Saito's color
29:
1.275 brouard 30: Revision 1.274 2017/06/29 09:47:08 brouard
31: Summary: Version 0.99r14
32:
1.274 brouard 33: Revision 1.273 2017/06/27 11:06:02 brouard
34: Summary: More documentation on projections
35:
1.273 brouard 36: Revision 1.272 2017/06/27 10:22:40 brouard
37: Summary: Color of backprojection changed from 6 to 5(yellow)
38:
1.272 brouard 39: Revision 1.271 2017/06/27 10:17:50 brouard
40: Summary: Some bug with rint
41:
1.271 brouard 42: Revision 1.270 2017/05/24 05:45:29 brouard
43: *** empty log message ***
44:
1.270 brouard 45: Revision 1.269 2017/05/23 08:39:25 brouard
46: Summary: Code into subroutine, cleanings
47:
1.269 brouard 48: Revision 1.268 2017/05/18 20:09:32 brouard
49: Summary: backprojection and confidence intervals of backprevalence
50:
1.268 brouard 51: Revision 1.267 2017/05/13 10:25:05 brouard
52: Summary: temporary save for backprojection
53:
1.267 brouard 54: Revision 1.266 2017/05/13 07:26:12 brouard
55: Summary: Version 0.99r13 (improvements and bugs fixed)
56:
1.266 brouard 57: Revision 1.265 2017/04/26 16:22:11 brouard
58: Summary: imach 0.99r13 Some bugs fixed
59:
1.265 brouard 60: Revision 1.264 2017/04/26 06:01:29 brouard
61: Summary: Labels in graphs
62:
1.264 brouard 63: Revision 1.263 2017/04/24 15:23:15 brouard
64: Summary: to save
65:
1.263 brouard 66: Revision 1.262 2017/04/18 16:48:12 brouard
67: *** empty log message ***
68:
1.262 brouard 69: Revision 1.261 2017/04/05 10:14:09 brouard
70: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
71:
1.261 brouard 72: Revision 1.260 2017/04/04 17:46:59 brouard
73: Summary: Gnuplot indexations fixed (humm)
74:
1.260 brouard 75: Revision 1.259 2017/04/04 13:01:16 brouard
76: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
77:
1.259 brouard 78: Revision 1.258 2017/04/03 10:17:47 brouard
79: Summary: Version 0.99r12
80:
81: Some cleanings, conformed with updated documentation.
82:
1.258 brouard 83: Revision 1.257 2017/03/29 16:53:30 brouard
84: Summary: Temp
85:
1.257 brouard 86: Revision 1.256 2017/03/27 05:50:23 brouard
87: Summary: Temporary
88:
1.256 brouard 89: Revision 1.255 2017/03/08 16:02:28 brouard
90: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
91:
1.255 brouard 92: Revision 1.254 2017/03/08 07:13:00 brouard
93: Summary: Fixing data parameter line
94:
1.254 brouard 95: Revision 1.253 2016/12/15 11:59:41 brouard
96: Summary: 0.99 in progress
97:
1.253 brouard 98: Revision 1.252 2016/09/15 21:15:37 brouard
99: *** empty log message ***
100:
1.252 brouard 101: Revision 1.251 2016/09/15 15:01:13 brouard
102: Summary: not working
103:
1.251 brouard 104: Revision 1.250 2016/09/08 16:07:27 brouard
105: Summary: continue
106:
1.250 brouard 107: Revision 1.249 2016/09/07 17:14:18 brouard
108: Summary: Starting values from frequencies
109:
1.249 brouard 110: Revision 1.248 2016/09/07 14:10:18 brouard
111: *** empty log message ***
112:
1.248 brouard 113: Revision 1.247 2016/09/02 11:11:21 brouard
114: *** empty log message ***
115:
1.247 brouard 116: Revision 1.246 2016/09/02 08:49:22 brouard
117: *** empty log message ***
118:
1.246 brouard 119: Revision 1.245 2016/09/02 07:25:01 brouard
120: *** empty log message ***
121:
1.245 brouard 122: Revision 1.244 2016/09/02 07:17:34 brouard
123: *** empty log message ***
124:
1.244 brouard 125: Revision 1.243 2016/09/02 06:45:35 brouard
126: *** empty log message ***
127:
1.243 brouard 128: Revision 1.242 2016/08/30 15:01:20 brouard
129: Summary: Fixing a lots
130:
1.242 brouard 131: Revision 1.241 2016/08/29 17:17:25 brouard
132: Summary: gnuplot problem in Back projection to fix
133:
1.241 brouard 134: Revision 1.240 2016/08/29 07:53:18 brouard
135: Summary: Better
136:
1.240 brouard 137: Revision 1.239 2016/08/26 15:51:03 brouard
138: Summary: Improvement in Powell output in order to copy and paste
139:
140: Author:
141:
1.239 brouard 142: Revision 1.238 2016/08/26 14:23:35 brouard
143: Summary: Starting tests of 0.99
144:
1.238 brouard 145: Revision 1.237 2016/08/26 09:20:19 brouard
146: Summary: to valgrind
147:
1.237 brouard 148: Revision 1.236 2016/08/25 10:50:18 brouard
149: *** empty log message ***
150:
1.236 brouard 151: Revision 1.235 2016/08/25 06:59:23 brouard
152: *** empty log message ***
153:
1.235 brouard 154: Revision 1.234 2016/08/23 16:51:20 brouard
155: *** empty log message ***
156:
1.234 brouard 157: Revision 1.233 2016/08/23 07:40:50 brouard
158: Summary: not working
159:
1.233 brouard 160: Revision 1.232 2016/08/22 14:20:21 brouard
161: Summary: not working
162:
1.232 brouard 163: Revision 1.231 2016/08/22 07:17:15 brouard
164: Summary: not working
165:
1.231 brouard 166: Revision 1.230 2016/08/22 06:55:53 brouard
167: Summary: Not working
168:
1.230 brouard 169: Revision 1.229 2016/07/23 09:45:53 brouard
170: Summary: Completing for func too
171:
1.229 brouard 172: Revision 1.228 2016/07/22 17:45:30 brouard
173: Summary: Fixing some arrays, still debugging
174:
1.227 brouard 175: Revision 1.226 2016/07/12 18:42:34 brouard
176: Summary: temp
177:
1.226 brouard 178: Revision 1.225 2016/07/12 08:40:03 brouard
179: Summary: saving but not running
180:
1.225 brouard 181: Revision 1.224 2016/07/01 13:16:01 brouard
182: Summary: Fixes
183:
1.224 brouard 184: Revision 1.223 2016/02/19 09:23:35 brouard
185: Summary: temporary
186:
1.223 brouard 187: Revision 1.222 2016/02/17 08:14:50 brouard
188: Summary: Probably last 0.98 stable version 0.98r6
189:
1.222 brouard 190: Revision 1.221 2016/02/15 23:35:36 brouard
191: Summary: minor bug
192:
1.220 brouard 193: Revision 1.219 2016/02/15 00:48:12 brouard
194: *** empty log message ***
195:
1.219 brouard 196: Revision 1.218 2016/02/12 11:29:23 brouard
197: Summary: 0.99 Back projections
198:
1.218 brouard 199: Revision 1.217 2015/12/23 17:18:31 brouard
200: Summary: Experimental backcast
201:
1.217 brouard 202: Revision 1.216 2015/12/18 17:32:11 brouard
203: Summary: 0.98r4 Warning and status=-2
204:
205: Version 0.98r4 is now:
206: - displaying an error when status is -1, date of interview unknown and date of death known;
207: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
208: Older changes concerning s=-2, dating from 2005 have been supersed.
209:
1.216 brouard 210: Revision 1.215 2015/12/16 08:52:24 brouard
211: Summary: 0.98r4 working
212:
1.215 brouard 213: Revision 1.214 2015/12/16 06:57:54 brouard
214: Summary: temporary not working
215:
1.214 brouard 216: Revision 1.213 2015/12/11 18:22:17 brouard
217: Summary: 0.98r4
218:
1.213 brouard 219: Revision 1.212 2015/11/21 12:47:24 brouard
220: Summary: minor typo
221:
1.212 brouard 222: Revision 1.211 2015/11/21 12:41:11 brouard
223: Summary: 0.98r3 with some graph of projected cross-sectional
224:
225: Author: Nicolas Brouard
226:
1.211 brouard 227: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 228: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 229: Summary: Adding ftolpl parameter
230: Author: N Brouard
231:
232: We had difficulties to get smoothed confidence intervals. It was due
233: to the period prevalence which wasn't computed accurately. The inner
234: parameter ftolpl is now an outer parameter of the .imach parameter
235: file after estepm. If ftolpl is small 1.e-4 and estepm too,
236: computation are long.
237:
1.209 brouard 238: Revision 1.208 2015/11/17 14:31:57 brouard
239: Summary: temporary
240:
1.208 brouard 241: Revision 1.207 2015/10/27 17:36:57 brouard
242: *** empty log message ***
243:
1.207 brouard 244: Revision 1.206 2015/10/24 07:14:11 brouard
245: *** empty log message ***
246:
1.206 brouard 247: Revision 1.205 2015/10/23 15:50:53 brouard
248: Summary: 0.98r3 some clarification for graphs on likelihood contributions
249:
1.205 brouard 250: Revision 1.204 2015/10/01 16:20:26 brouard
251: Summary: Some new graphs of contribution to likelihood
252:
1.204 brouard 253: Revision 1.203 2015/09/30 17:45:14 brouard
254: Summary: looking at better estimation of the hessian
255:
256: Also a better criteria for convergence to the period prevalence And
257: therefore adding the number of years needed to converge. (The
258: prevalence in any alive state shold sum to one
259:
1.203 brouard 260: Revision 1.202 2015/09/22 19:45:16 brouard
261: Summary: Adding some overall graph on contribution to likelihood. Might change
262:
1.202 brouard 263: Revision 1.201 2015/09/15 17:34:58 brouard
264: Summary: 0.98r0
265:
266: - Some new graphs like suvival functions
267: - Some bugs fixed like model=1+age+V2.
268:
1.201 brouard 269: Revision 1.200 2015/09/09 16:53:55 brouard
270: Summary: Big bug thanks to Flavia
271:
272: Even model=1+age+V2. did not work anymore
273:
1.200 brouard 274: Revision 1.199 2015/09/07 14:09:23 brouard
275: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
276:
1.199 brouard 277: Revision 1.198 2015/09/03 07:14:39 brouard
278: Summary: 0.98q5 Flavia
279:
1.198 brouard 280: Revision 1.197 2015/09/01 18:24:39 brouard
281: *** empty log message ***
282:
1.197 brouard 283: Revision 1.196 2015/08/18 23:17:52 brouard
284: Summary: 0.98q5
285:
1.196 brouard 286: Revision 1.195 2015/08/18 16:28:39 brouard
287: Summary: Adding a hack for testing purpose
288:
289: After reading the title, ftol and model lines, if the comment line has
290: a q, starting with #q, the answer at the end of the run is quit. It
291: permits to run test files in batch with ctest. The former workaround was
292: $ echo q | imach foo.imach
293:
1.195 brouard 294: Revision 1.194 2015/08/18 13:32:00 brouard
295: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
296:
1.194 brouard 297: Revision 1.193 2015/08/04 07:17:42 brouard
298: Summary: 0.98q4
299:
1.193 brouard 300: Revision 1.192 2015/07/16 16:49:02 brouard
301: Summary: Fixing some outputs
302:
1.192 brouard 303: Revision 1.191 2015/07/14 10:00:33 brouard
304: Summary: Some fixes
305:
1.191 brouard 306: Revision 1.190 2015/05/05 08:51:13 brouard
307: Summary: Adding digits in output parameters (7 digits instead of 6)
308:
309: Fix 1+age+.
310:
1.190 brouard 311: Revision 1.189 2015/04/30 14:45:16 brouard
312: Summary: 0.98q2
313:
1.189 brouard 314: Revision 1.188 2015/04/30 08:27:53 brouard
315: *** empty log message ***
316:
1.188 brouard 317: Revision 1.187 2015/04/29 09:11:15 brouard
318: *** empty log message ***
319:
1.187 brouard 320: Revision 1.186 2015/04/23 12:01:52 brouard
321: Summary: V1*age is working now, version 0.98q1
322:
323: Some codes had been disabled in order to simplify and Vn*age was
324: working in the optimization phase, ie, giving correct MLE parameters,
325: but, as usual, outputs were not correct and program core dumped.
326:
1.186 brouard 327: Revision 1.185 2015/03/11 13:26:42 brouard
328: Summary: Inclusion of compile and links command line for Intel Compiler
329:
1.185 brouard 330: Revision 1.184 2015/03/11 11:52:39 brouard
331: Summary: Back from Windows 8. Intel Compiler
332:
1.184 brouard 333: Revision 1.183 2015/03/10 20:34:32 brouard
334: Summary: 0.98q0, trying with directest, mnbrak fixed
335:
336: We use directest instead of original Powell test; probably no
337: incidence on the results, but better justifications;
338: We fixed Numerical Recipes mnbrak routine which was wrong and gave
339: wrong results.
340:
1.183 brouard 341: Revision 1.182 2015/02/12 08:19:57 brouard
342: Summary: Trying to keep directest which seems simpler and more general
343: Author: Nicolas Brouard
344:
1.182 brouard 345: Revision 1.181 2015/02/11 23:22:24 brouard
346: Summary: Comments on Powell added
347:
348: Author:
349:
1.181 brouard 350: Revision 1.180 2015/02/11 17:33:45 brouard
351: Summary: Finishing move from main to function (hpijx and prevalence_limit)
352:
1.180 brouard 353: Revision 1.179 2015/01/04 09:57:06 brouard
354: Summary: back to OS/X
355:
1.179 brouard 356: Revision 1.178 2015/01/04 09:35:48 brouard
357: *** empty log message ***
358:
1.178 brouard 359: Revision 1.177 2015/01/03 18:40:56 brouard
360: Summary: Still testing ilc32 on OSX
361:
1.177 brouard 362: Revision 1.176 2015/01/03 16:45:04 brouard
363: *** empty log message ***
364:
1.176 brouard 365: Revision 1.175 2015/01/03 16:33:42 brouard
366: *** empty log message ***
367:
1.175 brouard 368: Revision 1.174 2015/01/03 16:15:49 brouard
369: Summary: Still in cross-compilation
370:
1.174 brouard 371: Revision 1.173 2015/01/03 12:06:26 brouard
372: Summary: trying to detect cross-compilation
373:
1.173 brouard 374: Revision 1.172 2014/12/27 12:07:47 brouard
375: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
376:
1.172 brouard 377: Revision 1.171 2014/12/23 13:26:59 brouard
378: Summary: Back from Visual C
379:
380: Still problem with utsname.h on Windows
381:
1.171 brouard 382: Revision 1.170 2014/12/23 11:17:12 brouard
383: Summary: Cleaning some \%% back to %%
384:
385: The escape was mandatory for a specific compiler (which one?), but too many warnings.
386:
1.170 brouard 387: Revision 1.169 2014/12/22 23:08:31 brouard
388: Summary: 0.98p
389:
390: Outputs some informations on compiler used, OS etc. Testing on different platforms.
391:
1.169 brouard 392: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 393: Summary: update
1.169 brouard 394:
1.168 brouard 395: Revision 1.167 2014/12/22 13:50:56 brouard
396: Summary: Testing uname and compiler version and if compiled 32 or 64
397:
398: Testing on Linux 64
399:
1.167 brouard 400: Revision 1.166 2014/12/22 11:40:47 brouard
401: *** empty log message ***
402:
1.166 brouard 403: Revision 1.165 2014/12/16 11:20:36 brouard
404: Summary: After compiling on Visual C
405:
406: * imach.c (Module): Merging 1.61 to 1.162
407:
1.165 brouard 408: Revision 1.164 2014/12/16 10:52:11 brouard
409: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
410:
411: * imach.c (Module): Merging 1.61 to 1.162
412:
1.164 brouard 413: Revision 1.163 2014/12/16 10:30:11 brouard
414: * imach.c (Module): Merging 1.61 to 1.162
415:
1.163 brouard 416: Revision 1.162 2014/09/25 11:43:39 brouard
417: Summary: temporary backup 0.99!
418:
1.162 brouard 419: Revision 1.1 2014/09/16 11:06:58 brouard
420: Summary: With some code (wrong) for nlopt
421:
422: Author:
423:
424: Revision 1.161 2014/09/15 20:41:41 brouard
425: Summary: Problem with macro SQR on Intel compiler
426:
1.161 brouard 427: Revision 1.160 2014/09/02 09:24:05 brouard
428: *** empty log message ***
429:
1.160 brouard 430: Revision 1.159 2014/09/01 10:34:10 brouard
431: Summary: WIN32
432: Author: Brouard
433:
1.159 brouard 434: Revision 1.158 2014/08/27 17:11:51 brouard
435: *** empty log message ***
436:
1.158 brouard 437: Revision 1.157 2014/08/27 16:26:55 brouard
438: Summary: Preparing windows Visual studio version
439: Author: Brouard
440:
441: In order to compile on Visual studio, time.h is now correct and time_t
442: and tm struct should be used. difftime should be used but sometimes I
443: just make the differences in raw time format (time(&now).
444: Trying to suppress #ifdef LINUX
445: Add xdg-open for __linux in order to open default browser.
446:
1.157 brouard 447: Revision 1.156 2014/08/25 20:10:10 brouard
448: *** empty log message ***
449:
1.156 brouard 450: Revision 1.155 2014/08/25 18:32:34 brouard
451: Summary: New compile, minor changes
452: Author: Brouard
453:
1.155 brouard 454: Revision 1.154 2014/06/20 17:32:08 brouard
455: Summary: Outputs now all graphs of convergence to period prevalence
456:
1.154 brouard 457: Revision 1.153 2014/06/20 16:45:46 brouard
458: Summary: If 3 live state, convergence to period prevalence on same graph
459: Author: Brouard
460:
1.153 brouard 461: Revision 1.152 2014/06/18 17:54:09 brouard
462: Summary: open browser, use gnuplot on same dir than imach if not found in the path
463:
1.152 brouard 464: Revision 1.151 2014/06/18 16:43:30 brouard
465: *** empty log message ***
466:
1.151 brouard 467: Revision 1.150 2014/06/18 16:42:35 brouard
468: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
469: Author: brouard
470:
1.150 brouard 471: Revision 1.149 2014/06/18 15:51:14 brouard
472: Summary: Some fixes in parameter files errors
473: Author: Nicolas Brouard
474:
1.149 brouard 475: Revision 1.148 2014/06/17 17:38:48 brouard
476: Summary: Nothing new
477: Author: Brouard
478:
479: Just a new packaging for OS/X version 0.98nS
480:
1.148 brouard 481: Revision 1.147 2014/06/16 10:33:11 brouard
482: *** empty log message ***
483:
1.147 brouard 484: Revision 1.146 2014/06/16 10:20:28 brouard
485: Summary: Merge
486: Author: Brouard
487:
488: Merge, before building revised version.
489:
1.146 brouard 490: Revision 1.145 2014/06/10 21:23:15 brouard
491: Summary: Debugging with valgrind
492: Author: Nicolas Brouard
493:
494: Lot of changes in order to output the results with some covariates
495: After the Edimburgh REVES conference 2014, it seems mandatory to
496: improve the code.
497: No more memory valgrind error but a lot has to be done in order to
498: continue the work of splitting the code into subroutines.
499: Also, decodemodel has been improved. Tricode is still not
500: optimal. nbcode should be improved. Documentation has been added in
501: the source code.
502:
1.144 brouard 503: Revision 1.143 2014/01/26 09:45:38 brouard
504: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
505:
506: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
507: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
508:
1.143 brouard 509: Revision 1.142 2014/01/26 03:57:36 brouard
510: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
511:
512: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
513:
1.142 brouard 514: Revision 1.141 2014/01/26 02:42:01 brouard
515: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
516:
1.141 brouard 517: Revision 1.140 2011/09/02 10:37:54 brouard
518: Summary: times.h is ok with mingw32 now.
519:
1.140 brouard 520: Revision 1.139 2010/06/14 07:50:17 brouard
521: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
522: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
523:
1.139 brouard 524: Revision 1.138 2010/04/30 18:19:40 brouard
525: *** empty log message ***
526:
1.138 brouard 527: Revision 1.137 2010/04/29 18:11:38 brouard
528: (Module): Checking covariates for more complex models
529: than V1+V2. A lot of change to be done. Unstable.
530:
1.137 brouard 531: Revision 1.136 2010/04/26 20:30:53 brouard
532: (Module): merging some libgsl code. Fixing computation
533: of likelione (using inter/intrapolation if mle = 0) in order to
534: get same likelihood as if mle=1.
535: Some cleaning of code and comments added.
536:
1.136 brouard 537: Revision 1.135 2009/10/29 15:33:14 brouard
538: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
539:
1.135 brouard 540: Revision 1.134 2009/10/29 13:18:53 brouard
541: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
542:
1.134 brouard 543: Revision 1.133 2009/07/06 10:21:25 brouard
544: just nforces
545:
1.133 brouard 546: Revision 1.132 2009/07/06 08:22:05 brouard
547: Many tings
548:
1.132 brouard 549: Revision 1.131 2009/06/20 16:22:47 brouard
550: Some dimensions resccaled
551:
1.131 brouard 552: Revision 1.130 2009/05/26 06:44:34 brouard
553: (Module): Max Covariate is now set to 20 instead of 8. A
554: lot of cleaning with variables initialized to 0. Trying to make
555: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
556:
1.130 brouard 557: Revision 1.129 2007/08/31 13:49:27 lievre
558: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
559:
1.129 lievre 560: Revision 1.128 2006/06/30 13:02:05 brouard
561: (Module): Clarifications on computing e.j
562:
1.128 brouard 563: Revision 1.127 2006/04/28 18:11:50 brouard
564: (Module): Yes the sum of survivors was wrong since
565: imach-114 because nhstepm was no more computed in the age
566: loop. Now we define nhstepma in the age loop.
567: (Module): In order to speed up (in case of numerous covariates) we
568: compute health expectancies (without variances) in a first step
569: and then all the health expectancies with variances or standard
570: deviation (needs data from the Hessian matrices) which slows the
571: computation.
572: In the future we should be able to stop the program is only health
573: expectancies and graph are needed without standard deviations.
574:
1.127 brouard 575: Revision 1.126 2006/04/28 17:23:28 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: Version 0.98h
580:
1.126 brouard 581: Revision 1.125 2006/04/04 15:20:31 lievre
582: Errors in calculation of health expectancies. Age was not initialized.
583: Forecasting file added.
584:
585: Revision 1.124 2006/03/22 17:13:53 lievre
586: Parameters are printed with %lf instead of %f (more numbers after the comma).
587: The log-likelihood is printed in the log file
588:
589: Revision 1.123 2006/03/20 10:52:43 brouard
590: * imach.c (Module): <title> changed, corresponds to .htm file
591: name. <head> headers where missing.
592:
593: * imach.c (Module): Weights can have a decimal point as for
594: English (a comma might work with a correct LC_NUMERIC environment,
595: otherwise the weight is truncated).
596: Modification of warning when the covariates values are not 0 or
597: 1.
598: Version 0.98g
599:
600: Revision 1.122 2006/03/20 09:45:41 brouard
601: (Module): Weights can have a decimal point as for
602: English (a comma might work with a correct LC_NUMERIC environment,
603: otherwise the weight is truncated).
604: Modification of warning when the covariates values are not 0 or
605: 1.
606: Version 0.98g
607:
608: Revision 1.121 2006/03/16 17:45:01 lievre
609: * imach.c (Module): Comments concerning covariates added
610:
611: * imach.c (Module): refinements in the computation of lli if
612: status=-2 in order to have more reliable computation if stepm is
613: not 1 month. Version 0.98f
614:
615: Revision 1.120 2006/03/16 15:10:38 lievre
616: (Module): refinements in the computation of lli if
617: status=-2 in order to have more reliable computation if stepm is
618: not 1 month. Version 0.98f
619:
620: Revision 1.119 2006/03/15 17:42:26 brouard
621: (Module): Bug if status = -2, the loglikelihood was
622: computed as likelihood omitting the logarithm. Version O.98e
623:
624: Revision 1.118 2006/03/14 18:20:07 brouard
625: (Module): varevsij Comments added explaining the second
626: table of variances if popbased=1 .
627: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
628: (Module): Function pstamp added
629: (Module): Version 0.98d
630:
631: Revision 1.117 2006/03/14 17:16:22 brouard
632: (Module): varevsij Comments added explaining the second
633: table of variances if popbased=1 .
634: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
635: (Module): Function pstamp added
636: (Module): Version 0.98d
637:
638: Revision 1.116 2006/03/06 10:29:27 brouard
639: (Module): Variance-covariance wrong links and
640: varian-covariance of ej. is needed (Saito).
641:
642: Revision 1.115 2006/02/27 12:17:45 brouard
643: (Module): One freematrix added in mlikeli! 0.98c
644:
645: Revision 1.114 2006/02/26 12:57:58 brouard
646: (Module): Some improvements in processing parameter
647: filename with strsep.
648:
649: Revision 1.113 2006/02/24 14:20:24 brouard
650: (Module): Memory leaks checks with valgrind and:
651: datafile was not closed, some imatrix were not freed and on matrix
652: allocation too.
653:
654: Revision 1.112 2006/01/30 09:55:26 brouard
655: (Module): Back to gnuplot.exe instead of wgnuplot.exe
656:
657: Revision 1.111 2006/01/25 20:38:18 brouard
658: (Module): Lots of cleaning and bugs added (Gompertz)
659: (Module): Comments can be added in data file. Missing date values
660: can be a simple dot '.'.
661:
662: Revision 1.110 2006/01/25 00:51:50 brouard
663: (Module): Lots of cleaning and bugs added (Gompertz)
664:
665: Revision 1.109 2006/01/24 19:37:15 brouard
666: (Module): Comments (lines starting with a #) are allowed in data.
667:
668: Revision 1.108 2006/01/19 18:05:42 lievre
669: Gnuplot problem appeared...
670: To be fixed
671:
672: Revision 1.107 2006/01/19 16:20:37 brouard
673: Test existence of gnuplot in imach path
674:
675: Revision 1.106 2006/01/19 13:24:36 brouard
676: Some cleaning and links added in html output
677:
678: Revision 1.105 2006/01/05 20:23:19 lievre
679: *** empty log message ***
680:
681: Revision 1.104 2005/09/30 16:11:43 lievre
682: (Module): sump fixed, loop imx fixed, and simplifications.
683: (Module): If the status is missing at the last wave but we know
684: that the person is alive, then we can code his/her status as -2
685: (instead of missing=-1 in earlier versions) and his/her
686: contributions to the likelihood is 1 - Prob of dying from last
687: health status (= 1-p13= p11+p12 in the easiest case of somebody in
688: the healthy state at last known wave). Version is 0.98
689:
690: Revision 1.103 2005/09/30 15:54:49 lievre
691: (Module): sump fixed, loop imx fixed, and simplifications.
692:
693: Revision 1.102 2004/09/15 17:31:30 brouard
694: Add the possibility to read data file including tab characters.
695:
696: Revision 1.101 2004/09/15 10:38:38 brouard
697: Fix on curr_time
698:
699: Revision 1.100 2004/07/12 18:29:06 brouard
700: Add version for Mac OS X. Just define UNIX in Makefile
701:
702: Revision 1.99 2004/06/05 08:57:40 brouard
703: *** empty log message ***
704:
705: Revision 1.98 2004/05/16 15:05:56 brouard
706: New version 0.97 . First attempt to estimate force of mortality
707: directly from the data i.e. without the need of knowing the health
708: state at each age, but using a Gompertz model: log u =a + b*age .
709: This is the basic analysis of mortality and should be done before any
710: other analysis, in order to test if the mortality estimated from the
711: cross-longitudinal survey is different from the mortality estimated
712: from other sources like vital statistic data.
713:
714: The same imach parameter file can be used but the option for mle should be -3.
715:
1.133 brouard 716: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 717: former routines in order to include the new code within the former code.
718:
719: The output is very simple: only an estimate of the intercept and of
720: the slope with 95% confident intervals.
721:
722: Current limitations:
723: A) Even if you enter covariates, i.e. with the
724: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
725: B) There is no computation of Life Expectancy nor Life Table.
726:
727: Revision 1.97 2004/02/20 13:25:42 lievre
728: Version 0.96d. Population forecasting command line is (temporarily)
729: suppressed.
730:
731: Revision 1.96 2003/07/15 15:38:55 brouard
732: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
733: rewritten within the same printf. Workaround: many printfs.
734:
735: Revision 1.95 2003/07/08 07:54:34 brouard
736: * imach.c (Repository):
737: (Repository): Using imachwizard code to output a more meaningful covariance
738: matrix (cov(a12,c31) instead of numbers.
739:
740: Revision 1.94 2003/06/27 13:00:02 brouard
741: Just cleaning
742:
743: Revision 1.93 2003/06/25 16:33:55 brouard
744: (Module): On windows (cygwin) function asctime_r doesn't
745: exist so I changed back to asctime which exists.
746: (Module): Version 0.96b
747:
748: Revision 1.92 2003/06/25 16:30:45 brouard
749: (Module): On windows (cygwin) function asctime_r doesn't
750: exist so I changed back to asctime which exists.
751:
752: Revision 1.91 2003/06/25 15:30:29 brouard
753: * imach.c (Repository): Duplicated warning errors corrected.
754: (Repository): Elapsed time after each iteration is now output. It
755: helps to forecast when convergence will be reached. Elapsed time
756: is stamped in powell. We created a new html file for the graphs
757: concerning matrix of covariance. It has extension -cov.htm.
758:
759: Revision 1.90 2003/06/24 12:34:15 brouard
760: (Module): Some bugs corrected for windows. Also, when
761: mle=-1 a template is output in file "or"mypar.txt with the design
762: of the covariance matrix to be input.
763:
764: Revision 1.89 2003/06/24 12:30:52 brouard
765: (Module): Some bugs corrected for windows. Also, when
766: mle=-1 a template is output in file "or"mypar.txt with the design
767: of the covariance matrix to be input.
768:
769: Revision 1.88 2003/06/23 17:54:56 brouard
770: * 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.
771:
772: Revision 1.87 2003/06/18 12:26:01 brouard
773: Version 0.96
774:
775: Revision 1.86 2003/06/17 20:04:08 brouard
776: (Module): Change position of html and gnuplot routines and added
777: routine fileappend.
778:
779: Revision 1.85 2003/06/17 13:12:43 brouard
780: * imach.c (Repository): Check when date of death was earlier that
781: current date of interview. It may happen when the death was just
782: prior to the death. In this case, dh was negative and likelihood
783: was wrong (infinity). We still send an "Error" but patch by
784: assuming that the date of death was just one stepm after the
785: interview.
786: (Repository): Because some people have very long ID (first column)
787: we changed int to long in num[] and we added a new lvector for
788: memory allocation. But we also truncated to 8 characters (left
789: truncation)
790: (Repository): No more line truncation errors.
791:
792: Revision 1.84 2003/06/13 21:44:43 brouard
793: * imach.c (Repository): Replace "freqsummary" at a correct
794: place. It differs from routine "prevalence" which may be called
795: many times. Probs is memory consuming and must be used with
796: parcimony.
797: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
798:
799: Revision 1.83 2003/06/10 13:39:11 lievre
800: *** empty log message ***
801:
802: Revision 1.82 2003/06/05 15:57:20 brouard
803: Add log in imach.c and fullversion number is now printed.
804:
805: */
806: /*
807: Interpolated Markov Chain
808:
809: Short summary of the programme:
810:
1.227 brouard 811: This program computes Healthy Life Expectancies or State-specific
812: (if states aren't health statuses) Expectancies from
813: cross-longitudinal data. Cross-longitudinal data consist in:
814:
815: -1- a first survey ("cross") where individuals from different ages
816: are interviewed on their health status or degree of disability (in
817: the case of a health survey which is our main interest)
818:
819: -2- at least a second wave of interviews ("longitudinal") which
820: measure each change (if any) in individual health status. Health
821: expectancies are computed from the time spent in each health state
822: according to a model. More health states you consider, more time is
823: necessary to reach the Maximum Likelihood of the parameters involved
824: in the model. The simplest model is the multinomial logistic model
825: where pij is the probability to be observed in state j at the second
826: wave conditional to be observed in state i at the first
827: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
828: etc , where 'age' is age and 'sex' is a covariate. If you want to
829: have a more complex model than "constant and age", you should modify
830: the program where the markup *Covariates have to be included here
831: again* invites you to do it. More covariates you add, slower the
1.126 brouard 832: convergence.
833:
834: The advantage of this computer programme, compared to a simple
835: multinomial logistic model, is clear when the delay between waves is not
836: identical for each individual. Also, if a individual missed an
837: intermediate interview, the information is lost, but taken into
838: account using an interpolation or extrapolation.
839:
840: hPijx is the probability to be observed in state i at age x+h
841: conditional to the observed state i at age x. The delay 'h' can be
842: split into an exact number (nh*stepm) of unobserved intermediate
843: states. This elementary transition (by month, quarter,
844: semester or year) is modelled as a multinomial logistic. The hPx
845: matrix is simply the matrix product of nh*stepm elementary matrices
846: and the contribution of each individual to the likelihood is simply
847: hPijx.
848:
849: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 850: of the life expectancies. It also computes the period (stable) prevalence.
851:
852: Back prevalence and projections:
1.227 brouard 853:
854: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
855: double agemaxpar, double ftolpl, int *ncvyearp, double
856: dateprev1,double dateprev2, int firstpass, int lastpass, int
857: mobilavproj)
858:
859: Computes the back prevalence limit for any combination of
860: covariate values k at any age between ageminpar and agemaxpar and
861: returns it in **bprlim. In the loops,
862:
863: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
864: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
865:
866: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 867: Computes for any combination of covariates k and any age between bage and fage
868: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
869: oldm=oldms;savm=savms;
1.227 brouard 870:
1.267 brouard 871: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 872: Computes the transition matrix starting at age 'age' over
873: 'nhstepm*hstepm*stepm' months (i.e. until
874: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 875: nhstepm*hstepm matrices.
876:
877: Returns p3mat[i][j][h] after calling
878: p3mat[i][j][h]=matprod2(newm,
879: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
880: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
881: oldm);
1.226 brouard 882:
883: Important routines
884:
885: - func (or funcone), computes logit (pij) distinguishing
886: o fixed variables (single or product dummies or quantitative);
887: o varying variables by:
888: (1) wave (single, product dummies, quantitative),
889: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
890: % fixed dummy (treated) or quantitative (not done because time-consuming);
891: % varying dummy (not done) or quantitative (not done);
892: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
893: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
894: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
895: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
896: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 897:
1.226 brouard 898:
899:
1.133 brouard 900: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
901: Institut national d'études démographiques, Paris.
1.126 brouard 902: This software have been partly granted by Euro-REVES, a concerted action
903: from the European Union.
904: It is copyrighted identically to a GNU software product, ie programme and
905: software can be distributed freely for non commercial use. Latest version
906: can be accessed at http://euroreves.ined.fr/imach .
907:
908: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
909: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
910:
911: **********************************************************************/
912: /*
913: main
914: read parameterfile
915: read datafile
916: concatwav
917: freqsummary
918: if (mle >= 1)
919: mlikeli
920: print results files
921: if mle==1
922: computes hessian
923: read end of parameter file: agemin, agemax, bage, fage, estepm
924: begin-prev-date,...
925: open gnuplot file
926: open html file
1.145 brouard 927: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
928: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
929: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
930: freexexit2 possible for memory heap.
931:
932: h Pij x | pij_nom ficrestpij
933: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
934: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
935: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
936:
937: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
938: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
939: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
940: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
941: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
942:
1.126 brouard 943: forecasting if prevfcast==1 prevforecast call prevalence()
944: health expectancies
945: Variance-covariance of DFLE
946: prevalence()
947: movingaverage()
948: varevsij()
949: if popbased==1 varevsij(,popbased)
950: total life expectancies
951: Variance of period (stable) prevalence
952: end
953: */
954:
1.187 brouard 955: /* #define DEBUG */
956: /* #define DEBUGBRENT */
1.203 brouard 957: /* #define DEBUGLINMIN */
958: /* #define DEBUGHESS */
959: #define DEBUGHESSIJ
1.224 brouard 960: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 961: #define POWELL /* Instead of NLOPT */
1.224 brouard 962: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 963: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
964: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 965:
966: #include <math.h>
967: #include <stdio.h>
968: #include <stdlib.h>
969: #include <string.h>
1.226 brouard 970: #include <ctype.h>
1.159 brouard 971:
972: #ifdef _WIN32
973: #include <io.h>
1.172 brouard 974: #include <windows.h>
975: #include <tchar.h>
1.159 brouard 976: #else
1.126 brouard 977: #include <unistd.h>
1.159 brouard 978: #endif
1.126 brouard 979:
980: #include <limits.h>
981: #include <sys/types.h>
1.171 brouard 982:
983: #if defined(__GNUC__)
984: #include <sys/utsname.h> /* Doesn't work on Windows */
985: #endif
986:
1.126 brouard 987: #include <sys/stat.h>
988: #include <errno.h>
1.159 brouard 989: /* extern int errno; */
1.126 brouard 990:
1.157 brouard 991: /* #ifdef LINUX */
992: /* #include <time.h> */
993: /* #include "timeval.h" */
994: /* #else */
995: /* #include <sys/time.h> */
996: /* #endif */
997:
1.126 brouard 998: #include <time.h>
999:
1.136 brouard 1000: #ifdef GSL
1001: #include <gsl/gsl_errno.h>
1002: #include <gsl/gsl_multimin.h>
1003: #endif
1004:
1.167 brouard 1005:
1.162 brouard 1006: #ifdef NLOPT
1007: #include <nlopt.h>
1008: typedef struct {
1009: double (* function)(double [] );
1010: } myfunc_data ;
1011: #endif
1012:
1.126 brouard 1013: /* #include <libintl.h> */
1014: /* #define _(String) gettext (String) */
1015:
1.251 brouard 1016: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1017:
1018: #define GNUPLOTPROGRAM "gnuplot"
1019: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1020: #define FILENAMELENGTH 132
1021:
1022: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1023: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1024:
1.144 brouard 1025: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1026: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1027:
1028: #define NINTERVMAX 8
1.144 brouard 1029: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1030: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1031: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1032: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1033: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1034: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 1035: #define MAXN 20000
1.144 brouard 1036: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1037: /* #define AGESUP 130 */
1038: #define AGESUP 150
1.268 brouard 1039: #define AGEINF 0
1.218 brouard 1040: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1041: #define AGEBASE 40
1.194 brouard 1042: #define AGEOVERFLOW 1.e20
1.164 brouard 1043: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1044: #ifdef _WIN32
1045: #define DIRSEPARATOR '\\'
1046: #define CHARSEPARATOR "\\"
1047: #define ODIRSEPARATOR '/'
1048: #else
1.126 brouard 1049: #define DIRSEPARATOR '/'
1050: #define CHARSEPARATOR "/"
1051: #define ODIRSEPARATOR '\\'
1052: #endif
1053:
1.283 ! brouard 1054: /* $Id: imach.c,v 1.282 2018/02/27 22:50:02 brouard Exp $ */
1.126 brouard 1055: /* $State: Exp $ */
1.196 brouard 1056: #include "version.h"
1057: char version[]=__IMACH_VERSION__;
1.283 ! brouard 1058: 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";
! 1059: char fullversion[]="$Revision: 1.282 $ $Date: 2018/02/27 22:50:02 $";
1.126 brouard 1060: char strstart[80];
1061: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1062: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1063: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1064: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1065: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1066: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1067: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1068: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1069: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1070: int cptcovprodnoage=0; /**< Number of covariate products without age */
1071: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1072: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1073: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1074: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1075: int nsd=0; /**< Total number of single dummy variables (output) */
1076: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1077: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1078: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1079: int ntveff=0; /**< ntveff number of effective time varying variables */
1080: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1081: int cptcov=0; /* Working variable */
1.218 brouard 1082: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 1083: int npar=NPARMAX;
1084: int nlstate=2; /* Number of live states */
1085: int ndeath=1; /* Number of dead states */
1.130 brouard 1086: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1087: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1088: int popbased=0;
1089:
1090: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1091: int maxwav=0; /* Maxim number of waves */
1092: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1093: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1094: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1095: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1096: int mle=1, weightopt=0;
1.126 brouard 1097: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1098: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1099: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1100: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1101: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1102: int selected(int kvar); /* Is covariate kvar selected for printing results */
1103:
1.130 brouard 1104: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1105: double **matprod2(); /* test */
1.126 brouard 1106: double **oldm, **newm, **savm; /* Working pointers to matrices */
1107: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1108: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1109:
1.136 brouard 1110: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1111: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1112: FILE *ficlog, *ficrespow;
1.130 brouard 1113: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1114: double fretone; /* Only one call to likelihood */
1.130 brouard 1115: long ipmx=0; /* Number of contributions */
1.126 brouard 1116: double sw; /* Sum of weights */
1117: char filerespow[FILENAMELENGTH];
1118: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1119: FILE *ficresilk;
1120: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1121: FILE *ficresprobmorprev;
1122: FILE *fichtm, *fichtmcov; /* Html File */
1123: FILE *ficreseij;
1124: char filerese[FILENAMELENGTH];
1125: FILE *ficresstdeij;
1126: char fileresstde[FILENAMELENGTH];
1127: FILE *ficrescveij;
1128: char filerescve[FILENAMELENGTH];
1129: FILE *ficresvij;
1130: char fileresv[FILENAMELENGTH];
1.269 brouard 1131:
1.126 brouard 1132: char title[MAXLINE];
1.234 brouard 1133: char model[MAXLINE]; /**< The model line */
1.217 brouard 1134: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1135: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1136: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1137: char command[FILENAMELENGTH];
1138: int outcmd=0;
1139:
1.217 brouard 1140: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1141: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1142: char filelog[FILENAMELENGTH]; /* Log file */
1143: char filerest[FILENAMELENGTH];
1144: char fileregp[FILENAMELENGTH];
1145: char popfile[FILENAMELENGTH];
1146:
1147: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1148:
1.157 brouard 1149: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1150: /* struct timezone tzp; */
1151: /* extern int gettimeofday(); */
1152: struct tm tml, *gmtime(), *localtime();
1153:
1154: extern time_t time();
1155:
1156: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1157: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1158: struct tm tm;
1159:
1.126 brouard 1160: char strcurr[80], strfor[80];
1161:
1162: char *endptr;
1163: long lval;
1164: double dval;
1165:
1166: #define NR_END 1
1167: #define FREE_ARG char*
1168: #define FTOL 1.0e-10
1169:
1170: #define NRANSI
1.240 brouard 1171: #define ITMAX 200
1172: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1173:
1174: #define TOL 2.0e-4
1175:
1176: #define CGOLD 0.3819660
1177: #define ZEPS 1.0e-10
1178: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1179:
1180: #define GOLD 1.618034
1181: #define GLIMIT 100.0
1182: #define TINY 1.0e-20
1183:
1184: static double maxarg1,maxarg2;
1185: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1186: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1187:
1188: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1189: #define rint(a) floor(a+0.5)
1.166 brouard 1190: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1191: #define mytinydouble 1.0e-16
1.166 brouard 1192: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1193: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1194: /* static double dsqrarg; */
1195: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1196: static double sqrarg;
1197: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1198: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1199: int agegomp= AGEGOMP;
1200:
1201: int imx;
1202: int stepm=1;
1203: /* Stepm, step in month: minimum step interpolation*/
1204:
1205: int estepm;
1206: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1207:
1208: int m,nb;
1209: long *num;
1.197 brouard 1210: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1211: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1212: covariate for which somebody answered excluding
1213: undefined. Usually 2: 0 and 1. */
1214: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1215: covariate for which somebody answered including
1216: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1217: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1218: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1219: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1220: double *ageexmed,*agecens;
1221: double dateintmean=0;
1222:
1223: double *weight;
1224: int **s; /* Status */
1.141 brouard 1225: double *agedc;
1.145 brouard 1226: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1227: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1228: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1229: double **coqvar; /* Fixed quantitative covariate nqv */
1230: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1231: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1232: double idx;
1233: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1234: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1235: /*k 1 2 3 4 5 6 7 8 9 */
1236: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1237: /* Tndvar[k] 1 2 3 4 5 */
1238: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1239: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1240: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1241: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1242: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1243: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1244: /* Tprod[i]=k 4 7 */
1245: /* Tage[i]=k 5 8 */
1246: /* */
1247: /* Type */
1248: /* V 1 2 3 4 5 */
1249: /* F F V V V */
1250: /* D Q D D Q */
1251: /* */
1252: int *TvarsD;
1253: int *TvarsDind;
1254: int *TvarsQ;
1255: int *TvarsQind;
1256:
1.235 brouard 1257: #define MAXRESULTLINES 10
1258: int nresult=0;
1.258 brouard 1259: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1260: int TKresult[MAXRESULTLINES];
1.237 brouard 1261: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1262: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1263: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1264: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1265: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1266: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1267:
1.234 brouard 1268: /* 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 1269: 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 */
1270: 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 */
1271: 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 */
1272: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1273: 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 */
1274: 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 1275: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1276: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1277: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1278: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1279: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1280: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1281: 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 */
1282: 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 */
1283:
1.230 brouard 1284: int *Tvarsel; /**< Selected covariates for output */
1285: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1286: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1287: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1288: 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 1289: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1290: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1291: int *Tage;
1.227 brouard 1292: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1293: 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 1294: 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*/
1295: 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 1296: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1297: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1298: int **Tvard;
1299: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1300: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1301: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1302: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1303: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1304: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1305: double *lsurv, *lpop, *tpop;
1306:
1.231 brouard 1307: #define FD 1; /* Fixed dummy covariate */
1308: #define FQ 2; /* Fixed quantitative covariate */
1309: #define FP 3; /* Fixed product covariate */
1310: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1311: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1312: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1313: #define VD 10; /* Varying dummy covariate */
1314: #define VQ 11; /* Varying quantitative covariate */
1315: #define VP 12; /* Varying product covariate */
1316: #define VPDD 13; /* Varying product dummy*dummy covariate */
1317: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1318: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1319: #define APFD 16; /* Age product * fixed dummy covariate */
1320: #define APFQ 17; /* Age product * fixed quantitative covariate */
1321: #define APVD 18; /* Age product * varying dummy covariate */
1322: #define APVQ 19; /* Age product * varying quantitative covariate */
1323:
1324: #define FTYPE 1; /* Fixed covariate */
1325: #define VTYPE 2; /* Varying covariate (loop in wave) */
1326: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1327:
1328: struct kmodel{
1329: int maintype; /* main type */
1330: int subtype; /* subtype */
1331: };
1332: struct kmodel modell[NCOVMAX];
1333:
1.143 brouard 1334: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1335: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1336:
1337: /**************** split *************************/
1338: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1339: {
1340: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1341: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1342: */
1343: char *ss; /* pointer */
1.186 brouard 1344: int l1=0, l2=0; /* length counters */
1.126 brouard 1345:
1346: l1 = strlen(path ); /* length of path */
1347: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1348: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1349: if ( ss == NULL ) { /* no directory, so determine current directory */
1350: strcpy( name, path ); /* we got the fullname name because no directory */
1351: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1352: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1353: /* get current working directory */
1354: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1355: #ifdef WIN32
1356: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1357: #else
1358: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1359: #endif
1.126 brouard 1360: return( GLOCK_ERROR_GETCWD );
1361: }
1362: /* got dirc from getcwd*/
1363: printf(" DIRC = %s \n",dirc);
1.205 brouard 1364: } else { /* strip directory from path */
1.126 brouard 1365: ss++; /* after this, the filename */
1366: l2 = strlen( ss ); /* length of filename */
1367: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1368: strcpy( name, ss ); /* save file name */
1369: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1370: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1371: printf(" DIRC2 = %s \n",dirc);
1372: }
1373: /* We add a separator at the end of dirc if not exists */
1374: l1 = strlen( dirc ); /* length of directory */
1375: if( dirc[l1-1] != DIRSEPARATOR ){
1376: dirc[l1] = DIRSEPARATOR;
1377: dirc[l1+1] = 0;
1378: printf(" DIRC3 = %s \n",dirc);
1379: }
1380: ss = strrchr( name, '.' ); /* find last / */
1381: if (ss >0){
1382: ss++;
1383: strcpy(ext,ss); /* save extension */
1384: l1= strlen( name);
1385: l2= strlen(ss)+1;
1386: strncpy( finame, name, l1-l2);
1387: finame[l1-l2]= 0;
1388: }
1389:
1390: return( 0 ); /* we're done */
1391: }
1392:
1393:
1394: /******************************************/
1395:
1396: void replace_back_to_slash(char *s, char*t)
1397: {
1398: int i;
1399: int lg=0;
1400: i=0;
1401: lg=strlen(t);
1402: for(i=0; i<= lg; i++) {
1403: (s[i] = t[i]);
1404: if (t[i]== '\\') s[i]='/';
1405: }
1406: }
1407:
1.132 brouard 1408: char *trimbb(char *out, char *in)
1.137 brouard 1409: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1410: char *s;
1411: s=out;
1412: while (*in != '\0'){
1.137 brouard 1413: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1414: in++;
1415: }
1416: *out++ = *in++;
1417: }
1418: *out='\0';
1419: return s;
1420: }
1421:
1.187 brouard 1422: /* char *substrchaine(char *out, char *in, char *chain) */
1423: /* { */
1424: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1425: /* char *s, *t; */
1426: /* t=in;s=out; */
1427: /* while ((*in != *chain) && (*in != '\0')){ */
1428: /* *out++ = *in++; */
1429: /* } */
1430:
1431: /* /\* *in matches *chain *\/ */
1432: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1433: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1434: /* } */
1435: /* in--; chain--; */
1436: /* while ( (*in != '\0')){ */
1437: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1438: /* *out++ = *in++; */
1439: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1440: /* } */
1441: /* *out='\0'; */
1442: /* out=s; */
1443: /* return out; */
1444: /* } */
1445: char *substrchaine(char *out, char *in, char *chain)
1446: {
1447: /* Substract chain 'chain' from 'in', return and output 'out' */
1448: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1449:
1450: char *strloc;
1451:
1452: strcpy (out, in);
1453: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1454: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1455: if(strloc != NULL){
1456: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1457: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1458: /* strcpy (strloc, strloc +strlen(chain));*/
1459: }
1460: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1461: return out;
1462: }
1463:
1464:
1.145 brouard 1465: char *cutl(char *blocc, char *alocc, char *in, char occ)
1466: {
1.187 brouard 1467: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1468: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1469: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1470: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1471: */
1.160 brouard 1472: char *s, *t;
1.145 brouard 1473: t=in;s=in;
1474: while ((*in != occ) && (*in != '\0')){
1475: *alocc++ = *in++;
1476: }
1477: if( *in == occ){
1478: *(alocc)='\0';
1479: s=++in;
1480: }
1481:
1482: if (s == t) {/* occ not found */
1483: *(alocc-(in-s))='\0';
1484: in=s;
1485: }
1486: while ( *in != '\0'){
1487: *blocc++ = *in++;
1488: }
1489:
1490: *blocc='\0';
1491: return t;
1492: }
1.137 brouard 1493: char *cutv(char *blocc, char *alocc, char *in, char occ)
1494: {
1.187 brouard 1495: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1496: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1497: gives blocc="abcdef2ghi" and alocc="j".
1498: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1499: */
1500: char *s, *t;
1501: t=in;s=in;
1502: while (*in != '\0'){
1503: while( *in == occ){
1504: *blocc++ = *in++;
1505: s=in;
1506: }
1507: *blocc++ = *in++;
1508: }
1509: if (s == t) /* occ not found */
1510: *(blocc-(in-s))='\0';
1511: else
1512: *(blocc-(in-s)-1)='\0';
1513: in=s;
1514: while ( *in != '\0'){
1515: *alocc++ = *in++;
1516: }
1517:
1518: *alocc='\0';
1519: return s;
1520: }
1521:
1.126 brouard 1522: int nbocc(char *s, char occ)
1523: {
1524: int i,j=0;
1525: int lg=20;
1526: i=0;
1527: lg=strlen(s);
1528: for(i=0; i<= lg; i++) {
1.234 brouard 1529: if (s[i] == occ ) j++;
1.126 brouard 1530: }
1531: return j;
1532: }
1533:
1.137 brouard 1534: /* void cutv(char *u,char *v, char*t, char occ) */
1535: /* { */
1536: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1537: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1538: /* gives u="abcdef2ghi" and v="j" *\/ */
1539: /* int i,lg,j,p=0; */
1540: /* i=0; */
1541: /* lg=strlen(t); */
1542: /* for(j=0; j<=lg-1; j++) { */
1543: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1544: /* } */
1.126 brouard 1545:
1.137 brouard 1546: /* for(j=0; j<p; j++) { */
1547: /* (u[j] = t[j]); */
1548: /* } */
1549: /* u[p]='\0'; */
1.126 brouard 1550:
1.137 brouard 1551: /* for(j=0; j<= lg; j++) { */
1552: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1553: /* } */
1554: /* } */
1.126 brouard 1555:
1.160 brouard 1556: #ifdef _WIN32
1557: char * strsep(char **pp, const char *delim)
1558: {
1559: char *p, *q;
1560:
1561: if ((p = *pp) == NULL)
1562: return 0;
1563: if ((q = strpbrk (p, delim)) != NULL)
1564: {
1565: *pp = q + 1;
1566: *q = '\0';
1567: }
1568: else
1569: *pp = 0;
1570: return p;
1571: }
1572: #endif
1573:
1.126 brouard 1574: /********************** nrerror ********************/
1575:
1576: void nrerror(char error_text[])
1577: {
1578: fprintf(stderr,"ERREUR ...\n");
1579: fprintf(stderr,"%s\n",error_text);
1580: exit(EXIT_FAILURE);
1581: }
1582: /*********************** vector *******************/
1583: double *vector(int nl, int nh)
1584: {
1585: double *v;
1586: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1587: if (!v) nrerror("allocation failure in vector");
1588: return v-nl+NR_END;
1589: }
1590:
1591: /************************ free vector ******************/
1592: void free_vector(double*v, int nl, int nh)
1593: {
1594: free((FREE_ARG)(v+nl-NR_END));
1595: }
1596:
1597: /************************ivector *******************************/
1598: int *ivector(long nl,long nh)
1599: {
1600: int *v;
1601: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1602: if (!v) nrerror("allocation failure in ivector");
1603: return v-nl+NR_END;
1604: }
1605:
1606: /******************free ivector **************************/
1607: void free_ivector(int *v, long nl, long nh)
1608: {
1609: free((FREE_ARG)(v+nl-NR_END));
1610: }
1611:
1612: /************************lvector *******************************/
1613: long *lvector(long nl,long nh)
1614: {
1615: long *v;
1616: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1617: if (!v) nrerror("allocation failure in ivector");
1618: return v-nl+NR_END;
1619: }
1620:
1621: /******************free lvector **************************/
1622: void free_lvector(long *v, long nl, long nh)
1623: {
1624: free((FREE_ARG)(v+nl-NR_END));
1625: }
1626:
1627: /******************* imatrix *******************************/
1628: int **imatrix(long nrl, long nrh, long ncl, long nch)
1629: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1630: {
1631: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1632: int **m;
1633:
1634: /* allocate pointers to rows */
1635: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1636: if (!m) nrerror("allocation failure 1 in matrix()");
1637: m += NR_END;
1638: m -= nrl;
1639:
1640:
1641: /* allocate rows and set pointers to them */
1642: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1643: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1644: m[nrl] += NR_END;
1645: m[nrl] -= ncl;
1646:
1647: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1648:
1649: /* return pointer to array of pointers to rows */
1650: return m;
1651: }
1652:
1653: /****************** free_imatrix *************************/
1654: void free_imatrix(m,nrl,nrh,ncl,nch)
1655: int **m;
1656: long nch,ncl,nrh,nrl;
1657: /* free an int matrix allocated by imatrix() */
1658: {
1659: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1660: free((FREE_ARG) (m+nrl-NR_END));
1661: }
1662:
1663: /******************* matrix *******************************/
1664: double **matrix(long nrl, long nrh, long ncl, long nch)
1665: {
1666: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1667: double **m;
1668:
1669: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1670: if (!m) nrerror("allocation failure 1 in matrix()");
1671: m += NR_END;
1672: m -= nrl;
1673:
1674: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1675: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1676: m[nrl] += NR_END;
1677: m[nrl] -= ncl;
1678:
1679: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1680: return m;
1.145 brouard 1681: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1682: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1683: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1684: */
1685: }
1686:
1687: /*************************free matrix ************************/
1688: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1689: {
1690: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1691: free((FREE_ARG)(m+nrl-NR_END));
1692: }
1693:
1694: /******************* ma3x *******************************/
1695: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1696: {
1697: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1698: double ***m;
1699:
1700: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1701: if (!m) nrerror("allocation failure 1 in matrix()");
1702: m += NR_END;
1703: m -= nrl;
1704:
1705: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1706: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1707: m[nrl] += NR_END;
1708: m[nrl] -= ncl;
1709:
1710: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1711:
1712: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1713: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1714: m[nrl][ncl] += NR_END;
1715: m[nrl][ncl] -= nll;
1716: for (j=ncl+1; j<=nch; j++)
1717: m[nrl][j]=m[nrl][j-1]+nlay;
1718:
1719: for (i=nrl+1; i<=nrh; i++) {
1720: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1721: for (j=ncl+1; j<=nch; j++)
1722: m[i][j]=m[i][j-1]+nlay;
1723: }
1724: return m;
1725: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1726: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1727: */
1728: }
1729:
1730: /*************************free ma3x ************************/
1731: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1732: {
1733: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1734: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1735: free((FREE_ARG)(m+nrl-NR_END));
1736: }
1737:
1738: /*************** function subdirf ***********/
1739: char *subdirf(char fileres[])
1740: {
1741: /* Caution optionfilefiname is hidden */
1742: strcpy(tmpout,optionfilefiname);
1743: strcat(tmpout,"/"); /* Add to the right */
1744: strcat(tmpout,fileres);
1745: return tmpout;
1746: }
1747:
1748: /*************** function subdirf2 ***********/
1749: char *subdirf2(char fileres[], char *preop)
1750: {
1751:
1752: /* Caution optionfilefiname is hidden */
1753: strcpy(tmpout,optionfilefiname);
1754: strcat(tmpout,"/");
1755: strcat(tmpout,preop);
1756: strcat(tmpout,fileres);
1757: return tmpout;
1758: }
1759:
1760: /*************** function subdirf3 ***********/
1761: char *subdirf3(char fileres[], char *preop, char *preop2)
1762: {
1763:
1764: /* Caution optionfilefiname is hidden */
1765: strcpy(tmpout,optionfilefiname);
1766: strcat(tmpout,"/");
1767: strcat(tmpout,preop);
1768: strcat(tmpout,preop2);
1769: strcat(tmpout,fileres);
1770: return tmpout;
1771: }
1.213 brouard 1772:
1773: /*************** function subdirfext ***********/
1774: char *subdirfext(char fileres[], char *preop, char *postop)
1775: {
1776:
1777: strcpy(tmpout,preop);
1778: strcat(tmpout,fileres);
1779: strcat(tmpout,postop);
1780: return tmpout;
1781: }
1.126 brouard 1782:
1.213 brouard 1783: /*************** function subdirfext3 ***********/
1784: char *subdirfext3(char fileres[], char *preop, char *postop)
1785: {
1786:
1787: /* Caution optionfilefiname is hidden */
1788: strcpy(tmpout,optionfilefiname);
1789: strcat(tmpout,"/");
1790: strcat(tmpout,preop);
1791: strcat(tmpout,fileres);
1792: strcat(tmpout,postop);
1793: return tmpout;
1794: }
1795:
1.162 brouard 1796: char *asc_diff_time(long time_sec, char ascdiff[])
1797: {
1798: long sec_left, days, hours, minutes;
1799: days = (time_sec) / (60*60*24);
1800: sec_left = (time_sec) % (60*60*24);
1801: hours = (sec_left) / (60*60) ;
1802: sec_left = (sec_left) %(60*60);
1803: minutes = (sec_left) /60;
1804: sec_left = (sec_left) % (60);
1805: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1806: return ascdiff;
1807: }
1808:
1.126 brouard 1809: /***************** f1dim *************************/
1810: extern int ncom;
1811: extern double *pcom,*xicom;
1812: extern double (*nrfunc)(double []);
1813:
1814: double f1dim(double x)
1815: {
1816: int j;
1817: double f;
1818: double *xt;
1819:
1820: xt=vector(1,ncom);
1821: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1822: f=(*nrfunc)(xt);
1823: free_vector(xt,1,ncom);
1824: return f;
1825: }
1826:
1827: /*****************brent *************************/
1828: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1829: {
1830: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1831: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1832: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1833: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1834: * returned function value.
1835: */
1.126 brouard 1836: int iter;
1837: double a,b,d,etemp;
1.159 brouard 1838: double fu=0,fv,fw,fx;
1.164 brouard 1839: double ftemp=0.;
1.126 brouard 1840: double p,q,r,tol1,tol2,u,v,w,x,xm;
1841: double e=0.0;
1842:
1843: a=(ax < cx ? ax : cx);
1844: b=(ax > cx ? ax : cx);
1845: x=w=v=bx;
1846: fw=fv=fx=(*f)(x);
1847: for (iter=1;iter<=ITMAX;iter++) {
1848: xm=0.5*(a+b);
1849: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1850: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1851: printf(".");fflush(stdout);
1852: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1853: #ifdef DEBUGBRENT
1.126 brouard 1854: 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);
1855: 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);
1856: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1857: #endif
1858: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1859: *xmin=x;
1860: return fx;
1861: }
1862: ftemp=fu;
1863: if (fabs(e) > tol1) {
1864: r=(x-w)*(fx-fv);
1865: q=(x-v)*(fx-fw);
1866: p=(x-v)*q-(x-w)*r;
1867: q=2.0*(q-r);
1868: if (q > 0.0) p = -p;
1869: q=fabs(q);
1870: etemp=e;
1871: e=d;
1872: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1873: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1874: else {
1.224 brouard 1875: d=p/q;
1876: u=x+d;
1877: if (u-a < tol2 || b-u < tol2)
1878: d=SIGN(tol1,xm-x);
1.126 brouard 1879: }
1880: } else {
1881: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1882: }
1883: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1884: fu=(*f)(u);
1885: if (fu <= fx) {
1886: if (u >= x) a=x; else b=x;
1887: SHFT(v,w,x,u)
1.183 brouard 1888: SHFT(fv,fw,fx,fu)
1889: } else {
1890: if (u < x) a=u; else b=u;
1891: if (fu <= fw || w == x) {
1.224 brouard 1892: v=w;
1893: w=u;
1894: fv=fw;
1895: fw=fu;
1.183 brouard 1896: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1897: v=u;
1898: fv=fu;
1.183 brouard 1899: }
1900: }
1.126 brouard 1901: }
1902: nrerror("Too many iterations in brent");
1903: *xmin=x;
1904: return fx;
1905: }
1906:
1907: /****************** mnbrak ***********************/
1908:
1909: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1910: double (*func)(double))
1.183 brouard 1911: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1912: the downhill direction (defined by the function as evaluated at the initial points) and returns
1913: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1914: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1915: */
1.126 brouard 1916: double ulim,u,r,q, dum;
1917: double fu;
1.187 brouard 1918:
1919: double scale=10.;
1920: int iterscale=0;
1921:
1922: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1923: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1924:
1925:
1926: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1927: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1928: /* *bx = *ax - (*ax - *bx)/scale; */
1929: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1930: /* } */
1931:
1.126 brouard 1932: if (*fb > *fa) {
1933: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1934: SHFT(dum,*fb,*fa,dum)
1935: }
1.126 brouard 1936: *cx=(*bx)+GOLD*(*bx-*ax);
1937: *fc=(*func)(*cx);
1.183 brouard 1938: #ifdef DEBUG
1.224 brouard 1939: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1940: 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 1941: #endif
1.224 brouard 1942: 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 1943: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1944: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1945: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1946: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1947: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1948: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1949: fu=(*func)(u);
1.163 brouard 1950: #ifdef DEBUG
1951: /* f(x)=A(x-u)**2+f(u) */
1952: double A, fparabu;
1953: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1954: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1955: 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);
1956: 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 1957: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1958: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1959: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1960: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1961: #endif
1.184 brouard 1962: #ifdef MNBRAKORIGINAL
1.183 brouard 1963: #else
1.191 brouard 1964: /* if (fu > *fc) { */
1965: /* #ifdef DEBUG */
1966: /* printf("mnbrak4 fu > fc \n"); */
1967: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1968: /* #endif */
1969: /* /\* 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 *\\/ *\/ */
1970: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1971: /* dum=u; /\* Shifting c and u *\/ */
1972: /* u = *cx; */
1973: /* *cx = dum; */
1974: /* dum = fu; */
1975: /* fu = *fc; */
1976: /* *fc =dum; */
1977: /* } else { /\* end *\/ */
1978: /* #ifdef DEBUG */
1979: /* printf("mnbrak3 fu < fc \n"); */
1980: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1981: /* #endif */
1982: /* dum=u; /\* Shifting c and u *\/ */
1983: /* u = *cx; */
1984: /* *cx = dum; */
1985: /* dum = fu; */
1986: /* fu = *fc; */
1987: /* *fc =dum; */
1988: /* } */
1.224 brouard 1989: #ifdef DEBUGMNBRAK
1990: double A, fparabu;
1991: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1992: fparabu= *fa - A*(*ax-u)*(*ax-u);
1993: 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);
1994: 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 1995: #endif
1.191 brouard 1996: dum=u; /* Shifting c and u */
1997: u = *cx;
1998: *cx = dum;
1999: dum = fu;
2000: fu = *fc;
2001: *fc =dum;
1.183 brouard 2002: #endif
1.162 brouard 2003: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2004: #ifdef DEBUG
1.224 brouard 2005: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2006: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2007: #endif
1.126 brouard 2008: fu=(*func)(u);
2009: if (fu < *fc) {
1.183 brouard 2010: #ifdef DEBUG
1.224 brouard 2011: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2012: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2013: #endif
2014: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2015: SHFT(*fb,*fc,fu,(*func)(u))
2016: #ifdef DEBUG
2017: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2018: #endif
2019: }
1.162 brouard 2020: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2021: #ifdef DEBUG
1.224 brouard 2022: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2023: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2024: #endif
1.126 brouard 2025: u=ulim;
2026: fu=(*func)(u);
1.183 brouard 2027: } else { /* u could be left to b (if r > q parabola has a maximum) */
2028: #ifdef DEBUG
1.224 brouard 2029: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2030: 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 2031: #endif
1.126 brouard 2032: u=(*cx)+GOLD*(*cx-*bx);
2033: fu=(*func)(u);
1.224 brouard 2034: #ifdef DEBUG
2035: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2036: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2037: #endif
1.183 brouard 2038: } /* end tests */
1.126 brouard 2039: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2040: SHFT(*fa,*fb,*fc,fu)
2041: #ifdef DEBUG
1.224 brouard 2042: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2043: 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 2044: #endif
2045: } /* 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 2046: }
2047:
2048: /*************** linmin ************************/
1.162 brouard 2049: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2050: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2051: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2052: the value of func at the returned location p . This is actually all accomplished by calling the
2053: routines mnbrak and brent .*/
1.126 brouard 2054: int ncom;
2055: double *pcom,*xicom;
2056: double (*nrfunc)(double []);
2057:
1.224 brouard 2058: #ifdef LINMINORIGINAL
1.126 brouard 2059: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2060: #else
2061: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2062: #endif
1.126 brouard 2063: {
2064: double brent(double ax, double bx, double cx,
2065: double (*f)(double), double tol, double *xmin);
2066: double f1dim(double x);
2067: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2068: double *fc, double (*func)(double));
2069: int j;
2070: double xx,xmin,bx,ax;
2071: double fx,fb,fa;
1.187 brouard 2072:
1.203 brouard 2073: #ifdef LINMINORIGINAL
2074: #else
2075: double scale=10., axs, xxs; /* Scale added for infinity */
2076: #endif
2077:
1.126 brouard 2078: ncom=n;
2079: pcom=vector(1,n);
2080: xicom=vector(1,n);
2081: nrfunc=func;
2082: for (j=1;j<=n;j++) {
2083: pcom[j]=p[j];
1.202 brouard 2084: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2085: }
1.187 brouard 2086:
1.203 brouard 2087: #ifdef LINMINORIGINAL
2088: xx=1.;
2089: #else
2090: axs=0.0;
2091: xxs=1.;
2092: do{
2093: xx= xxs;
2094: #endif
1.187 brouard 2095: ax=0.;
2096: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2097: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2098: /* 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)) */
2099: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2100: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2101: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2102: /* 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 2103: #ifdef LINMINORIGINAL
2104: #else
2105: if (fx != fx){
1.224 brouard 2106: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2107: printf("|");
2108: fprintf(ficlog,"|");
1.203 brouard 2109: #ifdef DEBUGLINMIN
1.224 brouard 2110: 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 2111: #endif
2112: }
1.224 brouard 2113: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2114: #endif
2115:
1.191 brouard 2116: #ifdef DEBUGLINMIN
2117: 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 2118: 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 2119: #endif
1.224 brouard 2120: #ifdef LINMINORIGINAL
2121: #else
2122: if(fb == fx){ /* Flat function in the direction */
2123: xmin=xx;
2124: *flat=1;
2125: }else{
2126: *flat=0;
2127: #endif
2128: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2129: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2130: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2131: /* fmin = f(p[j] + xmin * xi[j]) */
2132: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2133: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2134: #ifdef DEBUG
1.224 brouard 2135: 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);
2136: 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);
2137: #endif
2138: #ifdef LINMINORIGINAL
2139: #else
2140: }
1.126 brouard 2141: #endif
1.191 brouard 2142: #ifdef DEBUGLINMIN
2143: printf("linmin end ");
1.202 brouard 2144: fprintf(ficlog,"linmin end ");
1.191 brouard 2145: #endif
1.126 brouard 2146: for (j=1;j<=n;j++) {
1.203 brouard 2147: #ifdef LINMINORIGINAL
2148: xi[j] *= xmin;
2149: #else
2150: #ifdef DEBUGLINMIN
2151: if(xxs <1.0)
2152: printf(" before xi[%d]=%12.8f", j,xi[j]);
2153: #endif
2154: 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) */
2155: #ifdef DEBUGLINMIN
2156: if(xxs <1.0)
2157: 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 );
2158: #endif
2159: #endif
1.187 brouard 2160: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2161: }
1.191 brouard 2162: #ifdef DEBUGLINMIN
1.203 brouard 2163: printf("\n");
1.191 brouard 2164: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2165: 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 2166: for (j=1;j<=n;j++) {
1.202 brouard 2167: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2168: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2169: if(j % ncovmodel == 0){
1.191 brouard 2170: printf("\n");
1.202 brouard 2171: fprintf(ficlog,"\n");
2172: }
1.191 brouard 2173: }
1.203 brouard 2174: #else
1.191 brouard 2175: #endif
1.126 brouard 2176: free_vector(xicom,1,n);
2177: free_vector(pcom,1,n);
2178: }
2179:
2180:
2181: /*************** powell ************************/
1.162 brouard 2182: /*
2183: Minimization of a function func of n variables. Input consists of an initial starting point
2184: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2185: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2186: such that failure to decrease by more than this amount on one iteration signals doneness. On
2187: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2188: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2189: */
1.224 brouard 2190: #ifdef LINMINORIGINAL
2191: #else
2192: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2193: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2194: #endif
1.126 brouard 2195: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2196: double (*func)(double []))
2197: {
1.224 brouard 2198: #ifdef LINMINORIGINAL
2199: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2200: double (*func)(double []));
1.224 brouard 2201: #else
1.241 brouard 2202: void linmin(double p[], double xi[], int n, double *fret,
2203: double (*func)(double []),int *flat);
1.224 brouard 2204: #endif
1.239 brouard 2205: int i,ibig,j,jk,k;
1.126 brouard 2206: double del,t,*pt,*ptt,*xit;
1.181 brouard 2207: double directest;
1.126 brouard 2208: double fp,fptt;
2209: double *xits;
2210: int niterf, itmp;
1.224 brouard 2211: #ifdef LINMINORIGINAL
2212: #else
2213:
2214: flatdir=ivector(1,n);
2215: for (j=1;j<=n;j++) flatdir[j]=0;
2216: #endif
1.126 brouard 2217:
2218: pt=vector(1,n);
2219: ptt=vector(1,n);
2220: xit=vector(1,n);
2221: xits=vector(1,n);
2222: *fret=(*func)(p);
2223: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2224: rcurr_time = time(NULL);
1.126 brouard 2225: for (*iter=1;;++(*iter)) {
1.187 brouard 2226: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2227: ibig=0;
2228: del=0.0;
1.157 brouard 2229: rlast_time=rcurr_time;
2230: /* (void) gettimeofday(&curr_time,&tzp); */
2231: rcurr_time = time(NULL);
2232: curr_time = *localtime(&rcurr_time);
2233: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2234: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2235: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2236: for (i=1;i<=n;i++) {
1.126 brouard 2237: fprintf(ficrespow," %.12lf", p[i]);
2238: }
1.239 brouard 2239: fprintf(ficrespow,"\n");fflush(ficrespow);
2240: printf("\n#model= 1 + age ");
2241: fprintf(ficlog,"\n#model= 1 + age ");
2242: if(nagesqr==1){
1.241 brouard 2243: printf(" + age*age ");
2244: fprintf(ficlog," + age*age ");
1.239 brouard 2245: }
2246: for(j=1;j <=ncovmodel-2;j++){
2247: if(Typevar[j]==0) {
2248: printf(" + V%d ",Tvar[j]);
2249: fprintf(ficlog," + V%d ",Tvar[j]);
2250: }else if(Typevar[j]==1) {
2251: printf(" + V%d*age ",Tvar[j]);
2252: fprintf(ficlog," + V%d*age ",Tvar[j]);
2253: }else if(Typevar[j]==2) {
2254: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2255: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2256: }
2257: }
1.126 brouard 2258: printf("\n");
1.239 brouard 2259: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2260: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2261: fprintf(ficlog,"\n");
1.239 brouard 2262: for(i=1,jk=1; i <=nlstate; i++){
2263: for(k=1; k <=(nlstate+ndeath); k++){
2264: if (k != i) {
2265: printf("%d%d ",i,k);
2266: fprintf(ficlog,"%d%d ",i,k);
2267: for(j=1; j <=ncovmodel; j++){
2268: printf("%12.7f ",p[jk]);
2269: fprintf(ficlog,"%12.7f ",p[jk]);
2270: jk++;
2271: }
2272: printf("\n");
2273: fprintf(ficlog,"\n");
2274: }
2275: }
2276: }
1.241 brouard 2277: if(*iter <=3 && *iter >1){
1.157 brouard 2278: tml = *localtime(&rcurr_time);
2279: strcpy(strcurr,asctime(&tml));
2280: rforecast_time=rcurr_time;
1.126 brouard 2281: itmp = strlen(strcurr);
2282: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2283: strcurr[itmp-1]='\0';
1.162 brouard 2284: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2285: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2286: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2287: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2288: forecast_time = *localtime(&rforecast_time);
2289: strcpy(strfor,asctime(&forecast_time));
2290: itmp = strlen(strfor);
2291: if(strfor[itmp-1]=='\n')
2292: strfor[itmp-1]='\0';
2293: 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);
2294: 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 2295: }
2296: }
1.187 brouard 2297: for (i=1;i<=n;i++) { /* For each direction i */
2298: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2299: fptt=(*fret);
2300: #ifdef DEBUG
1.203 brouard 2301: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2302: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2303: #endif
1.203 brouard 2304: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2305: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2306: #ifdef LINMINORIGINAL
1.188 brouard 2307: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2308: #else
2309: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2310: flatdir[i]=flat; /* Function is vanishing in that direction i */
2311: #endif
2312: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2313: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2314: /* because that direction will be replaced unless the gain del is small */
2315: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2316: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2317: /* with the new direction. */
2318: del=fabs(fptt-(*fret));
2319: ibig=i;
1.126 brouard 2320: }
2321: #ifdef DEBUG
2322: printf("%d %.12e",i,(*fret));
2323: fprintf(ficlog,"%d %.12e",i,(*fret));
2324: for (j=1;j<=n;j++) {
1.224 brouard 2325: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2326: printf(" x(%d)=%.12e",j,xit[j]);
2327: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2328: }
2329: for(j=1;j<=n;j++) {
1.225 brouard 2330: printf(" p(%d)=%.12e",j,p[j]);
2331: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2332: }
2333: printf("\n");
2334: fprintf(ficlog,"\n");
2335: #endif
1.187 brouard 2336: } /* end loop on each direction i */
2337: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2338: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2339: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2340: for(j=1;j<=n;j++) {
1.225 brouard 2341: if(flatdir[j] >0){
2342: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2343: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2344: }
2345: /* printf("\n"); */
2346: /* fprintf(ficlog,"\n"); */
2347: }
1.243 brouard 2348: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2349: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2350: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2351: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2352: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2353: /* decreased of more than 3.84 */
2354: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2355: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2356: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2357:
1.188 brouard 2358: /* Starting the program with initial values given by a former maximization will simply change */
2359: /* the scales of the directions and the directions, because the are reset to canonical directions */
2360: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2361: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2362: #ifdef DEBUG
2363: int k[2],l;
2364: k[0]=1;
2365: k[1]=-1;
2366: printf("Max: %.12e",(*func)(p));
2367: fprintf(ficlog,"Max: %.12e",(*func)(p));
2368: for (j=1;j<=n;j++) {
2369: printf(" %.12e",p[j]);
2370: fprintf(ficlog," %.12e",p[j]);
2371: }
2372: printf("\n");
2373: fprintf(ficlog,"\n");
2374: for(l=0;l<=1;l++) {
2375: for (j=1;j<=n;j++) {
2376: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2377: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2378: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2379: }
2380: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2381: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2382: }
2383: #endif
2384:
1.224 brouard 2385: #ifdef LINMINORIGINAL
2386: #else
2387: free_ivector(flatdir,1,n);
2388: #endif
1.126 brouard 2389: free_vector(xit,1,n);
2390: free_vector(xits,1,n);
2391: free_vector(ptt,1,n);
2392: free_vector(pt,1,n);
2393: return;
1.192 brouard 2394: } /* enough precision */
1.240 brouard 2395: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2396: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2397: ptt[j]=2.0*p[j]-pt[j];
2398: xit[j]=p[j]-pt[j];
2399: pt[j]=p[j];
2400: }
1.181 brouard 2401: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2402: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2403: if (*iter <=4) {
1.225 brouard 2404: #else
2405: #endif
1.224 brouard 2406: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2407: #else
1.161 brouard 2408: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2409: #endif
1.162 brouard 2410: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2411: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2412: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2413: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2414: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2415: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2416: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2417: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2418: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2419: /* Even if f3 <f1, directest can be negative and t >0 */
2420: /* mu² and del² are equal when f3=f1 */
2421: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2422: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2423: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2424: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2425: #ifdef NRCORIGINAL
2426: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2427: #else
2428: 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 2429: t= t- del*SQR(fp-fptt);
1.183 brouard 2430: #endif
1.202 brouard 2431: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2432: #ifdef DEBUG
1.181 brouard 2433: 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);
2434: 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 2435: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2436: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2437: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2438: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2439: 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);
2440: 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);
2441: #endif
1.183 brouard 2442: #ifdef POWELLORIGINAL
2443: if (t < 0.0) { /* Then we use it for new direction */
2444: #else
1.182 brouard 2445: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2446: 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 2447: 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 2448: 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 2449: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2450: }
1.181 brouard 2451: if (directest < 0.0) { /* Then we use it for new direction */
2452: #endif
1.191 brouard 2453: #ifdef DEBUGLINMIN
1.234 brouard 2454: printf("Before linmin in direction P%d-P0\n",n);
2455: for (j=1;j<=n;j++) {
2456: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2457: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2458: if(j % ncovmodel == 0){
2459: printf("\n");
2460: fprintf(ficlog,"\n");
2461: }
2462: }
1.224 brouard 2463: #endif
2464: #ifdef LINMINORIGINAL
1.234 brouard 2465: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2466: #else
1.234 brouard 2467: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2468: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2469: #endif
1.234 brouard 2470:
1.191 brouard 2471: #ifdef DEBUGLINMIN
1.234 brouard 2472: for (j=1;j<=n;j++) {
2473: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2474: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2475: if(j % ncovmodel == 0){
2476: printf("\n");
2477: fprintf(ficlog,"\n");
2478: }
2479: }
1.224 brouard 2480: #endif
1.234 brouard 2481: for (j=1;j<=n;j++) {
2482: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2483: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2484: }
1.224 brouard 2485: #ifdef LINMINORIGINAL
2486: #else
1.234 brouard 2487: for (j=1, flatd=0;j<=n;j++) {
2488: if(flatdir[j]>0)
2489: flatd++;
2490: }
2491: if(flatd >0){
1.255 brouard 2492: printf("%d flat directions: ",flatd);
2493: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2494: for (j=1;j<=n;j++) {
2495: if(flatdir[j]>0){
2496: printf("%d ",j);
2497: fprintf(ficlog,"%d ",j);
2498: }
2499: }
2500: printf("\n");
2501: fprintf(ficlog,"\n");
2502: }
1.191 brouard 2503: #endif
1.234 brouard 2504: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2505: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2506:
1.126 brouard 2507: #ifdef DEBUG
1.234 brouard 2508: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2509: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2510: for(j=1;j<=n;j++){
2511: printf(" %lf",xit[j]);
2512: fprintf(ficlog," %lf",xit[j]);
2513: }
2514: printf("\n");
2515: fprintf(ficlog,"\n");
1.126 brouard 2516: #endif
1.192 brouard 2517: } /* end of t or directest negative */
1.224 brouard 2518: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2519: #else
1.234 brouard 2520: } /* end if (fptt < fp) */
1.192 brouard 2521: #endif
1.225 brouard 2522: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2523: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2524: #else
1.224 brouard 2525: #endif
1.234 brouard 2526: } /* loop iteration */
1.126 brouard 2527: }
1.234 brouard 2528:
1.126 brouard 2529: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2530:
1.235 brouard 2531: 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 2532: {
1.279 brouard 2533: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2534: * (and selected quantitative values in nres)
2535: * by left multiplying the unit
2536: * matrix by transitions matrix until convergence is reached with precision ftolpl
2537: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2538: * Wx is row vector: population in state 1, population in state 2, population dead
2539: * or prevalence in state 1, prevalence in state 2, 0
2540: * newm is the matrix after multiplications, its rows are identical at a factor.
2541: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2542: * Output is prlim.
2543: * Initial matrix pimij
2544: */
1.206 brouard 2545: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2546: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2547: /* 0, 0 , 1} */
2548: /*
2549: * and after some iteration: */
2550: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2551: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2552: /* 0, 0 , 1} */
2553: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2554: /* {0.51571254859325999, 0.4842874514067399, */
2555: /* 0.51326036147820708, 0.48673963852179264} */
2556: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2557:
1.126 brouard 2558: int i, ii,j,k;
1.209 brouard 2559: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2560: /* double **matprod2(); */ /* test */
1.218 brouard 2561: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2562: double **newm;
1.209 brouard 2563: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2564: int ncvloop=0;
1.169 brouard 2565:
1.209 brouard 2566: min=vector(1,nlstate);
2567: max=vector(1,nlstate);
2568: meandiff=vector(1,nlstate);
2569:
1.218 brouard 2570: /* Starting with matrix unity */
1.126 brouard 2571: for (ii=1;ii<=nlstate+ndeath;ii++)
2572: for (j=1;j<=nlstate+ndeath;j++){
2573: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2574: }
1.169 brouard 2575:
2576: cov[1]=1.;
2577:
2578: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2579: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2580: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2581: ncvloop++;
1.126 brouard 2582: newm=savm;
2583: /* Covariates have to be included here again */
1.138 brouard 2584: cov[2]=agefin;
1.187 brouard 2585: if(nagesqr==1)
2586: cov[3]= agefin*agefin;;
1.234 brouard 2587: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2588: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2589: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2590: /* 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 2591: }
2592: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2593: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2594: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2595: /* 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 2596: }
1.237 brouard 2597: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2598: if(Dummy[Tvar[Tage[k]]]){
2599: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2600: } else{
1.235 brouard 2601: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2602: }
1.235 brouard 2603: /* 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 2604: }
1.237 brouard 2605: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2606: /* 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 2607: if(Dummy[Tvard[k][1]==0]){
2608: if(Dummy[Tvard[k][2]==0]){
2609: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2610: }else{
2611: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2612: }
2613: }else{
2614: if(Dummy[Tvard[k][2]==0]){
2615: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2616: }else{
2617: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2618: }
2619: }
1.234 brouard 2620: }
1.138 brouard 2621: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2622: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2623: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2624: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2625: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2626: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2627: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2628:
1.126 brouard 2629: savm=oldm;
2630: oldm=newm;
1.209 brouard 2631:
2632: for(j=1; j<=nlstate; j++){
2633: max[j]=0.;
2634: min[j]=1.;
2635: }
2636: for(i=1;i<=nlstate;i++){
2637: sumnew=0;
2638: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2639: for(j=1; j<=nlstate; j++){
2640: prlim[i][j]= newm[i][j]/(1-sumnew);
2641: max[j]=FMAX(max[j],prlim[i][j]);
2642: min[j]=FMIN(min[j],prlim[i][j]);
2643: }
2644: }
2645:
1.126 brouard 2646: maxmax=0.;
1.209 brouard 2647: for(j=1; j<=nlstate; j++){
2648: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2649: maxmax=FMAX(maxmax,meandiff[j]);
2650: /* 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 2651: } /* j loop */
1.203 brouard 2652: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2653: /* 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 2654: if(maxmax < ftolpl){
1.209 brouard 2655: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2656: free_vector(min,1,nlstate);
2657: free_vector(max,1,nlstate);
2658: free_vector(meandiff,1,nlstate);
1.126 brouard 2659: return prlim;
2660: }
1.169 brouard 2661: } /* age loop */
1.208 brouard 2662: /* After some age loop it doesn't converge */
1.209 brouard 2663: 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 2664: 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 2665: /* 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); */
2666: free_vector(min,1,nlstate);
2667: free_vector(max,1,nlstate);
2668: free_vector(meandiff,1,nlstate);
1.208 brouard 2669:
1.169 brouard 2670: return prlim; /* should not reach here */
1.126 brouard 2671: }
2672:
1.217 brouard 2673:
2674: /**** Back Prevalence limit (stable or period prevalence) ****************/
2675:
1.218 brouard 2676: /* 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) */
2677: /* 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 2678: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2679: {
1.264 brouard 2680: /* 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 2681: matrix by transitions matrix until convergence is reached with precision ftolpl */
2682: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2683: /* Wx is row vector: population in state 1, population in state 2, population dead */
2684: /* or prevalence in state 1, prevalence in state 2, 0 */
2685: /* newm is the matrix after multiplications, its rows are identical at a factor */
2686: /* Initial matrix pimij */
2687: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2688: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2689: /* 0, 0 , 1} */
2690: /*
2691: * and after some iteration: */
2692: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2693: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2694: /* 0, 0 , 1} */
2695: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2696: /* {0.51571254859325999, 0.4842874514067399, */
2697: /* 0.51326036147820708, 0.48673963852179264} */
2698: /* If we start from prlim again, prlim tends to a constant matrix */
2699:
2700: int i, ii,j,k;
1.247 brouard 2701: int first=0;
1.217 brouard 2702: double *min, *max, *meandiff, maxmax,sumnew=0.;
2703: /* double **matprod2(); */ /* test */
2704: double **out, cov[NCOVMAX+1], **bmij();
2705: double **newm;
1.218 brouard 2706: double **dnewm, **doldm, **dsavm; /* for use */
2707: double **oldm, **savm; /* for use */
2708:
1.217 brouard 2709: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2710: int ncvloop=0;
2711:
2712: min=vector(1,nlstate);
2713: max=vector(1,nlstate);
2714: meandiff=vector(1,nlstate);
2715:
1.266 brouard 2716: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2717: oldm=oldms; savm=savms;
2718:
2719: /* Starting with matrix unity */
2720: for (ii=1;ii<=nlstate+ndeath;ii++)
2721: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2722: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2723: }
2724:
2725: cov[1]=1.;
2726:
2727: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2728: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2729: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2730: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2731: ncvloop++;
1.218 brouard 2732: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2733: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2734: /* Covariates have to be included here again */
2735: cov[2]=agefin;
2736: if(nagesqr==1)
2737: cov[3]= agefin*agefin;;
1.242 brouard 2738: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2739: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2740: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2741: /* 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 2742: }
2743: /* for (k=1; k<=cptcovn;k++) { */
2744: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2745: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2746: /* /\* 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])]); *\/ */
2747: /* } */
2748: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2749: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2750: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2751: /* 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]); */
2752: }
2753: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2754: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2755: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2756: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2757: for (k=1; k<=cptcovage;k++){ /* For product with age */
2758: if(Dummy[Tvar[Tage[k]]]){
2759: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2760: } else{
2761: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2762: }
2763: /* 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]); */
2764: }
2765: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2766: /* 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]); */
2767: if(Dummy[Tvard[k][1]==0]){
2768: if(Dummy[Tvard[k][2]==0]){
2769: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2770: }else{
2771: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2772: }
2773: }else{
2774: if(Dummy[Tvard[k][2]==0]){
2775: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2776: }else{
2777: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2778: }
2779: }
1.217 brouard 2780: }
2781:
2782: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2783: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2784: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2785: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2786: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2787: /* ij should be linked to the correct index of cov */
2788: /* age and covariate values ij are in 'cov', but we need to pass
2789: * ij for the observed prevalence at age and status and covariate
2790: * number: prevacurrent[(int)agefin][ii][ij]
2791: */
2792: /* 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 *\/ */
2793: /* 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 *\/ */
2794: 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 2795: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2796: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2797: /* for(i=1; i<=nlstate+ndeath; i++) { */
2798: /* printf("%d newm= ",i); */
2799: /* for(j=1;j<=nlstate+ndeath;j++) { */
2800: /* printf("%f ",newm[i][j]); */
2801: /* } */
2802: /* printf("oldm * "); */
2803: /* for(j=1;j<=nlstate+ndeath;j++) { */
2804: /* printf("%f ",oldm[i][j]); */
2805: /* } */
1.268 brouard 2806: /* printf(" bmmij "); */
1.266 brouard 2807: /* for(j=1;j<=nlstate+ndeath;j++) { */
2808: /* printf("%f ",pmmij[i][j]); */
2809: /* } */
2810: /* printf("\n"); */
2811: /* } */
2812: /* } */
1.217 brouard 2813: savm=oldm;
2814: oldm=newm;
1.266 brouard 2815:
1.217 brouard 2816: for(j=1; j<=nlstate; j++){
2817: max[j]=0.;
2818: min[j]=1.;
2819: }
2820: for(j=1; j<=nlstate; j++){
2821: for(i=1;i<=nlstate;i++){
1.234 brouard 2822: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2823: bprlim[i][j]= newm[i][j];
2824: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2825: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2826: }
2827: }
1.218 brouard 2828:
1.217 brouard 2829: maxmax=0.;
2830: for(i=1; i<=nlstate; i++){
2831: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2832: maxmax=FMAX(maxmax,meandiff[i]);
2833: /* 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 2834: } /* i loop */
1.217 brouard 2835: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2836: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2837: if(maxmax < ftolpl){
1.220 brouard 2838: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2839: free_vector(min,1,nlstate);
2840: free_vector(max,1,nlstate);
2841: free_vector(meandiff,1,nlstate);
2842: return bprlim;
2843: }
2844: } /* age loop */
2845: /* After some age loop it doesn't converge */
1.247 brouard 2846: if(first){
2847: first=1;
2848: 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\
2849: 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);
2850: }
2851: 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 2852: 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);
2853: /* 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); */
2854: free_vector(min,1,nlstate);
2855: free_vector(max,1,nlstate);
2856: free_vector(meandiff,1,nlstate);
2857:
2858: return bprlim; /* should not reach here */
2859: }
2860:
1.126 brouard 2861: /*************** transition probabilities ***************/
2862:
2863: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2864: {
1.138 brouard 2865: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2866: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2867: model to the ncovmodel covariates (including constant and age).
2868: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2869: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2870: ncth covariate in the global vector x is given by the formula:
2871: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2872: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2873: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2874: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2875: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2876: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2877: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2878: */
2879: double s1, lnpijopii;
1.126 brouard 2880: /*double t34;*/
1.164 brouard 2881: int i,j, nc, ii, jj;
1.126 brouard 2882:
1.223 brouard 2883: for(i=1; i<= nlstate; i++){
2884: for(j=1; j<i;j++){
2885: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2886: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2887: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2888: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2889: }
2890: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2891: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2892: }
2893: for(j=i+1; j<=nlstate+ndeath;j++){
2894: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2895: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2896: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2897: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2898: }
2899: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2900: }
2901: }
1.218 brouard 2902:
1.223 brouard 2903: for(i=1; i<= nlstate; i++){
2904: s1=0;
2905: for(j=1; j<i; j++){
2906: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2907: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2908: }
2909: for(j=i+1; j<=nlstate+ndeath; j++){
2910: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2911: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2912: }
2913: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2914: ps[i][i]=1./(s1+1.);
2915: /* Computing other pijs */
2916: for(j=1; j<i; j++)
2917: ps[i][j]= exp(ps[i][j])*ps[i][i];
2918: for(j=i+1; j<=nlstate+ndeath; j++)
2919: ps[i][j]= exp(ps[i][j])*ps[i][i];
2920: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2921: } /* end i */
1.218 brouard 2922:
1.223 brouard 2923: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2924: for(jj=1; jj<= nlstate+ndeath; jj++){
2925: ps[ii][jj]=0;
2926: ps[ii][ii]=1;
2927: }
2928: }
1.218 brouard 2929:
2930:
1.223 brouard 2931: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2932: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2933: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2934: /* } */
2935: /* printf("\n "); */
2936: /* } */
2937: /* printf("\n ");printf("%lf ",cov[2]);*/
2938: /*
2939: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2940: goto end;*/
1.266 brouard 2941: return ps; /* Pointer is unchanged since its call */
1.126 brouard 2942: }
2943:
1.218 brouard 2944: /*************** backward transition probabilities ***************/
2945:
2946: /* 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 ) */
2947: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2948: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2949: {
1.266 brouard 2950: /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
2951: * 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 2952: */
1.218 brouard 2953: int i, ii, j,k;
1.222 brouard 2954:
2955: double **out, **pmij();
2956: double sumnew=0.;
1.218 brouard 2957: double agefin;
1.268 brouard 2958: 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 2959: double **dnewm, **dsavm, **doldm;
2960: double **bbmij;
2961:
1.218 brouard 2962: doldm=ddoldms; /* global pointers */
1.222 brouard 2963: dnewm=ddnewms;
2964: dsavm=ddsavms;
2965:
2966: agefin=cov[2];
1.268 brouard 2967: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 2968: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 2969: the observed prevalence (with this covariate ij) at beginning of transition */
2970: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 2971:
2972: /* P_x */
1.266 brouard 2973: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 2974: /* outputs pmmij which is a stochastic matrix in row */
2975:
2976: /* Diag(w_x) */
2977: /* Problem with prevacurrent which can be zero */
2978: sumnew=0.;
1.269 brouard 2979: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 2980: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.269 brouard 2981: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 2982: sumnew+=prevacurrent[(int)agefin][ii][ij];
2983: }
2984: if(sumnew >0.01){ /* At least some value in the prevalence */
2985: for (ii=1;ii<=nlstate+ndeath;ii++){
2986: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 2987: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 2988: }
2989: }else{
2990: for (ii=1;ii<=nlstate+ndeath;ii++){
2991: for (j=1;j<=nlstate+ndeath;j++)
2992: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
2993: }
2994: /* if(sumnew <0.9){ */
2995: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
2996: /* } */
2997: }
2998: k3=0.0; /* We put the last diagonal to 0 */
2999: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
3000: doldm[ii][ii]= k3;
3001: }
3002: /* End doldm, At the end doldm is diag[(w_i)] */
3003:
3004: /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
3005: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
3006:
3007: /* Diag(Sum_i w^i_x p^ij_x */
3008: /* 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 3009: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3010: sumnew=0.;
1.222 brouard 3011: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3012: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3013: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3014: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3015: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3016: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3017: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3018: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3019: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3020: /* }else */
1.268 brouard 3021: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3022: } /*End ii */
3023: } /* 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 */
3024:
3025: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
3026: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3027: /* end bmij */
1.266 brouard 3028: return ps; /*pointer is unchanged */
1.218 brouard 3029: }
1.217 brouard 3030: /*************** transition probabilities ***************/
3031:
1.218 brouard 3032: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3033: {
3034: /* According to parameters values stored in x and the covariate's values stored in cov,
3035: computes the probability to be observed in state j being in state i by appying the
3036: model to the ncovmodel covariates (including constant and age).
3037: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3038: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3039: ncth covariate in the global vector x is given by the formula:
3040: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3041: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3042: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3043: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3044: Outputs ps[i][j] the probability to be observed in j being in j according to
3045: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3046: */
3047: double s1, lnpijopii;
3048: /*double t34;*/
3049: int i,j, nc, ii, jj;
3050:
1.234 brouard 3051: for(i=1; i<= nlstate; i++){
3052: for(j=1; j<i;j++){
3053: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3054: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3055: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3056: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3057: }
3058: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3059: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3060: }
3061: for(j=i+1; j<=nlstate+ndeath;j++){
3062: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3063: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3064: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3065: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3066: }
3067: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3068: }
3069: }
3070:
3071: for(i=1; i<= nlstate; i++){
3072: s1=0;
3073: for(j=1; j<i; j++){
3074: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3075: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3076: }
3077: for(j=i+1; j<=nlstate+ndeath; j++){
3078: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3079: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3080: }
3081: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3082: ps[i][i]=1./(s1+1.);
3083: /* Computing other pijs */
3084: for(j=1; j<i; j++)
3085: ps[i][j]= exp(ps[i][j])*ps[i][i];
3086: for(j=i+1; j<=nlstate+ndeath; j++)
3087: ps[i][j]= exp(ps[i][j])*ps[i][i];
3088: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3089: } /* end i */
3090:
3091: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3092: for(jj=1; jj<= nlstate+ndeath; jj++){
3093: ps[ii][jj]=0;
3094: ps[ii][ii]=1;
3095: }
3096: }
3097: /* Added for backcast */ /* Transposed matrix too */
3098: for(jj=1; jj<= nlstate+ndeath; jj++){
3099: s1=0.;
3100: for(ii=1; ii<= nlstate+ndeath; ii++){
3101: s1+=ps[ii][jj];
3102: }
3103: for(ii=1; ii<= nlstate; ii++){
3104: ps[ii][jj]=ps[ii][jj]/s1;
3105: }
3106: }
3107: /* Transposition */
3108: for(jj=1; jj<= nlstate+ndeath; jj++){
3109: for(ii=jj; ii<= nlstate+ndeath; ii++){
3110: s1=ps[ii][jj];
3111: ps[ii][jj]=ps[jj][ii];
3112: ps[jj][ii]=s1;
3113: }
3114: }
3115: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3116: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3117: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3118: /* } */
3119: /* printf("\n "); */
3120: /* } */
3121: /* printf("\n ");printf("%lf ",cov[2]);*/
3122: /*
3123: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3124: goto end;*/
3125: return ps;
1.217 brouard 3126: }
3127:
3128:
1.126 brouard 3129: /**************** Product of 2 matrices ******************/
3130:
1.145 brouard 3131: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3132: {
3133: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3134: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3135: /* in, b, out are matrice of pointers which should have been initialized
3136: before: only the contents of out is modified. The function returns
3137: a pointer to pointers identical to out */
1.145 brouard 3138: int i, j, k;
1.126 brouard 3139: for(i=nrl; i<= nrh; i++)
1.145 brouard 3140: for(k=ncolol; k<=ncoloh; k++){
3141: out[i][k]=0.;
3142: for(j=ncl; j<=nch; j++)
3143: out[i][k] +=in[i][j]*b[j][k];
3144: }
1.126 brouard 3145: return out;
3146: }
3147:
3148:
3149: /************* Higher Matrix Product ***************/
3150:
1.235 brouard 3151: 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 3152: {
1.218 brouard 3153: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3154: 'nhstepm*hstepm*stepm' months (i.e. until
3155: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3156: nhstepm*hstepm matrices.
3157: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3158: (typically every 2 years instead of every month which is too big
3159: for the memory).
3160: Model is determined by parameters x and covariates have to be
3161: included manually here.
3162:
3163: */
3164:
3165: int i, j, d, h, k;
1.131 brouard 3166: double **out, cov[NCOVMAX+1];
1.126 brouard 3167: double **newm;
1.187 brouard 3168: double agexact;
1.214 brouard 3169: double agebegin, ageend;
1.126 brouard 3170:
3171: /* Hstepm could be zero and should return the unit matrix */
3172: for (i=1;i<=nlstate+ndeath;i++)
3173: for (j=1;j<=nlstate+ndeath;j++){
3174: oldm[i][j]=(i==j ? 1.0 : 0.0);
3175: po[i][j][0]=(i==j ? 1.0 : 0.0);
3176: }
3177: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3178: for(h=1; h <=nhstepm; h++){
3179: for(d=1; d <=hstepm; d++){
3180: newm=savm;
3181: /* Covariates have to be included here again */
3182: cov[1]=1.;
1.214 brouard 3183: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3184: cov[2]=agexact;
3185: if(nagesqr==1)
1.227 brouard 3186: cov[3]= agexact*agexact;
1.235 brouard 3187: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3188: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3189: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3190: /* 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)); */
3191: }
3192: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3193: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3194: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3195: /* 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]); */
3196: }
3197: for (k=1; k<=cptcovage;k++){
3198: if(Dummy[Tvar[Tage[k]]]){
3199: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3200: } else{
3201: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3202: }
3203: /* 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]); */
3204: }
3205: for (k=1; k<=cptcovprod;k++){ /* */
3206: /* 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]); */
3207: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3208: }
3209: /* for (k=1; k<=cptcovn;k++) */
3210: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3211: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3212: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3213: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3214: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3215:
3216:
1.126 brouard 3217: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3218: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3219: /* right multiplication of oldm by the current matrix */
1.126 brouard 3220: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3221: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3222: /* if((int)age == 70){ */
3223: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3224: /* for(i=1; i<=nlstate+ndeath; i++) { */
3225: /* printf("%d pmmij ",i); */
3226: /* for(j=1;j<=nlstate+ndeath;j++) { */
3227: /* printf("%f ",pmmij[i][j]); */
3228: /* } */
3229: /* printf(" oldm "); */
3230: /* for(j=1;j<=nlstate+ndeath;j++) { */
3231: /* printf("%f ",oldm[i][j]); */
3232: /* } */
3233: /* printf("\n"); */
3234: /* } */
3235: /* } */
1.126 brouard 3236: savm=oldm;
3237: oldm=newm;
3238: }
3239: for(i=1; i<=nlstate+ndeath; i++)
3240: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3241: po[i][j][h]=newm[i][j];
3242: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3243: }
1.128 brouard 3244: /*printf("h=%d ",h);*/
1.126 brouard 3245: } /* end h */
1.267 brouard 3246: /* printf("\n H=%d \n",h); */
1.126 brouard 3247: return po;
3248: }
3249:
1.217 brouard 3250: /************* Higher Back Matrix Product ***************/
1.218 brouard 3251: /* 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 3252: 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 3253: {
1.266 brouard 3254: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3255: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3256: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3257: nhstepm*hstepm matrices.
3258: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3259: (typically every 2 years instead of every month which is too big
1.217 brouard 3260: for the memory).
1.218 brouard 3261: Model is determined by parameters x and covariates have to be
1.266 brouard 3262: included manually here. Then we use a call to bmij(x and cov)
3263: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3264: */
1.217 brouard 3265:
3266: int i, j, d, h, k;
1.266 brouard 3267: double **out, cov[NCOVMAX+1], **bmij();
3268: double **newm, ***newmm;
1.217 brouard 3269: double agexact;
3270: double agebegin, ageend;
1.222 brouard 3271: double **oldm, **savm;
1.217 brouard 3272:
1.266 brouard 3273: newmm=po; /* To be saved */
3274: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3275: /* Hstepm could be zero and should return the unit matrix */
3276: for (i=1;i<=nlstate+ndeath;i++)
3277: for (j=1;j<=nlstate+ndeath;j++){
3278: oldm[i][j]=(i==j ? 1.0 : 0.0);
3279: po[i][j][0]=(i==j ? 1.0 : 0.0);
3280: }
3281: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3282: for(h=1; h <=nhstepm; h++){
3283: for(d=1; d <=hstepm; d++){
3284: newm=savm;
3285: /* Covariates have to be included here again */
3286: cov[1]=1.;
1.271 brouard 3287: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3288: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3289: cov[2]=agexact;
3290: if(nagesqr==1)
1.222 brouard 3291: cov[3]= agexact*agexact;
1.266 brouard 3292: for (k=1; k<=cptcovn;k++){
3293: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3294: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3295: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3296: /* 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)); */
3297: }
1.267 brouard 3298: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3299: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3300: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3301: /* 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]); */
3302: }
3303: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3304: if(Dummy[Tvar[Tage[k]]]){
3305: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3306: } else{
3307: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3308: }
3309: /* 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]); */
3310: }
3311: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3312: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3313: }
1.217 brouard 3314: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3315: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3316:
1.218 brouard 3317: /* Careful transposed matrix */
1.266 brouard 3318: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3319: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3320: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3321: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3322: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3323: /* if((int)age == 70){ */
3324: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3325: /* for(i=1; i<=nlstate+ndeath; i++) { */
3326: /* printf("%d pmmij ",i); */
3327: /* for(j=1;j<=nlstate+ndeath;j++) { */
3328: /* printf("%f ",pmmij[i][j]); */
3329: /* } */
3330: /* printf(" oldm "); */
3331: /* for(j=1;j<=nlstate+ndeath;j++) { */
3332: /* printf("%f ",oldm[i][j]); */
3333: /* } */
3334: /* printf("\n"); */
3335: /* } */
3336: /* } */
3337: savm=oldm;
3338: oldm=newm;
3339: }
3340: for(i=1; i<=nlstate+ndeath; i++)
3341: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3342: po[i][j][h]=newm[i][j];
1.268 brouard 3343: /* if(h==nhstepm) */
3344: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3345: }
1.268 brouard 3346: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3347: } /* end h */
1.268 brouard 3348: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3349: return po;
3350: }
3351:
3352:
1.162 brouard 3353: #ifdef NLOPT
3354: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3355: double fret;
3356: double *xt;
3357: int j;
3358: myfunc_data *d2 = (myfunc_data *) pd;
3359: /* xt = (p1-1); */
3360: xt=vector(1,n);
3361: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3362:
3363: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3364: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3365: printf("Function = %.12lf ",fret);
3366: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3367: printf("\n");
3368: free_vector(xt,1,n);
3369: return fret;
3370: }
3371: #endif
1.126 brouard 3372:
3373: /*************** log-likelihood *************/
3374: double func( double *x)
3375: {
1.226 brouard 3376: int i, ii, j, k, mi, d, kk;
3377: int ioffset=0;
3378: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3379: double **out;
3380: double lli; /* Individual log likelihood */
3381: int s1, s2;
1.228 brouard 3382: 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 3383: double bbh, survp;
3384: long ipmx;
3385: double agexact;
3386: /*extern weight */
3387: /* We are differentiating ll according to initial status */
3388: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3389: /*for(i=1;i<imx;i++)
3390: printf(" %d\n",s[4][i]);
3391: */
1.162 brouard 3392:
1.226 brouard 3393: ++countcallfunc;
1.162 brouard 3394:
1.226 brouard 3395: cov[1]=1.;
1.126 brouard 3396:
1.226 brouard 3397: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3398: ioffset=0;
1.226 brouard 3399: if(mle==1){
3400: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3401: /* Computes the values of the ncovmodel covariates of the model
3402: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3403: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3404: to be observed in j being in i according to the model.
3405: */
1.243 brouard 3406: ioffset=2+nagesqr ;
1.233 brouard 3407: /* Fixed */
1.234 brouard 3408: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3409: 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)*/
3410: }
1.226 brouard 3411: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3412: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3413: has been calculated etc */
3414: /* For an individual i, wav[i] gives the number of effective waves */
3415: /* We compute the contribution to Likelihood of each effective transition
3416: mw[mi][i] is real wave of the mi th effectve wave */
3417: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3418: s2=s[mw[mi+1][i]][i];
3419: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3420: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3421: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3422: */
3423: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3424: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3425: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3426: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3427: }
3428: for (ii=1;ii<=nlstate+ndeath;ii++)
3429: for (j=1;j<=nlstate+ndeath;j++){
3430: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3431: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3432: }
3433: for(d=0; d<dh[mi][i]; d++){
3434: newm=savm;
3435: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3436: cov[2]=agexact;
3437: if(nagesqr==1)
3438: cov[3]= agexact*agexact; /* Should be changed here */
3439: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3440: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3441: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3442: else
3443: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3444: }
3445: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3446: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3447: savm=oldm;
3448: oldm=newm;
3449: } /* end mult */
3450:
3451: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3452: /* But now since version 0.9 we anticipate for bias at large stepm.
3453: * If stepm is larger than one month (smallest stepm) and if the exact delay
3454: * (in months) between two waves is not a multiple of stepm, we rounded to
3455: * the nearest (and in case of equal distance, to the lowest) interval but now
3456: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3457: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3458: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3459: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3460: * -stepm/2 to stepm/2 .
3461: * For stepm=1 the results are the same as for previous versions of Imach.
3462: * For stepm > 1 the results are less biased than in previous versions.
3463: */
1.234 brouard 3464: s1=s[mw[mi][i]][i];
3465: s2=s[mw[mi+1][i]][i];
3466: bbh=(double)bh[mi][i]/(double)stepm;
3467: /* bias bh is positive if real duration
3468: * is higher than the multiple of stepm and negative otherwise.
3469: */
3470: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3471: if( s2 > nlstate){
3472: /* i.e. if s2 is a death state and if the date of death is known
3473: then the contribution to the likelihood is the probability to
3474: die between last step unit time and current step unit time,
3475: which is also equal to probability to die before dh
3476: minus probability to die before dh-stepm .
3477: In version up to 0.92 likelihood was computed
3478: as if date of death was unknown. Death was treated as any other
3479: health state: the date of the interview describes the actual state
3480: and not the date of a change in health state. The former idea was
3481: to consider that at each interview the state was recorded
3482: (healthy, disable or death) and IMaCh was corrected; but when we
3483: introduced the exact date of death then we should have modified
3484: the contribution of an exact death to the likelihood. This new
3485: contribution is smaller and very dependent of the step unit
3486: stepm. It is no more the probability to die between last interview
3487: and month of death but the probability to survive from last
3488: interview up to one month before death multiplied by the
3489: probability to die within a month. Thanks to Chris
3490: Jackson for correcting this bug. Former versions increased
3491: mortality artificially. The bad side is that we add another loop
3492: which slows down the processing. The difference can be up to 10%
3493: lower mortality.
3494: */
3495: /* If, at the beginning of the maximization mostly, the
3496: cumulative probability or probability to be dead is
3497: constant (ie = 1) over time d, the difference is equal to
3498: 0. out[s1][3] = savm[s1][3]: probability, being at state
3499: s1 at precedent wave, to be dead a month before current
3500: wave is equal to probability, being at state s1 at
3501: precedent wave, to be dead at mont of the current
3502: wave. Then the observed probability (that this person died)
3503: is null according to current estimated parameter. In fact,
3504: it should be very low but not zero otherwise the log go to
3505: infinity.
3506: */
1.183 brouard 3507: /* #ifdef INFINITYORIGINAL */
3508: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3509: /* #else */
3510: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3511: /* lli=log(mytinydouble); */
3512: /* else */
3513: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3514: /* #endif */
1.226 brouard 3515: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3516:
1.226 brouard 3517: } else if ( s2==-1 ) { /* alive */
3518: for (j=1,survp=0. ; j<=nlstate; j++)
3519: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3520: /*survp += out[s1][j]; */
3521: lli= log(survp);
3522: }
3523: else if (s2==-4) {
3524: for (j=3,survp=0. ; j<=nlstate; j++)
3525: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3526: lli= log(survp);
3527: }
3528: else if (s2==-5) {
3529: for (j=1,survp=0. ; j<=2; j++)
3530: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3531: lli= log(survp);
3532: }
3533: else{
3534: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3535: /* 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 */
3536: }
3537: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3538: /*if(lli ==000.0)*/
3539: /*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); */
3540: ipmx +=1;
3541: sw += weight[i];
3542: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3543: /* if (lli < log(mytinydouble)){ */
3544: /* 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); */
3545: /* 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]); */
3546: /* } */
3547: } /* end of wave */
3548: } /* end of individual */
3549: } else if(mle==2){
3550: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3551: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3552: for(mi=1; mi<= wav[i]-1; mi++){
3553: for (ii=1;ii<=nlstate+ndeath;ii++)
3554: for (j=1;j<=nlstate+ndeath;j++){
3555: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3556: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3557: }
3558: for(d=0; d<=dh[mi][i]; d++){
3559: newm=savm;
3560: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3561: cov[2]=agexact;
3562: if(nagesqr==1)
3563: cov[3]= agexact*agexact;
3564: for (kk=1; kk<=cptcovage;kk++) {
3565: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3566: }
3567: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3568: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3569: savm=oldm;
3570: oldm=newm;
3571: } /* end mult */
3572:
3573: s1=s[mw[mi][i]][i];
3574: s2=s[mw[mi+1][i]][i];
3575: bbh=(double)bh[mi][i]/(double)stepm;
3576: 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 */
3577: ipmx +=1;
3578: sw += weight[i];
3579: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3580: } /* end of wave */
3581: } /* end of individual */
3582: } else if(mle==3){ /* exponential inter-extrapolation */
3583: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3584: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3585: for(mi=1; mi<= wav[i]-1; mi++){
3586: for (ii=1;ii<=nlstate+ndeath;ii++)
3587: for (j=1;j<=nlstate+ndeath;j++){
3588: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3589: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3590: }
3591: for(d=0; d<dh[mi][i]; d++){
3592: newm=savm;
3593: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3594: cov[2]=agexact;
3595: if(nagesqr==1)
3596: cov[3]= agexact*agexact;
3597: for (kk=1; kk<=cptcovage;kk++) {
3598: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3599: }
3600: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3601: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3602: savm=oldm;
3603: oldm=newm;
3604: } /* end mult */
3605:
3606: s1=s[mw[mi][i]][i];
3607: s2=s[mw[mi+1][i]][i];
3608: bbh=(double)bh[mi][i]/(double)stepm;
3609: 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 */
3610: ipmx +=1;
3611: sw += weight[i];
3612: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3613: } /* end of wave */
3614: } /* end of individual */
3615: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3616: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3617: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3618: for(mi=1; mi<= wav[i]-1; mi++){
3619: for (ii=1;ii<=nlstate+ndeath;ii++)
3620: for (j=1;j<=nlstate+ndeath;j++){
3621: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3622: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3623: }
3624: for(d=0; d<dh[mi][i]; d++){
3625: newm=savm;
3626: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3627: cov[2]=agexact;
3628: if(nagesqr==1)
3629: cov[3]= agexact*agexact;
3630: for (kk=1; kk<=cptcovage;kk++) {
3631: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3632: }
1.126 brouard 3633:
1.226 brouard 3634: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3635: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3636: savm=oldm;
3637: oldm=newm;
3638: } /* end mult */
3639:
3640: s1=s[mw[mi][i]][i];
3641: s2=s[mw[mi+1][i]][i];
3642: if( s2 > nlstate){
3643: lli=log(out[s1][s2] - savm[s1][s2]);
3644: } else if ( s2==-1 ) { /* alive */
3645: for (j=1,survp=0. ; j<=nlstate; j++)
3646: survp += out[s1][j];
3647: lli= log(survp);
3648: }else{
3649: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3650: }
3651: ipmx +=1;
3652: sw += weight[i];
3653: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3654: /* 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 3655: } /* end of wave */
3656: } /* end of individual */
3657: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3658: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3659: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3660: for(mi=1; mi<= wav[i]-1; mi++){
3661: for (ii=1;ii<=nlstate+ndeath;ii++)
3662: for (j=1;j<=nlstate+ndeath;j++){
3663: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3664: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3665: }
3666: for(d=0; d<dh[mi][i]; d++){
3667: newm=savm;
3668: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3669: cov[2]=agexact;
3670: if(nagesqr==1)
3671: cov[3]= agexact*agexact;
3672: for (kk=1; kk<=cptcovage;kk++) {
3673: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3674: }
1.126 brouard 3675:
1.226 brouard 3676: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3677: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3678: savm=oldm;
3679: oldm=newm;
3680: } /* end mult */
3681:
3682: s1=s[mw[mi][i]][i];
3683: s2=s[mw[mi+1][i]][i];
3684: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3685: ipmx +=1;
3686: sw += weight[i];
3687: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3688: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
3689: } /* end of wave */
3690: } /* end of individual */
3691: } /* End of if */
3692: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3693: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3694: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3695: return -l;
1.126 brouard 3696: }
3697:
3698: /*************** log-likelihood *************/
3699: double funcone( double *x)
3700: {
1.228 brouard 3701: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3702: int i, ii, j, k, mi, d, kk;
1.228 brouard 3703: int ioffset=0;
1.131 brouard 3704: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3705: double **out;
3706: double lli; /* Individual log likelihood */
3707: double llt;
3708: int s1, s2;
1.228 brouard 3709: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3710:
1.126 brouard 3711: double bbh, survp;
1.187 brouard 3712: double agexact;
1.214 brouard 3713: double agebegin, ageend;
1.126 brouard 3714: /*extern weight */
3715: /* We are differentiating ll according to initial status */
3716: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3717: /*for(i=1;i<imx;i++)
3718: printf(" %d\n",s[4][i]);
3719: */
3720: cov[1]=1.;
3721:
3722: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3723: ioffset=0;
3724: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3725: /* ioffset=2+nagesqr+cptcovage; */
3726: ioffset=2+nagesqr;
1.232 brouard 3727: /* Fixed */
1.224 brouard 3728: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3729: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3730: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3731: 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)*/
3732: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3733: /* cov[2+6]=covar[Tvar[6]][i]; */
3734: /* cov[2+6]=covar[2][i]; V2 */
3735: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3736: /* cov[2+7]=covar[Tvar[7]][i]; */
3737: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3738: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3739: /* cov[2+9]=covar[Tvar[9]][i]; */
3740: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3741: }
1.232 brouard 3742: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3743: /* 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?)*\/ */
3744: /* } */
1.231 brouard 3745: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3746: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3747: /* } */
1.225 brouard 3748:
1.233 brouard 3749:
3750: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3751: /* Wave varying (but not age varying) */
3752: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3753: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3754: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3755: }
1.232 brouard 3756: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3757: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3758: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3759: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3760: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3761: /* 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 3762: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3763: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3764: /* /\* 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]); *\/ */
3765: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3766: /* } */
1.126 brouard 3767: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3768: for (j=1;j<=nlstate+ndeath;j++){
3769: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3770: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3771: }
1.214 brouard 3772:
3773: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3774: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3775: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3776: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3777: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3778: and mw[mi+1][i]. dh depends on stepm.*/
3779: newm=savm;
1.247 brouard 3780: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3781: cov[2]=agexact;
3782: if(nagesqr==1)
3783: cov[3]= agexact*agexact;
3784: for (kk=1; kk<=cptcovage;kk++) {
3785: if(!FixedV[Tvar[Tage[kk]]])
3786: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3787: else
3788: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3789: }
3790: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3791: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3792: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3793: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3794: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3795: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3796: savm=oldm;
3797: oldm=newm;
1.126 brouard 3798: } /* end mult */
3799:
3800: s1=s[mw[mi][i]][i];
3801: s2=s[mw[mi+1][i]][i];
1.217 brouard 3802: /* if(s2==-1){ */
1.268 brouard 3803: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3804: /* /\* exit(1); *\/ */
3805: /* } */
1.126 brouard 3806: bbh=(double)bh[mi][i]/(double)stepm;
3807: /* bias is positive if real duration
3808: * is higher than the multiple of stepm and negative otherwise.
3809: */
3810: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3811: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3812: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3813: for (j=1,survp=0. ; j<=nlstate; j++)
3814: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3815: lli= log(survp);
1.126 brouard 3816: }else if (mle==1){
1.242 brouard 3817: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3818: } else if(mle==2){
1.242 brouard 3819: 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 3820: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3821: 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 3822: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3823: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3824: } else{ /* mle=0 back to 1 */
1.242 brouard 3825: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3826: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3827: } /* End of if */
3828: ipmx +=1;
3829: sw += weight[i];
3830: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3831: /*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 3832: if(globpr){
1.246 brouard 3833: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3834: %11.6f %11.6f %11.6f ", \
1.242 brouard 3835: 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 3836: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3837: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3838: llt +=ll[k]*gipmx/gsw;
3839: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3840: }
3841: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3842: }
1.232 brouard 3843: } /* end of wave */
3844: } /* end of individual */
3845: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3846: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3847: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3848: if(globpr==0){ /* First time we count the contributions and weights */
3849: gipmx=ipmx;
3850: gsw=sw;
3851: }
3852: return -l;
1.126 brouard 3853: }
3854:
3855:
3856: /*************** function likelione ***********/
3857: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3858: {
3859: /* This routine should help understanding what is done with
3860: the selection of individuals/waves and
3861: to check the exact contribution to the likelihood.
3862: Plotting could be done.
3863: */
3864: int k;
3865:
3866: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3867: strcpy(fileresilk,"ILK_");
1.202 brouard 3868: strcat(fileresilk,fileresu);
1.126 brouard 3869: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3870: printf("Problem with resultfile: %s\n", fileresilk);
3871: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3872: }
1.214 brouard 3873: 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");
3874: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3875: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3876: for(k=1; k<=nlstate; k++)
3877: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3878: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3879: }
3880:
3881: *fretone=(*funcone)(p);
3882: if(*globpri !=0){
3883: fclose(ficresilk);
1.205 brouard 3884: if (mle ==0)
3885: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3886: else if(mle >=1)
3887: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3888: 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 3889: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3890:
3891: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3892: 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 3893: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3894: }
1.207 brouard 3895: 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 3896: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3897: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3898: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3899: fflush(fichtm);
1.205 brouard 3900: }
1.126 brouard 3901: return;
3902: }
3903:
3904:
3905: /*********** Maximum Likelihood Estimation ***************/
3906:
3907: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3908: {
1.165 brouard 3909: int i,j, iter=0;
1.126 brouard 3910: double **xi;
3911: double fret;
3912: double fretone; /* Only one call to likelihood */
3913: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3914:
3915: #ifdef NLOPT
3916: int creturn;
3917: nlopt_opt opt;
3918: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3919: double *lb;
3920: double minf; /* the minimum objective value, upon return */
3921: double * p1; /* Shifted parameters from 0 instead of 1 */
3922: myfunc_data dinst, *d = &dinst;
3923: #endif
3924:
3925:
1.126 brouard 3926: xi=matrix(1,npar,1,npar);
3927: for (i=1;i<=npar;i++)
3928: for (j=1;j<=npar;j++)
3929: xi[i][j]=(i==j ? 1.0 : 0.0);
3930: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3931: strcpy(filerespow,"POW_");
1.126 brouard 3932: strcat(filerespow,fileres);
3933: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3934: printf("Problem with resultfile: %s\n", filerespow);
3935: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3936: }
3937: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3938: for (i=1;i<=nlstate;i++)
3939: for(j=1;j<=nlstate+ndeath;j++)
3940: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3941: fprintf(ficrespow,"\n");
1.162 brouard 3942: #ifdef POWELL
1.126 brouard 3943: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3944: #endif
1.126 brouard 3945:
1.162 brouard 3946: #ifdef NLOPT
3947: #ifdef NEWUOA
3948: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3949: #else
3950: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3951: #endif
3952: lb=vector(0,npar-1);
3953: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3954: nlopt_set_lower_bounds(opt, lb);
3955: nlopt_set_initial_step1(opt, 0.1);
3956:
3957: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3958: d->function = func;
3959: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3960: nlopt_set_min_objective(opt, myfunc, d);
3961: nlopt_set_xtol_rel(opt, ftol);
3962: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3963: printf("nlopt failed! %d\n",creturn);
3964: }
3965: else {
3966: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3967: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3968: iter=1; /* not equal */
3969: }
3970: nlopt_destroy(opt);
3971: #endif
1.126 brouard 3972: free_matrix(xi,1,npar,1,npar);
3973: fclose(ficrespow);
1.203 brouard 3974: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3975: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3976: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3977:
3978: }
3979:
3980: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3981: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3982: {
3983: double **a,**y,*x,pd;
1.203 brouard 3984: /* double **hess; */
1.164 brouard 3985: int i, j;
1.126 brouard 3986: int *indx;
3987:
3988: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3989: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3990: void lubksb(double **a, int npar, int *indx, double b[]) ;
3991: void ludcmp(double **a, int npar, int *indx, double *d) ;
3992: double gompertz(double p[]);
1.203 brouard 3993: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3994:
3995: printf("\nCalculation of the hessian matrix. Wait...\n");
3996: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3997: for (i=1;i<=npar;i++){
1.203 brouard 3998: printf("%d-",i);fflush(stdout);
3999: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 4000:
4001: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
4002:
4003: /* printf(" %f ",p[i]);
4004: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4005: }
4006:
4007: for (i=1;i<=npar;i++) {
4008: for (j=1;j<=npar;j++) {
4009: if (j>i) {
1.203 brouard 4010: printf(".%d-%d",i,j);fflush(stdout);
4011: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4012: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4013:
4014: hess[j][i]=hess[i][j];
4015: /*printf(" %lf ",hess[i][j]);*/
4016: }
4017: }
4018: }
4019: printf("\n");
4020: fprintf(ficlog,"\n");
4021:
4022: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4023: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4024:
4025: a=matrix(1,npar,1,npar);
4026: y=matrix(1,npar,1,npar);
4027: x=vector(1,npar);
4028: indx=ivector(1,npar);
4029: for (i=1;i<=npar;i++)
4030: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4031: ludcmp(a,npar,indx,&pd);
4032:
4033: for (j=1;j<=npar;j++) {
4034: for (i=1;i<=npar;i++) x[i]=0;
4035: x[j]=1;
4036: lubksb(a,npar,indx,x);
4037: for (i=1;i<=npar;i++){
4038: matcov[i][j]=x[i];
4039: }
4040: }
4041:
4042: printf("\n#Hessian matrix#\n");
4043: fprintf(ficlog,"\n#Hessian matrix#\n");
4044: for (i=1;i<=npar;i++) {
4045: for (j=1;j<=npar;j++) {
1.203 brouard 4046: printf("%.6e ",hess[i][j]);
4047: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4048: }
4049: printf("\n");
4050: fprintf(ficlog,"\n");
4051: }
4052:
1.203 brouard 4053: /* printf("\n#Covariance matrix#\n"); */
4054: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4055: /* for (i=1;i<=npar;i++) { */
4056: /* for (j=1;j<=npar;j++) { */
4057: /* printf("%.6e ",matcov[i][j]); */
4058: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4059: /* } */
4060: /* printf("\n"); */
4061: /* fprintf(ficlog,"\n"); */
4062: /* } */
4063:
1.126 brouard 4064: /* Recompute Inverse */
1.203 brouard 4065: /* for (i=1;i<=npar;i++) */
4066: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4067: /* ludcmp(a,npar,indx,&pd); */
4068:
4069: /* printf("\n#Hessian matrix recomputed#\n"); */
4070:
4071: /* for (j=1;j<=npar;j++) { */
4072: /* for (i=1;i<=npar;i++) x[i]=0; */
4073: /* x[j]=1; */
4074: /* lubksb(a,npar,indx,x); */
4075: /* for (i=1;i<=npar;i++){ */
4076: /* y[i][j]=x[i]; */
4077: /* printf("%.3e ",y[i][j]); */
4078: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4079: /* } */
4080: /* printf("\n"); */
4081: /* fprintf(ficlog,"\n"); */
4082: /* } */
4083:
4084: /* Verifying the inverse matrix */
4085: #ifdef DEBUGHESS
4086: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4087:
1.203 brouard 4088: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4089: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4090:
4091: for (j=1;j<=npar;j++) {
4092: for (i=1;i<=npar;i++){
1.203 brouard 4093: printf("%.2f ",y[i][j]);
4094: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4095: }
4096: printf("\n");
4097: fprintf(ficlog,"\n");
4098: }
1.203 brouard 4099: #endif
1.126 brouard 4100:
4101: free_matrix(a,1,npar,1,npar);
4102: free_matrix(y,1,npar,1,npar);
4103: free_vector(x,1,npar);
4104: free_ivector(indx,1,npar);
1.203 brouard 4105: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4106:
4107:
4108: }
4109:
4110: /*************** hessian matrix ****************/
4111: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4112: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4113: int i;
4114: int l=1, lmax=20;
1.203 brouard 4115: double k1,k2, res, fx;
1.132 brouard 4116: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4117: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4118: int k=0,kmax=10;
4119: double l1;
4120:
4121: fx=func(x);
4122: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4123: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4124: l1=pow(10,l);
4125: delts=delt;
4126: for(k=1 ; k <kmax; k=k+1){
4127: delt = delta*(l1*k);
4128: p2[theta]=x[theta] +delt;
1.145 brouard 4129: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4130: p2[theta]=x[theta]-delt;
4131: k2=func(p2)-fx;
4132: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4133: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4134:
1.203 brouard 4135: #ifdef DEBUGHESSII
1.126 brouard 4136: 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);
4137: 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);
4138: #endif
4139: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4140: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4141: k=kmax;
4142: }
4143: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4144: k=kmax; l=lmax*10;
1.126 brouard 4145: }
4146: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4147: delts=delt;
4148: }
1.203 brouard 4149: } /* End loop k */
1.126 brouard 4150: }
4151: delti[theta]=delts;
4152: return res;
4153:
4154: }
4155:
1.203 brouard 4156: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4157: {
4158: int i;
1.164 brouard 4159: int l=1, lmax=20;
1.126 brouard 4160: double k1,k2,k3,k4,res,fx;
1.132 brouard 4161: double p2[MAXPARM+1];
1.203 brouard 4162: int k, kmax=1;
4163: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4164:
4165: int firstime=0;
1.203 brouard 4166:
1.126 brouard 4167: fx=func(x);
1.203 brouard 4168: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4169: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4170: p2[thetai]=x[thetai]+delti[thetai]*k;
4171: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4172: k1=func(p2)-fx;
4173:
1.203 brouard 4174: p2[thetai]=x[thetai]+delti[thetai]*k;
4175: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4176: k2=func(p2)-fx;
4177:
1.203 brouard 4178: p2[thetai]=x[thetai]-delti[thetai]*k;
4179: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4180: k3=func(p2)-fx;
4181:
1.203 brouard 4182: p2[thetai]=x[thetai]-delti[thetai]*k;
4183: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4184: k4=func(p2)-fx;
1.203 brouard 4185: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4186: if(k1*k2*k3*k4 <0.){
1.208 brouard 4187: firstime=1;
1.203 brouard 4188: kmax=kmax+10;
1.208 brouard 4189: }
4190: if(kmax >=10 || firstime ==1){
1.246 brouard 4191: 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);
4192: 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 4193: 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);
4194: 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);
4195: }
4196: #ifdef DEBUGHESSIJ
4197: v1=hess[thetai][thetai];
4198: v2=hess[thetaj][thetaj];
4199: cv12=res;
4200: /* Computing eigen value of Hessian matrix */
4201: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4202: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4203: if ((lc2 <0) || (lc1 <0) ){
4204: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4205: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4206: 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);
4207: 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);
4208: }
1.126 brouard 4209: #endif
4210: }
4211: return res;
4212: }
4213:
1.203 brouard 4214: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4215: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4216: /* { */
4217: /* int i; */
4218: /* int l=1, lmax=20; */
4219: /* double k1,k2,k3,k4,res,fx; */
4220: /* double p2[MAXPARM+1]; */
4221: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4222: /* int k=0,kmax=10; */
4223: /* double l1; */
4224:
4225: /* fx=func(x); */
4226: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4227: /* l1=pow(10,l); */
4228: /* delts=delt; */
4229: /* for(k=1 ; k <kmax; k=k+1){ */
4230: /* delt = delti*(l1*k); */
4231: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4232: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4233: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4234: /* k1=func(p2)-fx; */
4235:
4236: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4237: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4238: /* k2=func(p2)-fx; */
4239:
4240: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4241: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4242: /* k3=func(p2)-fx; */
4243:
4244: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4245: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4246: /* k4=func(p2)-fx; */
4247: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4248: /* #ifdef DEBUGHESSIJ */
4249: /* 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); */
4250: /* 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); */
4251: /* #endif */
4252: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4253: /* k=kmax; */
4254: /* } */
4255: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4256: /* k=kmax; l=lmax*10; */
4257: /* } */
4258: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4259: /* delts=delt; */
4260: /* } */
4261: /* } /\* End loop k *\/ */
4262: /* } */
4263: /* delti[theta]=delts; */
4264: /* return res; */
4265: /* } */
4266:
4267:
1.126 brouard 4268: /************** Inverse of matrix **************/
4269: void ludcmp(double **a, int n, int *indx, double *d)
4270: {
4271: int i,imax,j,k;
4272: double big,dum,sum,temp;
4273: double *vv;
4274:
4275: vv=vector(1,n);
4276: *d=1.0;
4277: for (i=1;i<=n;i++) {
4278: big=0.0;
4279: for (j=1;j<=n;j++)
4280: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4281: if (big == 0.0){
4282: printf(" Singular Hessian matrix at row %d:\n",i);
4283: for (j=1;j<=n;j++) {
4284: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4285: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4286: }
4287: fflush(ficlog);
4288: fclose(ficlog);
4289: nrerror("Singular matrix in routine ludcmp");
4290: }
1.126 brouard 4291: vv[i]=1.0/big;
4292: }
4293: for (j=1;j<=n;j++) {
4294: for (i=1;i<j;i++) {
4295: sum=a[i][j];
4296: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4297: a[i][j]=sum;
4298: }
4299: big=0.0;
4300: for (i=j;i<=n;i++) {
4301: sum=a[i][j];
4302: for (k=1;k<j;k++)
4303: sum -= a[i][k]*a[k][j];
4304: a[i][j]=sum;
4305: if ( (dum=vv[i]*fabs(sum)) >= big) {
4306: big=dum;
4307: imax=i;
4308: }
4309: }
4310: if (j != imax) {
4311: for (k=1;k<=n;k++) {
4312: dum=a[imax][k];
4313: a[imax][k]=a[j][k];
4314: a[j][k]=dum;
4315: }
4316: *d = -(*d);
4317: vv[imax]=vv[j];
4318: }
4319: indx[j]=imax;
4320: if (a[j][j] == 0.0) a[j][j]=TINY;
4321: if (j != n) {
4322: dum=1.0/(a[j][j]);
4323: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4324: }
4325: }
4326: free_vector(vv,1,n); /* Doesn't work */
4327: ;
4328: }
4329:
4330: void lubksb(double **a, int n, int *indx, double b[])
4331: {
4332: int i,ii=0,ip,j;
4333: double sum;
4334:
4335: for (i=1;i<=n;i++) {
4336: ip=indx[i];
4337: sum=b[ip];
4338: b[ip]=b[i];
4339: if (ii)
4340: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4341: else if (sum) ii=i;
4342: b[i]=sum;
4343: }
4344: for (i=n;i>=1;i--) {
4345: sum=b[i];
4346: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4347: b[i]=sum/a[i][i];
4348: }
4349: }
4350:
4351: void pstamp(FILE *fichier)
4352: {
1.196 brouard 4353: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4354: }
4355:
1.253 brouard 4356:
4357:
1.126 brouard 4358: /************ Frequencies ********************/
1.251 brouard 4359: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4360: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4361: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4362: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4363:
1.265 brouard 4364: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4365: int iind=0, iage=0;
4366: int mi; /* Effective wave */
4367: int first;
4368: double ***freq; /* Frequencies */
1.268 brouard 4369: 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 */
4370: 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);
1.283 ! brouard 4371: double *meanq, *idq;
1.226 brouard 4372: double **meanqt;
4373: double *pp, **prop, *posprop, *pospropt;
4374: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4375: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4376: double agebegin, ageend;
4377:
4378: pp=vector(1,nlstate);
1.251 brouard 4379: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4380: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4381: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4382: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4383: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.283 ! brouard 4384: idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
1.226 brouard 4385: meanqt=matrix(1,lastpass,1,nqtveff);
4386: strcpy(fileresp,"P_");
4387: strcat(fileresp,fileresu);
4388: /*strcat(fileresphtm,fileresu);*/
4389: if((ficresp=fopen(fileresp,"w"))==NULL) {
4390: printf("Problem with prevalence resultfile: %s\n", fileresp);
4391: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4392: exit(0);
4393: }
1.240 brouard 4394:
1.226 brouard 4395: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4396: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4397: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4398: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4399: fflush(ficlog);
4400: exit(70);
4401: }
4402: else{
4403: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4404: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4405: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4406: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4407: }
1.237 brouard 4408: 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 4409:
1.226 brouard 4410: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4411: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4412: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4413: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4414: fflush(ficlog);
4415: exit(70);
1.240 brouard 4416: } else{
1.226 brouard 4417: 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 4418: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4419: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4420: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4421: }
1.240 brouard 4422: 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);
4423:
1.253 brouard 4424: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4425: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4426: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4427: j1=0;
1.126 brouard 4428:
1.227 brouard 4429: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4430: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4431: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4432:
4433:
1.226 brouard 4434: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4435: reference=low_education V1=0,V2=0
4436: med_educ V1=1 V2=0,
4437: high_educ V1=0 V2=1
4438: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4439: */
1.249 brouard 4440: dateintsum=0;
4441: k2cpt=0;
4442:
1.253 brouard 4443: if(cptcoveff == 0 )
1.265 brouard 4444: nl=1; /* Constant and age model only */
1.253 brouard 4445: else
4446: nl=2;
1.265 brouard 4447:
4448: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4449: /* Loop on nj=1 or 2 if dummy covariates j!=0
4450: * Loop on j1(1 to 2**cptcoveff) covariate combination
4451: * freq[s1][s2][iage] =0.
4452: * Loop on iind
4453: * ++freq[s1][s2][iage] weighted
4454: * end iind
4455: * if covariate and j!0
4456: * headers Variable on one line
4457: * endif cov j!=0
4458: * header of frequency table by age
4459: * Loop on age
4460: * pp[s1]+=freq[s1][s2][iage] weighted
4461: * pos+=freq[s1][s2][iage] weighted
4462: * Loop on s1 initial state
4463: * fprintf(ficresp
4464: * end s1
4465: * end age
4466: * if j!=0 computes starting values
4467: * end compute starting values
4468: * end j1
4469: * end nl
4470: */
1.253 brouard 4471: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4472: if(nj==1)
4473: j=0; /* First pass for the constant */
1.265 brouard 4474: else{
1.253 brouard 4475: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4476: }
1.251 brouard 4477: first=1;
1.265 brouard 4478: 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 4479: posproptt=0.;
4480: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4481: scanf("%d", i);*/
4482: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4483: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4484: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4485: freq[i][s2][m]=0;
1.251 brouard 4486:
4487: for (i=1; i<=nlstate; i++) {
1.240 brouard 4488: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4489: prop[i][m]=0;
4490: posprop[i]=0;
4491: pospropt[i]=0;
4492: }
1.283 ! brouard 4493: for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
! 4494: idq[z1]+=0.;
! 4495: meanq[z1]+=0.;
! 4496: }
! 4497: /* for (z1=1; z1<= nqtveff; z1++) { */
1.251 brouard 4498: /* for(m=1;m<=lastpass;m++){ */
1.283 ! brouard 4499: /* meanqt[m][z1]=0.; */
! 4500: /* } */
! 4501: /* } */
1.251 brouard 4502: /* dateintsum=0; */
4503: /* k2cpt=0; */
4504:
1.265 brouard 4505: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4506: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4507: bool=1;
4508: if(j !=0){
4509: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4510: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.283 ! brouard 4511: /* for (z1=1; z1<= nqfveff; z1++) { */
1.251 brouard 4512: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4513: /* } */
4514: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4515: /* if(Tvaraff[z1] ==-20){ */
4516: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4517: /* }else if(Tvaraff[z1] ==-10){ */
4518: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4519: /* }else */
4520: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4521: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4522: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4523: /* 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",
4524: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4525: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4526: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4527: } /* Onlyf fixed */
4528: } /* end z1 */
4529: } /* cptcovn > 0 */
4530: } /* end any */
4531: }/* end j==0 */
1.265 brouard 4532: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4533: /* for(m=firstpass; m<=lastpass; m++){ */
4534: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4535: m=mw[mi][iind];
4536: if(j!=0){
4537: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4538: for (z1=1; z1<=cptcoveff; z1++) {
4539: if( Fixed[Tmodelind[z1]]==1){
4540: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4541: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4542: value is -1, we don't select. It differs from the
4543: constant and age model which counts them. */
4544: bool=0; /* not selected */
4545: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4546: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4547: bool=0;
4548: }
4549: }
4550: }
4551: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4552: } /* end j==0 */
4553: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4554: if(bool==1){
4555: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4556: and mw[mi+1][iind]. dh depends on stepm. */
4557: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4558: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4559: if(m >=firstpass && m <=lastpass){
4560: k2=anint[m][iind]+(mint[m][iind]/12.);
4561: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4562: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4563: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4564: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4565: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4566: if (m<lastpass) {
4567: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4568: /* 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]); */
4569: if(s[m][iind]==-1)
4570: 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.));
4571: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4572: /* if((int)agev[m][iind] == 55) */
4573: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4574: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4575: 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 4576: }
1.283 ! brouard 4577: for (z1=1; z1<= nqfveff; z1++) {
! 4578: idq[z1]++;
! 4579: meanq[z1]+=covar[ncovcol+z1][iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
! 4580: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
! 4581: }
1.251 brouard 4582: } /* end if between passes */
4583: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4584: dateintsum=dateintsum+k2; /* on all covariates ?*/
4585: k2cpt++;
4586: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4587: }
1.251 brouard 4588: }else{
4589: bool=1;
4590: }/* end bool 2 */
4591: } /* end m */
4592: } /* end bool */
4593: } /* end iind = 1 to imx */
4594: /* prop[s][age] is feeded for any initial and valid live state as well as
4595: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4596:
4597:
4598: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4599: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4600: pstamp(ficresp);
1.251 brouard 4601: if (cptcoveff>0 && j!=0){
1.265 brouard 4602: pstamp(ficresp);
1.251 brouard 4603: printf( "\n#********** Variable ");
4604: fprintf(ficresp, "\n#********** Variable ");
4605: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4606: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4607: fprintf(ficlog, "\n#********** Variable ");
4608: for (z1=1; z1<=cptcoveff; z1++){
4609: if(!FixedV[Tvaraff[z1]]){
4610: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4611: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4612: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4613: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4614: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4615: }else{
1.251 brouard 4616: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4617: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4618: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4619: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4620: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4621: }
4622: }
4623: printf( "**********\n#");
4624: fprintf(ficresp, "**********\n#");
4625: fprintf(ficresphtm, "**********</h3>\n");
4626: fprintf(ficresphtmfr, "**********</h3>\n");
4627: fprintf(ficlog, "**********\n");
4628: }
1.283 ! brouard 4629: /*
! 4630: Printing means of quantitative variables if any
! 4631: */
! 4632: for (z1=1; z1<= nqfveff; z1++) {
! 4633: fprintf(ficresphtmfr,"V quantitative id %d, number of idividuals= %f, sum=%f", z1, idq[z1], meanq[z1]);
! 4634: fprintf(ficresphtmfr,", mean=%f<p>\n",meanq[z1]/idq[z1]);
! 4635: }
! 4636: /* for (z1=1; z1<= nqtveff; z1++) { */
! 4637: /* for(m=1;m<=lastpass;m++){ */
! 4638: /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
! 4639: /* } */
! 4640: /* } */
! 4641:
1.251 brouard 4642: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4643: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4644: fprintf(ficresp, " Age");
4645: 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 4646: for(i=1; i<=nlstate;i++) {
1.265 brouard 4647: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4648: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4649: }
1.265 brouard 4650: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4651: fprintf(ficresphtm, "\n");
4652:
4653: /* Header of frequency table by age */
4654: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4655: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4656: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4657: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4658: if(s2!=0 && m!=0)
4659: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4660: }
1.226 brouard 4661: }
1.251 brouard 4662: fprintf(ficresphtmfr, "\n");
4663:
4664: /* For each age */
4665: for(iage=iagemin; iage <= iagemax+3; iage++){
4666: fprintf(ficresphtm,"<tr>");
4667: if(iage==iagemax+1){
4668: fprintf(ficlog,"1");
4669: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4670: }else if(iage==iagemax+2){
4671: fprintf(ficlog,"0");
4672: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4673: }else if(iage==iagemax+3){
4674: fprintf(ficlog,"Total");
4675: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4676: }else{
1.240 brouard 4677: if(first==1){
1.251 brouard 4678: first=0;
4679: printf("See log file for details...\n");
4680: }
4681: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4682: fprintf(ficlog,"Age %d", iage);
4683: }
1.265 brouard 4684: for(s1=1; s1 <=nlstate ; s1++){
4685: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4686: pp[s1] += freq[s1][m][iage];
1.251 brouard 4687: }
1.265 brouard 4688: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4689: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4690: pos += freq[s1][m][iage];
4691: if(pp[s1]>=1.e-10){
1.251 brouard 4692: if(first==1){
1.265 brouard 4693: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4694: }
1.265 brouard 4695: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4696: }else{
4697: if(first==1)
1.265 brouard 4698: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4699: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4700: }
4701: }
4702:
1.265 brouard 4703: for(s1=1; s1 <=nlstate ; s1++){
4704: /* posprop[s1]=0; */
4705: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4706: pp[s1] += freq[s1][m][iage];
4707: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4708:
4709: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4710: pos += pp[s1]; /* pos is the total number of transitions until this age */
4711: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4712: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4713: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4714: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4715: }
4716:
4717: /* Writing ficresp */
4718: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4719: if( iage <= iagemax){
4720: fprintf(ficresp," %d",iage);
4721: }
4722: }else if( nj==2){
4723: if( iage <= iagemax){
4724: fprintf(ficresp," %d",iage);
4725: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4726: }
1.240 brouard 4727: }
1.265 brouard 4728: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4729: if(pos>=1.e-5){
1.251 brouard 4730: if(first==1)
1.265 brouard 4731: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4732: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4733: }else{
4734: if(first==1)
1.265 brouard 4735: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4736: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4737: }
4738: if( iage <= iagemax){
4739: if(pos>=1.e-5){
1.265 brouard 4740: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4741: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4742: }else if( nj==2){
4743: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4744: }
4745: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4746: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4747: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4748: } else{
4749: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4750: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4751: }
1.240 brouard 4752: }
1.265 brouard 4753: pospropt[s1] +=posprop[s1];
4754: } /* end loop s1 */
1.251 brouard 4755: /* pospropt=0.; */
1.265 brouard 4756: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4757: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4758: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4759: if(first==1){
1.265 brouard 4760: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4761: }
1.265 brouard 4762: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4763: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4764: }
1.265 brouard 4765: if(s1!=0 && m!=0)
4766: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4767: }
1.265 brouard 4768: } /* end loop s1 */
1.251 brouard 4769: posproptt=0.;
1.265 brouard 4770: for(s1=1; s1 <=nlstate; s1++){
4771: posproptt += pospropt[s1];
1.251 brouard 4772: }
4773: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4774: fprintf(ficresphtm,"</tr>\n");
4775: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4776: if(iage <= iagemax)
4777: fprintf(ficresp,"\n");
1.240 brouard 4778: }
1.251 brouard 4779: if(first==1)
4780: printf("Others in log...\n");
4781: fprintf(ficlog,"\n");
4782: } /* end loop age iage */
1.265 brouard 4783:
1.251 brouard 4784: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4785: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4786: if(posproptt < 1.e-5){
1.265 brouard 4787: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4788: }else{
1.265 brouard 4789: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4790: }
1.226 brouard 4791: }
1.251 brouard 4792: fprintf(ficresphtm,"</tr>\n");
4793: fprintf(ficresphtm,"</table>\n");
4794: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4795: if(posproptt < 1.e-5){
1.251 brouard 4796: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4797: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4798: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4799: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4800: invalidvarcomb[j1]=1;
1.226 brouard 4801: }else{
1.251 brouard 4802: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4803: invalidvarcomb[j1]=0;
1.226 brouard 4804: }
1.251 brouard 4805: fprintf(ficresphtmfr,"</table>\n");
4806: fprintf(ficlog,"\n");
4807: if(j!=0){
4808: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4809: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4810: for(k=1; k <=(nlstate+ndeath); k++){
4811: if (k != i) {
1.265 brouard 4812: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4813: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4814: if(j1==1){ /* All dummy covariates to zero */
4815: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4816: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4817: printf("%d%d ",i,k);
4818: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4819: 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]));
4820: 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]));
4821: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4822: }
1.253 brouard 4823: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4824: for(iage=iagemin; iage <= iagemax+3; iage++){
4825: x[iage]= (double)iage;
4826: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4827: /* 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 4828: }
1.268 brouard 4829: /* Some are not finite, but linreg will ignore these ages */
4830: no=0;
1.253 brouard 4831: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4832: pstart[s1]=b;
4833: pstart[s1-1]=a;
1.252 brouard 4834: }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 */
4835: 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]);
4836: 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 4837: 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 4838: printf("%d%d ",i,k);
4839: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4840: 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 4841: }else{ /* Other cases, like quantitative fixed or varying covariates */
4842: ;
4843: }
4844: /* printf("%12.7f )", param[i][jj][k]); */
4845: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4846: s1++;
1.251 brouard 4847: } /* end jj */
4848: } /* end k!= i */
4849: } /* end k */
1.265 brouard 4850: } /* end i, s1 */
1.251 brouard 4851: } /* end j !=0 */
4852: } /* end selected combination of covariate j1 */
4853: if(j==0){ /* We can estimate starting values from the occurences in each case */
4854: printf("#Freqsummary: Starting values for the constants:\n");
4855: fprintf(ficlog,"\n");
1.265 brouard 4856: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4857: for(k=1; k <=(nlstate+ndeath); k++){
4858: if (k != i) {
4859: printf("%d%d ",i,k);
4860: fprintf(ficlog,"%d%d ",i,k);
4861: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4862: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4863: if(jj==1){ /* Age has to be done */
1.265 brouard 4864: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4865: 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]));
4866: 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 4867: }
4868: /* printf("%12.7f )", param[i][jj][k]); */
4869: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4870: s1++;
1.250 brouard 4871: }
1.251 brouard 4872: printf("\n");
4873: fprintf(ficlog,"\n");
1.250 brouard 4874: }
4875: }
4876: }
1.251 brouard 4877: printf("#Freqsummary\n");
4878: fprintf(ficlog,"\n");
1.265 brouard 4879: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4880: for(s2=-1; s2 <=nlstate+ndeath; s2++){
4881: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
4882: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4883: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4884: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
4885: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
4886: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 4887: /* } */
4888: }
1.265 brouard 4889: } /* end loop s1 */
1.251 brouard 4890:
4891: printf("\n");
4892: fprintf(ficlog,"\n");
4893: } /* end j=0 */
1.249 brouard 4894: } /* end j */
1.252 brouard 4895:
1.253 brouard 4896: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4897: for(i=1, jk=1; i <=nlstate; i++){
4898: for(j=1; j <=nlstate+ndeath; j++){
4899: if(j!=i){
4900: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4901: printf("%1d%1d",i,j);
4902: fprintf(ficparo,"%1d%1d",i,j);
4903: for(k=1; k<=ncovmodel;k++){
4904: /* printf(" %lf",param[i][j][k]); */
4905: /* fprintf(ficparo," %lf",param[i][j][k]); */
4906: p[jk]=pstart[jk];
4907: printf(" %f ",pstart[jk]);
4908: fprintf(ficparo," %f ",pstart[jk]);
4909: jk++;
4910: }
4911: printf("\n");
4912: fprintf(ficparo,"\n");
4913: }
4914: }
4915: }
4916: } /* end mle=-2 */
1.226 brouard 4917: dateintmean=dateintsum/k2cpt;
1.240 brouard 4918:
1.226 brouard 4919: fclose(ficresp);
4920: fclose(ficresphtm);
4921: fclose(ficresphtmfr);
1.283 ! brouard 4922: free_vector(idq,1,nqfveff);
1.226 brouard 4923: free_vector(meanq,1,nqfveff);
4924: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 4925: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
4926: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 4927: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4928: free_vector(pospropt,1,nlstate);
4929: free_vector(posprop,1,nlstate);
1.251 brouard 4930: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4931: free_vector(pp,1,nlstate);
4932: /* End of freqsummary */
4933: }
1.126 brouard 4934:
1.268 brouard 4935: /* Simple linear regression */
4936: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
4937:
4938: /* y=a+bx regression */
4939: double sumx = 0.0; /* sum of x */
4940: double sumx2 = 0.0; /* sum of x**2 */
4941: double sumxy = 0.0; /* sum of x * y */
4942: double sumy = 0.0; /* sum of y */
4943: double sumy2 = 0.0; /* sum of y**2 */
4944: double sume2 = 0.0; /* sum of square or residuals */
4945: double yhat;
4946:
4947: double denom=0;
4948: int i;
4949: int ne=*no;
4950:
4951: for ( i=ifi, ne=0;i<=ila;i++) {
4952: if(!isfinite(x[i]) || !isfinite(y[i])){
4953: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4954: continue;
4955: }
4956: ne=ne+1;
4957: sumx += x[i];
4958: sumx2 += x[i]*x[i];
4959: sumxy += x[i] * y[i];
4960: sumy += y[i];
4961: sumy2 += y[i]*y[i];
4962: denom = (ne * sumx2 - sumx*sumx);
4963: /* 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); */
4964: }
4965:
4966: denom = (ne * sumx2 - sumx*sumx);
4967: if (denom == 0) {
4968: // vertical, slope m is infinity
4969: *b = INFINITY;
4970: *a = 0;
4971: if (r) *r = 0;
4972: return 1;
4973: }
4974:
4975: *b = (ne * sumxy - sumx * sumy) / denom;
4976: *a = (sumy * sumx2 - sumx * sumxy) / denom;
4977: if (r!=NULL) {
4978: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
4979: sqrt((sumx2 - sumx*sumx/ne) *
4980: (sumy2 - sumy*sumy/ne));
4981: }
4982: *no=ne;
4983: for ( i=ifi, ne=0;i<=ila;i++) {
4984: if(!isfinite(x[i]) || !isfinite(y[i])){
4985: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4986: continue;
4987: }
4988: ne=ne+1;
4989: yhat = y[i] - *a -*b* x[i];
4990: sume2 += yhat * yhat ;
4991:
4992: denom = (ne * sumx2 - sumx*sumx);
4993: /* 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); */
4994: }
4995: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
4996: *sa= *sb * sqrt(sumx2/ne);
4997:
4998: return 0;
4999: }
5000:
1.126 brouard 5001: /************ Prevalence ********************/
1.227 brouard 5002: 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)
5003: {
5004: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5005: in each health status at the date of interview (if between dateprev1 and dateprev2).
5006: We still use firstpass and lastpass as another selection.
5007: */
1.126 brouard 5008:
1.227 brouard 5009: int i, m, jk, j1, bool, z1,j, iv;
5010: int mi; /* Effective wave */
5011: int iage;
5012: double agebegin, ageend;
5013:
5014: double **prop;
5015: double posprop;
5016: double y2; /* in fractional years */
5017: int iagemin, iagemax;
5018: int first; /** to stop verbosity which is redirected to log file */
5019:
5020: iagemin= (int) agemin;
5021: iagemax= (int) agemax;
5022: /*pp=vector(1,nlstate);*/
1.251 brouard 5023: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5024: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5025: j1=0;
1.222 brouard 5026:
1.227 brouard 5027: /*j=cptcoveff;*/
5028: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5029:
1.227 brouard 5030: first=1;
5031: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5032: for (i=1; i<=nlstate; i++)
1.251 brouard 5033: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5034: prop[i][iage]=0.0;
5035: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5036: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5037: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5038:
5039: for (i=1; i<=imx; i++) { /* Each individual */
5040: bool=1;
5041: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5042: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5043: m=mw[mi][i];
5044: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5045: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5046: for (z1=1; z1<=cptcoveff; z1++){
5047: if( Fixed[Tmodelind[z1]]==1){
5048: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5049: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5050: bool=0;
5051: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5052: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5053: bool=0;
5054: }
5055: }
5056: if(bool==1){ /* Otherwise we skip that wave/person */
5057: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5058: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5059: if(m >=firstpass && m <=lastpass){
5060: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5061: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5062: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5063: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5064: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5065: 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);
5066: exit(1);
5067: }
5068: if (s[m][i]>0 && s[m][i]<=nlstate) {
5069: /*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]]);*/
5070: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5071: prop[s[m][i]][iagemax+3] += weight[i];
5072: } /* end valid statuses */
5073: } /* end selection of dates */
5074: } /* end selection of waves */
5075: } /* end bool */
5076: } /* end wave */
5077: } /* end individual */
5078: for(i=iagemin; i <= iagemax+3; i++){
5079: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5080: posprop += prop[jk][i];
5081: }
5082:
5083: for(jk=1; jk <=nlstate ; jk++){
5084: if( i <= iagemax){
5085: if(posprop>=1.e-5){
5086: probs[i][jk][j1]= prop[jk][i]/posprop;
5087: } else{
5088: if(first==1){
5089: first=0;
1.266 brouard 5090: 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]);
5091: 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]);
5092: }else{
5093: 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 5094: }
5095: }
5096: }
5097: }/* end jk */
5098: }/* end i */
1.222 brouard 5099: /*} *//* end i1 */
1.227 brouard 5100: } /* end j1 */
1.222 brouard 5101:
1.227 brouard 5102: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5103: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5104: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5105: } /* End of prevalence */
1.126 brouard 5106:
5107: /************* Waves Concatenation ***************/
5108:
5109: 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)
5110: {
5111: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
5112: Death is a valid wave (if date is known).
5113: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5114: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
5115: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 5116: */
1.126 brouard 5117:
1.224 brouard 5118: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5119: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5120: double sum=0., jmean=0.;*/
1.224 brouard 5121: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5122: int j, k=0,jk, ju, jl;
5123: double sum=0.;
5124: first=0;
1.214 brouard 5125: firstwo=0;
1.217 brouard 5126: firsthree=0;
1.218 brouard 5127: firstfour=0;
1.164 brouard 5128: jmin=100000;
1.126 brouard 5129: jmax=-1;
5130: jmean=0.;
1.224 brouard 5131:
5132: /* Treating live states */
1.214 brouard 5133: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5134: mi=0; /* First valid wave */
1.227 brouard 5135: mli=0; /* Last valid wave */
1.126 brouard 5136: m=firstpass;
1.214 brouard 5137: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5138: 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 */
5139: mli=m-1;/* mw[++mi][i]=m-1; */
5140: }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 */
5141: mw[++mi][i]=m;
5142: mli=m;
1.224 brouard 5143: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5144: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5145: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5146: }
1.227 brouard 5147: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5148: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5149: break;
1.224 brouard 5150: #else
1.227 brouard 5151: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5152: if(firsthree == 0){
1.262 brouard 5153: 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 5154: firsthree=1;
5155: }
1.262 brouard 5156: 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 5157: mw[++mi][i]=m;
5158: mli=m;
5159: }
5160: if(s[m][i]==-2){ /* Vital status is really unknown */
5161: nbwarn++;
5162: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5163: 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);
5164: 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);
5165: }
5166: break;
5167: }
5168: break;
1.224 brouard 5169: #endif
1.227 brouard 5170: }/* End m >= lastpass */
1.126 brouard 5171: }/* end while */
1.224 brouard 5172:
1.227 brouard 5173: /* 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 5174: /* After last pass */
1.224 brouard 5175: /* Treating death states */
1.214 brouard 5176: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5177: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5178: /* } */
1.126 brouard 5179: mi++; /* Death is another wave */
5180: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5181: /* Only death is a correct wave */
1.126 brouard 5182: mw[mi][i]=m;
1.257 brouard 5183: } /* else not in a death state */
1.224 brouard 5184: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5185: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5186: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5187: 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 */
5188: nbwarn++;
5189: if(firstfiv==0){
5190: 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 );
5191: firstfiv=1;
5192: }else{
5193: 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 );
5194: }
5195: }else{ /* Death occured afer last wave potential bias */
5196: nberr++;
5197: if(firstwo==0){
1.257 brouard 5198: 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 5199: firstwo=1;
5200: }
1.257 brouard 5201: 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 5202: }
1.257 brouard 5203: }else{ /* if date of interview is unknown */
1.227 brouard 5204: /* death is known but not confirmed by death status at any wave */
5205: if(firstfour==0){
5206: 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 );
5207: firstfour=1;
5208: }
5209: 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 5210: }
1.224 brouard 5211: } /* end if date of death is known */
5212: #endif
5213: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5214: /* wav[i]=mw[mi][i]; */
1.126 brouard 5215: if(mi==0){
5216: nbwarn++;
5217: if(first==0){
1.227 brouard 5218: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5219: first=1;
1.126 brouard 5220: }
5221: if(first==1){
1.227 brouard 5222: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5223: }
5224: } /* end mi==0 */
5225: } /* End individuals */
1.214 brouard 5226: /* wav and mw are no more changed */
1.223 brouard 5227:
1.214 brouard 5228:
1.126 brouard 5229: for(i=1; i<=imx; i++){
5230: for(mi=1; mi<wav[i];mi++){
5231: if (stepm <=0)
1.227 brouard 5232: dh[mi][i]=1;
1.126 brouard 5233: else{
1.260 brouard 5234: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5235: if (agedc[i] < 2*AGESUP) {
5236: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5237: if(j==0) j=1; /* Survives at least one month after exam */
5238: else if(j<0){
5239: nberr++;
5240: 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]);
5241: j=1; /* Temporary Dangerous patch */
5242: 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);
5243: 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]);
5244: 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);
5245: }
5246: k=k+1;
5247: if (j >= jmax){
5248: jmax=j;
5249: ijmax=i;
5250: }
5251: if (j <= jmin){
5252: jmin=j;
5253: ijmin=i;
5254: }
5255: sum=sum+j;
5256: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5257: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5258: }
5259: }
5260: else{
5261: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5262: /* 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 5263:
1.227 brouard 5264: k=k+1;
5265: if (j >= jmax) {
5266: jmax=j;
5267: ijmax=i;
5268: }
5269: else if (j <= jmin){
5270: jmin=j;
5271: ijmin=i;
5272: }
5273: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5274: /*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]);*/
5275: if(j<0){
5276: nberr++;
5277: 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]);
5278: 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]);
5279: }
5280: sum=sum+j;
5281: }
5282: jk= j/stepm;
5283: jl= j -jk*stepm;
5284: ju= j -(jk+1)*stepm;
5285: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5286: if(jl==0){
5287: dh[mi][i]=jk;
5288: bh[mi][i]=0;
5289: }else{ /* We want a negative bias in order to only have interpolation ie
5290: * to avoid the price of an extra matrix product in likelihood */
5291: dh[mi][i]=jk+1;
5292: bh[mi][i]=ju;
5293: }
5294: }else{
5295: if(jl <= -ju){
5296: dh[mi][i]=jk;
5297: bh[mi][i]=jl; /* bias is positive if real duration
5298: * is higher than the multiple of stepm and negative otherwise.
5299: */
5300: }
5301: else{
5302: dh[mi][i]=jk+1;
5303: bh[mi][i]=ju;
5304: }
5305: if(dh[mi][i]==0){
5306: dh[mi][i]=1; /* At least one step */
5307: bh[mi][i]=ju; /* At least one step */
5308: /* 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);*/
5309: }
5310: } /* end if mle */
1.126 brouard 5311: }
5312: } /* end wave */
5313: }
5314: jmean=sum/k;
5315: 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 5316: 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 5317: }
1.126 brouard 5318:
5319: /*********** Tricode ****************************/
1.220 brouard 5320: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5321: {
5322: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5323: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5324: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5325: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5326: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5327: */
1.130 brouard 5328:
1.242 brouard 5329: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5330: int modmaxcovj=0; /* Modality max of covariates j */
5331: int cptcode=0; /* Modality max of covariates j */
5332: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5333:
5334:
1.242 brouard 5335: /* cptcoveff=0; */
5336: /* *cptcov=0; */
1.126 brouard 5337:
1.242 brouard 5338: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 5339:
1.242 brouard 5340: /* Loop on covariates without age and products and no quantitative variable */
5341: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
5342: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5343: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5344: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5345: switch(Fixed[k]) {
5346: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5347: 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*/
5348: ij=(int)(covar[Tvar[k]][i]);
5349: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5350: * If product of Vn*Vm, still boolean *:
5351: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5352: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5353: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5354: modality of the nth covariate of individual i. */
5355: if (ij > modmaxcovj)
5356: modmaxcovj=ij;
5357: else if (ij < modmincovj)
5358: modmincovj=ij;
5359: if ((ij < -1) && (ij > NCOVMAX)){
5360: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5361: exit(1);
5362: }else
5363: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5364: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5365: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5366: /* getting the maximum value of the modality of the covariate
5367: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5368: female ies 1, then modmaxcovj=1.
5369: */
5370: } /* end for loop on individuals i */
5371: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5372: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5373: cptcode=modmaxcovj;
5374: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5375: /*for (i=0; i<=cptcode; i++) {*/
5376: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5377: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5378: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5379: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5380: if( j != -1){
5381: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5382: covariate for which somebody answered excluding
5383: undefined. Usually 2: 0 and 1. */
5384: }
5385: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5386: covariate for which somebody answered including
5387: undefined. Usually 3: -1, 0 and 1. */
5388: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5389: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5390: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5391:
1.242 brouard 5392: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5393: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5394: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5395: /* modmincovj=3; modmaxcovj = 7; */
5396: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5397: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5398: /* defining two dummy variables: variables V1_1 and V1_2.*/
5399: /* nbcode[Tvar[j]][ij]=k; */
5400: /* nbcode[Tvar[j]][1]=0; */
5401: /* nbcode[Tvar[j]][2]=1; */
5402: /* nbcode[Tvar[j]][3]=2; */
5403: /* To be continued (not working yet). */
5404: ij=0; /* ij is similar to i but can jump over null modalities */
5405: 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*/
5406: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5407: break;
5408: }
5409: ij++;
5410: 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*/
5411: cptcode = ij; /* New max modality for covar j */
5412: } /* end of loop on modality i=-1 to 1 or more */
5413: break;
5414: case 1: /* Testing on varying covariate, could be simple and
5415: * should look at waves or product of fixed *
5416: * varying. No time to test -1, assuming 0 and 1 only */
5417: ij=0;
5418: for(i=0; i<=1;i++){
5419: nbcode[Tvar[k]][++ij]=i;
5420: }
5421: break;
5422: default:
5423: break;
5424: } /* end switch */
5425: } /* end dummy test */
5426:
5427: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
5428: /* /\*recode from 0 *\/ */
5429: /* k is a modality. If we have model=V1+V1*sex */
5430: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
5431: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
5432: /* } */
5433: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
5434: /* if (ij > ncodemax[j]) { */
5435: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5436: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5437: /* break; */
5438: /* } */
5439: /* } /\* end of loop on modality k *\/ */
5440: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
5441:
5442: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5443: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5444: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5445: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5446: 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 */
5447: 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 */
5448: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5449: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5450:
5451: ij=0;
5452: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5453: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5454: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5455: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5456: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5457: /* If product not in single variable we don't print results */
5458: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5459: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5460: 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*/
5461: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5462: 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 */
5463: if(Fixed[k]!=0)
5464: anyvaryingduminmodel=1;
5465: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5466: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5467: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5468: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5469: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5470: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5471: }
5472: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5473: /* ij--; */
5474: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5475: *cptcov=ij; /*Number of total real effective covariates: effective
5476: * because they can be excluded from the model and real
5477: * if in the model but excluded because missing values, but how to get k from ij?*/
5478: for(j=ij+1; j<= cptcovt; j++){
5479: Tvaraff[j]=0;
5480: Tmodelind[j]=0;
5481: }
5482: for(j=ntveff+1; j<= cptcovt; j++){
5483: TmodelInvind[j]=0;
5484: }
5485: /* To be sorted */
5486: ;
5487: }
1.126 brouard 5488:
1.145 brouard 5489:
1.126 brouard 5490: /*********** Health Expectancies ****************/
5491:
1.235 brouard 5492: 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 5493:
5494: {
5495: /* Health expectancies, no variances */
1.164 brouard 5496: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5497: int nhstepma, nstepma; /* Decreasing with age */
5498: double age, agelim, hf;
5499: double ***p3mat;
5500: double eip;
5501:
1.238 brouard 5502: /* pstamp(ficreseij); */
1.126 brouard 5503: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5504: fprintf(ficreseij,"# Age");
5505: for(i=1; i<=nlstate;i++){
5506: for(j=1; j<=nlstate;j++){
5507: fprintf(ficreseij," e%1d%1d ",i,j);
5508: }
5509: fprintf(ficreseij," e%1d. ",i);
5510: }
5511: fprintf(ficreseij,"\n");
5512:
5513:
5514: if(estepm < stepm){
5515: printf ("Problem %d lower than %d\n",estepm, stepm);
5516: }
5517: else hstepm=estepm;
5518: /* We compute the life expectancy from trapezoids spaced every estepm months
5519: * This is mainly to measure the difference between two models: for example
5520: * if stepm=24 months pijx are given only every 2 years and by summing them
5521: * we are calculating an estimate of the Life Expectancy assuming a linear
5522: * progression in between and thus overestimating or underestimating according
5523: * to the curvature of the survival function. If, for the same date, we
5524: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5525: * to compare the new estimate of Life expectancy with the same linear
5526: * hypothesis. A more precise result, taking into account a more precise
5527: * curvature will be obtained if estepm is as small as stepm. */
5528:
5529: /* For example we decided to compute the life expectancy with the smallest unit */
5530: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5531: nhstepm is the number of hstepm from age to agelim
5532: nstepm is the number of stepm from age to agelin.
1.270 brouard 5533: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5534: and note for a fixed period like estepm months */
5535: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5536: survival function given by stepm (the optimization length). Unfortunately it
5537: means that if the survival funtion is printed only each two years of age and if
5538: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5539: results. So we changed our mind and took the option of the best precision.
5540: */
5541: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5542:
5543: agelim=AGESUP;
5544: /* If stepm=6 months */
5545: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5546: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5547:
5548: /* nhstepm age range expressed in number of stepm */
5549: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5550: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5551: /* if (stepm >= YEARM) hstepm=1;*/
5552: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5553: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5554:
5555: for (age=bage; age<=fage; age ++){
5556: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5557: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5558: /* if (stepm >= YEARM) hstepm=1;*/
5559: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5560:
5561: /* If stepm=6 months */
5562: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5563: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5564:
1.235 brouard 5565: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5566:
5567: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5568:
5569: printf("%d|",(int)age);fflush(stdout);
5570: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5571:
5572: /* Computing expectancies */
5573: for(i=1; i<=nlstate;i++)
5574: for(j=1; j<=nlstate;j++)
5575: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5576: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5577:
5578: /* 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]);*/
5579:
5580: }
5581:
5582: fprintf(ficreseij,"%3.0f",age );
5583: for(i=1; i<=nlstate;i++){
5584: eip=0;
5585: for(j=1; j<=nlstate;j++){
5586: eip +=eij[i][j][(int)age];
5587: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5588: }
5589: fprintf(ficreseij,"%9.4f", eip );
5590: }
5591: fprintf(ficreseij,"\n");
5592:
5593: }
5594: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5595: printf("\n");
5596: fprintf(ficlog,"\n");
5597:
5598: }
5599:
1.235 brouard 5600: 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 5601:
5602: {
5603: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5604: to initial status i, ei. .
1.126 brouard 5605: */
5606: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5607: int nhstepma, nstepma; /* Decreasing with age */
5608: double age, agelim, hf;
5609: double ***p3matp, ***p3matm, ***varhe;
5610: double **dnewm,**doldm;
5611: double *xp, *xm;
5612: double **gp, **gm;
5613: double ***gradg, ***trgradg;
5614: int theta;
5615:
5616: double eip, vip;
5617:
5618: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5619: xp=vector(1,npar);
5620: xm=vector(1,npar);
5621: dnewm=matrix(1,nlstate*nlstate,1,npar);
5622: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5623:
5624: pstamp(ficresstdeij);
5625: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5626: fprintf(ficresstdeij,"# Age");
5627: for(i=1; i<=nlstate;i++){
5628: for(j=1; j<=nlstate;j++)
5629: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5630: fprintf(ficresstdeij," e%1d. ",i);
5631: }
5632: fprintf(ficresstdeij,"\n");
5633:
5634: pstamp(ficrescveij);
5635: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5636: fprintf(ficrescveij,"# Age");
5637: for(i=1; i<=nlstate;i++)
5638: for(j=1; j<=nlstate;j++){
5639: cptj= (j-1)*nlstate+i;
5640: for(i2=1; i2<=nlstate;i2++)
5641: for(j2=1; j2<=nlstate;j2++){
5642: cptj2= (j2-1)*nlstate+i2;
5643: if(cptj2 <= cptj)
5644: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5645: }
5646: }
5647: fprintf(ficrescveij,"\n");
5648:
5649: if(estepm < stepm){
5650: printf ("Problem %d lower than %d\n",estepm, stepm);
5651: }
5652: else hstepm=estepm;
5653: /* We compute the life expectancy from trapezoids spaced every estepm months
5654: * This is mainly to measure the difference between two models: for example
5655: * if stepm=24 months pijx are given only every 2 years and by summing them
5656: * we are calculating an estimate of the Life Expectancy assuming a linear
5657: * progression in between and thus overestimating or underestimating according
5658: * to the curvature of the survival function. If, for the same date, we
5659: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5660: * to compare the new estimate of Life expectancy with the same linear
5661: * hypothesis. A more precise result, taking into account a more precise
5662: * curvature will be obtained if estepm is as small as stepm. */
5663:
5664: /* For example we decided to compute the life expectancy with the smallest unit */
5665: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5666: nhstepm is the number of hstepm from age to agelim
5667: nstepm is the number of stepm from age to agelin.
5668: Look at hpijx to understand the reason of that which relies in memory size
5669: and note for a fixed period like estepm months */
5670: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5671: survival function given by stepm (the optimization length). Unfortunately it
5672: means that if the survival funtion is printed only each two years of age and if
5673: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5674: results. So we changed our mind and took the option of the best precision.
5675: */
5676: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5677:
5678: /* If stepm=6 months */
5679: /* nhstepm age range expressed in number of stepm */
5680: agelim=AGESUP;
5681: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5682: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5683: /* if (stepm >= YEARM) hstepm=1;*/
5684: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5685:
5686: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5687: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5688: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5689: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5690: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5691: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5692:
5693: for (age=bage; age<=fage; age ++){
5694: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5695: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5696: /* if (stepm >= YEARM) hstepm=1;*/
5697: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5698:
1.126 brouard 5699: /* If stepm=6 months */
5700: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5701: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5702:
5703: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5704:
1.126 brouard 5705: /* Computing Variances of health expectancies */
5706: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5707: decrease memory allocation */
5708: for(theta=1; theta <=npar; theta++){
5709: for(i=1; i<=npar; i++){
1.222 brouard 5710: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5711: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5712: }
1.235 brouard 5713: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5714: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5715:
1.126 brouard 5716: for(j=1; j<= nlstate; j++){
1.222 brouard 5717: for(i=1; i<=nlstate; i++){
5718: for(h=0; h<=nhstepm-1; h++){
5719: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5720: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5721: }
5722: }
1.126 brouard 5723: }
1.218 brouard 5724:
1.126 brouard 5725: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5726: for(h=0; h<=nhstepm-1; h++){
5727: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5728: }
1.126 brouard 5729: }/* End theta */
5730:
5731:
5732: for(h=0; h<=nhstepm-1; h++)
5733: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5734: for(theta=1; theta <=npar; theta++)
5735: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5736:
1.218 brouard 5737:
1.222 brouard 5738: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5739: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5740: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5741:
1.222 brouard 5742: printf("%d|",(int)age);fflush(stdout);
5743: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5744: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5745: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5746: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5747: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5748: for(ij=1;ij<=nlstate*nlstate;ij++)
5749: for(ji=1;ji<=nlstate*nlstate;ji++)
5750: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5751: }
5752: }
1.218 brouard 5753:
1.126 brouard 5754: /* Computing expectancies */
1.235 brouard 5755: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5756: for(i=1; i<=nlstate;i++)
5757: for(j=1; j<=nlstate;j++)
1.222 brouard 5758: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5759: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5760:
1.222 brouard 5761: /* 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 5762:
1.222 brouard 5763: }
1.269 brouard 5764:
5765: /* Standard deviation of expectancies ij */
1.126 brouard 5766: fprintf(ficresstdeij,"%3.0f",age );
5767: for(i=1; i<=nlstate;i++){
5768: eip=0.;
5769: vip=0.;
5770: for(j=1; j<=nlstate;j++){
1.222 brouard 5771: eip += eij[i][j][(int)age];
5772: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5773: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5774: 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 5775: }
5776: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5777: }
5778: fprintf(ficresstdeij,"\n");
1.218 brouard 5779:
1.269 brouard 5780: /* Variance of expectancies ij */
1.126 brouard 5781: fprintf(ficrescveij,"%3.0f",age );
5782: for(i=1; i<=nlstate;i++)
5783: for(j=1; j<=nlstate;j++){
1.222 brouard 5784: cptj= (j-1)*nlstate+i;
5785: for(i2=1; i2<=nlstate;i2++)
5786: for(j2=1; j2<=nlstate;j2++){
5787: cptj2= (j2-1)*nlstate+i2;
5788: if(cptj2 <= cptj)
5789: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5790: }
1.126 brouard 5791: }
5792: fprintf(ficrescveij,"\n");
1.218 brouard 5793:
1.126 brouard 5794: }
5795: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5796: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5797: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5798: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5799: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5800: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5801: printf("\n");
5802: fprintf(ficlog,"\n");
1.218 brouard 5803:
1.126 brouard 5804: free_vector(xm,1,npar);
5805: free_vector(xp,1,npar);
5806: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5807: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5808: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5809: }
1.218 brouard 5810:
1.126 brouard 5811: /************ Variance ******************/
1.235 brouard 5812: 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 5813: {
1.279 brouard 5814: /** Variance of health expectancies
5815: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5816: * double **newm;
5817: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5818: */
1.218 brouard 5819:
5820: /* int movingaverage(); */
5821: double **dnewm,**doldm;
5822: double **dnewmp,**doldmp;
5823: int i, j, nhstepm, hstepm, h, nstepm ;
5824: int k;
5825: double *xp;
1.279 brouard 5826: double **gp, **gm; /**< for var eij */
5827: double ***gradg, ***trgradg; /**< for var eij */
5828: double **gradgp, **trgradgp; /**< for var p point j */
5829: double *gpp, *gmp; /**< for var p point j */
5830: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5831: double ***p3mat;
5832: double age,agelim, hf;
5833: /* double ***mobaverage; */
5834: int theta;
5835: char digit[4];
5836: char digitp[25];
5837:
5838: char fileresprobmorprev[FILENAMELENGTH];
5839:
5840: if(popbased==1){
5841: if(mobilav!=0)
5842: strcpy(digitp,"-POPULBASED-MOBILAV_");
5843: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5844: }
5845: else
5846: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5847:
1.218 brouard 5848: /* if (mobilav!=0) { */
5849: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5850: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5851: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5852: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5853: /* } */
5854: /* } */
5855:
5856: strcpy(fileresprobmorprev,"PRMORPREV-");
5857: sprintf(digit,"%-d",ij);
5858: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5859: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5860: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5861: strcat(fileresprobmorprev,fileresu);
5862: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5863: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5864: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5865: }
5866: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5867: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5868: pstamp(ficresprobmorprev);
5869: 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 5870: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5871: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5872: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5873: }
5874: for(j=1;j<=cptcoveff;j++)
5875: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5876: fprintf(ficresprobmorprev,"\n");
5877:
1.218 brouard 5878: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5879: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5880: fprintf(ficresprobmorprev," p.%-d SE",j);
5881: for(i=1; i<=nlstate;i++)
5882: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5883: }
5884: fprintf(ficresprobmorprev,"\n");
5885:
5886: fprintf(ficgp,"\n# Routine varevsij");
5887: fprintf(ficgp,"\nunset title \n");
5888: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5889: 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");
5890: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 5891:
1.218 brouard 5892: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5893: pstamp(ficresvij);
5894: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5895: if(popbased==1)
5896: 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);
5897: else
5898: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5899: fprintf(ficresvij,"# Age");
5900: for(i=1; i<=nlstate;i++)
5901: for(j=1; j<=nlstate;j++)
5902: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5903: fprintf(ficresvij,"\n");
5904:
5905: xp=vector(1,npar);
5906: dnewm=matrix(1,nlstate,1,npar);
5907: doldm=matrix(1,nlstate,1,nlstate);
5908: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5909: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5910:
5911: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5912: gpp=vector(nlstate+1,nlstate+ndeath);
5913: gmp=vector(nlstate+1,nlstate+ndeath);
5914: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5915:
1.218 brouard 5916: if(estepm < stepm){
5917: printf ("Problem %d lower than %d\n",estepm, stepm);
5918: }
5919: else hstepm=estepm;
5920: /* For example we decided to compute the life expectancy with the smallest unit */
5921: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5922: nhstepm is the number of hstepm from age to agelim
5923: nstepm is the number of stepm from age to agelim.
5924: Look at function hpijx to understand why because of memory size limitations,
5925: we decided (b) to get a life expectancy respecting the most precise curvature of the
5926: survival function given by stepm (the optimization length). Unfortunately it
5927: means that if the survival funtion is printed every two years of age and if
5928: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5929: results. So we changed our mind and took the option of the best precision.
5930: */
5931: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5932: agelim = AGESUP;
5933: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5934: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5935: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5936: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5937: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5938: gp=matrix(0,nhstepm,1,nlstate);
5939: gm=matrix(0,nhstepm,1,nlstate);
5940:
5941:
5942: for(theta=1; theta <=npar; theta++){
5943: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5944: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5945: }
1.279 brouard 5946: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
5947: * returns into prlim .
5948: */
1.242 brouard 5949: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 5950:
5951: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 5952: if (popbased==1) {
5953: if(mobilav ==0){
5954: for(i=1; i<=nlstate;i++)
5955: prlim[i][i]=probs[(int)age][i][ij];
5956: }else{ /* mobilav */
5957: for(i=1; i<=nlstate;i++)
5958: prlim[i][i]=mobaverage[(int)age][i][ij];
5959: }
5960: }
1.279 brouard 5961: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
5962: */
5963: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
5964: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
5965: * at horizon h in state j including mortality.
5966: */
1.218 brouard 5967: for(j=1; j<= nlstate; j++){
5968: for(h=0; h<=nhstepm; h++){
5969: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5970: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5971: }
5972: }
1.279 brouard 5973: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 5974: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 5975: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 5976: */
5977: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5978: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5979: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 5980: }
5981:
5982: /* Again with minus shift */
1.218 brouard 5983:
5984: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5985: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5986:
1.242 brouard 5987: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 5988:
5989: if (popbased==1) {
5990: if(mobilav ==0){
5991: for(i=1; i<=nlstate;i++)
5992: prlim[i][i]=probs[(int)age][i][ij];
5993: }else{ /* mobilav */
5994: for(i=1; i<=nlstate;i++)
5995: prlim[i][i]=mobaverage[(int)age][i][ij];
5996: }
5997: }
5998:
1.235 brouard 5999: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 6000:
6001: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
6002: for(h=0; h<=nhstepm; h++){
6003: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
6004: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
6005: }
6006: }
6007: /* This for computing probability of death (h=1 means
6008: computed over hstepm matrices product = hstepm*stepm months)
6009: as a weighted average of prlim.
6010: */
6011: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6012: for(i=1,gmp[j]=0.; i<= nlstate; i++)
6013: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6014: }
1.279 brouard 6015: /* end shifting computations */
6016:
6017: /**< Computing gradient matrix at horizon h
6018: */
1.218 brouard 6019: for(j=1; j<= nlstate; j++) /* vareij */
6020: for(h=0; h<=nhstepm; h++){
6021: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
6022: }
1.279 brouard 6023: /**< Gradient of overall mortality p.3 (or p.j)
6024: */
6025: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6026: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6027: }
6028:
6029: } /* End theta */
1.279 brouard 6030:
6031: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6032: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6033:
6034: for(h=0; h<=nhstepm; h++) /* veij */
6035: for(j=1; j<=nlstate;j++)
6036: for(theta=1; theta <=npar; theta++)
6037: trgradg[h][j][theta]=gradg[h][theta][j];
6038:
6039: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6040: for(theta=1; theta <=npar; theta++)
6041: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6042: /**< as well as its transposed matrix
6043: */
1.218 brouard 6044:
6045: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6046: for(i=1;i<=nlstate;i++)
6047: for(j=1;j<=nlstate;j++)
6048: vareij[i][j][(int)age] =0.;
1.279 brouard 6049:
6050: /* Computing trgradg by matcov by gradg at age and summing over h
6051: * and k (nhstepm) formula 15 of article
6052: * Lievre-Brouard-Heathcote
6053: */
6054:
1.218 brouard 6055: for(h=0;h<=nhstepm;h++){
6056: for(k=0;k<=nhstepm;k++){
6057: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6058: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6059: for(i=1;i<=nlstate;i++)
6060: for(j=1;j<=nlstate;j++)
6061: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6062: }
6063: }
6064:
1.279 brouard 6065: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6066: * p.j overall mortality formula 49 but computed directly because
6067: * we compute the grad (wix pijx) instead of grad (pijx),even if
6068: * wix is independent of theta.
6069: */
1.218 brouard 6070: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6071: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6072: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6073: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6074: varppt[j][i]=doldmp[j][i];
6075: /* end ppptj */
6076: /* x centered again */
6077:
1.242 brouard 6078: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6079:
6080: if (popbased==1) {
6081: if(mobilav ==0){
6082: for(i=1; i<=nlstate;i++)
6083: prlim[i][i]=probs[(int)age][i][ij];
6084: }else{ /* mobilav */
6085: for(i=1; i<=nlstate;i++)
6086: prlim[i][i]=mobaverage[(int)age][i][ij];
6087: }
6088: }
6089:
6090: /* This for computing probability of death (h=1 means
6091: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6092: as a weighted average of prlim.
6093: */
1.235 brouard 6094: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6095: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6096: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6097: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6098: }
6099: /* end probability of death */
6100:
6101: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6102: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6103: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6104: for(i=1; i<=nlstate;i++){
6105: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6106: }
6107: }
6108: fprintf(ficresprobmorprev,"\n");
6109:
6110: fprintf(ficresvij,"%.0f ",age );
6111: for(i=1; i<=nlstate;i++)
6112: for(j=1; j<=nlstate;j++){
6113: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6114: }
6115: fprintf(ficresvij,"\n");
6116: free_matrix(gp,0,nhstepm,1,nlstate);
6117: free_matrix(gm,0,nhstepm,1,nlstate);
6118: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6119: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6120: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6121: } /* End age */
6122: free_vector(gpp,nlstate+1,nlstate+ndeath);
6123: free_vector(gmp,nlstate+1,nlstate+ndeath);
6124: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6125: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6126: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6127: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6128: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6129: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6130: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6131: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6132: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6133: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6134: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6135: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6136: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6137: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6138: 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);
6139: /* 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 6140: */
1.218 brouard 6141: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6142: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6143:
1.218 brouard 6144: free_vector(xp,1,npar);
6145: free_matrix(doldm,1,nlstate,1,nlstate);
6146: free_matrix(dnewm,1,nlstate,1,npar);
6147: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6148: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6149: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6150: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6151: fclose(ficresprobmorprev);
6152: fflush(ficgp);
6153: fflush(fichtm);
6154: } /* end varevsij */
1.126 brouard 6155:
6156: /************ Variance of prevlim ******************/
1.269 brouard 6157: 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 6158: {
1.205 brouard 6159: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6160: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6161:
1.268 brouard 6162: double **dnewmpar,**doldm;
1.126 brouard 6163: int i, j, nhstepm, hstepm;
6164: double *xp;
6165: double *gp, *gm;
6166: double **gradg, **trgradg;
1.208 brouard 6167: double **mgm, **mgp;
1.126 brouard 6168: double age,agelim;
6169: int theta;
6170:
6171: pstamp(ficresvpl);
6172: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.241 brouard 6173: fprintf(ficresvpl,"# Age ");
6174: if(nresult >=1)
6175: fprintf(ficresvpl," Result# ");
1.126 brouard 6176: for(i=1; i<=nlstate;i++)
6177: fprintf(ficresvpl," %1d-%1d",i,i);
6178: fprintf(ficresvpl,"\n");
6179:
6180: xp=vector(1,npar);
1.268 brouard 6181: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6182: doldm=matrix(1,nlstate,1,nlstate);
6183:
6184: hstepm=1*YEARM; /* Every year of age */
6185: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6186: agelim = AGESUP;
6187: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6188: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6189: if (stepm >= YEARM) hstepm=1;
6190: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6191: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6192: mgp=matrix(1,npar,1,nlstate);
6193: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6194: gp=vector(1,nlstate);
6195: gm=vector(1,nlstate);
6196:
6197: for(theta=1; theta <=npar; theta++){
6198: for(i=1; i<=npar; i++){ /* Computes gradient */
6199: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6200: }
1.209 brouard 6201: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6202: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6203: else
1.235 brouard 6204: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6205: for(i=1;i<=nlstate;i++){
1.126 brouard 6206: gp[i] = prlim[i][i];
1.208 brouard 6207: mgp[theta][i] = prlim[i][i];
6208: }
1.126 brouard 6209: for(i=1; i<=npar; i++) /* Computes gradient */
6210: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 6211: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6212: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6213: else
1.235 brouard 6214: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6215: for(i=1;i<=nlstate;i++){
1.126 brouard 6216: gm[i] = prlim[i][i];
1.208 brouard 6217: mgm[theta][i] = prlim[i][i];
6218: }
1.126 brouard 6219: for(i=1;i<=nlstate;i++)
6220: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6221: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6222: } /* End theta */
6223:
6224: trgradg =matrix(1,nlstate,1,npar);
6225:
6226: for(j=1; j<=nlstate;j++)
6227: for(theta=1; theta <=npar; theta++)
6228: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6229: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6230: /* printf("\nmgm mgp %d ",(int)age); */
6231: /* for(j=1; j<=nlstate;j++){ */
6232: /* printf(" %d ",j); */
6233: /* for(theta=1; theta <=npar; theta++) */
6234: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6235: /* printf("\n "); */
6236: /* } */
6237: /* } */
6238: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6239: /* printf("\n gradg %d ",(int)age); */
6240: /* for(j=1; j<=nlstate;j++){ */
6241: /* printf("%d ",j); */
6242: /* for(theta=1; theta <=npar; theta++) */
6243: /* printf("%d %lf ",theta,gradg[theta][j]); */
6244: /* printf("\n "); */
6245: /* } */
6246: /* } */
1.126 brouard 6247:
6248: for(i=1;i<=nlstate;i++)
6249: varpl[i][(int)age] =0.;
1.209 brouard 6250: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6251: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6252: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6253: }else{
1.268 brouard 6254: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6255: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6256: }
1.126 brouard 6257: for(i=1;i<=nlstate;i++)
6258: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6259:
6260: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6261: if(nresult >=1)
6262: fprintf(ficresvpl,"%d ",nres );
1.126 brouard 6263: for(i=1; i<=nlstate;i++)
6264: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
6265: fprintf(ficresvpl,"\n");
6266: free_vector(gp,1,nlstate);
6267: free_vector(gm,1,nlstate);
1.208 brouard 6268: free_matrix(mgm,1,npar,1,nlstate);
6269: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6270: free_matrix(gradg,1,npar,1,nlstate);
6271: free_matrix(trgradg,1,nlstate,1,npar);
6272: } /* End age */
6273:
6274: free_vector(xp,1,npar);
6275: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6276: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6277:
6278: }
6279:
6280:
6281: /************ Variance of backprevalence limit ******************/
1.269 brouard 6282: 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 6283: {
6284: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6285: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6286:
6287: double **dnewmpar,**doldm;
6288: int i, j, nhstepm, hstepm;
6289: double *xp;
6290: double *gp, *gm;
6291: double **gradg, **trgradg;
6292: double **mgm, **mgp;
6293: double age,agelim;
6294: int theta;
6295:
6296: pstamp(ficresvbl);
6297: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6298: fprintf(ficresvbl,"# Age ");
6299: if(nresult >=1)
6300: fprintf(ficresvbl," Result# ");
6301: for(i=1; i<=nlstate;i++)
6302: fprintf(ficresvbl," %1d-%1d",i,i);
6303: fprintf(ficresvbl,"\n");
6304:
6305: xp=vector(1,npar);
6306: dnewmpar=matrix(1,nlstate,1,npar);
6307: doldm=matrix(1,nlstate,1,nlstate);
6308:
6309: hstepm=1*YEARM; /* Every year of age */
6310: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6311: agelim = AGEINF;
6312: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6313: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6314: if (stepm >= YEARM) hstepm=1;
6315: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6316: gradg=matrix(1,npar,1,nlstate);
6317: mgp=matrix(1,npar,1,nlstate);
6318: mgm=matrix(1,npar,1,nlstate);
6319: gp=vector(1,nlstate);
6320: gm=vector(1,nlstate);
6321:
6322: for(theta=1; theta <=npar; theta++){
6323: for(i=1; i<=npar; i++){ /* Computes gradient */
6324: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6325: }
6326: if(mobilavproj > 0 )
6327: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6328: else
6329: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6330: for(i=1;i<=nlstate;i++){
6331: gp[i] = bprlim[i][i];
6332: mgp[theta][i] = bprlim[i][i];
6333: }
6334: for(i=1; i<=npar; i++) /* Computes gradient */
6335: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6336: if(mobilavproj > 0 )
6337: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6338: else
6339: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6340: for(i=1;i<=nlstate;i++){
6341: gm[i] = bprlim[i][i];
6342: mgm[theta][i] = bprlim[i][i];
6343: }
6344: for(i=1;i<=nlstate;i++)
6345: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6346: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6347: } /* End theta */
6348:
6349: trgradg =matrix(1,nlstate,1,npar);
6350:
6351: for(j=1; j<=nlstate;j++)
6352: for(theta=1; theta <=npar; theta++)
6353: trgradg[j][theta]=gradg[theta][j];
6354: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6355: /* printf("\nmgm mgp %d ",(int)age); */
6356: /* for(j=1; j<=nlstate;j++){ */
6357: /* printf(" %d ",j); */
6358: /* for(theta=1; theta <=npar; theta++) */
6359: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6360: /* printf("\n "); */
6361: /* } */
6362: /* } */
6363: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6364: /* printf("\n gradg %d ",(int)age); */
6365: /* for(j=1; j<=nlstate;j++){ */
6366: /* printf("%d ",j); */
6367: /* for(theta=1; theta <=npar; theta++) */
6368: /* printf("%d %lf ",theta,gradg[theta][j]); */
6369: /* printf("\n "); */
6370: /* } */
6371: /* } */
6372:
6373: for(i=1;i<=nlstate;i++)
6374: varbpl[i][(int)age] =0.;
6375: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6376: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6377: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6378: }else{
6379: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6380: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6381: }
6382: for(i=1;i<=nlstate;i++)
6383: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6384:
6385: fprintf(ficresvbl,"%.0f ",age );
6386: if(nresult >=1)
6387: fprintf(ficresvbl,"%d ",nres );
6388: for(i=1; i<=nlstate;i++)
6389: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6390: fprintf(ficresvbl,"\n");
6391: free_vector(gp,1,nlstate);
6392: free_vector(gm,1,nlstate);
6393: free_matrix(mgm,1,npar,1,nlstate);
6394: free_matrix(mgp,1,npar,1,nlstate);
6395: free_matrix(gradg,1,npar,1,nlstate);
6396: free_matrix(trgradg,1,nlstate,1,npar);
6397: } /* End age */
6398:
6399: free_vector(xp,1,npar);
6400: free_matrix(doldm,1,nlstate,1,npar);
6401: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6402:
6403: }
6404:
6405: /************ Variance of one-step probabilities ******************/
6406: 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 6407: {
6408: int i, j=0, k1, l1, tj;
6409: int k2, l2, j1, z1;
6410: int k=0, l;
6411: int first=1, first1, first2;
6412: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6413: double **dnewm,**doldm;
6414: double *xp;
6415: double *gp, *gm;
6416: double **gradg, **trgradg;
6417: double **mu;
6418: double age, cov[NCOVMAX+1];
6419: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6420: int theta;
6421: char fileresprob[FILENAMELENGTH];
6422: char fileresprobcov[FILENAMELENGTH];
6423: char fileresprobcor[FILENAMELENGTH];
6424: double ***varpij;
6425:
6426: strcpy(fileresprob,"PROB_");
6427: strcat(fileresprob,fileres);
6428: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6429: printf("Problem with resultfile: %s\n", fileresprob);
6430: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6431: }
6432: strcpy(fileresprobcov,"PROBCOV_");
6433: strcat(fileresprobcov,fileresu);
6434: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6435: printf("Problem with resultfile: %s\n", fileresprobcov);
6436: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6437: }
6438: strcpy(fileresprobcor,"PROBCOR_");
6439: strcat(fileresprobcor,fileresu);
6440: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6441: printf("Problem with resultfile: %s\n", fileresprobcor);
6442: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6443: }
6444: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6445: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6446: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6447: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6448: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6449: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6450: pstamp(ficresprob);
6451: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6452: fprintf(ficresprob,"# Age");
6453: pstamp(ficresprobcov);
6454: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6455: fprintf(ficresprobcov,"# Age");
6456: pstamp(ficresprobcor);
6457: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6458: fprintf(ficresprobcor,"# Age");
1.126 brouard 6459:
6460:
1.222 brouard 6461: for(i=1; i<=nlstate;i++)
6462: for(j=1; j<=(nlstate+ndeath);j++){
6463: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6464: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6465: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6466: }
6467: /* fprintf(ficresprob,"\n");
6468: fprintf(ficresprobcov,"\n");
6469: fprintf(ficresprobcor,"\n");
6470: */
6471: xp=vector(1,npar);
6472: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6473: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6474: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6475: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6476: first=1;
6477: fprintf(ficgp,"\n# Routine varprob");
6478: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6479: fprintf(fichtm,"\n");
6480:
1.266 brouard 6481: 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 6482: 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);
6483: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6484: and drawn. It helps understanding how is the covariance between two incidences.\
6485: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6486: 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 6487: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6488: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6489: standard deviations wide on each axis. <br>\
6490: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6491: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6492: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6493:
1.222 brouard 6494: cov[1]=1;
6495: /* tj=cptcoveff; */
1.225 brouard 6496: tj = (int) pow(2,cptcoveff);
1.222 brouard 6497: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6498: j1=0;
1.224 brouard 6499: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6500: if (cptcovn>0) {
6501: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6502: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6503: fprintf(ficresprob, "**********\n#\n");
6504: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6505: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6506: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6507:
1.222 brouard 6508: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6509: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6510: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6511:
6512:
1.222 brouard 6513: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6514: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6515: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6516:
1.222 brouard 6517: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6518: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6519: fprintf(ficresprobcor, "**********\n#");
6520: if(invalidvarcomb[j1]){
6521: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6522: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6523: continue;
6524: }
6525: }
6526: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6527: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6528: gp=vector(1,(nlstate)*(nlstate+ndeath));
6529: gm=vector(1,(nlstate)*(nlstate+ndeath));
6530: for (age=bage; age<=fage; age ++){
6531: cov[2]=age;
6532: if(nagesqr==1)
6533: cov[3]= age*age;
6534: for (k=1; k<=cptcovn;k++) {
6535: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6536: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6537: * 1 1 1 1 1
6538: * 2 2 1 1 1
6539: * 3 1 2 1 1
6540: */
6541: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6542: }
6543: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6544: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6545: for (k=1; k<=cptcovprod;k++)
6546: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6547:
6548:
1.222 brouard 6549: for(theta=1; theta <=npar; theta++){
6550: for(i=1; i<=npar; i++)
6551: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6552:
1.222 brouard 6553: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6554:
1.222 brouard 6555: k=0;
6556: for(i=1; i<= (nlstate); i++){
6557: for(j=1; j<=(nlstate+ndeath);j++){
6558: k=k+1;
6559: gp[k]=pmmij[i][j];
6560: }
6561: }
1.220 brouard 6562:
1.222 brouard 6563: for(i=1; i<=npar; i++)
6564: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6565:
1.222 brouard 6566: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6567: k=0;
6568: for(i=1; i<=(nlstate); i++){
6569: for(j=1; j<=(nlstate+ndeath);j++){
6570: k=k+1;
6571: gm[k]=pmmij[i][j];
6572: }
6573: }
1.220 brouard 6574:
1.222 brouard 6575: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6576: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6577: }
1.126 brouard 6578:
1.222 brouard 6579: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6580: for(theta=1; theta <=npar; theta++)
6581: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6582:
1.222 brouard 6583: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6584: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6585:
1.222 brouard 6586: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6587:
1.222 brouard 6588: k=0;
6589: for(i=1; i<=(nlstate); i++){
6590: for(j=1; j<=(nlstate+ndeath);j++){
6591: k=k+1;
6592: mu[k][(int) age]=pmmij[i][j];
6593: }
6594: }
6595: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6596: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6597: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6598:
1.222 brouard 6599: /*printf("\n%d ",(int)age);
6600: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6601: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6602: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6603: }*/
1.220 brouard 6604:
1.222 brouard 6605: fprintf(ficresprob,"\n%d ",(int)age);
6606: fprintf(ficresprobcov,"\n%d ",(int)age);
6607: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6608:
1.222 brouard 6609: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6610: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6611: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6612: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6613: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6614: }
6615: i=0;
6616: for (k=1; k<=(nlstate);k++){
6617: for (l=1; l<=(nlstate+ndeath);l++){
6618: i++;
6619: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6620: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6621: for (j=1; j<=i;j++){
6622: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6623: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6624: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6625: }
6626: }
6627: }/* end of loop for state */
6628: } /* end of loop for age */
6629: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6630: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6631: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6632: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6633:
6634: /* Confidence intervalle of pij */
6635: /*
6636: fprintf(ficgp,"\nunset parametric;unset label");
6637: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6638: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6639: 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);
6640: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6641: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6642: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6643: */
6644:
6645: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6646: first1=1;first2=2;
6647: for (k2=1; k2<=(nlstate);k2++){
6648: for (l2=1; l2<=(nlstate+ndeath);l2++){
6649: if(l2==k2) continue;
6650: j=(k2-1)*(nlstate+ndeath)+l2;
6651: for (k1=1; k1<=(nlstate);k1++){
6652: for (l1=1; l1<=(nlstate+ndeath);l1++){
6653: if(l1==k1) continue;
6654: i=(k1-1)*(nlstate+ndeath)+l1;
6655: if(i<=j) continue;
6656: for (age=bage; age<=fage; age ++){
6657: if ((int)age %5==0){
6658: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6659: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6660: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6661: mu1=mu[i][(int) age]/stepm*YEARM ;
6662: mu2=mu[j][(int) age]/stepm*YEARM;
6663: c12=cv12/sqrt(v1*v2);
6664: /* Computing eigen value of matrix of covariance */
6665: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6666: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6667: if ((lc2 <0) || (lc1 <0) ){
6668: if(first2==1){
6669: first1=0;
6670: 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);
6671: }
6672: 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);
6673: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6674: /* lc2=fabs(lc2); */
6675: }
1.220 brouard 6676:
1.222 brouard 6677: /* Eigen vectors */
1.280 brouard 6678: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6679: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6680: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6681: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6682: }else
6683: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6684: /*v21=sqrt(1.-v11*v11); *//* error */
6685: v21=(lc1-v1)/cv12*v11;
6686: v12=-v21;
6687: v22=v11;
6688: tnalp=v21/v11;
6689: if(first1==1){
6690: first1=0;
6691: 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);
6692: }
6693: 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);
6694: /*printf(fignu*/
6695: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6696: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6697: if(first==1){
6698: first=0;
6699: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6700: fprintf(ficgp,"\nset parametric;unset label");
6701: 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);
6702: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6703: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6704: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6705: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6706: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6707: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6708: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6709: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6710: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6711: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6712: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6713: 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 6714: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6715: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6716: }else{
6717: first=0;
6718: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6719: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6720: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6721: 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 6722: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6723: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6724: }/* if first */
6725: } /* age mod 5 */
6726: } /* end loop age */
6727: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6728: first=1;
6729: } /*l12 */
6730: } /* k12 */
6731: } /*l1 */
6732: }/* k1 */
6733: } /* loop on combination of covariates j1 */
6734: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6735: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6736: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6737: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6738: free_vector(xp,1,npar);
6739: fclose(ficresprob);
6740: fclose(ficresprobcov);
6741: fclose(ficresprobcor);
6742: fflush(ficgp);
6743: fflush(fichtmcov);
6744: }
1.126 brouard 6745:
6746:
6747: /******************* Printing html file ***********/
1.201 brouard 6748: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6749: int lastpass, int stepm, int weightopt, char model[],\
6750: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.258 brouard 6751: int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
1.273 brouard 6752: double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
6753: double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
1.237 brouard 6754: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6755:
6756: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6757: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6758: </ul>");
1.237 brouard 6759: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6760: </ul>", model);
1.214 brouard 6761: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6762: 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",
6763: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6764: 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 6765: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6766: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6767: fprintf(fichtm,"\
6768: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6769: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6770: fprintf(fichtm,"\
1.217 brouard 6771: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6772: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6773: fprintf(fichtm,"\
1.126 brouard 6774: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6775: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6776: fprintf(fichtm,"\
1.217 brouard 6777: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6778: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6779: fprintf(fichtm,"\
1.211 brouard 6780: - (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 6781: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6782: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6783: if(prevfcast==1){
6784: fprintf(fichtm,"\
6785: - Prevalence projections by age and states: \
1.201 brouard 6786: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6787: }
1.126 brouard 6788:
6789:
1.225 brouard 6790: m=pow(2,cptcoveff);
1.222 brouard 6791: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6792:
1.264 brouard 6793: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6794:
6795: jj1=0;
6796:
6797: fprintf(fichtm," \n<ul>");
6798: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6799: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6800: if(m != 1 && TKresult[nres]!= k1)
6801: continue;
6802: jj1++;
6803: if (cptcovn > 0) {
6804: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6805: for (cpt=1; cpt<=cptcoveff;cpt++){
6806: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6807: }
6808: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6809: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6810: }
6811: fprintf(fichtm,"\">");
6812:
6813: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6814: fprintf(fichtm,"************ Results for covariates");
6815: for (cpt=1; cpt<=cptcoveff;cpt++){
6816: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6817: }
6818: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6819: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6820: }
6821: if(invalidvarcomb[k1]){
6822: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6823: continue;
6824: }
6825: fprintf(fichtm,"</a></li>");
6826: } /* cptcovn >0 */
6827: }
6828: fprintf(fichtm," \n</ul>");
6829:
1.222 brouard 6830: jj1=0;
1.237 brouard 6831:
6832: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6833: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6834: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6835: continue;
1.220 brouard 6836:
1.222 brouard 6837: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6838: jj1++;
6839: if (cptcovn > 0) {
1.264 brouard 6840: fprintf(fichtm,"\n<p><a name=\"rescov");
6841: for (cpt=1; cpt<=cptcoveff;cpt++){
6842: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6843: }
6844: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6845: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6846: }
6847: fprintf(fichtm,"\"</a>");
6848:
1.222 brouard 6849: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6850: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6851: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6852: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6853: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6854: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6855: }
1.237 brouard 6856: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6857: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6858: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6859: }
6860:
1.230 brouard 6861: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6862: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6863: if(invalidvarcomb[k1]){
6864: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6865: printf("\nCombination (%d) ignored because no cases \n",k1);
6866: continue;
6867: }
6868: }
6869: /* aij, bij */
1.259 brouard 6870: 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 6871: <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 6872: /* Pij */
1.241 brouard 6873: 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> \
6874: <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 6875: /* Quasi-incidences */
6876: 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 6877: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6878: 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 6879: 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> \
6880: <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 6881: /* Survival functions (period) in state j */
6882: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6883: 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> \
6884: <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 6885: }
6886: /* State specific survival functions (period) */
6887: for(cpt=1; cpt<=nlstate;cpt++){
6888: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6889: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.283 ! brouard 6890: <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 6891: }
6892: /* Period (stable) prevalence in each health state */
6893: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6894: 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> \
6895: <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 6896: }
6897: if(backcast==1){
6898: /* Period (stable) back prevalence in each health state */
6899: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6900: 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 6901: <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 6902: }
1.217 brouard 6903: }
1.222 brouard 6904: if(prevfcast==1){
6905: /* Projection of prevalence up to period (stable) prevalence in each health state */
6906: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6907: 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> \
6908: <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 6909: }
6910: }
1.268 brouard 6911: if(backcast==1){
6912: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
6913: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6914: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
6915: 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 \
6916: 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) \
6917: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
6918: <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 6919: }
6920: }
1.220 brouard 6921:
1.222 brouard 6922: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 6923: 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> \
6924: <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 6925: }
6926: /* } /\* end i1 *\/ */
6927: }/* End k1 */
6928: fprintf(fichtm,"</ul>");
1.126 brouard 6929:
1.222 brouard 6930: fprintf(fichtm,"\
1.126 brouard 6931: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6932: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6933: - 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 6934: But because parameters are usually highly correlated (a higher incidence of disability \
6935: and a higher incidence of recovery can give very close observed transition) it might \
6936: be very useful to look not only at linear confidence intervals estimated from the \
6937: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6938: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6939: covariance matrix of the one-step probabilities. \
6940: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6941:
1.222 brouard 6942: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6943: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6944: fprintf(fichtm,"\
1.126 brouard 6945: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6946: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6947:
1.222 brouard 6948: fprintf(fichtm,"\
1.126 brouard 6949: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6950: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6951: fprintf(fichtm,"\
1.126 brouard 6952: - 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): \
6953: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6954: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6955: fprintf(fichtm,"\
1.126 brouard 6956: - (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): \
6957: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6958: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6959: fprintf(fichtm,"\
1.128 brouard 6960: - 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 6961: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6962: fprintf(fichtm,"\
1.128 brouard 6963: - 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 6964: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6965: fprintf(fichtm,"\
1.126 brouard 6966: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6967: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6968:
6969: /* if(popforecast==1) fprintf(fichtm,"\n */
6970: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6971: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6972: /* <br>",fileres,fileres,fileres,fileres); */
6973: /* else */
6974: /* 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 6975: fflush(fichtm);
6976: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6977:
1.225 brouard 6978: m=pow(2,cptcoveff);
1.222 brouard 6979: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6980:
1.222 brouard 6981: jj1=0;
1.237 brouard 6982:
1.241 brouard 6983: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 6984: for(k1=1; k1<=m;k1++){
1.253 brouard 6985: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6986: continue;
1.222 brouard 6987: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6988: jj1++;
1.126 brouard 6989: if (cptcovn > 0) {
6990: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6991: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 6992: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
6993: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6994: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6995: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6996: }
6997:
1.126 brouard 6998: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6999:
1.222 brouard 7000: if(invalidvarcomb[k1]){
7001: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
7002: continue;
7003: }
1.126 brouard 7004: }
7005: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 7006: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 7007: 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 7008: <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 7009: }
7010: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 7011: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
7012: true period expectancies (those weighted with period prevalences are also\
7013: drawn in addition to the population based expectancies computed using\
1.241 brouard 7014: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
7015: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 7016: /* } /\* end i1 *\/ */
7017: }/* End k1 */
1.241 brouard 7018: }/* End nres */
1.222 brouard 7019: fprintf(fichtm,"</ul>");
7020: fflush(fichtm);
1.126 brouard 7021: }
7022:
7023: /******************* Gnuplot file **************/
1.270 brouard 7024: 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 7025:
7026: char dirfileres[132],optfileres[132];
1.264 brouard 7027: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7028: 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 7029: int lv=0, vlv=0, kl=0;
1.130 brouard 7030: int ng=0;
1.201 brouard 7031: int vpopbased;
1.223 brouard 7032: int ioffset; /* variable offset for columns */
1.270 brouard 7033: int iyearc=1; /* variable column for year of projection */
7034: int iagec=1; /* variable column for age of projection */
1.235 brouard 7035: int nres=0; /* Index of resultline */
1.266 brouard 7036: int istart=1; /* For starting graphs in projections */
1.219 brouard 7037:
1.126 brouard 7038: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7039: /* printf("Problem with file %s",optionfilegnuplot); */
7040: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7041: /* } */
7042:
7043: /*#ifdef windows */
7044: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7045: /*#endif */
1.225 brouard 7046: m=pow(2,cptcoveff);
1.126 brouard 7047:
1.274 brouard 7048: /* diagram of the model */
7049: fprintf(ficgp,"\n#Diagram of the model \n");
7050: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7051: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7052: 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);
7053:
7054: 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);
7055: fprintf(ficgp,"\n#show arrow\nunset label\n");
7056: 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);
7057: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7058: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7059: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7060: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7061:
1.202 brouard 7062: /* Contribution to likelihood */
7063: /* Plot the probability implied in the likelihood */
1.223 brouard 7064: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7065: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7066: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7067: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7068: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7069: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7070: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7071: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7072: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7073: 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));
7074: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7075: 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));
7076: for (i=1; i<= nlstate ; i ++) {
7077: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7078: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7079: 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);
7080: for (j=2; j<= nlstate+ndeath ; j ++) {
7081: 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);
7082: }
7083: fprintf(ficgp,";\nset out; unset ylabel;\n");
7084: }
7085: /* 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 */
7086: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7087: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7088: fprintf(ficgp,"\nset out;unset log\n");
7089: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7090:
1.126 brouard 7091: strcpy(dirfileres,optionfilefiname);
7092: strcpy(optfileres,"vpl");
1.223 brouard 7093: /* 1eme*/
1.238 brouard 7094: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7095: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7096: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7097: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7098: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7099: continue;
7100: /* We are interested in selected combination by the resultline */
1.246 brouard 7101: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.238 brouard 7102: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7103: strcpy(gplotlabel,"(");
1.238 brouard 7104: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7105: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7106: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7107: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7108: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7109: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7110: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7111: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7112: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7113: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7114: }
7115: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7116: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7117: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7118: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7119: }
7120: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7121: /* printf("\n#\n"); */
1.238 brouard 7122: fprintf(ficgp,"\n#\n");
7123: if(invalidvarcomb[k1]){
1.260 brouard 7124: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7125: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7126: continue;
7127: }
1.235 brouard 7128:
1.241 brouard 7129: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7130: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7131: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7132: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7133: 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);
7134: /* 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); */
7135: /* k1-1 error should be nres-1*/
1.238 brouard 7136: for (i=1; i<= nlstate ; i ++) {
7137: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7138: else fprintf(ficgp," %%*lf (%%*lf)");
7139: }
1.260 brouard 7140: 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 7141: for (i=1; i<= nlstate ; i ++) {
7142: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7143: else fprintf(ficgp," %%*lf (%%*lf)");
7144: }
1.260 brouard 7145: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7146: for (i=1; i<= nlstate ; i ++) {
7147: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7148: else fprintf(ficgp," %%*lf (%%*lf)");
7149: }
1.265 brouard 7150: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7151:
7152: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7153: if(cptcoveff ==0){
1.271 brouard 7154: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7155: }else{
7156: kl=0;
7157: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7158: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7159: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7160: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7161: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7162: vlv= nbcode[Tvaraff[k]][lv];
7163: kl++;
7164: /* 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 *\/ */
7165: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7166: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7167: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7168: if(k==cptcoveff){
7169: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7170: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7171: }else{
7172: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7173: kl++;
7174: }
7175: } /* end covariate */
7176: } /* end if no covariate */
7177:
1.238 brouard 7178: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
7179: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7180: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7181: if(cptcoveff ==0){
1.245 brouard 7182: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7183: }else{
7184: kl=0;
7185: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7186: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7187: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7188: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7189: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7190: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7191: kl++;
1.238 brouard 7192: /* 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 *\/ */
7193: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7194: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7195: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7196: if(k==cptcoveff){
1.245 brouard 7197: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7198: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7199: }else{
7200: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7201: kl++;
7202: }
7203: } /* end covariate */
7204: } /* end if no covariate */
1.268 brouard 7205: if(backcast == 1){
7206: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7207: /* k1-1 error should be nres-1*/
7208: for (i=1; i<= nlstate ; i ++) {
7209: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7210: else fprintf(ficgp," %%*lf (%%*lf)");
7211: }
1.271 brouard 7212: 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 7213: for (i=1; i<= nlstate ; i ++) {
7214: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7215: else fprintf(ficgp," %%*lf (%%*lf)");
7216: }
1.276 brouard 7217: 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 7218: for (i=1; i<= nlstate ; i ++) {
7219: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7220: else fprintf(ficgp," %%*lf (%%*lf)");
7221: }
1.274 brouard 7222: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7223: } /* end if backprojcast */
1.238 brouard 7224: } /* end if backcast */
1.276 brouard 7225: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7226: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7227: } /* nres */
1.201 brouard 7228: } /* k1 */
7229: } /* cpt */
1.235 brouard 7230:
7231:
1.126 brouard 7232: /*2 eme*/
1.238 brouard 7233: for (k1=1; k1<= m ; k1 ++){
7234: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7235: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7236: continue;
7237: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7238: strcpy(gplotlabel,"(");
1.238 brouard 7239: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7240: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7241: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7242: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7243: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7244: vlv= nbcode[Tvaraff[k]][lv];
7245: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7246: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7247: }
1.237 brouard 7248: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7249: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7250: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7251: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7252: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7253: }
1.264 brouard 7254: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7255: fprintf(ficgp,"\n#\n");
1.223 brouard 7256: if(invalidvarcomb[k1]){
7257: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7258: continue;
7259: }
1.219 brouard 7260:
1.241 brouard 7261: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7262: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7263: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7264: if(vpopbased==0){
1.238 brouard 7265: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7266: }else
1.238 brouard 7267: fprintf(ficgp,"\nreplot ");
7268: for (i=1; i<= nlstate+1 ; i ++) {
7269: k=2*i;
1.261 brouard 7270: 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 7271: for (j=1; j<= nlstate+1 ; j ++) {
7272: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7273: else fprintf(ficgp," %%*lf (%%*lf)");
7274: }
7275: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7276: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7277: 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 7278: for (j=1; j<= nlstate+1 ; j ++) {
7279: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7280: else fprintf(ficgp," %%*lf (%%*lf)");
7281: }
7282: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7283: 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 7284: for (j=1; j<= nlstate+1 ; j ++) {
7285: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7286: else fprintf(ficgp," %%*lf (%%*lf)");
7287: }
7288: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7289: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7290: } /* state */
7291: } /* vpopbased */
1.264 brouard 7292: 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 7293: } /* end nres */
7294: } /* k1 end 2 eme*/
7295:
7296:
7297: /*3eme*/
7298: for (k1=1; k1<= m ; k1 ++){
7299: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7300: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7301: continue;
7302:
7303: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7304: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7305: strcpy(gplotlabel,"(");
1.238 brouard 7306: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7307: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7308: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7309: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7310: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7311: vlv= nbcode[Tvaraff[k]][lv];
7312: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7313: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7314: }
7315: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7316: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7317: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7318: }
1.264 brouard 7319: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7320: fprintf(ficgp,"\n#\n");
7321: if(invalidvarcomb[k1]){
7322: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7323: continue;
7324: }
7325:
7326: /* k=2+nlstate*(2*cpt-2); */
7327: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7328: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7329: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7330: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7331: 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 7332: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7333: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7334: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7335: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7336: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7337: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7338:
1.238 brouard 7339: */
7340: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7341: 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 7342: /* 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 7343:
1.238 brouard 7344: }
1.261 brouard 7345: 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 7346: }
1.264 brouard 7347: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7348: } /* end nres */
7349: } /* end kl 3eme */
1.126 brouard 7350:
1.223 brouard 7351: /* 4eme */
1.201 brouard 7352: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7353: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7354: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7355: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7356: continue;
1.238 brouard 7357: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7358: strcpy(gplotlabel,"(");
1.238 brouard 7359: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7360: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7361: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7362: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7363: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7364: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7365: vlv= nbcode[Tvaraff[k]][lv];
7366: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7367: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7368: }
7369: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7370: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7371: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7372: }
1.264 brouard 7373: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7374: fprintf(ficgp,"\n#\n");
7375: if(invalidvarcomb[k1]){
7376: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7377: continue;
1.223 brouard 7378: }
1.238 brouard 7379:
1.241 brouard 7380: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7381: 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 7382: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7383: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7384: k=3;
7385: for (i=1; i<= nlstate ; i ++){
7386: if(i==1){
7387: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7388: }else{
7389: fprintf(ficgp,", '' ");
7390: }
7391: l=(nlstate+ndeath)*(i-1)+1;
7392: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7393: for (j=2; j<= nlstate+ndeath ; j ++)
7394: fprintf(ficgp,"+$%d",k+l+j-1);
7395: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7396: } /* nlstate */
1.264 brouard 7397: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7398: } /* end cpt state*/
7399: } /* end nres */
7400: } /* end covariate k1 */
7401:
1.220 brouard 7402: /* 5eme */
1.201 brouard 7403: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7404: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7405: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7406: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7407: continue;
1.238 brouard 7408: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7409: strcpy(gplotlabel,"(");
1.238 brouard 7410: 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);
7411: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7412: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7413: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7414: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7415: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7416: vlv= nbcode[Tvaraff[k]][lv];
7417: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7418: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7419: }
7420: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7421: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7422: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7423: }
1.264 brouard 7424: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7425: fprintf(ficgp,"\n#\n");
7426: if(invalidvarcomb[k1]){
7427: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7428: continue;
7429: }
1.227 brouard 7430:
1.241 brouard 7431: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7432: 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 7433: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7434: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7435: k=3;
7436: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7437: if(j==1)
7438: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7439: else
7440: fprintf(ficgp,", '' ");
7441: l=(nlstate+ndeath)*(cpt-1) +j;
7442: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7443: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7444: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7445: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7446: } /* nlstate */
7447: fprintf(ficgp,", '' ");
7448: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7449: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7450: l=(nlstate+ndeath)*(cpt-1) +j;
7451: if(j < nlstate)
7452: fprintf(ficgp,"$%d +",k+l);
7453: else
7454: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7455: }
1.264 brouard 7456: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7457: } /* end cpt state*/
7458: } /* end covariate */
7459: } /* end nres */
1.227 brouard 7460:
1.220 brouard 7461: /* 6eme */
1.202 brouard 7462: /* CV preval stable (period) for each covariate */
1.237 brouard 7463: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7464: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7465: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7466: continue;
1.255 brouard 7467: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7468: strcpy(gplotlabel,"(");
1.211 brouard 7469: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7470: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7471: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7472: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7473: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7474: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7475: vlv= nbcode[Tvaraff[k]][lv];
7476: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7477: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7478: }
1.237 brouard 7479: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7480: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7481: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7482: }
1.264 brouard 7483: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7484: fprintf(ficgp,"\n#\n");
1.223 brouard 7485: if(invalidvarcomb[k1]){
1.227 brouard 7486: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7487: continue;
1.223 brouard 7488: }
1.227 brouard 7489:
1.241 brouard 7490: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7491: 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 7492: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7493: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7494: k=3; /* Offset */
1.255 brouard 7495: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7496: if(i==1)
7497: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7498: else
7499: fprintf(ficgp,", '' ");
1.255 brouard 7500: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7501: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7502: for (j=2; j<= nlstate ; j ++)
7503: fprintf(ficgp,"+$%d",k+l+j-1);
7504: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7505: } /* nlstate */
1.264 brouard 7506: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7507: } /* end cpt state*/
7508: } /* end covariate */
1.227 brouard 7509:
7510:
1.220 brouard 7511: /* 7eme */
1.218 brouard 7512: if(backcast == 1){
1.217 brouard 7513: /* CV back preval stable (period) for each covariate */
1.237 brouard 7514: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7515: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7516: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7517: continue;
1.268 brouard 7518: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7519: strcpy(gplotlabel,"(");
7520: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7521: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7522: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7523: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7524: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7525: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7526: vlv= nbcode[Tvaraff[k]][lv];
7527: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7528: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7529: }
1.237 brouard 7530: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7531: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7532: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7533: }
1.264 brouard 7534: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7535: fprintf(ficgp,"\n#\n");
7536: if(invalidvarcomb[k1]){
7537: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7538: continue;
7539: }
7540:
1.241 brouard 7541: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7542: 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 7543: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7544: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7545: k=3; /* Offset */
1.268 brouard 7546: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7547: if(i==1)
7548: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7549: else
7550: fprintf(ficgp,", '' ");
7551: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7552: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7553: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7554: /* 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 7555: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7556: /* for (j=2; j<= nlstate ; j ++) */
7557: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7558: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7559: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7560: } /* nlstate */
1.264 brouard 7561: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7562: } /* end cpt state*/
7563: } /* end covariate */
7564: } /* End if backcast */
7565:
1.223 brouard 7566: /* 8eme */
1.218 brouard 7567: if(prevfcast==1){
7568: /* Projection from cross-sectional to stable (period) for each covariate */
7569:
1.237 brouard 7570: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7571: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7572: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7573: continue;
1.211 brouard 7574: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7575: strcpy(gplotlabel,"(");
1.227 brouard 7576: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
7577: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7578: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7579: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7580: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7581: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7582: vlv= nbcode[Tvaraff[k]][lv];
7583: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7584: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7585: }
1.237 brouard 7586: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7587: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7588: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7589: }
1.264 brouard 7590: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7591: fprintf(ficgp,"\n#\n");
7592: if(invalidvarcomb[k1]){
7593: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7594: continue;
7595: }
7596:
7597: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7598: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7599: 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 7600: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7601: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7602:
7603: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7604: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7605: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7606: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7607: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7608: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7609: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7610: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7611: if(i==istart){
1.227 brouard 7612: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7613: }else{
7614: fprintf(ficgp,",\\\n '' ");
7615: }
7616: if(cptcoveff ==0){ /* No covariate */
7617: ioffset=2; /* Age is in 2 */
7618: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7619: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7620: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7621: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7622: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7623: if(i==nlstate+1){
1.270 brouard 7624: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7625: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7626: fprintf(ficgp,",\\\n '' ");
7627: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7628: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7629: offyear, \
1.268 brouard 7630: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7631: }else
1.227 brouard 7632: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7633: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7634: }else{ /* more than 2 covariates */
1.270 brouard 7635: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7636: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7637: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7638: iyearc=ioffset-1;
7639: iagec=ioffset;
1.227 brouard 7640: fprintf(ficgp," u %d:(",ioffset);
7641: kl=0;
7642: strcpy(gplotcondition,"(");
7643: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7644: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7645: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7646: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7647: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7648: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7649: kl++;
7650: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7651: kl++;
7652: if(k <cptcoveff && cptcoveff>1)
7653: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7654: }
7655: strcpy(gplotcondition+strlen(gplotcondition),")");
7656: /* 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 *\/ */
7657: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7658: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7659: /* '' 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*/
7660: if(i==nlstate+1){
1.270 brouard 7661: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7662: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7663: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7664: fprintf(ficgp," u %d:(",iagec);
7665: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7666: iyearc, iagec, offyear, \
7667: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7668: /* '' 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 7669: }else{
7670: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7671: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7672: }
7673: } /* end if covariate */
7674: } /* nlstate */
1.264 brouard 7675: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7676: } /* end cpt state*/
7677: } /* end covariate */
7678: } /* End if prevfcast */
1.227 brouard 7679:
1.268 brouard 7680: if(backcast==1){
7681: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7682:
7683: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7684: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7685: if(m != 1 && TKresult[nres]!= k1)
7686: continue;
7687: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7688: strcpy(gplotlabel,"(");
7689: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7690: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7691: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7692: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7693: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7694: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7695: vlv= nbcode[Tvaraff[k]][lv];
7696: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7697: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7698: }
7699: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7700: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7701: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7702: }
7703: strcpy(gplotlabel+strlen(gplotlabel),")");
7704: fprintf(ficgp,"\n#\n");
7705: if(invalidvarcomb[k1]){
7706: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7707: continue;
7708: }
7709:
7710: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7711: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7712: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7713: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7714: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7715:
7716: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7717: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7718: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7719: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7720: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7721: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7722: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7723: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7724: if(i==istart){
7725: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7726: }else{
7727: fprintf(ficgp,",\\\n '' ");
7728: }
7729: if(cptcoveff ==0){ /* No covariate */
7730: ioffset=2; /* Age is in 2 */
7731: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7732: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7733: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7734: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7735: fprintf(ficgp," u %d:(", ioffset);
7736: if(i==nlstate+1){
1.270 brouard 7737: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7738: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7739: fprintf(ficgp,",\\\n '' ");
7740: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7741: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7742: offbyear, \
7743: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7744: }else
7745: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7746: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7747: }else{ /* more than 2 covariates */
1.270 brouard 7748: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7749: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7750: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7751: iyearc=ioffset-1;
7752: iagec=ioffset;
1.268 brouard 7753: fprintf(ficgp," u %d:(",ioffset);
7754: kl=0;
7755: strcpy(gplotcondition,"(");
7756: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7757: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7758: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7759: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7760: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7761: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7762: kl++;
7763: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7764: kl++;
7765: if(k <cptcoveff && cptcoveff>1)
7766: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7767: }
7768: strcpy(gplotcondition+strlen(gplotcondition),")");
7769: /* 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 *\/ */
7770: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7771: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7772: /* '' 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*/
7773: if(i==nlstate+1){
1.270 brouard 7774: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7775: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7776: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7777: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7778: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7779: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7780: iyearc,iagec,offbyear, \
7781: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7782: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7783: }else{
7784: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7785: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7786: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7787: }
7788: } /* end if covariate */
7789: } /* nlstate */
7790: fprintf(ficgp,"\nset out; unset label;\n");
7791: } /* end cpt state*/
7792: } /* end covariate */
7793: } /* End if backcast */
7794:
1.227 brouard 7795:
1.238 brouard 7796: /* 9eme writing MLE parameters */
7797: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7798: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7799: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7800: for(k=1; k <=(nlstate+ndeath); k++){
7801: if (k != i) {
1.227 brouard 7802: fprintf(ficgp,"# current state %d\n",k);
7803: for(j=1; j <=ncovmodel; j++){
7804: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7805: jk++;
7806: }
7807: fprintf(ficgp,"\n");
1.126 brouard 7808: }
7809: }
1.223 brouard 7810: }
1.187 brouard 7811: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7812:
1.145 brouard 7813: /*goto avoid;*/
1.238 brouard 7814: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7815: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7816: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7817: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7818: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7819: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7820: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7821: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7822: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7823: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7824: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7825: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7826: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7827: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7828: fprintf(ficgp,"#\n");
1.223 brouard 7829: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7830: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7831: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7832: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7833: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7834: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7835: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7836: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7837: continue;
1.264 brouard 7838: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7839: strcpy(gplotlabel,"(");
1.276 brouard 7840: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7841: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7842: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7843: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7844: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7845: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7846: vlv= nbcode[Tvaraff[k]][lv];
7847: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7848: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7849: }
1.237 brouard 7850: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7851: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7852: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7853: }
1.264 brouard 7854: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7855: fprintf(ficgp,"\n#\n");
1.264 brouard 7856: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7857: fprintf(ficgp,"\nset key outside ");
7858: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7859: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7860: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7861: if (ng==1){
7862: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7863: fprintf(ficgp,"\nunset log y");
7864: }else if (ng==2){
7865: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7866: fprintf(ficgp,"\nset log y");
7867: }else if (ng==3){
7868: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7869: fprintf(ficgp,"\nset log y");
7870: }else
7871: fprintf(ficgp,"\nunset title ");
7872: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7873: i=1;
7874: for(k2=1; k2<=nlstate; k2++) {
7875: k3=i;
7876: for(k=1; k<=(nlstate+ndeath); k++) {
7877: if (k != k2){
7878: switch( ng) {
7879: case 1:
7880: if(nagesqr==0)
7881: fprintf(ficgp," p%d+p%d*x",i,i+1);
7882: else /* nagesqr =1 */
7883: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7884: break;
7885: case 2: /* ng=2 */
7886: if(nagesqr==0)
7887: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7888: else /* nagesqr =1 */
7889: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7890: break;
7891: case 3:
7892: if(nagesqr==0)
7893: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7894: else /* nagesqr =1 */
7895: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7896: break;
7897: }
7898: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7899: ijp=1; /* product no age */
7900: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7901: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7902: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 7903: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7904: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
7905: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7906: if(DummyV[j]==0){
7907: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
7908: }else{ /* quantitative */
7909: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
7910: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7911: }
7912: ij++;
1.237 brouard 7913: }
1.268 brouard 7914: }
7915: }else if(cptcovprod >0){
7916: if(j==Tprod[ijp]) { /* */
7917: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
7918: if(ijp <=cptcovprod) { /* Product */
7919: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
7920: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
7921: /* 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)]); */
7922: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
7923: }else{ /* Vn is dummy and Vm is quanti */
7924: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
7925: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7926: }
7927: }else{ /* Vn*Vm Vn is quanti */
7928: if(DummyV[Tvard[ijp][2]]==0){
7929: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
7930: }else{ /* Both quanti */
7931: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7932: }
1.237 brouard 7933: }
1.268 brouard 7934: ijp++;
1.237 brouard 7935: }
1.268 brouard 7936: } /* end Tprod */
1.237 brouard 7937: } else{ /* simple covariate */
1.264 brouard 7938: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 7939: if(Dummy[j]==0){
7940: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
7941: }else{ /* quantitative */
7942: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 7943: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 7944: }
1.237 brouard 7945: } /* end simple */
7946: } /* end j */
1.223 brouard 7947: }else{
7948: i=i-ncovmodel;
7949: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
7950: fprintf(ficgp," (1.");
7951: }
1.227 brouard 7952:
1.223 brouard 7953: if(ng != 1){
7954: fprintf(ficgp,")/(1");
1.227 brouard 7955:
1.264 brouard 7956: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 7957: if(nagesqr==0)
1.264 brouard 7958: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 7959: else /* nagesqr =1 */
1.264 brouard 7960: 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 7961:
1.223 brouard 7962: ij=1;
7963: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 7964: if(cptcovage >0){
7965: if((j-2)==Tage[ij]) { /* Bug valgrind */
7966: if(ij <=cptcovage) { /* Bug valgrind */
7967: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
7968: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7969: ij++;
7970: }
7971: }
7972: }else
7973: 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 7974: }
7975: fprintf(ficgp,")");
7976: }
7977: fprintf(ficgp,")");
7978: if(ng ==2)
1.276 brouard 7979: 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 7980: else /* ng= 3 */
1.276 brouard 7981: 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 7982: }else{ /* end ng <> 1 */
7983: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 7984: 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 7985: }
7986: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
7987: fprintf(ficgp,",");
7988: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
7989: fprintf(ficgp,",");
7990: i=i+ncovmodel;
7991: } /* end k */
7992: } /* end k2 */
1.276 brouard 7993: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
7994: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 7995: } /* end k1 */
1.223 brouard 7996: } /* end ng */
7997: /* avoid: */
7998: fflush(ficgp);
1.126 brouard 7999: } /* end gnuplot */
8000:
8001:
8002: /*************** Moving average **************/
1.219 brouard 8003: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 8004: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 8005:
1.222 brouard 8006: int i, cpt, cptcod;
8007: int modcovmax =1;
8008: int mobilavrange, mob;
8009: int iage=0;
8010:
1.266 brouard 8011: double sum=0., sumr=0.;
1.222 brouard 8012: double age;
1.266 brouard 8013: double *sumnewp, *sumnewm, *sumnewmr;
8014: double *agemingood, *agemaxgood;
8015: double *agemingoodr, *agemaxgoodr;
1.222 brouard 8016:
8017:
1.278 brouard 8018: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
8019: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 8020:
8021: sumnewp = vector(1,ncovcombmax);
8022: sumnewm = vector(1,ncovcombmax);
1.266 brouard 8023: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 8024: agemingood = vector(1,ncovcombmax);
1.266 brouard 8025: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8026: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8027: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8028:
8029: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8030: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8031: sumnewp[cptcod]=0.;
1.266 brouard 8032: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8033: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8034: }
8035: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8036:
1.266 brouard 8037: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8038: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8039: else mobilavrange=mobilav;
8040: for (age=bage; age<=fage; age++)
8041: for (i=1; i<=nlstate;i++)
8042: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8043: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8044: /* We keep the original values on the extreme ages bage, fage and for
8045: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8046: we use a 5 terms etc. until the borders are no more concerned.
8047: */
8048: for (mob=3;mob <=mobilavrange;mob=mob+2){
8049: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8050: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8051: sumnewm[cptcod]=0.;
8052: for (i=1; i<=nlstate;i++){
1.222 brouard 8053: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8054: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8055: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8056: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8057: }
8058: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8059: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8060: } /* end i */
8061: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8062: } /* end cptcod */
1.222 brouard 8063: }/* end age */
8064: }/* end mob */
1.266 brouard 8065: }else{
8066: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8067: return -1;
1.266 brouard 8068: }
8069:
8070: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8071: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8072: if(invalidvarcomb[cptcod]){
8073: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8074: continue;
8075: }
1.219 brouard 8076:
1.266 brouard 8077: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8078: sumnewm[cptcod]=0.;
8079: sumnewmr[cptcod]=0.;
8080: for (i=1; i<=nlstate;i++){
8081: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8082: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8083: }
8084: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8085: agemingoodr[cptcod]=age;
8086: }
8087: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8088: agemingood[cptcod]=age;
8089: }
8090: } /* age */
8091: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8092: sumnewm[cptcod]=0.;
1.266 brouard 8093: sumnewmr[cptcod]=0.;
1.222 brouard 8094: for (i=1; i<=nlstate;i++){
8095: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8096: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8097: }
8098: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8099: agemaxgoodr[cptcod]=age;
1.222 brouard 8100: }
8101: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8102: agemaxgood[cptcod]=age;
8103: }
8104: } /* age */
8105: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8106: /* but they will change */
8107: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8108: sumnewm[cptcod]=0.;
8109: sumnewmr[cptcod]=0.;
8110: for (i=1; i<=nlstate;i++){
8111: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8112: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8113: }
8114: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8115: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8116: agemaxgoodr[cptcod]=age; /* age min */
8117: for (i=1; i<=nlstate;i++)
8118: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8119: }else{ /* bad we change the value with the values of good ages */
8120: for (i=1; i<=nlstate;i++){
8121: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8122: } /* i */
8123: } /* end bad */
8124: }else{
8125: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8126: agemaxgood[cptcod]=age;
8127: }else{ /* bad we change the value with the values of good ages */
8128: for (i=1; i<=nlstate;i++){
8129: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8130: } /* i */
8131: } /* end bad */
8132: }/* end else */
8133: sum=0.;sumr=0.;
8134: for (i=1; i<=nlstate;i++){
8135: sum+=mobaverage[(int)age][i][cptcod];
8136: sumr+=probs[(int)age][i][cptcod];
8137: }
8138: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8139: 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 8140: } /* end bad */
8141: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8142: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8143: 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 8144: } /* end bad */
8145: }/* age */
1.266 brouard 8146:
8147: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8148: sumnewm[cptcod]=0.;
1.266 brouard 8149: sumnewmr[cptcod]=0.;
1.222 brouard 8150: for (i=1; i<=nlstate;i++){
8151: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8152: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8153: }
8154: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8155: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8156: agemingoodr[cptcod]=age;
8157: for (i=1; i<=nlstate;i++)
8158: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8159: }else{ /* bad we change the value with the values of good ages */
8160: for (i=1; i<=nlstate;i++){
8161: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8162: } /* i */
8163: } /* end bad */
8164: }else{
8165: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8166: agemingood[cptcod]=age;
8167: }else{ /* bad */
8168: for (i=1; i<=nlstate;i++){
8169: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8170: } /* i */
8171: } /* end bad */
8172: }/* end else */
8173: sum=0.;sumr=0.;
8174: for (i=1; i<=nlstate;i++){
8175: sum+=mobaverage[(int)age][i][cptcod];
8176: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8177: }
1.266 brouard 8178: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8179: 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 8180: } /* end bad */
8181: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8182: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8183: 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 8184: } /* end bad */
8185: }/* age */
1.266 brouard 8186:
1.222 brouard 8187:
8188: for (age=bage; age<=fage; age++){
1.235 brouard 8189: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8190: sumnewp[cptcod]=0.;
8191: sumnewm[cptcod]=0.;
8192: for (i=1; i<=nlstate;i++){
8193: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8194: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8195: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8196: }
8197: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8198: }
8199: /* printf("\n"); */
8200: /* } */
1.266 brouard 8201:
1.222 brouard 8202: /* brutal averaging */
1.266 brouard 8203: /* for (i=1; i<=nlstate;i++){ */
8204: /* for (age=1; age<=bage; age++){ */
8205: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8206: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8207: /* } */
8208: /* for (age=fage; age<=AGESUP; age++){ */
8209: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8210: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8211: /* } */
8212: /* } /\* end i status *\/ */
8213: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8214: /* for (age=1; age<=AGESUP; age++){ */
8215: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8216: /* mobaverage[(int)age][i][cptcod]=0.; */
8217: /* } */
8218: /* } */
1.222 brouard 8219: }/* end cptcod */
1.266 brouard 8220: free_vector(agemaxgoodr,1, ncovcombmax);
8221: free_vector(agemaxgood,1, ncovcombmax);
8222: free_vector(agemingood,1, ncovcombmax);
8223: free_vector(agemingoodr,1, ncovcombmax);
8224: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8225: free_vector(sumnewm,1, ncovcombmax);
8226: free_vector(sumnewp,1, ncovcombmax);
8227: return 0;
8228: }/* End movingaverage */
1.218 brouard 8229:
1.126 brouard 8230:
8231: /************** Forecasting ******************/
1.269 brouard 8232: 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 8233: /* proj1, year, month, day of starting projection
8234: agemin, agemax range of age
8235: dateprev1 dateprev2 range of dates during which prevalence is computed
8236: anproj2 year of en of projection (same day and month as proj1).
8237: */
1.267 brouard 8238: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8239: double agec; /* generic age */
8240: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
8241: double *popeffectif,*popcount;
8242: double ***p3mat;
1.218 brouard 8243: /* double ***mobaverage; */
1.126 brouard 8244: char fileresf[FILENAMELENGTH];
8245:
8246: agelim=AGESUP;
1.211 brouard 8247: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8248: in each health status at the date of interview (if between dateprev1 and dateprev2).
8249: We still use firstpass and lastpass as another selection.
8250: */
1.214 brouard 8251: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8252: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8253:
1.201 brouard 8254: strcpy(fileresf,"F_");
8255: strcat(fileresf,fileresu);
1.126 brouard 8256: if((ficresf=fopen(fileresf,"w"))==NULL) {
8257: printf("Problem with forecast resultfile: %s\n", fileresf);
8258: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8259: }
1.235 brouard 8260: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8261: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8262:
1.225 brouard 8263: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8264:
8265:
8266: stepsize=(int) (stepm+YEARM-1)/YEARM;
8267: if (stepm<=12) stepsize=1;
8268: if(estepm < stepm){
8269: printf ("Problem %d lower than %d\n",estepm, stepm);
8270: }
1.270 brouard 8271: else{
8272: hstepm=estepm;
8273: }
8274: if(estepm > stepm){ /* Yes every two year */
8275: stepsize=2;
8276: }
1.126 brouard 8277:
8278: hstepm=hstepm/stepm;
8279: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8280: fractional in yp1 */
8281: anprojmean=yp;
8282: yp2=modf((yp1*12),&yp);
8283: mprojmean=yp;
8284: yp1=modf((yp2*30.5),&yp);
8285: jprojmean=yp;
8286: if(jprojmean==0) jprojmean=1;
8287: if(mprojmean==0) jprojmean=1;
8288:
1.227 brouard 8289: i1=pow(2,cptcoveff);
1.126 brouard 8290: if (cptcovn < 1){i1=1;}
8291:
8292: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
8293:
8294: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8295:
1.126 brouard 8296: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8297: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8298: for(k=1; k<=i1;k++){
1.253 brouard 8299: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8300: continue;
1.227 brouard 8301: if(invalidvarcomb[k]){
8302: printf("\nCombination (%d) projection ignored because no cases \n",k);
8303: continue;
8304: }
8305: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8306: for(j=1;j<=cptcoveff;j++) {
8307: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8308: }
1.235 brouard 8309: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8310: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8311: }
1.227 brouard 8312: fprintf(ficresf," yearproj age");
8313: for(j=1; j<=nlstate+ndeath;j++){
8314: for(i=1; i<=nlstate;i++)
8315: fprintf(ficresf," p%d%d",i,j);
8316: fprintf(ficresf," wp.%d",j);
8317: }
8318: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
8319: fprintf(ficresf,"\n");
8320: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.270 brouard 8321: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8322: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8323: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8324: nhstepm = nhstepm/hstepm;
8325: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8326: oldm=oldms;savm=savms;
1.268 brouard 8327: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8328: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8329: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8330: for (h=0; h<=nhstepm; h++){
8331: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8332: break;
8333: }
8334: }
8335: fprintf(ficresf,"\n");
8336: for(j=1;j<=cptcoveff;j++)
8337: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8338: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
8339:
8340: for(j=1; j<=nlstate+ndeath;j++) {
8341: ppij=0.;
8342: for(i=1; i<=nlstate;i++) {
1.278 brouard 8343: if (mobilav>=1)
8344: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8345: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8346: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8347: }
1.268 brouard 8348: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8349: } /* end i */
8350: fprintf(ficresf," %.3f", ppij);
8351: }/* end j */
1.227 brouard 8352: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8353: } /* end agec */
1.266 brouard 8354: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8355: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8356: } /* end yearp */
8357: } /* end k */
1.219 brouard 8358:
1.126 brouard 8359: fclose(ficresf);
1.215 brouard 8360: printf("End of Computing forecasting \n");
8361: fprintf(ficlog,"End of Computing forecasting\n");
8362:
1.126 brouard 8363: }
8364:
1.269 brouard 8365: /************** Back Forecasting ******************/
8366: 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 8367: /* back1, year, month, day of starting backection
8368: agemin, agemax range of age
8369: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8370: anback2 year of end of backprojection (same day and month as back1).
8371: prevacurrent and prev are prevalences.
1.267 brouard 8372: */
8373: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8374: double agec; /* generic age */
1.268 brouard 8375: double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.267 brouard 8376: double *popeffectif,*popcount;
8377: double ***p3mat;
8378: /* double ***mobaverage; */
8379: char fileresfb[FILENAMELENGTH];
8380:
1.268 brouard 8381: agelim=AGEINF;
1.267 brouard 8382: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8383: in each health status at the date of interview (if between dateprev1 and dateprev2).
8384: We still use firstpass and lastpass as another selection.
8385: */
8386: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8387: /* firstpass, lastpass, stepm, weightopt, model); */
8388:
8389: /*Do we need to compute prevalence again?*/
8390:
8391: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8392:
8393: strcpy(fileresfb,"FB_");
8394: strcat(fileresfb,fileresu);
8395: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8396: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8397: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8398: }
8399: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8400: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8401:
8402: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8403:
8404:
8405: stepsize=(int) (stepm+YEARM-1)/YEARM;
8406: if (stepm<=12) stepsize=1;
8407: if(estepm < stepm){
8408: printf ("Problem %d lower than %d\n",estepm, stepm);
8409: }
1.270 brouard 8410: else{
8411: hstepm=estepm;
8412: }
8413: if(estepm >= stepm){ /* Yes every two year */
8414: stepsize=2;
8415: }
1.267 brouard 8416:
8417: hstepm=hstepm/stepm;
8418: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8419: fractional in yp1 */
8420: anprojmean=yp;
8421: yp2=modf((yp1*12),&yp);
8422: mprojmean=yp;
8423: yp1=modf((yp2*30.5),&yp);
8424: jprojmean=yp;
8425: if(jprojmean==0) jprojmean=1;
8426: if(mprojmean==0) jprojmean=1;
8427:
8428: i1=pow(2,cptcoveff);
8429: if (cptcovn < 1){i1=1;}
8430:
8431: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.268 brouard 8432: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8433:
8434: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8435:
8436: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8437: for(k=1; k<=i1;k++){
8438: if(i1 != 1 && TKresult[nres]!= k)
8439: continue;
8440: if(invalidvarcomb[k]){
8441: printf("\nCombination (%d) projection ignored because no cases \n",k);
8442: continue;
8443: }
1.268 brouard 8444: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8445: for(j=1;j<=cptcoveff;j++) {
8446: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8447: }
8448: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8449: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8450: }
8451: fprintf(ficresfb," yearbproj age");
8452: for(j=1; j<=nlstate+ndeath;j++){
8453: for(i=1; i<=nlstate;i++)
1.268 brouard 8454: fprintf(ficresfb," b%d%d",i,j);
8455: fprintf(ficresfb," b.%d",j);
1.267 brouard 8456: }
8457: for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
8458: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8459: fprintf(ficresfb,"\n");
8460: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
1.273 brouard 8461: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8462: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8463: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8464: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8465: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8466: nhstepm = nhstepm/hstepm;
8467: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8468: oldm=oldms;savm=savms;
1.268 brouard 8469: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8470: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8471: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8472: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8473: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8474: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8475: for (h=0; h<=nhstepm; h++){
1.268 brouard 8476: if (h*hstepm/YEARM*stepm ==-yearp) {
8477: break;
8478: }
8479: }
8480: fprintf(ficresfb,"\n");
8481: for(j=1;j<=cptcoveff;j++)
8482: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8483: fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
8484: for(i=1; i<=nlstate+ndeath;i++) {
8485: ppij=0.;ppi=0.;
8486: for(j=1; j<=nlstate;j++) {
8487: /* if (mobilav==1) */
1.269 brouard 8488: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8489: ppi=ppi+prevacurrent[(int)agec][j][k];
8490: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8491: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8492: /* else { */
8493: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8494: /* } */
1.268 brouard 8495: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8496: } /* end j */
8497: if(ppi <0.99){
8498: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8499: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8500: }
8501: fprintf(ficresfb," %.3f", ppij);
8502: }/* end j */
1.267 brouard 8503: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8504: } /* end agec */
8505: } /* end yearp */
8506: } /* end k */
1.217 brouard 8507:
1.267 brouard 8508: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8509:
1.267 brouard 8510: fclose(ficresfb);
8511: printf("End of Computing Back forecasting \n");
8512: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8513:
1.267 brouard 8514: }
1.217 brouard 8515:
1.269 brouard 8516: /* Variance of prevalence limit: varprlim */
8517: 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){
8518: /*------- Variance of period (stable) prevalence------*/
8519:
8520: char fileresvpl[FILENAMELENGTH];
8521: FILE *ficresvpl;
8522: double **oldm, **savm;
8523: double **varpl; /* Variances of prevalence limits by age */
8524: int i1, k, nres, j ;
8525:
8526: strcpy(fileresvpl,"VPL_");
8527: strcat(fileresvpl,fileresu);
8528: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8529: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8530: exit(0);
8531: }
8532: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8533: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
8534:
8535: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8536: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8537:
8538: i1=pow(2,cptcoveff);
8539: if (cptcovn < 1){i1=1;}
8540:
8541: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8542: for(k=1; k<=i1;k++){
8543: if(i1 != 1 && TKresult[nres]!= k)
8544: continue;
8545: fprintf(ficresvpl,"\n#****** ");
8546: printf("\n#****** ");
8547: fprintf(ficlog,"\n#****** ");
8548: for(j=1;j<=cptcoveff;j++) {
8549: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8550: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8551: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8552: }
8553: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8554: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8555: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8556: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8557: }
8558: fprintf(ficresvpl,"******\n");
8559: printf("******\n");
8560: fprintf(ficlog,"******\n");
8561:
8562: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8563: oldm=oldms;savm=savms;
8564: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8565: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8566: /*}*/
8567: }
8568:
8569: fclose(ficresvpl);
8570: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8571: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
8572:
8573: }
8574: /* Variance of back prevalence: varbprlim */
8575: 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){
8576: /*------- Variance of back (stable) prevalence------*/
8577:
8578: char fileresvbl[FILENAMELENGTH];
8579: FILE *ficresvbl;
8580:
8581: double **oldm, **savm;
8582: double **varbpl; /* Variances of back prevalence limits by age */
8583: int i1, k, nres, j ;
8584:
8585: strcpy(fileresvbl,"VBL_");
8586: strcat(fileresvbl,fileresu);
8587: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8588: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8589: exit(0);
8590: }
8591: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8592: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8593:
8594:
8595: i1=pow(2,cptcoveff);
8596: if (cptcovn < 1){i1=1;}
8597:
8598: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8599: for(k=1; k<=i1;k++){
8600: if(i1 != 1 && TKresult[nres]!= k)
8601: continue;
8602: fprintf(ficresvbl,"\n#****** ");
8603: printf("\n#****** ");
8604: fprintf(ficlog,"\n#****** ");
8605: for(j=1;j<=cptcoveff;j++) {
8606: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8607: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8608: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8609: }
8610: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8611: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8612: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8613: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8614: }
8615: fprintf(ficresvbl,"******\n");
8616: printf("******\n");
8617: fprintf(ficlog,"******\n");
8618:
8619: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8620: oldm=oldms;savm=savms;
8621:
8622: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8623: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8624: /*}*/
8625: }
8626:
8627: fclose(ficresvbl);
8628: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8629: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8630:
8631: } /* End of varbprlim */
8632:
1.126 brouard 8633: /************** Forecasting *****not tested NB*************/
1.227 brouard 8634: /* 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 8635:
1.227 brouard 8636: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8637: /* int *popage; */
8638: /* double calagedatem, agelim, kk1, kk2; */
8639: /* double *popeffectif,*popcount; */
8640: /* double ***p3mat,***tabpop,***tabpopprev; */
8641: /* /\* double ***mobaverage; *\/ */
8642: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8643:
1.227 brouard 8644: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8645: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8646: /* agelim=AGESUP; */
8647: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8648:
1.227 brouard 8649: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8650:
8651:
1.227 brouard 8652: /* strcpy(filerespop,"POP_"); */
8653: /* strcat(filerespop,fileresu); */
8654: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8655: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8656: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8657: /* } */
8658: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8659: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8660:
1.227 brouard 8661: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8662:
1.227 brouard 8663: /* /\* if (mobilav!=0) { *\/ */
8664: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8665: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8666: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8667: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8668: /* /\* } *\/ */
8669: /* /\* } *\/ */
1.126 brouard 8670:
1.227 brouard 8671: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8672: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8673:
1.227 brouard 8674: /* agelim=AGESUP; */
1.126 brouard 8675:
1.227 brouard 8676: /* hstepm=1; */
8677: /* hstepm=hstepm/stepm; */
1.218 brouard 8678:
1.227 brouard 8679: /* if (popforecast==1) { */
8680: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8681: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8682: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8683: /* } */
8684: /* popage=ivector(0,AGESUP); */
8685: /* popeffectif=vector(0,AGESUP); */
8686: /* popcount=vector(0,AGESUP); */
1.126 brouard 8687:
1.227 brouard 8688: /* i=1; */
8689: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8690:
1.227 brouard 8691: /* imx=i; */
8692: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8693: /* } */
1.218 brouard 8694:
1.227 brouard 8695: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8696: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8697: /* k=k+1; */
8698: /* fprintf(ficrespop,"\n#******"); */
8699: /* for(j=1;j<=cptcoveff;j++) { */
8700: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8701: /* } */
8702: /* fprintf(ficrespop,"******\n"); */
8703: /* fprintf(ficrespop,"# Age"); */
8704: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8705: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8706:
1.227 brouard 8707: /* for (cpt=0; cpt<=0;cpt++) { */
8708: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8709:
1.227 brouard 8710: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8711: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8712: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8713:
1.227 brouard 8714: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8715: /* oldm=oldms;savm=savms; */
8716: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8717:
1.227 brouard 8718: /* for (h=0; h<=nhstepm; h++){ */
8719: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8720: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8721: /* } */
8722: /* for(j=1; j<=nlstate+ndeath;j++) { */
8723: /* kk1=0.;kk2=0; */
8724: /* for(i=1; i<=nlstate;i++) { */
8725: /* if (mobilav==1) */
8726: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8727: /* else { */
8728: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8729: /* } */
8730: /* } */
8731: /* if (h==(int)(calagedatem+12*cpt)){ */
8732: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8733: /* /\*fprintf(ficrespop," %.3f", kk1); */
8734: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8735: /* } */
8736: /* } */
8737: /* for(i=1; i<=nlstate;i++){ */
8738: /* kk1=0.; */
8739: /* for(j=1; j<=nlstate;j++){ */
8740: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8741: /* } */
8742: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8743: /* } */
1.218 brouard 8744:
1.227 brouard 8745: /* if (h==(int)(calagedatem+12*cpt)) */
8746: /* for(j=1; j<=nlstate;j++) */
8747: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8748: /* } */
8749: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8750: /* } */
8751: /* } */
1.218 brouard 8752:
1.227 brouard 8753: /* /\******\/ */
1.218 brouard 8754:
1.227 brouard 8755: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8756: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8757: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8758: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8759: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8760:
1.227 brouard 8761: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8762: /* oldm=oldms;savm=savms; */
8763: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8764: /* for (h=0; h<=nhstepm; h++){ */
8765: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8766: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8767: /* } */
8768: /* for(j=1; j<=nlstate+ndeath;j++) { */
8769: /* kk1=0.;kk2=0; */
8770: /* for(i=1; i<=nlstate;i++) { */
8771: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8772: /* } */
8773: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8774: /* } */
8775: /* } */
8776: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8777: /* } */
8778: /* } */
8779: /* } */
8780: /* } */
1.218 brouard 8781:
1.227 brouard 8782: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8783:
1.227 brouard 8784: /* if (popforecast==1) { */
8785: /* free_ivector(popage,0,AGESUP); */
8786: /* free_vector(popeffectif,0,AGESUP); */
8787: /* free_vector(popcount,0,AGESUP); */
8788: /* } */
8789: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8790: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8791: /* fclose(ficrespop); */
8792: /* } /\* End of popforecast *\/ */
1.218 brouard 8793:
1.126 brouard 8794: int fileappend(FILE *fichier, char *optionfich)
8795: {
8796: if((fichier=fopen(optionfich,"a"))==NULL) {
8797: printf("Problem with file: %s\n", optionfich);
8798: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8799: return (0);
8800: }
8801: fflush(fichier);
8802: return (1);
8803: }
8804:
8805:
8806: /**************** function prwizard **********************/
8807: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8808: {
8809:
8810: /* Wizard to print covariance matrix template */
8811:
1.164 brouard 8812: char ca[32], cb[32];
8813: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8814: int numlinepar;
8815:
8816: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8817: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8818: for(i=1; i <=nlstate; i++){
8819: jj=0;
8820: for(j=1; j <=nlstate+ndeath; j++){
8821: if(j==i) continue;
8822: jj++;
8823: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8824: printf("%1d%1d",i,j);
8825: fprintf(ficparo,"%1d%1d",i,j);
8826: for(k=1; k<=ncovmodel;k++){
8827: /* printf(" %lf",param[i][j][k]); */
8828: /* fprintf(ficparo," %lf",param[i][j][k]); */
8829: printf(" 0.");
8830: fprintf(ficparo," 0.");
8831: }
8832: printf("\n");
8833: fprintf(ficparo,"\n");
8834: }
8835: }
8836: printf("# Scales (for hessian or gradient estimation)\n");
8837: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8838: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8839: for(i=1; i <=nlstate; i++){
8840: jj=0;
8841: for(j=1; j <=nlstate+ndeath; j++){
8842: if(j==i) continue;
8843: jj++;
8844: fprintf(ficparo,"%1d%1d",i,j);
8845: printf("%1d%1d",i,j);
8846: fflush(stdout);
8847: for(k=1; k<=ncovmodel;k++){
8848: /* printf(" %le",delti3[i][j][k]); */
8849: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8850: printf(" 0.");
8851: fprintf(ficparo," 0.");
8852: }
8853: numlinepar++;
8854: printf("\n");
8855: fprintf(ficparo,"\n");
8856: }
8857: }
8858: printf("# Covariance matrix\n");
8859: /* # 121 Var(a12)\n\ */
8860: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8861: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8862: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8863: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8864: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8865: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8866: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8867: fflush(stdout);
8868: fprintf(ficparo,"# Covariance matrix\n");
8869: /* # 121 Var(a12)\n\ */
8870: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8871: /* # ...\n\ */
8872: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8873:
8874: for(itimes=1;itimes<=2;itimes++){
8875: jj=0;
8876: for(i=1; i <=nlstate; i++){
8877: for(j=1; j <=nlstate+ndeath; j++){
8878: if(j==i) continue;
8879: for(k=1; k<=ncovmodel;k++){
8880: jj++;
8881: ca[0]= k+'a'-1;ca[1]='\0';
8882: if(itimes==1){
8883: printf("#%1d%1d%d",i,j,k);
8884: fprintf(ficparo,"#%1d%1d%d",i,j,k);
8885: }else{
8886: printf("%1d%1d%d",i,j,k);
8887: fprintf(ficparo,"%1d%1d%d",i,j,k);
8888: /* printf(" %.5le",matcov[i][j]); */
8889: }
8890: ll=0;
8891: for(li=1;li <=nlstate; li++){
8892: for(lj=1;lj <=nlstate+ndeath; lj++){
8893: if(lj==li) continue;
8894: for(lk=1;lk<=ncovmodel;lk++){
8895: ll++;
8896: if(ll<=jj){
8897: cb[0]= lk +'a'-1;cb[1]='\0';
8898: if(ll<jj){
8899: if(itimes==1){
8900: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8901: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8902: }else{
8903: printf(" 0.");
8904: fprintf(ficparo," 0.");
8905: }
8906: }else{
8907: if(itimes==1){
8908: printf(" Var(%s%1d%1d)",ca,i,j);
8909: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
8910: }else{
8911: printf(" 0.");
8912: fprintf(ficparo," 0.");
8913: }
8914: }
8915: }
8916: } /* end lk */
8917: } /* end lj */
8918: } /* end li */
8919: printf("\n");
8920: fprintf(ficparo,"\n");
8921: numlinepar++;
8922: } /* end k*/
8923: } /*end j */
8924: } /* end i */
8925: } /* end itimes */
8926:
8927: } /* end of prwizard */
8928: /******************* Gompertz Likelihood ******************************/
8929: double gompertz(double x[])
8930: {
8931: double A,B,L=0.0,sump=0.,num=0.;
8932: int i,n=0; /* n is the size of the sample */
8933:
1.220 brouard 8934: for (i=1;i<=imx ; i++) {
1.126 brouard 8935: sump=sump+weight[i];
8936: /* sump=sump+1;*/
8937: num=num+1;
8938: }
8939:
8940:
8941: /* for (i=0; i<=imx; i++)
8942: 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]);*/
8943:
8944: for (i=1;i<=imx ; i++)
8945: {
8946: if (cens[i] == 1 && wav[i]>1)
8947: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
8948:
8949: if (cens[i] == 0 && wav[i]>1)
8950: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
8951: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
8952:
8953: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8954: if (wav[i] > 1 ) { /* ??? */
8955: L=L+A*weight[i];
8956: /* 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]);*/
8957: }
8958: }
8959:
8960: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8961:
8962: return -2*L*num/sump;
8963: }
8964:
1.136 brouard 8965: #ifdef GSL
8966: /******************* Gompertz_f Likelihood ******************************/
8967: double gompertz_f(const gsl_vector *v, void *params)
8968: {
8969: double A,B,LL=0.0,sump=0.,num=0.;
8970: double *x= (double *) v->data;
8971: int i,n=0; /* n is the size of the sample */
8972:
8973: for (i=0;i<=imx-1 ; i++) {
8974: sump=sump+weight[i];
8975: /* sump=sump+1;*/
8976: num=num+1;
8977: }
8978:
8979:
8980: /* for (i=0; i<=imx; i++)
8981: 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]);*/
8982: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
8983: for (i=1;i<=imx ; i++)
8984: {
8985: if (cens[i] == 1 && wav[i]>1)
8986: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
8987:
8988: if (cens[i] == 0 && wav[i]>1)
8989: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
8990: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
8991:
8992: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8993: if (wav[i] > 1 ) { /* ??? */
8994: LL=LL+A*weight[i];
8995: /* 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]);*/
8996: }
8997: }
8998:
8999: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
9000: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
9001:
9002: return -2*LL*num/sump;
9003: }
9004: #endif
9005:
1.126 brouard 9006: /******************* Printing html file ***********/
1.201 brouard 9007: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 9008: int lastpass, int stepm, int weightopt, char model[],\
9009: int imx, double p[],double **matcov,double agemortsup){
9010: int i,k;
9011:
9012: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
9013: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
9014: for (i=1;i<=2;i++)
9015: 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 9016: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 9017: fprintf(fichtm,"</ul>");
9018:
9019: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
9020:
9021: 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>");
9022:
9023: for (k=agegomp;k<(agemortsup-2);k++)
9024: 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]);
9025:
9026:
9027: fflush(fichtm);
9028: }
9029:
9030: /******************* Gnuplot file **************/
1.201 brouard 9031: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9032:
9033: char dirfileres[132],optfileres[132];
1.164 brouard 9034:
1.126 brouard 9035: int ng;
9036:
9037:
9038: /*#ifdef windows */
9039: fprintf(ficgp,"cd \"%s\" \n",pathc);
9040: /*#endif */
9041:
9042:
9043: strcpy(dirfileres,optionfilefiname);
9044: strcpy(optfileres,"vpl");
1.199 brouard 9045: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9046: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9047: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9048: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9049: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9050:
9051: }
9052:
1.136 brouard 9053: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9054: {
1.126 brouard 9055:
1.136 brouard 9056: /*-------- data file ----------*/
9057: FILE *fic;
9058: char dummy[]=" ";
1.240 brouard 9059: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9060: int lstra;
1.136 brouard 9061: int linei, month, year,iout;
9062: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9063: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9064: char *stratrunc;
1.223 brouard 9065:
1.240 brouard 9066: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9067: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9068:
1.240 brouard 9069: for(v=1; v <=ncovcol;v++){
9070: DummyV[v]=0;
9071: FixedV[v]=0;
9072: }
9073: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9074: DummyV[v]=1;
9075: FixedV[v]=0;
9076: }
9077: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9078: DummyV[v]=0;
9079: FixedV[v]=1;
9080: }
9081: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9082: DummyV[v]=1;
9083: FixedV[v]=1;
9084: }
9085: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9086: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9087: 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]);
9088: }
1.126 brouard 9089:
1.136 brouard 9090: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9091: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9092: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9093: }
1.126 brouard 9094:
1.136 brouard 9095: i=1;
9096: linei=0;
9097: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9098: linei=linei+1;
9099: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9100: if(line[j] == '\t')
9101: line[j] = ' ';
9102: }
9103: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9104: ;
9105: };
9106: line[j+1]=0; /* Trims blanks at end of line */
9107: if(line[0]=='#'){
9108: fprintf(ficlog,"Comment line\n%s\n",line);
9109: printf("Comment line\n%s\n",line);
9110: continue;
9111: }
9112: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9113: strcpy(line, linetmp);
1.223 brouard 9114:
9115: /* Loops on waves */
9116: for (j=maxwav;j>=1;j--){
9117: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9118: cutv(stra, strb, line, ' ');
9119: if(strb[0]=='.') { /* Missing value */
9120: lval=-1;
9121: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9122: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9123: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9124: 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);
9125: 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);
9126: return 1;
9127: }
9128: }else{
9129: errno=0;
9130: /* what_kind_of_number(strb); */
9131: dval=strtod(strb,&endptr);
9132: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9133: /* if(strb != endptr && *endptr == '\0') */
9134: /* dval=dlval; */
9135: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9136: if( strb[0]=='\0' || (*endptr != '\0')){
9137: 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);
9138: 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);
9139: return 1;
9140: }
9141: cotqvar[j][iv][i]=dval;
9142: cotvar[j][ntv+iv][i]=dval;
9143: }
9144: strcpy(line,stra);
1.223 brouard 9145: }/* end loop ntqv */
1.225 brouard 9146:
1.223 brouard 9147: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9148: cutv(stra, strb, line, ' ');
9149: if(strb[0]=='.') { /* Missing value */
9150: lval=-1;
9151: }else{
9152: errno=0;
9153: lval=strtol(strb,&endptr,10);
9154: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9155: if( strb[0]=='\0' || (*endptr != '\0')){
9156: 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);
9157: 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);
9158: return 1;
9159: }
9160: }
9161: if(lval <-1 || lval >1){
9162: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9163: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9164: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9165: For example, for multinomial values like 1, 2 and 3,\n \
9166: build V1=0 V2=0 for the reference value (1),\n \
9167: V1=1 V2=0 for (2) \n \
1.223 brouard 9168: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9169: output of IMaCh is often meaningless.\n \
1.223 brouard 9170: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9171: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9172: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9173: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9174: For example, for multinomial values like 1, 2 and 3,\n \
9175: build V1=0 V2=0 for the reference value (1),\n \
9176: V1=1 V2=0 for (2) \n \
1.223 brouard 9177: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9178: output of IMaCh is often meaningless.\n \
1.223 brouard 9179: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9180: return 1;
9181: }
9182: cotvar[j][iv][i]=(double)(lval);
9183: strcpy(line,stra);
1.223 brouard 9184: }/* end loop ntv */
1.225 brouard 9185:
1.223 brouard 9186: /* Statuses at wave */
1.137 brouard 9187: cutv(stra, strb, line, ' ');
1.223 brouard 9188: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9189: lval=-1;
1.136 brouard 9190: }else{
1.238 brouard 9191: errno=0;
9192: lval=strtol(strb,&endptr,10);
9193: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9194: if( strb[0]=='\0' || (*endptr != '\0')){
9195: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
9196: 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);
9197: return 1;
9198: }
1.136 brouard 9199: }
1.225 brouard 9200:
1.136 brouard 9201: s[j][i]=lval;
1.225 brouard 9202:
1.223 brouard 9203: /* Date of Interview */
1.136 brouard 9204: strcpy(line,stra);
9205: cutv(stra, strb,line,' ');
1.169 brouard 9206: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9207: }
1.169 brouard 9208: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9209: month=99;
9210: year=9999;
1.136 brouard 9211: }else{
1.225 brouard 9212: 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);
9213: 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);
9214: return 1;
1.136 brouard 9215: }
9216: anint[j][i]= (double) year;
9217: mint[j][i]= (double)month;
9218: strcpy(line,stra);
1.223 brouard 9219: } /* End loop on waves */
1.225 brouard 9220:
1.223 brouard 9221: /* Date of death */
1.136 brouard 9222: cutv(stra, strb,line,' ');
1.169 brouard 9223: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9224: }
1.169 brouard 9225: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9226: month=99;
9227: year=9999;
9228: }else{
1.141 brouard 9229: 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 9230: 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);
9231: return 1;
1.136 brouard 9232: }
9233: andc[i]=(double) year;
9234: moisdc[i]=(double) month;
9235: strcpy(line,stra);
9236:
1.223 brouard 9237: /* Date of birth */
1.136 brouard 9238: cutv(stra, strb,line,' ');
1.169 brouard 9239: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9240: }
1.169 brouard 9241: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9242: month=99;
9243: year=9999;
9244: }else{
1.141 brouard 9245: 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);
9246: 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 9247: return 1;
1.136 brouard 9248: }
9249: if (year==9999) {
1.141 brouard 9250: 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);
9251: 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 9252: return 1;
9253:
1.136 brouard 9254: }
9255: annais[i]=(double)(year);
9256: moisnais[i]=(double)(month);
9257: strcpy(line,stra);
1.225 brouard 9258:
1.223 brouard 9259: /* Sample weight */
1.136 brouard 9260: cutv(stra, strb,line,' ');
9261: errno=0;
9262: dval=strtod(strb,&endptr);
9263: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9264: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9265: 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 9266: fflush(ficlog);
9267: return 1;
9268: }
9269: weight[i]=dval;
9270: strcpy(line,stra);
1.225 brouard 9271:
1.223 brouard 9272: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9273: cutv(stra, strb, line, ' ');
9274: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9275: lval=-1;
1.223 brouard 9276: }else{
1.225 brouard 9277: errno=0;
9278: /* what_kind_of_number(strb); */
9279: dval=strtod(strb,&endptr);
9280: /* if(strb != endptr && *endptr == '\0') */
9281: /* dval=dlval; */
9282: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9283: if( strb[0]=='\0' || (*endptr != '\0')){
9284: 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);
9285: 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);
9286: return 1;
9287: }
9288: coqvar[iv][i]=dval;
1.226 brouard 9289: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9290: }
9291: strcpy(line,stra);
9292: }/* end loop nqv */
1.136 brouard 9293:
1.223 brouard 9294: /* Covariate values */
1.136 brouard 9295: for (j=ncovcol;j>=1;j--){
9296: cutv(stra, strb,line,' ');
1.223 brouard 9297: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9298: lval=-1;
1.136 brouard 9299: }else{
1.225 brouard 9300: errno=0;
9301: lval=strtol(strb,&endptr,10);
9302: if( strb[0]=='\0' || (*endptr != '\0')){
9303: 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);
9304: 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);
9305: return 1;
9306: }
1.136 brouard 9307: }
9308: if(lval <-1 || lval >1){
1.225 brouard 9309: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9310: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9311: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9312: For example, for multinomial values like 1, 2 and 3,\n \
9313: build V1=0 V2=0 for the reference value (1),\n \
9314: V1=1 V2=0 for (2) \n \
1.136 brouard 9315: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9316: output of IMaCh is often meaningless.\n \
1.136 brouard 9317: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9318: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9319: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9320: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9321: For example, for multinomial values like 1, 2 and 3,\n \
9322: build V1=0 V2=0 for the reference value (1),\n \
9323: V1=1 V2=0 for (2) \n \
1.136 brouard 9324: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9325: output of IMaCh is often meaningless.\n \
1.136 brouard 9326: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9327: return 1;
1.136 brouard 9328: }
9329: covar[j][i]=(double)(lval);
9330: strcpy(line,stra);
9331: }
9332: lstra=strlen(stra);
1.225 brouard 9333:
1.136 brouard 9334: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9335: stratrunc = &(stra[lstra-9]);
9336: num[i]=atol(stratrunc);
9337: }
9338: else
9339: num[i]=atol(stra);
9340: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9341: 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;}*/
9342:
9343: i=i+1;
9344: } /* End loop reading data */
1.225 brouard 9345:
1.136 brouard 9346: *imax=i-1; /* Number of individuals */
9347: fclose(fic);
1.225 brouard 9348:
1.136 brouard 9349: return (0);
1.164 brouard 9350: /* endread: */
1.225 brouard 9351: printf("Exiting readdata: ");
9352: fclose(fic);
9353: return (1);
1.223 brouard 9354: }
1.126 brouard 9355:
1.234 brouard 9356: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9357: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9358: while (*p2 == ' ')
1.234 brouard 9359: p2++;
9360: /* while ((*p1++ = *p2++) !=0) */
9361: /* ; */
9362: /* do */
9363: /* while (*p2 == ' ') */
9364: /* p2++; */
9365: /* while (*p1++ == *p2++); */
9366: *stri=p2;
1.145 brouard 9367: }
9368:
1.235 brouard 9369: int decoderesult ( char resultline[], int nres)
1.230 brouard 9370: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9371: {
1.235 brouard 9372: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9373: char resultsav[MAXLINE];
1.234 brouard 9374: int resultmodel[MAXLINE];
9375: int modelresult[MAXLINE];
1.230 brouard 9376: char stra[80], strb[80], strc[80], strd[80],stre[80];
9377:
1.234 brouard 9378: removefirstspace(&resultline);
1.233 brouard 9379: printf("decoderesult:%s\n",resultline);
1.230 brouard 9380:
9381: if (strstr(resultline,"v") !=0){
9382: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9383: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9384: return 1;
9385: }
9386: trimbb(resultsav, resultline);
9387: if (strlen(resultsav) >1){
9388: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9389: }
1.253 brouard 9390: if(j == 0){ /* Resultline but no = */
9391: TKresult[nres]=0; /* Combination for the nresult and the model */
9392: return (0);
9393: }
9394:
1.234 brouard 9395: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9396: 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);
9397: 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);
9398: }
9399: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9400: if(nbocc(resultsav,'=') >1){
9401: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9402: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9403: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9404: }else
9405: cutl(strc,strd,resultsav,'=');
1.230 brouard 9406: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9407:
1.230 brouard 9408: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9409: Tvarsel[k]=atoi(strc);
9410: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9411: /* cptcovsel++; */
9412: if (nbocc(stra,'=') >0)
9413: strcpy(resultsav,stra); /* and analyzes it */
9414: }
1.235 brouard 9415: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9416: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9417: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9418: match=0;
1.236 brouard 9419: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9420: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9421: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9422: match=1;
9423: break;
9424: }
9425: }
9426: if(match == 0){
9427: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9428: }
9429: }
9430: }
1.235 brouard 9431: /* Checking for missing or useless values in comparison of current model needs */
9432: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9433: match=0;
1.235 brouard 9434: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9435: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9436: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9437: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9438: ++match;
9439: }
9440: }
9441: }
9442: if(match == 0){
9443: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9444: }else if(match > 1){
9445: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9446: }
9447: }
1.235 brouard 9448:
1.234 brouard 9449: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9450: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9451: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9452: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9453: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9454: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9455: /* 1 0 0 0 */
9456: /* 2 1 0 0 */
9457: /* 3 0 1 0 */
9458: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9459: /* 5 0 0 1 */
9460: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9461: /* 7 0 1 1 */
9462: /* 8 1 1 1 */
1.237 brouard 9463: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9464: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9465: /* V5*age V5 known which value for nres? */
9466: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9467: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9468: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9469: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9470: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9471: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9472: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9473: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9474: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9475: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9476: k4++;;
9477: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9478: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9479: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9480: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9481: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9482: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9483: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9484: k4q++;;
9485: }
9486: }
1.234 brouard 9487:
1.235 brouard 9488: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9489: return (0);
9490: }
1.235 brouard 9491:
1.230 brouard 9492: int decodemodel( char model[], int lastobs)
9493: /**< This routine decodes the model and returns:
1.224 brouard 9494: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9495: * - nagesqr = 1 if age*age in the model, otherwise 0.
9496: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9497: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9498: * - cptcovage number of covariates with age*products =2
9499: * - cptcovs number of simple covariates
9500: * - 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
9501: * which is a new column after the 9 (ncovcol) variables.
9502: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9503: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9504: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9505: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9506: */
1.136 brouard 9507: {
1.238 brouard 9508: int i, j, k, ks, v;
1.227 brouard 9509: int j1, k1, k2, k3, k4;
1.136 brouard 9510: char modelsav[80];
1.145 brouard 9511: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9512: char *strpt;
1.136 brouard 9513:
1.145 brouard 9514: /*removespace(model);*/
1.136 brouard 9515: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9516: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9517: if (strstr(model,"AGE") !=0){
1.192 brouard 9518: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9519: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9520: return 1;
9521: }
1.141 brouard 9522: if (strstr(model,"v") !=0){
9523: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9524: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9525: return 1;
9526: }
1.187 brouard 9527: strcpy(modelsav,model);
9528: if ((strpt=strstr(model,"age*age")) !=0){
9529: printf(" strpt=%s, model=%s\n",strpt, model);
9530: if(strpt != model){
1.234 brouard 9531: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9532: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9533: corresponding column of parameters.\n",model);
1.234 brouard 9534: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9535: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9536: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9537: return 1;
1.225 brouard 9538: }
1.187 brouard 9539: nagesqr=1;
9540: if (strstr(model,"+age*age") !=0)
1.234 brouard 9541: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9542: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9543: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9544: else
1.234 brouard 9545: substrchaine(modelsav, model, "age*age");
1.187 brouard 9546: }else
9547: nagesqr=0;
9548: if (strlen(modelsav) >1){
9549: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9550: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9551: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9552: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9553: * cst, age and age*age
9554: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9555: /* including age products which are counted in cptcovage.
9556: * but the covariates which are products must be treated
9557: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9558: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9559: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9560:
9561:
1.187 brouard 9562: /* Design
9563: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9564: * < ncovcol=8 >
9565: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9566: * k= 1 2 3 4 5 6 7 8
9567: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9568: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9569: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9570: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9571: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9572: * Tage[++cptcovage]=k
9573: * if products, new covar are created after ncovcol with k1
9574: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9575: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9576: * 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
9577: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9578: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9579: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9580: * < ncovcol=8 >
9581: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9582: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9583: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9584: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9585: * p Tprod[1]@2={ 6, 5}
9586: *p Tvard[1][1]@4= {7, 8, 5, 6}
9587: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9588: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9589: *How to reorganize?
9590: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9591: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9592: * {2, 1, 4, 8, 5, 6, 3, 7}
9593: * Struct []
9594: */
1.225 brouard 9595:
1.187 brouard 9596: /* This loop fills the array Tvar from the string 'model'.*/
9597: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9598: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9599: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9600: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9601: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9602: /* k=1 Tvar[1]=2 (from V2) */
9603: /* k=5 Tvar[5] */
9604: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9605: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9606: /* } */
1.198 brouard 9607: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9608: /*
9609: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9610: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9611: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9612: }
1.187 brouard 9613: cptcovage=0;
9614: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9615: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9616: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9617: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9618: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9619: /*scanf("%d",i);*/
9620: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9621: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9622: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9623: /* covar is not filled and then is empty */
9624: cptcovprod--;
9625: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9626: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9627: Typevar[k]=1; /* 1 for age product */
9628: cptcovage++; /* Sums the number of covariates which include age as a product */
9629: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9630: /*printf("stre=%s ", stre);*/
9631: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9632: cptcovprod--;
9633: cutl(stre,strb,strc,'V');
9634: Tvar[k]=atoi(stre);
9635: Typevar[k]=1; /* 1 for age product */
9636: cptcovage++;
9637: Tage[cptcovage]=k;
9638: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9639: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9640: cptcovn++;
9641: cptcovprodnoage++;k1++;
9642: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9643: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9644: because this model-covariate is a construction we invent a new column
9645: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9646: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9647: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9648: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9649: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9650: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9651: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9652: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9653: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9654: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9655: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9656: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9657: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9658: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9659: for (i=1; i<=lastobs;i++){
9660: /* Computes the new covariate which is a product of
9661: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9662: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9663: }
9664: } /* End age is not in the model */
9665: } /* End if model includes a product */
9666: else { /* no more sum */
9667: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9668: /* scanf("%d",i);*/
9669: cutl(strd,strc,strb,'V');
9670: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9671: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9672: Tvar[k]=atoi(strd);
9673: Typevar[k]=0; /* 0 for simple covariates */
9674: }
9675: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9676: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9677: scanf("%d",i);*/
1.187 brouard 9678: } /* end of loop + on total covariates */
9679: } /* end if strlen(modelsave == 0) age*age might exist */
9680: } /* end if strlen(model == 0) */
1.136 brouard 9681:
9682: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9683: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9684:
1.136 brouard 9685: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9686: printf("cptcovprod=%d ", cptcovprod);
9687: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9688: scanf("%d ",i);*/
9689:
9690:
1.230 brouard 9691: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9692: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9693: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9694: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9695: k = 1 2 3 4 5 6 7 8 9
9696: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9697: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9698: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9699: Dummy[k] 1 0 0 0 3 1 1 2 3
9700: Tmodelind[combination of covar]=k;
1.225 brouard 9701: */
9702: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9703: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9704: /* 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 9705: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9706: printf("Model=%s\n\
9707: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9708: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9709: 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);
9710: fprintf(ficlog,"Model=%s\n\
9711: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9712: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9713: 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);
1.240 brouard 9714: for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9715: 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 */
9716: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9717: Fixed[k]= 0;
9718: Dummy[k]= 0;
1.225 brouard 9719: ncoveff++;
1.232 brouard 9720: ncovf++;
1.234 brouard 9721: nsd++;
9722: modell[k].maintype= FTYPE;
9723: TvarsD[nsd]=Tvar[k];
9724: TvarsDind[nsd]=k;
9725: TvarF[ncovf]=Tvar[k];
9726: TvarFind[ncovf]=k;
9727: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9728: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9729: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9730: Fixed[k]= 0;
9731: Dummy[k]= 0;
9732: ncoveff++;
9733: ncovf++;
9734: modell[k].maintype= FTYPE;
9735: TvarF[ncovf]=Tvar[k];
9736: TvarFind[ncovf]=k;
1.230 brouard 9737: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9738: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9739: }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 9740: Fixed[k]= 0;
9741: Dummy[k]= 1;
1.230 brouard 9742: nqfveff++;
1.234 brouard 9743: modell[k].maintype= FTYPE;
9744: modell[k].subtype= FQ;
9745: nsq++;
9746: TvarsQ[nsq]=Tvar[k];
9747: TvarsQind[nsq]=k;
1.232 brouard 9748: ncovf++;
1.234 brouard 9749: TvarF[ncovf]=Tvar[k];
9750: TvarFind[ncovf]=k;
1.231 brouard 9751: 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 9752: 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 9753: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9754: Fixed[k]= 1;
9755: Dummy[k]= 0;
1.225 brouard 9756: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9757: modell[k].maintype= VTYPE;
9758: modell[k].subtype= VD;
9759: nsd++;
9760: TvarsD[nsd]=Tvar[k];
9761: TvarsDind[nsd]=k;
9762: ncovv++; /* Only simple time varying variables */
9763: TvarV[ncovv]=Tvar[k];
1.242 brouard 9764: 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 9765: 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 */
9766: 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 9767: 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);
9768: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9769: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9770: Fixed[k]= 1;
9771: Dummy[k]= 1;
9772: nqtveff++;
9773: modell[k].maintype= VTYPE;
9774: modell[k].subtype= VQ;
9775: ncovv++; /* Only simple time varying variables */
9776: nsq++;
9777: TvarsQ[nsq]=Tvar[k];
9778: TvarsQind[nsq]=k;
9779: TvarV[ncovv]=Tvar[k];
1.242 brouard 9780: 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 9781: 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 */
9782: 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 9783: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9784: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9785: 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 9786: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9787: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9788: ncova++;
9789: TvarA[ncova]=Tvar[k];
9790: TvarAind[ncova]=k;
1.231 brouard 9791: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9792: Fixed[k]= 2;
9793: Dummy[k]= 2;
9794: modell[k].maintype= ATYPE;
9795: modell[k].subtype= APFD;
9796: /* ncoveff++; */
1.227 brouard 9797: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 9798: Fixed[k]= 2;
9799: Dummy[k]= 3;
9800: modell[k].maintype= ATYPE;
9801: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
9802: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 9803: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 9804: Fixed[k]= 3;
9805: Dummy[k]= 2;
9806: modell[k].maintype= ATYPE;
9807: modell[k].subtype= APVD; /* Product age * varying dummy */
9808: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 9809: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9810: Fixed[k]= 3;
9811: Dummy[k]= 3;
9812: modell[k].maintype= ATYPE;
9813: modell[k].subtype= APVQ; /* Product age * varying quantitative */
9814: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 9815: }
9816: }else if (Typevar[k] == 2) { /* product without age */
9817: k1=Tposprod[k];
9818: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 9819: if(Tvard[k1][2] <=ncovcol){
9820: Fixed[k]= 1;
9821: Dummy[k]= 0;
9822: modell[k].maintype= FTYPE;
9823: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
9824: ncovf++; /* Fixed variables without age */
9825: TvarF[ncovf]=Tvar[k];
9826: TvarFind[ncovf]=k;
9827: }else if(Tvard[k1][2] <=ncovcol+nqv){
9828: Fixed[k]= 0; /* or 2 ?*/
9829: Dummy[k]= 1;
9830: modell[k].maintype= FTYPE;
9831: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
9832: ncovf++; /* Varying variables without age */
9833: TvarF[ncovf]=Tvar[k];
9834: TvarFind[ncovf]=k;
9835: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9836: Fixed[k]= 1;
9837: Dummy[k]= 0;
9838: modell[k].maintype= VTYPE;
9839: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
9840: ncovv++; /* Varying variables without age */
9841: TvarV[ncovv]=Tvar[k];
9842: TvarVind[ncovv]=k;
9843: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9844: Fixed[k]= 1;
9845: Dummy[k]= 1;
9846: modell[k].maintype= VTYPE;
9847: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
9848: ncovv++; /* Varying variables without age */
9849: TvarV[ncovv]=Tvar[k];
9850: TvarVind[ncovv]=k;
9851: }
1.227 brouard 9852: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 9853: if(Tvard[k1][2] <=ncovcol){
9854: Fixed[k]= 0; /* or 2 ?*/
9855: Dummy[k]= 1;
9856: modell[k].maintype= FTYPE;
9857: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
9858: ncovf++; /* Fixed variables without age */
9859: TvarF[ncovf]=Tvar[k];
9860: TvarFind[ncovf]=k;
9861: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9862: Fixed[k]= 1;
9863: Dummy[k]= 1;
9864: modell[k].maintype= VTYPE;
9865: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
9866: ncovv++; /* Varying variables without age */
9867: TvarV[ncovv]=Tvar[k];
9868: TvarVind[ncovv]=k;
9869: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9870: Fixed[k]= 1;
9871: Dummy[k]= 1;
9872: modell[k].maintype= VTYPE;
9873: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
9874: ncovv++; /* Varying variables without age */
9875: TvarV[ncovv]=Tvar[k];
9876: TvarVind[ncovv]=k;
9877: ncovv++; /* Varying variables without age */
9878: TvarV[ncovv]=Tvar[k];
9879: TvarVind[ncovv]=k;
9880: }
1.227 brouard 9881: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 9882: if(Tvard[k1][2] <=ncovcol){
9883: Fixed[k]= 1;
9884: Dummy[k]= 1;
9885: modell[k].maintype= VTYPE;
9886: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
9887: ncovv++; /* Varying variables without age */
9888: TvarV[ncovv]=Tvar[k];
9889: TvarVind[ncovv]=k;
9890: }else if(Tvard[k1][2] <=ncovcol+nqv){
9891: Fixed[k]= 1;
9892: Dummy[k]= 1;
9893: modell[k].maintype= VTYPE;
9894: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
9895: ncovv++; /* Varying variables without age */
9896: TvarV[ncovv]=Tvar[k];
9897: TvarVind[ncovv]=k;
9898: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9899: Fixed[k]= 1;
9900: Dummy[k]= 0;
9901: modell[k].maintype= VTYPE;
9902: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
9903: ncovv++; /* Varying variables without age */
9904: TvarV[ncovv]=Tvar[k];
9905: TvarVind[ncovv]=k;
9906: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9907: Fixed[k]= 1;
9908: Dummy[k]= 1;
9909: modell[k].maintype= VTYPE;
9910: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
9911: ncovv++; /* Varying variables without age */
9912: TvarV[ncovv]=Tvar[k];
9913: TvarVind[ncovv]=k;
9914: }
1.227 brouard 9915: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9916: if(Tvard[k1][2] <=ncovcol){
9917: Fixed[k]= 1;
9918: Dummy[k]= 1;
9919: modell[k].maintype= VTYPE;
9920: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
9921: ncovv++; /* Varying variables without age */
9922: TvarV[ncovv]=Tvar[k];
9923: TvarVind[ncovv]=k;
9924: }else if(Tvard[k1][2] <=ncovcol+nqv){
9925: Fixed[k]= 1;
9926: Dummy[k]= 1;
9927: modell[k].maintype= VTYPE;
9928: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
9929: ncovv++; /* Varying variables without age */
9930: TvarV[ncovv]=Tvar[k];
9931: TvarVind[ncovv]=k;
9932: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9933: Fixed[k]= 1;
9934: Dummy[k]= 1;
9935: modell[k].maintype= VTYPE;
9936: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
9937: ncovv++; /* Varying variables without age */
9938: TvarV[ncovv]=Tvar[k];
9939: TvarVind[ncovv]=k;
9940: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9941: Fixed[k]= 1;
9942: Dummy[k]= 1;
9943: modell[k].maintype= VTYPE;
9944: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
9945: ncovv++; /* Varying variables without age */
9946: TvarV[ncovv]=Tvar[k];
9947: TvarVind[ncovv]=k;
9948: }
1.227 brouard 9949: }else{
1.240 brouard 9950: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9951: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9952: } /*end k1*/
1.225 brouard 9953: }else{
1.226 brouard 9954: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
9955: 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 9956: }
1.227 brouard 9957: 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 9958: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 9959: 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]);
9960: }
9961: /* Searching for doublons in the model */
9962: for(k1=1; k1<= cptcovt;k1++){
9963: for(k2=1; k2 <k1;k2++){
9964: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234 brouard 9965: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
9966: if(Tvar[k1]==Tvar[k2]){
9967: 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[Tvar[k1]],Dummy[Tvar[k1]]);
9968: 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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
9969: return(1);
9970: }
9971: }else if (Typevar[k1] ==2){
9972: k3=Tposprod[k1];
9973: k4=Tposprod[k2];
9974: 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])) ){
9975: 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]]);
9976: 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);
9977: return(1);
9978: }
9979: }
1.227 brouard 9980: }
9981: }
1.225 brouard 9982: }
9983: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
9984: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 9985: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
9986: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 9987: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 9988: /*endread:*/
1.225 brouard 9989: printf("Exiting decodemodel: ");
9990: return (1);
1.136 brouard 9991: }
9992:
1.169 brouard 9993: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 9994: {/* Check ages at death */
1.136 brouard 9995: int i, m;
1.218 brouard 9996: int firstone=0;
9997:
1.136 brouard 9998: for (i=1; i<=imx; i++) {
9999: for(m=2; (m<= maxwav); m++) {
10000: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
10001: anint[m][i]=9999;
1.216 brouard 10002: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
10003: s[m][i]=-1;
1.136 brouard 10004: }
10005: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 10006: *nberr = *nberr + 1;
1.218 brouard 10007: if(firstone == 0){
10008: firstone=1;
1.260 brouard 10009: 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 10010: }
1.262 brouard 10011: 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 10012: s[m][i]=-1; /* Droping the death status */
1.136 brouard 10013: }
10014: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 10015: (*nberr)++;
1.259 brouard 10016: 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 10017: 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 10018: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 10019: }
10020: }
10021: }
10022:
10023: for (i=1; i<=imx; i++) {
10024: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10025: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10026: 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 10027: if (s[m][i] >= nlstate+1) {
1.169 brouard 10028: if(agedc[i]>0){
10029: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10030: agev[m][i]=agedc[i];
1.214 brouard 10031: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10032: }else {
1.136 brouard 10033: if ((int)andc[i]!=9999){
10034: nbwarn++;
10035: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10036: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10037: agev[m][i]=-1;
10038: }
10039: }
1.169 brouard 10040: } /* agedc > 0 */
1.214 brouard 10041: } /* end if */
1.136 brouard 10042: else if(s[m][i] !=9){ /* Standard case, age in fractional
10043: years but with the precision of a month */
10044: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10045: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10046: agev[m][i]=1;
10047: else if(agev[m][i] < *agemin){
10048: *agemin=agev[m][i];
10049: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10050: }
10051: else if(agev[m][i] >*agemax){
10052: *agemax=agev[m][i];
1.156 brouard 10053: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10054: }
10055: /*agev[m][i]=anint[m][i]-annais[i];*/
10056: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10057: } /* en if 9*/
1.136 brouard 10058: else { /* =9 */
1.214 brouard 10059: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10060: agev[m][i]=1;
10061: s[m][i]=-1;
10062: }
10063: }
1.214 brouard 10064: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10065: agev[m][i]=1;
1.214 brouard 10066: else{
10067: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10068: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10069: agev[m][i]=0;
10070: }
10071: } /* End for lastpass */
10072: }
1.136 brouard 10073:
10074: for (i=1; i<=imx; i++) {
10075: for(m=firstpass; (m<=lastpass); m++){
10076: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10077: (*nberr)++;
1.136 brouard 10078: 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);
10079: 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);
10080: return 1;
10081: }
10082: }
10083: }
10084:
10085: /*for (i=1; i<=imx; i++){
10086: for (m=firstpass; (m<lastpass); m++){
10087: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10088: }
10089:
10090: }*/
10091:
10092:
1.139 brouard 10093: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10094: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10095:
10096: return (0);
1.164 brouard 10097: /* endread:*/
1.136 brouard 10098: printf("Exiting calandcheckages: ");
10099: return (1);
10100: }
10101:
1.172 brouard 10102: #if defined(_MSC_VER)
10103: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10104: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10105: //#include "stdafx.h"
10106: //#include <stdio.h>
10107: //#include <tchar.h>
10108: //#include <windows.h>
10109: //#include <iostream>
10110: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10111:
10112: LPFN_ISWOW64PROCESS fnIsWow64Process;
10113:
10114: BOOL IsWow64()
10115: {
10116: BOOL bIsWow64 = FALSE;
10117:
10118: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10119: // (HANDLE, PBOOL);
10120:
10121: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10122:
10123: HMODULE module = GetModuleHandle(_T("kernel32"));
10124: const char funcName[] = "IsWow64Process";
10125: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10126: GetProcAddress(module, funcName);
10127:
10128: if (NULL != fnIsWow64Process)
10129: {
10130: if (!fnIsWow64Process(GetCurrentProcess(),
10131: &bIsWow64))
10132: //throw std::exception("Unknown error");
10133: printf("Unknown error\n");
10134: }
10135: return bIsWow64 != FALSE;
10136: }
10137: #endif
1.177 brouard 10138:
1.191 brouard 10139: void syscompilerinfo(int logged)
1.167 brouard 10140: {
10141: /* #include "syscompilerinfo.h"*/
1.185 brouard 10142: /* command line Intel compiler 32bit windows, XP compatible:*/
10143: /* /GS /W3 /Gy
10144: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10145: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10146: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10147: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10148: */
10149: /* 64 bits */
1.185 brouard 10150: /*
10151: /GS /W3 /Gy
10152: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10153: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10154: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10155: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10156: /* Optimization are useless and O3 is slower than O2 */
10157: /*
10158: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10159: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10160: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10161: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10162: */
1.186 brouard 10163: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10164: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10165: /PDB:"visual studio
10166: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10167: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10168: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10169: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10170: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10171: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10172: uiAccess='false'"
10173: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10174: /NOLOGO /TLBID:1
10175: */
1.177 brouard 10176: #if defined __INTEL_COMPILER
1.178 brouard 10177: #if defined(__GNUC__)
10178: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10179: #endif
1.177 brouard 10180: #elif defined(__GNUC__)
1.179 brouard 10181: #ifndef __APPLE__
1.174 brouard 10182: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10183: #endif
1.177 brouard 10184: struct utsname sysInfo;
1.178 brouard 10185: int cross = CROSS;
10186: if (cross){
10187: printf("Cross-");
1.191 brouard 10188: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10189: }
1.174 brouard 10190: #endif
10191:
1.171 brouard 10192: #include <stdint.h>
1.178 brouard 10193:
1.191 brouard 10194: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10195: #if defined(__clang__)
1.191 brouard 10196: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10197: #endif
10198: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10199: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10200: #endif
10201: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10202: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10203: #endif
10204: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10205: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10206: #endif
10207: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10208: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10209: #endif
10210: #if defined(_MSC_VER)
1.191 brouard 10211: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10212: #endif
10213: #if defined(__PGI)
1.191 brouard 10214: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10215: #endif
10216: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10217: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10218: #endif
1.191 brouard 10219: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10220:
1.167 brouard 10221: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10222: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10223: // Windows (x64 and x86)
1.191 brouard 10224: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10225: #elif __unix__ // all unices, not all compilers
10226: // Unix
1.191 brouard 10227: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10228: #elif __linux__
10229: // linux
1.191 brouard 10230: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10231: #elif __APPLE__
1.174 brouard 10232: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10233: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10234: #endif
10235:
10236: /* __MINGW32__ */
10237: /* __CYGWIN__ */
10238: /* __MINGW64__ */
10239: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10240: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10241: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10242: /* _WIN64 // Defined for applications for Win64. */
10243: /* _M_X64 // Defined for compilations that target x64 processors. */
10244: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10245:
1.167 brouard 10246: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10247: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10248: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10249: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10250: #else
1.191 brouard 10251: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10252: #endif
10253:
1.169 brouard 10254: #if defined(__GNUC__)
10255: # if defined(__GNUC_PATCHLEVEL__)
10256: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10257: + __GNUC_MINOR__ * 100 \
10258: + __GNUC_PATCHLEVEL__)
10259: # else
10260: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10261: + __GNUC_MINOR__ * 100)
10262: # endif
1.174 brouard 10263: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10264: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10265:
10266: if (uname(&sysInfo) != -1) {
10267: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10268: 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 10269: }
10270: else
10271: perror("uname() error");
1.179 brouard 10272: //#ifndef __INTEL_COMPILER
10273: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10274: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10275: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10276: #endif
1.169 brouard 10277: #endif
1.172 brouard 10278:
10279: // void main()
10280: // {
1.169 brouard 10281: #if defined(_MSC_VER)
1.174 brouard 10282: if (IsWow64()){
1.191 brouard 10283: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10284: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10285: }
10286: else{
1.191 brouard 10287: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10288: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10289: }
1.172 brouard 10290: // printf("\nPress Enter to continue...");
10291: // getchar();
10292: // }
10293:
1.169 brouard 10294: #endif
10295:
1.167 brouard 10296:
1.219 brouard 10297: }
1.136 brouard 10298:
1.219 brouard 10299: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 10300: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 brouard 10301: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10302: /* double ftolpl = 1.e-10; */
1.180 brouard 10303: double age, agebase, agelim;
1.203 brouard 10304: double tot;
1.180 brouard 10305:
1.202 brouard 10306: strcpy(filerespl,"PL_");
10307: strcat(filerespl,fileresu);
10308: if((ficrespl=fopen(filerespl,"w"))==NULL) {
10309: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10310: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10311: }
1.227 brouard 10312: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
10313: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10314: pstamp(ficrespl);
1.203 brouard 10315: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10316: fprintf(ficrespl,"#Age ");
10317: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10318: fprintf(ficrespl,"\n");
1.180 brouard 10319:
1.219 brouard 10320: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10321:
1.219 brouard 10322: agebase=ageminpar;
10323: agelim=agemaxpar;
1.180 brouard 10324:
1.227 brouard 10325: /* i1=pow(2,ncoveff); */
1.234 brouard 10326: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10327: if (cptcovn < 1){i1=1;}
1.180 brouard 10328:
1.238 brouard 10329: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10330: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10331: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10332: continue;
1.235 brouard 10333:
1.238 brouard 10334: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10335: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10336: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10337: /* k=k+1; */
10338: /* to clean */
10339: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10340: fprintf(ficrespl,"#******");
10341: printf("#******");
10342: fprintf(ficlog,"#******");
10343: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10344: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10345: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10346: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10347: }
10348: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10349: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10350: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10351: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10352: }
10353: fprintf(ficrespl,"******\n");
10354: printf("******\n");
10355: fprintf(ficlog,"******\n");
10356: if(invalidvarcomb[k]){
10357: printf("\nCombination (%d) ignored because no case \n",k);
10358: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10359: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10360: continue;
10361: }
1.219 brouard 10362:
1.238 brouard 10363: fprintf(ficrespl,"#Age ");
10364: for(j=1;j<=cptcoveff;j++) {
10365: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10366: }
10367: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10368: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10369:
1.238 brouard 10370: for (age=agebase; age<=agelim; age++){
10371: /* for (age=agebase; age<=agebase; age++){ */
10372: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10373: fprintf(ficrespl,"%.0f ",age );
10374: for(j=1;j<=cptcoveff;j++)
10375: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10376: tot=0.;
10377: for(i=1; i<=nlstate;i++){
10378: tot += prlim[i][i];
10379: fprintf(ficrespl," %.5f", prlim[i][i]);
10380: }
10381: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10382: } /* Age */
10383: /* was end of cptcod */
10384: } /* cptcov */
10385: } /* nres */
1.219 brouard 10386: return 0;
1.180 brouard 10387: }
10388:
1.218 brouard 10389: 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){
10390: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10391:
10392: /* Computes the back prevalence limit for any combination of covariate values
10393: * at any age between ageminpar and agemaxpar
10394: */
1.235 brouard 10395: int i, j, k, i1, nres=0 ;
1.217 brouard 10396: /* double ftolpl = 1.e-10; */
10397: double age, agebase, agelim;
10398: double tot;
1.218 brouard 10399: /* double ***mobaverage; */
10400: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10401:
10402: strcpy(fileresplb,"PLB_");
10403: strcat(fileresplb,fileresu);
10404: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
10405: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10406: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10407: }
10408: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10409: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10410: pstamp(ficresplb);
10411: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
10412: fprintf(ficresplb,"#Age ");
10413: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10414: fprintf(ficresplb,"\n");
10415:
1.218 brouard 10416:
10417: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10418:
10419: agebase=ageminpar;
10420: agelim=agemaxpar;
10421:
10422:
1.227 brouard 10423: i1=pow(2,cptcoveff);
1.218 brouard 10424: if (cptcovn < 1){i1=1;}
1.227 brouard 10425:
1.238 brouard 10426: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10427: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10428: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10429: continue;
10430: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10431: fprintf(ficresplb,"#******");
10432: printf("#******");
10433: fprintf(ficlog,"#******");
10434: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10435: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10436: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10437: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10438: }
10439: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10440: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10441: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10442: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10443: }
10444: fprintf(ficresplb,"******\n");
10445: printf("******\n");
10446: fprintf(ficlog,"******\n");
10447: if(invalidvarcomb[k]){
10448: printf("\nCombination (%d) ignored because no cases \n",k);
10449: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10450: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10451: continue;
10452: }
1.218 brouard 10453:
1.238 brouard 10454: fprintf(ficresplb,"#Age ");
10455: for(j=1;j<=cptcoveff;j++) {
10456: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10457: }
10458: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10459: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10460:
10461:
1.238 brouard 10462: for (age=agebase; age<=agelim; age++){
10463: /* for (age=agebase; age<=agebase; age++){ */
10464: if(mobilavproj > 0){
10465: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10466: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10467: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10468: }else if (mobilavproj == 0){
10469: 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);
10470: 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);
10471: exit(1);
10472: }else{
10473: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10474: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10475: /* printf("TOTOT\n"); */
10476: /* exit(1); */
1.238 brouard 10477: }
10478: fprintf(ficresplb,"%.0f ",age );
10479: for(j=1;j<=cptcoveff;j++)
10480: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10481: tot=0.;
10482: for(i=1; i<=nlstate;i++){
10483: tot += bprlim[i][i];
10484: fprintf(ficresplb," %.5f", bprlim[i][i]);
10485: }
10486: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10487: } /* Age */
10488: /* was end of cptcod */
1.255 brouard 10489: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10490: } /* end of any combination */
10491: } /* end of nres */
1.218 brouard 10492: /* hBijx(p, bage, fage); */
10493: /* fclose(ficrespijb); */
10494:
10495: return 0;
1.217 brouard 10496: }
1.218 brouard 10497:
1.180 brouard 10498: int hPijx(double *p, int bage, int fage){
10499: /*------------- h Pij x at various ages ------------*/
10500:
10501: int stepsize;
10502: int agelim;
10503: int hstepm;
10504: int nhstepm;
1.235 brouard 10505: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10506:
10507: double agedeb;
10508: double ***p3mat;
10509:
1.201 brouard 10510: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10511: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10512: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10513: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10514: }
10515: printf("Computing pij: result on file '%s' \n", filerespij);
10516: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10517:
10518: stepsize=(int) (stepm+YEARM-1)/YEARM;
10519: /*if (stepm<=24) stepsize=2;*/
10520:
10521: agelim=AGESUP;
10522: hstepm=stepsize*YEARM; /* Every year of age */
10523: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10524:
1.180 brouard 10525: /* hstepm=1; aff par mois*/
10526: pstamp(ficrespij);
10527: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10528: i1= pow(2,cptcoveff);
1.218 brouard 10529: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10530: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10531: /* k=k+1; */
1.235 brouard 10532: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10533: for(k=1; k<=i1;k++){
1.253 brouard 10534: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10535: continue;
1.183 brouard 10536: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10537: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10538: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10539: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10540: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10541: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10542: }
1.183 brouard 10543: fprintf(ficrespij,"******\n");
10544:
10545: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10546: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10547: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10548:
10549: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10550:
1.183 brouard 10551: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10552: oldm=oldms;savm=savms;
1.235 brouard 10553: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10554: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10555: for(i=1; i<=nlstate;i++)
10556: for(j=1; j<=nlstate+ndeath;j++)
10557: fprintf(ficrespij," %1d-%1d",i,j);
10558: fprintf(ficrespij,"\n");
10559: for (h=0; h<=nhstepm; h++){
10560: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10561: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10562: for(i=1; i<=nlstate;i++)
10563: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10564: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10565: fprintf(ficrespij,"\n");
10566: }
1.183 brouard 10567: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10568: fprintf(ficrespij,"\n");
10569: }
1.180 brouard 10570: /*}*/
10571: }
1.218 brouard 10572: return 0;
1.180 brouard 10573: }
1.218 brouard 10574:
10575: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10576: /*------------- h Bij x at various ages ------------*/
10577:
10578: int stepsize;
1.218 brouard 10579: /* int agelim; */
10580: int ageminl;
1.217 brouard 10581: int hstepm;
10582: int nhstepm;
1.238 brouard 10583: int h, i, i1, j, k, nres;
1.218 brouard 10584:
1.217 brouard 10585: double agedeb;
10586: double ***p3mat;
1.218 brouard 10587:
10588: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10589: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10590: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10591: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10592: }
10593: printf("Computing pij back: result on file '%s' \n", filerespijb);
10594: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10595:
10596: stepsize=(int) (stepm+YEARM-1)/YEARM;
10597: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10598:
1.218 brouard 10599: /* agelim=AGESUP; */
10600: ageminl=30;
10601: hstepm=stepsize*YEARM; /* Every year of age */
10602: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10603:
10604: /* hstepm=1; aff par mois*/
10605: pstamp(ficrespijb);
1.255 brouard 10606: 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 10607: i1= pow(2,cptcoveff);
1.218 brouard 10608: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10609: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10610: /* k=k+1; */
1.238 brouard 10611: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10612: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10613: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10614: continue;
10615: fprintf(ficrespijb,"\n#****** ");
10616: for(j=1;j<=cptcoveff;j++)
10617: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10618: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10619: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10620: }
10621: fprintf(ficrespijb,"******\n");
1.264 brouard 10622: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10623: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10624: continue;
10625: }
10626:
10627: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10628: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10629: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
10630: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10631: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
10632:
10633: /* nhstepm=nhstepm*YEARM; aff par mois*/
10634:
1.266 brouard 10635: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10636: /* and memory limitations if stepm is small */
10637:
1.238 brouard 10638: /* oldm=oldms;savm=savms; */
10639: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10640: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10641: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10642: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10643: for(i=1; i<=nlstate;i++)
10644: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10645: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10646: fprintf(ficrespijb,"\n");
1.238 brouard 10647: for (h=0; h<=nhstepm; h++){
10648: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10649: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10650: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10651: for(i=1; i<=nlstate;i++)
10652: for(j=1; j<=nlstate+ndeath;j++)
10653: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10654: fprintf(ficrespijb,"\n");
10655: }
10656: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10657: fprintf(ficrespijb,"\n");
10658: } /* end age deb */
10659: } /* end combination */
10660: } /* end nres */
1.218 brouard 10661: return 0;
10662: } /* hBijx */
1.217 brouard 10663:
1.180 brouard 10664:
1.136 brouard 10665: /***********************************************/
10666: /**************** Main Program *****************/
10667: /***********************************************/
10668:
10669: int main(int argc, char *argv[])
10670: {
10671: #ifdef GSL
10672: const gsl_multimin_fminimizer_type *T;
10673: size_t iteri = 0, it;
10674: int rval = GSL_CONTINUE;
10675: int status = GSL_SUCCESS;
10676: double ssval;
10677: #endif
10678: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 10679: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 10680: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10681: int jj, ll, li, lj, lk;
1.136 brouard 10682: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10683: int num_filled;
1.136 brouard 10684: int itimes;
10685: int NDIM=2;
10686: int vpopbased=0;
1.235 brouard 10687: int nres=0;
1.258 brouard 10688: int endishere=0;
1.277 brouard 10689: int noffset=0;
1.274 brouard 10690: int ncurrv=0; /* Temporary variable */
10691:
1.164 brouard 10692: char ca[32], cb[32];
1.136 brouard 10693: /* FILE *fichtm; *//* Html File */
10694: /* FILE *ficgp;*/ /*Gnuplot File */
10695: struct stat info;
1.191 brouard 10696: double agedeb=0.;
1.194 brouard 10697:
10698: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10699: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10700:
1.165 brouard 10701: double fret;
1.191 brouard 10702: double dum=0.; /* Dummy variable */
1.136 brouard 10703: double ***p3mat;
1.218 brouard 10704: /* double ***mobaverage; */
1.164 brouard 10705:
10706: char line[MAXLINE];
1.197 brouard 10707: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10708:
1.234 brouard 10709: char modeltemp[MAXLINE];
1.230 brouard 10710: char resultline[MAXLINE];
10711:
1.136 brouard 10712: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10713: char *tok, *val; /* pathtot */
1.136 brouard 10714: int firstobs=1, lastobs=10;
1.195 brouard 10715: int c, h , cpt, c2;
1.191 brouard 10716: int jl=0;
10717: int i1, j1, jk, stepsize=0;
1.194 brouard 10718: int count=0;
10719:
1.164 brouard 10720: int *tab;
1.136 brouard 10721: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 10722: int backcast=0;
1.136 brouard 10723: int mobilav=0,popforecast=0;
1.191 brouard 10724: int hstepm=0, nhstepm=0;
1.136 brouard 10725: int agemortsup;
10726: float sumlpop=0.;
10727: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10728: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10729:
1.191 brouard 10730: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10731: double ftolpl=FTOL;
10732: double **prlim;
1.217 brouard 10733: double **bprlim;
1.136 brouard 10734: double ***param; /* Matrix of parameters */
1.251 brouard 10735: double ***paramstart; /* Matrix of starting parameter values */
10736: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10737: double **matcov; /* Matrix of covariance */
1.203 brouard 10738: double **hess; /* Hessian matrix */
1.136 brouard 10739: double ***delti3; /* Scale */
10740: double *delti; /* Scale */
10741: double ***eij, ***vareij;
10742: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10743:
1.136 brouard 10744: double *epj, vepp;
1.164 brouard 10745:
1.273 brouard 10746: double dateprev1, dateprev2;
10747: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
10748: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
1.217 brouard 10749:
1.136 brouard 10750: double **ximort;
1.145 brouard 10751: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10752: int *dcwave;
10753:
1.164 brouard 10754: char z[1]="c";
1.136 brouard 10755:
10756: /*char *strt;*/
10757: char strtend[80];
1.126 brouard 10758:
1.164 brouard 10759:
1.126 brouard 10760: /* setlocale (LC_ALL, ""); */
10761: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10762: /* textdomain (PACKAGE); */
10763: /* setlocale (LC_CTYPE, ""); */
10764: /* setlocale (LC_MESSAGES, ""); */
10765:
10766: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10767: rstart_time = time(NULL);
10768: /* (void) gettimeofday(&start_time,&tzp);*/
10769: start_time = *localtime(&rstart_time);
1.126 brouard 10770: curr_time=start_time;
1.157 brouard 10771: /*tml = *localtime(&start_time.tm_sec);*/
10772: /* strcpy(strstart,asctime(&tml)); */
10773: strcpy(strstart,asctime(&start_time));
1.126 brouard 10774:
10775: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10776: /* tp.tm_sec = tp.tm_sec +86400; */
10777: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10778: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10779: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10780: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10781: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 10782: /* strt=asctime(&tmg); */
10783: /* printf("Time(after) =%s",strstart); */
10784: /* (void) time (&time_value);
10785: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
10786: * tm = *localtime(&time_value);
10787: * strstart=asctime(&tm);
10788: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
10789: */
10790:
10791: nberr=0; /* Number of errors and warnings */
10792: nbwarn=0;
1.184 brouard 10793: #ifdef WIN32
10794: _getcwd(pathcd, size);
10795: #else
1.126 brouard 10796: getcwd(pathcd, size);
1.184 brouard 10797: #endif
1.191 brouard 10798: syscompilerinfo(0);
1.196 brouard 10799: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 10800: if(argc <=1){
10801: printf("\nEnter the parameter file name: ");
1.205 brouard 10802: if(!fgets(pathr,FILENAMELENGTH,stdin)){
10803: printf("ERROR Empty parameter file name\n");
10804: goto end;
10805: }
1.126 brouard 10806: i=strlen(pathr);
10807: if(pathr[i-1]=='\n')
10808: pathr[i-1]='\0';
1.156 brouard 10809: i=strlen(pathr);
1.205 brouard 10810: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 10811: pathr[i-1]='\0';
1.205 brouard 10812: }
10813: i=strlen(pathr);
10814: if( i==0 ){
10815: printf("ERROR Empty parameter file name\n");
10816: goto end;
10817: }
10818: for (tok = pathr; tok != NULL; ){
1.126 brouard 10819: printf("Pathr |%s|\n",pathr);
10820: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
10821: printf("val= |%s| pathr=%s\n",val,pathr);
10822: strcpy (pathtot, val);
10823: if(pathr[0] == '\0') break; /* Dirty */
10824: }
10825: }
1.281 brouard 10826: else if (argc<=2){
10827: strcpy(pathtot,argv[1]);
10828: }
1.126 brouard 10829: else{
10830: strcpy(pathtot,argv[1]);
1.281 brouard 10831: strcpy(z,argv[2]);
10832: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 10833: }
10834: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
10835: /*cygwin_split_path(pathtot,path,optionfile);
10836: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
10837: /* cutv(path,optionfile,pathtot,'\\');*/
10838:
10839: /* Split argv[0], imach program to get pathimach */
10840: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
10841: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10842: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10843: /* strcpy(pathimach,argv[0]); */
10844: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
10845: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
10846: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 10847: #ifdef WIN32
10848: _chdir(path); /* Can be a relative path */
10849: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
10850: #else
1.126 brouard 10851: chdir(path); /* Can be a relative path */
1.184 brouard 10852: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
10853: #endif
10854: printf("Current directory %s!\n",pathcd);
1.126 brouard 10855: strcpy(command,"mkdir ");
10856: strcat(command,optionfilefiname);
10857: if((outcmd=system(command)) != 0){
1.169 brouard 10858: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 10859: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
10860: /* fclose(ficlog); */
10861: /* exit(1); */
10862: }
10863: /* if((imk=mkdir(optionfilefiname))<0){ */
10864: /* perror("mkdir"); */
10865: /* } */
10866:
10867: /*-------- arguments in the command line --------*/
10868:
1.186 brouard 10869: /* Main Log file */
1.126 brouard 10870: strcat(filelog, optionfilefiname);
10871: strcat(filelog,".log"); /* */
10872: if((ficlog=fopen(filelog,"w"))==NULL) {
10873: printf("Problem with logfile %s\n",filelog);
10874: goto end;
10875: }
10876: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 10877: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 10878: fprintf(ficlog,"\nEnter the parameter file name: \n");
10879: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
10880: path=%s \n\
10881: optionfile=%s\n\
10882: optionfilext=%s\n\
1.156 brouard 10883: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 10884:
1.197 brouard 10885: syscompilerinfo(1);
1.167 brouard 10886:
1.126 brouard 10887: printf("Local time (at start):%s",strstart);
10888: fprintf(ficlog,"Local time (at start): %s",strstart);
10889: fflush(ficlog);
10890: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 10891: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 10892:
10893: /* */
10894: strcpy(fileres,"r");
10895: strcat(fileres, optionfilefiname);
1.201 brouard 10896: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 10897: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 10898: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 10899:
1.186 brouard 10900: /* Main ---------arguments file --------*/
1.126 brouard 10901:
10902: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 10903: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
10904: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 10905: fflush(ficlog);
1.149 brouard 10906: /* goto end; */
10907: exit(70);
1.126 brouard 10908: }
10909:
10910: strcpy(filereso,"o");
1.201 brouard 10911: strcat(filereso,fileresu);
1.126 brouard 10912: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
10913: printf("Problem with Output resultfile: %s\n", filereso);
10914: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
10915: fflush(ficlog);
10916: goto end;
10917: }
1.278 brouard 10918: /*-------- Rewriting parameter file ----------*/
10919: strcpy(rfileres,"r"); /* "Rparameterfile */
10920: strcat(rfileres,optionfilefiname); /* Parameter file first name */
10921: strcat(rfileres,"."); /* */
10922: strcat(rfileres,optionfilext); /* Other files have txt extension */
10923: if((ficres =fopen(rfileres,"w"))==NULL) {
10924: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
10925: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
10926: fflush(ficlog);
10927: goto end;
10928: }
10929: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 10930:
1.278 brouard 10931:
1.126 brouard 10932: /* Reads comments: lines beginning with '#' */
10933: numlinepar=0;
1.277 brouard 10934: /* Is it a BOM UTF-8 Windows file? */
10935: /* First parameter line */
1.197 brouard 10936: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 10937: noffset=0;
10938: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
10939: {
10940: noffset=noffset+3;
10941: printf("# File is an UTF8 Bom.\n"); // 0xBF
10942: }
10943: else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
10944: {
10945: noffset=noffset+2;
10946: printf("# File is an UTF16BE BOM file\n");
10947: }
10948: else if( line[0] == 0 && line[1] == 0)
10949: {
10950: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
10951: noffset=noffset+4;
10952: printf("# File is an UTF16BE BOM file\n");
10953: }
10954: } else{
10955: ;/*printf(" Not a BOM file\n");*/
10956: }
10957:
1.197 brouard 10958: /* If line starts with a # it is a comment */
1.277 brouard 10959: if (line[noffset] == '#') {
1.197 brouard 10960: numlinepar++;
10961: fputs(line,stdout);
10962: fputs(line,ficparo);
1.278 brouard 10963: fputs(line,ficres);
1.197 brouard 10964: fputs(line,ficlog);
10965: continue;
10966: }else
10967: break;
10968: }
10969: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
10970: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
10971: if (num_filled != 5) {
10972: printf("Should be 5 parameters\n");
1.283 ! brouard 10973: fprintf(ficlog,"Should be 5 parameters\n");
1.197 brouard 10974: }
1.126 brouard 10975: numlinepar++;
1.197 brouard 10976: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.283 ! brouard 10977: fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
! 10978: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
! 10979: fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
1.197 brouard 10980: }
10981: /* Second parameter line */
10982: while(fgets(line, MAXLINE, ficpar)) {
1.283 ! brouard 10983: /* while(fscanf(ficpar,"%[^\n]", line)) { */
! 10984: /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
1.197 brouard 10985: if (line[0] == '#') {
10986: numlinepar++;
1.283 ! brouard 10987: printf("%s",line);
! 10988: fprintf(ficres,"%s",line);
! 10989: fprintf(ficparo,"%s",line);
! 10990: fprintf(ficlog,"%s",line);
1.197 brouard 10991: continue;
10992: }else
10993: break;
10994: }
1.223 brouard 10995: 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", \
10996: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
10997: if (num_filled != 11) {
10998: 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 10999: printf("but line=%s\n",line);
1.283 ! brouard 11000: 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");
! 11001: fprintf(ficlog,"but line=%s\n",line);
1.197 brouard 11002: }
1.223 brouard 11003: 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 11004: 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);
! 11005: 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, mle, weightopt);
! 11006: 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 11007: }
1.203 brouard 11008: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 11009: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 11010: /* Third parameter line */
11011: while(fgets(line, MAXLINE, ficpar)) {
11012: /* If line starts with a # it is a comment */
11013: if (line[0] == '#') {
11014: numlinepar++;
1.283 ! brouard 11015: printf("%s",line);
! 11016: fprintf(ficres,"%s",line);
! 11017: fprintf(ficparo,"%s",line);
! 11018: fprintf(ficlog,"%s",line);
1.197 brouard 11019: continue;
11020: }else
11021: break;
11022: }
1.201 brouard 11023: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 11024: if (num_filled != 1){
11025: printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
11026: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
1.197 brouard 11027: model[0]='\0';
11028: goto end;
11029: }
11030: else{
11031: if (model[0]=='+'){
11032: for(i=1; i<=strlen(model);i++)
11033: modeltemp[i-1]=model[i];
1.201 brouard 11034: strcpy(model,modeltemp);
1.197 brouard 11035: }
11036: }
1.199 brouard 11037: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11038: printf("model=1+age+%s\n",model);fflush(stdout);
1.283 ! brouard 11039: fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
! 11040: fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
! 11041: fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11042: }
11043: /* 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); */
11044: /* numlinepar=numlinepar+3; /\* In general *\/ */
11045: /* 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 11046: /* 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); */
! 11047: /* 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 11048: fflush(ficlog);
1.190 brouard 11049: /* if(model[0]=='#'|| model[0]== '\0'){ */
11050: if(model[0]=='#'){
1.279 brouard 11051: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11052: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11053: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11054: if(mle != -1){
1.279 brouard 11055: 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 11056: exit(1);
11057: }
11058: }
1.126 brouard 11059: while((c=getc(ficpar))=='#' && c!= EOF){
11060: ungetc(c,ficpar);
11061: fgets(line, MAXLINE, ficpar);
11062: numlinepar++;
1.195 brouard 11063: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11064: z[0]=line[1];
11065: }
11066: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11067: fputs(line, stdout);
11068: //puts(line);
1.126 brouard 11069: fputs(line,ficparo);
11070: fputs(line,ficlog);
11071: }
11072: ungetc(c,ficpar);
11073:
11074:
1.145 brouard 11075: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.268 brouard 11076: if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
11077: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
11078: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11079: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11080: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11081: v1+v2*age+v2*v3 makes cptcovn = 3
11082: */
11083: if (strlen(model)>1)
1.187 brouard 11084: 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 11085: else
1.187 brouard 11086: ncovmodel=2; /* Constant and age */
1.133 brouard 11087: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11088: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11089: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11090: 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);
11091: 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);
11092: fflush(stdout);
11093: fclose (ficlog);
11094: goto end;
11095: }
1.126 brouard 11096: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11097: delti=delti3[1][1];
11098: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11099: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11100: /* We could also provide initial parameters values giving by simple logistic regression
11101: * only one way, that is without matrix product. We will have nlstate maximizations */
11102: /* for(i=1;i<nlstate;i++){ */
11103: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11104: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11105: /* } */
1.126 brouard 11106: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11107: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11108: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11109: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11110: fclose (ficparo);
11111: fclose (ficlog);
11112: goto end;
11113: exit(0);
1.220 brouard 11114: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11115: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11116: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11117: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11118: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11119: matcov=matrix(1,npar,1,npar);
1.203 brouard 11120: hess=matrix(1,npar,1,npar);
1.220 brouard 11121: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11122: /* Read guessed parameters */
1.126 brouard 11123: /* Reads comments: lines beginning with '#' */
11124: while((c=getc(ficpar))=='#' && c!= EOF){
11125: ungetc(c,ficpar);
11126: fgets(line, MAXLINE, ficpar);
11127: numlinepar++;
1.141 brouard 11128: fputs(line,stdout);
1.126 brouard 11129: fputs(line,ficparo);
11130: fputs(line,ficlog);
11131: }
11132: ungetc(c,ficpar);
11133:
11134: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11135: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11136: for(i=1; i <=nlstate; i++){
1.234 brouard 11137: j=0;
1.126 brouard 11138: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11139: if(jj==i) continue;
11140: j++;
11141: fscanf(ficpar,"%1d%1d",&i1,&j1);
11142: if ((i1 != i) || (j1 != jj)){
11143: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11144: It might be a problem of design; if ncovcol and the model are correct\n \
11145: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11146: exit(1);
11147: }
11148: fprintf(ficparo,"%1d%1d",i1,j1);
11149: if(mle==1)
11150: printf("%1d%1d",i,jj);
11151: fprintf(ficlog,"%1d%1d",i,jj);
11152: for(k=1; k<=ncovmodel;k++){
11153: fscanf(ficpar," %lf",¶m[i][j][k]);
11154: if(mle==1){
11155: printf(" %lf",param[i][j][k]);
11156: fprintf(ficlog," %lf",param[i][j][k]);
11157: }
11158: else
11159: fprintf(ficlog," %lf",param[i][j][k]);
11160: fprintf(ficparo," %lf",param[i][j][k]);
11161: }
11162: fscanf(ficpar,"\n");
11163: numlinepar++;
11164: if(mle==1)
11165: printf("\n");
11166: fprintf(ficlog,"\n");
11167: fprintf(ficparo,"\n");
1.126 brouard 11168: }
11169: }
11170: fflush(ficlog);
1.234 brouard 11171:
1.251 brouard 11172: /* Reads parameters values */
1.126 brouard 11173: p=param[1][1];
1.251 brouard 11174: pstart=paramstart[1][1];
1.126 brouard 11175:
11176: /* Reads comments: lines beginning with '#' */
11177: while((c=getc(ficpar))=='#' && c!= EOF){
11178: ungetc(c,ficpar);
11179: fgets(line, MAXLINE, ficpar);
11180: numlinepar++;
1.141 brouard 11181: fputs(line,stdout);
1.126 brouard 11182: fputs(line,ficparo);
11183: fputs(line,ficlog);
11184: }
11185: ungetc(c,ficpar);
11186:
11187: for(i=1; i <=nlstate; i++){
11188: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11189: fscanf(ficpar,"%1d%1d",&i1,&j1);
11190: if ( (i1-i) * (j1-j) != 0){
11191: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11192: exit(1);
11193: }
11194: printf("%1d%1d",i,j);
11195: fprintf(ficparo,"%1d%1d",i1,j1);
11196: fprintf(ficlog,"%1d%1d",i1,j1);
11197: for(k=1; k<=ncovmodel;k++){
11198: fscanf(ficpar,"%le",&delti3[i][j][k]);
11199: printf(" %le",delti3[i][j][k]);
11200: fprintf(ficparo," %le",delti3[i][j][k]);
11201: fprintf(ficlog," %le",delti3[i][j][k]);
11202: }
11203: fscanf(ficpar,"\n");
11204: numlinepar++;
11205: printf("\n");
11206: fprintf(ficparo,"\n");
11207: fprintf(ficlog,"\n");
1.126 brouard 11208: }
11209: }
11210: fflush(ficlog);
1.234 brouard 11211:
1.145 brouard 11212: /* Reads covariance matrix */
1.126 brouard 11213: delti=delti3[1][1];
1.220 brouard 11214:
11215:
1.126 brouard 11216: /* 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 11217:
1.126 brouard 11218: /* Reads comments: lines beginning with '#' */
11219: while((c=getc(ficpar))=='#' && c!= EOF){
11220: ungetc(c,ficpar);
11221: fgets(line, MAXLINE, ficpar);
11222: numlinepar++;
1.141 brouard 11223: fputs(line,stdout);
1.126 brouard 11224: fputs(line,ficparo);
11225: fputs(line,ficlog);
11226: }
11227: ungetc(c,ficpar);
1.220 brouard 11228:
1.126 brouard 11229: matcov=matrix(1,npar,1,npar);
1.203 brouard 11230: hess=matrix(1,npar,1,npar);
1.131 brouard 11231: for(i=1; i <=npar; i++)
11232: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11233:
1.194 brouard 11234: /* Scans npar lines */
1.126 brouard 11235: for(i=1; i <=npar; i++){
1.226 brouard 11236: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11237: if(count != 3){
1.226 brouard 11238: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11239: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11240: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11241: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11242: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11243: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11244: exit(1);
1.220 brouard 11245: }else{
1.226 brouard 11246: if(mle==1)
11247: printf("%1d%1d%d",i1,j1,jk);
11248: }
11249: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11250: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11251: for(j=1; j <=i; j++){
1.226 brouard 11252: fscanf(ficpar," %le",&matcov[i][j]);
11253: if(mle==1){
11254: printf(" %.5le",matcov[i][j]);
11255: }
11256: fprintf(ficlog," %.5le",matcov[i][j]);
11257: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11258: }
11259: fscanf(ficpar,"\n");
11260: numlinepar++;
11261: if(mle==1)
1.220 brouard 11262: printf("\n");
1.126 brouard 11263: fprintf(ficlog,"\n");
11264: fprintf(ficparo,"\n");
11265: }
1.194 brouard 11266: /* End of read covariance matrix npar lines */
1.126 brouard 11267: for(i=1; i <=npar; i++)
11268: for(j=i+1;j<=npar;j++)
1.226 brouard 11269: matcov[i][j]=matcov[j][i];
1.126 brouard 11270:
11271: if(mle==1)
11272: printf("\n");
11273: fprintf(ficlog,"\n");
11274:
11275: fflush(ficlog);
11276:
11277: } /* End of mle != -3 */
1.218 brouard 11278:
1.186 brouard 11279: /* Main data
11280: */
1.126 brouard 11281: n= lastobs;
11282: num=lvector(1,n);
11283: moisnais=vector(1,n);
11284: annais=vector(1,n);
11285: moisdc=vector(1,n);
11286: andc=vector(1,n);
1.220 brouard 11287: weight=vector(1,n);
1.126 brouard 11288: agedc=vector(1,n);
11289: cod=ivector(1,n);
1.220 brouard 11290: for(i=1;i<=n;i++){
1.234 brouard 11291: num[i]=0;
11292: moisnais[i]=0;
11293: annais[i]=0;
11294: moisdc[i]=0;
11295: andc[i]=0;
11296: agedc[i]=0;
11297: cod[i]=0;
11298: weight[i]=1.0; /* Equal weights, 1 by default */
11299: }
1.126 brouard 11300: mint=matrix(1,maxwav,1,n);
11301: anint=matrix(1,maxwav,1,n);
1.131 brouard 11302: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11303: tab=ivector(1,NCOVMAX);
1.144 brouard 11304: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11305: 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 11306:
1.136 brouard 11307: /* Reads data from file datafile */
11308: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11309: goto end;
11310:
11311: /* Calculation of the number of parameters from char model */
1.234 brouard 11312: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11313: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11314: k=3 V4 Tvar[k=3]= 4 (from V4)
11315: k=2 V1 Tvar[k=2]= 1 (from V1)
11316: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11317: */
11318:
11319: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11320: TvarsDind=ivector(1,NCOVMAX); /* */
11321: TvarsD=ivector(1,NCOVMAX); /* */
11322: TvarsQind=ivector(1,NCOVMAX); /* */
11323: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11324: TvarF=ivector(1,NCOVMAX); /* */
11325: TvarFind=ivector(1,NCOVMAX); /* */
11326: TvarV=ivector(1,NCOVMAX); /* */
11327: TvarVind=ivector(1,NCOVMAX); /* */
11328: TvarA=ivector(1,NCOVMAX); /* */
11329: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11330: TvarFD=ivector(1,NCOVMAX); /* */
11331: TvarFDind=ivector(1,NCOVMAX); /* */
11332: TvarFQ=ivector(1,NCOVMAX); /* */
11333: TvarFQind=ivector(1,NCOVMAX); /* */
11334: TvarVD=ivector(1,NCOVMAX); /* */
11335: TvarVDind=ivector(1,NCOVMAX); /* */
11336: TvarVQ=ivector(1,NCOVMAX); /* */
11337: TvarVQind=ivector(1,NCOVMAX); /* */
11338:
1.230 brouard 11339: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11340: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11341: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11342: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11343: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11344: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11345: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11346: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11347: */
11348: /* For model-covariate k tells which data-covariate to use but
11349: because this model-covariate is a construction we invent a new column
11350: ncovcol + k1
11351: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11352: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11353: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11354: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11355: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11356: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11357: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11358: */
1.145 brouard 11359: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11360: 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 11361: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11362: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11363: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11364: 4 covariates (3 plus signs)
11365: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11366: */
1.230 brouard 11367: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11368: * individual dummy, fixed or varying:
11369: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11370: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11371: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11372: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11373: * Tmodelind[1]@9={9,0,3,2,}*/
11374: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11375: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11376: * individual quantitative, fixed or varying:
11377: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11378: * 3, 1, 0, 0, 0, 0, 0, 0},
11379: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11380: /* Main decodemodel */
11381:
1.187 brouard 11382:
1.223 brouard 11383: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11384: goto end;
11385:
1.137 brouard 11386: if((double)(lastobs-imx)/(double)imx > 1.10){
11387: nbwarn++;
11388: 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);
11389: 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);
11390: }
1.136 brouard 11391: /* if(mle==1){*/
1.137 brouard 11392: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11393: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11394: }
11395:
11396: /*-calculation of age at interview from date of interview and age at death -*/
11397: agev=matrix(1,maxwav,1,imx);
11398:
11399: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11400: goto end;
11401:
1.126 brouard 11402:
1.136 brouard 11403: agegomp=(int)agemin;
11404: free_vector(moisnais,1,n);
11405: free_vector(annais,1,n);
1.126 brouard 11406: /* free_matrix(mint,1,maxwav,1,n);
11407: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11408: /* free_vector(moisdc,1,n); */
11409: /* free_vector(andc,1,n); */
1.145 brouard 11410: /* */
11411:
1.126 brouard 11412: wav=ivector(1,imx);
1.214 brouard 11413: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11414: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11415: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11416: 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.*/
11417: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11418: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11419:
11420: /* Concatenates waves */
1.214 brouard 11421: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11422: Death is a valid wave (if date is known).
11423: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11424: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11425: and mw[mi+1][i]. dh depends on stepm.
11426: */
11427:
1.126 brouard 11428: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11429: /* Concatenates waves */
1.145 brouard 11430:
1.215 brouard 11431: free_vector(moisdc,1,n);
11432: free_vector(andc,1,n);
11433:
1.126 brouard 11434: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11435: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11436: ncodemax[1]=1;
1.145 brouard 11437: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11438: cptcoveff=0;
1.220 brouard 11439: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11440: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11441: }
11442:
11443: ncovcombmax=pow(2,cptcoveff);
11444: invalidvarcomb=ivector(1, ncovcombmax);
11445: for(i=1;i<ncovcombmax;i++)
11446: invalidvarcomb[i]=0;
11447:
1.211 brouard 11448: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11449: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11450: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11451:
1.200 brouard 11452: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11453: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11454: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11455: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11456: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11457: * (currently 0 or 1) in the data.
11458: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11459: * corresponding modality (h,j).
11460: */
11461:
1.145 brouard 11462: h=0;
11463: /*if (cptcovn > 0) */
1.126 brouard 11464: m=pow(2,cptcoveff);
11465:
1.144 brouard 11466: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11467: * For k=4 covariates, h goes from 1 to m=2**k
11468: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11469: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11470: * h\k 1 2 3 4
1.143 brouard 11471: *______________________________
11472: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11473: * 2 2 1 1 1
11474: * 3 i=2 1 2 1 1
11475: * 4 2 2 1 1
11476: * 5 i=3 1 i=2 1 2 1
11477: * 6 2 1 2 1
11478: * 7 i=4 1 2 2 1
11479: * 8 2 2 2 1
1.197 brouard 11480: * 9 i=5 1 i=3 1 i=2 1 2
11481: * 10 2 1 1 2
11482: * 11 i=6 1 2 1 2
11483: * 12 2 2 1 2
11484: * 13 i=7 1 i=4 1 2 2
11485: * 14 2 1 2 2
11486: * 15 i=8 1 2 2 2
11487: * 16 2 2 2 2
1.143 brouard 11488: */
1.212 brouard 11489: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11490: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11491: * and the value of each covariate?
11492: * V1=1, V2=1, V3=2, V4=1 ?
11493: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11494: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11495: * In order to get the real value in the data, we use nbcode
11496: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11497: * We are keeping this crazy system in order to be able (in the future?)
11498: * to have more than 2 values (0 or 1) for a covariate.
11499: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11500: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11501: * bbbbbbbb
11502: * 76543210
11503: * h-1 00000101 (6-1=5)
1.219 brouard 11504: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11505: * &
11506: * 1 00000001 (1)
1.219 brouard 11507: * 00000000 = 1 & ((h-1) >> (k-1))
11508: * +1= 00000001 =1
1.211 brouard 11509: *
11510: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11511: * h' 1101 =2^3+2^2+0x2^1+2^0
11512: * >>k' 11
11513: * & 00000001
11514: * = 00000001
11515: * +1 = 00000010=2 = codtabm(14,3)
11516: * Reverse h=6 and m=16?
11517: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11518: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11519: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11520: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11521: * V3=decodtabm(14,3,2**4)=2
11522: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11523: *(h-1) >> (j-1) 0011 =13 >> 2
11524: * &1 000000001
11525: * = 000000001
11526: * +1= 000000010 =2
11527: * 2211
11528: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11529: * V3=2
1.220 brouard 11530: * codtabm and decodtabm are identical
1.211 brouard 11531: */
11532:
1.145 brouard 11533:
11534: free_ivector(Ndum,-1,NCOVMAX);
11535:
11536:
1.126 brouard 11537:
1.186 brouard 11538: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11539: strcpy(optionfilegnuplot,optionfilefiname);
11540: if(mle==-3)
1.201 brouard 11541: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11542: strcat(optionfilegnuplot,".gp");
11543:
11544: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11545: printf("Problem with file %s",optionfilegnuplot);
11546: }
11547: else{
1.204 brouard 11548: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11549: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11550: //fprintf(ficgp,"set missing 'NaNq'\n");
11551: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11552: }
11553: /* fclose(ficgp);*/
1.186 brouard 11554:
11555:
11556: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11557:
11558: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11559: if(mle==-3)
1.201 brouard 11560: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11561: strcat(optionfilehtm,".htm");
11562: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11563: printf("Problem with %s \n",optionfilehtm);
11564: exit(0);
1.126 brouard 11565: }
11566:
11567: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11568: strcat(optionfilehtmcov,"-cov.htm");
11569: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11570: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11571: }
11572: else{
11573: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11574: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11575: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11576: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11577: }
11578:
1.213 brouard 11579: 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 11580: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11581: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11582: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11583: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11584: \n\
11585: <hr size=\"2\" color=\"#EC5E5E\">\
11586: <ul><li><h4>Parameter files</h4>\n\
11587: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11588: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11589: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11590: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11591: - Date and time at start: %s</ul>\n",\
11592: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11593: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11594: fileres,fileres,\
11595: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11596: fflush(fichtm);
11597:
11598: strcpy(pathr,path);
11599: strcat(pathr,optionfilefiname);
1.184 brouard 11600: #ifdef WIN32
11601: _chdir(optionfilefiname); /* Move to directory named optionfile */
11602: #else
1.126 brouard 11603: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11604: #endif
11605:
1.126 brouard 11606:
1.220 brouard 11607: /* Calculates basic frequencies. Computes observed prevalence at single age
11608: and for any valid combination of covariates
1.126 brouard 11609: and prints on file fileres'p'. */
1.251 brouard 11610: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11611: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11612:
11613: fprintf(fichtm,"\n");
1.274 brouard 11614: fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\
11615: ftol, stepm);
11616: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11617: ncurrv=1;
11618: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11619: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11620: ncurrv=i;
11621: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
11622: fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);
11623: ncurrv=i;
11624: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
11625: fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);
11626: ncurrv=i;
11627: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11628: 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", \
11629: nlstate, ndeath, maxwav, mle, weightopt);
11630:
11631: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11632: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11633:
11634:
11635: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11636: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11637: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11638: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11639: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11640: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11641: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11642: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11643: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11644:
1.126 brouard 11645: /* For Powell, parameters are in a vector p[] starting at p[1]
11646: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11647: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11648:
11649: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11650: /* For mortality only */
1.126 brouard 11651: if (mle==-3){
1.136 brouard 11652: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11653: for(i=1;i<=NDIM;i++)
11654: for(j=1;j<=NDIM;j++)
11655: ximort[i][j]=0.;
1.186 brouard 11656: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 11657: cens=ivector(1,n);
11658: ageexmed=vector(1,n);
11659: agecens=vector(1,n);
11660: dcwave=ivector(1,n);
1.223 brouard 11661:
1.126 brouard 11662: for (i=1; i<=imx; i++){
11663: dcwave[i]=-1;
11664: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11665: if (s[m][i]>nlstate) {
11666: dcwave[i]=m;
11667: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11668: break;
11669: }
1.126 brouard 11670: }
1.226 brouard 11671:
1.126 brouard 11672: for (i=1; i<=imx; i++) {
11673: if (wav[i]>0){
1.226 brouard 11674: ageexmed[i]=agev[mw[1][i]][i];
11675: j=wav[i];
11676: agecens[i]=1.;
11677:
11678: if (ageexmed[i]> 1 && wav[i] > 0){
11679: agecens[i]=agev[mw[j][i]][i];
11680: cens[i]= 1;
11681: }else if (ageexmed[i]< 1)
11682: cens[i]= -1;
11683: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11684: cens[i]=0 ;
1.126 brouard 11685: }
11686: else cens[i]=-1;
11687: }
11688:
11689: for (i=1;i<=NDIM;i++) {
11690: for (j=1;j<=NDIM;j++)
1.226 brouard 11691: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11692: }
11693:
1.145 brouard 11694: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 11695: /*printf("%lf %lf", p[1], p[2]);*/
11696:
11697:
1.136 brouard 11698: #ifdef GSL
11699: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11700: #else
1.126 brouard 11701: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11702: #endif
1.201 brouard 11703: strcpy(filerespow,"POW-MORT_");
11704: strcat(filerespow,fileresu);
1.126 brouard 11705: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11706: printf("Problem with resultfile: %s\n", filerespow);
11707: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11708: }
1.136 brouard 11709: #ifdef GSL
11710: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11711: #else
1.126 brouard 11712: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11713: #endif
1.126 brouard 11714: /* for (i=1;i<=nlstate;i++)
11715: for(j=1;j<=nlstate+ndeath;j++)
11716: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11717: */
11718: fprintf(ficrespow,"\n");
1.136 brouard 11719: #ifdef GSL
11720: /* gsl starts here */
11721: T = gsl_multimin_fminimizer_nmsimplex;
11722: gsl_multimin_fminimizer *sfm = NULL;
11723: gsl_vector *ss, *x;
11724: gsl_multimin_function minex_func;
11725:
11726: /* Initial vertex size vector */
11727: ss = gsl_vector_alloc (NDIM);
11728:
11729: if (ss == NULL){
11730: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11731: }
11732: /* Set all step sizes to 1 */
11733: gsl_vector_set_all (ss, 0.001);
11734:
11735: /* Starting point */
1.126 brouard 11736:
1.136 brouard 11737: x = gsl_vector_alloc (NDIM);
11738:
11739: if (x == NULL){
11740: gsl_vector_free(ss);
11741: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11742: }
11743:
11744: /* Initialize method and iterate */
11745: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11746: /* gsl_vector_set(x, 0, 0.0268); */
11747: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11748: gsl_vector_set(x, 0, p[1]);
11749: gsl_vector_set(x, 1, p[2]);
11750:
11751: minex_func.f = &gompertz_f;
11752: minex_func.n = NDIM;
11753: minex_func.params = (void *)&p; /* ??? */
11754:
11755: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11756: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
11757:
11758: printf("Iterations beginning .....\n\n");
11759: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
11760:
11761: iteri=0;
11762: while (rval == GSL_CONTINUE){
11763: iteri++;
11764: status = gsl_multimin_fminimizer_iterate(sfm);
11765:
11766: if (status) printf("error: %s\n", gsl_strerror (status));
11767: fflush(0);
11768:
11769: if (status)
11770: break;
11771:
11772: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
11773: ssval = gsl_multimin_fminimizer_size (sfm);
11774:
11775: if (rval == GSL_SUCCESS)
11776: printf ("converged to a local maximum at\n");
11777:
11778: printf("%5d ", iteri);
11779: for (it = 0; it < NDIM; it++){
11780: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
11781: }
11782: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
11783: }
11784:
11785: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
11786:
11787: gsl_vector_free(x); /* initial values */
11788: gsl_vector_free(ss); /* inital step size */
11789: for (it=0; it<NDIM; it++){
11790: p[it+1]=gsl_vector_get(sfm->x,it);
11791: fprintf(ficrespow," %.12lf", p[it]);
11792: }
11793: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
11794: #endif
11795: #ifdef POWELL
11796: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
11797: #endif
1.126 brouard 11798: fclose(ficrespow);
11799:
1.203 brouard 11800: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 11801:
11802: for(i=1; i <=NDIM; i++)
11803: for(j=i+1;j<=NDIM;j++)
1.220 brouard 11804: matcov[i][j]=matcov[j][i];
1.126 brouard 11805:
11806: printf("\nCovariance matrix\n ");
1.203 brouard 11807: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 11808: for(i=1; i <=NDIM; i++) {
11809: for(j=1;j<=NDIM;j++){
1.220 brouard 11810: printf("%f ",matcov[i][j]);
11811: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 11812: }
1.203 brouard 11813: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 11814: }
11815:
11816: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 11817: for (i=1;i<=NDIM;i++) {
1.126 brouard 11818: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 11819: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
11820: }
1.126 brouard 11821: lsurv=vector(1,AGESUP);
11822: lpop=vector(1,AGESUP);
11823: tpop=vector(1,AGESUP);
11824: lsurv[agegomp]=100000;
11825:
11826: for (k=agegomp;k<=AGESUP;k++) {
11827: agemortsup=k;
11828: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
11829: }
11830:
11831: for (k=agegomp;k<agemortsup;k++)
11832: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
11833:
11834: for (k=agegomp;k<agemortsup;k++){
11835: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
11836: sumlpop=sumlpop+lpop[k];
11837: }
11838:
11839: tpop[agegomp]=sumlpop;
11840: for (k=agegomp;k<(agemortsup-3);k++){
11841: /* tpop[k+1]=2;*/
11842: tpop[k+1]=tpop[k]-lpop[k];
11843: }
11844:
11845:
11846: printf("\nAge lx qx dx Lx Tx e(x)\n");
11847: for (k=agegomp;k<(agemortsup-2);k++)
11848: 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]);
11849:
11850:
11851: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 11852: ageminpar=50;
11853: agemaxpar=100;
1.194 brouard 11854: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
11855: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11856: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11857: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
11858: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11859: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11860: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 11861: }else{
11862: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
11863: 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 11864: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 11865: }
1.201 brouard 11866: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 11867: stepm, weightopt,\
11868: model,imx,p,matcov,agemortsup);
11869:
11870: free_vector(lsurv,1,AGESUP);
11871: free_vector(lpop,1,AGESUP);
11872: free_vector(tpop,1,AGESUP);
1.220 brouard 11873: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 11874: free_ivector(cens,1,n);
11875: free_vector(agecens,1,n);
11876: free_ivector(dcwave,1,n);
1.220 brouard 11877: #ifdef GSL
1.136 brouard 11878: #endif
1.186 brouard 11879: } /* Endof if mle==-3 mortality only */
1.205 brouard 11880: /* Standard */
11881: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
11882: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11883: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 11884: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 11885: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11886: for (k=1; k<=npar;k++)
11887: printf(" %d %8.5f",k,p[k]);
11888: printf("\n");
1.205 brouard 11889: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
11890: /* mlikeli uses func not funcone */
1.247 brouard 11891: /* for(i=1;i<nlstate;i++){ */
11892: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11893: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11894: /* } */
1.205 brouard 11895: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
11896: }
11897: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
11898: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11899: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
11900: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11901: }
11902: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 11903: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11904: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11905: for (k=1; k<=npar;k++)
11906: printf(" %d %8.5f",k,p[k]);
11907: printf("\n");
11908:
11909: /*--------- results files --------------*/
1.283 ! brouard 11910: /* 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 11911:
11912:
11913: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11914: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11915: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11916: for(i=1,jk=1; i <=nlstate; i++){
11917: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 11918: if (k != i) {
11919: printf("%d%d ",i,k);
11920: fprintf(ficlog,"%d%d ",i,k);
11921: fprintf(ficres,"%1d%1d ",i,k);
11922: for(j=1; j <=ncovmodel; j++){
11923: printf("%12.7f ",p[jk]);
11924: fprintf(ficlog,"%12.7f ",p[jk]);
11925: fprintf(ficres,"%12.7f ",p[jk]);
11926: jk++;
11927: }
11928: printf("\n");
11929: fprintf(ficlog,"\n");
11930: fprintf(ficres,"\n");
11931: }
1.126 brouard 11932: }
11933: }
1.203 brouard 11934: if(mle != 0){
11935: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 11936: ftolhess=ftol; /* Usually correct */
1.203 brouard 11937: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
11938: 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");
11939: 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");
11940: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 11941: for(k=1; k <=(nlstate+ndeath); k++){
11942: if (k != i) {
11943: printf("%d%d ",i,k);
11944: fprintf(ficlog,"%d%d ",i,k);
11945: for(j=1; j <=ncovmodel; j++){
11946: 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]));
11947: 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]));
11948: jk++;
11949: }
11950: printf("\n");
11951: fprintf(ficlog,"\n");
11952: }
11953: }
1.193 brouard 11954: }
1.203 brouard 11955: } /* end of hesscov and Wald tests */
1.225 brouard 11956:
1.203 brouard 11957: /* */
1.126 brouard 11958: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
11959: printf("# Scales (for hessian or gradient estimation)\n");
11960: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
11961: for(i=1,jk=1; i <=nlstate; i++){
11962: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 11963: if (j!=i) {
11964: fprintf(ficres,"%1d%1d",i,j);
11965: printf("%1d%1d",i,j);
11966: fprintf(ficlog,"%1d%1d",i,j);
11967: for(k=1; k<=ncovmodel;k++){
11968: printf(" %.5e",delti[jk]);
11969: fprintf(ficlog," %.5e",delti[jk]);
11970: fprintf(ficres," %.5e",delti[jk]);
11971: jk++;
11972: }
11973: printf("\n");
11974: fprintf(ficlog,"\n");
11975: fprintf(ficres,"\n");
11976: }
1.126 brouard 11977: }
11978: }
11979:
11980: 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 11981: if(mle >= 1) /* To big for the screen */
1.126 brouard 11982: 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");
11983: 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");
11984: /* # 121 Var(a12)\n\ */
11985: /* # 122 Cov(b12,a12) Var(b12)\n\ */
11986: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
11987: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
11988: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
11989: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
11990: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
11991: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
11992:
11993:
11994: /* Just to have a covariance matrix which will be more understandable
11995: even is we still don't want to manage dictionary of variables
11996: */
11997: for(itimes=1;itimes<=2;itimes++){
11998: jj=0;
11999: for(i=1; i <=nlstate; i++){
1.225 brouard 12000: for(j=1; j <=nlstate+ndeath; j++){
12001: if(j==i) continue;
12002: for(k=1; k<=ncovmodel;k++){
12003: jj++;
12004: ca[0]= k+'a'-1;ca[1]='\0';
12005: if(itimes==1){
12006: if(mle>=1)
12007: printf("#%1d%1d%d",i,j,k);
12008: fprintf(ficlog,"#%1d%1d%d",i,j,k);
12009: fprintf(ficres,"#%1d%1d%d",i,j,k);
12010: }else{
12011: if(mle>=1)
12012: printf("%1d%1d%d",i,j,k);
12013: fprintf(ficlog,"%1d%1d%d",i,j,k);
12014: fprintf(ficres,"%1d%1d%d",i,j,k);
12015: }
12016: ll=0;
12017: for(li=1;li <=nlstate; li++){
12018: for(lj=1;lj <=nlstate+ndeath; lj++){
12019: if(lj==li) continue;
12020: for(lk=1;lk<=ncovmodel;lk++){
12021: ll++;
12022: if(ll<=jj){
12023: cb[0]= lk +'a'-1;cb[1]='\0';
12024: if(ll<jj){
12025: if(itimes==1){
12026: if(mle>=1)
12027: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12028: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12029: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
12030: }else{
12031: if(mle>=1)
12032: printf(" %.5e",matcov[jj][ll]);
12033: fprintf(ficlog," %.5e",matcov[jj][ll]);
12034: fprintf(ficres," %.5e",matcov[jj][ll]);
12035: }
12036: }else{
12037: if(itimes==1){
12038: if(mle>=1)
12039: printf(" Var(%s%1d%1d)",ca,i,j);
12040: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12041: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12042: }else{
12043: if(mle>=1)
12044: printf(" %.7e",matcov[jj][ll]);
12045: fprintf(ficlog," %.7e",matcov[jj][ll]);
12046: fprintf(ficres," %.7e",matcov[jj][ll]);
12047: }
12048: }
12049: }
12050: } /* end lk */
12051: } /* end lj */
12052: } /* end li */
12053: if(mle>=1)
12054: printf("\n");
12055: fprintf(ficlog,"\n");
12056: fprintf(ficres,"\n");
12057: numlinepar++;
12058: } /* end k*/
12059: } /*end j */
1.126 brouard 12060: } /* end i */
12061: } /* end itimes */
12062:
12063: fflush(ficlog);
12064: fflush(ficres);
1.225 brouard 12065: while(fgets(line, MAXLINE, ficpar)) {
12066: /* If line starts with a # it is a comment */
12067: if (line[0] == '#') {
12068: numlinepar++;
12069: fputs(line,stdout);
12070: fputs(line,ficparo);
12071: fputs(line,ficlog);
12072: continue;
12073: }else
12074: break;
12075: }
12076:
1.209 brouard 12077: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12078: /* ungetc(c,ficpar); */
12079: /* fgets(line, MAXLINE, ficpar); */
12080: /* fputs(line,stdout); */
12081: /* fputs(line,ficparo); */
12082: /* } */
12083: /* ungetc(c,ficpar); */
1.126 brouard 12084:
12085: estepm=0;
1.209 brouard 12086: 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 12087:
12088: if (num_filled != 6) {
12089: 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);
12090: 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);
12091: goto end;
12092: }
12093: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12094: }
12095: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12096: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12097:
1.209 brouard 12098: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12099: if (estepm==0 || estepm < stepm) estepm=stepm;
12100: if (fage <= 2) {
12101: bage = ageminpar;
12102: fage = agemaxpar;
12103: }
12104:
12105: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12106: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12107: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12108:
1.186 brouard 12109: /* Other stuffs, more or less useful */
1.254 brouard 12110: while(fgets(line, MAXLINE, ficpar)) {
12111: /* If line starts with a # it is a comment */
12112: if (line[0] == '#') {
12113: numlinepar++;
12114: fputs(line,stdout);
12115: fputs(line,ficparo);
12116: fputs(line,ficlog);
12117: continue;
12118: }else
12119: break;
12120: }
12121:
12122: 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){
12123:
12124: if (num_filled != 7) {
12125: 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);
12126: 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);
12127: goto end;
12128: }
12129: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12130: 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);
12131: 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);
12132: 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 12133: }
1.254 brouard 12134:
12135: while(fgets(line, MAXLINE, ficpar)) {
12136: /* If line starts with a # it is a comment */
12137: if (line[0] == '#') {
12138: numlinepar++;
12139: fputs(line,stdout);
12140: fputs(line,ficparo);
12141: fputs(line,ficlog);
12142: continue;
12143: }else
12144: break;
1.126 brouard 12145: }
12146:
12147:
12148: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12149: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12150:
1.254 brouard 12151: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12152: if (num_filled != 1) {
12153: 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);
12154: 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);
12155: goto end;
12156: }
12157: printf("pop_based=%d\n",popbased);
12158: fprintf(ficlog,"pop_based=%d\n",popbased);
12159: fprintf(ficparo,"pop_based=%d\n",popbased);
12160: fprintf(ficres,"pop_based=%d\n",popbased);
12161: }
12162:
1.258 brouard 12163: /* Results */
12164: nresult=0;
12165: do{
12166: if(!fgets(line, MAXLINE, ficpar)){
12167: endishere=1;
12168: parameterline=14;
12169: }else if (line[0] == '#') {
12170: /* If line starts with a # it is a comment */
1.254 brouard 12171: numlinepar++;
12172: fputs(line,stdout);
12173: fputs(line,ficparo);
12174: fputs(line,ficlog);
12175: continue;
1.258 brouard 12176: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12177: parameterline=11;
12178: else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
12179: parameterline=12;
12180: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12181: parameterline=13;
12182: else{
12183: parameterline=14;
1.254 brouard 12184: }
1.258 brouard 12185: switch (parameterline){
12186: case 11:
12187: 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){
12188: if (num_filled != 8) {
12189: 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);
12190: 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);
12191: goto end;
12192: }
12193: 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);
12194: 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);
12195: 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);
12196: 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);
12197: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12198: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12199: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
12200:
1.258 brouard 12201: }
1.254 brouard 12202: break;
1.258 brouard 12203: case 12:
12204: /*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);*/
12205: 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){
12206: if (num_filled != 8) {
1.262 brouard 12207: 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);
12208: 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 12209: goto end;
12210: }
12211: 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);
12212: 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);
12213: 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);
12214: 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);
12215: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12216: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12217: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.258 brouard 12218: }
1.230 brouard 12219: break;
1.258 brouard 12220: case 13:
12221: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12222: if (num_filled == 0){
12223: resultline[0]='\0';
12224: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12225: 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);
12226: break;
12227: } else if (num_filled != 1){
12228: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12229: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12230: }
12231: nresult++; /* Sum of resultlines */
12232: printf("Result %d: result=%s\n",nresult, resultline);
12233: if(nresult > MAXRESULTLINES){
12234: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12235: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12236: goto end;
12237: }
12238: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12239: fprintf(ficparo,"result: %s\n",resultline);
12240: fprintf(ficres,"result: %s\n",resultline);
12241: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12242: break;
1.258 brouard 12243: case 14:
1.259 brouard 12244: if(ncovmodel >2 && nresult==0 ){
12245: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12246: goto end;
12247: }
1.259 brouard 12248: break;
1.258 brouard 12249: default:
12250: nresult=1;
12251: decoderesult(".",nresult ); /* No covariate */
12252: }
12253: } /* End switch parameterline */
12254: }while(endishere==0); /* End do */
1.126 brouard 12255:
1.230 brouard 12256: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12257: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12258:
12259: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12260: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12261: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12262: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12263: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12264: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12265: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12266: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12267: }else{
1.270 brouard 12268: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
12269: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
1.220 brouard 12270: }
12271: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.258 brouard 12272: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
1.273 brouard 12273: jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
1.220 brouard 12274:
1.225 brouard 12275: /*------------ free_vector -------------*/
12276: /* chdir(path); */
1.220 brouard 12277:
1.215 brouard 12278: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12279: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12280: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12281: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 12282: free_lvector(num,1,n);
12283: free_vector(agedc,1,n);
12284: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12285: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12286: fclose(ficparo);
12287: fclose(ficres);
1.220 brouard 12288:
12289:
1.186 brouard 12290: /* Other results (useful)*/
1.220 brouard 12291:
12292:
1.126 brouard 12293: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12294: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12295: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12296: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12297: fclose(ficrespl);
12298:
12299: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12300: /*#include "hpijx.h"*/
12301: hPijx(p, bage, fage);
1.145 brouard 12302: fclose(ficrespij);
1.227 brouard 12303:
1.220 brouard 12304: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12305: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12306: k=1;
1.126 brouard 12307: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12308:
1.269 brouard 12309: /* Prevalence for each covariate combination in probs[age][status][cov] */
12310: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12311: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12312: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12313: for(k=1;k<=ncovcombmax;k++)
12314: probs[i][j][k]=0.;
1.269 brouard 12315: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12316: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12317: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12318: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12319: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12320: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12321: for(k=1;k<=ncovcombmax;k++)
12322: mobaverages[i][j][k]=0.;
1.219 brouard 12323: mobaverage=mobaverages;
12324: if (mobilav!=0) {
1.235 brouard 12325: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12326: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12327: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12328: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12329: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12330: }
1.269 brouard 12331: } else if (mobilavproj !=0) {
1.235 brouard 12332: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12333: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12334: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12335: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12336: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12337: }
1.269 brouard 12338: }else{
12339: printf("Internal error moving average\n");
12340: fflush(stdout);
12341: exit(1);
1.219 brouard 12342: }
12343: }/* end if moving average */
1.227 brouard 12344:
1.126 brouard 12345: /*---------- Forecasting ------------------*/
12346: if(prevfcast==1){
12347: /* if(stepm ==1){*/
1.269 brouard 12348: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 12349: }
1.269 brouard 12350:
12351: /* Backcasting */
1.217 brouard 12352: if(backcast==1){
1.219 brouard 12353: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12354: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12355: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12356:
12357: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12358:
12359: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12360:
1.219 brouard 12361: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12362: fclose(ficresplb);
12363:
1.222 brouard 12364: hBijx(p, bage, fage, mobaverage);
12365: fclose(ficrespijb);
1.219 brouard 12366:
1.269 brouard 12367: prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
12368: mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
12369: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12370:
12371:
1.269 brouard 12372: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12373: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12374: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12375: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.269 brouard 12376: } /* end Backcasting */
1.268 brouard 12377:
1.186 brouard 12378:
12379: /* ------ Other prevalence ratios------------ */
1.126 brouard 12380:
1.215 brouard 12381: free_ivector(wav,1,imx);
12382: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12383: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12384: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12385:
12386:
1.127 brouard 12387: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12388:
1.201 brouard 12389: strcpy(filerese,"E_");
12390: strcat(filerese,fileresu);
1.126 brouard 12391: if((ficreseij=fopen(filerese,"w"))==NULL) {
12392: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12393: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12394: }
1.208 brouard 12395: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12396: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12397:
12398: pstamp(ficreseij);
1.219 brouard 12399:
1.235 brouard 12400: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12401: if (cptcovn < 1){i1=1;}
12402:
12403: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12404: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12405: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12406: continue;
1.219 brouard 12407: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12408: printf("\n#****** ");
1.225 brouard 12409: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12410: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12411: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12412: }
12413: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12414: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12415: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12416: }
12417: fprintf(ficreseij,"******\n");
1.235 brouard 12418: printf("******\n");
1.219 brouard 12419:
12420: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12421: oldm=oldms;savm=savms;
1.235 brouard 12422: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12423:
1.219 brouard 12424: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12425: }
12426: fclose(ficreseij);
1.208 brouard 12427: printf("done evsij\n");fflush(stdout);
12428: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12429:
1.218 brouard 12430:
1.227 brouard 12431: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12432:
1.201 brouard 12433: strcpy(filerest,"T_");
12434: strcat(filerest,fileresu);
1.127 brouard 12435: if((ficrest=fopen(filerest,"w"))==NULL) {
12436: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12437: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12438: }
1.208 brouard 12439: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12440: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12441: strcpy(fileresstde,"STDE_");
12442: strcat(fileresstde,fileresu);
1.126 brouard 12443: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12444: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12445: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12446: }
1.227 brouard 12447: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12448: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12449:
1.201 brouard 12450: strcpy(filerescve,"CVE_");
12451: strcat(filerescve,fileresu);
1.126 brouard 12452: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12453: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12454: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12455: }
1.227 brouard 12456: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12457: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12458:
1.201 brouard 12459: strcpy(fileresv,"V_");
12460: strcat(fileresv,fileresu);
1.126 brouard 12461: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12462: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12463: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12464: }
1.227 brouard 12465: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12466: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12467:
1.235 brouard 12468: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12469: if (cptcovn < 1){i1=1;}
12470:
12471: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12472: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12473: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12474: continue;
1.242 brouard 12475: printf("\n#****** Result for:");
12476: fprintf(ficrest,"\n#****** Result for:");
12477: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12478: for(j=1;j<=cptcoveff;j++){
12479: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12480: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12481: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12482: }
1.235 brouard 12483: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12484: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12485: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12486: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12487: }
1.208 brouard 12488: fprintf(ficrest,"******\n");
1.227 brouard 12489: fprintf(ficlog,"******\n");
12490: printf("******\n");
1.208 brouard 12491:
12492: fprintf(ficresstdeij,"\n#****** ");
12493: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12494: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12495: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12496: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12497: }
1.235 brouard 12498: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12499: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12500: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12501: }
1.208 brouard 12502: fprintf(ficresstdeij,"******\n");
12503: fprintf(ficrescveij,"******\n");
12504:
12505: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12506: /* pstamp(ficresvij); */
1.225 brouard 12507: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12508: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12509: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12510: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12511: }
1.208 brouard 12512: fprintf(ficresvij,"******\n");
12513:
12514: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12515: oldm=oldms;savm=savms;
1.235 brouard 12516: printf(" cvevsij ");
12517: fprintf(ficlog, " cvevsij ");
12518: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12519: printf(" end cvevsij \n ");
12520: fprintf(ficlog, " end cvevsij \n ");
12521:
12522: /*
12523: */
12524: /* goto endfree; */
12525:
12526: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12527: pstamp(ficrest);
12528:
1.269 brouard 12529: epj=vector(1,nlstate+1);
1.208 brouard 12530: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12531: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12532: cptcod= 0; /* To be deleted */
12533: printf("varevsij vpopbased=%d \n",vpopbased);
12534: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12535: 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 12536: 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 ");
12537: if(vpopbased==1)
12538: 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);
12539: else
12540: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
12541: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12542: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12543: fprintf(ficrest,"\n");
12544: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
12545: printf("Computing age specific period (stable) prevalences in each health state \n");
12546: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
12547: for(age=bage; age <=fage ;age++){
1.235 brouard 12548: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12549: if (vpopbased==1) {
12550: if(mobilav ==0){
12551: for(i=1; i<=nlstate;i++)
12552: prlim[i][i]=probs[(int)age][i][k];
12553: }else{ /* mobilav */
12554: for(i=1; i<=nlstate;i++)
12555: prlim[i][i]=mobaverage[(int)age][i][k];
12556: }
12557: }
1.219 brouard 12558:
1.227 brouard 12559: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12560: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12561: /* printf(" age %4.0f ",age); */
12562: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12563: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12564: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12565: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12566: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12567: }
12568: epj[nlstate+1] +=epj[j];
12569: }
12570: /* printf(" age %4.0f \n",age); */
1.219 brouard 12571:
1.227 brouard 12572: for(i=1, vepp=0.;i <=nlstate;i++)
12573: for(j=1;j <=nlstate;j++)
12574: vepp += vareij[i][j][(int)age];
12575: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12576: for(j=1;j <=nlstate;j++){
12577: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12578: }
12579: fprintf(ficrest,"\n");
12580: }
1.208 brouard 12581: } /* End vpopbased */
1.269 brouard 12582: free_vector(epj,1,nlstate+1);
1.208 brouard 12583: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12584: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12585: printf("done selection\n");fflush(stdout);
12586: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12587:
1.235 brouard 12588: } /* End k selection */
1.227 brouard 12589:
12590: printf("done State-specific expectancies\n");fflush(stdout);
12591: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12592:
1.269 brouard 12593: /* variance-covariance of period prevalence*/
12594: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12595:
1.227 brouard 12596:
12597: free_vector(weight,1,n);
12598: free_imatrix(Tvard,1,NCOVMAX,1,2);
12599: free_imatrix(s,1,maxwav+1,1,n);
12600: free_matrix(anint,1,maxwav,1,n);
12601: free_matrix(mint,1,maxwav,1,n);
12602: free_ivector(cod,1,n);
12603: free_ivector(tab,1,NCOVMAX);
12604: fclose(ficresstdeij);
12605: fclose(ficrescveij);
12606: fclose(ficresvij);
12607: fclose(ficrest);
12608: fclose(ficpar);
12609:
12610:
1.126 brouard 12611: /*---------- End : free ----------------*/
1.219 brouard 12612: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12613: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12614: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12615: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12616: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12617: } /* mle==-3 arrives here for freeing */
1.227 brouard 12618: /* endfree:*/
12619: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12620: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12621: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.268 brouard 12622: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
12623: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
12624: if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
1.227 brouard 12625: free_matrix(covar,0,NCOVMAX,1,n);
12626: free_matrix(matcov,1,npar,1,npar);
12627: free_matrix(hess,1,npar,1,npar);
12628: /*free_vector(delti,1,npar);*/
12629: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12630: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12631: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12632: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12633:
12634: free_ivector(ncodemax,1,NCOVMAX);
12635: free_ivector(ncodemaxwundef,1,NCOVMAX);
12636: free_ivector(Dummy,-1,NCOVMAX);
12637: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12638: free_ivector(DummyV,1,NCOVMAX);
12639: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12640: free_ivector(Typevar,-1,NCOVMAX);
12641: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12642: free_ivector(TvarsQ,1,NCOVMAX);
12643: free_ivector(TvarsQind,1,NCOVMAX);
12644: free_ivector(TvarsD,1,NCOVMAX);
12645: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12646: free_ivector(TvarFD,1,NCOVMAX);
12647: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12648: free_ivector(TvarF,1,NCOVMAX);
12649: free_ivector(TvarFind,1,NCOVMAX);
12650: free_ivector(TvarV,1,NCOVMAX);
12651: free_ivector(TvarVind,1,NCOVMAX);
12652: free_ivector(TvarA,1,NCOVMAX);
12653: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12654: free_ivector(TvarFQ,1,NCOVMAX);
12655: free_ivector(TvarFQind,1,NCOVMAX);
12656: free_ivector(TvarVD,1,NCOVMAX);
12657: free_ivector(TvarVDind,1,NCOVMAX);
12658: free_ivector(TvarVQ,1,NCOVMAX);
12659: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12660: free_ivector(Tvarsel,1,NCOVMAX);
12661: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12662: free_ivector(Tposprod,1,NCOVMAX);
12663: free_ivector(Tprod,1,NCOVMAX);
12664: free_ivector(Tvaraff,1,NCOVMAX);
12665: free_ivector(invalidvarcomb,1,ncovcombmax);
12666: free_ivector(Tage,1,NCOVMAX);
12667: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12668: free_ivector(TmodelInvind,1,NCOVMAX);
12669: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12670:
12671: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12672: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12673: fflush(fichtm);
12674: fflush(ficgp);
12675:
1.227 brouard 12676:
1.126 brouard 12677: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12678: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12679: 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 12680: }else{
12681: printf("End of Imach\n");
12682: fprintf(ficlog,"End of Imach\n");
12683: }
12684: printf("See log file on %s\n",filelog);
12685: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12686: /*(void) gettimeofday(&end_time,&tzp);*/
12687: rend_time = time(NULL);
12688: end_time = *localtime(&rend_time);
12689: /* tml = *localtime(&end_time.tm_sec); */
12690: strcpy(strtend,asctime(&end_time));
1.126 brouard 12691: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
12692: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 12693: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 12694:
1.157 brouard 12695: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
12696: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
12697: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 12698: /* printf("Total time was %d uSec.\n", total_usecs);*/
12699: /* if(fileappend(fichtm,optionfilehtm)){ */
12700: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12701: fclose(fichtm);
12702: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12703: fclose(fichtmcov);
12704: fclose(ficgp);
12705: fclose(ficlog);
12706: /*------ End -----------*/
1.227 brouard 12707:
1.281 brouard 12708:
12709: /* Executes gnuplot */
1.227 brouard 12710:
12711: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 12712: #ifdef WIN32
1.227 brouard 12713: if (_chdir(pathcd) != 0)
12714: printf("Can't move to directory %s!\n",path);
12715: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 12716: #else
1.227 brouard 12717: if(chdir(pathcd) != 0)
12718: printf("Can't move to directory %s!\n", path);
12719: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 12720: #endif
1.126 brouard 12721: printf("Current directory %s!\n",pathcd);
12722: /*strcat(plotcmd,CHARSEPARATOR);*/
12723: sprintf(plotcmd,"gnuplot");
1.157 brouard 12724: #ifdef _WIN32
1.126 brouard 12725: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
12726: #endif
12727: if(!stat(plotcmd,&info)){
1.158 brouard 12728: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12729: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 12730: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 12731: }else
12732: strcpy(pplotcmd,plotcmd);
1.157 brouard 12733: #ifdef __unix
1.126 brouard 12734: strcpy(plotcmd,GNUPLOTPROGRAM);
12735: if(!stat(plotcmd,&info)){
1.158 brouard 12736: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12737: }else
12738: strcpy(pplotcmd,plotcmd);
12739: #endif
12740: }else
12741: strcpy(pplotcmd,plotcmd);
12742:
12743: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 12744: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 12745:
1.126 brouard 12746: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 12747: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 12748: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 12749: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 12750: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 12751: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 12752: }
1.158 brouard 12753: printf(" Successful, please wait...");
1.126 brouard 12754: while (z[0] != 'q') {
12755: /* chdir(path); */
1.154 brouard 12756: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 12757: scanf("%s",z);
12758: /* if (z[0] == 'c') system("./imach"); */
12759: if (z[0] == 'e') {
1.158 brouard 12760: #ifdef __APPLE__
1.152 brouard 12761: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 12762: #elif __linux
12763: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 12764: #else
1.152 brouard 12765: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 12766: #endif
12767: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
12768: system(pplotcmd);
1.126 brouard 12769: }
12770: else if (z[0] == 'g') system(plotcmd);
12771: else if (z[0] == 'q') exit(0);
12772: }
1.227 brouard 12773: end:
1.126 brouard 12774: while (z[0] != 'q') {
1.195 brouard 12775: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 12776: scanf("%s",z);
12777: }
1.283 ! brouard 12778: printf("End\n");
1.282 brouard 12779: exit(0);
1.126 brouard 12780: }
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