Annotation of imach/src/imach.c, revision 1.282
1.282 ! brouard 1: /* $Id: imach.c,v 1.281 2018/02/27 19:25:23 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.282 ! brouard 4: Revision 1.281 2018/02/27 19:25:23 brouard
! 5: Summary: Adding second argument for quitting
! 6:
1.281 brouard 7: Revision 1.280 2018/02/21 07:58:13 brouard
8: Summary: 0.99r15
9:
10: New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
11:
1.280 brouard 12: Revision 1.279 2017/07/20 13:35:01 brouard
13: Summary: temporary working
14:
1.279 brouard 15: Revision 1.278 2017/07/19 14:09:02 brouard
16: Summary: Bug for mobil_average=0 and prevforecast fixed(?)
17:
1.278 brouard 18: Revision 1.277 2017/07/17 08:53:49 brouard
19: Summary: BOM files can be read now
20:
1.277 brouard 21: Revision 1.276 2017/06/30 15:48:31 brouard
22: Summary: Graphs improvements
23:
1.276 brouard 24: Revision 1.275 2017/06/30 13:39:33 brouard
25: Summary: Saito's color
26:
1.275 brouard 27: Revision 1.274 2017/06/29 09:47:08 brouard
28: Summary: Version 0.99r14
29:
1.274 brouard 30: Revision 1.273 2017/06/27 11:06:02 brouard
31: Summary: More documentation on projections
32:
1.273 brouard 33: Revision 1.272 2017/06/27 10:22:40 brouard
34: Summary: Color of backprojection changed from 6 to 5(yellow)
35:
1.272 brouard 36: Revision 1.271 2017/06/27 10:17:50 brouard
37: Summary: Some bug with rint
38:
1.271 brouard 39: Revision 1.270 2017/05/24 05:45:29 brouard
40: *** empty log message ***
41:
1.270 brouard 42: Revision 1.269 2017/05/23 08:39:25 brouard
43: Summary: Code into subroutine, cleanings
44:
1.269 brouard 45: Revision 1.268 2017/05/18 20:09:32 brouard
46: Summary: backprojection and confidence intervals of backprevalence
47:
1.268 brouard 48: Revision 1.267 2017/05/13 10:25:05 brouard
49: Summary: temporary save for backprojection
50:
1.267 brouard 51: Revision 1.266 2017/05/13 07:26:12 brouard
52: Summary: Version 0.99r13 (improvements and bugs fixed)
53:
1.266 brouard 54: Revision 1.265 2017/04/26 16:22:11 brouard
55: Summary: imach 0.99r13 Some bugs fixed
56:
1.265 brouard 57: Revision 1.264 2017/04/26 06:01:29 brouard
58: Summary: Labels in graphs
59:
1.264 brouard 60: Revision 1.263 2017/04/24 15:23:15 brouard
61: Summary: to save
62:
1.263 brouard 63: Revision 1.262 2017/04/18 16:48:12 brouard
64: *** empty log message ***
65:
1.262 brouard 66: Revision 1.261 2017/04/05 10:14:09 brouard
67: Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
68:
1.261 brouard 69: Revision 1.260 2017/04/04 17:46:59 brouard
70: Summary: Gnuplot indexations fixed (humm)
71:
1.260 brouard 72: Revision 1.259 2017/04/04 13:01:16 brouard
73: Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
74:
1.259 brouard 75: Revision 1.258 2017/04/03 10:17:47 brouard
76: Summary: Version 0.99r12
77:
78: Some cleanings, conformed with updated documentation.
79:
1.258 brouard 80: Revision 1.257 2017/03/29 16:53:30 brouard
81: Summary: Temp
82:
1.257 brouard 83: Revision 1.256 2017/03/27 05:50:23 brouard
84: Summary: Temporary
85:
1.256 brouard 86: Revision 1.255 2017/03/08 16:02:28 brouard
87: Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
88:
1.255 brouard 89: Revision 1.254 2017/03/08 07:13:00 brouard
90: Summary: Fixing data parameter line
91:
1.254 brouard 92: Revision 1.253 2016/12/15 11:59:41 brouard
93: Summary: 0.99 in progress
94:
1.253 brouard 95: Revision 1.252 2016/09/15 21:15:37 brouard
96: *** empty log message ***
97:
1.252 brouard 98: Revision 1.251 2016/09/15 15:01:13 brouard
99: Summary: not working
100:
1.251 brouard 101: Revision 1.250 2016/09/08 16:07:27 brouard
102: Summary: continue
103:
1.250 brouard 104: Revision 1.249 2016/09/07 17:14:18 brouard
105: Summary: Starting values from frequencies
106:
1.249 brouard 107: Revision 1.248 2016/09/07 14:10:18 brouard
108: *** empty log message ***
109:
1.248 brouard 110: Revision 1.247 2016/09/02 11:11:21 brouard
111: *** empty log message ***
112:
1.247 brouard 113: Revision 1.246 2016/09/02 08:49:22 brouard
114: *** empty log message ***
115:
1.246 brouard 116: Revision 1.245 2016/09/02 07:25:01 brouard
117: *** empty log message ***
118:
1.245 brouard 119: Revision 1.244 2016/09/02 07:17:34 brouard
120: *** empty log message ***
121:
1.244 brouard 122: Revision 1.243 2016/09/02 06:45:35 brouard
123: *** empty log message ***
124:
1.243 brouard 125: Revision 1.242 2016/08/30 15:01:20 brouard
126: Summary: Fixing a lots
127:
1.242 brouard 128: Revision 1.241 2016/08/29 17:17:25 brouard
129: Summary: gnuplot problem in Back projection to fix
130:
1.241 brouard 131: Revision 1.240 2016/08/29 07:53:18 brouard
132: Summary: Better
133:
1.240 brouard 134: Revision 1.239 2016/08/26 15:51:03 brouard
135: Summary: Improvement in Powell output in order to copy and paste
136:
137: Author:
138:
1.239 brouard 139: Revision 1.238 2016/08/26 14:23:35 brouard
140: Summary: Starting tests of 0.99
141:
1.238 brouard 142: Revision 1.237 2016/08/26 09:20:19 brouard
143: Summary: to valgrind
144:
1.237 brouard 145: Revision 1.236 2016/08/25 10:50:18 brouard
146: *** empty log message ***
147:
1.236 brouard 148: Revision 1.235 2016/08/25 06:59:23 brouard
149: *** empty log message ***
150:
1.235 brouard 151: Revision 1.234 2016/08/23 16:51:20 brouard
152: *** empty log message ***
153:
1.234 brouard 154: Revision 1.233 2016/08/23 07:40:50 brouard
155: Summary: not working
156:
1.233 brouard 157: Revision 1.232 2016/08/22 14:20:21 brouard
158: Summary: not working
159:
1.232 brouard 160: Revision 1.231 2016/08/22 07:17:15 brouard
161: Summary: not working
162:
1.231 brouard 163: Revision 1.230 2016/08/22 06:55:53 brouard
164: Summary: Not working
165:
1.230 brouard 166: Revision 1.229 2016/07/23 09:45:53 brouard
167: Summary: Completing for func too
168:
1.229 brouard 169: Revision 1.228 2016/07/22 17:45:30 brouard
170: Summary: Fixing some arrays, still debugging
171:
1.227 brouard 172: Revision 1.226 2016/07/12 18:42:34 brouard
173: Summary: temp
174:
1.226 brouard 175: Revision 1.225 2016/07/12 08:40:03 brouard
176: Summary: saving but not running
177:
1.225 brouard 178: Revision 1.224 2016/07/01 13:16:01 brouard
179: Summary: Fixes
180:
1.224 brouard 181: Revision 1.223 2016/02/19 09:23:35 brouard
182: Summary: temporary
183:
1.223 brouard 184: Revision 1.222 2016/02/17 08:14:50 brouard
185: Summary: Probably last 0.98 stable version 0.98r6
186:
1.222 brouard 187: Revision 1.221 2016/02/15 23:35:36 brouard
188: Summary: minor bug
189:
1.220 brouard 190: Revision 1.219 2016/02/15 00:48:12 brouard
191: *** empty log message ***
192:
1.219 brouard 193: Revision 1.218 2016/02/12 11:29:23 brouard
194: Summary: 0.99 Back projections
195:
1.218 brouard 196: Revision 1.217 2015/12/23 17:18:31 brouard
197: Summary: Experimental backcast
198:
1.217 brouard 199: Revision 1.216 2015/12/18 17:32:11 brouard
200: Summary: 0.98r4 Warning and status=-2
201:
202: Version 0.98r4 is now:
203: - displaying an error when status is -1, date of interview unknown and date of death known;
204: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
205: Older changes concerning s=-2, dating from 2005 have been supersed.
206:
1.216 brouard 207: Revision 1.215 2015/12/16 08:52:24 brouard
208: Summary: 0.98r4 working
209:
1.215 brouard 210: Revision 1.214 2015/12/16 06:57:54 brouard
211: Summary: temporary not working
212:
1.214 brouard 213: Revision 1.213 2015/12/11 18:22:17 brouard
214: Summary: 0.98r4
215:
1.213 brouard 216: Revision 1.212 2015/11/21 12:47:24 brouard
217: Summary: minor typo
218:
1.212 brouard 219: Revision 1.211 2015/11/21 12:41:11 brouard
220: Summary: 0.98r3 with some graph of projected cross-sectional
221:
222: Author: Nicolas Brouard
223:
1.211 brouard 224: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 225: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 226: Summary: Adding ftolpl parameter
227: Author: N Brouard
228:
229: We had difficulties to get smoothed confidence intervals. It was due
230: to the period prevalence which wasn't computed accurately. The inner
231: parameter ftolpl is now an outer parameter of the .imach parameter
232: file after estepm. If ftolpl is small 1.e-4 and estepm too,
233: computation are long.
234:
1.209 brouard 235: Revision 1.208 2015/11/17 14:31:57 brouard
236: Summary: temporary
237:
1.208 brouard 238: Revision 1.207 2015/10/27 17:36:57 brouard
239: *** empty log message ***
240:
1.207 brouard 241: Revision 1.206 2015/10/24 07:14:11 brouard
242: *** empty log message ***
243:
1.206 brouard 244: Revision 1.205 2015/10/23 15:50:53 brouard
245: Summary: 0.98r3 some clarification for graphs on likelihood contributions
246:
1.205 brouard 247: Revision 1.204 2015/10/01 16:20:26 brouard
248: Summary: Some new graphs of contribution to likelihood
249:
1.204 brouard 250: Revision 1.203 2015/09/30 17:45:14 brouard
251: Summary: looking at better estimation of the hessian
252:
253: Also a better criteria for convergence to the period prevalence And
254: therefore adding the number of years needed to converge. (The
255: prevalence in any alive state shold sum to one
256:
1.203 brouard 257: Revision 1.202 2015/09/22 19:45:16 brouard
258: Summary: Adding some overall graph on contribution to likelihood. Might change
259:
1.202 brouard 260: Revision 1.201 2015/09/15 17:34:58 brouard
261: Summary: 0.98r0
262:
263: - Some new graphs like suvival functions
264: - Some bugs fixed like model=1+age+V2.
265:
1.201 brouard 266: Revision 1.200 2015/09/09 16:53:55 brouard
267: Summary: Big bug thanks to Flavia
268:
269: Even model=1+age+V2. did not work anymore
270:
1.200 brouard 271: Revision 1.199 2015/09/07 14:09:23 brouard
272: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
273:
1.199 brouard 274: Revision 1.198 2015/09/03 07:14:39 brouard
275: Summary: 0.98q5 Flavia
276:
1.198 brouard 277: Revision 1.197 2015/09/01 18:24:39 brouard
278: *** empty log message ***
279:
1.197 brouard 280: Revision 1.196 2015/08/18 23:17:52 brouard
281: Summary: 0.98q5
282:
1.196 brouard 283: Revision 1.195 2015/08/18 16:28:39 brouard
284: Summary: Adding a hack for testing purpose
285:
286: After reading the title, ftol and model lines, if the comment line has
287: a q, starting with #q, the answer at the end of the run is quit. It
288: permits to run test files in batch with ctest. The former workaround was
289: $ echo q | imach foo.imach
290:
1.195 brouard 291: Revision 1.194 2015/08/18 13:32:00 brouard
292: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
293:
1.194 brouard 294: Revision 1.193 2015/08/04 07:17:42 brouard
295: Summary: 0.98q4
296:
1.193 brouard 297: Revision 1.192 2015/07/16 16:49:02 brouard
298: Summary: Fixing some outputs
299:
1.192 brouard 300: Revision 1.191 2015/07/14 10:00:33 brouard
301: Summary: Some fixes
302:
1.191 brouard 303: Revision 1.190 2015/05/05 08:51:13 brouard
304: Summary: Adding digits in output parameters (7 digits instead of 6)
305:
306: Fix 1+age+.
307:
1.190 brouard 308: Revision 1.189 2015/04/30 14:45:16 brouard
309: Summary: 0.98q2
310:
1.189 brouard 311: Revision 1.188 2015/04/30 08:27:53 brouard
312: *** empty log message ***
313:
1.188 brouard 314: Revision 1.187 2015/04/29 09:11:15 brouard
315: *** empty log message ***
316:
1.187 brouard 317: Revision 1.186 2015/04/23 12:01:52 brouard
318: Summary: V1*age is working now, version 0.98q1
319:
320: Some codes had been disabled in order to simplify and Vn*age was
321: working in the optimization phase, ie, giving correct MLE parameters,
322: but, as usual, outputs were not correct and program core dumped.
323:
1.186 brouard 324: Revision 1.185 2015/03/11 13:26:42 brouard
325: Summary: Inclusion of compile and links command line for Intel Compiler
326:
1.185 brouard 327: Revision 1.184 2015/03/11 11:52:39 brouard
328: Summary: Back from Windows 8. Intel Compiler
329:
1.184 brouard 330: Revision 1.183 2015/03/10 20:34:32 brouard
331: Summary: 0.98q0, trying with directest, mnbrak fixed
332:
333: We use directest instead of original Powell test; probably no
334: incidence on the results, but better justifications;
335: We fixed Numerical Recipes mnbrak routine which was wrong and gave
336: wrong results.
337:
1.183 brouard 338: Revision 1.182 2015/02/12 08:19:57 brouard
339: Summary: Trying to keep directest which seems simpler and more general
340: Author: Nicolas Brouard
341:
1.182 brouard 342: Revision 1.181 2015/02/11 23:22:24 brouard
343: Summary: Comments on Powell added
344:
345: Author:
346:
1.181 brouard 347: Revision 1.180 2015/02/11 17:33:45 brouard
348: Summary: Finishing move from main to function (hpijx and prevalence_limit)
349:
1.180 brouard 350: Revision 1.179 2015/01/04 09:57:06 brouard
351: Summary: back to OS/X
352:
1.179 brouard 353: Revision 1.178 2015/01/04 09:35:48 brouard
354: *** empty log message ***
355:
1.178 brouard 356: Revision 1.177 2015/01/03 18:40:56 brouard
357: Summary: Still testing ilc32 on OSX
358:
1.177 brouard 359: Revision 1.176 2015/01/03 16:45:04 brouard
360: *** empty log message ***
361:
1.176 brouard 362: Revision 1.175 2015/01/03 16:33:42 brouard
363: *** empty log message ***
364:
1.175 brouard 365: Revision 1.174 2015/01/03 16:15:49 brouard
366: Summary: Still in cross-compilation
367:
1.174 brouard 368: Revision 1.173 2015/01/03 12:06:26 brouard
369: Summary: trying to detect cross-compilation
370:
1.173 brouard 371: Revision 1.172 2014/12/27 12:07:47 brouard
372: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
373:
1.172 brouard 374: Revision 1.171 2014/12/23 13:26:59 brouard
375: Summary: Back from Visual C
376:
377: Still problem with utsname.h on Windows
378:
1.171 brouard 379: Revision 1.170 2014/12/23 11:17:12 brouard
380: Summary: Cleaning some \%% back to %%
381:
382: The escape was mandatory for a specific compiler (which one?), but too many warnings.
383:
1.170 brouard 384: Revision 1.169 2014/12/22 23:08:31 brouard
385: Summary: 0.98p
386:
387: Outputs some informations on compiler used, OS etc. Testing on different platforms.
388:
1.169 brouard 389: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 390: Summary: update
1.169 brouard 391:
1.168 brouard 392: Revision 1.167 2014/12/22 13:50:56 brouard
393: Summary: Testing uname and compiler version and if compiled 32 or 64
394:
395: Testing on Linux 64
396:
1.167 brouard 397: Revision 1.166 2014/12/22 11:40:47 brouard
398: *** empty log message ***
399:
1.166 brouard 400: Revision 1.165 2014/12/16 11:20:36 brouard
401: Summary: After compiling on Visual C
402:
403: * imach.c (Module): Merging 1.61 to 1.162
404:
1.165 brouard 405: Revision 1.164 2014/12/16 10:52:11 brouard
406: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
407:
408: * imach.c (Module): Merging 1.61 to 1.162
409:
1.164 brouard 410: Revision 1.163 2014/12/16 10:30:11 brouard
411: * imach.c (Module): Merging 1.61 to 1.162
412:
1.163 brouard 413: Revision 1.162 2014/09/25 11:43:39 brouard
414: Summary: temporary backup 0.99!
415:
1.162 brouard 416: Revision 1.1 2014/09/16 11:06:58 brouard
417: Summary: With some code (wrong) for nlopt
418:
419: Author:
420:
421: Revision 1.161 2014/09/15 20:41:41 brouard
422: Summary: Problem with macro SQR on Intel compiler
423:
1.161 brouard 424: Revision 1.160 2014/09/02 09:24:05 brouard
425: *** empty log message ***
426:
1.160 brouard 427: Revision 1.159 2014/09/01 10:34:10 brouard
428: Summary: WIN32
429: Author: Brouard
430:
1.159 brouard 431: Revision 1.158 2014/08/27 17:11:51 brouard
432: *** empty log message ***
433:
1.158 brouard 434: Revision 1.157 2014/08/27 16:26:55 brouard
435: Summary: Preparing windows Visual studio version
436: Author: Brouard
437:
438: In order to compile on Visual studio, time.h is now correct and time_t
439: and tm struct should be used. difftime should be used but sometimes I
440: just make the differences in raw time format (time(&now).
441: Trying to suppress #ifdef LINUX
442: Add xdg-open for __linux in order to open default browser.
443:
1.157 brouard 444: Revision 1.156 2014/08/25 20:10:10 brouard
445: *** empty log message ***
446:
1.156 brouard 447: Revision 1.155 2014/08/25 18:32:34 brouard
448: Summary: New compile, minor changes
449: Author: Brouard
450:
1.155 brouard 451: Revision 1.154 2014/06/20 17:32:08 brouard
452: Summary: Outputs now all graphs of convergence to period prevalence
453:
1.154 brouard 454: Revision 1.153 2014/06/20 16:45:46 brouard
455: Summary: If 3 live state, convergence to period prevalence on same graph
456: Author: Brouard
457:
1.153 brouard 458: Revision 1.152 2014/06/18 17:54:09 brouard
459: Summary: open browser, use gnuplot on same dir than imach if not found in the path
460:
1.152 brouard 461: Revision 1.151 2014/06/18 16:43:30 brouard
462: *** empty log message ***
463:
1.151 brouard 464: Revision 1.150 2014/06/18 16:42:35 brouard
465: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
466: Author: brouard
467:
1.150 brouard 468: Revision 1.149 2014/06/18 15:51:14 brouard
469: Summary: Some fixes in parameter files errors
470: Author: Nicolas Brouard
471:
1.149 brouard 472: Revision 1.148 2014/06/17 17:38:48 brouard
473: Summary: Nothing new
474: Author: Brouard
475:
476: Just a new packaging for OS/X version 0.98nS
477:
1.148 brouard 478: Revision 1.147 2014/06/16 10:33:11 brouard
479: *** empty log message ***
480:
1.147 brouard 481: Revision 1.146 2014/06/16 10:20:28 brouard
482: Summary: Merge
483: Author: Brouard
484:
485: Merge, before building revised version.
486:
1.146 brouard 487: Revision 1.145 2014/06/10 21:23:15 brouard
488: Summary: Debugging with valgrind
489: Author: Nicolas Brouard
490:
491: Lot of changes in order to output the results with some covariates
492: After the Edimburgh REVES conference 2014, it seems mandatory to
493: improve the code.
494: No more memory valgrind error but a lot has to be done in order to
495: continue the work of splitting the code into subroutines.
496: Also, decodemodel has been improved. Tricode is still not
497: optimal. nbcode should be improved. Documentation has been added in
498: the source code.
499:
1.144 brouard 500: Revision 1.143 2014/01/26 09:45:38 brouard
501: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
502:
503: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
504: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
505:
1.143 brouard 506: Revision 1.142 2014/01/26 03:57:36 brouard
507: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
508:
509: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
510:
1.142 brouard 511: Revision 1.141 2014/01/26 02:42:01 brouard
512: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
513:
1.141 brouard 514: Revision 1.140 2011/09/02 10:37:54 brouard
515: Summary: times.h is ok with mingw32 now.
516:
1.140 brouard 517: Revision 1.139 2010/06/14 07:50:17 brouard
518: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
519: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
520:
1.139 brouard 521: Revision 1.138 2010/04/30 18:19:40 brouard
522: *** empty log message ***
523:
1.138 brouard 524: Revision 1.137 2010/04/29 18:11:38 brouard
525: (Module): Checking covariates for more complex models
526: than V1+V2. A lot of change to be done. Unstable.
527:
1.137 brouard 528: Revision 1.136 2010/04/26 20:30:53 brouard
529: (Module): merging some libgsl code. Fixing computation
530: of likelione (using inter/intrapolation if mle = 0) in order to
531: get same likelihood as if mle=1.
532: Some cleaning of code and comments added.
533:
1.136 brouard 534: Revision 1.135 2009/10/29 15:33:14 brouard
535: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
536:
1.135 brouard 537: Revision 1.134 2009/10/29 13:18:53 brouard
538: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
539:
1.134 brouard 540: Revision 1.133 2009/07/06 10:21:25 brouard
541: just nforces
542:
1.133 brouard 543: Revision 1.132 2009/07/06 08:22:05 brouard
544: Many tings
545:
1.132 brouard 546: Revision 1.131 2009/06/20 16:22:47 brouard
547: Some dimensions resccaled
548:
1.131 brouard 549: Revision 1.130 2009/05/26 06:44:34 brouard
550: (Module): Max Covariate is now set to 20 instead of 8. A
551: lot of cleaning with variables initialized to 0. Trying to make
552: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
553:
1.130 brouard 554: Revision 1.129 2007/08/31 13:49:27 lievre
555: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
556:
1.129 lievre 557: Revision 1.128 2006/06/30 13:02:05 brouard
558: (Module): Clarifications on computing e.j
559:
1.128 brouard 560: Revision 1.127 2006/04/28 18:11:50 brouard
561: (Module): Yes the sum of survivors was wrong since
562: imach-114 because nhstepm was no more computed in the age
563: loop. Now we define nhstepma in the age loop.
564: (Module): In order to speed up (in case of numerous covariates) we
565: compute health expectancies (without variances) in a first step
566: and then all the health expectancies with variances or standard
567: deviation (needs data from the Hessian matrices) which slows the
568: computation.
569: In the future we should be able to stop the program is only health
570: expectancies and graph are needed without standard deviations.
571:
1.127 brouard 572: Revision 1.126 2006/04/28 17:23:28 brouard
573: (Module): Yes the sum of survivors was wrong since
574: imach-114 because nhstepm was no more computed in the age
575: loop. Now we define nhstepma in the age loop.
576: Version 0.98h
577:
1.126 brouard 578: Revision 1.125 2006/04/04 15:20:31 lievre
579: Errors in calculation of health expectancies. Age was not initialized.
580: Forecasting file added.
581:
582: Revision 1.124 2006/03/22 17:13:53 lievre
583: Parameters are printed with %lf instead of %f (more numbers after the comma).
584: The log-likelihood is printed in the log file
585:
586: Revision 1.123 2006/03/20 10:52:43 brouard
587: * imach.c (Module): <title> changed, corresponds to .htm file
588: name. <head> headers where missing.
589:
590: * imach.c (Module): Weights can have a decimal point as for
591: English (a comma might work with a correct LC_NUMERIC environment,
592: otherwise the weight is truncated).
593: Modification of warning when the covariates values are not 0 or
594: 1.
595: Version 0.98g
596:
597: Revision 1.122 2006/03/20 09:45:41 brouard
598: (Module): Weights can have a decimal point as for
599: English (a comma might work with a correct LC_NUMERIC environment,
600: otherwise the weight is truncated).
601: Modification of warning when the covariates values are not 0 or
602: 1.
603: Version 0.98g
604:
605: Revision 1.121 2006/03/16 17:45:01 lievre
606: * imach.c (Module): Comments concerning covariates added
607:
608: * imach.c (Module): refinements in the computation of lli if
609: status=-2 in order to have more reliable computation if stepm is
610: not 1 month. Version 0.98f
611:
612: Revision 1.120 2006/03/16 15:10:38 lievre
613: (Module): refinements in the computation of lli if
614: status=-2 in order to have more reliable computation if stepm is
615: not 1 month. Version 0.98f
616:
617: Revision 1.119 2006/03/15 17:42:26 brouard
618: (Module): Bug if status = -2, the loglikelihood was
619: computed as likelihood omitting the logarithm. Version O.98e
620:
621: Revision 1.118 2006/03/14 18:20:07 brouard
622: (Module): varevsij Comments added explaining the second
623: table of variances if popbased=1 .
624: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
625: (Module): Function pstamp added
626: (Module): Version 0.98d
627:
628: Revision 1.117 2006/03/14 17:16:22 brouard
629: (Module): varevsij Comments added explaining the second
630: table of variances if popbased=1 .
631: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
632: (Module): Function pstamp added
633: (Module): Version 0.98d
634:
635: Revision 1.116 2006/03/06 10:29:27 brouard
636: (Module): Variance-covariance wrong links and
637: varian-covariance of ej. is needed (Saito).
638:
639: Revision 1.115 2006/02/27 12:17:45 brouard
640: (Module): One freematrix added in mlikeli! 0.98c
641:
642: Revision 1.114 2006/02/26 12:57:58 brouard
643: (Module): Some improvements in processing parameter
644: filename with strsep.
645:
646: Revision 1.113 2006/02/24 14:20:24 brouard
647: (Module): Memory leaks checks with valgrind and:
648: datafile was not closed, some imatrix were not freed and on matrix
649: allocation too.
650:
651: Revision 1.112 2006/01/30 09:55:26 brouard
652: (Module): Back to gnuplot.exe instead of wgnuplot.exe
653:
654: Revision 1.111 2006/01/25 20:38:18 brouard
655: (Module): Lots of cleaning and bugs added (Gompertz)
656: (Module): Comments can be added in data file. Missing date values
657: can be a simple dot '.'.
658:
659: Revision 1.110 2006/01/25 00:51:50 brouard
660: (Module): Lots of cleaning and bugs added (Gompertz)
661:
662: Revision 1.109 2006/01/24 19:37:15 brouard
663: (Module): Comments (lines starting with a #) are allowed in data.
664:
665: Revision 1.108 2006/01/19 18:05:42 lievre
666: Gnuplot problem appeared...
667: To be fixed
668:
669: Revision 1.107 2006/01/19 16:20:37 brouard
670: Test existence of gnuplot in imach path
671:
672: Revision 1.106 2006/01/19 13:24:36 brouard
673: Some cleaning and links added in html output
674:
675: Revision 1.105 2006/01/05 20:23:19 lievre
676: *** empty log message ***
677:
678: Revision 1.104 2005/09/30 16:11:43 lievre
679: (Module): sump fixed, loop imx fixed, and simplifications.
680: (Module): If the status is missing at the last wave but we know
681: that the person is alive, then we can code his/her status as -2
682: (instead of missing=-1 in earlier versions) and his/her
683: contributions to the likelihood is 1 - Prob of dying from last
684: health status (= 1-p13= p11+p12 in the easiest case of somebody in
685: the healthy state at last known wave). Version is 0.98
686:
687: Revision 1.103 2005/09/30 15:54:49 lievre
688: (Module): sump fixed, loop imx fixed, and simplifications.
689:
690: Revision 1.102 2004/09/15 17:31:30 brouard
691: Add the possibility to read data file including tab characters.
692:
693: Revision 1.101 2004/09/15 10:38:38 brouard
694: Fix on curr_time
695:
696: Revision 1.100 2004/07/12 18:29:06 brouard
697: Add version for Mac OS X. Just define UNIX in Makefile
698:
699: Revision 1.99 2004/06/05 08:57:40 brouard
700: *** empty log message ***
701:
702: Revision 1.98 2004/05/16 15:05:56 brouard
703: New version 0.97 . First attempt to estimate force of mortality
704: directly from the data i.e. without the need of knowing the health
705: state at each age, but using a Gompertz model: log u =a + b*age .
706: This is the basic analysis of mortality and should be done before any
707: other analysis, in order to test if the mortality estimated from the
708: cross-longitudinal survey is different from the mortality estimated
709: from other sources like vital statistic data.
710:
711: The same imach parameter file can be used but the option for mle should be -3.
712:
1.133 brouard 713: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 714: former routines in order to include the new code within the former code.
715:
716: The output is very simple: only an estimate of the intercept and of
717: the slope with 95% confident intervals.
718:
719: Current limitations:
720: A) Even if you enter covariates, i.e. with the
721: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
722: B) There is no computation of Life Expectancy nor Life Table.
723:
724: Revision 1.97 2004/02/20 13:25:42 lievre
725: Version 0.96d. Population forecasting command line is (temporarily)
726: suppressed.
727:
728: Revision 1.96 2003/07/15 15:38:55 brouard
729: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
730: rewritten within the same printf. Workaround: many printfs.
731:
732: Revision 1.95 2003/07/08 07:54:34 brouard
733: * imach.c (Repository):
734: (Repository): Using imachwizard code to output a more meaningful covariance
735: matrix (cov(a12,c31) instead of numbers.
736:
737: Revision 1.94 2003/06/27 13:00:02 brouard
738: Just cleaning
739:
740: Revision 1.93 2003/06/25 16:33:55 brouard
741: (Module): On windows (cygwin) function asctime_r doesn't
742: exist so I changed back to asctime which exists.
743: (Module): Version 0.96b
744:
745: Revision 1.92 2003/06/25 16:30:45 brouard
746: (Module): On windows (cygwin) function asctime_r doesn't
747: exist so I changed back to asctime which exists.
748:
749: Revision 1.91 2003/06/25 15:30:29 brouard
750: * imach.c (Repository): Duplicated warning errors corrected.
751: (Repository): Elapsed time after each iteration is now output. It
752: helps to forecast when convergence will be reached. Elapsed time
753: is stamped in powell. We created a new html file for the graphs
754: concerning matrix of covariance. It has extension -cov.htm.
755:
756: Revision 1.90 2003/06/24 12:34:15 brouard
757: (Module): Some bugs corrected for windows. Also, when
758: mle=-1 a template is output in file "or"mypar.txt with the design
759: of the covariance matrix to be input.
760:
761: Revision 1.89 2003/06/24 12:30:52 brouard
762: (Module): Some bugs corrected for windows. Also, when
763: mle=-1 a template is output in file "or"mypar.txt with the design
764: of the covariance matrix to be input.
765:
766: Revision 1.88 2003/06/23 17:54:56 brouard
767: * 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.
768:
769: Revision 1.87 2003/06/18 12:26:01 brouard
770: Version 0.96
771:
772: Revision 1.86 2003/06/17 20:04:08 brouard
773: (Module): Change position of html and gnuplot routines and added
774: routine fileappend.
775:
776: Revision 1.85 2003/06/17 13:12:43 brouard
777: * imach.c (Repository): Check when date of death was earlier that
778: current date of interview. It may happen when the death was just
779: prior to the death. In this case, dh was negative and likelihood
780: was wrong (infinity). We still send an "Error" but patch by
781: assuming that the date of death was just one stepm after the
782: interview.
783: (Repository): Because some people have very long ID (first column)
784: we changed int to long in num[] and we added a new lvector for
785: memory allocation. But we also truncated to 8 characters (left
786: truncation)
787: (Repository): No more line truncation errors.
788:
789: Revision 1.84 2003/06/13 21:44:43 brouard
790: * imach.c (Repository): Replace "freqsummary" at a correct
791: place. It differs from routine "prevalence" which may be called
792: many times. Probs is memory consuming and must be used with
793: parcimony.
794: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
795:
796: Revision 1.83 2003/06/10 13:39:11 lievre
797: *** empty log message ***
798:
799: Revision 1.82 2003/06/05 15:57:20 brouard
800: Add log in imach.c and fullversion number is now printed.
801:
802: */
803: /*
804: Interpolated Markov Chain
805:
806: Short summary of the programme:
807:
1.227 brouard 808: This program computes Healthy Life Expectancies or State-specific
809: (if states aren't health statuses) Expectancies from
810: cross-longitudinal data. Cross-longitudinal data consist in:
811:
812: -1- a first survey ("cross") where individuals from different ages
813: are interviewed on their health status or degree of disability (in
814: the case of a health survey which is our main interest)
815:
816: -2- at least a second wave of interviews ("longitudinal") which
817: measure each change (if any) in individual health status. Health
818: expectancies are computed from the time spent in each health state
819: according to a model. More health states you consider, more time is
820: necessary to reach the Maximum Likelihood of the parameters involved
821: in the model. The simplest model is the multinomial logistic model
822: where pij is the probability to be observed in state j at the second
823: wave conditional to be observed in state i at the first
824: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
825: etc , where 'age' is age and 'sex' is a covariate. If you want to
826: have a more complex model than "constant and age", you should modify
827: the program where the markup *Covariates have to be included here
828: again* invites you to do it. More covariates you add, slower the
1.126 brouard 829: convergence.
830:
831: The advantage of this computer programme, compared to a simple
832: multinomial logistic model, is clear when the delay between waves is not
833: identical for each individual. Also, if a individual missed an
834: intermediate interview, the information is lost, but taken into
835: account using an interpolation or extrapolation.
836:
837: hPijx is the probability to be observed in state i at age x+h
838: conditional to the observed state i at age x. The delay 'h' can be
839: split into an exact number (nh*stepm) of unobserved intermediate
840: states. This elementary transition (by month, quarter,
841: semester or year) is modelled as a multinomial logistic. The hPx
842: matrix is simply the matrix product of nh*stepm elementary matrices
843: and the contribution of each individual to the likelihood is simply
844: hPijx.
845:
846: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 847: of the life expectancies. It also computes the period (stable) prevalence.
848:
849: Back prevalence and projections:
1.227 brouard 850:
851: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
852: double agemaxpar, double ftolpl, int *ncvyearp, double
853: dateprev1,double dateprev2, int firstpass, int lastpass, int
854: mobilavproj)
855:
856: Computes the back prevalence limit for any combination of
857: covariate values k at any age between ageminpar and agemaxpar and
858: returns it in **bprlim. In the loops,
859:
860: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
861: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
862:
863: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 864: Computes for any combination of covariates k and any age between bage and fage
865: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
866: oldm=oldms;savm=savms;
1.227 brouard 867:
1.267 brouard 868: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.218 brouard 869: Computes the transition matrix starting at age 'age' over
870: 'nhstepm*hstepm*stepm' months (i.e. until
871: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 872: nhstepm*hstepm matrices.
873:
874: Returns p3mat[i][j][h] after calling
875: p3mat[i][j][h]=matprod2(newm,
876: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
877: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
878: oldm);
1.226 brouard 879:
880: Important routines
881:
882: - func (or funcone), computes logit (pij) distinguishing
883: o fixed variables (single or product dummies or quantitative);
884: o varying variables by:
885: (1) wave (single, product dummies, quantitative),
886: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
887: % fixed dummy (treated) or quantitative (not done because time-consuming);
888: % varying dummy (not done) or quantitative (not done);
889: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
890: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
891: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
892: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
893: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 894:
1.226 brouard 895:
896:
1.133 brouard 897: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
898: Institut national d'études démographiques, Paris.
1.126 brouard 899: This software have been partly granted by Euro-REVES, a concerted action
900: from the European Union.
901: It is copyrighted identically to a GNU software product, ie programme and
902: software can be distributed freely for non commercial use. Latest version
903: can be accessed at http://euroreves.ined.fr/imach .
904:
905: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
906: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
907:
908: **********************************************************************/
909: /*
910: main
911: read parameterfile
912: read datafile
913: concatwav
914: freqsummary
915: if (mle >= 1)
916: mlikeli
917: print results files
918: if mle==1
919: computes hessian
920: read end of parameter file: agemin, agemax, bage, fage, estepm
921: begin-prev-date,...
922: open gnuplot file
923: open html file
1.145 brouard 924: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
925: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
926: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
927: freexexit2 possible for memory heap.
928:
929: h Pij x | pij_nom ficrestpij
930: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
931: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
932: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
933:
934: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
935: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
936: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
937: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
938: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
939:
1.126 brouard 940: forecasting if prevfcast==1 prevforecast call prevalence()
941: health expectancies
942: Variance-covariance of DFLE
943: prevalence()
944: movingaverage()
945: varevsij()
946: if popbased==1 varevsij(,popbased)
947: total life expectancies
948: Variance of period (stable) prevalence
949: end
950: */
951:
1.187 brouard 952: /* #define DEBUG */
953: /* #define DEBUGBRENT */
1.203 brouard 954: /* #define DEBUGLINMIN */
955: /* #define DEBUGHESS */
956: #define DEBUGHESSIJ
1.224 brouard 957: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 958: #define POWELL /* Instead of NLOPT */
1.224 brouard 959: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 960: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
961: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 962:
963: #include <math.h>
964: #include <stdio.h>
965: #include <stdlib.h>
966: #include <string.h>
1.226 brouard 967: #include <ctype.h>
1.159 brouard 968:
969: #ifdef _WIN32
970: #include <io.h>
1.172 brouard 971: #include <windows.h>
972: #include <tchar.h>
1.159 brouard 973: #else
1.126 brouard 974: #include <unistd.h>
1.159 brouard 975: #endif
1.126 brouard 976:
977: #include <limits.h>
978: #include <sys/types.h>
1.171 brouard 979:
980: #if defined(__GNUC__)
981: #include <sys/utsname.h> /* Doesn't work on Windows */
982: #endif
983:
1.126 brouard 984: #include <sys/stat.h>
985: #include <errno.h>
1.159 brouard 986: /* extern int errno; */
1.126 brouard 987:
1.157 brouard 988: /* #ifdef LINUX */
989: /* #include <time.h> */
990: /* #include "timeval.h" */
991: /* #else */
992: /* #include <sys/time.h> */
993: /* #endif */
994:
1.126 brouard 995: #include <time.h>
996:
1.136 brouard 997: #ifdef GSL
998: #include <gsl/gsl_errno.h>
999: #include <gsl/gsl_multimin.h>
1000: #endif
1001:
1.167 brouard 1002:
1.162 brouard 1003: #ifdef NLOPT
1004: #include <nlopt.h>
1005: typedef struct {
1006: double (* function)(double [] );
1007: } myfunc_data ;
1008: #endif
1009:
1.126 brouard 1010: /* #include <libintl.h> */
1011: /* #define _(String) gettext (String) */
1012:
1.251 brouard 1013: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 1014:
1015: #define GNUPLOTPROGRAM "gnuplot"
1016: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
1017: #define FILENAMELENGTH 132
1018:
1019: #define GLOCK_ERROR_NOPATH -1 /* empty path */
1020: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
1021:
1.144 brouard 1022: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
1023: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 1024:
1025: #define NINTERVMAX 8
1.144 brouard 1026: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
1027: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
1028: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 1029: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 1030: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
1031: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 1032: #define MAXN 20000
1.144 brouard 1033: #define YEARM 12. /**< Number of months per year */
1.218 brouard 1034: /* #define AGESUP 130 */
1035: #define AGESUP 150
1.268 brouard 1036: #define AGEINF 0
1.218 brouard 1037: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 1038: #define AGEBASE 40
1.194 brouard 1039: #define AGEOVERFLOW 1.e20
1.164 brouard 1040: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 1041: #ifdef _WIN32
1042: #define DIRSEPARATOR '\\'
1043: #define CHARSEPARATOR "\\"
1044: #define ODIRSEPARATOR '/'
1045: #else
1.126 brouard 1046: #define DIRSEPARATOR '/'
1047: #define CHARSEPARATOR "/"
1048: #define ODIRSEPARATOR '\\'
1049: #endif
1050:
1.282 ! brouard 1051: /* $Id: imach.c,v 1.281 2018/02/27 19:25:23 brouard Exp $ */
1.126 brouard 1052: /* $State: Exp $ */
1.196 brouard 1053: #include "version.h"
1054: char version[]=__IMACH_VERSION__;
1.224 brouard 1055: char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
1.282 ! brouard 1056: char fullversion[]="$Revision: 1.281 $ $Date: 2018/02/27 19:25:23 $";
1.126 brouard 1057: char strstart[80];
1058: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 1059: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 1060: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 1061: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
1062: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
1063: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 1064: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
1065: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 1066: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
1067: int cptcovprodnoage=0; /**< Number of covariate products without age */
1068: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 1069: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
1070: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 1071: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 1072: int nsd=0; /**< Total number of single dummy variables (output) */
1073: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 1074: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 1075: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 1076: int ntveff=0; /**< ntveff number of effective time varying variables */
1077: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 1078: int cptcov=0; /* Working variable */
1.218 brouard 1079: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 1080: int npar=NPARMAX;
1081: int nlstate=2; /* Number of live states */
1082: int ndeath=1; /* Number of dead states */
1.130 brouard 1083: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 1084: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 1085: int popbased=0;
1086:
1087: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1088: int maxwav=0; /* Maxim number of waves */
1089: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1090: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1091: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1092: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1093: int mle=1, weightopt=0;
1.126 brouard 1094: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1095: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1096: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1097: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1098: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1099: int selected(int kvar); /* Is covariate kvar selected for printing results */
1100:
1.130 brouard 1101: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1102: double **matprod2(); /* test */
1.126 brouard 1103: double **oldm, **newm, **savm; /* Working pointers to matrices */
1104: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1105: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1106:
1.136 brouard 1107: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1108: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1109: FILE *ficlog, *ficrespow;
1.130 brouard 1110: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1111: double fretone; /* Only one call to likelihood */
1.130 brouard 1112: long ipmx=0; /* Number of contributions */
1.126 brouard 1113: double sw; /* Sum of weights */
1114: char filerespow[FILENAMELENGTH];
1115: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1116: FILE *ficresilk;
1117: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1118: FILE *ficresprobmorprev;
1119: FILE *fichtm, *fichtmcov; /* Html File */
1120: FILE *ficreseij;
1121: char filerese[FILENAMELENGTH];
1122: FILE *ficresstdeij;
1123: char fileresstde[FILENAMELENGTH];
1124: FILE *ficrescveij;
1125: char filerescve[FILENAMELENGTH];
1126: FILE *ficresvij;
1127: char fileresv[FILENAMELENGTH];
1.269 brouard 1128:
1.126 brouard 1129: char title[MAXLINE];
1.234 brouard 1130: char model[MAXLINE]; /**< The model line */
1.217 brouard 1131: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1132: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1133: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1134: char command[FILENAMELENGTH];
1135: int outcmd=0;
1136:
1.217 brouard 1137: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1138: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1139: char filelog[FILENAMELENGTH]; /* Log file */
1140: char filerest[FILENAMELENGTH];
1141: char fileregp[FILENAMELENGTH];
1142: char popfile[FILENAMELENGTH];
1143:
1144: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1145:
1.157 brouard 1146: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1147: /* struct timezone tzp; */
1148: /* extern int gettimeofday(); */
1149: struct tm tml, *gmtime(), *localtime();
1150:
1151: extern time_t time();
1152:
1153: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1154: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1155: struct tm tm;
1156:
1.126 brouard 1157: char strcurr[80], strfor[80];
1158:
1159: char *endptr;
1160: long lval;
1161: double dval;
1162:
1163: #define NR_END 1
1164: #define FREE_ARG char*
1165: #define FTOL 1.0e-10
1166:
1167: #define NRANSI
1.240 brouard 1168: #define ITMAX 200
1169: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1170:
1171: #define TOL 2.0e-4
1172:
1173: #define CGOLD 0.3819660
1174: #define ZEPS 1.0e-10
1175: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1176:
1177: #define GOLD 1.618034
1178: #define GLIMIT 100.0
1179: #define TINY 1.0e-20
1180:
1181: static double maxarg1,maxarg2;
1182: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1183: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1184:
1185: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1186: #define rint(a) floor(a+0.5)
1.166 brouard 1187: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1188: #define mytinydouble 1.0e-16
1.166 brouard 1189: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1190: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1191: /* static double dsqrarg; */
1192: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1193: static double sqrarg;
1194: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1195: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1196: int agegomp= AGEGOMP;
1197:
1198: int imx;
1199: int stepm=1;
1200: /* Stepm, step in month: minimum step interpolation*/
1201:
1202: int estepm;
1203: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1204:
1205: int m,nb;
1206: long *num;
1.197 brouard 1207: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1208: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1209: covariate for which somebody answered excluding
1210: undefined. Usually 2: 0 and 1. */
1211: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1212: covariate for which somebody answered including
1213: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1214: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1215: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1216: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1217: double *ageexmed,*agecens;
1218: double dateintmean=0;
1219:
1220: double *weight;
1221: int **s; /* Status */
1.141 brouard 1222: double *agedc;
1.145 brouard 1223: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1224: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1225: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.268 brouard 1226: double **coqvar; /* Fixed quantitative covariate nqv */
1227: double ***cotvar; /* Time varying covariate ntv */
1.225 brouard 1228: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1229: double idx;
1230: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1231: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1232: /*k 1 2 3 4 5 6 7 8 9 */
1233: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1234: /* Tndvar[k] 1 2 3 4 5 */
1235: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1236: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1237: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1238: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1239: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1240: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1241: /* Tprod[i]=k 4 7 */
1242: /* Tage[i]=k 5 8 */
1243: /* */
1244: /* Type */
1245: /* V 1 2 3 4 5 */
1246: /* F F V V V */
1247: /* D Q D D Q */
1248: /* */
1249: int *TvarsD;
1250: int *TvarsDind;
1251: int *TvarsQ;
1252: int *TvarsQind;
1253:
1.235 brouard 1254: #define MAXRESULTLINES 10
1255: int nresult=0;
1.258 brouard 1256: int parameterline=0; /* # of the parameter (type) line */
1.235 brouard 1257: int TKresult[MAXRESULTLINES];
1.237 brouard 1258: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1259: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1260: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1261: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1262: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1263: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1264:
1.234 brouard 1265: /* 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 1266: 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 */
1267: 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 */
1268: 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 */
1269: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1270: 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 */
1271: 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 1272: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1273: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1274: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1275: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1276: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1277: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1278: 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 */
1279: 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 */
1280:
1.230 brouard 1281: int *Tvarsel; /**< Selected covariates for output */
1282: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1283: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1284: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1285: 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 1286: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1287: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1288: int *Tage;
1.227 brouard 1289: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1290: 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 1291: 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*/
1292: 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 1293: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1294: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1295: int **Tvard;
1296: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1297: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1298: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1299: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1300: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1301: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1302: double *lsurv, *lpop, *tpop;
1303:
1.231 brouard 1304: #define FD 1; /* Fixed dummy covariate */
1305: #define FQ 2; /* Fixed quantitative covariate */
1306: #define FP 3; /* Fixed product covariate */
1307: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1308: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1309: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1310: #define VD 10; /* Varying dummy covariate */
1311: #define VQ 11; /* Varying quantitative covariate */
1312: #define VP 12; /* Varying product covariate */
1313: #define VPDD 13; /* Varying product dummy*dummy covariate */
1314: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1315: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1316: #define APFD 16; /* Age product * fixed dummy covariate */
1317: #define APFQ 17; /* Age product * fixed quantitative covariate */
1318: #define APVD 18; /* Age product * varying dummy covariate */
1319: #define APVQ 19; /* Age product * varying quantitative covariate */
1320:
1321: #define FTYPE 1; /* Fixed covariate */
1322: #define VTYPE 2; /* Varying covariate (loop in wave) */
1323: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1324:
1325: struct kmodel{
1326: int maintype; /* main type */
1327: int subtype; /* subtype */
1328: };
1329: struct kmodel modell[NCOVMAX];
1330:
1.143 brouard 1331: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1332: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1333:
1334: /**************** split *************************/
1335: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1336: {
1337: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1338: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1339: */
1340: char *ss; /* pointer */
1.186 brouard 1341: int l1=0, l2=0; /* length counters */
1.126 brouard 1342:
1343: l1 = strlen(path ); /* length of path */
1344: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1345: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1346: if ( ss == NULL ) { /* no directory, so determine current directory */
1347: strcpy( name, path ); /* we got the fullname name because no directory */
1348: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1349: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1350: /* get current working directory */
1351: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1352: #ifdef WIN32
1353: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1354: #else
1355: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1356: #endif
1.126 brouard 1357: return( GLOCK_ERROR_GETCWD );
1358: }
1359: /* got dirc from getcwd*/
1360: printf(" DIRC = %s \n",dirc);
1.205 brouard 1361: } else { /* strip directory from path */
1.126 brouard 1362: ss++; /* after this, the filename */
1363: l2 = strlen( ss ); /* length of filename */
1364: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1365: strcpy( name, ss ); /* save file name */
1366: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1367: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1368: printf(" DIRC2 = %s \n",dirc);
1369: }
1370: /* We add a separator at the end of dirc if not exists */
1371: l1 = strlen( dirc ); /* length of directory */
1372: if( dirc[l1-1] != DIRSEPARATOR ){
1373: dirc[l1] = DIRSEPARATOR;
1374: dirc[l1+1] = 0;
1375: printf(" DIRC3 = %s \n",dirc);
1376: }
1377: ss = strrchr( name, '.' ); /* find last / */
1378: if (ss >0){
1379: ss++;
1380: strcpy(ext,ss); /* save extension */
1381: l1= strlen( name);
1382: l2= strlen(ss)+1;
1383: strncpy( finame, name, l1-l2);
1384: finame[l1-l2]= 0;
1385: }
1386:
1387: return( 0 ); /* we're done */
1388: }
1389:
1390:
1391: /******************************************/
1392:
1393: void replace_back_to_slash(char *s, char*t)
1394: {
1395: int i;
1396: int lg=0;
1397: i=0;
1398: lg=strlen(t);
1399: for(i=0; i<= lg; i++) {
1400: (s[i] = t[i]);
1401: if (t[i]== '\\') s[i]='/';
1402: }
1403: }
1404:
1.132 brouard 1405: char *trimbb(char *out, char *in)
1.137 brouard 1406: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1407: char *s;
1408: s=out;
1409: while (*in != '\0'){
1.137 brouard 1410: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1411: in++;
1412: }
1413: *out++ = *in++;
1414: }
1415: *out='\0';
1416: return s;
1417: }
1418:
1.187 brouard 1419: /* char *substrchaine(char *out, char *in, char *chain) */
1420: /* { */
1421: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1422: /* char *s, *t; */
1423: /* t=in;s=out; */
1424: /* while ((*in != *chain) && (*in != '\0')){ */
1425: /* *out++ = *in++; */
1426: /* } */
1427:
1428: /* /\* *in matches *chain *\/ */
1429: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1430: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1431: /* } */
1432: /* in--; chain--; */
1433: /* while ( (*in != '\0')){ */
1434: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1435: /* *out++ = *in++; */
1436: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1437: /* } */
1438: /* *out='\0'; */
1439: /* out=s; */
1440: /* return out; */
1441: /* } */
1442: char *substrchaine(char *out, char *in, char *chain)
1443: {
1444: /* Substract chain 'chain' from 'in', return and output 'out' */
1445: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1446:
1447: char *strloc;
1448:
1449: strcpy (out, in);
1450: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1451: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1452: if(strloc != NULL){
1453: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1454: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1455: /* strcpy (strloc, strloc +strlen(chain));*/
1456: }
1457: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1458: return out;
1459: }
1460:
1461:
1.145 brouard 1462: char *cutl(char *blocc, char *alocc, char *in, char occ)
1463: {
1.187 brouard 1464: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1465: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1466: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1467: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1468: */
1.160 brouard 1469: char *s, *t;
1.145 brouard 1470: t=in;s=in;
1471: while ((*in != occ) && (*in != '\0')){
1472: *alocc++ = *in++;
1473: }
1474: if( *in == occ){
1475: *(alocc)='\0';
1476: s=++in;
1477: }
1478:
1479: if (s == t) {/* occ not found */
1480: *(alocc-(in-s))='\0';
1481: in=s;
1482: }
1483: while ( *in != '\0'){
1484: *blocc++ = *in++;
1485: }
1486:
1487: *blocc='\0';
1488: return t;
1489: }
1.137 brouard 1490: char *cutv(char *blocc, char *alocc, char *in, char occ)
1491: {
1.187 brouard 1492: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1493: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1494: gives blocc="abcdef2ghi" and alocc="j".
1495: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1496: */
1497: char *s, *t;
1498: t=in;s=in;
1499: while (*in != '\0'){
1500: while( *in == occ){
1501: *blocc++ = *in++;
1502: s=in;
1503: }
1504: *blocc++ = *in++;
1505: }
1506: if (s == t) /* occ not found */
1507: *(blocc-(in-s))='\0';
1508: else
1509: *(blocc-(in-s)-1)='\0';
1510: in=s;
1511: while ( *in != '\0'){
1512: *alocc++ = *in++;
1513: }
1514:
1515: *alocc='\0';
1516: return s;
1517: }
1518:
1.126 brouard 1519: int nbocc(char *s, char occ)
1520: {
1521: int i,j=0;
1522: int lg=20;
1523: i=0;
1524: lg=strlen(s);
1525: for(i=0; i<= lg; i++) {
1.234 brouard 1526: if (s[i] == occ ) j++;
1.126 brouard 1527: }
1528: return j;
1529: }
1530:
1.137 brouard 1531: /* void cutv(char *u,char *v, char*t, char occ) */
1532: /* { */
1533: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1534: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1535: /* gives u="abcdef2ghi" and v="j" *\/ */
1536: /* int i,lg,j,p=0; */
1537: /* i=0; */
1538: /* lg=strlen(t); */
1539: /* for(j=0; j<=lg-1; j++) { */
1540: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1541: /* } */
1.126 brouard 1542:
1.137 brouard 1543: /* for(j=0; j<p; j++) { */
1544: /* (u[j] = t[j]); */
1545: /* } */
1546: /* u[p]='\0'; */
1.126 brouard 1547:
1.137 brouard 1548: /* for(j=0; j<= lg; j++) { */
1549: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1550: /* } */
1551: /* } */
1.126 brouard 1552:
1.160 brouard 1553: #ifdef _WIN32
1554: char * strsep(char **pp, const char *delim)
1555: {
1556: char *p, *q;
1557:
1558: if ((p = *pp) == NULL)
1559: return 0;
1560: if ((q = strpbrk (p, delim)) != NULL)
1561: {
1562: *pp = q + 1;
1563: *q = '\0';
1564: }
1565: else
1566: *pp = 0;
1567: return p;
1568: }
1569: #endif
1570:
1.126 brouard 1571: /********************** nrerror ********************/
1572:
1573: void nrerror(char error_text[])
1574: {
1575: fprintf(stderr,"ERREUR ...\n");
1576: fprintf(stderr,"%s\n",error_text);
1577: exit(EXIT_FAILURE);
1578: }
1579: /*********************** vector *******************/
1580: double *vector(int nl, int nh)
1581: {
1582: double *v;
1583: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1584: if (!v) nrerror("allocation failure in vector");
1585: return v-nl+NR_END;
1586: }
1587:
1588: /************************ free vector ******************/
1589: void free_vector(double*v, int nl, int nh)
1590: {
1591: free((FREE_ARG)(v+nl-NR_END));
1592: }
1593:
1594: /************************ivector *******************************/
1595: int *ivector(long nl,long nh)
1596: {
1597: int *v;
1598: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1599: if (!v) nrerror("allocation failure in ivector");
1600: return v-nl+NR_END;
1601: }
1602:
1603: /******************free ivector **************************/
1604: void free_ivector(int *v, long nl, long nh)
1605: {
1606: free((FREE_ARG)(v+nl-NR_END));
1607: }
1608:
1609: /************************lvector *******************************/
1610: long *lvector(long nl,long nh)
1611: {
1612: long *v;
1613: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1614: if (!v) nrerror("allocation failure in ivector");
1615: return v-nl+NR_END;
1616: }
1617:
1618: /******************free lvector **************************/
1619: void free_lvector(long *v, long nl, long nh)
1620: {
1621: free((FREE_ARG)(v+nl-NR_END));
1622: }
1623:
1624: /******************* imatrix *******************************/
1625: int **imatrix(long nrl, long nrh, long ncl, long nch)
1626: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1627: {
1628: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1629: int **m;
1630:
1631: /* allocate pointers to rows */
1632: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1633: if (!m) nrerror("allocation failure 1 in matrix()");
1634: m += NR_END;
1635: m -= nrl;
1636:
1637:
1638: /* allocate rows and set pointers to them */
1639: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1640: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1641: m[nrl] += NR_END;
1642: m[nrl] -= ncl;
1643:
1644: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1645:
1646: /* return pointer to array of pointers to rows */
1647: return m;
1648: }
1649:
1650: /****************** free_imatrix *************************/
1651: void free_imatrix(m,nrl,nrh,ncl,nch)
1652: int **m;
1653: long nch,ncl,nrh,nrl;
1654: /* free an int matrix allocated by imatrix() */
1655: {
1656: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1657: free((FREE_ARG) (m+nrl-NR_END));
1658: }
1659:
1660: /******************* matrix *******************************/
1661: double **matrix(long nrl, long nrh, long ncl, long nch)
1662: {
1663: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1664: double **m;
1665:
1666: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1667: if (!m) nrerror("allocation failure 1 in matrix()");
1668: m += NR_END;
1669: m -= nrl;
1670:
1671: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1672: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1673: m[nrl] += NR_END;
1674: m[nrl] -= ncl;
1675:
1676: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1677: return m;
1.145 brouard 1678: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1679: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1680: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1681: */
1682: }
1683:
1684: /*************************free matrix ************************/
1685: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1686: {
1687: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1688: free((FREE_ARG)(m+nrl-NR_END));
1689: }
1690:
1691: /******************* ma3x *******************************/
1692: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1693: {
1694: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1695: double ***m;
1696:
1697: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1698: if (!m) nrerror("allocation failure 1 in matrix()");
1699: m += NR_END;
1700: m -= nrl;
1701:
1702: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1703: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1704: m[nrl] += NR_END;
1705: m[nrl] -= ncl;
1706:
1707: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1708:
1709: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1710: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1711: m[nrl][ncl] += NR_END;
1712: m[nrl][ncl] -= nll;
1713: for (j=ncl+1; j<=nch; j++)
1714: m[nrl][j]=m[nrl][j-1]+nlay;
1715:
1716: for (i=nrl+1; i<=nrh; i++) {
1717: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1718: for (j=ncl+1; j<=nch; j++)
1719: m[i][j]=m[i][j-1]+nlay;
1720: }
1721: return m;
1722: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1723: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1724: */
1725: }
1726:
1727: /*************************free ma3x ************************/
1728: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1729: {
1730: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1731: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1732: free((FREE_ARG)(m+nrl-NR_END));
1733: }
1734:
1735: /*************** function subdirf ***********/
1736: char *subdirf(char fileres[])
1737: {
1738: /* Caution optionfilefiname is hidden */
1739: strcpy(tmpout,optionfilefiname);
1740: strcat(tmpout,"/"); /* Add to the right */
1741: strcat(tmpout,fileres);
1742: return tmpout;
1743: }
1744:
1745: /*************** function subdirf2 ***********/
1746: char *subdirf2(char fileres[], char *preop)
1747: {
1748:
1749: /* Caution optionfilefiname is hidden */
1750: strcpy(tmpout,optionfilefiname);
1751: strcat(tmpout,"/");
1752: strcat(tmpout,preop);
1753: strcat(tmpout,fileres);
1754: return tmpout;
1755: }
1756:
1757: /*************** function subdirf3 ***********/
1758: char *subdirf3(char fileres[], char *preop, char *preop2)
1759: {
1760:
1761: /* Caution optionfilefiname is hidden */
1762: strcpy(tmpout,optionfilefiname);
1763: strcat(tmpout,"/");
1764: strcat(tmpout,preop);
1765: strcat(tmpout,preop2);
1766: strcat(tmpout,fileres);
1767: return tmpout;
1768: }
1.213 brouard 1769:
1770: /*************** function subdirfext ***********/
1771: char *subdirfext(char fileres[], char *preop, char *postop)
1772: {
1773:
1774: strcpy(tmpout,preop);
1775: strcat(tmpout,fileres);
1776: strcat(tmpout,postop);
1777: return tmpout;
1778: }
1.126 brouard 1779:
1.213 brouard 1780: /*************** function subdirfext3 ***********/
1781: char *subdirfext3(char fileres[], char *preop, char *postop)
1782: {
1783:
1784: /* Caution optionfilefiname is hidden */
1785: strcpy(tmpout,optionfilefiname);
1786: strcat(tmpout,"/");
1787: strcat(tmpout,preop);
1788: strcat(tmpout,fileres);
1789: strcat(tmpout,postop);
1790: return tmpout;
1791: }
1792:
1.162 brouard 1793: char *asc_diff_time(long time_sec, char ascdiff[])
1794: {
1795: long sec_left, days, hours, minutes;
1796: days = (time_sec) / (60*60*24);
1797: sec_left = (time_sec) % (60*60*24);
1798: hours = (sec_left) / (60*60) ;
1799: sec_left = (sec_left) %(60*60);
1800: minutes = (sec_left) /60;
1801: sec_left = (sec_left) % (60);
1802: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1803: return ascdiff;
1804: }
1805:
1.126 brouard 1806: /***************** f1dim *************************/
1807: extern int ncom;
1808: extern double *pcom,*xicom;
1809: extern double (*nrfunc)(double []);
1810:
1811: double f1dim(double x)
1812: {
1813: int j;
1814: double f;
1815: double *xt;
1816:
1817: xt=vector(1,ncom);
1818: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1819: f=(*nrfunc)(xt);
1820: free_vector(xt,1,ncom);
1821: return f;
1822: }
1823:
1824: /*****************brent *************************/
1825: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1826: {
1827: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1828: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1829: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1830: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1831: * returned function value.
1832: */
1.126 brouard 1833: int iter;
1834: double a,b,d,etemp;
1.159 brouard 1835: double fu=0,fv,fw,fx;
1.164 brouard 1836: double ftemp=0.;
1.126 brouard 1837: double p,q,r,tol1,tol2,u,v,w,x,xm;
1838: double e=0.0;
1839:
1840: a=(ax < cx ? ax : cx);
1841: b=(ax > cx ? ax : cx);
1842: x=w=v=bx;
1843: fw=fv=fx=(*f)(x);
1844: for (iter=1;iter<=ITMAX;iter++) {
1845: xm=0.5*(a+b);
1846: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1847: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1848: printf(".");fflush(stdout);
1849: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1850: #ifdef DEBUGBRENT
1.126 brouard 1851: 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);
1852: 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);
1853: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1854: #endif
1855: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1856: *xmin=x;
1857: return fx;
1858: }
1859: ftemp=fu;
1860: if (fabs(e) > tol1) {
1861: r=(x-w)*(fx-fv);
1862: q=(x-v)*(fx-fw);
1863: p=(x-v)*q-(x-w)*r;
1864: q=2.0*(q-r);
1865: if (q > 0.0) p = -p;
1866: q=fabs(q);
1867: etemp=e;
1868: e=d;
1869: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1870: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1871: else {
1.224 brouard 1872: d=p/q;
1873: u=x+d;
1874: if (u-a < tol2 || b-u < tol2)
1875: d=SIGN(tol1,xm-x);
1.126 brouard 1876: }
1877: } else {
1878: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1879: }
1880: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1881: fu=(*f)(u);
1882: if (fu <= fx) {
1883: if (u >= x) a=x; else b=x;
1884: SHFT(v,w,x,u)
1.183 brouard 1885: SHFT(fv,fw,fx,fu)
1886: } else {
1887: if (u < x) a=u; else b=u;
1888: if (fu <= fw || w == x) {
1.224 brouard 1889: v=w;
1890: w=u;
1891: fv=fw;
1892: fw=fu;
1.183 brouard 1893: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1894: v=u;
1895: fv=fu;
1.183 brouard 1896: }
1897: }
1.126 brouard 1898: }
1899: nrerror("Too many iterations in brent");
1900: *xmin=x;
1901: return fx;
1902: }
1903:
1904: /****************** mnbrak ***********************/
1905:
1906: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1907: double (*func)(double))
1.183 brouard 1908: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1909: the downhill direction (defined by the function as evaluated at the initial points) and returns
1910: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1911: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1912: */
1.126 brouard 1913: double ulim,u,r,q, dum;
1914: double fu;
1.187 brouard 1915:
1916: double scale=10.;
1917: int iterscale=0;
1918:
1919: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1920: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1921:
1922:
1923: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1924: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1925: /* *bx = *ax - (*ax - *bx)/scale; */
1926: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1927: /* } */
1928:
1.126 brouard 1929: if (*fb > *fa) {
1930: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1931: SHFT(dum,*fb,*fa,dum)
1932: }
1.126 brouard 1933: *cx=(*bx)+GOLD*(*bx-*ax);
1934: *fc=(*func)(*cx);
1.183 brouard 1935: #ifdef DEBUG
1.224 brouard 1936: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1937: 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 1938: #endif
1.224 brouard 1939: 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 1940: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1941: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1942: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1943: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1944: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1945: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1946: fu=(*func)(u);
1.163 brouard 1947: #ifdef DEBUG
1948: /* f(x)=A(x-u)**2+f(u) */
1949: double A, fparabu;
1950: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1951: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1952: 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);
1953: 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 1954: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1955: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1956: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1957: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1958: #endif
1.184 brouard 1959: #ifdef MNBRAKORIGINAL
1.183 brouard 1960: #else
1.191 brouard 1961: /* if (fu > *fc) { */
1962: /* #ifdef DEBUG */
1963: /* printf("mnbrak4 fu > fc \n"); */
1964: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1965: /* #endif */
1966: /* /\* 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 *\\/ *\/ */
1967: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1968: /* dum=u; /\* Shifting c and u *\/ */
1969: /* u = *cx; */
1970: /* *cx = dum; */
1971: /* dum = fu; */
1972: /* fu = *fc; */
1973: /* *fc =dum; */
1974: /* } else { /\* end *\/ */
1975: /* #ifdef DEBUG */
1976: /* printf("mnbrak3 fu < fc \n"); */
1977: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1978: /* #endif */
1979: /* dum=u; /\* Shifting c and u *\/ */
1980: /* u = *cx; */
1981: /* *cx = dum; */
1982: /* dum = fu; */
1983: /* fu = *fc; */
1984: /* *fc =dum; */
1985: /* } */
1.224 brouard 1986: #ifdef DEBUGMNBRAK
1987: double A, fparabu;
1988: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1989: fparabu= *fa - A*(*ax-u)*(*ax-u);
1990: 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);
1991: 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 1992: #endif
1.191 brouard 1993: dum=u; /* Shifting c and u */
1994: u = *cx;
1995: *cx = dum;
1996: dum = fu;
1997: fu = *fc;
1998: *fc =dum;
1.183 brouard 1999: #endif
1.162 brouard 2000: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 2001: #ifdef DEBUG
1.224 brouard 2002: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
2003: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 2004: #endif
1.126 brouard 2005: fu=(*func)(u);
2006: if (fu < *fc) {
1.183 brouard 2007: #ifdef DEBUG
1.224 brouard 2008: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2009: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
2010: #endif
2011: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
2012: SHFT(*fb,*fc,fu,(*func)(u))
2013: #ifdef DEBUG
2014: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 2015: #endif
2016: }
1.162 brouard 2017: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 2018: #ifdef DEBUG
1.224 brouard 2019: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
2020: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 2021: #endif
1.126 brouard 2022: u=ulim;
2023: fu=(*func)(u);
1.183 brouard 2024: } else { /* u could be left to b (if r > q parabola has a maximum) */
2025: #ifdef DEBUG
1.224 brouard 2026: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
2027: 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 2028: #endif
1.126 brouard 2029: u=(*cx)+GOLD*(*cx-*bx);
2030: fu=(*func)(u);
1.224 brouard 2031: #ifdef DEBUG
2032: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2033: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
2034: #endif
1.183 brouard 2035: } /* end tests */
1.126 brouard 2036: SHFT(*ax,*bx,*cx,u)
1.183 brouard 2037: SHFT(*fa,*fb,*fc,fu)
2038: #ifdef DEBUG
1.224 brouard 2039: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
2040: 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 2041: #endif
2042: } /* 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 2043: }
2044:
2045: /*************** linmin ************************/
1.162 brouard 2046: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
2047: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
2048: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
2049: the value of func at the returned location p . This is actually all accomplished by calling the
2050: routines mnbrak and brent .*/
1.126 brouard 2051: int ncom;
2052: double *pcom,*xicom;
2053: double (*nrfunc)(double []);
2054:
1.224 brouard 2055: #ifdef LINMINORIGINAL
1.126 brouard 2056: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 2057: #else
2058: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
2059: #endif
1.126 brouard 2060: {
2061: double brent(double ax, double bx, double cx,
2062: double (*f)(double), double tol, double *xmin);
2063: double f1dim(double x);
2064: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
2065: double *fc, double (*func)(double));
2066: int j;
2067: double xx,xmin,bx,ax;
2068: double fx,fb,fa;
1.187 brouard 2069:
1.203 brouard 2070: #ifdef LINMINORIGINAL
2071: #else
2072: double scale=10., axs, xxs; /* Scale added for infinity */
2073: #endif
2074:
1.126 brouard 2075: ncom=n;
2076: pcom=vector(1,n);
2077: xicom=vector(1,n);
2078: nrfunc=func;
2079: for (j=1;j<=n;j++) {
2080: pcom[j]=p[j];
1.202 brouard 2081: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 2082: }
1.187 brouard 2083:
1.203 brouard 2084: #ifdef LINMINORIGINAL
2085: xx=1.;
2086: #else
2087: axs=0.0;
2088: xxs=1.;
2089: do{
2090: xx= xxs;
2091: #endif
1.187 brouard 2092: ax=0.;
2093: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2094: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2095: /* 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)) */
2096: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2097: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2098: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2099: /* 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 2100: #ifdef LINMINORIGINAL
2101: #else
2102: if (fx != fx){
1.224 brouard 2103: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2104: printf("|");
2105: fprintf(ficlog,"|");
1.203 brouard 2106: #ifdef DEBUGLINMIN
1.224 brouard 2107: 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 2108: #endif
2109: }
1.224 brouard 2110: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2111: #endif
2112:
1.191 brouard 2113: #ifdef DEBUGLINMIN
2114: 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 2115: 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 2116: #endif
1.224 brouard 2117: #ifdef LINMINORIGINAL
2118: #else
2119: if(fb == fx){ /* Flat function in the direction */
2120: xmin=xx;
2121: *flat=1;
2122: }else{
2123: *flat=0;
2124: #endif
2125: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2126: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2127: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2128: /* fmin = f(p[j] + xmin * xi[j]) */
2129: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2130: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2131: #ifdef DEBUG
1.224 brouard 2132: 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);
2133: 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);
2134: #endif
2135: #ifdef LINMINORIGINAL
2136: #else
2137: }
1.126 brouard 2138: #endif
1.191 brouard 2139: #ifdef DEBUGLINMIN
2140: printf("linmin end ");
1.202 brouard 2141: fprintf(ficlog,"linmin end ");
1.191 brouard 2142: #endif
1.126 brouard 2143: for (j=1;j<=n;j++) {
1.203 brouard 2144: #ifdef LINMINORIGINAL
2145: xi[j] *= xmin;
2146: #else
2147: #ifdef DEBUGLINMIN
2148: if(xxs <1.0)
2149: printf(" before xi[%d]=%12.8f", j,xi[j]);
2150: #endif
2151: 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) */
2152: #ifdef DEBUGLINMIN
2153: if(xxs <1.0)
2154: 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 );
2155: #endif
2156: #endif
1.187 brouard 2157: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2158: }
1.191 brouard 2159: #ifdef DEBUGLINMIN
1.203 brouard 2160: printf("\n");
1.191 brouard 2161: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2162: 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 2163: for (j=1;j<=n;j++) {
1.202 brouard 2164: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2165: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2166: if(j % ncovmodel == 0){
1.191 brouard 2167: printf("\n");
1.202 brouard 2168: fprintf(ficlog,"\n");
2169: }
1.191 brouard 2170: }
1.203 brouard 2171: #else
1.191 brouard 2172: #endif
1.126 brouard 2173: free_vector(xicom,1,n);
2174: free_vector(pcom,1,n);
2175: }
2176:
2177:
2178: /*************** powell ************************/
1.162 brouard 2179: /*
2180: Minimization of a function func of n variables. Input consists of an initial starting point
2181: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2182: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2183: such that failure to decrease by more than this amount on one iteration signals doneness. On
2184: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2185: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2186: */
1.224 brouard 2187: #ifdef LINMINORIGINAL
2188: #else
2189: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2190: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2191: #endif
1.126 brouard 2192: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2193: double (*func)(double []))
2194: {
1.224 brouard 2195: #ifdef LINMINORIGINAL
2196: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2197: double (*func)(double []));
1.224 brouard 2198: #else
1.241 brouard 2199: void linmin(double p[], double xi[], int n, double *fret,
2200: double (*func)(double []),int *flat);
1.224 brouard 2201: #endif
1.239 brouard 2202: int i,ibig,j,jk,k;
1.126 brouard 2203: double del,t,*pt,*ptt,*xit;
1.181 brouard 2204: double directest;
1.126 brouard 2205: double fp,fptt;
2206: double *xits;
2207: int niterf, itmp;
1.224 brouard 2208: #ifdef LINMINORIGINAL
2209: #else
2210:
2211: flatdir=ivector(1,n);
2212: for (j=1;j<=n;j++) flatdir[j]=0;
2213: #endif
1.126 brouard 2214:
2215: pt=vector(1,n);
2216: ptt=vector(1,n);
2217: xit=vector(1,n);
2218: xits=vector(1,n);
2219: *fret=(*func)(p);
2220: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2221: rcurr_time = time(NULL);
1.126 brouard 2222: for (*iter=1;;++(*iter)) {
1.187 brouard 2223: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2224: ibig=0;
2225: del=0.0;
1.157 brouard 2226: rlast_time=rcurr_time;
2227: /* (void) gettimeofday(&curr_time,&tzp); */
2228: rcurr_time = time(NULL);
2229: curr_time = *localtime(&rcurr_time);
2230: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2231: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2232: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2233: for (i=1;i<=n;i++) {
1.126 brouard 2234: fprintf(ficrespow," %.12lf", p[i]);
2235: }
1.239 brouard 2236: fprintf(ficrespow,"\n");fflush(ficrespow);
2237: printf("\n#model= 1 + age ");
2238: fprintf(ficlog,"\n#model= 1 + age ");
2239: if(nagesqr==1){
1.241 brouard 2240: printf(" + age*age ");
2241: fprintf(ficlog," + age*age ");
1.239 brouard 2242: }
2243: for(j=1;j <=ncovmodel-2;j++){
2244: if(Typevar[j]==0) {
2245: printf(" + V%d ",Tvar[j]);
2246: fprintf(ficlog," + V%d ",Tvar[j]);
2247: }else if(Typevar[j]==1) {
2248: printf(" + V%d*age ",Tvar[j]);
2249: fprintf(ficlog," + V%d*age ",Tvar[j]);
2250: }else if(Typevar[j]==2) {
2251: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2252: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2253: }
2254: }
1.126 brouard 2255: printf("\n");
1.239 brouard 2256: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2257: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2258: fprintf(ficlog,"\n");
1.239 brouard 2259: for(i=1,jk=1; i <=nlstate; i++){
2260: for(k=1; k <=(nlstate+ndeath); k++){
2261: if (k != i) {
2262: printf("%d%d ",i,k);
2263: fprintf(ficlog,"%d%d ",i,k);
2264: for(j=1; j <=ncovmodel; j++){
2265: printf("%12.7f ",p[jk]);
2266: fprintf(ficlog,"%12.7f ",p[jk]);
2267: jk++;
2268: }
2269: printf("\n");
2270: fprintf(ficlog,"\n");
2271: }
2272: }
2273: }
1.241 brouard 2274: if(*iter <=3 && *iter >1){
1.157 brouard 2275: tml = *localtime(&rcurr_time);
2276: strcpy(strcurr,asctime(&tml));
2277: rforecast_time=rcurr_time;
1.126 brouard 2278: itmp = strlen(strcurr);
2279: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2280: strcurr[itmp-1]='\0';
1.162 brouard 2281: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2282: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2283: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2284: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2285: forecast_time = *localtime(&rforecast_time);
2286: strcpy(strfor,asctime(&forecast_time));
2287: itmp = strlen(strfor);
2288: if(strfor[itmp-1]=='\n')
2289: strfor[itmp-1]='\0';
2290: 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);
2291: 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 2292: }
2293: }
1.187 brouard 2294: for (i=1;i<=n;i++) { /* For each direction i */
2295: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2296: fptt=(*fret);
2297: #ifdef DEBUG
1.203 brouard 2298: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2299: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2300: #endif
1.203 brouard 2301: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2302: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2303: #ifdef LINMINORIGINAL
1.188 brouard 2304: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2305: #else
2306: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2307: flatdir[i]=flat; /* Function is vanishing in that direction i */
2308: #endif
2309: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2310: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2311: /* because that direction will be replaced unless the gain del is small */
2312: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2313: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2314: /* with the new direction. */
2315: del=fabs(fptt-(*fret));
2316: ibig=i;
1.126 brouard 2317: }
2318: #ifdef DEBUG
2319: printf("%d %.12e",i,(*fret));
2320: fprintf(ficlog,"%d %.12e",i,(*fret));
2321: for (j=1;j<=n;j++) {
1.224 brouard 2322: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2323: printf(" x(%d)=%.12e",j,xit[j]);
2324: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2325: }
2326: for(j=1;j<=n;j++) {
1.225 brouard 2327: printf(" p(%d)=%.12e",j,p[j]);
2328: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2329: }
2330: printf("\n");
2331: fprintf(ficlog,"\n");
2332: #endif
1.187 brouard 2333: } /* end loop on each direction i */
2334: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2335: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2336: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2337: for(j=1;j<=n;j++) {
1.225 brouard 2338: if(flatdir[j] >0){
2339: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2340: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2341: }
2342: /* printf("\n"); */
2343: /* fprintf(ficlog,"\n"); */
2344: }
1.243 brouard 2345: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2346: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2347: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2348: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2349: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2350: /* decreased of more than 3.84 */
2351: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2352: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2353: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2354:
1.188 brouard 2355: /* Starting the program with initial values given by a former maximization will simply change */
2356: /* the scales of the directions and the directions, because the are reset to canonical directions */
2357: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2358: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2359: #ifdef DEBUG
2360: int k[2],l;
2361: k[0]=1;
2362: k[1]=-1;
2363: printf("Max: %.12e",(*func)(p));
2364: fprintf(ficlog,"Max: %.12e",(*func)(p));
2365: for (j=1;j<=n;j++) {
2366: printf(" %.12e",p[j]);
2367: fprintf(ficlog," %.12e",p[j]);
2368: }
2369: printf("\n");
2370: fprintf(ficlog,"\n");
2371: for(l=0;l<=1;l++) {
2372: for (j=1;j<=n;j++) {
2373: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2374: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2375: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2376: }
2377: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2378: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2379: }
2380: #endif
2381:
1.224 brouard 2382: #ifdef LINMINORIGINAL
2383: #else
2384: free_ivector(flatdir,1,n);
2385: #endif
1.126 brouard 2386: free_vector(xit,1,n);
2387: free_vector(xits,1,n);
2388: free_vector(ptt,1,n);
2389: free_vector(pt,1,n);
2390: return;
1.192 brouard 2391: } /* enough precision */
1.240 brouard 2392: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2393: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2394: ptt[j]=2.0*p[j]-pt[j];
2395: xit[j]=p[j]-pt[j];
2396: pt[j]=p[j];
2397: }
1.181 brouard 2398: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2399: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2400: if (*iter <=4) {
1.225 brouard 2401: #else
2402: #endif
1.224 brouard 2403: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2404: #else
1.161 brouard 2405: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2406: #endif
1.162 brouard 2407: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2408: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2409: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2410: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2411: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2412: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2413: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2414: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2415: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2416: /* Even if f3 <f1, directest can be negative and t >0 */
2417: /* mu² and del² are equal when f3=f1 */
2418: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2419: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2420: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2421: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2422: #ifdef NRCORIGINAL
2423: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2424: #else
2425: 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 2426: t= t- del*SQR(fp-fptt);
1.183 brouard 2427: #endif
1.202 brouard 2428: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2429: #ifdef DEBUG
1.181 brouard 2430: 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);
2431: 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 2432: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2433: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2434: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2435: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2436: 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);
2437: 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);
2438: #endif
1.183 brouard 2439: #ifdef POWELLORIGINAL
2440: if (t < 0.0) { /* Then we use it for new direction */
2441: #else
1.182 brouard 2442: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2443: 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 2444: 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 2445: 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 2446: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2447: }
1.181 brouard 2448: if (directest < 0.0) { /* Then we use it for new direction */
2449: #endif
1.191 brouard 2450: #ifdef DEBUGLINMIN
1.234 brouard 2451: printf("Before linmin in direction P%d-P0\n",n);
2452: for (j=1;j<=n;j++) {
2453: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2454: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2455: if(j % ncovmodel == 0){
2456: printf("\n");
2457: fprintf(ficlog,"\n");
2458: }
2459: }
1.224 brouard 2460: #endif
2461: #ifdef LINMINORIGINAL
1.234 brouard 2462: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2463: #else
1.234 brouard 2464: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2465: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2466: #endif
1.234 brouard 2467:
1.191 brouard 2468: #ifdef DEBUGLINMIN
1.234 brouard 2469: for (j=1;j<=n;j++) {
2470: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2471: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2472: if(j % ncovmodel == 0){
2473: printf("\n");
2474: fprintf(ficlog,"\n");
2475: }
2476: }
1.224 brouard 2477: #endif
1.234 brouard 2478: for (j=1;j<=n;j++) {
2479: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2480: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2481: }
1.224 brouard 2482: #ifdef LINMINORIGINAL
2483: #else
1.234 brouard 2484: for (j=1, flatd=0;j<=n;j++) {
2485: if(flatdir[j]>0)
2486: flatd++;
2487: }
2488: if(flatd >0){
1.255 brouard 2489: printf("%d flat directions: ",flatd);
2490: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2491: for (j=1;j<=n;j++) {
2492: if(flatdir[j]>0){
2493: printf("%d ",j);
2494: fprintf(ficlog,"%d ",j);
2495: }
2496: }
2497: printf("\n");
2498: fprintf(ficlog,"\n");
2499: }
1.191 brouard 2500: #endif
1.234 brouard 2501: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2502: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2503:
1.126 brouard 2504: #ifdef DEBUG
1.234 brouard 2505: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2506: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2507: for(j=1;j<=n;j++){
2508: printf(" %lf",xit[j]);
2509: fprintf(ficlog," %lf",xit[j]);
2510: }
2511: printf("\n");
2512: fprintf(ficlog,"\n");
1.126 brouard 2513: #endif
1.192 brouard 2514: } /* end of t or directest negative */
1.224 brouard 2515: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2516: #else
1.234 brouard 2517: } /* end if (fptt < fp) */
1.192 brouard 2518: #endif
1.225 brouard 2519: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2520: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2521: #else
1.224 brouard 2522: #endif
1.234 brouard 2523: } /* loop iteration */
1.126 brouard 2524: }
1.234 brouard 2525:
1.126 brouard 2526: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2527:
1.235 brouard 2528: 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 2529: {
1.279 brouard 2530: /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
2531: * (and selected quantitative values in nres)
2532: * by left multiplying the unit
2533: * matrix by transitions matrix until convergence is reached with precision ftolpl
2534: * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
2535: * Wx is row vector: population in state 1, population in state 2, population dead
2536: * or prevalence in state 1, prevalence in state 2, 0
2537: * newm is the matrix after multiplications, its rows are identical at a factor.
2538: * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
2539: * Output is prlim.
2540: * Initial matrix pimij
2541: */
1.206 brouard 2542: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2543: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2544: /* 0, 0 , 1} */
2545: /*
2546: * and after some iteration: */
2547: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2548: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2549: /* 0, 0 , 1} */
2550: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2551: /* {0.51571254859325999, 0.4842874514067399, */
2552: /* 0.51326036147820708, 0.48673963852179264} */
2553: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2554:
1.126 brouard 2555: int i, ii,j,k;
1.209 brouard 2556: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2557: /* double **matprod2(); */ /* test */
1.218 brouard 2558: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2559: double **newm;
1.209 brouard 2560: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2561: int ncvloop=0;
1.169 brouard 2562:
1.209 brouard 2563: min=vector(1,nlstate);
2564: max=vector(1,nlstate);
2565: meandiff=vector(1,nlstate);
2566:
1.218 brouard 2567: /* Starting with matrix unity */
1.126 brouard 2568: for (ii=1;ii<=nlstate+ndeath;ii++)
2569: for (j=1;j<=nlstate+ndeath;j++){
2570: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2571: }
1.169 brouard 2572:
2573: cov[1]=1.;
2574:
2575: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2576: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2577: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2578: ncvloop++;
1.126 brouard 2579: newm=savm;
2580: /* Covariates have to be included here again */
1.138 brouard 2581: cov[2]=agefin;
1.187 brouard 2582: if(nagesqr==1)
2583: cov[3]= agefin*agefin;;
1.234 brouard 2584: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2585: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2586: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2587: /* 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 2588: }
2589: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2590: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2591: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2592: /* 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 2593: }
1.237 brouard 2594: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2595: if(Dummy[Tvar[Tage[k]]]){
2596: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2597: } else{
1.235 brouard 2598: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2599: }
1.235 brouard 2600: /* 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 2601: }
1.237 brouard 2602: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2603: /* 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 2604: if(Dummy[Tvard[k][1]==0]){
2605: if(Dummy[Tvard[k][2]==0]){
2606: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2607: }else{
2608: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2609: }
2610: }else{
2611: if(Dummy[Tvard[k][2]==0]){
2612: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2613: }else{
2614: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2615: }
2616: }
1.234 brouard 2617: }
1.138 brouard 2618: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2619: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2620: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2621: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2622: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2623: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2624: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2625:
1.126 brouard 2626: savm=oldm;
2627: oldm=newm;
1.209 brouard 2628:
2629: for(j=1; j<=nlstate; j++){
2630: max[j]=0.;
2631: min[j]=1.;
2632: }
2633: for(i=1;i<=nlstate;i++){
2634: sumnew=0;
2635: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2636: for(j=1; j<=nlstate; j++){
2637: prlim[i][j]= newm[i][j]/(1-sumnew);
2638: max[j]=FMAX(max[j],prlim[i][j]);
2639: min[j]=FMIN(min[j],prlim[i][j]);
2640: }
2641: }
2642:
1.126 brouard 2643: maxmax=0.;
1.209 brouard 2644: for(j=1; j<=nlstate; j++){
2645: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2646: maxmax=FMAX(maxmax,meandiff[j]);
2647: /* 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 2648: } /* j loop */
1.203 brouard 2649: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2650: /* 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 2651: if(maxmax < ftolpl){
1.209 brouard 2652: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2653: free_vector(min,1,nlstate);
2654: free_vector(max,1,nlstate);
2655: free_vector(meandiff,1,nlstate);
1.126 brouard 2656: return prlim;
2657: }
1.169 brouard 2658: } /* age loop */
1.208 brouard 2659: /* After some age loop it doesn't converge */
1.209 brouard 2660: 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 2661: 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 2662: /* 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); */
2663: free_vector(min,1,nlstate);
2664: free_vector(max,1,nlstate);
2665: free_vector(meandiff,1,nlstate);
1.208 brouard 2666:
1.169 brouard 2667: return prlim; /* should not reach here */
1.126 brouard 2668: }
2669:
1.217 brouard 2670:
2671: /**** Back Prevalence limit (stable or period prevalence) ****************/
2672:
1.218 brouard 2673: /* 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) */
2674: /* 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 2675: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2676: {
1.264 brouard 2677: /* 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 2678: matrix by transitions matrix until convergence is reached with precision ftolpl */
2679: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2680: /* Wx is row vector: population in state 1, population in state 2, population dead */
2681: /* or prevalence in state 1, prevalence in state 2, 0 */
2682: /* newm is the matrix after multiplications, its rows are identical at a factor */
2683: /* Initial matrix pimij */
2684: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2685: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2686: /* 0, 0 , 1} */
2687: /*
2688: * and after some iteration: */
2689: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2690: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2691: /* 0, 0 , 1} */
2692: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2693: /* {0.51571254859325999, 0.4842874514067399, */
2694: /* 0.51326036147820708, 0.48673963852179264} */
2695: /* If we start from prlim again, prlim tends to a constant matrix */
2696:
2697: int i, ii,j,k;
1.247 brouard 2698: int first=0;
1.217 brouard 2699: double *min, *max, *meandiff, maxmax,sumnew=0.;
2700: /* double **matprod2(); */ /* test */
2701: double **out, cov[NCOVMAX+1], **bmij();
2702: double **newm;
1.218 brouard 2703: double **dnewm, **doldm, **dsavm; /* for use */
2704: double **oldm, **savm; /* for use */
2705:
1.217 brouard 2706: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2707: int ncvloop=0;
2708:
2709: min=vector(1,nlstate);
2710: max=vector(1,nlstate);
2711: meandiff=vector(1,nlstate);
2712:
1.266 brouard 2713: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2714: oldm=oldms; savm=savms;
2715:
2716: /* Starting with matrix unity */
2717: for (ii=1;ii<=nlstate+ndeath;ii++)
2718: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2719: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2720: }
2721:
2722: cov[1]=1.;
2723:
2724: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2725: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2726: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2727: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2728: ncvloop++;
1.218 brouard 2729: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2730: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2731: /* Covariates have to be included here again */
2732: cov[2]=agefin;
2733: if(nagesqr==1)
2734: cov[3]= agefin*agefin;;
1.242 brouard 2735: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2736: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2737: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.264 brouard 2738: /* 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 2739: }
2740: /* for (k=1; k<=cptcovn;k++) { */
2741: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2742: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2743: /* /\* 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])]); *\/ */
2744: /* } */
2745: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2746: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2747: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2748: /* 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]); */
2749: }
2750: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2751: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2752: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2753: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2754: for (k=1; k<=cptcovage;k++){ /* For product with age */
2755: if(Dummy[Tvar[Tage[k]]]){
2756: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2757: } else{
2758: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2759: }
2760: /* 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]); */
2761: }
2762: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2763: /* 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]); */
2764: if(Dummy[Tvard[k][1]==0]){
2765: if(Dummy[Tvard[k][2]==0]){
2766: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2767: }else{
2768: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2769: }
2770: }else{
2771: if(Dummy[Tvard[k][2]==0]){
2772: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2773: }else{
2774: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2775: }
2776: }
1.217 brouard 2777: }
2778:
2779: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2780: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2781: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2782: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2783: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2784: /* ij should be linked to the correct index of cov */
2785: /* age and covariate values ij are in 'cov', but we need to pass
2786: * ij for the observed prevalence at age and status and covariate
2787: * number: prevacurrent[(int)agefin][ii][ij]
2788: */
2789: /* 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 *\/ */
2790: /* 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 *\/ */
2791: 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 2792: /* if((int)age == 86 || (int)age == 87){ */
1.266 brouard 2793: /* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
2794: /* for(i=1; i<=nlstate+ndeath; i++) { */
2795: /* printf("%d newm= ",i); */
2796: /* for(j=1;j<=nlstate+ndeath;j++) { */
2797: /* printf("%f ",newm[i][j]); */
2798: /* } */
2799: /* printf("oldm * "); */
2800: /* for(j=1;j<=nlstate+ndeath;j++) { */
2801: /* printf("%f ",oldm[i][j]); */
2802: /* } */
1.268 brouard 2803: /* printf(" bmmij "); */
1.266 brouard 2804: /* for(j=1;j<=nlstate+ndeath;j++) { */
2805: /* printf("%f ",pmmij[i][j]); */
2806: /* } */
2807: /* printf("\n"); */
2808: /* } */
2809: /* } */
1.217 brouard 2810: savm=oldm;
2811: oldm=newm;
1.266 brouard 2812:
1.217 brouard 2813: for(j=1; j<=nlstate; j++){
2814: max[j]=0.;
2815: min[j]=1.;
2816: }
2817: for(j=1; j<=nlstate; j++){
2818: for(i=1;i<=nlstate;i++){
1.234 brouard 2819: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2820: bprlim[i][j]= newm[i][j];
2821: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2822: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2823: }
2824: }
1.218 brouard 2825:
1.217 brouard 2826: maxmax=0.;
2827: for(i=1; i<=nlstate; i++){
2828: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2829: maxmax=FMAX(maxmax,meandiff[i]);
2830: /* 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 2831: } /* i loop */
1.217 brouard 2832: *ncvyear= -( (int)age- (int)agefin);
1.268 brouard 2833: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2834: if(maxmax < ftolpl){
1.220 brouard 2835: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2836: free_vector(min,1,nlstate);
2837: free_vector(max,1,nlstate);
2838: free_vector(meandiff,1,nlstate);
2839: return bprlim;
2840: }
2841: } /* age loop */
2842: /* After some age loop it doesn't converge */
1.247 brouard 2843: if(first){
2844: first=1;
2845: 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\
2846: 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);
2847: }
2848: 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 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: /* 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); */
2851: free_vector(min,1,nlstate);
2852: free_vector(max,1,nlstate);
2853: free_vector(meandiff,1,nlstate);
2854:
2855: return bprlim; /* should not reach here */
2856: }
2857:
1.126 brouard 2858: /*************** transition probabilities ***************/
2859:
2860: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2861: {
1.138 brouard 2862: /* According to parameters values stored in x and the covariate's values stored in cov,
1.266 brouard 2863: computes the probability to be observed in state j (after stepm years) being in state i by appying the
1.138 brouard 2864: model to the ncovmodel covariates (including constant and age).
2865: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2866: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2867: ncth covariate in the global vector x is given by the formula:
2868: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2869: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2870: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2871: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1.266 brouard 2872: Outputs ps[i][j] or probability to be observed in j being in i according to
1.138 brouard 2873: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1.266 brouard 2874: Sum on j ps[i][j] should equal to 1.
1.138 brouard 2875: */
2876: double s1, lnpijopii;
1.126 brouard 2877: /*double t34;*/
1.164 brouard 2878: int i,j, nc, ii, jj;
1.126 brouard 2879:
1.223 brouard 2880: for(i=1; i<= nlstate; i++){
2881: for(j=1; j<i;j++){
2882: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2883: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2884: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2885: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2886: }
2887: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2888: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2889: }
2890: for(j=i+1; j<=nlstate+ndeath;j++){
2891: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2892: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2893: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2894: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2895: }
2896: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2897: }
2898: }
1.218 brouard 2899:
1.223 brouard 2900: for(i=1; i<= nlstate; i++){
2901: s1=0;
2902: for(j=1; j<i; j++){
2903: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2904: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2905: }
2906: for(j=i+1; j<=nlstate+ndeath; j++){
2907: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2908: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2909: }
2910: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2911: ps[i][i]=1./(s1+1.);
2912: /* Computing other pijs */
2913: for(j=1; j<i; j++)
2914: ps[i][j]= exp(ps[i][j])*ps[i][i];
2915: for(j=i+1; j<=nlstate+ndeath; j++)
2916: ps[i][j]= exp(ps[i][j])*ps[i][i];
2917: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2918: } /* end i */
1.218 brouard 2919:
1.223 brouard 2920: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2921: for(jj=1; jj<= nlstate+ndeath; jj++){
2922: ps[ii][jj]=0;
2923: ps[ii][ii]=1;
2924: }
2925: }
1.218 brouard 2926:
2927:
1.223 brouard 2928: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2929: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2930: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2931: /* } */
2932: /* printf("\n "); */
2933: /* } */
2934: /* printf("\n ");printf("%lf ",cov[2]);*/
2935: /*
2936: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2937: goto end;*/
1.266 brouard 2938: return ps; /* Pointer is unchanged since its call */
1.126 brouard 2939: }
2940:
1.218 brouard 2941: /*************** backward transition probabilities ***************/
2942:
2943: /* 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 ) */
2944: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2945: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2946: {
1.266 brouard 2947: /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
2948: * 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 2949: */
1.218 brouard 2950: int i, ii, j,k;
1.222 brouard 2951:
2952: double **out, **pmij();
2953: double sumnew=0.;
1.218 brouard 2954: double agefin;
1.268 brouard 2955: 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 2956: double **dnewm, **dsavm, **doldm;
2957: double **bbmij;
2958:
1.218 brouard 2959: doldm=ddoldms; /* global pointers */
1.222 brouard 2960: dnewm=ddnewms;
2961: dsavm=ddsavms;
2962:
2963: agefin=cov[2];
1.268 brouard 2964: /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
1.222 brouard 2965: /* bmij *//* age is cov[2], ij is included in cov, but we need for
1.266 brouard 2966: the observed prevalence (with this covariate ij) at beginning of transition */
2967: /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.268 brouard 2968:
2969: /* P_x */
1.266 brouard 2970: pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
1.268 brouard 2971: /* outputs pmmij which is a stochastic matrix in row */
2972:
2973: /* Diag(w_x) */
2974: /* Problem with prevacurrent which can be zero */
2975: sumnew=0.;
1.269 brouard 2976: /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
1.268 brouard 2977: for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
1.269 brouard 2978: /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
1.268 brouard 2979: sumnew+=prevacurrent[(int)agefin][ii][ij];
2980: }
2981: if(sumnew >0.01){ /* At least some value in the prevalence */
2982: for (ii=1;ii<=nlstate+ndeath;ii++){
2983: for (j=1;j<=nlstate+ndeath;j++)
1.269 brouard 2984: doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
1.268 brouard 2985: }
2986: }else{
2987: for (ii=1;ii<=nlstate+ndeath;ii++){
2988: for (j=1;j<=nlstate+ndeath;j++)
2989: doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
2990: }
2991: /* if(sumnew <0.9){ */
2992: /* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
2993: /* } */
2994: }
2995: k3=0.0; /* We put the last diagonal to 0 */
2996: for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
2997: doldm[ii][ii]= k3;
2998: }
2999: /* End doldm, At the end doldm is diag[(w_i)] */
3000:
3001: /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
3002: bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
3003:
3004: /* Diag(Sum_i w^i_x p^ij_x */
3005: /* 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 3006: for (j=1;j<=nlstate+ndeath;j++){
1.268 brouard 3007: sumnew=0.;
1.222 brouard 3008: for (ii=1;ii<=nlstate;ii++){
1.266 brouard 3009: /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
1.268 brouard 3010: sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
1.222 brouard 3011: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
1.268 brouard 3012: for (ii=1;ii<=nlstate+ndeath;ii++){
1.222 brouard 3013: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
1.268 brouard 3014: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3015: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
1.268 brouard 3016: /* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
1.222 brouard 3017: /* }else */
1.268 brouard 3018: dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
3019: } /*End ii */
3020: } /* 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 */
3021:
3022: ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
3023: /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
1.222 brouard 3024: /* end bmij */
1.266 brouard 3025: return ps; /*pointer is unchanged */
1.218 brouard 3026: }
1.217 brouard 3027: /*************** transition probabilities ***************/
3028:
1.218 brouard 3029: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 3030: {
3031: /* According to parameters values stored in x and the covariate's values stored in cov,
3032: computes the probability to be observed in state j being in state i by appying the
3033: model to the ncovmodel covariates (including constant and age).
3034: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
3035: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
3036: ncth covariate in the global vector x is given by the formula:
3037: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
3038: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
3039: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
3040: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
3041: Outputs ps[i][j] the probability to be observed in j being in j according to
3042: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
3043: */
3044: double s1, lnpijopii;
3045: /*double t34;*/
3046: int i,j, nc, ii, jj;
3047:
1.234 brouard 3048: for(i=1; i<= nlstate; i++){
3049: for(j=1; j<i;j++){
3050: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3051: /*lnpijopii += param[i][j][nc]*cov[nc];*/
3052: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
3053: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3054: }
3055: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3056: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
3057: }
3058: for(j=i+1; j<=nlstate+ndeath;j++){
3059: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
3060: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
3061: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
3062: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
3063: }
3064: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
3065: }
3066: }
3067:
3068: for(i=1; i<= nlstate; i++){
3069: s1=0;
3070: for(j=1; j<i; j++){
3071: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3072: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3073: }
3074: for(j=i+1; j<=nlstate+ndeath; j++){
3075: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
3076: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
3077: }
3078: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
3079: ps[i][i]=1./(s1+1.);
3080: /* Computing other pijs */
3081: for(j=1; j<i; j++)
3082: ps[i][j]= exp(ps[i][j])*ps[i][i];
3083: for(j=i+1; j<=nlstate+ndeath; j++)
3084: ps[i][j]= exp(ps[i][j])*ps[i][i];
3085: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
3086: } /* end i */
3087:
3088: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
3089: for(jj=1; jj<= nlstate+ndeath; jj++){
3090: ps[ii][jj]=0;
3091: ps[ii][ii]=1;
3092: }
3093: }
3094: /* Added for backcast */ /* Transposed matrix too */
3095: for(jj=1; jj<= nlstate+ndeath; jj++){
3096: s1=0.;
3097: for(ii=1; ii<= nlstate+ndeath; ii++){
3098: s1+=ps[ii][jj];
3099: }
3100: for(ii=1; ii<= nlstate; ii++){
3101: ps[ii][jj]=ps[ii][jj]/s1;
3102: }
3103: }
3104: /* Transposition */
3105: for(jj=1; jj<= nlstate+ndeath; jj++){
3106: for(ii=jj; ii<= nlstate+ndeath; ii++){
3107: s1=ps[ii][jj];
3108: ps[ii][jj]=ps[jj][ii];
3109: ps[jj][ii]=s1;
3110: }
3111: }
3112: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
3113: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
3114: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
3115: /* } */
3116: /* printf("\n "); */
3117: /* } */
3118: /* printf("\n ");printf("%lf ",cov[2]);*/
3119: /*
3120: for(i=1; i<= npar; i++) printf("%f ",x[i]);
3121: goto end;*/
3122: return ps;
1.217 brouard 3123: }
3124:
3125:
1.126 brouard 3126: /**************** Product of 2 matrices ******************/
3127:
1.145 brouard 3128: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 3129: {
3130: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
3131: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
3132: /* in, b, out are matrice of pointers which should have been initialized
3133: before: only the contents of out is modified. The function returns
3134: a pointer to pointers identical to out */
1.145 brouard 3135: int i, j, k;
1.126 brouard 3136: for(i=nrl; i<= nrh; i++)
1.145 brouard 3137: for(k=ncolol; k<=ncoloh; k++){
3138: out[i][k]=0.;
3139: for(j=ncl; j<=nch; j++)
3140: out[i][k] +=in[i][j]*b[j][k];
3141: }
1.126 brouard 3142: return out;
3143: }
3144:
3145:
3146: /************* Higher Matrix Product ***************/
3147:
1.235 brouard 3148: 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 3149: {
1.218 brouard 3150: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3151: 'nhstepm*hstepm*stepm' months (i.e. until
3152: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3153: nhstepm*hstepm matrices.
3154: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3155: (typically every 2 years instead of every month which is too big
3156: for the memory).
3157: Model is determined by parameters x and covariates have to be
3158: included manually here.
3159:
3160: */
3161:
3162: int i, j, d, h, k;
1.131 brouard 3163: double **out, cov[NCOVMAX+1];
1.126 brouard 3164: double **newm;
1.187 brouard 3165: double agexact;
1.214 brouard 3166: double agebegin, ageend;
1.126 brouard 3167:
3168: /* Hstepm could be zero and should return the unit matrix */
3169: for (i=1;i<=nlstate+ndeath;i++)
3170: for (j=1;j<=nlstate+ndeath;j++){
3171: oldm[i][j]=(i==j ? 1.0 : 0.0);
3172: po[i][j][0]=(i==j ? 1.0 : 0.0);
3173: }
3174: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3175: for(h=1; h <=nhstepm; h++){
3176: for(d=1; d <=hstepm; d++){
3177: newm=savm;
3178: /* Covariates have to be included here again */
3179: cov[1]=1.;
1.214 brouard 3180: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3181: cov[2]=agexact;
3182: if(nagesqr==1)
1.227 brouard 3183: cov[3]= agexact*agexact;
1.235 brouard 3184: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3185: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3186: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3187: /* 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)); */
3188: }
3189: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3190: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3191: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3192: /* 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]); */
3193: }
3194: for (k=1; k<=cptcovage;k++){
3195: if(Dummy[Tvar[Tage[k]]]){
3196: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3197: } else{
3198: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3199: }
3200: /* 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]); */
3201: }
3202: for (k=1; k<=cptcovprod;k++){ /* */
3203: /* 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]); */
3204: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3205: }
3206: /* for (k=1; k<=cptcovn;k++) */
3207: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3208: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3209: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3210: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3211: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3212:
3213:
1.126 brouard 3214: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3215: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3216: /* right multiplication of oldm by the current matrix */
1.126 brouard 3217: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3218: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3219: /* if((int)age == 70){ */
3220: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3221: /* for(i=1; i<=nlstate+ndeath; i++) { */
3222: /* printf("%d pmmij ",i); */
3223: /* for(j=1;j<=nlstate+ndeath;j++) { */
3224: /* printf("%f ",pmmij[i][j]); */
3225: /* } */
3226: /* printf(" oldm "); */
3227: /* for(j=1;j<=nlstate+ndeath;j++) { */
3228: /* printf("%f ",oldm[i][j]); */
3229: /* } */
3230: /* printf("\n"); */
3231: /* } */
3232: /* } */
1.126 brouard 3233: savm=oldm;
3234: oldm=newm;
3235: }
3236: for(i=1; i<=nlstate+ndeath; i++)
3237: for(j=1;j<=nlstate+ndeath;j++) {
1.267 brouard 3238: po[i][j][h]=newm[i][j];
3239: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3240: }
1.128 brouard 3241: /*printf("h=%d ",h);*/
1.126 brouard 3242: } /* end h */
1.267 brouard 3243: /* printf("\n H=%d \n",h); */
1.126 brouard 3244: return po;
3245: }
3246:
1.217 brouard 3247: /************* Higher Back Matrix Product ***************/
1.218 brouard 3248: /* 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 3249: 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 3250: {
1.266 brouard 3251: /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
1.217 brouard 3252: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3253: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3254: nhstepm*hstepm matrices.
3255: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3256: (typically every 2 years instead of every month which is too big
1.217 brouard 3257: for the memory).
1.218 brouard 3258: Model is determined by parameters x and covariates have to be
1.266 brouard 3259: included manually here. Then we use a call to bmij(x and cov)
3260: The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
1.222 brouard 3261: */
1.217 brouard 3262:
3263: int i, j, d, h, k;
1.266 brouard 3264: double **out, cov[NCOVMAX+1], **bmij();
3265: double **newm, ***newmm;
1.217 brouard 3266: double agexact;
3267: double agebegin, ageend;
1.222 brouard 3268: double **oldm, **savm;
1.217 brouard 3269:
1.266 brouard 3270: newmm=po; /* To be saved */
3271: oldm=oldms;savm=savms; /* Global pointers */
1.217 brouard 3272: /* Hstepm could be zero and should return the unit matrix */
3273: for (i=1;i<=nlstate+ndeath;i++)
3274: for (j=1;j<=nlstate+ndeath;j++){
3275: oldm[i][j]=(i==j ? 1.0 : 0.0);
3276: po[i][j][0]=(i==j ? 1.0 : 0.0);
3277: }
3278: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3279: for(h=1; h <=nhstepm; h++){
3280: for(d=1; d <=hstepm; d++){
3281: newm=savm;
3282: /* Covariates have to be included here again */
3283: cov[1]=1.;
1.271 brouard 3284: agexact=age-( (h-1)*hstepm + (d) )*stepm/YEARM; /* age just before transition, d or d-1? */
1.217 brouard 3285: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3286: cov[2]=agexact;
3287: if(nagesqr==1)
1.222 brouard 3288: cov[3]= agexact*agexact;
1.266 brouard 3289: for (k=1; k<=cptcovn;k++){
3290: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3291: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
3292: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3293: /* 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)); */
3294: }
1.267 brouard 3295: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3296: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3297: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3298: /* 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]); */
3299: }
3300: for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
3301: if(Dummy[Tvar[Tage[k]]]){
3302: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3303: } else{
3304: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3305: }
3306: /* 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]); */
3307: }
3308: for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
1.222 brouard 3309: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.267 brouard 3310: }
1.217 brouard 3311: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3312: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.267 brouard 3313:
1.218 brouard 3314: /* Careful transposed matrix */
1.266 brouard 3315: /* age is in cov[2], prevacurrent at beginning of transition. */
1.218 brouard 3316: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3317: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3318: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3319: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3320: /* if((int)age == 70){ */
3321: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3322: /* for(i=1; i<=nlstate+ndeath; i++) { */
3323: /* printf("%d pmmij ",i); */
3324: /* for(j=1;j<=nlstate+ndeath;j++) { */
3325: /* printf("%f ",pmmij[i][j]); */
3326: /* } */
3327: /* printf(" oldm "); */
3328: /* for(j=1;j<=nlstate+ndeath;j++) { */
3329: /* printf("%f ",oldm[i][j]); */
3330: /* } */
3331: /* printf("\n"); */
3332: /* } */
3333: /* } */
3334: savm=oldm;
3335: oldm=newm;
3336: }
3337: for(i=1; i<=nlstate+ndeath; i++)
3338: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3339: po[i][j][h]=newm[i][j];
1.268 brouard 3340: /* if(h==nhstepm) */
3341: /* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
1.217 brouard 3342: }
1.268 brouard 3343: /* printf("h=%d %.1f ",h, agexact); */
1.217 brouard 3344: } /* end h */
1.268 brouard 3345: /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
1.217 brouard 3346: return po;
3347: }
3348:
3349:
1.162 brouard 3350: #ifdef NLOPT
3351: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3352: double fret;
3353: double *xt;
3354: int j;
3355: myfunc_data *d2 = (myfunc_data *) pd;
3356: /* xt = (p1-1); */
3357: xt=vector(1,n);
3358: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3359:
3360: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3361: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3362: printf("Function = %.12lf ",fret);
3363: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3364: printf("\n");
3365: free_vector(xt,1,n);
3366: return fret;
3367: }
3368: #endif
1.126 brouard 3369:
3370: /*************** log-likelihood *************/
3371: double func( double *x)
3372: {
1.226 brouard 3373: int i, ii, j, k, mi, d, kk;
3374: int ioffset=0;
3375: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3376: double **out;
3377: double lli; /* Individual log likelihood */
3378: int s1, s2;
1.228 brouard 3379: 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 3380: double bbh, survp;
3381: long ipmx;
3382: double agexact;
3383: /*extern weight */
3384: /* We are differentiating ll according to initial status */
3385: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3386: /*for(i=1;i<imx;i++)
3387: printf(" %d\n",s[4][i]);
3388: */
1.162 brouard 3389:
1.226 brouard 3390: ++countcallfunc;
1.162 brouard 3391:
1.226 brouard 3392: cov[1]=1.;
1.126 brouard 3393:
1.226 brouard 3394: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3395: ioffset=0;
1.226 brouard 3396: if(mle==1){
3397: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3398: /* Computes the values of the ncovmodel covariates of the model
3399: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3400: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3401: to be observed in j being in i according to the model.
3402: */
1.243 brouard 3403: ioffset=2+nagesqr ;
1.233 brouard 3404: /* Fixed */
1.234 brouard 3405: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3406: 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)*/
3407: }
1.226 brouard 3408: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3409: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3410: has been calculated etc */
3411: /* For an individual i, wav[i] gives the number of effective waves */
3412: /* We compute the contribution to Likelihood of each effective transition
3413: mw[mi][i] is real wave of the mi th effectve wave */
3414: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3415: s2=s[mw[mi+1][i]][i];
3416: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3417: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3418: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3419: */
3420: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3421: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3422: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3423: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3424: }
3425: for (ii=1;ii<=nlstate+ndeath;ii++)
3426: for (j=1;j<=nlstate+ndeath;j++){
3427: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3428: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3429: }
3430: for(d=0; d<dh[mi][i]; d++){
3431: newm=savm;
3432: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3433: cov[2]=agexact;
3434: if(nagesqr==1)
3435: cov[3]= agexact*agexact; /* Should be changed here */
3436: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3437: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3438: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3439: else
3440: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3441: }
3442: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3443: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3444: savm=oldm;
3445: oldm=newm;
3446: } /* end mult */
3447:
3448: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3449: /* But now since version 0.9 we anticipate for bias at large stepm.
3450: * If stepm is larger than one month (smallest stepm) and if the exact delay
3451: * (in months) between two waves is not a multiple of stepm, we rounded to
3452: * the nearest (and in case of equal distance, to the lowest) interval but now
3453: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3454: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3455: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3456: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3457: * -stepm/2 to stepm/2 .
3458: * For stepm=1 the results are the same as for previous versions of Imach.
3459: * For stepm > 1 the results are less biased than in previous versions.
3460: */
1.234 brouard 3461: s1=s[mw[mi][i]][i];
3462: s2=s[mw[mi+1][i]][i];
3463: bbh=(double)bh[mi][i]/(double)stepm;
3464: /* bias bh is positive if real duration
3465: * is higher than the multiple of stepm and negative otherwise.
3466: */
3467: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3468: if( s2 > nlstate){
3469: /* i.e. if s2 is a death state and if the date of death is known
3470: then the contribution to the likelihood is the probability to
3471: die between last step unit time and current step unit time,
3472: which is also equal to probability to die before dh
3473: minus probability to die before dh-stepm .
3474: In version up to 0.92 likelihood was computed
3475: as if date of death was unknown. Death was treated as any other
3476: health state: the date of the interview describes the actual state
3477: and not the date of a change in health state. The former idea was
3478: to consider that at each interview the state was recorded
3479: (healthy, disable or death) and IMaCh was corrected; but when we
3480: introduced the exact date of death then we should have modified
3481: the contribution of an exact death to the likelihood. This new
3482: contribution is smaller and very dependent of the step unit
3483: stepm. It is no more the probability to die between last interview
3484: and month of death but the probability to survive from last
3485: interview up to one month before death multiplied by the
3486: probability to die within a month. Thanks to Chris
3487: Jackson for correcting this bug. Former versions increased
3488: mortality artificially. The bad side is that we add another loop
3489: which slows down the processing. The difference can be up to 10%
3490: lower mortality.
3491: */
3492: /* If, at the beginning of the maximization mostly, the
3493: cumulative probability or probability to be dead is
3494: constant (ie = 1) over time d, the difference is equal to
3495: 0. out[s1][3] = savm[s1][3]: probability, being at state
3496: s1 at precedent wave, to be dead a month before current
3497: wave is equal to probability, being at state s1 at
3498: precedent wave, to be dead at mont of the current
3499: wave. Then the observed probability (that this person died)
3500: is null according to current estimated parameter. In fact,
3501: it should be very low but not zero otherwise the log go to
3502: infinity.
3503: */
1.183 brouard 3504: /* #ifdef INFINITYORIGINAL */
3505: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3506: /* #else */
3507: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3508: /* lli=log(mytinydouble); */
3509: /* else */
3510: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3511: /* #endif */
1.226 brouard 3512: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3513:
1.226 brouard 3514: } else if ( s2==-1 ) { /* alive */
3515: for (j=1,survp=0. ; j<=nlstate; j++)
3516: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3517: /*survp += out[s1][j]; */
3518: lli= log(survp);
3519: }
3520: else if (s2==-4) {
3521: for (j=3,survp=0. ; j<=nlstate; j++)
3522: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3523: lli= log(survp);
3524: }
3525: else if (s2==-5) {
3526: for (j=1,survp=0. ; j<=2; j++)
3527: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3528: lli= log(survp);
3529: }
3530: else{
3531: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3532: /* 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 */
3533: }
3534: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3535: /*if(lli ==000.0)*/
3536: /*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); */
3537: ipmx +=1;
3538: sw += weight[i];
3539: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3540: /* if (lli < log(mytinydouble)){ */
3541: /* 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); */
3542: /* 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]); */
3543: /* } */
3544: } /* end of wave */
3545: } /* end of individual */
3546: } else if(mle==2){
3547: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3548: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3549: for(mi=1; mi<= wav[i]-1; mi++){
3550: for (ii=1;ii<=nlstate+ndeath;ii++)
3551: for (j=1;j<=nlstate+ndeath;j++){
3552: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3553: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3554: }
3555: for(d=0; d<=dh[mi][i]; d++){
3556: newm=savm;
3557: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3558: cov[2]=agexact;
3559: if(nagesqr==1)
3560: cov[3]= agexact*agexact;
3561: for (kk=1; kk<=cptcovage;kk++) {
3562: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3563: }
3564: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3565: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3566: savm=oldm;
3567: oldm=newm;
3568: } /* end mult */
3569:
3570: s1=s[mw[mi][i]][i];
3571: s2=s[mw[mi+1][i]][i];
3572: bbh=(double)bh[mi][i]/(double)stepm;
3573: 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 */
3574: ipmx +=1;
3575: sw += weight[i];
3576: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3577: } /* end of wave */
3578: } /* end of individual */
3579: } else if(mle==3){ /* exponential inter-extrapolation */
3580: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3581: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3582: for(mi=1; mi<= wav[i]-1; mi++){
3583: for (ii=1;ii<=nlstate+ndeath;ii++)
3584: for (j=1;j<=nlstate+ndeath;j++){
3585: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3586: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3587: }
3588: for(d=0; d<dh[mi][i]; d++){
3589: newm=savm;
3590: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3591: cov[2]=agexact;
3592: if(nagesqr==1)
3593: cov[3]= agexact*agexact;
3594: for (kk=1; kk<=cptcovage;kk++) {
3595: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3596: }
3597: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3598: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3599: savm=oldm;
3600: oldm=newm;
3601: } /* end mult */
3602:
3603: s1=s[mw[mi][i]][i];
3604: s2=s[mw[mi+1][i]][i];
3605: bbh=(double)bh[mi][i]/(double)stepm;
3606: 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 */
3607: ipmx +=1;
3608: sw += weight[i];
3609: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3610: } /* end of wave */
3611: } /* end of individual */
3612: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3613: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3614: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3615: for(mi=1; mi<= wav[i]-1; mi++){
3616: for (ii=1;ii<=nlstate+ndeath;ii++)
3617: for (j=1;j<=nlstate+ndeath;j++){
3618: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3619: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3620: }
3621: for(d=0; d<dh[mi][i]; d++){
3622: newm=savm;
3623: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3624: cov[2]=agexact;
3625: if(nagesqr==1)
3626: cov[3]= agexact*agexact;
3627: for (kk=1; kk<=cptcovage;kk++) {
3628: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3629: }
1.126 brouard 3630:
1.226 brouard 3631: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3632: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3633: savm=oldm;
3634: oldm=newm;
3635: } /* end mult */
3636:
3637: s1=s[mw[mi][i]][i];
3638: s2=s[mw[mi+1][i]][i];
3639: if( s2 > nlstate){
3640: lli=log(out[s1][s2] - savm[s1][s2]);
3641: } else if ( s2==-1 ) { /* alive */
3642: for (j=1,survp=0. ; j<=nlstate; j++)
3643: survp += out[s1][j];
3644: lli= log(survp);
3645: }else{
3646: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3647: }
3648: ipmx +=1;
3649: sw += weight[i];
3650: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3651: /* 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 3652: } /* end of wave */
3653: } /* end of individual */
3654: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3655: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3656: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3657: for(mi=1; mi<= wav[i]-1; mi++){
3658: for (ii=1;ii<=nlstate+ndeath;ii++)
3659: for (j=1;j<=nlstate+ndeath;j++){
3660: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3661: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3662: }
3663: for(d=0; d<dh[mi][i]; d++){
3664: newm=savm;
3665: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3666: cov[2]=agexact;
3667: if(nagesqr==1)
3668: cov[3]= agexact*agexact;
3669: for (kk=1; kk<=cptcovage;kk++) {
3670: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3671: }
1.126 brouard 3672:
1.226 brouard 3673: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3674: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3675: savm=oldm;
3676: oldm=newm;
3677: } /* end mult */
3678:
3679: s1=s[mw[mi][i]][i];
3680: s2=s[mw[mi+1][i]][i];
3681: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3682: ipmx +=1;
3683: sw += weight[i];
3684: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3685: /*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]);*/
3686: } /* end of wave */
3687: } /* end of individual */
3688: } /* End of if */
3689: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3690: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3691: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3692: return -l;
1.126 brouard 3693: }
3694:
3695: /*************** log-likelihood *************/
3696: double funcone( double *x)
3697: {
1.228 brouard 3698: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3699: int i, ii, j, k, mi, d, kk;
1.228 brouard 3700: int ioffset=0;
1.131 brouard 3701: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3702: double **out;
3703: double lli; /* Individual log likelihood */
3704: double llt;
3705: int s1, s2;
1.228 brouard 3706: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3707:
1.126 brouard 3708: double bbh, survp;
1.187 brouard 3709: double agexact;
1.214 brouard 3710: double agebegin, ageend;
1.126 brouard 3711: /*extern weight */
3712: /* We are differentiating ll according to initial status */
3713: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3714: /*for(i=1;i<imx;i++)
3715: printf(" %d\n",s[4][i]);
3716: */
3717: cov[1]=1.;
3718:
3719: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3720: ioffset=0;
3721: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3722: /* ioffset=2+nagesqr+cptcovage; */
3723: ioffset=2+nagesqr;
1.232 brouard 3724: /* Fixed */
1.224 brouard 3725: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3726: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3727: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3728: 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)*/
3729: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3730: /* cov[2+6]=covar[Tvar[6]][i]; */
3731: /* cov[2+6]=covar[2][i]; V2 */
3732: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3733: /* cov[2+7]=covar[Tvar[7]][i]; */
3734: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3735: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3736: /* cov[2+9]=covar[Tvar[9]][i]; */
3737: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3738: }
1.232 brouard 3739: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3740: /* 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?)*\/ */
3741: /* } */
1.231 brouard 3742: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3743: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3744: /* } */
1.225 brouard 3745:
1.233 brouard 3746:
3747: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3748: /* Wave varying (but not age varying) */
3749: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3750: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3751: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3752: }
1.232 brouard 3753: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3754: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3755: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3756: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3757: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3758: /* 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 3759: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3760: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3761: /* /\* 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]); *\/ */
3762: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3763: /* } */
1.126 brouard 3764: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3765: for (j=1;j<=nlstate+ndeath;j++){
3766: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3767: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3768: }
1.214 brouard 3769:
3770: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3771: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3772: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3773: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3774: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3775: and mw[mi+1][i]. dh depends on stepm.*/
3776: newm=savm;
1.247 brouard 3777: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3778: cov[2]=agexact;
3779: if(nagesqr==1)
3780: cov[3]= agexact*agexact;
3781: for (kk=1; kk<=cptcovage;kk++) {
3782: if(!FixedV[Tvar[Tage[kk]]])
3783: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3784: else
3785: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3786: }
3787: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3788: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3789: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3790: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3791: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3792: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3793: savm=oldm;
3794: oldm=newm;
1.126 brouard 3795: } /* end mult */
3796:
3797: s1=s[mw[mi][i]][i];
3798: s2=s[mw[mi+1][i]][i];
1.217 brouard 3799: /* if(s2==-1){ */
1.268 brouard 3800: /* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
1.217 brouard 3801: /* /\* exit(1); *\/ */
3802: /* } */
1.126 brouard 3803: bbh=(double)bh[mi][i]/(double)stepm;
3804: /* bias is positive if real duration
3805: * is higher than the multiple of stepm and negative otherwise.
3806: */
3807: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3808: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3809: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3810: for (j=1,survp=0. ; j<=nlstate; j++)
3811: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3812: lli= log(survp);
1.126 brouard 3813: }else if (mle==1){
1.242 brouard 3814: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3815: } else if(mle==2){
1.242 brouard 3816: 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 3817: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3818: 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 3819: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3820: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3821: } else{ /* mle=0 back to 1 */
1.242 brouard 3822: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3823: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3824: } /* End of if */
3825: ipmx +=1;
3826: sw += weight[i];
3827: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3828: /*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 3829: if(globpr){
1.246 brouard 3830: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3831: %11.6f %11.6f %11.6f ", \
1.242 brouard 3832: 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 3833: 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
1.242 brouard 3834: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3835: llt +=ll[k]*gipmx/gsw;
3836: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3837: }
3838: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3839: }
1.232 brouard 3840: } /* end of wave */
3841: } /* end of individual */
3842: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3843: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3844: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3845: if(globpr==0){ /* First time we count the contributions and weights */
3846: gipmx=ipmx;
3847: gsw=sw;
3848: }
3849: return -l;
1.126 brouard 3850: }
3851:
3852:
3853: /*************** function likelione ***********/
3854: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3855: {
3856: /* This routine should help understanding what is done with
3857: the selection of individuals/waves and
3858: to check the exact contribution to the likelihood.
3859: Plotting could be done.
3860: */
3861: int k;
3862:
3863: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3864: strcpy(fileresilk,"ILK_");
1.202 brouard 3865: strcat(fileresilk,fileresu);
1.126 brouard 3866: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3867: printf("Problem with resultfile: %s\n", fileresilk);
3868: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3869: }
1.214 brouard 3870: 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");
3871: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3872: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3873: for(k=1; k<=nlstate; k++)
3874: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3875: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3876: }
3877:
3878: *fretone=(*funcone)(p);
3879: if(*globpri !=0){
3880: fclose(ficresilk);
1.205 brouard 3881: if (mle ==0)
3882: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3883: else if(mle >=1)
3884: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3885: 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 3886: fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);
1.208 brouard 3887:
3888: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3889: 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 3890: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3891: }
1.207 brouard 3892: 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 3893: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3894: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3895: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3896: fflush(fichtm);
1.205 brouard 3897: }
1.126 brouard 3898: return;
3899: }
3900:
3901:
3902: /*********** Maximum Likelihood Estimation ***************/
3903:
3904: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3905: {
1.165 brouard 3906: int i,j, iter=0;
1.126 brouard 3907: double **xi;
3908: double fret;
3909: double fretone; /* Only one call to likelihood */
3910: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3911:
3912: #ifdef NLOPT
3913: int creturn;
3914: nlopt_opt opt;
3915: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3916: double *lb;
3917: double minf; /* the minimum objective value, upon return */
3918: double * p1; /* Shifted parameters from 0 instead of 1 */
3919: myfunc_data dinst, *d = &dinst;
3920: #endif
3921:
3922:
1.126 brouard 3923: xi=matrix(1,npar,1,npar);
3924: for (i=1;i<=npar;i++)
3925: for (j=1;j<=npar;j++)
3926: xi[i][j]=(i==j ? 1.0 : 0.0);
3927: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3928: strcpy(filerespow,"POW_");
1.126 brouard 3929: strcat(filerespow,fileres);
3930: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3931: printf("Problem with resultfile: %s\n", filerespow);
3932: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3933: }
3934: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3935: for (i=1;i<=nlstate;i++)
3936: for(j=1;j<=nlstate+ndeath;j++)
3937: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3938: fprintf(ficrespow,"\n");
1.162 brouard 3939: #ifdef POWELL
1.126 brouard 3940: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3941: #endif
1.126 brouard 3942:
1.162 brouard 3943: #ifdef NLOPT
3944: #ifdef NEWUOA
3945: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3946: #else
3947: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3948: #endif
3949: lb=vector(0,npar-1);
3950: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3951: nlopt_set_lower_bounds(opt, lb);
3952: nlopt_set_initial_step1(opt, 0.1);
3953:
3954: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3955: d->function = func;
3956: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3957: nlopt_set_min_objective(opt, myfunc, d);
3958: nlopt_set_xtol_rel(opt, ftol);
3959: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3960: printf("nlopt failed! %d\n",creturn);
3961: }
3962: else {
3963: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3964: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3965: iter=1; /* not equal */
3966: }
3967: nlopt_destroy(opt);
3968: #endif
1.126 brouard 3969: free_matrix(xi,1,npar,1,npar);
3970: fclose(ficrespow);
1.203 brouard 3971: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3972: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3973: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3974:
3975: }
3976:
3977: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3978: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3979: {
3980: double **a,**y,*x,pd;
1.203 brouard 3981: /* double **hess; */
1.164 brouard 3982: int i, j;
1.126 brouard 3983: int *indx;
3984:
3985: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3986: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3987: void lubksb(double **a, int npar, int *indx, double b[]) ;
3988: void ludcmp(double **a, int npar, int *indx, double *d) ;
3989: double gompertz(double p[]);
1.203 brouard 3990: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3991:
3992: printf("\nCalculation of the hessian matrix. Wait...\n");
3993: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3994: for (i=1;i<=npar;i++){
1.203 brouard 3995: printf("%d-",i);fflush(stdout);
3996: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3997:
3998: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3999:
4000: /* printf(" %f ",p[i]);
4001: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
4002: }
4003:
4004: for (i=1;i<=npar;i++) {
4005: for (j=1;j<=npar;j++) {
4006: if (j>i) {
1.203 brouard 4007: printf(".%d-%d",i,j);fflush(stdout);
4008: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
4009: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 4010:
4011: hess[j][i]=hess[i][j];
4012: /*printf(" %lf ",hess[i][j]);*/
4013: }
4014: }
4015: }
4016: printf("\n");
4017: fprintf(ficlog,"\n");
4018:
4019: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
4020: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
4021:
4022: a=matrix(1,npar,1,npar);
4023: y=matrix(1,npar,1,npar);
4024: x=vector(1,npar);
4025: indx=ivector(1,npar);
4026: for (i=1;i<=npar;i++)
4027: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
4028: ludcmp(a,npar,indx,&pd);
4029:
4030: for (j=1;j<=npar;j++) {
4031: for (i=1;i<=npar;i++) x[i]=0;
4032: x[j]=1;
4033: lubksb(a,npar,indx,x);
4034: for (i=1;i<=npar;i++){
4035: matcov[i][j]=x[i];
4036: }
4037: }
4038:
4039: printf("\n#Hessian matrix#\n");
4040: fprintf(ficlog,"\n#Hessian matrix#\n");
4041: for (i=1;i<=npar;i++) {
4042: for (j=1;j<=npar;j++) {
1.203 brouard 4043: printf("%.6e ",hess[i][j]);
4044: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 4045: }
4046: printf("\n");
4047: fprintf(ficlog,"\n");
4048: }
4049:
1.203 brouard 4050: /* printf("\n#Covariance matrix#\n"); */
4051: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
4052: /* for (i=1;i<=npar;i++) { */
4053: /* for (j=1;j<=npar;j++) { */
4054: /* printf("%.6e ",matcov[i][j]); */
4055: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
4056: /* } */
4057: /* printf("\n"); */
4058: /* fprintf(ficlog,"\n"); */
4059: /* } */
4060:
1.126 brouard 4061: /* Recompute Inverse */
1.203 brouard 4062: /* for (i=1;i<=npar;i++) */
4063: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
4064: /* ludcmp(a,npar,indx,&pd); */
4065:
4066: /* printf("\n#Hessian matrix recomputed#\n"); */
4067:
4068: /* for (j=1;j<=npar;j++) { */
4069: /* for (i=1;i<=npar;i++) x[i]=0; */
4070: /* x[j]=1; */
4071: /* lubksb(a,npar,indx,x); */
4072: /* for (i=1;i<=npar;i++){ */
4073: /* y[i][j]=x[i]; */
4074: /* printf("%.3e ",y[i][j]); */
4075: /* fprintf(ficlog,"%.3e ",y[i][j]); */
4076: /* } */
4077: /* printf("\n"); */
4078: /* fprintf(ficlog,"\n"); */
4079: /* } */
4080:
4081: /* Verifying the inverse matrix */
4082: #ifdef DEBUGHESS
4083: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 4084:
1.203 brouard 4085: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
4086: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 4087:
4088: for (j=1;j<=npar;j++) {
4089: for (i=1;i<=npar;i++){
1.203 brouard 4090: printf("%.2f ",y[i][j]);
4091: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 4092: }
4093: printf("\n");
4094: fprintf(ficlog,"\n");
4095: }
1.203 brouard 4096: #endif
1.126 brouard 4097:
4098: free_matrix(a,1,npar,1,npar);
4099: free_matrix(y,1,npar,1,npar);
4100: free_vector(x,1,npar);
4101: free_ivector(indx,1,npar);
1.203 brouard 4102: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 4103:
4104:
4105: }
4106:
4107: /*************** hessian matrix ****************/
4108: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 4109: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 4110: int i;
4111: int l=1, lmax=20;
1.203 brouard 4112: double k1,k2, res, fx;
1.132 brouard 4113: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 4114: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
4115: int k=0,kmax=10;
4116: double l1;
4117:
4118: fx=func(x);
4119: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 4120: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 4121: l1=pow(10,l);
4122: delts=delt;
4123: for(k=1 ; k <kmax; k=k+1){
4124: delt = delta*(l1*k);
4125: p2[theta]=x[theta] +delt;
1.145 brouard 4126: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 4127: p2[theta]=x[theta]-delt;
4128: k2=func(p2)-fx;
4129: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 4130: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 4131:
1.203 brouard 4132: #ifdef DEBUGHESSII
1.126 brouard 4133: 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);
4134: 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);
4135: #endif
4136: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
4137: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
4138: k=kmax;
4139: }
4140: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 4141: k=kmax; l=lmax*10;
1.126 brouard 4142: }
4143: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
4144: delts=delt;
4145: }
1.203 brouard 4146: } /* End loop k */
1.126 brouard 4147: }
4148: delti[theta]=delts;
4149: return res;
4150:
4151: }
4152:
1.203 brouard 4153: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4154: {
4155: int i;
1.164 brouard 4156: int l=1, lmax=20;
1.126 brouard 4157: double k1,k2,k3,k4,res,fx;
1.132 brouard 4158: double p2[MAXPARM+1];
1.203 brouard 4159: int k, kmax=1;
4160: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4161:
4162: int firstime=0;
1.203 brouard 4163:
1.126 brouard 4164: fx=func(x);
1.203 brouard 4165: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4166: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4167: p2[thetai]=x[thetai]+delti[thetai]*k;
4168: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4169: k1=func(p2)-fx;
4170:
1.203 brouard 4171: p2[thetai]=x[thetai]+delti[thetai]*k;
4172: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4173: k2=func(p2)-fx;
4174:
1.203 brouard 4175: p2[thetai]=x[thetai]-delti[thetai]*k;
4176: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4177: k3=func(p2)-fx;
4178:
1.203 brouard 4179: p2[thetai]=x[thetai]-delti[thetai]*k;
4180: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4181: k4=func(p2)-fx;
1.203 brouard 4182: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4183: if(k1*k2*k3*k4 <0.){
1.208 brouard 4184: firstime=1;
1.203 brouard 4185: kmax=kmax+10;
1.208 brouard 4186: }
4187: if(kmax >=10 || firstime ==1){
1.246 brouard 4188: 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);
4189: 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 4190: 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);
4191: 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);
4192: }
4193: #ifdef DEBUGHESSIJ
4194: v1=hess[thetai][thetai];
4195: v2=hess[thetaj][thetaj];
4196: cv12=res;
4197: /* Computing eigen value of Hessian matrix */
4198: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4199: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4200: if ((lc2 <0) || (lc1 <0) ){
4201: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4202: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4203: 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);
4204: 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);
4205: }
1.126 brouard 4206: #endif
4207: }
4208: return res;
4209: }
4210:
1.203 brouard 4211: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4212: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4213: /* { */
4214: /* int i; */
4215: /* int l=1, lmax=20; */
4216: /* double k1,k2,k3,k4,res,fx; */
4217: /* double p2[MAXPARM+1]; */
4218: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4219: /* int k=0,kmax=10; */
4220: /* double l1; */
4221:
4222: /* fx=func(x); */
4223: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4224: /* l1=pow(10,l); */
4225: /* delts=delt; */
4226: /* for(k=1 ; k <kmax; k=k+1){ */
4227: /* delt = delti*(l1*k); */
4228: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4229: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4230: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4231: /* k1=func(p2)-fx; */
4232:
4233: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4234: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4235: /* k2=func(p2)-fx; */
4236:
4237: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4238: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4239: /* k3=func(p2)-fx; */
4240:
4241: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4242: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4243: /* k4=func(p2)-fx; */
4244: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4245: /* #ifdef DEBUGHESSIJ */
4246: /* 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); */
4247: /* 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); */
4248: /* #endif */
4249: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4250: /* k=kmax; */
4251: /* } */
4252: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4253: /* k=kmax; l=lmax*10; */
4254: /* } */
4255: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4256: /* delts=delt; */
4257: /* } */
4258: /* } /\* End loop k *\/ */
4259: /* } */
4260: /* delti[theta]=delts; */
4261: /* return res; */
4262: /* } */
4263:
4264:
1.126 brouard 4265: /************** Inverse of matrix **************/
4266: void ludcmp(double **a, int n, int *indx, double *d)
4267: {
4268: int i,imax,j,k;
4269: double big,dum,sum,temp;
4270: double *vv;
4271:
4272: vv=vector(1,n);
4273: *d=1.0;
4274: for (i=1;i<=n;i++) {
4275: big=0.0;
4276: for (j=1;j<=n;j++)
4277: if ((temp=fabs(a[i][j])) > big) big=temp;
1.256 brouard 4278: if (big == 0.0){
4279: printf(" Singular Hessian matrix at row %d:\n",i);
4280: for (j=1;j<=n;j++) {
4281: printf(" a[%d][%d]=%f,",i,j,a[i][j]);
4282: fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
4283: }
4284: fflush(ficlog);
4285: fclose(ficlog);
4286: nrerror("Singular matrix in routine ludcmp");
4287: }
1.126 brouard 4288: vv[i]=1.0/big;
4289: }
4290: for (j=1;j<=n;j++) {
4291: for (i=1;i<j;i++) {
4292: sum=a[i][j];
4293: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4294: a[i][j]=sum;
4295: }
4296: big=0.0;
4297: for (i=j;i<=n;i++) {
4298: sum=a[i][j];
4299: for (k=1;k<j;k++)
4300: sum -= a[i][k]*a[k][j];
4301: a[i][j]=sum;
4302: if ( (dum=vv[i]*fabs(sum)) >= big) {
4303: big=dum;
4304: imax=i;
4305: }
4306: }
4307: if (j != imax) {
4308: for (k=1;k<=n;k++) {
4309: dum=a[imax][k];
4310: a[imax][k]=a[j][k];
4311: a[j][k]=dum;
4312: }
4313: *d = -(*d);
4314: vv[imax]=vv[j];
4315: }
4316: indx[j]=imax;
4317: if (a[j][j] == 0.0) a[j][j]=TINY;
4318: if (j != n) {
4319: dum=1.0/(a[j][j]);
4320: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4321: }
4322: }
4323: free_vector(vv,1,n); /* Doesn't work */
4324: ;
4325: }
4326:
4327: void lubksb(double **a, int n, int *indx, double b[])
4328: {
4329: int i,ii=0,ip,j;
4330: double sum;
4331:
4332: for (i=1;i<=n;i++) {
4333: ip=indx[i];
4334: sum=b[ip];
4335: b[ip]=b[i];
4336: if (ii)
4337: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4338: else if (sum) ii=i;
4339: b[i]=sum;
4340: }
4341: for (i=n;i>=1;i--) {
4342: sum=b[i];
4343: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4344: b[i]=sum/a[i][i];
4345: }
4346: }
4347:
4348: void pstamp(FILE *fichier)
4349: {
1.196 brouard 4350: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4351: }
4352:
1.253 brouard 4353:
4354:
1.126 brouard 4355: /************ Frequencies ********************/
1.251 brouard 4356: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4357: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4358: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4359: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4360:
1.265 brouard 4361: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
1.226 brouard 4362: int iind=0, iage=0;
4363: int mi; /* Effective wave */
4364: int first;
4365: double ***freq; /* Frequencies */
1.268 brouard 4366: 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 */
4367: 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);
1.226 brouard 4368: double *meanq;
4369: double **meanqt;
4370: double *pp, **prop, *posprop, *pospropt;
4371: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4372: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4373: double agebegin, ageend;
4374:
4375: pp=vector(1,nlstate);
1.251 brouard 4376: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4377: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4378: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4379: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4380: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
4381: meanqt=matrix(1,lastpass,1,nqtveff);
4382: strcpy(fileresp,"P_");
4383: strcat(fileresp,fileresu);
4384: /*strcat(fileresphtm,fileresu);*/
4385: if((ficresp=fopen(fileresp,"w"))==NULL) {
4386: printf("Problem with prevalence resultfile: %s\n", fileresp);
4387: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4388: exit(0);
4389: }
1.240 brouard 4390:
1.226 brouard 4391: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4392: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4393: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4394: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4395: fflush(ficlog);
4396: exit(70);
4397: }
4398: else{
4399: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4400: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4401: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4402: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4403: }
1.237 brouard 4404: 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 4405:
1.226 brouard 4406: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4407: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4408: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4409: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4410: fflush(ficlog);
4411: exit(70);
1.240 brouard 4412: } else{
1.226 brouard 4413: 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 4414: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4415: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4416: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4417: }
1.240 brouard 4418: 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);
4419:
1.253 brouard 4420: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4421: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4422: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4423: j1=0;
1.126 brouard 4424:
1.227 brouard 4425: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4426: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4427: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4428:
4429:
1.226 brouard 4430: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4431: reference=low_education V1=0,V2=0
4432: med_educ V1=1 V2=0,
4433: high_educ V1=0 V2=1
4434: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4435: */
1.249 brouard 4436: dateintsum=0;
4437: k2cpt=0;
4438:
1.253 brouard 4439: if(cptcoveff == 0 )
1.265 brouard 4440: nl=1; /* Constant and age model only */
1.253 brouard 4441: else
4442: nl=2;
1.265 brouard 4443:
4444: /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
4445: /* Loop on nj=1 or 2 if dummy covariates j!=0
4446: * Loop on j1(1 to 2**cptcoveff) covariate combination
4447: * freq[s1][s2][iage] =0.
4448: * Loop on iind
4449: * ++freq[s1][s2][iage] weighted
4450: * end iind
4451: * if covariate and j!0
4452: * headers Variable on one line
4453: * endif cov j!=0
4454: * header of frequency table by age
4455: * Loop on age
4456: * pp[s1]+=freq[s1][s2][iage] weighted
4457: * pos+=freq[s1][s2][iage] weighted
4458: * Loop on s1 initial state
4459: * fprintf(ficresp
4460: * end s1
4461: * end age
4462: * if j!=0 computes starting values
4463: * end compute starting values
4464: * end j1
4465: * end nl
4466: */
1.253 brouard 4467: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4468: if(nj==1)
4469: j=0; /* First pass for the constant */
1.265 brouard 4470: else{
1.253 brouard 4471: j=cptcoveff; /* Other passes for the covariate values */
1.265 brouard 4472: }
1.251 brouard 4473: first=1;
1.265 brouard 4474: 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 4475: posproptt=0.;
4476: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4477: scanf("%d", i);*/
4478: for (i=-5; i<=nlstate+ndeath; i++)
1.265 brouard 4479: for (s2=-5; s2<=nlstate+ndeath; s2++)
1.251 brouard 4480: for(m=iagemin; m <= iagemax+3; m++)
1.265 brouard 4481: freq[i][s2][m]=0;
1.251 brouard 4482:
4483: for (i=1; i<=nlstate; i++) {
1.240 brouard 4484: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4485: prop[i][m]=0;
4486: posprop[i]=0;
4487: pospropt[i]=0;
4488: }
4489: /* for (z1=1; z1<= nqfveff; z1++) { */
4490: /* meanq[z1]+=0.; */
4491: /* for(m=1;m<=lastpass;m++){ */
4492: /* meanqt[m][z1]=0.; */
4493: /* } */
4494: /* } */
4495:
4496: /* dateintsum=0; */
4497: /* k2cpt=0; */
4498:
1.265 brouard 4499: /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
1.251 brouard 4500: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4501: bool=1;
4502: if(j !=0){
4503: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4504: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4505: /* for (z1=1; z1<= nqfveff; z1++) { */
4506: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4507: /* } */
4508: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4509: /* if(Tvaraff[z1] ==-20){ */
4510: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4511: /* }else if(Tvaraff[z1] ==-10){ */
4512: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4513: /* }else */
4514: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
1.265 brouard 4515: /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
1.251 brouard 4516: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4517: /* 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",
4518: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4519: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4520: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4521: } /* Onlyf fixed */
4522: } /* end z1 */
4523: } /* cptcovn > 0 */
4524: } /* end any */
4525: }/* end j==0 */
1.265 brouard 4526: if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
1.251 brouard 4527: /* for(m=firstpass; m<=lastpass; m++){ */
4528: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4529: m=mw[mi][iind];
4530: if(j!=0){
4531: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4532: for (z1=1; z1<=cptcoveff; z1++) {
4533: if( Fixed[Tmodelind[z1]]==1){
4534: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4535: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4536: value is -1, we don't select. It differs from the
4537: constant and age model which counts them. */
4538: bool=0; /* not selected */
4539: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4540: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4541: bool=0;
4542: }
4543: }
4544: }
4545: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4546: } /* end j==0 */
4547: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4548: if(bool==1){
4549: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4550: and mw[mi+1][iind]. dh depends on stepm. */
4551: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4552: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4553: if(m >=firstpass && m <=lastpass){
4554: k2=anint[m][iind]+(mint[m][iind]/12.);
4555: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4556: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4557: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4558: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4559: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4560: if (m<lastpass) {
4561: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4562: /* 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]); */
4563: if(s[m][iind]==-1)
4564: 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.));
4565: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4566: /* if((int)agev[m][iind] == 55) */
4567: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4568: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4569: 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 4570: }
1.251 brouard 4571: } /* end if between passes */
4572: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4573: dateintsum=dateintsum+k2; /* on all covariates ?*/
4574: k2cpt++;
4575: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4576: }
1.251 brouard 4577: }else{
4578: bool=1;
4579: }/* end bool 2 */
4580: } /* end m */
4581: } /* end bool */
4582: } /* end iind = 1 to imx */
4583: /* prop[s][age] is feeded for any initial and valid live state as well as
4584: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4585:
4586:
4587: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1.265 brouard 4588: if(cptcoveff==0 && nj==1) /* no covariate and first pass */
4589: pstamp(ficresp);
1.251 brouard 4590: if (cptcoveff>0 && j!=0){
1.265 brouard 4591: pstamp(ficresp);
1.251 brouard 4592: printf( "\n#********** Variable ");
4593: fprintf(ficresp, "\n#********** Variable ");
4594: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4595: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4596: fprintf(ficlog, "\n#********** Variable ");
4597: for (z1=1; z1<=cptcoveff; z1++){
4598: if(!FixedV[Tvaraff[z1]]){
4599: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4600: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4601: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4602: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4603: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4604: }else{
1.251 brouard 4605: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4606: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4607: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4608: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4609: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4610: }
4611: }
4612: printf( "**********\n#");
4613: fprintf(ficresp, "**********\n#");
4614: fprintf(ficresphtm, "**********</h3>\n");
4615: fprintf(ficresphtmfr, "**********</h3>\n");
4616: fprintf(ficlog, "**********\n");
4617: }
4618: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.265 brouard 4619: if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
4620: fprintf(ficresp, " Age");
4621: 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 4622: for(i=1; i<=nlstate;i++) {
1.265 brouard 4623: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
1.251 brouard 4624: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4625: }
1.265 brouard 4626: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
1.251 brouard 4627: fprintf(ficresphtm, "\n");
4628:
4629: /* Header of frequency table by age */
4630: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4631: fprintf(ficresphtmfr,"<th>Age</th> ");
1.265 brouard 4632: for(s2=-1; s2 <=nlstate+ndeath; s2++){
1.251 brouard 4633: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4634: if(s2!=0 && m!=0)
4635: fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
1.240 brouard 4636: }
1.226 brouard 4637: }
1.251 brouard 4638: fprintf(ficresphtmfr, "\n");
4639:
4640: /* For each age */
4641: for(iage=iagemin; iage <= iagemax+3; iage++){
4642: fprintf(ficresphtm,"<tr>");
4643: if(iage==iagemax+1){
4644: fprintf(ficlog,"1");
4645: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4646: }else if(iage==iagemax+2){
4647: fprintf(ficlog,"0");
4648: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4649: }else if(iage==iagemax+3){
4650: fprintf(ficlog,"Total");
4651: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4652: }else{
1.240 brouard 4653: if(first==1){
1.251 brouard 4654: first=0;
4655: printf("See log file for details...\n");
4656: }
4657: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4658: fprintf(ficlog,"Age %d", iage);
4659: }
1.265 brouard 4660: for(s1=1; s1 <=nlstate ; s1++){
4661: for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
4662: pp[s1] += freq[s1][m][iage];
1.251 brouard 4663: }
1.265 brouard 4664: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4665: for(m=-1, pos=0; m <=0 ; m++)
1.265 brouard 4666: pos += freq[s1][m][iage];
4667: if(pp[s1]>=1.e-10){
1.251 brouard 4668: if(first==1){
1.265 brouard 4669: printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4670: }
1.265 brouard 4671: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
1.251 brouard 4672: }else{
4673: if(first==1)
1.265 brouard 4674: printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
4675: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
1.240 brouard 4676: }
4677: }
4678:
1.265 brouard 4679: for(s1=1; s1 <=nlstate ; s1++){
4680: /* posprop[s1]=0; */
4681: for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4682: pp[s1] += freq[s1][m][iage];
4683: } /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
4684:
4685: for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
4686: pos += pp[s1]; /* pos is the total number of transitions until this age */
4687: posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
4688: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4689: pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
4690: from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4691: }
4692:
4693: /* Writing ficresp */
4694: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4695: if( iage <= iagemax){
4696: fprintf(ficresp," %d",iage);
4697: }
4698: }else if( nj==2){
4699: if( iage <= iagemax){
4700: fprintf(ficresp," %d",iage);
4701: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4702: }
1.240 brouard 4703: }
1.265 brouard 4704: for(s1=1; s1 <=nlstate ; s1++){
1.240 brouard 4705: if(pos>=1.e-5){
1.251 brouard 4706: if(first==1)
1.265 brouard 4707: printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
4708: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
1.251 brouard 4709: }else{
4710: if(first==1)
1.265 brouard 4711: printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
4712: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
1.251 brouard 4713: }
4714: if( iage <= iagemax){
4715: if(pos>=1.e-5){
1.265 brouard 4716: if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
4717: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4718: }else if( nj==2){
4719: fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4720: }
4721: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
4722: /*probs[iage][s1][j1]= pp[s1]/pos;*/
4723: /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
4724: } else{
4725: if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
4726: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
1.251 brouard 4727: }
1.240 brouard 4728: }
1.265 brouard 4729: pospropt[s1] +=posprop[s1];
4730: } /* end loop s1 */
1.251 brouard 4731: /* pospropt=0.; */
1.265 brouard 4732: for(s1=-1; s1 <=nlstate+ndeath; s1++){
1.251 brouard 4733: for(m=-1; m <=nlstate+ndeath; m++){
1.265 brouard 4734: if(freq[s1][m][iage] !=0 ) { /* minimizing output */
1.251 brouard 4735: if(first==1){
1.265 brouard 4736: printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4737: }
1.265 brouard 4738: /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
4739: fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
1.251 brouard 4740: }
1.265 brouard 4741: if(s1!=0 && m!=0)
4742: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
1.240 brouard 4743: }
1.265 brouard 4744: } /* end loop s1 */
1.251 brouard 4745: posproptt=0.;
1.265 brouard 4746: for(s1=1; s1 <=nlstate; s1++){
4747: posproptt += pospropt[s1];
1.251 brouard 4748: }
4749: fprintf(ficresphtmfr,"</tr>\n ");
1.265 brouard 4750: fprintf(ficresphtm,"</tr>\n");
4751: if((cptcoveff==0 && nj==1)|| nj==2 ) {
4752: if(iage <= iagemax)
4753: fprintf(ficresp,"\n");
1.240 brouard 4754: }
1.251 brouard 4755: if(first==1)
4756: printf("Others in log...\n");
4757: fprintf(ficlog,"\n");
4758: } /* end loop age iage */
1.265 brouard 4759:
1.251 brouard 4760: fprintf(ficresphtm,"<tr><th>Tot</th>");
1.265 brouard 4761: for(s1=1; s1 <=nlstate ; s1++){
1.251 brouard 4762: if(posproptt < 1.e-5){
1.265 brouard 4763: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
1.251 brouard 4764: }else{
1.265 brouard 4765: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
1.240 brouard 4766: }
1.226 brouard 4767: }
1.251 brouard 4768: fprintf(ficresphtm,"</tr>\n");
4769: fprintf(ficresphtm,"</table>\n");
4770: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4771: if(posproptt < 1.e-5){
1.251 brouard 4772: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4773: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
1.260 brouard 4774: fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
4775: printf("# This combination (%d) is not valid and no result will be produced\n",j1);
1.251 brouard 4776: invalidvarcomb[j1]=1;
1.226 brouard 4777: }else{
1.251 brouard 4778: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4779: invalidvarcomb[j1]=0;
1.226 brouard 4780: }
1.251 brouard 4781: fprintf(ficresphtmfr,"</table>\n");
4782: fprintf(ficlog,"\n");
4783: if(j!=0){
4784: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
1.265 brouard 4785: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4786: for(k=1; k <=(nlstate+ndeath); k++){
4787: if (k != i) {
1.265 brouard 4788: for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
1.253 brouard 4789: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4790: if(j1==1){ /* All dummy covariates to zero */
4791: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4792: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4793: printf("%d%d ",i,k);
4794: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4795: 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]));
4796: 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]));
4797: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4798: }
1.253 brouard 4799: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4800: for(iage=iagemin; iage <= iagemax+3; iage++){
4801: x[iage]= (double)iage;
4802: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
1.265 brouard 4803: /* 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 4804: }
1.268 brouard 4805: /* Some are not finite, but linreg will ignore these ages */
4806: no=0;
1.253 brouard 4807: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
1.265 brouard 4808: pstart[s1]=b;
4809: pstart[s1-1]=a;
1.252 brouard 4810: }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 */
4811: 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]);
4812: 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 4813: 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 4814: printf("%d%d ",i,k);
4815: fprintf(ficlog,"%d%d ",i,k);
1.265 brouard 4816: 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 4817: }else{ /* Other cases, like quantitative fixed or varying covariates */
4818: ;
4819: }
4820: /* printf("%12.7f )", param[i][jj][k]); */
4821: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4822: s1++;
1.251 brouard 4823: } /* end jj */
4824: } /* end k!= i */
4825: } /* end k */
1.265 brouard 4826: } /* end i, s1 */
1.251 brouard 4827: } /* end j !=0 */
4828: } /* end selected combination of covariate j1 */
4829: if(j==0){ /* We can estimate starting values from the occurences in each case */
4830: printf("#Freqsummary: Starting values for the constants:\n");
4831: fprintf(ficlog,"\n");
1.265 brouard 4832: for(i=1,s1=1; i <=nlstate; i++){
1.251 brouard 4833: for(k=1; k <=(nlstate+ndeath); k++){
4834: if (k != i) {
4835: printf("%d%d ",i,k);
4836: fprintf(ficlog,"%d%d ",i,k);
4837: for(jj=1; jj <=ncovmodel; jj++){
1.265 brouard 4838: pstart[s1]=p[s1]; /* Setting pstart to p values by default */
1.253 brouard 4839: if(jj==1){ /* Age has to be done */
1.265 brouard 4840: pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
4841: 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]));
4842: 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 4843: }
4844: /* printf("%12.7f )", param[i][jj][k]); */
4845: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
1.265 brouard 4846: s1++;
1.250 brouard 4847: }
1.251 brouard 4848: printf("\n");
4849: fprintf(ficlog,"\n");
1.250 brouard 4850: }
4851: }
4852: }
1.251 brouard 4853: printf("#Freqsummary\n");
4854: fprintf(ficlog,"\n");
1.265 brouard 4855: for(s1=-1; s1 <=nlstate+ndeath; s1++){
4856: for(s2=-1; s2 <=nlstate+ndeath; s2++){
4857: /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
4858: printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4859: fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
4860: /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
4861: /* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
4862: /* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
1.251 brouard 4863: /* } */
4864: }
1.265 brouard 4865: } /* end loop s1 */
1.251 brouard 4866:
4867: printf("\n");
4868: fprintf(ficlog,"\n");
4869: } /* end j=0 */
1.249 brouard 4870: } /* end j */
1.252 brouard 4871:
1.253 brouard 4872: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4873: for(i=1, jk=1; i <=nlstate; i++){
4874: for(j=1; j <=nlstate+ndeath; j++){
4875: if(j!=i){
4876: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4877: printf("%1d%1d",i,j);
4878: fprintf(ficparo,"%1d%1d",i,j);
4879: for(k=1; k<=ncovmodel;k++){
4880: /* printf(" %lf",param[i][j][k]); */
4881: /* fprintf(ficparo," %lf",param[i][j][k]); */
4882: p[jk]=pstart[jk];
4883: printf(" %f ",pstart[jk]);
4884: fprintf(ficparo," %f ",pstart[jk]);
4885: jk++;
4886: }
4887: printf("\n");
4888: fprintf(ficparo,"\n");
4889: }
4890: }
4891: }
4892: } /* end mle=-2 */
1.226 brouard 4893: dateintmean=dateintsum/k2cpt;
1.240 brouard 4894:
1.226 brouard 4895: fclose(ficresp);
4896: fclose(ficresphtm);
4897: fclose(ficresphtmfr);
4898: free_vector(meanq,1,nqfveff);
4899: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 4900: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
4901: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 4902: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4903: free_vector(pospropt,1,nlstate);
4904: free_vector(posprop,1,nlstate);
1.251 brouard 4905: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4906: free_vector(pp,1,nlstate);
4907: /* End of freqsummary */
4908: }
1.126 brouard 4909:
1.268 brouard 4910: /* Simple linear regression */
4911: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
4912:
4913: /* y=a+bx regression */
4914: double sumx = 0.0; /* sum of x */
4915: double sumx2 = 0.0; /* sum of x**2 */
4916: double sumxy = 0.0; /* sum of x * y */
4917: double sumy = 0.0; /* sum of y */
4918: double sumy2 = 0.0; /* sum of y**2 */
4919: double sume2 = 0.0; /* sum of square or residuals */
4920: double yhat;
4921:
4922: double denom=0;
4923: int i;
4924: int ne=*no;
4925:
4926: for ( i=ifi, ne=0;i<=ila;i++) {
4927: if(!isfinite(x[i]) || !isfinite(y[i])){
4928: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4929: continue;
4930: }
4931: ne=ne+1;
4932: sumx += x[i];
4933: sumx2 += x[i]*x[i];
4934: sumxy += x[i] * y[i];
4935: sumy += y[i];
4936: sumy2 += y[i]*y[i];
4937: denom = (ne * sumx2 - sumx*sumx);
4938: /* 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); */
4939: }
4940:
4941: denom = (ne * sumx2 - sumx*sumx);
4942: if (denom == 0) {
4943: // vertical, slope m is infinity
4944: *b = INFINITY;
4945: *a = 0;
4946: if (r) *r = 0;
4947: return 1;
4948: }
4949:
4950: *b = (ne * sumxy - sumx * sumy) / denom;
4951: *a = (sumy * sumx2 - sumx * sumxy) / denom;
4952: if (r!=NULL) {
4953: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
4954: sqrt((sumx2 - sumx*sumx/ne) *
4955: (sumy2 - sumy*sumy/ne));
4956: }
4957: *no=ne;
4958: for ( i=ifi, ne=0;i<=ila;i++) {
4959: if(!isfinite(x[i]) || !isfinite(y[i])){
4960: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4961: continue;
4962: }
4963: ne=ne+1;
4964: yhat = y[i] - *a -*b* x[i];
4965: sume2 += yhat * yhat ;
4966:
4967: denom = (ne * sumx2 - sumx*sumx);
4968: /* 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); */
4969: }
4970: *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
4971: *sa= *sb * sqrt(sumx2/ne);
4972:
4973: return 0;
4974: }
4975:
1.126 brouard 4976: /************ Prevalence ********************/
1.227 brouard 4977: 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)
4978: {
4979: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4980: in each health status at the date of interview (if between dateprev1 and dateprev2).
4981: We still use firstpass and lastpass as another selection.
4982: */
1.126 brouard 4983:
1.227 brouard 4984: int i, m, jk, j1, bool, z1,j, iv;
4985: int mi; /* Effective wave */
4986: int iage;
4987: double agebegin, ageend;
4988:
4989: double **prop;
4990: double posprop;
4991: double y2; /* in fractional years */
4992: int iagemin, iagemax;
4993: int first; /** to stop verbosity which is redirected to log file */
4994:
4995: iagemin= (int) agemin;
4996: iagemax= (int) agemax;
4997: /*pp=vector(1,nlstate);*/
1.251 brouard 4998: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 4999: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
5000: j1=0;
1.222 brouard 5001:
1.227 brouard 5002: /*j=cptcoveff;*/
5003: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 5004:
1.227 brouard 5005: first=1;
5006: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
5007: for (i=1; i<=nlstate; i++)
1.251 brouard 5008: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 5009: prop[i][iage]=0.0;
5010: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
5011: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
5012: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
5013:
5014: for (i=1; i<=imx; i++) { /* Each individual */
5015: bool=1;
5016: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
5017: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
5018: m=mw[mi][i];
5019: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
5020: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
5021: for (z1=1; z1<=cptcoveff; z1++){
5022: if( Fixed[Tmodelind[z1]]==1){
5023: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
5024: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
5025: bool=0;
5026: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
5027: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
5028: bool=0;
5029: }
5030: }
5031: if(bool==1){ /* Otherwise we skip that wave/person */
5032: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
5033: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
5034: if(m >=firstpass && m <=lastpass){
5035: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
5036: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
5037: if(agev[m][i]==0) agev[m][i]=iagemax+1;
5038: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 5039: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 5040: 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);
5041: exit(1);
5042: }
5043: if (s[m][i]>0 && s[m][i]<=nlstate) {
5044: /*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]]);*/
5045: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
5046: prop[s[m][i]][iagemax+3] += weight[i];
5047: } /* end valid statuses */
5048: } /* end selection of dates */
5049: } /* end selection of waves */
5050: } /* end bool */
5051: } /* end wave */
5052: } /* end individual */
5053: for(i=iagemin; i <= iagemax+3; i++){
5054: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
5055: posprop += prop[jk][i];
5056: }
5057:
5058: for(jk=1; jk <=nlstate ; jk++){
5059: if( i <= iagemax){
5060: if(posprop>=1.e-5){
5061: probs[i][jk][j1]= prop[jk][i]/posprop;
5062: } else{
5063: if(first==1){
5064: first=0;
1.266 brouard 5065: 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]);
5066: 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]);
5067: }else{
5068: 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 5069: }
5070: }
5071: }
5072: }/* end jk */
5073: }/* end i */
1.222 brouard 5074: /*} *//* end i1 */
1.227 brouard 5075: } /* end j1 */
1.222 brouard 5076:
1.227 brouard 5077: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
5078: /*free_vector(pp,1,nlstate);*/
1.251 brouard 5079: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 5080: } /* End of prevalence */
1.126 brouard 5081:
5082: /************* Waves Concatenation ***************/
5083:
5084: 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)
5085: {
5086: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
5087: Death is a valid wave (if date is known).
5088: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
5089: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
5090: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 5091: */
1.126 brouard 5092:
1.224 brouard 5093: int i=0, mi=0, m=0, mli=0;
1.126 brouard 5094: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
5095: double sum=0., jmean=0.;*/
1.224 brouard 5096: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 5097: int j, k=0,jk, ju, jl;
5098: double sum=0.;
5099: first=0;
1.214 brouard 5100: firstwo=0;
1.217 brouard 5101: firsthree=0;
1.218 brouard 5102: firstfour=0;
1.164 brouard 5103: jmin=100000;
1.126 brouard 5104: jmax=-1;
5105: jmean=0.;
1.224 brouard 5106:
5107: /* Treating live states */
1.214 brouard 5108: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 5109: mi=0; /* First valid wave */
1.227 brouard 5110: mli=0; /* Last valid wave */
1.126 brouard 5111: m=firstpass;
1.214 brouard 5112: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 5113: 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 */
5114: mli=m-1;/* mw[++mi][i]=m-1; */
5115: }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 */
5116: mw[++mi][i]=m;
5117: mli=m;
1.224 brouard 5118: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
5119: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 5120: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 5121: }
1.227 brouard 5122: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 5123: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 5124: break;
1.224 brouard 5125: #else
1.227 brouard 5126: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
5127: if(firsthree == 0){
1.262 brouard 5128: 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 5129: firsthree=1;
5130: }
1.262 brouard 5131: 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 5132: mw[++mi][i]=m;
5133: mli=m;
5134: }
5135: if(s[m][i]==-2){ /* Vital status is really unknown */
5136: nbwarn++;
5137: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
5138: 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);
5139: 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);
5140: }
5141: break;
5142: }
5143: break;
1.224 brouard 5144: #endif
1.227 brouard 5145: }/* End m >= lastpass */
1.126 brouard 5146: }/* end while */
1.224 brouard 5147:
1.227 brouard 5148: /* 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 5149: /* After last pass */
1.224 brouard 5150: /* Treating death states */
1.214 brouard 5151: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 5152: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
5153: /* } */
1.126 brouard 5154: mi++; /* Death is another wave */
5155: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 5156: /* Only death is a correct wave */
1.126 brouard 5157: mw[mi][i]=m;
1.257 brouard 5158: } /* else not in a death state */
1.224 brouard 5159: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.257 brouard 5160: else if ((int) andc[i] != 9999) { /* Date of death is known */
1.218 brouard 5161: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 5162: 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 */
5163: nbwarn++;
5164: if(firstfiv==0){
5165: 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 );
5166: firstfiv=1;
5167: }else{
5168: 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 );
5169: }
5170: }else{ /* Death occured afer last wave potential bias */
5171: nberr++;
5172: if(firstwo==0){
1.257 brouard 5173: 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 5174: firstwo=1;
5175: }
1.257 brouard 5176: 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 5177: }
1.257 brouard 5178: }else{ /* if date of interview is unknown */
1.227 brouard 5179: /* death is known but not confirmed by death status at any wave */
5180: if(firstfour==0){
5181: 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 );
5182: firstfour=1;
5183: }
5184: 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 5185: }
1.224 brouard 5186: } /* end if date of death is known */
5187: #endif
5188: wav[i]=mi; /* mi should be the last effective wave (or mli) */
5189: /* wav[i]=mw[mi][i]; */
1.126 brouard 5190: if(mi==0){
5191: nbwarn++;
5192: if(first==0){
1.227 brouard 5193: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
5194: first=1;
1.126 brouard 5195: }
5196: if(first==1){
1.227 brouard 5197: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 5198: }
5199: } /* end mi==0 */
5200: } /* End individuals */
1.214 brouard 5201: /* wav and mw are no more changed */
1.223 brouard 5202:
1.214 brouard 5203:
1.126 brouard 5204: for(i=1; i<=imx; i++){
5205: for(mi=1; mi<wav[i];mi++){
5206: if (stepm <=0)
1.227 brouard 5207: dh[mi][i]=1;
1.126 brouard 5208: else{
1.260 brouard 5209: if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
1.227 brouard 5210: if (agedc[i] < 2*AGESUP) {
5211: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5212: if(j==0) j=1; /* Survives at least one month after exam */
5213: else if(j<0){
5214: nberr++;
5215: 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]);
5216: j=1; /* Temporary Dangerous patch */
5217: 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);
5218: 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]);
5219: 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);
5220: }
5221: k=k+1;
5222: if (j >= jmax){
5223: jmax=j;
5224: ijmax=i;
5225: }
5226: if (j <= jmin){
5227: jmin=j;
5228: ijmin=i;
5229: }
5230: sum=sum+j;
5231: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5232: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5233: }
5234: }
5235: else{
5236: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5237: /* 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 5238:
1.227 brouard 5239: k=k+1;
5240: if (j >= jmax) {
5241: jmax=j;
5242: ijmax=i;
5243: }
5244: else if (j <= jmin){
5245: jmin=j;
5246: ijmin=i;
5247: }
5248: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5249: /*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]);*/
5250: if(j<0){
5251: nberr++;
5252: 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]);
5253: 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]);
5254: }
5255: sum=sum+j;
5256: }
5257: jk= j/stepm;
5258: jl= j -jk*stepm;
5259: ju= j -(jk+1)*stepm;
5260: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5261: if(jl==0){
5262: dh[mi][i]=jk;
5263: bh[mi][i]=0;
5264: }else{ /* We want a negative bias in order to only have interpolation ie
5265: * to avoid the price of an extra matrix product in likelihood */
5266: dh[mi][i]=jk+1;
5267: bh[mi][i]=ju;
5268: }
5269: }else{
5270: if(jl <= -ju){
5271: dh[mi][i]=jk;
5272: bh[mi][i]=jl; /* bias is positive if real duration
5273: * is higher than the multiple of stepm and negative otherwise.
5274: */
5275: }
5276: else{
5277: dh[mi][i]=jk+1;
5278: bh[mi][i]=ju;
5279: }
5280: if(dh[mi][i]==0){
5281: dh[mi][i]=1; /* At least one step */
5282: bh[mi][i]=ju; /* At least one step */
5283: /* 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);*/
5284: }
5285: } /* end if mle */
1.126 brouard 5286: }
5287: } /* end wave */
5288: }
5289: jmean=sum/k;
5290: 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 5291: 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 5292: }
1.126 brouard 5293:
5294: /*********** Tricode ****************************/
1.220 brouard 5295: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5296: {
5297: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5298: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5299: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5300: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5301: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5302: */
1.130 brouard 5303:
1.242 brouard 5304: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5305: int modmaxcovj=0; /* Modality max of covariates j */
5306: int cptcode=0; /* Modality max of covariates j */
5307: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5308:
5309:
1.242 brouard 5310: /* cptcoveff=0; */
5311: /* *cptcov=0; */
1.126 brouard 5312:
1.242 brouard 5313: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 5314:
1.242 brouard 5315: /* Loop on covariates without age and products and no quantitative variable */
5316: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
5317: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5318: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5319: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5320: switch(Fixed[k]) {
5321: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5322: 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*/
5323: ij=(int)(covar[Tvar[k]][i]);
5324: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5325: * If product of Vn*Vm, still boolean *:
5326: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5327: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5328: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5329: modality of the nth covariate of individual i. */
5330: if (ij > modmaxcovj)
5331: modmaxcovj=ij;
5332: else if (ij < modmincovj)
5333: modmincovj=ij;
5334: if ((ij < -1) && (ij > NCOVMAX)){
5335: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5336: exit(1);
5337: }else
5338: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5339: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5340: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5341: /* getting the maximum value of the modality of the covariate
5342: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5343: female ies 1, then modmaxcovj=1.
5344: */
5345: } /* end for loop on individuals i */
5346: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5347: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5348: cptcode=modmaxcovj;
5349: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5350: /*for (i=0; i<=cptcode; i++) {*/
5351: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5352: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5353: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5354: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5355: if( j != -1){
5356: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5357: covariate for which somebody answered excluding
5358: undefined. Usually 2: 0 and 1. */
5359: }
5360: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5361: covariate for which somebody answered including
5362: undefined. Usually 3: -1, 0 and 1. */
5363: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5364: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5365: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5366:
1.242 brouard 5367: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5368: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5369: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5370: /* modmincovj=3; modmaxcovj = 7; */
5371: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5372: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5373: /* defining two dummy variables: variables V1_1 and V1_2.*/
5374: /* nbcode[Tvar[j]][ij]=k; */
5375: /* nbcode[Tvar[j]][1]=0; */
5376: /* nbcode[Tvar[j]][2]=1; */
5377: /* nbcode[Tvar[j]][3]=2; */
5378: /* To be continued (not working yet). */
5379: ij=0; /* ij is similar to i but can jump over null modalities */
5380: 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*/
5381: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5382: break;
5383: }
5384: ij++;
5385: 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*/
5386: cptcode = ij; /* New max modality for covar j */
5387: } /* end of loop on modality i=-1 to 1 or more */
5388: break;
5389: case 1: /* Testing on varying covariate, could be simple and
5390: * should look at waves or product of fixed *
5391: * varying. No time to test -1, assuming 0 and 1 only */
5392: ij=0;
5393: for(i=0; i<=1;i++){
5394: nbcode[Tvar[k]][++ij]=i;
5395: }
5396: break;
5397: default:
5398: break;
5399: } /* end switch */
5400: } /* end dummy test */
5401:
5402: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
5403: /* /\*recode from 0 *\/ */
5404: /* k is a modality. If we have model=V1+V1*sex */
5405: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
5406: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
5407: /* } */
5408: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
5409: /* if (ij > ncodemax[j]) { */
5410: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5411: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5412: /* break; */
5413: /* } */
5414: /* } /\* end of loop on modality k *\/ */
5415: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
5416:
5417: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5418: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5419: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5420: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5421: 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 */
5422: 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 */
5423: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5424: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5425:
5426: ij=0;
5427: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5428: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5429: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5430: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5431: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5432: /* If product not in single variable we don't print results */
5433: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5434: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5435: 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*/
5436: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5437: 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 */
5438: if(Fixed[k]!=0)
5439: anyvaryingduminmodel=1;
5440: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5441: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5442: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5443: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5444: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5445: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5446: }
5447: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5448: /* ij--; */
5449: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5450: *cptcov=ij; /*Number of total real effective covariates: effective
5451: * because they can be excluded from the model and real
5452: * if in the model but excluded because missing values, but how to get k from ij?*/
5453: for(j=ij+1; j<= cptcovt; j++){
5454: Tvaraff[j]=0;
5455: Tmodelind[j]=0;
5456: }
5457: for(j=ntveff+1; j<= cptcovt; j++){
5458: TmodelInvind[j]=0;
5459: }
5460: /* To be sorted */
5461: ;
5462: }
1.126 brouard 5463:
1.145 brouard 5464:
1.126 brouard 5465: /*********** Health Expectancies ****************/
5466:
1.235 brouard 5467: 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 5468:
5469: {
5470: /* Health expectancies, no variances */
1.164 brouard 5471: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5472: int nhstepma, nstepma; /* Decreasing with age */
5473: double age, agelim, hf;
5474: double ***p3mat;
5475: double eip;
5476:
1.238 brouard 5477: /* pstamp(ficreseij); */
1.126 brouard 5478: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5479: fprintf(ficreseij,"# Age");
5480: for(i=1; i<=nlstate;i++){
5481: for(j=1; j<=nlstate;j++){
5482: fprintf(ficreseij," e%1d%1d ",i,j);
5483: }
5484: fprintf(ficreseij," e%1d. ",i);
5485: }
5486: fprintf(ficreseij,"\n");
5487:
5488:
5489: if(estepm < stepm){
5490: printf ("Problem %d lower than %d\n",estepm, stepm);
5491: }
5492: else hstepm=estepm;
5493: /* We compute the life expectancy from trapezoids spaced every estepm months
5494: * This is mainly to measure the difference between two models: for example
5495: * if stepm=24 months pijx are given only every 2 years and by summing them
5496: * we are calculating an estimate of the Life Expectancy assuming a linear
5497: * progression in between and thus overestimating or underestimating according
5498: * to the curvature of the survival function. If, for the same date, we
5499: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5500: * to compare the new estimate of Life expectancy with the same linear
5501: * hypothesis. A more precise result, taking into account a more precise
5502: * curvature will be obtained if estepm is as small as stepm. */
5503:
5504: /* For example we decided to compute the life expectancy with the smallest unit */
5505: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5506: nhstepm is the number of hstepm from age to agelim
5507: nstepm is the number of stepm from age to agelin.
1.270 brouard 5508: Look at hpijx to understand the reason which relies in memory size consideration
1.126 brouard 5509: and note for a fixed period like estepm months */
5510: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5511: survival function given by stepm (the optimization length). Unfortunately it
5512: means that if the survival funtion is printed only each two years of age and if
5513: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5514: results. So we changed our mind and took the option of the best precision.
5515: */
5516: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5517:
5518: agelim=AGESUP;
5519: /* If stepm=6 months */
5520: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5521: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5522:
5523: /* nhstepm age range expressed in number of stepm */
5524: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5525: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5526: /* if (stepm >= YEARM) hstepm=1;*/
5527: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5528: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5529:
5530: for (age=bage; age<=fage; age ++){
5531: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5532: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5533: /* if (stepm >= YEARM) hstepm=1;*/
5534: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5535:
5536: /* If stepm=6 months */
5537: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5538: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5539:
1.235 brouard 5540: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5541:
5542: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5543:
5544: printf("%d|",(int)age);fflush(stdout);
5545: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5546:
5547: /* Computing expectancies */
5548: for(i=1; i<=nlstate;i++)
5549: for(j=1; j<=nlstate;j++)
5550: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5551: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5552:
5553: /* 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]);*/
5554:
5555: }
5556:
5557: fprintf(ficreseij,"%3.0f",age );
5558: for(i=1; i<=nlstate;i++){
5559: eip=0;
5560: for(j=1; j<=nlstate;j++){
5561: eip +=eij[i][j][(int)age];
5562: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5563: }
5564: fprintf(ficreseij,"%9.4f", eip );
5565: }
5566: fprintf(ficreseij,"\n");
5567:
5568: }
5569: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5570: printf("\n");
5571: fprintf(ficlog,"\n");
5572:
5573: }
5574:
1.235 brouard 5575: 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 5576:
5577: {
5578: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5579: to initial status i, ei. .
1.126 brouard 5580: */
5581: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5582: int nhstepma, nstepma; /* Decreasing with age */
5583: double age, agelim, hf;
5584: double ***p3matp, ***p3matm, ***varhe;
5585: double **dnewm,**doldm;
5586: double *xp, *xm;
5587: double **gp, **gm;
5588: double ***gradg, ***trgradg;
5589: int theta;
5590:
5591: double eip, vip;
5592:
5593: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5594: xp=vector(1,npar);
5595: xm=vector(1,npar);
5596: dnewm=matrix(1,nlstate*nlstate,1,npar);
5597: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5598:
5599: pstamp(ficresstdeij);
5600: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5601: fprintf(ficresstdeij,"# Age");
5602: for(i=1; i<=nlstate;i++){
5603: for(j=1; j<=nlstate;j++)
5604: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5605: fprintf(ficresstdeij," e%1d. ",i);
5606: }
5607: fprintf(ficresstdeij,"\n");
5608:
5609: pstamp(ficrescveij);
5610: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5611: fprintf(ficrescveij,"# Age");
5612: for(i=1; i<=nlstate;i++)
5613: for(j=1; j<=nlstate;j++){
5614: cptj= (j-1)*nlstate+i;
5615: for(i2=1; i2<=nlstate;i2++)
5616: for(j2=1; j2<=nlstate;j2++){
5617: cptj2= (j2-1)*nlstate+i2;
5618: if(cptj2 <= cptj)
5619: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5620: }
5621: }
5622: fprintf(ficrescveij,"\n");
5623:
5624: if(estepm < stepm){
5625: printf ("Problem %d lower than %d\n",estepm, stepm);
5626: }
5627: else hstepm=estepm;
5628: /* We compute the life expectancy from trapezoids spaced every estepm months
5629: * This is mainly to measure the difference between two models: for example
5630: * if stepm=24 months pijx are given only every 2 years and by summing them
5631: * we are calculating an estimate of the Life Expectancy assuming a linear
5632: * progression in between and thus overestimating or underestimating according
5633: * to the curvature of the survival function. If, for the same date, we
5634: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5635: * to compare the new estimate of Life expectancy with the same linear
5636: * hypothesis. A more precise result, taking into account a more precise
5637: * curvature will be obtained if estepm is as small as stepm. */
5638:
5639: /* For example we decided to compute the life expectancy with the smallest unit */
5640: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5641: nhstepm is the number of hstepm from age to agelim
5642: nstepm is the number of stepm from age to agelin.
5643: Look at hpijx to understand the reason of that which relies in memory size
5644: and note for a fixed period like estepm months */
5645: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5646: survival function given by stepm (the optimization length). Unfortunately it
5647: means that if the survival funtion is printed only each two years of age and if
5648: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5649: results. So we changed our mind and took the option of the best precision.
5650: */
5651: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5652:
5653: /* If stepm=6 months */
5654: /* nhstepm age range expressed in number of stepm */
5655: agelim=AGESUP;
5656: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5657: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5658: /* if (stepm >= YEARM) hstepm=1;*/
5659: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5660:
5661: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5662: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5663: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5664: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5665: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5666: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5667:
5668: for (age=bage; age<=fage; age ++){
5669: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5670: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5671: /* if (stepm >= YEARM) hstepm=1;*/
5672: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5673:
1.126 brouard 5674: /* If stepm=6 months */
5675: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5676: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5677:
5678: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5679:
1.126 brouard 5680: /* Computing Variances of health expectancies */
5681: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5682: decrease memory allocation */
5683: for(theta=1; theta <=npar; theta++){
5684: for(i=1; i<=npar; i++){
1.222 brouard 5685: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5686: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5687: }
1.235 brouard 5688: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5689: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5690:
1.126 brouard 5691: for(j=1; j<= nlstate; j++){
1.222 brouard 5692: for(i=1; i<=nlstate; i++){
5693: for(h=0; h<=nhstepm-1; h++){
5694: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5695: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5696: }
5697: }
1.126 brouard 5698: }
1.218 brouard 5699:
1.126 brouard 5700: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5701: for(h=0; h<=nhstepm-1; h++){
5702: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5703: }
1.126 brouard 5704: }/* End theta */
5705:
5706:
5707: for(h=0; h<=nhstepm-1; h++)
5708: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5709: for(theta=1; theta <=npar; theta++)
5710: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5711:
1.218 brouard 5712:
1.222 brouard 5713: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5714: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5715: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5716:
1.222 brouard 5717: printf("%d|",(int)age);fflush(stdout);
5718: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5719: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5720: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5721: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5722: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5723: for(ij=1;ij<=nlstate*nlstate;ij++)
5724: for(ji=1;ji<=nlstate*nlstate;ji++)
5725: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5726: }
5727: }
1.218 brouard 5728:
1.126 brouard 5729: /* Computing expectancies */
1.235 brouard 5730: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5731: for(i=1; i<=nlstate;i++)
5732: for(j=1; j<=nlstate;j++)
1.222 brouard 5733: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5734: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5735:
1.222 brouard 5736: /* 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 5737:
1.222 brouard 5738: }
1.269 brouard 5739:
5740: /* Standard deviation of expectancies ij */
1.126 brouard 5741: fprintf(ficresstdeij,"%3.0f",age );
5742: for(i=1; i<=nlstate;i++){
5743: eip=0.;
5744: vip=0.;
5745: for(j=1; j<=nlstate;j++){
1.222 brouard 5746: eip += eij[i][j][(int)age];
5747: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5748: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5749: 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 5750: }
5751: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5752: }
5753: fprintf(ficresstdeij,"\n");
1.218 brouard 5754:
1.269 brouard 5755: /* Variance of expectancies ij */
1.126 brouard 5756: fprintf(ficrescveij,"%3.0f",age );
5757: for(i=1; i<=nlstate;i++)
5758: for(j=1; j<=nlstate;j++){
1.222 brouard 5759: cptj= (j-1)*nlstate+i;
5760: for(i2=1; i2<=nlstate;i2++)
5761: for(j2=1; j2<=nlstate;j2++){
5762: cptj2= (j2-1)*nlstate+i2;
5763: if(cptj2 <= cptj)
5764: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5765: }
1.126 brouard 5766: }
5767: fprintf(ficrescveij,"\n");
1.218 brouard 5768:
1.126 brouard 5769: }
5770: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5771: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5772: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5773: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5774: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5775: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5776: printf("\n");
5777: fprintf(ficlog,"\n");
1.218 brouard 5778:
1.126 brouard 5779: free_vector(xm,1,npar);
5780: free_vector(xp,1,npar);
5781: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5782: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5783: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5784: }
1.218 brouard 5785:
1.126 brouard 5786: /************ Variance ******************/
1.235 brouard 5787: 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 5788: {
1.279 brouard 5789: /** Variance of health expectancies
5790: * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
5791: * double **newm;
5792: * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
5793: */
1.218 brouard 5794:
5795: /* int movingaverage(); */
5796: double **dnewm,**doldm;
5797: double **dnewmp,**doldmp;
5798: int i, j, nhstepm, hstepm, h, nstepm ;
5799: int k;
5800: double *xp;
1.279 brouard 5801: double **gp, **gm; /**< for var eij */
5802: double ***gradg, ***trgradg; /**< for var eij */
5803: double **gradgp, **trgradgp; /**< for var p point j */
5804: double *gpp, *gmp; /**< for var p point j */
5805: double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
1.218 brouard 5806: double ***p3mat;
5807: double age,agelim, hf;
5808: /* double ***mobaverage; */
5809: int theta;
5810: char digit[4];
5811: char digitp[25];
5812:
5813: char fileresprobmorprev[FILENAMELENGTH];
5814:
5815: if(popbased==1){
5816: if(mobilav!=0)
5817: strcpy(digitp,"-POPULBASED-MOBILAV_");
5818: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5819: }
5820: else
5821: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5822:
1.218 brouard 5823: /* if (mobilav!=0) { */
5824: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5825: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5826: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5827: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5828: /* } */
5829: /* } */
5830:
5831: strcpy(fileresprobmorprev,"PRMORPREV-");
5832: sprintf(digit,"%-d",ij);
5833: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5834: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5835: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5836: strcat(fileresprobmorprev,fileresu);
5837: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5838: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5839: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5840: }
5841: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5842: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5843: pstamp(ficresprobmorprev);
5844: 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 5845: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5846: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5847: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5848: }
5849: for(j=1;j<=cptcoveff;j++)
5850: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5851: fprintf(ficresprobmorprev,"\n");
5852:
1.218 brouard 5853: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5854: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5855: fprintf(ficresprobmorprev," p.%-d SE",j);
5856: for(i=1; i<=nlstate;i++)
5857: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5858: }
5859: fprintf(ficresprobmorprev,"\n");
5860:
5861: fprintf(ficgp,"\n# Routine varevsij");
5862: fprintf(ficgp,"\nunset title \n");
5863: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5864: 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");
5865: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
1.279 brouard 5866:
1.218 brouard 5867: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5868: pstamp(ficresvij);
5869: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5870: if(popbased==1)
5871: 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);
5872: else
5873: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5874: fprintf(ficresvij,"# Age");
5875: for(i=1; i<=nlstate;i++)
5876: for(j=1; j<=nlstate;j++)
5877: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5878: fprintf(ficresvij,"\n");
5879:
5880: xp=vector(1,npar);
5881: dnewm=matrix(1,nlstate,1,npar);
5882: doldm=matrix(1,nlstate,1,nlstate);
5883: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5884: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5885:
5886: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5887: gpp=vector(nlstate+1,nlstate+ndeath);
5888: gmp=vector(nlstate+1,nlstate+ndeath);
5889: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5890:
1.218 brouard 5891: if(estepm < stepm){
5892: printf ("Problem %d lower than %d\n",estepm, stepm);
5893: }
5894: else hstepm=estepm;
5895: /* For example we decided to compute the life expectancy with the smallest unit */
5896: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5897: nhstepm is the number of hstepm from age to agelim
5898: nstepm is the number of stepm from age to agelim.
5899: Look at function hpijx to understand why because of memory size limitations,
5900: we decided (b) to get a life expectancy respecting the most precise curvature of the
5901: survival function given by stepm (the optimization length). Unfortunately it
5902: means that if the survival funtion is printed every two years of age and if
5903: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5904: results. So we changed our mind and took the option of the best precision.
5905: */
5906: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5907: agelim = AGESUP;
5908: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5909: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5910: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5911: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5912: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5913: gp=matrix(0,nhstepm,1,nlstate);
5914: gm=matrix(0,nhstepm,1,nlstate);
5915:
5916:
5917: for(theta=1; theta <=npar; theta++){
5918: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5919: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5920: }
1.279 brouard 5921: /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
5922: * returns into prlim .
5923: */
1.242 brouard 5924: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.279 brouard 5925:
5926: /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
1.218 brouard 5927: if (popbased==1) {
5928: if(mobilav ==0){
5929: for(i=1; i<=nlstate;i++)
5930: prlim[i][i]=probs[(int)age][i][ij];
5931: }else{ /* mobilav */
5932: for(i=1; i<=nlstate;i++)
5933: prlim[i][i]=mobaverage[(int)age][i][ij];
5934: }
5935: }
1.279 brouard 5936: /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
5937: */
5938: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
5939: /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
5940: * at horizon h in state j including mortality.
5941: */
1.218 brouard 5942: for(j=1; j<= nlstate; j++){
5943: for(h=0; h<=nhstepm; h++){
5944: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5945: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5946: }
5947: }
1.279 brouard 5948: /* Next for computing shifted+ probability of death (h=1 means
1.218 brouard 5949: computed over hstepm matrices product = hstepm*stepm months)
1.279 brouard 5950: as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
1.218 brouard 5951: */
5952: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5953: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5954: gpp[j] += prlim[i][i]*p3mat[i][j][1];
1.279 brouard 5955: }
5956:
5957: /* Again with minus shift */
1.218 brouard 5958:
5959: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5960: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5961:
1.242 brouard 5962: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 5963:
5964: if (popbased==1) {
5965: if(mobilav ==0){
5966: for(i=1; i<=nlstate;i++)
5967: prlim[i][i]=probs[(int)age][i][ij];
5968: }else{ /* mobilav */
5969: for(i=1; i<=nlstate;i++)
5970: prlim[i][i]=mobaverage[(int)age][i][ij];
5971: }
5972: }
5973:
1.235 brouard 5974: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 5975:
5976: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5977: for(h=0; h<=nhstepm; h++){
5978: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5979: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5980: }
5981: }
5982: /* This for computing probability of death (h=1 means
5983: computed over hstepm matrices product = hstepm*stepm months)
5984: as a weighted average of prlim.
5985: */
5986: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5987: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5988: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5989: }
1.279 brouard 5990: /* end shifting computations */
5991:
5992: /**< Computing gradient matrix at horizon h
5993: */
1.218 brouard 5994: for(j=1; j<= nlstate; j++) /* vareij */
5995: for(h=0; h<=nhstepm; h++){
5996: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5997: }
1.279 brouard 5998: /**< Gradient of overall mortality p.3 (or p.j)
5999: */
6000: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
1.218 brouard 6001: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
6002: }
6003:
6004: } /* End theta */
1.279 brouard 6005:
6006: /* We got the gradient matrix for each theta and state j */
1.218 brouard 6007: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
6008:
6009: for(h=0; h<=nhstepm; h++) /* veij */
6010: for(j=1; j<=nlstate;j++)
6011: for(theta=1; theta <=npar; theta++)
6012: trgradg[h][j][theta]=gradg[h][theta][j];
6013:
6014: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
6015: for(theta=1; theta <=npar; theta++)
6016: trgradgp[j][theta]=gradgp[theta][j];
1.279 brouard 6017: /**< as well as its transposed matrix
6018: */
1.218 brouard 6019:
6020: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
6021: for(i=1;i<=nlstate;i++)
6022: for(j=1;j<=nlstate;j++)
6023: vareij[i][j][(int)age] =0.;
1.279 brouard 6024:
6025: /* Computing trgradg by matcov by gradg at age and summing over h
6026: * and k (nhstepm) formula 15 of article
6027: * Lievre-Brouard-Heathcote
6028: */
6029:
1.218 brouard 6030: for(h=0;h<=nhstepm;h++){
6031: for(k=0;k<=nhstepm;k++){
6032: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
6033: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
6034: for(i=1;i<=nlstate;i++)
6035: for(j=1;j<=nlstate;j++)
6036: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
6037: }
6038: }
6039:
1.279 brouard 6040: /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
6041: * p.j overall mortality formula 49 but computed directly because
6042: * we compute the grad (wix pijx) instead of grad (pijx),even if
6043: * wix is independent of theta.
6044: */
1.218 brouard 6045: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
6046: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
6047: for(j=nlstate+1;j<=nlstate+ndeath;j++)
6048: for(i=nlstate+1;i<=nlstate+ndeath;i++)
6049: varppt[j][i]=doldmp[j][i];
6050: /* end ppptj */
6051: /* x centered again */
6052:
1.242 brouard 6053: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 6054:
6055: if (popbased==1) {
6056: if(mobilav ==0){
6057: for(i=1; i<=nlstate;i++)
6058: prlim[i][i]=probs[(int)age][i][ij];
6059: }else{ /* mobilav */
6060: for(i=1; i<=nlstate;i++)
6061: prlim[i][i]=mobaverage[(int)age][i][ij];
6062: }
6063: }
6064:
6065: /* This for computing probability of death (h=1 means
6066: computed over hstepm (estepm) matrices product = hstepm*stepm months)
6067: as a weighted average of prlim.
6068: */
1.235 brouard 6069: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 6070: for(j=nlstate+1;j<=nlstate+ndeath;j++){
6071: for(i=1,gmp[j]=0.;i<= nlstate; i++)
6072: gmp[j] += prlim[i][i]*p3mat[i][j][1];
6073: }
6074: /* end probability of death */
6075:
6076: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
6077: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
6078: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
6079: for(i=1; i<=nlstate;i++){
6080: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
6081: }
6082: }
6083: fprintf(ficresprobmorprev,"\n");
6084:
6085: fprintf(ficresvij,"%.0f ",age );
6086: for(i=1; i<=nlstate;i++)
6087: for(j=1; j<=nlstate;j++){
6088: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
6089: }
6090: fprintf(ficresvij,"\n");
6091: free_matrix(gp,0,nhstepm,1,nlstate);
6092: free_matrix(gm,0,nhstepm,1,nlstate);
6093: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
6094: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
6095: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6096: } /* End age */
6097: free_vector(gpp,nlstate+1,nlstate+ndeath);
6098: free_vector(gmp,nlstate+1,nlstate+ndeath);
6099: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
6100: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
6101: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
6102: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
6103: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
6104: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
6105: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
6106: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
6107: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
6108: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
6109: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
6110: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
6111: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
6112: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
6113: 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);
6114: /* 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 6115: */
1.218 brouard 6116: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
6117: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 6118:
1.218 brouard 6119: free_vector(xp,1,npar);
6120: free_matrix(doldm,1,nlstate,1,nlstate);
6121: free_matrix(dnewm,1,nlstate,1,npar);
6122: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6123: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
6124: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
6125: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6126: fclose(ficresprobmorprev);
6127: fflush(ficgp);
6128: fflush(fichtm);
6129: } /* end varevsij */
1.126 brouard 6130:
6131: /************ Variance of prevlim ******************/
1.269 brouard 6132: 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 6133: {
1.205 brouard 6134: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 6135: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 6136:
1.268 brouard 6137: double **dnewmpar,**doldm;
1.126 brouard 6138: int i, j, nhstepm, hstepm;
6139: double *xp;
6140: double *gp, *gm;
6141: double **gradg, **trgradg;
1.208 brouard 6142: double **mgm, **mgp;
1.126 brouard 6143: double age,agelim;
6144: int theta;
6145:
6146: pstamp(ficresvpl);
6147: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.241 brouard 6148: fprintf(ficresvpl,"# Age ");
6149: if(nresult >=1)
6150: fprintf(ficresvpl," Result# ");
1.126 brouard 6151: for(i=1; i<=nlstate;i++)
6152: fprintf(ficresvpl," %1d-%1d",i,i);
6153: fprintf(ficresvpl,"\n");
6154:
6155: xp=vector(1,npar);
1.268 brouard 6156: dnewmpar=matrix(1,nlstate,1,npar);
1.126 brouard 6157: doldm=matrix(1,nlstate,1,nlstate);
6158:
6159: hstepm=1*YEARM; /* Every year of age */
6160: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6161: agelim = AGESUP;
6162: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
6163: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6164: if (stepm >= YEARM) hstepm=1;
6165: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6166: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 6167: mgp=matrix(1,npar,1,nlstate);
6168: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 6169: gp=vector(1,nlstate);
6170: gm=vector(1,nlstate);
6171:
6172: for(theta=1; theta <=npar; theta++){
6173: for(i=1; i<=npar; i++){ /* Computes gradient */
6174: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6175: }
1.209 brouard 6176: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6177: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6178: else
1.235 brouard 6179: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6180: for(i=1;i<=nlstate;i++){
1.126 brouard 6181: gp[i] = prlim[i][i];
1.208 brouard 6182: mgp[theta][i] = prlim[i][i];
6183: }
1.126 brouard 6184: for(i=1; i<=npar; i++) /* Computes gradient */
6185: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 6186: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 6187: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 6188: else
1.235 brouard 6189: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 6190: for(i=1;i<=nlstate;i++){
1.126 brouard 6191: gm[i] = prlim[i][i];
1.208 brouard 6192: mgm[theta][i] = prlim[i][i];
6193: }
1.126 brouard 6194: for(i=1;i<=nlstate;i++)
6195: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 6196: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 6197: } /* End theta */
6198:
6199: trgradg =matrix(1,nlstate,1,npar);
6200:
6201: for(j=1; j<=nlstate;j++)
6202: for(theta=1; theta <=npar; theta++)
6203: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 6204: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6205: /* printf("\nmgm mgp %d ",(int)age); */
6206: /* for(j=1; j<=nlstate;j++){ */
6207: /* printf(" %d ",j); */
6208: /* for(theta=1; theta <=npar; theta++) */
6209: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6210: /* printf("\n "); */
6211: /* } */
6212: /* } */
6213: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6214: /* printf("\n gradg %d ",(int)age); */
6215: /* for(j=1; j<=nlstate;j++){ */
6216: /* printf("%d ",j); */
6217: /* for(theta=1; theta <=npar; theta++) */
6218: /* printf("%d %lf ",theta,gradg[theta][j]); */
6219: /* printf("\n "); */
6220: /* } */
6221: /* } */
1.126 brouard 6222:
6223: for(i=1;i<=nlstate;i++)
6224: varpl[i][(int)age] =0.;
1.209 brouard 6225: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.268 brouard 6226: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6227: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6228: }else{
1.268 brouard 6229: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6230: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 6231: }
1.126 brouard 6232: for(i=1;i<=nlstate;i++)
6233: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6234:
6235: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6236: if(nresult >=1)
6237: fprintf(ficresvpl,"%d ",nres );
1.126 brouard 6238: for(i=1; i<=nlstate;i++)
6239: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
6240: fprintf(ficresvpl,"\n");
6241: free_vector(gp,1,nlstate);
6242: free_vector(gm,1,nlstate);
1.208 brouard 6243: free_matrix(mgm,1,npar,1,nlstate);
6244: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6245: free_matrix(gradg,1,npar,1,nlstate);
6246: free_matrix(trgradg,1,nlstate,1,npar);
6247: } /* End age */
6248:
6249: free_vector(xp,1,npar);
6250: free_matrix(doldm,1,nlstate,1,npar);
1.268 brouard 6251: free_matrix(dnewmpar,1,nlstate,1,nlstate);
6252:
6253: }
6254:
6255:
6256: /************ Variance of backprevalence limit ******************/
1.269 brouard 6257: 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 6258: {
6259: /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
6260: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
6261:
6262: double **dnewmpar,**doldm;
6263: int i, j, nhstepm, hstepm;
6264: double *xp;
6265: double *gp, *gm;
6266: double **gradg, **trgradg;
6267: double **mgm, **mgp;
6268: double age,agelim;
6269: int theta;
6270:
6271: pstamp(ficresvbl);
6272: fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
6273: fprintf(ficresvbl,"# Age ");
6274: if(nresult >=1)
6275: fprintf(ficresvbl," Result# ");
6276: for(i=1; i<=nlstate;i++)
6277: fprintf(ficresvbl," %1d-%1d",i,i);
6278: fprintf(ficresvbl,"\n");
6279:
6280: xp=vector(1,npar);
6281: dnewmpar=matrix(1,nlstate,1,npar);
6282: doldm=matrix(1,nlstate,1,nlstate);
6283:
6284: hstepm=1*YEARM; /* Every year of age */
6285: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
6286: agelim = AGEINF;
6287: for (age=fage; age>=bage; age --){ /* If stepm=6 months */
6288: nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6289: if (stepm >= YEARM) hstepm=1;
6290: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6291: gradg=matrix(1,npar,1,nlstate);
6292: mgp=matrix(1,npar,1,nlstate);
6293: mgm=matrix(1,npar,1,nlstate);
6294: gp=vector(1,nlstate);
6295: gm=vector(1,nlstate);
6296:
6297: for(theta=1; theta <=npar; theta++){
6298: for(i=1; i<=npar; i++){ /* Computes gradient */
6299: xp[i] = x[i] + (i==theta ?delti[theta]:0);
6300: }
6301: if(mobilavproj > 0 )
6302: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6303: else
6304: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6305: for(i=1;i<=nlstate;i++){
6306: gp[i] = bprlim[i][i];
6307: mgp[theta][i] = bprlim[i][i];
6308: }
6309: for(i=1; i<=npar; i++) /* Computes gradient */
6310: xp[i] = x[i] - (i==theta ?delti[theta]:0);
6311: if(mobilavproj > 0 )
6312: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6313: else
6314: bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
6315: for(i=1;i<=nlstate;i++){
6316: gm[i] = bprlim[i][i];
6317: mgm[theta][i] = bprlim[i][i];
6318: }
6319: for(i=1;i<=nlstate;i++)
6320: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
6321: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
6322: } /* End theta */
6323:
6324: trgradg =matrix(1,nlstate,1,npar);
6325:
6326: for(j=1; j<=nlstate;j++)
6327: for(theta=1; theta <=npar; theta++)
6328: trgradg[j][theta]=gradg[theta][j];
6329: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6330: /* printf("\nmgm mgp %d ",(int)age); */
6331: /* for(j=1; j<=nlstate;j++){ */
6332: /* printf(" %d ",j); */
6333: /* for(theta=1; theta <=npar; theta++) */
6334: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
6335: /* printf("\n "); */
6336: /* } */
6337: /* } */
6338: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
6339: /* printf("\n gradg %d ",(int)age); */
6340: /* for(j=1; j<=nlstate;j++){ */
6341: /* printf("%d ",j); */
6342: /* for(theta=1; theta <=npar; theta++) */
6343: /* printf("%d %lf ",theta,gradg[theta][j]); */
6344: /* printf("\n "); */
6345: /* } */
6346: /* } */
6347:
6348: for(i=1;i<=nlstate;i++)
6349: varbpl[i][(int)age] =0.;
6350: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
6351: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6352: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6353: }else{
6354: matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
6355: matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
6356: }
6357: for(i=1;i<=nlstate;i++)
6358: varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6359:
6360: fprintf(ficresvbl,"%.0f ",age );
6361: if(nresult >=1)
6362: fprintf(ficresvbl,"%d ",nres );
6363: for(i=1; i<=nlstate;i++)
6364: fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
6365: fprintf(ficresvbl,"\n");
6366: free_vector(gp,1,nlstate);
6367: free_vector(gm,1,nlstate);
6368: free_matrix(mgm,1,npar,1,nlstate);
6369: free_matrix(mgp,1,npar,1,nlstate);
6370: free_matrix(gradg,1,npar,1,nlstate);
6371: free_matrix(trgradg,1,nlstate,1,npar);
6372: } /* End age */
6373:
6374: free_vector(xp,1,npar);
6375: free_matrix(doldm,1,nlstate,1,npar);
6376: free_matrix(dnewmpar,1,nlstate,1,nlstate);
1.126 brouard 6377:
6378: }
6379:
6380: /************ Variance of one-step probabilities ******************/
6381: 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 6382: {
6383: int i, j=0, k1, l1, tj;
6384: int k2, l2, j1, z1;
6385: int k=0, l;
6386: int first=1, first1, first2;
6387: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6388: double **dnewm,**doldm;
6389: double *xp;
6390: double *gp, *gm;
6391: double **gradg, **trgradg;
6392: double **mu;
6393: double age, cov[NCOVMAX+1];
6394: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6395: int theta;
6396: char fileresprob[FILENAMELENGTH];
6397: char fileresprobcov[FILENAMELENGTH];
6398: char fileresprobcor[FILENAMELENGTH];
6399: double ***varpij;
6400:
6401: strcpy(fileresprob,"PROB_");
6402: strcat(fileresprob,fileres);
6403: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6404: printf("Problem with resultfile: %s\n", fileresprob);
6405: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6406: }
6407: strcpy(fileresprobcov,"PROBCOV_");
6408: strcat(fileresprobcov,fileresu);
6409: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6410: printf("Problem with resultfile: %s\n", fileresprobcov);
6411: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6412: }
6413: strcpy(fileresprobcor,"PROBCOR_");
6414: strcat(fileresprobcor,fileresu);
6415: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6416: printf("Problem with resultfile: %s\n", fileresprobcor);
6417: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6418: }
6419: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6420: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6421: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6422: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6423: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6424: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6425: pstamp(ficresprob);
6426: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6427: fprintf(ficresprob,"# Age");
6428: pstamp(ficresprobcov);
6429: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6430: fprintf(ficresprobcov,"# Age");
6431: pstamp(ficresprobcor);
6432: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6433: fprintf(ficresprobcor,"# Age");
1.126 brouard 6434:
6435:
1.222 brouard 6436: for(i=1; i<=nlstate;i++)
6437: for(j=1; j<=(nlstate+ndeath);j++){
6438: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6439: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6440: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6441: }
6442: /* fprintf(ficresprob,"\n");
6443: fprintf(ficresprobcov,"\n");
6444: fprintf(ficresprobcor,"\n");
6445: */
6446: xp=vector(1,npar);
6447: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6448: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6449: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6450: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6451: first=1;
6452: fprintf(ficgp,"\n# Routine varprob");
6453: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6454: fprintf(fichtm,"\n");
6455:
1.266 brouard 6456: 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 6457: 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);
6458: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6459: and drawn. It helps understanding how is the covariance between two incidences.\
6460: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6461: 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 6462: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6463: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6464: standard deviations wide on each axis. <br>\
6465: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6466: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6467: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6468:
1.222 brouard 6469: cov[1]=1;
6470: /* tj=cptcoveff; */
1.225 brouard 6471: tj = (int) pow(2,cptcoveff);
1.222 brouard 6472: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6473: j1=0;
1.224 brouard 6474: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6475: if (cptcovn>0) {
6476: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6477: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6478: fprintf(ficresprob, "**********\n#\n");
6479: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6480: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6481: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6482:
1.222 brouard 6483: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6484: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6485: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6486:
6487:
1.222 brouard 6488: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6489: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6490: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6491:
1.222 brouard 6492: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6493: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6494: fprintf(ficresprobcor, "**********\n#");
6495: if(invalidvarcomb[j1]){
6496: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6497: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6498: continue;
6499: }
6500: }
6501: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6502: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6503: gp=vector(1,(nlstate)*(nlstate+ndeath));
6504: gm=vector(1,(nlstate)*(nlstate+ndeath));
6505: for (age=bage; age<=fage; age ++){
6506: cov[2]=age;
6507: if(nagesqr==1)
6508: cov[3]= age*age;
6509: for (k=1; k<=cptcovn;k++) {
6510: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6511: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6512: * 1 1 1 1 1
6513: * 2 2 1 1 1
6514: * 3 1 2 1 1
6515: */
6516: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6517: }
6518: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6519: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6520: for (k=1; k<=cptcovprod;k++)
6521: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6522:
6523:
1.222 brouard 6524: for(theta=1; theta <=npar; theta++){
6525: for(i=1; i<=npar; i++)
6526: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6527:
1.222 brouard 6528: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6529:
1.222 brouard 6530: k=0;
6531: for(i=1; i<= (nlstate); i++){
6532: for(j=1; j<=(nlstate+ndeath);j++){
6533: k=k+1;
6534: gp[k]=pmmij[i][j];
6535: }
6536: }
1.220 brouard 6537:
1.222 brouard 6538: for(i=1; i<=npar; i++)
6539: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6540:
1.222 brouard 6541: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6542: k=0;
6543: for(i=1; i<=(nlstate); i++){
6544: for(j=1; j<=(nlstate+ndeath);j++){
6545: k=k+1;
6546: gm[k]=pmmij[i][j];
6547: }
6548: }
1.220 brouard 6549:
1.222 brouard 6550: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6551: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6552: }
1.126 brouard 6553:
1.222 brouard 6554: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6555: for(theta=1; theta <=npar; theta++)
6556: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6557:
1.222 brouard 6558: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6559: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6560:
1.222 brouard 6561: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6562:
1.222 brouard 6563: k=0;
6564: for(i=1; i<=(nlstate); i++){
6565: for(j=1; j<=(nlstate+ndeath);j++){
6566: k=k+1;
6567: mu[k][(int) age]=pmmij[i][j];
6568: }
6569: }
6570: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6571: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6572: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6573:
1.222 brouard 6574: /*printf("\n%d ",(int)age);
6575: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6576: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6577: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6578: }*/
1.220 brouard 6579:
1.222 brouard 6580: fprintf(ficresprob,"\n%d ",(int)age);
6581: fprintf(ficresprobcov,"\n%d ",(int)age);
6582: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6583:
1.222 brouard 6584: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6585: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6586: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6587: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6588: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6589: }
6590: i=0;
6591: for (k=1; k<=(nlstate);k++){
6592: for (l=1; l<=(nlstate+ndeath);l++){
6593: i++;
6594: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6595: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6596: for (j=1; j<=i;j++){
6597: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6598: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6599: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6600: }
6601: }
6602: }/* end of loop for state */
6603: } /* end of loop for age */
6604: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6605: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6606: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6607: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6608:
6609: /* Confidence intervalle of pij */
6610: /*
6611: fprintf(ficgp,"\nunset parametric;unset label");
6612: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6613: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6614: 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);
6615: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6616: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6617: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6618: */
6619:
6620: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6621: first1=1;first2=2;
6622: for (k2=1; k2<=(nlstate);k2++){
6623: for (l2=1; l2<=(nlstate+ndeath);l2++){
6624: if(l2==k2) continue;
6625: j=(k2-1)*(nlstate+ndeath)+l2;
6626: for (k1=1; k1<=(nlstate);k1++){
6627: for (l1=1; l1<=(nlstate+ndeath);l1++){
6628: if(l1==k1) continue;
6629: i=(k1-1)*(nlstate+ndeath)+l1;
6630: if(i<=j) continue;
6631: for (age=bage; age<=fage; age ++){
6632: if ((int)age %5==0){
6633: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6634: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6635: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6636: mu1=mu[i][(int) age]/stepm*YEARM ;
6637: mu2=mu[j][(int) age]/stepm*YEARM;
6638: c12=cv12/sqrt(v1*v2);
6639: /* Computing eigen value of matrix of covariance */
6640: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6641: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6642: if ((lc2 <0) || (lc1 <0) ){
6643: if(first2==1){
6644: first1=0;
6645: 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);
6646: }
6647: 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);
6648: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6649: /* lc2=fabs(lc2); */
6650: }
1.220 brouard 6651:
1.222 brouard 6652: /* Eigen vectors */
1.280 brouard 6653: if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
6654: printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6655: fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
6656: v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
6657: }else
6658: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
1.222 brouard 6659: /*v21=sqrt(1.-v11*v11); *//* error */
6660: v21=(lc1-v1)/cv12*v11;
6661: v12=-v21;
6662: v22=v11;
6663: tnalp=v21/v11;
6664: if(first1==1){
6665: first1=0;
6666: 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);
6667: }
6668: 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);
6669: /*printf(fignu*/
6670: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6671: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6672: if(first==1){
6673: first=0;
6674: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6675: fprintf(ficgp,"\nset parametric;unset label");
6676: 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);
6677: fprintf(ficgp,"\nset ter svg size 640, 480");
1.266 brouard 6678: fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6679: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6680: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6681: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6682: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6683: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6684: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6685: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6686: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6687: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6688: 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 6689: mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
6690: mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
1.222 brouard 6691: }else{
6692: first=0;
6693: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6694: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6695: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6696: 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 6697: mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
6698: mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
1.222 brouard 6699: }/* if first */
6700: } /* age mod 5 */
6701: } /* end loop age */
6702: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6703: first=1;
6704: } /*l12 */
6705: } /* k12 */
6706: } /*l1 */
6707: }/* k1 */
6708: } /* loop on combination of covariates j1 */
6709: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6710: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6711: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6712: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6713: free_vector(xp,1,npar);
6714: fclose(ficresprob);
6715: fclose(ficresprobcov);
6716: fclose(ficresprobcor);
6717: fflush(ficgp);
6718: fflush(fichtmcov);
6719: }
1.126 brouard 6720:
6721:
6722: /******************* Printing html file ***********/
1.201 brouard 6723: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6724: int lastpass, int stepm, int weightopt, char model[],\
6725: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.258 brouard 6726: int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
1.273 brouard 6727: double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
6728: double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
1.237 brouard 6729: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6730:
6731: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6732: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6733: </ul>");
1.237 brouard 6734: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6735: </ul>", model);
1.214 brouard 6736: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6737: 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",
6738: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6739: 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 6740: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6741: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6742: fprintf(fichtm,"\
6743: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6744: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6745: fprintf(fichtm,"\
1.217 brouard 6746: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6747: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6748: fprintf(fichtm,"\
1.126 brouard 6749: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6750: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6751: fprintf(fichtm,"\
1.217 brouard 6752: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6753: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6754: fprintf(fichtm,"\
1.211 brouard 6755: - (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 6756: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6757: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6758: if(prevfcast==1){
6759: fprintf(fichtm,"\
6760: - Prevalence projections by age and states: \
1.201 brouard 6761: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6762: }
1.126 brouard 6763:
6764:
1.225 brouard 6765: m=pow(2,cptcoveff);
1.222 brouard 6766: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6767:
1.264 brouard 6768: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
6769:
6770: jj1=0;
6771:
6772: fprintf(fichtm," \n<ul>");
6773: for(nres=1; nres <= nresult; nres++) /* For each resultline */
6774: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
6775: if(m != 1 && TKresult[nres]!= k1)
6776: continue;
6777: jj1++;
6778: if (cptcovn > 0) {
6779: fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
6780: for (cpt=1; cpt<=cptcoveff;cpt++){
6781: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6782: }
6783: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6784: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6785: }
6786: fprintf(fichtm,"\">");
6787:
6788: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
6789: fprintf(fichtm,"************ Results for covariates");
6790: for (cpt=1; cpt<=cptcoveff;cpt++){
6791: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6792: }
6793: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6794: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6795: }
6796: if(invalidvarcomb[k1]){
6797: fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
6798: continue;
6799: }
6800: fprintf(fichtm,"</a></li>");
6801: } /* cptcovn >0 */
6802: }
6803: fprintf(fichtm," \n</ul>");
6804:
1.222 brouard 6805: jj1=0;
1.237 brouard 6806:
6807: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6808: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6809: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6810: continue;
1.220 brouard 6811:
1.222 brouard 6812: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6813: jj1++;
6814: if (cptcovn > 0) {
1.264 brouard 6815: fprintf(fichtm,"\n<p><a name=\"rescov");
6816: for (cpt=1; cpt<=cptcoveff;cpt++){
6817: fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6818: }
6819: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6820: fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
6821: }
6822: fprintf(fichtm,"\"</a>");
6823:
1.222 brouard 6824: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6825: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6826: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6827: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6828: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6829: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6830: }
1.237 brouard 6831: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6832: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6833: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6834: }
6835:
1.230 brouard 6836: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6837: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6838: if(invalidvarcomb[k1]){
6839: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6840: printf("\nCombination (%d) ignored because no cases \n",k1);
6841: continue;
6842: }
6843: }
6844: /* aij, bij */
1.259 brouard 6845: 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 6846: <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 6847: /* Pij */
1.241 brouard 6848: 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> \
6849: <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 6850: /* Quasi-incidences */
6851: 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 6852: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6853: 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 6854: 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> \
6855: <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 6856: /* Survival functions (period) in state j */
6857: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6858: 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> \
6859: <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 6860: }
6861: /* State specific survival functions (period) */
6862: for(cpt=1; cpt<=nlstate;cpt++){
6863: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6864: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.241 brouard 6865: <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 6866: }
6867: /* Period (stable) prevalence in each health state */
6868: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6869: 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> \
6870: <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 6871: }
6872: if(backcast==1){
6873: /* Period (stable) back prevalence in each health state */
6874: for(cpt=1; cpt<=nlstate;cpt++){
1.264 brouard 6875: 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 6876: <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 6877: }
1.217 brouard 6878: }
1.222 brouard 6879: if(prevfcast==1){
6880: /* Projection of prevalence up to period (stable) prevalence in each health state */
6881: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6882: 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> \
6883: <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 6884: }
6885: }
1.268 brouard 6886: if(backcast==1){
6887: /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
6888: for(cpt=1; cpt<=nlstate;cpt++){
1.273 brouard 6889: fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
6890: 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 \
6891: 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) \
6892: with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
6893: <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 6894: }
6895: }
1.220 brouard 6896:
1.222 brouard 6897: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 6898: 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> \
6899: <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 6900: }
6901: /* } /\* end i1 *\/ */
6902: }/* End k1 */
6903: fprintf(fichtm,"</ul>");
1.126 brouard 6904:
1.222 brouard 6905: fprintf(fichtm,"\
1.126 brouard 6906: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6907: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6908: - 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 6909: But because parameters are usually highly correlated (a higher incidence of disability \
6910: and a higher incidence of recovery can give very close observed transition) it might \
6911: be very useful to look not only at linear confidence intervals estimated from the \
6912: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6913: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6914: covariance matrix of the one-step probabilities. \
6915: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6916:
1.222 brouard 6917: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6918: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6919: fprintf(fichtm,"\
1.126 brouard 6920: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6921: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6922:
1.222 brouard 6923: fprintf(fichtm,"\
1.126 brouard 6924: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6925: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6926: fprintf(fichtm,"\
1.126 brouard 6927: - 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): \
6928: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6929: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6930: fprintf(fichtm,"\
1.126 brouard 6931: - (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): \
6932: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6933: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6934: fprintf(fichtm,"\
1.128 brouard 6935: - 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 6936: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6937: fprintf(fichtm,"\
1.128 brouard 6938: - 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 6939: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6940: fprintf(fichtm,"\
1.126 brouard 6941: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6942: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6943:
6944: /* if(popforecast==1) fprintf(fichtm,"\n */
6945: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6946: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6947: /* <br>",fileres,fileres,fileres,fileres); */
6948: /* else */
6949: /* 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 6950: fflush(fichtm);
6951: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6952:
1.225 brouard 6953: m=pow(2,cptcoveff);
1.222 brouard 6954: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6955:
1.222 brouard 6956: jj1=0;
1.237 brouard 6957:
1.241 brouard 6958: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 6959: for(k1=1; k1<=m;k1++){
1.253 brouard 6960: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6961: continue;
1.222 brouard 6962: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6963: jj1++;
1.126 brouard 6964: if (cptcovn > 0) {
6965: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6966: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 6967: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
6968: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6969: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6970: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6971: }
6972:
1.126 brouard 6973: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6974:
1.222 brouard 6975: if(invalidvarcomb[k1]){
6976: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6977: continue;
6978: }
1.126 brouard 6979: }
6980: for(cpt=1; cpt<=nlstate;cpt++) {
1.258 brouard 6981: fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
1.241 brouard 6982: 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 6983: <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 6984: }
6985: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6986: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6987: true period expectancies (those weighted with period prevalences are also\
6988: drawn in addition to the population based expectancies computed using\
1.241 brouard 6989: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
6990: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 6991: /* } /\* end i1 *\/ */
6992: }/* End k1 */
1.241 brouard 6993: }/* End nres */
1.222 brouard 6994: fprintf(fichtm,"</ul>");
6995: fflush(fichtm);
1.126 brouard 6996: }
6997:
6998: /******************* Gnuplot file **************/
1.270 brouard 6999: 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 7000:
7001: char dirfileres[132],optfileres[132];
1.264 brouard 7002: char gplotcondition[132], gplotlabel[132];
1.237 brouard 7003: 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 7004: int lv=0, vlv=0, kl=0;
1.130 brouard 7005: int ng=0;
1.201 brouard 7006: int vpopbased;
1.223 brouard 7007: int ioffset; /* variable offset for columns */
1.270 brouard 7008: int iyearc=1; /* variable column for year of projection */
7009: int iagec=1; /* variable column for age of projection */
1.235 brouard 7010: int nres=0; /* Index of resultline */
1.266 brouard 7011: int istart=1; /* For starting graphs in projections */
1.219 brouard 7012:
1.126 brouard 7013: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
7014: /* printf("Problem with file %s",optionfilegnuplot); */
7015: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
7016: /* } */
7017:
7018: /*#ifdef windows */
7019: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 7020: /*#endif */
1.225 brouard 7021: m=pow(2,cptcoveff);
1.126 brouard 7022:
1.274 brouard 7023: /* diagram of the model */
7024: fprintf(ficgp,"\n#Diagram of the model \n");
7025: fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
7026: fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
7027: 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);
7028:
7029: 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);
7030: fprintf(ficgp,"\n#show arrow\nunset label\n");
7031: 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);
7032: fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
7033: fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
7034: fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
7035: fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
7036:
1.202 brouard 7037: /* Contribution to likelihood */
7038: /* Plot the probability implied in the likelihood */
1.223 brouard 7039: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
7040: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
7041: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
7042: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 7043: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 7044: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
7045: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 7046: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
7047: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
7048: 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));
7049: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
7050: 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));
7051: for (i=1; i<= nlstate ; i ++) {
7052: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
7053: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
7054: 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);
7055: for (j=2; j<= nlstate+ndeath ; j ++) {
7056: 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);
7057: }
7058: fprintf(ficgp,";\nset out; unset ylabel;\n");
7059: }
7060: /* 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 */
7061: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
7062: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
7063: fprintf(ficgp,"\nset out;unset log\n");
7064: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 7065:
1.126 brouard 7066: strcpy(dirfileres,optionfilefiname);
7067: strcpy(optfileres,"vpl");
1.223 brouard 7068: /* 1eme*/
1.238 brouard 7069: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
7070: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 7071: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 7072: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 7073: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7074: continue;
7075: /* We are interested in selected combination by the resultline */
1.246 brouard 7076: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.238 brouard 7077: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
1.264 brouard 7078: strcpy(gplotlabel,"(");
1.238 brouard 7079: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
7080: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
7081: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7082: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7083: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7084: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
7085: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 7086: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 7087: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7088: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7089: }
7090: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 7091: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 7092: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7093: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7094: }
7095: strcpy(gplotlabel+strlen(gplotlabel),")");
1.246 brouard 7096: /* printf("\n#\n"); */
1.238 brouard 7097: fprintf(ficgp,"\n#\n");
7098: if(invalidvarcomb[k1]){
1.260 brouard 7099: /*k1=k1-1;*/ /* To be checked */
1.238 brouard 7100: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7101: continue;
7102: }
1.235 brouard 7103:
1.241 brouard 7104: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
7105: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
1.276 brouard 7106: /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
7107: fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
1.260 brouard 7108: 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);
7109: /* 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); */
7110: /* k1-1 error should be nres-1*/
1.238 brouard 7111: for (i=1; i<= nlstate ; i ++) {
7112: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7113: else fprintf(ficgp," %%*lf (%%*lf)");
7114: }
1.260 brouard 7115: 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 7116: for (i=1; i<= nlstate ; i ++) {
7117: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7118: else fprintf(ficgp," %%*lf (%%*lf)");
7119: }
1.260 brouard 7120: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
1.238 brouard 7121: for (i=1; i<= nlstate ; i ++) {
7122: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7123: else fprintf(ficgp," %%*lf (%%*lf)");
7124: }
1.265 brouard 7125: /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
7126:
7127: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
7128: if(cptcoveff ==0){
1.271 brouard 7129: fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
1.265 brouard 7130: }else{
7131: kl=0;
7132: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7133: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7134: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7135: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7136: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7137: vlv= nbcode[Tvaraff[k]][lv];
7138: kl++;
7139: /* 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 *\/ */
7140: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7141: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7142: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7143: if(k==cptcoveff){
7144: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
7145: 2+cptcoveff*2+3*(cpt-1), cpt ); /* 4 or 6 ?*/
7146: }else{
7147: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7148: kl++;
7149: }
7150: } /* end covariate */
7151: } /* end if no covariate */
7152:
1.238 brouard 7153: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
7154: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 7155: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 7156: if(cptcoveff ==0){
1.245 brouard 7157: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 7158: }else{
7159: kl=0;
7160: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
7161: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7162: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7163: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7164: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7165: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 7166: kl++;
1.238 brouard 7167: /* 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 *\/ */
7168: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7169: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7170: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
7171: if(k==cptcoveff){
1.245 brouard 7172: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 7173: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 7174: }else{
7175: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
7176: kl++;
7177: }
7178: } /* end covariate */
7179: } /* end if no covariate */
1.268 brouard 7180: if(backcast == 1){
7181: fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
7182: /* k1-1 error should be nres-1*/
7183: for (i=1; i<= nlstate ; i ++) {
7184: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7185: else fprintf(ficgp," %%*lf (%%*lf)");
7186: }
1.271 brouard 7187: 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 7188: for (i=1; i<= nlstate ; i ++) {
7189: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7190: else fprintf(ficgp," %%*lf (%%*lf)");
7191: }
1.276 brouard 7192: 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 7193: for (i=1; i<= nlstate ; i ++) {
7194: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
7195: else fprintf(ficgp," %%*lf (%%*lf)");
7196: }
1.274 brouard 7197: fprintf(ficgp,"\" t\"\" w l lt 4");
1.268 brouard 7198: } /* end if backprojcast */
1.238 brouard 7199: } /* end if backcast */
1.276 brouard 7200: /* fprintf(ficgp,"\nset out ;unset label;\n"); */
7201: fprintf(ficgp,"\nset out ;unset title;\n");
1.238 brouard 7202: } /* nres */
1.201 brouard 7203: } /* k1 */
7204: } /* cpt */
1.235 brouard 7205:
7206:
1.126 brouard 7207: /*2 eme*/
1.238 brouard 7208: for (k1=1; k1<= m ; k1 ++){
7209: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7210: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7211: continue;
7212: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.264 brouard 7213: strcpy(gplotlabel,"(");
1.238 brouard 7214: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 7215: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 7216: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7217: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7218: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7219: vlv= nbcode[Tvaraff[k]][lv];
7220: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7221: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7222: }
1.237 brouard 7223: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 7224: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7225: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 7226: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7227: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7228: }
1.264 brouard 7229: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7230: fprintf(ficgp,"\n#\n");
1.223 brouard 7231: if(invalidvarcomb[k1]){
7232: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7233: continue;
7234: }
1.219 brouard 7235:
1.241 brouard 7236: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 7237: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.264 brouard 7238: fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
7239: if(vpopbased==0){
1.238 brouard 7240: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
1.264 brouard 7241: }else
1.238 brouard 7242: fprintf(ficgp,"\nreplot ");
7243: for (i=1; i<= nlstate+1 ; i ++) {
7244: k=2*i;
1.261 brouard 7245: 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 7246: for (j=1; j<= nlstate+1 ; j ++) {
7247: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7248: else fprintf(ficgp," %%*lf (%%*lf)");
7249: }
7250: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
7251: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
1.261 brouard 7252: 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 7253: for (j=1; j<= nlstate+1 ; j ++) {
7254: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7255: else fprintf(ficgp," %%*lf (%%*lf)");
7256: }
7257: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.261 brouard 7258: 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 7259: for (j=1; j<= nlstate+1 ; j ++) {
7260: if (j==i) fprintf(ficgp," %%lf (%%lf)");
7261: else fprintf(ficgp," %%*lf (%%*lf)");
7262: }
7263: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
7264: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
7265: } /* state */
7266: } /* vpopbased */
1.264 brouard 7267: 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 7268: } /* end nres */
7269: } /* k1 end 2 eme*/
7270:
7271:
7272: /*3eme*/
7273: for (k1=1; k1<= m ; k1 ++){
7274: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7275: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 7276: continue;
7277:
7278: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.261 brouard 7279: fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
1.264 brouard 7280: strcpy(gplotlabel,"(");
1.238 brouard 7281: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7282: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7283: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7284: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7285: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7286: vlv= nbcode[Tvaraff[k]][lv];
7287: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7288: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7289: }
7290: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7291: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7292: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7293: }
1.264 brouard 7294: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7295: fprintf(ficgp,"\n#\n");
7296: if(invalidvarcomb[k1]){
7297: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7298: continue;
7299: }
7300:
7301: /* k=2+nlstate*(2*cpt-2); */
7302: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 7303: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.264 brouard 7304: fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
1.238 brouard 7305: fprintf(ficgp,"set ter svg size 640, 480\n\
1.261 brouard 7306: 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 7307: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7308: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7309: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
7310: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
7311: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
7312: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 7313:
1.238 brouard 7314: */
7315: for (i=1; i< nlstate ; i ++) {
1.261 brouard 7316: 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 7317: /* 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 7318:
1.238 brouard 7319: }
1.261 brouard 7320: 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 7321: }
1.264 brouard 7322: fprintf(ficgp,"\nunset label;\n");
1.238 brouard 7323: } /* end nres */
7324: } /* end kl 3eme */
1.126 brouard 7325:
1.223 brouard 7326: /* 4eme */
1.201 brouard 7327: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 7328: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
7329: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7330: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 7331: continue;
1.238 brouard 7332: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
1.264 brouard 7333: strcpy(gplotlabel,"(");
1.238 brouard 7334: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
7335: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7336: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7337: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7338: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7339: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7340: vlv= nbcode[Tvaraff[k]][lv];
7341: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7342: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7343: }
7344: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7345: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7346: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7347: }
1.264 brouard 7348: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7349: fprintf(ficgp,"\n#\n");
7350: if(invalidvarcomb[k1]){
7351: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7352: continue;
1.223 brouard 7353: }
1.238 brouard 7354:
1.241 brouard 7355: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.264 brouard 7356: 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 7357: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7358: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7359: k=3;
7360: for (i=1; i<= nlstate ; i ++){
7361: if(i==1){
7362: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7363: }else{
7364: fprintf(ficgp,", '' ");
7365: }
7366: l=(nlstate+ndeath)*(i-1)+1;
7367: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7368: for (j=2; j<= nlstate+ndeath ; j ++)
7369: fprintf(ficgp,"+$%d",k+l+j-1);
7370: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
7371: } /* nlstate */
1.264 brouard 7372: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7373: } /* end cpt state*/
7374: } /* end nres */
7375: } /* end covariate k1 */
7376:
1.220 brouard 7377: /* 5eme */
1.201 brouard 7378: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 7379: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
7380: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7381: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 7382: continue;
1.238 brouard 7383: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.264 brouard 7384: strcpy(gplotlabel,"(");
1.238 brouard 7385: 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);
7386: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7387: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7388: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7389: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7390: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7391: vlv= nbcode[Tvaraff[k]][lv];
7392: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7393: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.238 brouard 7394: }
7395: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7396: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7397: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 7398: }
1.264 brouard 7399: strcpy(gplotlabel+strlen(gplotlabel),")");
1.238 brouard 7400: fprintf(ficgp,"\n#\n");
7401: if(invalidvarcomb[k1]){
7402: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7403: continue;
7404: }
1.227 brouard 7405:
1.241 brouard 7406: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.264 brouard 7407: 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 7408: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
7409: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7410: k=3;
7411: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7412: if(j==1)
7413: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7414: else
7415: fprintf(ficgp,", '' ");
7416: l=(nlstate+ndeath)*(cpt-1) +j;
7417: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
7418: /* for (i=2; i<= nlstate+ndeath ; i ++) */
7419: /* fprintf(ficgp,"+$%d",k+l+i-1); */
7420: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
7421: } /* nlstate */
7422: fprintf(ficgp,", '' ");
7423: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
7424: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
7425: l=(nlstate+ndeath)*(cpt-1) +j;
7426: if(j < nlstate)
7427: fprintf(ficgp,"$%d +",k+l);
7428: else
7429: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
7430: }
1.264 brouard 7431: fprintf(ficgp,"\nset out; unset label;\n");
1.238 brouard 7432: } /* end cpt state*/
7433: } /* end covariate */
7434: } /* end nres */
1.227 brouard 7435:
1.220 brouard 7436: /* 6eme */
1.202 brouard 7437: /* CV preval stable (period) for each covariate */
1.237 brouard 7438: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7439: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7440: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7441: continue;
1.255 brouard 7442: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.264 brouard 7443: strcpy(gplotlabel,"(");
1.211 brouard 7444: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 7445: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 7446: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7447: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7448: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7449: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7450: vlv= nbcode[Tvaraff[k]][lv];
7451: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7452: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 7453: }
1.237 brouard 7454: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7455: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7456: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7457: }
1.264 brouard 7458: strcpy(gplotlabel+strlen(gplotlabel),")");
1.211 brouard 7459: fprintf(ficgp,"\n#\n");
1.223 brouard 7460: if(invalidvarcomb[k1]){
1.227 brouard 7461: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7462: continue;
1.223 brouard 7463: }
1.227 brouard 7464:
1.241 brouard 7465: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.264 brouard 7466: 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 7467: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7468: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 7469: k=3; /* Offset */
1.255 brouard 7470: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7471: if(i==1)
7472: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
7473: else
7474: fprintf(ficgp,", '' ");
1.255 brouard 7475: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7476: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
7477: for (j=2; j<= nlstate ; j ++)
7478: fprintf(ficgp,"+$%d",k+l+j-1);
7479: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 7480: } /* nlstate */
1.264 brouard 7481: fprintf(ficgp,"\nset out; unset label;\n");
1.153 brouard 7482: } /* end cpt state*/
7483: } /* end covariate */
1.227 brouard 7484:
7485:
1.220 brouard 7486: /* 7eme */
1.218 brouard 7487: if(backcast == 1){
1.217 brouard 7488: /* CV back preval stable (period) for each covariate */
1.237 brouard 7489: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7490: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7491: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7492: continue;
1.268 brouard 7493: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
1.264 brouard 7494: strcpy(gplotlabel,"(");
7495: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 7496: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
7497: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
7498: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7499: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 7500: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 7501: vlv= nbcode[Tvaraff[k]][lv];
7502: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7503: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7504: }
1.237 brouard 7505: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7506: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7507: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7508: }
1.264 brouard 7509: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7510: fprintf(ficgp,"\n#\n");
7511: if(invalidvarcomb[k1]){
7512: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7513: continue;
7514: }
7515:
1.241 brouard 7516: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.268 brouard 7517: 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 7518: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7519: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7520: k=3; /* Offset */
1.268 brouard 7521: for (i=1; i<= nlstate ; i ++){ /* State of arrival */
1.227 brouard 7522: if(i==1)
7523: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7524: else
7525: fprintf(ficgp,", '' ");
7526: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 brouard 7527: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7528: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7529: /* 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 7530: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7531: /* for (j=2; j<= nlstate ; j ++) */
7532: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7533: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
1.268 brouard 7534: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
1.227 brouard 7535: } /* nlstate */
1.264 brouard 7536: fprintf(ficgp,"\nset out; unset label;\n");
1.218 brouard 7537: } /* end cpt state*/
7538: } /* end covariate */
7539: } /* End if backcast */
7540:
1.223 brouard 7541: /* 8eme */
1.218 brouard 7542: if(prevfcast==1){
7543: /* Projection from cross-sectional to stable (period) for each covariate */
7544:
1.237 brouard 7545: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7546: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7547: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7548: continue;
1.211 brouard 7549: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.264 brouard 7550: strcpy(gplotlabel,"(");
1.227 brouard 7551: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
7552: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7553: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7554: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7555: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7556: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7557: vlv= nbcode[Tvaraff[k]][lv];
7558: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.264 brouard 7559: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
1.227 brouard 7560: }
1.237 brouard 7561: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7562: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7563: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7564: }
1.264 brouard 7565: strcpy(gplotlabel+strlen(gplotlabel),")");
1.227 brouard 7566: fprintf(ficgp,"\n#\n");
7567: if(invalidvarcomb[k1]){
7568: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7569: continue;
7570: }
7571:
7572: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7573: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.264 brouard 7574: 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 7575: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7576: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.266 brouard 7577:
7578: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7579: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7580: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7581: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
1.227 brouard 7582: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7583: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7584: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7585: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
1.266 brouard 7586: if(i==istart){
1.227 brouard 7587: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7588: }else{
7589: fprintf(ficgp,",\\\n '' ");
7590: }
7591: if(cptcoveff ==0){ /* No covariate */
7592: ioffset=2; /* Age is in 2 */
7593: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7594: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7595: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7596: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7597: fprintf(ficgp," u %d:(", ioffset);
1.266 brouard 7598: if(i==nlstate+1){
1.270 brouard 7599: fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
1.266 brouard 7600: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7601: fprintf(ficgp,",\\\n '' ");
7602: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7603: fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
1.266 brouard 7604: offyear, \
1.268 brouard 7605: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
1.266 brouard 7606: }else
1.227 brouard 7607: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7608: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7609: }else{ /* more than 2 covariates */
1.270 brouard 7610: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7611: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7612: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7613: iyearc=ioffset-1;
7614: iagec=ioffset;
1.227 brouard 7615: fprintf(ficgp," u %d:(",ioffset);
7616: kl=0;
7617: strcpy(gplotcondition,"(");
7618: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7619: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7620: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7621: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7622: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7623: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7624: kl++;
7625: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7626: kl++;
7627: if(k <cptcoveff && cptcoveff>1)
7628: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7629: }
7630: strcpy(gplotcondition+strlen(gplotcondition),")");
7631: /* 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 *\/ */
7632: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7633: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7634: /* '' 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*/
7635: if(i==nlstate+1){
1.270 brouard 7636: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
7637: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
1.266 brouard 7638: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7639: fprintf(ficgp," u %d:(",iagec);
7640: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
7641: iyearc, iagec, offyear, \
7642: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
1.266 brouard 7643: /* '' 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 7644: }else{
7645: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7646: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7647: }
7648: } /* end if covariate */
7649: } /* nlstate */
1.264 brouard 7650: fprintf(ficgp,"\nset out; unset label;\n");
1.223 brouard 7651: } /* end cpt state*/
7652: } /* end covariate */
7653: } /* End if prevfcast */
1.227 brouard 7654:
1.268 brouard 7655: if(backcast==1){
7656: /* Back projection from cross-sectional to stable (mixed) for each covariate */
7657:
7658: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7659: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
7660: if(m != 1 && TKresult[nres]!= k1)
7661: continue;
7662: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
7663: strcpy(gplotlabel,"(");
7664: fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
7665: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7666: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7667: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7668: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7669: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7670: vlv= nbcode[Tvaraff[k]][lv];
7671: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7672: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7673: }
7674: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7675: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7676: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7677: }
7678: strcpy(gplotlabel+strlen(gplotlabel),")");
7679: fprintf(ficgp,"\n#\n");
7680: if(invalidvarcomb[k1]){
7681: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7682: continue;
7683: }
7684:
7685: fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
7686: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
7687: fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
7688: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
7689: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
7690:
7691: /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
7692: istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
7693: /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
7694: for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7695: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7696: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7697: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7698: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7699: if(i==istart){
7700: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
7701: }else{
7702: fprintf(ficgp,",\\\n '' ");
7703: }
7704: if(cptcoveff ==0){ /* No covariate */
7705: ioffset=2; /* Age is in 2 */
7706: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7707: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7708: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7709: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7710: fprintf(ficgp," u %d:(", ioffset);
7711: if(i==nlstate+1){
1.270 brouard 7712: fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
1.268 brouard 7713: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7714: fprintf(ficgp,",\\\n '' ");
7715: fprintf(ficgp," u %d:(",ioffset);
1.270 brouard 7716: fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
1.268 brouard 7717: offbyear, \
7718: ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
7719: }else
7720: fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
7721: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
7722: }else{ /* more than 2 covariates */
1.270 brouard 7723: ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
7724: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7725: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7726: iyearc=ioffset-1;
7727: iagec=ioffset;
1.268 brouard 7728: fprintf(ficgp," u %d:(",ioffset);
7729: kl=0;
7730: strcpy(gplotcondition,"(");
7731: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7732: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7733: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7734: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7735: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7736: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7737: kl++;
7738: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7739: kl++;
7740: if(k <cptcoveff && cptcoveff>1)
7741: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7742: }
7743: strcpy(gplotcondition+strlen(gplotcondition),")");
7744: /* 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 *\/ */
7745: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7746: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7747: /* '' 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*/
7748: if(i==nlstate+1){
1.270 brouard 7749: fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
7750: ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
1.268 brouard 7751: fprintf(ficgp,",\\\n '' ");
1.270 brouard 7752: fprintf(ficgp," u %d:(",iagec);
1.268 brouard 7753: /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
1.270 brouard 7754: fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
7755: iyearc,iagec,offbyear, \
7756: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
1.268 brouard 7757: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
7758: }else{
7759: /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
7760: fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
7761: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
7762: }
7763: } /* end if covariate */
7764: } /* nlstate */
7765: fprintf(ficgp,"\nset out; unset label;\n");
7766: } /* end cpt state*/
7767: } /* end covariate */
7768: } /* End if backcast */
7769:
1.227 brouard 7770:
1.238 brouard 7771: /* 9eme writing MLE parameters */
7772: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7773: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7774: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7775: for(k=1; k <=(nlstate+ndeath); k++){
7776: if (k != i) {
1.227 brouard 7777: fprintf(ficgp,"# current state %d\n",k);
7778: for(j=1; j <=ncovmodel; j++){
7779: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7780: jk++;
7781: }
7782: fprintf(ficgp,"\n");
1.126 brouard 7783: }
7784: }
1.223 brouard 7785: }
1.187 brouard 7786: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7787:
1.145 brouard 7788: /*goto avoid;*/
1.238 brouard 7789: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7790: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7791: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7792: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7793: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7794: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7795: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7796: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7797: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7798: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7799: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7800: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7801: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7802: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7803: fprintf(ficgp,"#\n");
1.223 brouard 7804: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7805: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7806: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7807: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.264 brouard 7808: fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7809: for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
1.237 brouard 7810: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.264 brouard 7811: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7812: continue;
1.264 brouard 7813: fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
7814: strcpy(gplotlabel,"(");
1.276 brouard 7815: /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
1.264 brouard 7816: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7817: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7818: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7819: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7820: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7821: vlv= nbcode[Tvaraff[k]][lv];
7822: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7823: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
7824: }
1.237 brouard 7825: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7826: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.264 brouard 7827: sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.237 brouard 7828: }
1.264 brouard 7829: strcpy(gplotlabel+strlen(gplotlabel),")");
1.237 brouard 7830: fprintf(ficgp,"\n#\n");
1.264 brouard 7831: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
1.276 brouard 7832: fprintf(ficgp,"\nset key outside ");
7833: /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
7834: fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
1.223 brouard 7835: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7836: if (ng==1){
7837: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7838: fprintf(ficgp,"\nunset log y");
7839: }else if (ng==2){
7840: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7841: fprintf(ficgp,"\nset log y");
7842: }else if (ng==3){
7843: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7844: fprintf(ficgp,"\nset log y");
7845: }else
7846: fprintf(ficgp,"\nunset title ");
7847: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7848: i=1;
7849: for(k2=1; k2<=nlstate; k2++) {
7850: k3=i;
7851: for(k=1; k<=(nlstate+ndeath); k++) {
7852: if (k != k2){
7853: switch( ng) {
7854: case 1:
7855: if(nagesqr==0)
7856: fprintf(ficgp," p%d+p%d*x",i,i+1);
7857: else /* nagesqr =1 */
7858: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7859: break;
7860: case 2: /* ng=2 */
7861: if(nagesqr==0)
7862: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7863: else /* nagesqr =1 */
7864: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7865: break;
7866: case 3:
7867: if(nagesqr==0)
7868: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7869: else /* nagesqr =1 */
7870: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7871: break;
7872: }
7873: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7874: ijp=1; /* product no age */
7875: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7876: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7877: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.268 brouard 7878: if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7879: if(j==Tage[ij]) { /* Product by age To be looked at!!*/
7880: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
7881: if(DummyV[j]==0){
7882: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
7883: }else{ /* quantitative */
7884: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
7885: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7886: }
7887: ij++;
1.237 brouard 7888: }
1.268 brouard 7889: }
7890: }else if(cptcovprod >0){
7891: if(j==Tprod[ijp]) { /* */
7892: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
7893: if(ijp <=cptcovprod) { /* Product */
7894: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
7895: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
7896: /* 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)]); */
7897: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
7898: }else{ /* Vn is dummy and Vm is quanti */
7899: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
7900: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7901: }
7902: }else{ /* Vn*Vm Vn is quanti */
7903: if(DummyV[Tvard[ijp][2]]==0){
7904: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
7905: }else{ /* Both quanti */
7906: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7907: }
1.237 brouard 7908: }
1.268 brouard 7909: ijp++;
1.237 brouard 7910: }
1.268 brouard 7911: } /* end Tprod */
1.237 brouard 7912: } else{ /* simple covariate */
1.264 brouard 7913: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
1.237 brouard 7914: if(Dummy[j]==0){
7915: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
7916: }else{ /* quantitative */
7917: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.264 brouard 7918: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
1.223 brouard 7919: }
1.237 brouard 7920: } /* end simple */
7921: } /* end j */
1.223 brouard 7922: }else{
7923: i=i-ncovmodel;
7924: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
7925: fprintf(ficgp," (1.");
7926: }
1.227 brouard 7927:
1.223 brouard 7928: if(ng != 1){
7929: fprintf(ficgp,")/(1");
1.227 brouard 7930:
1.264 brouard 7931: for(cpt=1; cpt <=nlstate; cpt++){
1.223 brouard 7932: if(nagesqr==0)
1.264 brouard 7933: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
1.223 brouard 7934: else /* nagesqr =1 */
1.264 brouard 7935: 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 7936:
1.223 brouard 7937: ij=1;
7938: for(j=3; j <=ncovmodel-nagesqr; j++){
1.268 brouard 7939: if(cptcovage >0){
7940: if((j-2)==Tage[ij]) { /* Bug valgrind */
7941: if(ij <=cptcovage) { /* Bug valgrind */
7942: fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
7943: /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
7944: ij++;
7945: }
7946: }
7947: }else
7948: 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 7949: }
7950: fprintf(ficgp,")");
7951: }
7952: fprintf(ficgp,")");
7953: if(ng ==2)
1.276 brouard 7954: 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 7955: else /* ng= 3 */
1.276 brouard 7956: 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 7957: }else{ /* end ng <> 1 */
7958: if( k !=k2) /* logit p11 is hard to draw */
1.276 brouard 7959: 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 7960: }
7961: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
7962: fprintf(ficgp,",");
7963: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
7964: fprintf(ficgp,",");
7965: i=i+ncovmodel;
7966: } /* end k */
7967: } /* end k2 */
1.276 brouard 7968: /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
7969: fprintf(ficgp,"\n set out; unset title;set key default;\n");
1.264 brouard 7970: } /* end k1 */
1.223 brouard 7971: } /* end ng */
7972: /* avoid: */
7973: fflush(ficgp);
1.126 brouard 7974: } /* end gnuplot */
7975:
7976:
7977: /*************** Moving average **************/
1.219 brouard 7978: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 7979: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 7980:
1.222 brouard 7981: int i, cpt, cptcod;
7982: int modcovmax =1;
7983: int mobilavrange, mob;
7984: int iage=0;
7985:
1.266 brouard 7986: double sum=0., sumr=0.;
1.222 brouard 7987: double age;
1.266 brouard 7988: double *sumnewp, *sumnewm, *sumnewmr;
7989: double *agemingood, *agemaxgood;
7990: double *agemingoodr, *agemaxgoodr;
1.222 brouard 7991:
7992:
1.278 brouard 7993: /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
7994: /* a covariate has 2 modalities, should be equal to ncovcombmax */
1.222 brouard 7995:
7996: sumnewp = vector(1,ncovcombmax);
7997: sumnewm = vector(1,ncovcombmax);
1.266 brouard 7998: sumnewmr = vector(1,ncovcombmax);
1.222 brouard 7999: agemingood = vector(1,ncovcombmax);
1.266 brouard 8000: agemingoodr = vector(1,ncovcombmax);
1.222 brouard 8001: agemaxgood = vector(1,ncovcombmax);
1.266 brouard 8002: agemaxgoodr = vector(1,ncovcombmax);
1.222 brouard 8003:
8004: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.266 brouard 8005: sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
1.222 brouard 8006: sumnewp[cptcod]=0.;
1.266 brouard 8007: agemingood[cptcod]=0, agemingoodr[cptcod]=0;
8008: agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
1.222 brouard 8009: }
8010: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
8011:
1.266 brouard 8012: if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
8013: if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
1.222 brouard 8014: else mobilavrange=mobilav;
8015: for (age=bage; age<=fage; age++)
8016: for (i=1; i<=nlstate;i++)
8017: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
8018: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8019: /* We keep the original values on the extreme ages bage, fage and for
8020: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
8021: we use a 5 terms etc. until the borders are no more concerned.
8022: */
8023: for (mob=3;mob <=mobilavrange;mob=mob+2){
8024: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.266 brouard 8025: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
8026: sumnewm[cptcod]=0.;
8027: for (i=1; i<=nlstate;i++){
1.222 brouard 8028: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
8029: for (cpt=1;cpt<=(mob-1)/2;cpt++){
8030: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
8031: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
8032: }
8033: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
1.266 brouard 8034: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8035: } /* end i */
8036: if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
8037: } /* end cptcod */
1.222 brouard 8038: }/* end age */
8039: }/* end mob */
1.266 brouard 8040: }else{
8041: printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
1.222 brouard 8042: return -1;
1.266 brouard 8043: }
8044:
8045: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
1.222 brouard 8046: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
8047: if(invalidvarcomb[cptcod]){
8048: printf("\nCombination (%d) ignored because no cases \n",cptcod);
8049: continue;
8050: }
1.219 brouard 8051:
1.266 brouard 8052: for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
8053: sumnewm[cptcod]=0.;
8054: sumnewmr[cptcod]=0.;
8055: for (i=1; i<=nlstate;i++){
8056: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8057: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8058: }
8059: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8060: agemingoodr[cptcod]=age;
8061: }
8062: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8063: agemingood[cptcod]=age;
8064: }
8065: } /* age */
8066: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
1.222 brouard 8067: sumnewm[cptcod]=0.;
1.266 brouard 8068: sumnewmr[cptcod]=0.;
1.222 brouard 8069: for (i=1; i<=nlstate;i++){
8070: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8071: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8072: }
8073: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8074: agemaxgoodr[cptcod]=age;
1.222 brouard 8075: }
8076: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.266 brouard 8077: agemaxgood[cptcod]=age;
8078: }
8079: } /* age */
8080: /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
8081: /* but they will change */
8082: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
8083: sumnewm[cptcod]=0.;
8084: sumnewmr[cptcod]=0.;
8085: for (i=1; i<=nlstate;i++){
8086: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8087: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8088: }
8089: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8090: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
8091: agemaxgoodr[cptcod]=age; /* age min */
8092: for (i=1; i<=nlstate;i++)
8093: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8094: }else{ /* bad we change the value with the values of good ages */
8095: for (i=1; i<=nlstate;i++){
8096: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
8097: } /* i */
8098: } /* end bad */
8099: }else{
8100: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8101: agemaxgood[cptcod]=age;
8102: }else{ /* bad we change the value with the values of good ages */
8103: for (i=1; i<=nlstate;i++){
8104: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
8105: } /* i */
8106: } /* end bad */
8107: }/* end else */
8108: sum=0.;sumr=0.;
8109: for (i=1; i<=nlstate;i++){
8110: sum+=mobaverage[(int)age][i][cptcod];
8111: sumr+=probs[(int)age][i][cptcod];
8112: }
8113: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8114: 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 8115: } /* end bad */
8116: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8117: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8118: 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 8119: } /* end bad */
8120: }/* age */
1.266 brouard 8121:
8122: for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
1.222 brouard 8123: sumnewm[cptcod]=0.;
1.266 brouard 8124: sumnewmr[cptcod]=0.;
1.222 brouard 8125: for (i=1; i<=nlstate;i++){
8126: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
1.266 brouard 8127: sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
8128: }
8129: if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
8130: if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
8131: agemingoodr[cptcod]=age;
8132: for (i=1; i<=nlstate;i++)
8133: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
8134: }else{ /* bad we change the value with the values of good ages */
8135: for (i=1; i<=nlstate;i++){
8136: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
8137: } /* i */
8138: } /* end bad */
8139: }else{
8140: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
8141: agemingood[cptcod]=age;
8142: }else{ /* bad */
8143: for (i=1; i<=nlstate;i++){
8144: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
8145: } /* i */
8146: } /* end bad */
8147: }/* end else */
8148: sum=0.;sumr=0.;
8149: for (i=1; i<=nlstate;i++){
8150: sum+=mobaverage[(int)age][i][cptcod];
8151: sumr+=mobaverage[(int)age][i][cptcod];
1.222 brouard 8152: }
1.266 brouard 8153: if(fabs(sum - 1.) > 1.e-3) { /* bad */
1.268 brouard 8154: 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 8155: } /* end bad */
8156: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
8157: if(fabs(sumr - 1.) > 1.e-3) { /* bad */
1.268 brouard 8158: 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 8159: } /* end bad */
8160: }/* age */
1.266 brouard 8161:
1.222 brouard 8162:
8163: for (age=bage; age<=fage; age++){
1.235 brouard 8164: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 8165: sumnewp[cptcod]=0.;
8166: sumnewm[cptcod]=0.;
8167: for (i=1; i<=nlstate;i++){
8168: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
8169: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
8170: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
8171: }
8172: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
8173: }
8174: /* printf("\n"); */
8175: /* } */
1.266 brouard 8176:
1.222 brouard 8177: /* brutal averaging */
1.266 brouard 8178: /* for (i=1; i<=nlstate;i++){ */
8179: /* for (age=1; age<=bage; age++){ */
8180: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
8181: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8182: /* } */
8183: /* for (age=fage; age<=AGESUP; age++){ */
8184: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
8185: /* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
8186: /* } */
8187: /* } /\* end i status *\/ */
8188: /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
8189: /* for (age=1; age<=AGESUP; age++){ */
8190: /* /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
8191: /* mobaverage[(int)age][i][cptcod]=0.; */
8192: /* } */
8193: /* } */
1.222 brouard 8194: }/* end cptcod */
1.266 brouard 8195: free_vector(agemaxgoodr,1, ncovcombmax);
8196: free_vector(agemaxgood,1, ncovcombmax);
8197: free_vector(agemingood,1, ncovcombmax);
8198: free_vector(agemingoodr,1, ncovcombmax);
8199: free_vector(sumnewmr,1, ncovcombmax);
1.222 brouard 8200: free_vector(sumnewm,1, ncovcombmax);
8201: free_vector(sumnewp,1, ncovcombmax);
8202: return 0;
8203: }/* End movingaverage */
1.218 brouard 8204:
1.126 brouard 8205:
8206: /************** Forecasting ******************/
1.269 brouard 8207: 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 8208: /* proj1, year, month, day of starting projection
8209: agemin, agemax range of age
8210: dateprev1 dateprev2 range of dates during which prevalence is computed
8211: anproj2 year of en of projection (same day and month as proj1).
8212: */
1.267 brouard 8213: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 8214: double agec; /* generic age */
8215: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
8216: double *popeffectif,*popcount;
8217: double ***p3mat;
1.218 brouard 8218: /* double ***mobaverage; */
1.126 brouard 8219: char fileresf[FILENAMELENGTH];
8220:
8221: agelim=AGESUP;
1.211 brouard 8222: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8223: in each health status at the date of interview (if between dateprev1 and dateprev2).
8224: We still use firstpass and lastpass as another selection.
8225: */
1.214 brouard 8226: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8227: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 8228:
1.201 brouard 8229: strcpy(fileresf,"F_");
8230: strcat(fileresf,fileresu);
1.126 brouard 8231: if((ficresf=fopen(fileresf,"w"))==NULL) {
8232: printf("Problem with forecast resultfile: %s\n", fileresf);
8233: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
8234: }
1.235 brouard 8235: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
8236: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 8237:
1.225 brouard 8238: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 8239:
8240:
8241: stepsize=(int) (stepm+YEARM-1)/YEARM;
8242: if (stepm<=12) stepsize=1;
8243: if(estepm < stepm){
8244: printf ("Problem %d lower than %d\n",estepm, stepm);
8245: }
1.270 brouard 8246: else{
8247: hstepm=estepm;
8248: }
8249: if(estepm > stepm){ /* Yes every two year */
8250: stepsize=2;
8251: }
1.126 brouard 8252:
8253: hstepm=hstepm/stepm;
8254: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8255: fractional in yp1 */
8256: anprojmean=yp;
8257: yp2=modf((yp1*12),&yp);
8258: mprojmean=yp;
8259: yp1=modf((yp2*30.5),&yp);
8260: jprojmean=yp;
8261: if(jprojmean==0) jprojmean=1;
8262: if(mprojmean==0) jprojmean=1;
8263:
1.227 brouard 8264: i1=pow(2,cptcoveff);
1.126 brouard 8265: if (cptcovn < 1){i1=1;}
8266:
8267: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
8268:
8269: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 8270:
1.126 brouard 8271: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 8272: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8273: for(k=1; k<=i1;k++){
1.253 brouard 8274: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 8275: continue;
1.227 brouard 8276: if(invalidvarcomb[k]){
8277: printf("\nCombination (%d) projection ignored because no cases \n",k);
8278: continue;
8279: }
8280: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
8281: for(j=1;j<=cptcoveff;j++) {
8282: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8283: }
1.235 brouard 8284: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 8285: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 8286: }
1.227 brouard 8287: fprintf(ficresf," yearproj age");
8288: for(j=1; j<=nlstate+ndeath;j++){
8289: for(i=1; i<=nlstate;i++)
8290: fprintf(ficresf," p%d%d",i,j);
8291: fprintf(ficresf," wp.%d",j);
8292: }
8293: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
8294: fprintf(ficresf,"\n");
8295: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
1.270 brouard 8296: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
8297: for (agec=fage; agec>=(bage); agec--){
1.227 brouard 8298: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
8299: nhstepm = nhstepm/hstepm;
8300: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8301: oldm=oldms;savm=savms;
1.268 brouard 8302: /* We compute pii at age agec over nhstepm);*/
1.235 brouard 8303: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.268 brouard 8304: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
1.227 brouard 8305: for (h=0; h<=nhstepm; h++){
8306: if (h*hstepm/YEARM*stepm ==yearp) {
1.268 brouard 8307: break;
8308: }
8309: }
8310: fprintf(ficresf,"\n");
8311: for(j=1;j<=cptcoveff;j++)
8312: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8313: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
8314:
8315: for(j=1; j<=nlstate+ndeath;j++) {
8316: ppij=0.;
8317: for(i=1; i<=nlstate;i++) {
1.278 brouard 8318: if (mobilav>=1)
8319: ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
8320: else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
8321: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
8322: }
1.268 brouard 8323: fprintf(ficresf," %.3f", p3mat[i][j][h]);
8324: } /* end i */
8325: fprintf(ficresf," %.3f", ppij);
8326: }/* end j */
1.227 brouard 8327: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8328: } /* end agec */
1.266 brouard 8329: /* diffyear=(int) anproj1+yearp-ageminpar-1; */
8330: /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
1.227 brouard 8331: } /* end yearp */
8332: } /* end k */
1.219 brouard 8333:
1.126 brouard 8334: fclose(ficresf);
1.215 brouard 8335: printf("End of Computing forecasting \n");
8336: fprintf(ficlog,"End of Computing forecasting\n");
8337:
1.126 brouard 8338: }
8339:
1.269 brouard 8340: /************** Back Forecasting ******************/
8341: 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 8342: /* back1, year, month, day of starting backection
8343: agemin, agemax range of age
8344: dateprev1 dateprev2 range of dates during which prevalence is computed
1.269 brouard 8345: anback2 year of end of backprojection (same day and month as back1).
8346: prevacurrent and prev are prevalences.
1.267 brouard 8347: */
8348: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
8349: double agec; /* generic age */
1.268 brouard 8350: double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
1.267 brouard 8351: double *popeffectif,*popcount;
8352: double ***p3mat;
8353: /* double ***mobaverage; */
8354: char fileresfb[FILENAMELENGTH];
8355:
1.268 brouard 8356: agelim=AGEINF;
1.267 brouard 8357: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
8358: in each health status at the date of interview (if between dateprev1 and dateprev2).
8359: We still use firstpass and lastpass as another selection.
8360: */
8361: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
8362: /* firstpass, lastpass, stepm, weightopt, model); */
8363:
8364: /*Do we need to compute prevalence again?*/
8365:
8366: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
8367:
8368: strcpy(fileresfb,"FB_");
8369: strcat(fileresfb,fileresu);
8370: if((ficresfb=fopen(fileresfb,"w"))==NULL) {
8371: printf("Problem with back forecast resultfile: %s\n", fileresfb);
8372: fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
8373: }
8374: printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8375: fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
8376:
8377: if (cptcoveff==0) ncodemax[cptcoveff]=1;
8378:
8379:
8380: stepsize=(int) (stepm+YEARM-1)/YEARM;
8381: if (stepm<=12) stepsize=1;
8382: if(estepm < stepm){
8383: printf ("Problem %d lower than %d\n",estepm, stepm);
8384: }
1.270 brouard 8385: else{
8386: hstepm=estepm;
8387: }
8388: if(estepm >= stepm){ /* Yes every two year */
8389: stepsize=2;
8390: }
1.267 brouard 8391:
8392: hstepm=hstepm/stepm;
8393: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
8394: fractional in yp1 */
8395: anprojmean=yp;
8396: yp2=modf((yp1*12),&yp);
8397: mprojmean=yp;
8398: yp1=modf((yp2*30.5),&yp);
8399: jprojmean=yp;
8400: if(jprojmean==0) jprojmean=1;
8401: if(mprojmean==0) jprojmean=1;
8402:
8403: i1=pow(2,cptcoveff);
8404: if (cptcovn < 1){i1=1;}
8405:
8406: fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.268 brouard 8407: printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
1.267 brouard 8408:
8409: fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
8410:
8411: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8412: for(k=1; k<=i1;k++){
8413: if(i1 != 1 && TKresult[nres]!= k)
8414: continue;
8415: if(invalidvarcomb[k]){
8416: printf("\nCombination (%d) projection ignored because no cases \n",k);
8417: continue;
8418: }
1.268 brouard 8419: fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
1.267 brouard 8420: for(j=1;j<=cptcoveff;j++) {
8421: fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8422: }
8423: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
8424: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
8425: }
8426: fprintf(ficresfb," yearbproj age");
8427: for(j=1; j<=nlstate+ndeath;j++){
8428: for(i=1; i<=nlstate;i++)
1.268 brouard 8429: fprintf(ficresfb," b%d%d",i,j);
8430: fprintf(ficresfb," b.%d",j);
1.267 brouard 8431: }
8432: for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
8433: /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
8434: fprintf(ficresfb,"\n");
8435: fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
1.273 brouard 8436: /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
1.270 brouard 8437: /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
8438: for (agec=bage; agec<=fage; agec++){ /* testing */
1.268 brouard 8439: /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
1.271 brouard 8440: nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
1.267 brouard 8441: nhstepm = nhstepm/hstepm;
8442: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8443: oldm=oldms;savm=savms;
1.268 brouard 8444: /* computes hbxij at age agec over 1 to nhstepm */
1.271 brouard 8445: /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
1.267 brouard 8446: hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.268 brouard 8447: /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
8448: /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
8449: /* printf(" agec=%.2f\n",agec);fflush(stdout); */
1.267 brouard 8450: for (h=0; h<=nhstepm; h++){
1.268 brouard 8451: if (h*hstepm/YEARM*stepm ==-yearp) {
8452: break;
8453: }
8454: }
8455: fprintf(ficresfb,"\n");
8456: for(j=1;j<=cptcoveff;j++)
8457: fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8458: fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
8459: for(i=1; i<=nlstate+ndeath;i++) {
8460: ppij=0.;ppi=0.;
8461: for(j=1; j<=nlstate;j++) {
8462: /* if (mobilav==1) */
1.269 brouard 8463: ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
8464: ppi=ppi+prevacurrent[(int)agec][j][k];
8465: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
8466: /* ppi=ppi+mobaverage[(int)agec][j][k]; */
1.267 brouard 8467: /* else { */
8468: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
8469: /* } */
1.268 brouard 8470: fprintf(ficresfb," %.3f", p3mat[i][j][h]);
8471: } /* end j */
8472: if(ppi <0.99){
8473: printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8474: fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
8475: }
8476: fprintf(ficresfb," %.3f", ppij);
8477: }/* end j */
1.267 brouard 8478: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8479: } /* end agec */
8480: } /* end yearp */
8481: } /* end k */
1.217 brouard 8482:
1.267 brouard 8483: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
1.217 brouard 8484:
1.267 brouard 8485: fclose(ficresfb);
8486: printf("End of Computing Back forecasting \n");
8487: fprintf(ficlog,"End of Computing Back forecasting\n");
1.218 brouard 8488:
1.267 brouard 8489: }
1.217 brouard 8490:
1.269 brouard 8491: /* Variance of prevalence limit: varprlim */
8492: 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){
8493: /*------- Variance of period (stable) prevalence------*/
8494:
8495: char fileresvpl[FILENAMELENGTH];
8496: FILE *ficresvpl;
8497: double **oldm, **savm;
8498: double **varpl; /* Variances of prevalence limits by age */
8499: int i1, k, nres, j ;
8500:
8501: strcpy(fileresvpl,"VPL_");
8502: strcat(fileresvpl,fileresu);
8503: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8504: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8505: exit(0);
8506: }
8507: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8508: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
8509:
8510: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8511: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8512:
8513: i1=pow(2,cptcoveff);
8514: if (cptcovn < 1){i1=1;}
8515:
8516: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8517: for(k=1; k<=i1;k++){
8518: if(i1 != 1 && TKresult[nres]!= k)
8519: continue;
8520: fprintf(ficresvpl,"\n#****** ");
8521: printf("\n#****** ");
8522: fprintf(ficlog,"\n#****** ");
8523: for(j=1;j<=cptcoveff;j++) {
8524: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8525: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8526: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8527: }
8528: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8529: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8530: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8531: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8532: }
8533: fprintf(ficresvpl,"******\n");
8534: printf("******\n");
8535: fprintf(ficlog,"******\n");
8536:
8537: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8538: oldm=oldms;savm=savms;
8539: varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
8540: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
8541: /*}*/
8542: }
8543:
8544: fclose(ficresvpl);
8545: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8546: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
8547:
8548: }
8549: /* Variance of back prevalence: varbprlim */
8550: 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){
8551: /*------- Variance of back (stable) prevalence------*/
8552:
8553: char fileresvbl[FILENAMELENGTH];
8554: FILE *ficresvbl;
8555:
8556: double **oldm, **savm;
8557: double **varbpl; /* Variances of back prevalence limits by age */
8558: int i1, k, nres, j ;
8559:
8560: strcpy(fileresvbl,"VBL_");
8561: strcat(fileresvbl,fileresu);
8562: if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
8563: printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
8564: exit(0);
8565: }
8566: printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
8567: fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
8568:
8569:
8570: i1=pow(2,cptcoveff);
8571: if (cptcovn < 1){i1=1;}
8572:
8573: for(nres=1; nres <= nresult; nres++) /* For each resultline */
8574: for(k=1; k<=i1;k++){
8575: if(i1 != 1 && TKresult[nres]!= k)
8576: continue;
8577: fprintf(ficresvbl,"\n#****** ");
8578: printf("\n#****** ");
8579: fprintf(ficlog,"\n#****** ");
8580: for(j=1;j<=cptcoveff;j++) {
8581: fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8582: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8583: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8584: }
8585: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
8586: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8587: fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8588: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
8589: }
8590: fprintf(ficresvbl,"******\n");
8591: printf("******\n");
8592: fprintf(ficlog,"******\n");
8593:
8594: varbpl=matrix(1,nlstate,(int) bage, (int) fage);
8595: oldm=oldms;savm=savms;
8596:
8597: varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
8598: free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
8599: /*}*/
8600: }
8601:
8602: fclose(ficresvbl);
8603: printf("done variance-covariance of back prevalence\n");fflush(stdout);
8604: fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
8605:
8606: } /* End of varbprlim */
8607:
1.126 brouard 8608: /************** Forecasting *****not tested NB*************/
1.227 brouard 8609: /* 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 8610:
1.227 brouard 8611: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
8612: /* int *popage; */
8613: /* double calagedatem, agelim, kk1, kk2; */
8614: /* double *popeffectif,*popcount; */
8615: /* double ***p3mat,***tabpop,***tabpopprev; */
8616: /* /\* double ***mobaverage; *\/ */
8617: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 8618:
1.227 brouard 8619: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8620: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8621: /* agelim=AGESUP; */
8622: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 8623:
1.227 brouard 8624: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 8625:
8626:
1.227 brouard 8627: /* strcpy(filerespop,"POP_"); */
8628: /* strcat(filerespop,fileresu); */
8629: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
8630: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
8631: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
8632: /* } */
8633: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
8634: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 8635:
1.227 brouard 8636: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 8637:
1.227 brouard 8638: /* /\* if (mobilav!=0) { *\/ */
8639: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
8640: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
8641: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8642: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
8643: /* /\* } *\/ */
8644: /* /\* } *\/ */
1.126 brouard 8645:
1.227 brouard 8646: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
8647: /* if (stepm<=12) stepsize=1; */
1.126 brouard 8648:
1.227 brouard 8649: /* agelim=AGESUP; */
1.126 brouard 8650:
1.227 brouard 8651: /* hstepm=1; */
8652: /* hstepm=hstepm/stepm; */
1.218 brouard 8653:
1.227 brouard 8654: /* if (popforecast==1) { */
8655: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
8656: /* printf("Problem with population file : %s\n",popfile);exit(0); */
8657: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
8658: /* } */
8659: /* popage=ivector(0,AGESUP); */
8660: /* popeffectif=vector(0,AGESUP); */
8661: /* popcount=vector(0,AGESUP); */
1.126 brouard 8662:
1.227 brouard 8663: /* i=1; */
8664: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 8665:
1.227 brouard 8666: /* imx=i; */
8667: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
8668: /* } */
1.218 brouard 8669:
1.227 brouard 8670: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
8671: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
8672: /* k=k+1; */
8673: /* fprintf(ficrespop,"\n#******"); */
8674: /* for(j=1;j<=cptcoveff;j++) { */
8675: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
8676: /* } */
8677: /* fprintf(ficrespop,"******\n"); */
8678: /* fprintf(ficrespop,"# Age"); */
8679: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
8680: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 8681:
1.227 brouard 8682: /* for (cpt=0; cpt<=0;cpt++) { */
8683: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 8684:
1.227 brouard 8685: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8686: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8687: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8688:
1.227 brouard 8689: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8690: /* oldm=oldms;savm=savms; */
8691: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 8692:
1.227 brouard 8693: /* for (h=0; h<=nhstepm; h++){ */
8694: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8695: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8696: /* } */
8697: /* for(j=1; j<=nlstate+ndeath;j++) { */
8698: /* kk1=0.;kk2=0; */
8699: /* for(i=1; i<=nlstate;i++) { */
8700: /* if (mobilav==1) */
8701: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
8702: /* else { */
8703: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
8704: /* } */
8705: /* } */
8706: /* if (h==(int)(calagedatem+12*cpt)){ */
8707: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
8708: /* /\*fprintf(ficrespop," %.3f", kk1); */
8709: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
8710: /* } */
8711: /* } */
8712: /* for(i=1; i<=nlstate;i++){ */
8713: /* kk1=0.; */
8714: /* for(j=1; j<=nlstate;j++){ */
8715: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
8716: /* } */
8717: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
8718: /* } */
1.218 brouard 8719:
1.227 brouard 8720: /* if (h==(int)(calagedatem+12*cpt)) */
8721: /* for(j=1; j<=nlstate;j++) */
8722: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
8723: /* } */
8724: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8725: /* } */
8726: /* } */
1.218 brouard 8727:
1.227 brouard 8728: /* /\******\/ */
1.218 brouard 8729:
1.227 brouard 8730: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
8731: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
8732: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
8733: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
8734: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 8735:
1.227 brouard 8736: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8737: /* oldm=oldms;savm=savms; */
8738: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8739: /* for (h=0; h<=nhstepm; h++){ */
8740: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
8741: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
8742: /* } */
8743: /* for(j=1; j<=nlstate+ndeath;j++) { */
8744: /* kk1=0.;kk2=0; */
8745: /* for(i=1; i<=nlstate;i++) { */
8746: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
8747: /* } */
8748: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
8749: /* } */
8750: /* } */
8751: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
8752: /* } */
8753: /* } */
8754: /* } */
8755: /* } */
1.218 brouard 8756:
1.227 brouard 8757: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 8758:
1.227 brouard 8759: /* if (popforecast==1) { */
8760: /* free_ivector(popage,0,AGESUP); */
8761: /* free_vector(popeffectif,0,AGESUP); */
8762: /* free_vector(popcount,0,AGESUP); */
8763: /* } */
8764: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8765: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
8766: /* fclose(ficrespop); */
8767: /* } /\* End of popforecast *\/ */
1.218 brouard 8768:
1.126 brouard 8769: int fileappend(FILE *fichier, char *optionfich)
8770: {
8771: if((fichier=fopen(optionfich,"a"))==NULL) {
8772: printf("Problem with file: %s\n", optionfich);
8773: fprintf(ficlog,"Problem with file: %s\n", optionfich);
8774: return (0);
8775: }
8776: fflush(fichier);
8777: return (1);
8778: }
8779:
8780:
8781: /**************** function prwizard **********************/
8782: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
8783: {
8784:
8785: /* Wizard to print covariance matrix template */
8786:
1.164 brouard 8787: char ca[32], cb[32];
8788: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 8789: int numlinepar;
8790:
8791: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8792: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8793: for(i=1; i <=nlstate; i++){
8794: jj=0;
8795: for(j=1; j <=nlstate+ndeath; j++){
8796: if(j==i) continue;
8797: jj++;
8798: /*ca[0]= k+'a'-1;ca[1]='\0';*/
8799: printf("%1d%1d",i,j);
8800: fprintf(ficparo,"%1d%1d",i,j);
8801: for(k=1; k<=ncovmodel;k++){
8802: /* printf(" %lf",param[i][j][k]); */
8803: /* fprintf(ficparo," %lf",param[i][j][k]); */
8804: printf(" 0.");
8805: fprintf(ficparo," 0.");
8806: }
8807: printf("\n");
8808: fprintf(ficparo,"\n");
8809: }
8810: }
8811: printf("# Scales (for hessian or gradient estimation)\n");
8812: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
8813: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
8814: for(i=1; i <=nlstate; i++){
8815: jj=0;
8816: for(j=1; j <=nlstate+ndeath; j++){
8817: if(j==i) continue;
8818: jj++;
8819: fprintf(ficparo,"%1d%1d",i,j);
8820: printf("%1d%1d",i,j);
8821: fflush(stdout);
8822: for(k=1; k<=ncovmodel;k++){
8823: /* printf(" %le",delti3[i][j][k]); */
8824: /* fprintf(ficparo," %le",delti3[i][j][k]); */
8825: printf(" 0.");
8826: fprintf(ficparo," 0.");
8827: }
8828: numlinepar++;
8829: printf("\n");
8830: fprintf(ficparo,"\n");
8831: }
8832: }
8833: printf("# Covariance matrix\n");
8834: /* # 121 Var(a12)\n\ */
8835: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8836: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8837: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8838: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8839: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8840: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8841: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8842: fflush(stdout);
8843: fprintf(ficparo,"# Covariance matrix\n");
8844: /* # 121 Var(a12)\n\ */
8845: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8846: /* # ...\n\ */
8847: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8848:
8849: for(itimes=1;itimes<=2;itimes++){
8850: jj=0;
8851: for(i=1; i <=nlstate; i++){
8852: for(j=1; j <=nlstate+ndeath; j++){
8853: if(j==i) continue;
8854: for(k=1; k<=ncovmodel;k++){
8855: jj++;
8856: ca[0]= k+'a'-1;ca[1]='\0';
8857: if(itimes==1){
8858: printf("#%1d%1d%d",i,j,k);
8859: fprintf(ficparo,"#%1d%1d%d",i,j,k);
8860: }else{
8861: printf("%1d%1d%d",i,j,k);
8862: fprintf(ficparo,"%1d%1d%d",i,j,k);
8863: /* printf(" %.5le",matcov[i][j]); */
8864: }
8865: ll=0;
8866: for(li=1;li <=nlstate; li++){
8867: for(lj=1;lj <=nlstate+ndeath; lj++){
8868: if(lj==li) continue;
8869: for(lk=1;lk<=ncovmodel;lk++){
8870: ll++;
8871: if(ll<=jj){
8872: cb[0]= lk +'a'-1;cb[1]='\0';
8873: if(ll<jj){
8874: if(itimes==1){
8875: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8876: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8877: }else{
8878: printf(" 0.");
8879: fprintf(ficparo," 0.");
8880: }
8881: }else{
8882: if(itimes==1){
8883: printf(" Var(%s%1d%1d)",ca,i,j);
8884: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
8885: }else{
8886: printf(" 0.");
8887: fprintf(ficparo," 0.");
8888: }
8889: }
8890: }
8891: } /* end lk */
8892: } /* end lj */
8893: } /* end li */
8894: printf("\n");
8895: fprintf(ficparo,"\n");
8896: numlinepar++;
8897: } /* end k*/
8898: } /*end j */
8899: } /* end i */
8900: } /* end itimes */
8901:
8902: } /* end of prwizard */
8903: /******************* Gompertz Likelihood ******************************/
8904: double gompertz(double x[])
8905: {
8906: double A,B,L=0.0,sump=0.,num=0.;
8907: int i,n=0; /* n is the size of the sample */
8908:
1.220 brouard 8909: for (i=1;i<=imx ; i++) {
1.126 brouard 8910: sump=sump+weight[i];
8911: /* sump=sump+1;*/
8912: num=num+1;
8913: }
8914:
8915:
8916: /* for (i=0; i<=imx; i++)
8917: 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]);*/
8918:
8919: for (i=1;i<=imx ; i++)
8920: {
8921: if (cens[i] == 1 && wav[i]>1)
8922: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
8923:
8924: if (cens[i] == 0 && wav[i]>1)
8925: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
8926: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
8927:
8928: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8929: if (wav[i] > 1 ) { /* ??? */
8930: L=L+A*weight[i];
8931: /* 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]);*/
8932: }
8933: }
8934:
8935: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8936:
8937: return -2*L*num/sump;
8938: }
8939:
1.136 brouard 8940: #ifdef GSL
8941: /******************* Gompertz_f Likelihood ******************************/
8942: double gompertz_f(const gsl_vector *v, void *params)
8943: {
8944: double A,B,LL=0.0,sump=0.,num=0.;
8945: double *x= (double *) v->data;
8946: int i,n=0; /* n is the size of the sample */
8947:
8948: for (i=0;i<=imx-1 ; i++) {
8949: sump=sump+weight[i];
8950: /* sump=sump+1;*/
8951: num=num+1;
8952: }
8953:
8954:
8955: /* for (i=0; i<=imx; i++)
8956: 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]);*/
8957: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
8958: for (i=1;i<=imx ; i++)
8959: {
8960: if (cens[i] == 1 && wav[i]>1)
8961: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
8962:
8963: if (cens[i] == 0 && wav[i]>1)
8964: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
8965: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
8966:
8967: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8968: if (wav[i] > 1 ) { /* ??? */
8969: LL=LL+A*weight[i];
8970: /* 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]);*/
8971: }
8972: }
8973:
8974: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8975: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
8976:
8977: return -2*LL*num/sump;
8978: }
8979: #endif
8980:
1.126 brouard 8981: /******************* Printing html file ***********/
1.201 brouard 8982: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 8983: int lastpass, int stepm, int weightopt, char model[],\
8984: int imx, double p[],double **matcov,double agemortsup){
8985: int i,k;
8986:
8987: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
8988: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
8989: for (i=1;i<=2;i++)
8990: 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 8991: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 8992: fprintf(fichtm,"</ul>");
8993:
8994: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
8995:
8996: 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>");
8997:
8998: for (k=agegomp;k<(agemortsup-2);k++)
8999: 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]);
9000:
9001:
9002: fflush(fichtm);
9003: }
9004:
9005: /******************* Gnuplot file **************/
1.201 brouard 9006: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 9007:
9008: char dirfileres[132],optfileres[132];
1.164 brouard 9009:
1.126 brouard 9010: int ng;
9011:
9012:
9013: /*#ifdef windows */
9014: fprintf(ficgp,"cd \"%s\" \n",pathc);
9015: /*#endif */
9016:
9017:
9018: strcpy(dirfileres,optionfilefiname);
9019: strcpy(optfileres,"vpl");
1.199 brouard 9020: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 9021: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 9022: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 9023: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 9024: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
9025:
9026: }
9027:
1.136 brouard 9028: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
9029: {
1.126 brouard 9030:
1.136 brouard 9031: /*-------- data file ----------*/
9032: FILE *fic;
9033: char dummy[]=" ";
1.240 brouard 9034: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 9035: int lstra;
1.136 brouard 9036: int linei, month, year,iout;
9037: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 9038: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 9039: char *stratrunc;
1.223 brouard 9040:
1.240 brouard 9041: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
9042: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 9043:
1.240 brouard 9044: for(v=1; v <=ncovcol;v++){
9045: DummyV[v]=0;
9046: FixedV[v]=0;
9047: }
9048: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
9049: DummyV[v]=1;
9050: FixedV[v]=0;
9051: }
9052: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
9053: DummyV[v]=0;
9054: FixedV[v]=1;
9055: }
9056: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
9057: DummyV[v]=1;
9058: FixedV[v]=1;
9059: }
9060: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
9061: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
9062: 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]);
9063: }
1.126 brouard 9064:
1.136 brouard 9065: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 9066: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
9067: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 9068: }
1.126 brouard 9069:
1.136 brouard 9070: i=1;
9071: linei=0;
9072: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
9073: linei=linei+1;
9074: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
9075: if(line[j] == '\t')
9076: line[j] = ' ';
9077: }
9078: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
9079: ;
9080: };
9081: line[j+1]=0; /* Trims blanks at end of line */
9082: if(line[0]=='#'){
9083: fprintf(ficlog,"Comment line\n%s\n",line);
9084: printf("Comment line\n%s\n",line);
9085: continue;
9086: }
9087: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 9088: strcpy(line, linetmp);
1.223 brouard 9089:
9090: /* Loops on waves */
9091: for (j=maxwav;j>=1;j--){
9092: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 9093: cutv(stra, strb, line, ' ');
9094: if(strb[0]=='.') { /* Missing value */
9095: lval=-1;
9096: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
9097: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
9098: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
9099: 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);
9100: 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);
9101: return 1;
9102: }
9103: }else{
9104: errno=0;
9105: /* what_kind_of_number(strb); */
9106: dval=strtod(strb,&endptr);
9107: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
9108: /* if(strb != endptr && *endptr == '\0') */
9109: /* dval=dlval; */
9110: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9111: if( strb[0]=='\0' || (*endptr != '\0')){
9112: 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);
9113: 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);
9114: return 1;
9115: }
9116: cotqvar[j][iv][i]=dval;
9117: cotvar[j][ntv+iv][i]=dval;
9118: }
9119: strcpy(line,stra);
1.223 brouard 9120: }/* end loop ntqv */
1.225 brouard 9121:
1.223 brouard 9122: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 9123: cutv(stra, strb, line, ' ');
9124: if(strb[0]=='.') { /* Missing value */
9125: lval=-1;
9126: }else{
9127: errno=0;
9128: lval=strtol(strb,&endptr,10);
9129: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9130: if( strb[0]=='\0' || (*endptr != '\0')){
9131: 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);
9132: 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);
9133: return 1;
9134: }
9135: }
9136: if(lval <-1 || lval >1){
9137: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9138: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9139: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9140: For example, for multinomial values like 1, 2 and 3,\n \
9141: build V1=0 V2=0 for the reference value (1),\n \
9142: V1=1 V2=0 for (2) \n \
1.223 brouard 9143: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9144: output of IMaCh is often meaningless.\n \
1.223 brouard 9145: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 9146: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 9147: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9148: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 9149: For example, for multinomial values like 1, 2 and 3,\n \
9150: build V1=0 V2=0 for the reference value (1),\n \
9151: V1=1 V2=0 for (2) \n \
1.223 brouard 9152: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 9153: output of IMaCh is often meaningless.\n \
1.223 brouard 9154: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 9155: return 1;
9156: }
9157: cotvar[j][iv][i]=(double)(lval);
9158: strcpy(line,stra);
1.223 brouard 9159: }/* end loop ntv */
1.225 brouard 9160:
1.223 brouard 9161: /* Statuses at wave */
1.137 brouard 9162: cutv(stra, strb, line, ' ');
1.223 brouard 9163: if(strb[0]=='.') { /* Missing value */
1.238 brouard 9164: lval=-1;
1.136 brouard 9165: }else{
1.238 brouard 9166: errno=0;
9167: lval=strtol(strb,&endptr,10);
9168: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
9169: if( strb[0]=='\0' || (*endptr != '\0')){
9170: 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);
9171: 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);
9172: return 1;
9173: }
1.136 brouard 9174: }
1.225 brouard 9175:
1.136 brouard 9176: s[j][i]=lval;
1.225 brouard 9177:
1.223 brouard 9178: /* Date of Interview */
1.136 brouard 9179: strcpy(line,stra);
9180: cutv(stra, strb,line,' ');
1.169 brouard 9181: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9182: }
1.169 brouard 9183: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 9184: month=99;
9185: year=9999;
1.136 brouard 9186: }else{
1.225 brouard 9187: 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);
9188: 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);
9189: return 1;
1.136 brouard 9190: }
9191: anint[j][i]= (double) year;
9192: mint[j][i]= (double)month;
9193: strcpy(line,stra);
1.223 brouard 9194: } /* End loop on waves */
1.225 brouard 9195:
1.223 brouard 9196: /* Date of death */
1.136 brouard 9197: cutv(stra, strb,line,' ');
1.169 brouard 9198: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9199: }
1.169 brouard 9200: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 9201: month=99;
9202: year=9999;
9203: }else{
1.141 brouard 9204: 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 9205: 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);
9206: return 1;
1.136 brouard 9207: }
9208: andc[i]=(double) year;
9209: moisdc[i]=(double) month;
9210: strcpy(line,stra);
9211:
1.223 brouard 9212: /* Date of birth */
1.136 brouard 9213: cutv(stra, strb,line,' ');
1.169 brouard 9214: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 9215: }
1.169 brouard 9216: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 9217: month=99;
9218: year=9999;
9219: }else{
1.141 brouard 9220: 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);
9221: 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 9222: return 1;
1.136 brouard 9223: }
9224: if (year==9999) {
1.141 brouard 9225: 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);
9226: 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 9227: return 1;
9228:
1.136 brouard 9229: }
9230: annais[i]=(double)(year);
9231: moisnais[i]=(double)(month);
9232: strcpy(line,stra);
1.225 brouard 9233:
1.223 brouard 9234: /* Sample weight */
1.136 brouard 9235: cutv(stra, strb,line,' ');
9236: errno=0;
9237: dval=strtod(strb,&endptr);
9238: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 9239: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
9240: 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 9241: fflush(ficlog);
9242: return 1;
9243: }
9244: weight[i]=dval;
9245: strcpy(line,stra);
1.225 brouard 9246:
1.223 brouard 9247: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
9248: cutv(stra, strb, line, ' ');
9249: if(strb[0]=='.') { /* Missing value */
1.225 brouard 9250: lval=-1;
1.223 brouard 9251: }else{
1.225 brouard 9252: errno=0;
9253: /* what_kind_of_number(strb); */
9254: dval=strtod(strb,&endptr);
9255: /* if(strb != endptr && *endptr == '\0') */
9256: /* dval=dlval; */
9257: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
9258: if( strb[0]=='\0' || (*endptr != '\0')){
9259: 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);
9260: 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);
9261: return 1;
9262: }
9263: coqvar[iv][i]=dval;
1.226 brouard 9264: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 9265: }
9266: strcpy(line,stra);
9267: }/* end loop nqv */
1.136 brouard 9268:
1.223 brouard 9269: /* Covariate values */
1.136 brouard 9270: for (j=ncovcol;j>=1;j--){
9271: cutv(stra, strb,line,' ');
1.223 brouard 9272: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 9273: lval=-1;
1.136 brouard 9274: }else{
1.225 brouard 9275: errno=0;
9276: lval=strtol(strb,&endptr,10);
9277: if( strb[0]=='\0' || (*endptr != '\0')){
9278: 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);
9279: 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);
9280: return 1;
9281: }
1.136 brouard 9282: }
9283: if(lval <-1 || lval >1){
1.225 brouard 9284: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9285: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9286: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9287: For example, for multinomial values like 1, 2 and 3,\n \
9288: build V1=0 V2=0 for the reference value (1),\n \
9289: V1=1 V2=0 for (2) \n \
1.136 brouard 9290: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9291: output of IMaCh is often meaningless.\n \
1.136 brouard 9292: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 9293: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 9294: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
9295: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 9296: For example, for multinomial values like 1, 2 and 3,\n \
9297: build V1=0 V2=0 for the reference value (1),\n \
9298: V1=1 V2=0 for (2) \n \
1.136 brouard 9299: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 9300: output of IMaCh is often meaningless.\n \
1.136 brouard 9301: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 9302: return 1;
1.136 brouard 9303: }
9304: covar[j][i]=(double)(lval);
9305: strcpy(line,stra);
9306: }
9307: lstra=strlen(stra);
1.225 brouard 9308:
1.136 brouard 9309: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
9310: stratrunc = &(stra[lstra-9]);
9311: num[i]=atol(stratrunc);
9312: }
9313: else
9314: num[i]=atol(stra);
9315: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
9316: 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;}*/
9317:
9318: i=i+1;
9319: } /* End loop reading data */
1.225 brouard 9320:
1.136 brouard 9321: *imax=i-1; /* Number of individuals */
9322: fclose(fic);
1.225 brouard 9323:
1.136 brouard 9324: return (0);
1.164 brouard 9325: /* endread: */
1.225 brouard 9326: printf("Exiting readdata: ");
9327: fclose(fic);
9328: return (1);
1.223 brouard 9329: }
1.126 brouard 9330:
1.234 brouard 9331: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 9332: char *p1 = *stri, *p2 = *stri;
1.235 brouard 9333: while (*p2 == ' ')
1.234 brouard 9334: p2++;
9335: /* while ((*p1++ = *p2++) !=0) */
9336: /* ; */
9337: /* do */
9338: /* while (*p2 == ' ') */
9339: /* p2++; */
9340: /* while (*p1++ == *p2++); */
9341: *stri=p2;
1.145 brouard 9342: }
9343:
1.235 brouard 9344: int decoderesult ( char resultline[], int nres)
1.230 brouard 9345: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
9346: {
1.235 brouard 9347: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 9348: char resultsav[MAXLINE];
1.234 brouard 9349: int resultmodel[MAXLINE];
9350: int modelresult[MAXLINE];
1.230 brouard 9351: char stra[80], strb[80], strc[80], strd[80],stre[80];
9352:
1.234 brouard 9353: removefirstspace(&resultline);
1.233 brouard 9354: printf("decoderesult:%s\n",resultline);
1.230 brouard 9355:
9356: if (strstr(resultline,"v") !=0){
9357: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
9358: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
9359: return 1;
9360: }
9361: trimbb(resultsav, resultline);
9362: if (strlen(resultsav) >1){
9363: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
9364: }
1.253 brouard 9365: if(j == 0){ /* Resultline but no = */
9366: TKresult[nres]=0; /* Combination for the nresult and the model */
9367: return (0);
9368: }
9369:
1.234 brouard 9370: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
9371: 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);
9372: 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);
9373: }
9374: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
9375: if(nbocc(resultsav,'=') >1){
9376: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
9377: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
9378: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
9379: }else
9380: cutl(strc,strd,resultsav,'=');
1.230 brouard 9381: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 9382:
1.230 brouard 9383: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
9384: Tvarsel[k]=atoi(strc);
9385: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
9386: /* cptcovsel++; */
9387: if (nbocc(stra,'=') >0)
9388: strcpy(resultsav,stra); /* and analyzes it */
9389: }
1.235 brouard 9390: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 9391: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9392: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 9393: match=0;
1.236 brouard 9394: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 9395: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 9396: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 9397: match=1;
9398: break;
9399: }
9400: }
9401: if(match == 0){
9402: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9403: }
9404: }
9405: }
1.235 brouard 9406: /* Checking for missing or useless values in comparison of current model needs */
9407: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 9408: match=0;
1.235 brouard 9409: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9410: if(Typevar[k1]==0){ /* Single */
1.237 brouard 9411: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 9412: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 9413: ++match;
9414: }
9415: }
9416: }
9417: if(match == 0){
9418: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
9419: }else if(match > 1){
9420: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
9421: }
9422: }
1.235 brouard 9423:
1.234 brouard 9424: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 9425: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9426: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
9427: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
9428: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
9429: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
9430: /* 1 0 0 0 */
9431: /* 2 1 0 0 */
9432: /* 3 0 1 0 */
9433: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
9434: /* 5 0 0 1 */
9435: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
9436: /* 7 0 1 1 */
9437: /* 8 1 1 1 */
1.237 brouard 9438: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
9439: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
9440: /* V5*age V5 known which value for nres? */
9441: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 9442: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
9443: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 9444: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 9445: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
9446: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 9447: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
9448: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
9449: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 9450: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
9451: k4++;;
9452: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
9453: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
9454: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 9455: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
9456: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
9457: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 9458: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
9459: k4q++;;
9460: }
9461: }
1.234 brouard 9462:
1.235 brouard 9463: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 9464: return (0);
9465: }
1.235 brouard 9466:
1.230 brouard 9467: int decodemodel( char model[], int lastobs)
9468: /**< This routine decodes the model and returns:
1.224 brouard 9469: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
9470: * - nagesqr = 1 if age*age in the model, otherwise 0.
9471: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
9472: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
9473: * - cptcovage number of covariates with age*products =2
9474: * - cptcovs number of simple covariates
9475: * - 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
9476: * which is a new column after the 9 (ncovcol) variables.
9477: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
9478: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
9479: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
9480: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
9481: */
1.136 brouard 9482: {
1.238 brouard 9483: int i, j, k, ks, v;
1.227 brouard 9484: int j1, k1, k2, k3, k4;
1.136 brouard 9485: char modelsav[80];
1.145 brouard 9486: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 9487: char *strpt;
1.136 brouard 9488:
1.145 brouard 9489: /*removespace(model);*/
1.136 brouard 9490: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 9491: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 9492: if (strstr(model,"AGE") !=0){
1.192 brouard 9493: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
9494: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 9495: return 1;
9496: }
1.141 brouard 9497: if (strstr(model,"v") !=0){
9498: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
9499: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
9500: return 1;
9501: }
1.187 brouard 9502: strcpy(modelsav,model);
9503: if ((strpt=strstr(model,"age*age")) !=0){
9504: printf(" strpt=%s, model=%s\n",strpt, model);
9505: if(strpt != model){
1.234 brouard 9506: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9507: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9508: corresponding column of parameters.\n",model);
1.234 brouard 9509: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 9510: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 9511: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 9512: return 1;
1.225 brouard 9513: }
1.187 brouard 9514: nagesqr=1;
9515: if (strstr(model,"+age*age") !=0)
1.234 brouard 9516: substrchaine(modelsav, model, "+age*age");
1.187 brouard 9517: else if (strstr(model,"age*age+") !=0)
1.234 brouard 9518: substrchaine(modelsav, model, "age*age+");
1.187 brouard 9519: else
1.234 brouard 9520: substrchaine(modelsav, model, "age*age");
1.187 brouard 9521: }else
9522: nagesqr=0;
9523: if (strlen(modelsav) >1){
9524: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
9525: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 9526: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 9527: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 9528: * cst, age and age*age
9529: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
9530: /* including age products which are counted in cptcovage.
9531: * but the covariates which are products must be treated
9532: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 9533: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
9534: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 9535:
9536:
1.187 brouard 9537: /* Design
9538: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
9539: * < ncovcol=8 >
9540: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
9541: * k= 1 2 3 4 5 6 7 8
9542: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
9543: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 9544: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
9545: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 9546: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
9547: * Tage[++cptcovage]=k
9548: * if products, new covar are created after ncovcol with k1
9549: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
9550: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
9551: * 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
9552: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
9553: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
9554: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
9555: * < ncovcol=8 >
9556: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
9557: * k= 1 2 3 4 5 6 7 8 9 10 11 12
9558: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
9559: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9560: * p Tprod[1]@2={ 6, 5}
9561: *p Tvard[1][1]@4= {7, 8, 5, 6}
9562: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
9563: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
9564: *How to reorganize?
9565: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
9566: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
9567: * {2, 1, 4, 8, 5, 6, 3, 7}
9568: * Struct []
9569: */
1.225 brouard 9570:
1.187 brouard 9571: /* This loop fills the array Tvar from the string 'model'.*/
9572: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
9573: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
9574: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
9575: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
9576: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
9577: /* k=1 Tvar[1]=2 (from V2) */
9578: /* k=5 Tvar[5] */
9579: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 9580: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 9581: /* } */
1.198 brouard 9582: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 9583: /*
9584: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 9585: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
9586: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
9587: }
1.187 brouard 9588: cptcovage=0;
9589: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 9590: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 9591: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 9592: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
9593: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
9594: /*scanf("%d",i);*/
9595: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
9596: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
9597: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
9598: /* covar is not filled and then is empty */
9599: cptcovprod--;
9600: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
9601: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
9602: Typevar[k]=1; /* 1 for age product */
9603: cptcovage++; /* Sums the number of covariates which include age as a product */
9604: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
9605: /*printf("stre=%s ", stre);*/
9606: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
9607: cptcovprod--;
9608: cutl(stre,strb,strc,'V');
9609: Tvar[k]=atoi(stre);
9610: Typevar[k]=1; /* 1 for age product */
9611: cptcovage++;
9612: Tage[cptcovage]=k;
9613: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
9614: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
9615: cptcovn++;
9616: cptcovprodnoage++;k1++;
9617: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
9618: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
9619: because this model-covariate is a construction we invent a new column
9620: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
9621: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
9622: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
9623: Typevar[k]=2; /* 2 for double fixed dummy covariates */
9624: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
9625: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
9626: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
9627: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
9628: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
9629: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
9630: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
9631: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 9632: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 9633: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
9634: for (i=1; i<=lastobs;i++){
9635: /* Computes the new covariate which is a product of
9636: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
9637: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
9638: }
9639: } /* End age is not in the model */
9640: } /* End if model includes a product */
9641: else { /* no more sum */
9642: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
9643: /* scanf("%d",i);*/
9644: cutl(strd,strc,strb,'V');
9645: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
9646: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
9647: Tvar[k]=atoi(strd);
9648: Typevar[k]=0; /* 0 for simple covariates */
9649: }
9650: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 9651: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 9652: scanf("%d",i);*/
1.187 brouard 9653: } /* end of loop + on total covariates */
9654: } /* end if strlen(modelsave == 0) age*age might exist */
9655: } /* end if strlen(model == 0) */
1.136 brouard 9656:
9657: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
9658: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 9659:
1.136 brouard 9660: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 9661: printf("cptcovprod=%d ", cptcovprod);
9662: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
9663: scanf("%d ",i);*/
9664:
9665:
1.230 brouard 9666: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
9667: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 9668: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
9669: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
9670: k = 1 2 3 4 5 6 7 8 9
9671: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
9672: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 9673: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
9674: Dummy[k] 1 0 0 0 3 1 1 2 3
9675: Tmodelind[combination of covar]=k;
1.225 brouard 9676: */
9677: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 9678: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 9679: /* 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 9680: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 9681: printf("Model=%s\n\
9682: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9683: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9684: 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);
9685: fprintf(ficlog,"Model=%s\n\
9686: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
9687: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
9688: 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 9689: for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 9690: 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 */
9691: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 9692: Fixed[k]= 0;
9693: Dummy[k]= 0;
1.225 brouard 9694: ncoveff++;
1.232 brouard 9695: ncovf++;
1.234 brouard 9696: nsd++;
9697: modell[k].maintype= FTYPE;
9698: TvarsD[nsd]=Tvar[k];
9699: TvarsDind[nsd]=k;
9700: TvarF[ncovf]=Tvar[k];
9701: TvarFind[ncovf]=k;
9702: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9703: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
9704: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
9705: Fixed[k]= 0;
9706: Dummy[k]= 0;
9707: ncoveff++;
9708: ncovf++;
9709: modell[k].maintype= FTYPE;
9710: TvarF[ncovf]=Tvar[k];
9711: TvarFind[ncovf]=k;
1.230 brouard 9712: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 9713: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 9714: }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 9715: Fixed[k]= 0;
9716: Dummy[k]= 1;
1.230 brouard 9717: nqfveff++;
1.234 brouard 9718: modell[k].maintype= FTYPE;
9719: modell[k].subtype= FQ;
9720: nsq++;
9721: TvarsQ[nsq]=Tvar[k];
9722: TvarsQind[nsq]=k;
1.232 brouard 9723: ncovf++;
1.234 brouard 9724: TvarF[ncovf]=Tvar[k];
9725: TvarFind[ncovf]=k;
1.231 brouard 9726: 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 9727: 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 9728: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 9729: Fixed[k]= 1;
9730: Dummy[k]= 0;
1.225 brouard 9731: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 9732: modell[k].maintype= VTYPE;
9733: modell[k].subtype= VD;
9734: nsd++;
9735: TvarsD[nsd]=Tvar[k];
9736: TvarsDind[nsd]=k;
9737: ncovv++; /* Only simple time varying variables */
9738: TvarV[ncovv]=Tvar[k];
1.242 brouard 9739: 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 9740: 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 */
9741: 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 9742: 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);
9743: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 9744: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 9745: Fixed[k]= 1;
9746: Dummy[k]= 1;
9747: nqtveff++;
9748: modell[k].maintype= VTYPE;
9749: modell[k].subtype= VQ;
9750: ncovv++; /* Only simple time varying variables */
9751: nsq++;
9752: TvarsQ[nsq]=Tvar[k];
9753: TvarsQind[nsq]=k;
9754: TvarV[ncovv]=Tvar[k];
1.242 brouard 9755: 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 9756: 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 */
9757: 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 9758: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
9759: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
9760: 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 9761: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 9762: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 9763: ncova++;
9764: TvarA[ncova]=Tvar[k];
9765: TvarAind[ncova]=k;
1.231 brouard 9766: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 9767: Fixed[k]= 2;
9768: Dummy[k]= 2;
9769: modell[k].maintype= ATYPE;
9770: modell[k].subtype= APFD;
9771: /* ncoveff++; */
1.227 brouard 9772: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 9773: Fixed[k]= 2;
9774: Dummy[k]= 3;
9775: modell[k].maintype= ATYPE;
9776: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
9777: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 9778: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 9779: Fixed[k]= 3;
9780: Dummy[k]= 2;
9781: modell[k].maintype= ATYPE;
9782: modell[k].subtype= APVD; /* Product age * varying dummy */
9783: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 9784: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9785: Fixed[k]= 3;
9786: Dummy[k]= 3;
9787: modell[k].maintype= ATYPE;
9788: modell[k].subtype= APVQ; /* Product age * varying quantitative */
9789: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 9790: }
9791: }else if (Typevar[k] == 2) { /* product without age */
9792: k1=Tposprod[k];
9793: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 9794: if(Tvard[k1][2] <=ncovcol){
9795: Fixed[k]= 1;
9796: Dummy[k]= 0;
9797: modell[k].maintype= FTYPE;
9798: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
9799: ncovf++; /* Fixed variables without age */
9800: TvarF[ncovf]=Tvar[k];
9801: TvarFind[ncovf]=k;
9802: }else if(Tvard[k1][2] <=ncovcol+nqv){
9803: Fixed[k]= 0; /* or 2 ?*/
9804: Dummy[k]= 1;
9805: modell[k].maintype= FTYPE;
9806: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
9807: ncovf++; /* Varying variables without age */
9808: TvarF[ncovf]=Tvar[k];
9809: TvarFind[ncovf]=k;
9810: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9811: Fixed[k]= 1;
9812: Dummy[k]= 0;
9813: modell[k].maintype= VTYPE;
9814: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
9815: ncovv++; /* Varying variables without age */
9816: TvarV[ncovv]=Tvar[k];
9817: TvarVind[ncovv]=k;
9818: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9819: Fixed[k]= 1;
9820: Dummy[k]= 1;
9821: modell[k].maintype= VTYPE;
9822: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
9823: ncovv++; /* Varying variables without age */
9824: TvarV[ncovv]=Tvar[k];
9825: TvarVind[ncovv]=k;
9826: }
1.227 brouard 9827: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 9828: if(Tvard[k1][2] <=ncovcol){
9829: Fixed[k]= 0; /* or 2 ?*/
9830: Dummy[k]= 1;
9831: modell[k].maintype= FTYPE;
9832: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
9833: ncovf++; /* Fixed variables without age */
9834: TvarF[ncovf]=Tvar[k];
9835: TvarFind[ncovf]=k;
9836: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9837: Fixed[k]= 1;
9838: Dummy[k]= 1;
9839: modell[k].maintype= VTYPE;
9840: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
9841: ncovv++; /* Varying variables without age */
9842: TvarV[ncovv]=Tvar[k];
9843: TvarVind[ncovv]=k;
9844: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9845: Fixed[k]= 1;
9846: Dummy[k]= 1;
9847: modell[k].maintype= VTYPE;
9848: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
9849: ncovv++; /* Varying variables without age */
9850: TvarV[ncovv]=Tvar[k];
9851: TvarVind[ncovv]=k;
9852: ncovv++; /* Varying variables without age */
9853: TvarV[ncovv]=Tvar[k];
9854: TvarVind[ncovv]=k;
9855: }
1.227 brouard 9856: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 9857: if(Tvard[k1][2] <=ncovcol){
9858: Fixed[k]= 1;
9859: Dummy[k]= 1;
9860: modell[k].maintype= VTYPE;
9861: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
9862: ncovv++; /* Varying variables without age */
9863: TvarV[ncovv]=Tvar[k];
9864: TvarVind[ncovv]=k;
9865: }else if(Tvard[k1][2] <=ncovcol+nqv){
9866: Fixed[k]= 1;
9867: Dummy[k]= 1;
9868: modell[k].maintype= VTYPE;
9869: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
9870: ncovv++; /* Varying variables without age */
9871: TvarV[ncovv]=Tvar[k];
9872: TvarVind[ncovv]=k;
9873: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9874: Fixed[k]= 1;
9875: Dummy[k]= 0;
9876: modell[k].maintype= VTYPE;
9877: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
9878: ncovv++; /* Varying variables without age */
9879: TvarV[ncovv]=Tvar[k];
9880: TvarVind[ncovv]=k;
9881: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9882: Fixed[k]= 1;
9883: Dummy[k]= 1;
9884: modell[k].maintype= VTYPE;
9885: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
9886: ncovv++; /* Varying variables without age */
9887: TvarV[ncovv]=Tvar[k];
9888: TvarVind[ncovv]=k;
9889: }
1.227 brouard 9890: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 9891: if(Tvard[k1][2] <=ncovcol){
9892: Fixed[k]= 1;
9893: Dummy[k]= 1;
9894: modell[k].maintype= VTYPE;
9895: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
9896: ncovv++; /* Varying variables without age */
9897: TvarV[ncovv]=Tvar[k];
9898: TvarVind[ncovv]=k;
9899: }else if(Tvard[k1][2] <=ncovcol+nqv){
9900: Fixed[k]= 1;
9901: Dummy[k]= 1;
9902: modell[k].maintype= VTYPE;
9903: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
9904: ncovv++; /* Varying variables without age */
9905: TvarV[ncovv]=Tvar[k];
9906: TvarVind[ncovv]=k;
9907: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9908: Fixed[k]= 1;
9909: Dummy[k]= 1;
9910: modell[k].maintype= VTYPE;
9911: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
9912: ncovv++; /* Varying variables without age */
9913: TvarV[ncovv]=Tvar[k];
9914: TvarVind[ncovv]=k;
9915: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9916: Fixed[k]= 1;
9917: Dummy[k]= 1;
9918: modell[k].maintype= VTYPE;
9919: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
9920: ncovv++; /* Varying variables without age */
9921: TvarV[ncovv]=Tvar[k];
9922: TvarVind[ncovv]=k;
9923: }
1.227 brouard 9924: }else{
1.240 brouard 9925: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9926: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9927: } /*end k1*/
1.225 brouard 9928: }else{
1.226 brouard 9929: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
9930: 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 9931: }
1.227 brouard 9932: 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 9933: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 9934: 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]);
9935: }
9936: /* Searching for doublons in the model */
9937: for(k1=1; k1<= cptcovt;k1++){
9938: for(k2=1; k2 <k1;k2++){
9939: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234 brouard 9940: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
9941: if(Tvar[k1]==Tvar[k2]){
9942: 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]]);
9943: 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);
9944: return(1);
9945: }
9946: }else if (Typevar[k1] ==2){
9947: k3=Tposprod[k1];
9948: k4=Tposprod[k2];
9949: 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])) ){
9950: 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]]);
9951: 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);
9952: return(1);
9953: }
9954: }
1.227 brouard 9955: }
9956: }
1.225 brouard 9957: }
9958: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
9959: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 9960: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
9961: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 9962: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 9963: /*endread:*/
1.225 brouard 9964: printf("Exiting decodemodel: ");
9965: return (1);
1.136 brouard 9966: }
9967:
1.169 brouard 9968: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 9969: {/* Check ages at death */
1.136 brouard 9970: int i, m;
1.218 brouard 9971: int firstone=0;
9972:
1.136 brouard 9973: for (i=1; i<=imx; i++) {
9974: for(m=2; (m<= maxwav); m++) {
9975: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
9976: anint[m][i]=9999;
1.216 brouard 9977: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
9978: s[m][i]=-1;
1.136 brouard 9979: }
9980: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.260 brouard 9981: *nberr = *nberr + 1;
1.218 brouard 9982: if(firstone == 0){
9983: firstone=1;
1.260 brouard 9984: 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 9985: }
1.262 brouard 9986: 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 9987: s[m][i]=-1; /* Droping the death status */
1.136 brouard 9988: }
9989: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 9990: (*nberr)++;
1.259 brouard 9991: 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 9992: 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 9993: s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
1.136 brouard 9994: }
9995: }
9996: }
9997:
9998: for (i=1; i<=imx; i++) {
9999: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
10000: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 10001: 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 10002: if (s[m][i] >= nlstate+1) {
1.169 brouard 10003: if(agedc[i]>0){
10004: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 10005: agev[m][i]=agedc[i];
1.214 brouard 10006: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 10007: }else {
1.136 brouard 10008: if ((int)andc[i]!=9999){
10009: nbwarn++;
10010: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
10011: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
10012: agev[m][i]=-1;
10013: }
10014: }
1.169 brouard 10015: } /* agedc > 0 */
1.214 brouard 10016: } /* end if */
1.136 brouard 10017: else if(s[m][i] !=9){ /* Standard case, age in fractional
10018: years but with the precision of a month */
10019: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
10020: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
10021: agev[m][i]=1;
10022: else if(agev[m][i] < *agemin){
10023: *agemin=agev[m][i];
10024: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
10025: }
10026: else if(agev[m][i] >*agemax){
10027: *agemax=agev[m][i];
1.156 brouard 10028: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 10029: }
10030: /*agev[m][i]=anint[m][i]-annais[i];*/
10031: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 10032: } /* en if 9*/
1.136 brouard 10033: else { /* =9 */
1.214 brouard 10034: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 10035: agev[m][i]=1;
10036: s[m][i]=-1;
10037: }
10038: }
1.214 brouard 10039: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 10040: agev[m][i]=1;
1.214 brouard 10041: else{
10042: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10043: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
10044: agev[m][i]=0;
10045: }
10046: } /* End for lastpass */
10047: }
1.136 brouard 10048:
10049: for (i=1; i<=imx; i++) {
10050: for(m=firstpass; (m<=lastpass); m++){
10051: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 10052: (*nberr)++;
1.136 brouard 10053: 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);
10054: 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);
10055: return 1;
10056: }
10057: }
10058: }
10059:
10060: /*for (i=1; i<=imx; i++){
10061: for (m=firstpass; (m<lastpass); m++){
10062: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
10063: }
10064:
10065: }*/
10066:
10067:
1.139 brouard 10068: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
10069: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 10070:
10071: return (0);
1.164 brouard 10072: /* endread:*/
1.136 brouard 10073: printf("Exiting calandcheckages: ");
10074: return (1);
10075: }
10076:
1.172 brouard 10077: #if defined(_MSC_VER)
10078: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10079: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
10080: //#include "stdafx.h"
10081: //#include <stdio.h>
10082: //#include <tchar.h>
10083: //#include <windows.h>
10084: //#include <iostream>
10085: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
10086:
10087: LPFN_ISWOW64PROCESS fnIsWow64Process;
10088:
10089: BOOL IsWow64()
10090: {
10091: BOOL bIsWow64 = FALSE;
10092:
10093: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
10094: // (HANDLE, PBOOL);
10095:
10096: //LPFN_ISWOW64PROCESS fnIsWow64Process;
10097:
10098: HMODULE module = GetModuleHandle(_T("kernel32"));
10099: const char funcName[] = "IsWow64Process";
10100: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
10101: GetProcAddress(module, funcName);
10102:
10103: if (NULL != fnIsWow64Process)
10104: {
10105: if (!fnIsWow64Process(GetCurrentProcess(),
10106: &bIsWow64))
10107: //throw std::exception("Unknown error");
10108: printf("Unknown error\n");
10109: }
10110: return bIsWow64 != FALSE;
10111: }
10112: #endif
1.177 brouard 10113:
1.191 brouard 10114: void syscompilerinfo(int logged)
1.167 brouard 10115: {
10116: /* #include "syscompilerinfo.h"*/
1.185 brouard 10117: /* command line Intel compiler 32bit windows, XP compatible:*/
10118: /* /GS /W3 /Gy
10119: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
10120: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
10121: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 10122: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
10123: */
10124: /* 64 bits */
1.185 brouard 10125: /*
10126: /GS /W3 /Gy
10127: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
10128: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
10129: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
10130: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
10131: /* Optimization are useless and O3 is slower than O2 */
10132: /*
10133: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
10134: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
10135: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
10136: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
10137: */
1.186 brouard 10138: /* Link is */ /* /OUT:"visual studio
1.185 brouard 10139: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
10140: /PDB:"visual studio
10141: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
10142: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
10143: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
10144: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
10145: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
10146: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
10147: uiAccess='false'"
10148: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
10149: /NOLOGO /TLBID:1
10150: */
1.177 brouard 10151: #if defined __INTEL_COMPILER
1.178 brouard 10152: #if defined(__GNUC__)
10153: struct utsname sysInfo; /* For Intel on Linux and OS/X */
10154: #endif
1.177 brouard 10155: #elif defined(__GNUC__)
1.179 brouard 10156: #ifndef __APPLE__
1.174 brouard 10157: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 10158: #endif
1.177 brouard 10159: struct utsname sysInfo;
1.178 brouard 10160: int cross = CROSS;
10161: if (cross){
10162: printf("Cross-");
1.191 brouard 10163: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 10164: }
1.174 brouard 10165: #endif
10166:
1.171 brouard 10167: #include <stdint.h>
1.178 brouard 10168:
1.191 brouard 10169: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 10170: #if defined(__clang__)
1.191 brouard 10171: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 10172: #endif
10173: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 10174: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 10175: #endif
10176: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 10177: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 10178: #endif
10179: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 10180: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 10181: #endif
10182: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 10183: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 10184: #endif
10185: #if defined(_MSC_VER)
1.191 brouard 10186: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 10187: #endif
10188: #if defined(__PGI)
1.191 brouard 10189: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 10190: #endif
10191: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 10192: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 10193: #endif
1.191 brouard 10194: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 10195:
1.167 brouard 10196: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
10197: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
10198: // Windows (x64 and x86)
1.191 brouard 10199: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 10200: #elif __unix__ // all unices, not all compilers
10201: // Unix
1.191 brouard 10202: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 10203: #elif __linux__
10204: // linux
1.191 brouard 10205: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 10206: #elif __APPLE__
1.174 brouard 10207: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 10208: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 10209: #endif
10210:
10211: /* __MINGW32__ */
10212: /* __CYGWIN__ */
10213: /* __MINGW64__ */
10214: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
10215: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
10216: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
10217: /* _WIN64 // Defined for applications for Win64. */
10218: /* _M_X64 // Defined for compilations that target x64 processors. */
10219: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 10220:
1.167 brouard 10221: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 10222: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 10223: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 10224: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 10225: #else
1.191 brouard 10226: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 10227: #endif
10228:
1.169 brouard 10229: #if defined(__GNUC__)
10230: # if defined(__GNUC_PATCHLEVEL__)
10231: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10232: + __GNUC_MINOR__ * 100 \
10233: + __GNUC_PATCHLEVEL__)
10234: # else
10235: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
10236: + __GNUC_MINOR__ * 100)
10237: # endif
1.174 brouard 10238: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 10239: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 10240:
10241: if (uname(&sysInfo) != -1) {
10242: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 10243: 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 10244: }
10245: else
10246: perror("uname() error");
1.179 brouard 10247: //#ifndef __INTEL_COMPILER
10248: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 10249: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 10250: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 10251: #endif
1.169 brouard 10252: #endif
1.172 brouard 10253:
10254: // void main()
10255: // {
1.169 brouard 10256: #if defined(_MSC_VER)
1.174 brouard 10257: if (IsWow64()){
1.191 brouard 10258: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
10259: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 10260: }
10261: else{
1.191 brouard 10262: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
10263: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 10264: }
1.172 brouard 10265: // printf("\nPress Enter to continue...");
10266: // getchar();
10267: // }
10268:
1.169 brouard 10269: #endif
10270:
1.167 brouard 10271:
1.219 brouard 10272: }
1.136 brouard 10273:
1.219 brouard 10274: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 10275: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 brouard 10276: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 10277: /* double ftolpl = 1.e-10; */
1.180 brouard 10278: double age, agebase, agelim;
1.203 brouard 10279: double tot;
1.180 brouard 10280:
1.202 brouard 10281: strcpy(filerespl,"PL_");
10282: strcat(filerespl,fileresu);
10283: if((ficrespl=fopen(filerespl,"w"))==NULL) {
10284: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10285: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
10286: }
1.227 brouard 10287: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
10288: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 10289: pstamp(ficrespl);
1.203 brouard 10290: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 10291: fprintf(ficrespl,"#Age ");
10292: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
10293: fprintf(ficrespl,"\n");
1.180 brouard 10294:
1.219 brouard 10295: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 10296:
1.219 brouard 10297: agebase=ageminpar;
10298: agelim=agemaxpar;
1.180 brouard 10299:
1.227 brouard 10300: /* i1=pow(2,ncoveff); */
1.234 brouard 10301: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 10302: if (cptcovn < 1){i1=1;}
1.180 brouard 10303:
1.238 brouard 10304: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
10305: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 10306: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10307: continue;
1.235 brouard 10308:
1.238 brouard 10309: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10310: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
10311: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
10312: /* k=k+1; */
10313: /* to clean */
10314: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10315: fprintf(ficrespl,"#******");
10316: printf("#******");
10317: fprintf(ficlog,"#******");
10318: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10319: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
10320: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10321: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10322: }
10323: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10324: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10325: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10326: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10327: }
10328: fprintf(ficrespl,"******\n");
10329: printf("******\n");
10330: fprintf(ficlog,"******\n");
10331: if(invalidvarcomb[k]){
10332: printf("\nCombination (%d) ignored because no case \n",k);
10333: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
10334: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
10335: continue;
10336: }
1.219 brouard 10337:
1.238 brouard 10338: fprintf(ficrespl,"#Age ");
10339: for(j=1;j<=cptcoveff;j++) {
10340: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10341: }
10342: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
10343: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 10344:
1.238 brouard 10345: for (age=agebase; age<=agelim; age++){
10346: /* for (age=agebase; age<=agebase; age++){ */
10347: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
10348: fprintf(ficrespl,"%.0f ",age );
10349: for(j=1;j<=cptcoveff;j++)
10350: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10351: tot=0.;
10352: for(i=1; i<=nlstate;i++){
10353: tot += prlim[i][i];
10354: fprintf(ficrespl," %.5f", prlim[i][i]);
10355: }
10356: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
10357: } /* Age */
10358: /* was end of cptcod */
10359: } /* cptcov */
10360: } /* nres */
1.219 brouard 10361: return 0;
1.180 brouard 10362: }
10363:
1.218 brouard 10364: 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){
10365: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10366:
10367: /* Computes the back prevalence limit for any combination of covariate values
10368: * at any age between ageminpar and agemaxpar
10369: */
1.235 brouard 10370: int i, j, k, i1, nres=0 ;
1.217 brouard 10371: /* double ftolpl = 1.e-10; */
10372: double age, agebase, agelim;
10373: double tot;
1.218 brouard 10374: /* double ***mobaverage; */
10375: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 10376:
10377: strcpy(fileresplb,"PLB_");
10378: strcat(fileresplb,fileresu);
10379: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
10380: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10381: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
10382: }
10383: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10384: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
10385: pstamp(ficresplb);
10386: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
10387: fprintf(ficresplb,"#Age ");
10388: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
10389: fprintf(ficresplb,"\n");
10390:
1.218 brouard 10391:
10392: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
10393:
10394: agebase=ageminpar;
10395: agelim=agemaxpar;
10396:
10397:
1.227 brouard 10398: i1=pow(2,cptcoveff);
1.218 brouard 10399: if (cptcovn < 1){i1=1;}
1.227 brouard 10400:
1.238 brouard 10401: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10402: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10403: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10404: continue;
10405: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
10406: fprintf(ficresplb,"#******");
10407: printf("#******");
10408: fprintf(ficlog,"#******");
10409: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
10410: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10411: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10412: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10413: }
10414: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10415: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10416: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10417: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10418: }
10419: fprintf(ficresplb,"******\n");
10420: printf("******\n");
10421: fprintf(ficlog,"******\n");
10422: if(invalidvarcomb[k]){
10423: printf("\nCombination (%d) ignored because no cases \n",k);
10424: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
10425: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
10426: continue;
10427: }
1.218 brouard 10428:
1.238 brouard 10429: fprintf(ficresplb,"#Age ");
10430: for(j=1;j<=cptcoveff;j++) {
10431: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10432: }
10433: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
10434: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 10435:
10436:
1.238 brouard 10437: for (age=agebase; age<=agelim; age++){
10438: /* for (age=agebase; age<=agebase; age++){ */
10439: if(mobilavproj > 0){
10440: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
10441: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10442: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 10443: }else if (mobilavproj == 0){
10444: 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);
10445: 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);
10446: exit(1);
10447: }else{
10448: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 10449: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.266 brouard 10450: /* printf("TOTOT\n"); */
10451: /* exit(1); */
1.238 brouard 10452: }
10453: fprintf(ficresplb,"%.0f ",age );
10454: for(j=1;j<=cptcoveff;j++)
10455: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10456: tot=0.;
10457: for(i=1; i<=nlstate;i++){
10458: tot += bprlim[i][i];
10459: fprintf(ficresplb," %.5f", bprlim[i][i]);
10460: }
10461: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
10462: } /* Age */
10463: /* was end of cptcod */
1.255 brouard 10464: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 10465: } /* end of any combination */
10466: } /* end of nres */
1.218 brouard 10467: /* hBijx(p, bage, fage); */
10468: /* fclose(ficrespijb); */
10469:
10470: return 0;
1.217 brouard 10471: }
1.218 brouard 10472:
1.180 brouard 10473: int hPijx(double *p, int bage, int fage){
10474: /*------------- h Pij x at various ages ------------*/
10475:
10476: int stepsize;
10477: int agelim;
10478: int hstepm;
10479: int nhstepm;
1.235 brouard 10480: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 10481:
10482: double agedeb;
10483: double ***p3mat;
10484:
1.201 brouard 10485: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 10486: if((ficrespij=fopen(filerespij,"w"))==NULL) {
10487: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
10488: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
10489: }
10490: printf("Computing pij: result on file '%s' \n", filerespij);
10491: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
10492:
10493: stepsize=(int) (stepm+YEARM-1)/YEARM;
10494: /*if (stepm<=24) stepsize=2;*/
10495:
10496: agelim=AGESUP;
10497: hstepm=stepsize*YEARM; /* Every year of age */
10498: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 10499:
1.180 brouard 10500: /* hstepm=1; aff par mois*/
10501: pstamp(ficrespij);
10502: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 10503: i1= pow(2,cptcoveff);
1.218 brouard 10504: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10505: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10506: /* k=k+1; */
1.235 brouard 10507: for(nres=1; nres <= nresult; nres++) /* For each resultline */
10508: for(k=1; k<=i1;k++){
1.253 brouard 10509: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 10510: continue;
1.183 brouard 10511: fprintf(ficrespij,"\n#****** ");
1.227 brouard 10512: for(j=1;j<=cptcoveff;j++)
1.198 brouard 10513: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 10514: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
10515: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10516: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
10517: }
1.183 brouard 10518: fprintf(ficrespij,"******\n");
10519:
10520: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
10521: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10522: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
10523:
10524: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 10525:
1.183 brouard 10526: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10527: oldm=oldms;savm=savms;
1.235 brouard 10528: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 10529: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
10530: for(i=1; i<=nlstate;i++)
10531: for(j=1; j<=nlstate+ndeath;j++)
10532: fprintf(ficrespij," %1d-%1d",i,j);
10533: fprintf(ficrespij,"\n");
10534: for (h=0; h<=nhstepm; h++){
10535: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10536: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 10537: for(i=1; i<=nlstate;i++)
10538: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 10539: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 10540: fprintf(ficrespij,"\n");
10541: }
1.183 brouard 10542: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10543: fprintf(ficrespij,"\n");
10544: }
1.180 brouard 10545: /*}*/
10546: }
1.218 brouard 10547: return 0;
1.180 brouard 10548: }
1.218 brouard 10549:
10550: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 10551: /*------------- h Bij x at various ages ------------*/
10552:
10553: int stepsize;
1.218 brouard 10554: /* int agelim; */
10555: int ageminl;
1.217 brouard 10556: int hstepm;
10557: int nhstepm;
1.238 brouard 10558: int h, i, i1, j, k, nres;
1.218 brouard 10559:
1.217 brouard 10560: double agedeb;
10561: double ***p3mat;
1.218 brouard 10562:
10563: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
10564: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
10565: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10566: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
10567: }
10568: printf("Computing pij back: result on file '%s' \n", filerespijb);
10569: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
10570:
10571: stepsize=(int) (stepm+YEARM-1)/YEARM;
10572: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 10573:
1.218 brouard 10574: /* agelim=AGESUP; */
10575: ageminl=30;
10576: hstepm=stepsize*YEARM; /* Every year of age */
10577: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
10578:
10579: /* hstepm=1; aff par mois*/
10580: pstamp(ficrespijb);
1.255 brouard 10581: 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 10582: i1= pow(2,cptcoveff);
1.218 brouard 10583: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
10584: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
10585: /* k=k+1; */
1.238 brouard 10586: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
10587: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 10588: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 10589: continue;
10590: fprintf(ficrespijb,"\n#****** ");
10591: for(j=1;j<=cptcoveff;j++)
10592: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10593: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
10594: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
10595: }
10596: fprintf(ficrespijb,"******\n");
1.264 brouard 10597: if(invalidvarcomb[k]){ /* Is it necessary here? */
1.238 brouard 10598: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
10599: continue;
10600: }
10601:
10602: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
10603: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
10604: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
10605: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
10606: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
10607:
10608: /* nhstepm=nhstepm*YEARM; aff par mois*/
10609:
1.266 brouard 10610: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
10611: /* and memory limitations if stepm is small */
10612:
1.238 brouard 10613: /* oldm=oldms;savm=savms; */
10614: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.267 brouard 10615: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
1.238 brouard 10616: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 brouard 10617: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 10618: for(i=1; i<=nlstate;i++)
10619: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 10620: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 10621: fprintf(ficrespijb,"\n");
1.238 brouard 10622: for (h=0; h<=nhstepm; h++){
10623: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
10624: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
10625: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
10626: for(i=1; i<=nlstate;i++)
10627: for(j=1; j<=nlstate+ndeath;j++)
10628: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
10629: fprintf(ficrespijb,"\n");
10630: }
10631: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
10632: fprintf(ficrespijb,"\n");
10633: } /* end age deb */
10634: } /* end combination */
10635: } /* end nres */
1.218 brouard 10636: return 0;
10637: } /* hBijx */
1.217 brouard 10638:
1.180 brouard 10639:
1.136 brouard 10640: /***********************************************/
10641: /**************** Main Program *****************/
10642: /***********************************************/
10643:
10644: int main(int argc, char *argv[])
10645: {
10646: #ifdef GSL
10647: const gsl_multimin_fminimizer_type *T;
10648: size_t iteri = 0, it;
10649: int rval = GSL_CONTINUE;
10650: int status = GSL_SUCCESS;
10651: double ssval;
10652: #endif
10653: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 10654: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 10655: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 10656: int jj, ll, li, lj, lk;
1.136 brouard 10657: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 10658: int num_filled;
1.136 brouard 10659: int itimes;
10660: int NDIM=2;
10661: int vpopbased=0;
1.235 brouard 10662: int nres=0;
1.258 brouard 10663: int endishere=0;
1.277 brouard 10664: int noffset=0;
1.274 brouard 10665: int ncurrv=0; /* Temporary variable */
10666:
1.164 brouard 10667: char ca[32], cb[32];
1.136 brouard 10668: /* FILE *fichtm; *//* Html File */
10669: /* FILE *ficgp;*/ /*Gnuplot File */
10670: struct stat info;
1.191 brouard 10671: double agedeb=0.;
1.194 brouard 10672:
10673: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 10674: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 10675:
1.165 brouard 10676: double fret;
1.191 brouard 10677: double dum=0.; /* Dummy variable */
1.136 brouard 10678: double ***p3mat;
1.218 brouard 10679: /* double ***mobaverage; */
1.164 brouard 10680:
10681: char line[MAXLINE];
1.197 brouard 10682: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
10683:
1.234 brouard 10684: char modeltemp[MAXLINE];
1.230 brouard 10685: char resultline[MAXLINE];
10686:
1.136 brouard 10687: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 10688: char *tok, *val; /* pathtot */
1.136 brouard 10689: int firstobs=1, lastobs=10;
1.195 brouard 10690: int c, h , cpt, c2;
1.191 brouard 10691: int jl=0;
10692: int i1, j1, jk, stepsize=0;
1.194 brouard 10693: int count=0;
10694:
1.164 brouard 10695: int *tab;
1.136 brouard 10696: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 10697: int backcast=0;
1.136 brouard 10698: int mobilav=0,popforecast=0;
1.191 brouard 10699: int hstepm=0, nhstepm=0;
1.136 brouard 10700: int agemortsup;
10701: float sumlpop=0.;
10702: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
10703: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
10704:
1.191 brouard 10705: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 10706: double ftolpl=FTOL;
10707: double **prlim;
1.217 brouard 10708: double **bprlim;
1.136 brouard 10709: double ***param; /* Matrix of parameters */
1.251 brouard 10710: double ***paramstart; /* Matrix of starting parameter values */
10711: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 10712: double **matcov; /* Matrix of covariance */
1.203 brouard 10713: double **hess; /* Hessian matrix */
1.136 brouard 10714: double ***delti3; /* Scale */
10715: double *delti; /* Scale */
10716: double ***eij, ***vareij;
10717: double **varpl; /* Variances of prevalence limits by age */
1.269 brouard 10718:
1.136 brouard 10719: double *epj, vepp;
1.164 brouard 10720:
1.273 brouard 10721: double dateprev1, dateprev2;
10722: double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
10723: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
1.217 brouard 10724:
1.136 brouard 10725: double **ximort;
1.145 brouard 10726: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 10727: int *dcwave;
10728:
1.164 brouard 10729: char z[1]="c";
1.136 brouard 10730:
10731: /*char *strt;*/
10732: char strtend[80];
1.126 brouard 10733:
1.164 brouard 10734:
1.126 brouard 10735: /* setlocale (LC_ALL, ""); */
10736: /* bindtextdomain (PACKAGE, LOCALEDIR); */
10737: /* textdomain (PACKAGE); */
10738: /* setlocale (LC_CTYPE, ""); */
10739: /* setlocale (LC_MESSAGES, ""); */
10740:
10741: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 10742: rstart_time = time(NULL);
10743: /* (void) gettimeofday(&start_time,&tzp);*/
10744: start_time = *localtime(&rstart_time);
1.126 brouard 10745: curr_time=start_time;
1.157 brouard 10746: /*tml = *localtime(&start_time.tm_sec);*/
10747: /* strcpy(strstart,asctime(&tml)); */
10748: strcpy(strstart,asctime(&start_time));
1.126 brouard 10749:
10750: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 10751: /* tp.tm_sec = tp.tm_sec +86400; */
10752: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 10753: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
10754: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
10755: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 10756: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 10757: /* strt=asctime(&tmg); */
10758: /* printf("Time(after) =%s",strstart); */
10759: /* (void) time (&time_value);
10760: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
10761: * tm = *localtime(&time_value);
10762: * strstart=asctime(&tm);
10763: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
10764: */
10765:
10766: nberr=0; /* Number of errors and warnings */
10767: nbwarn=0;
1.184 brouard 10768: #ifdef WIN32
10769: _getcwd(pathcd, size);
10770: #else
1.126 brouard 10771: getcwd(pathcd, size);
1.184 brouard 10772: #endif
1.191 brouard 10773: syscompilerinfo(0);
1.196 brouard 10774: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 10775: if(argc <=1){
10776: printf("\nEnter the parameter file name: ");
1.205 brouard 10777: if(!fgets(pathr,FILENAMELENGTH,stdin)){
10778: printf("ERROR Empty parameter file name\n");
10779: goto end;
10780: }
1.126 brouard 10781: i=strlen(pathr);
10782: if(pathr[i-1]=='\n')
10783: pathr[i-1]='\0';
1.156 brouard 10784: i=strlen(pathr);
1.205 brouard 10785: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 10786: pathr[i-1]='\0';
1.205 brouard 10787: }
10788: i=strlen(pathr);
10789: if( i==0 ){
10790: printf("ERROR Empty parameter file name\n");
10791: goto end;
10792: }
10793: for (tok = pathr; tok != NULL; ){
1.126 brouard 10794: printf("Pathr |%s|\n",pathr);
10795: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
10796: printf("val= |%s| pathr=%s\n",val,pathr);
10797: strcpy (pathtot, val);
10798: if(pathr[0] == '\0') break; /* Dirty */
10799: }
10800: }
1.281 brouard 10801: else if (argc<=2){
10802: strcpy(pathtot,argv[1]);
10803: }
1.126 brouard 10804: else{
10805: strcpy(pathtot,argv[1]);
1.281 brouard 10806: strcpy(z,argv[2]);
10807: printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
1.126 brouard 10808: }
10809: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
10810: /*cygwin_split_path(pathtot,path,optionfile);
10811: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
10812: /* cutv(path,optionfile,pathtot,'\\');*/
10813:
10814: /* Split argv[0], imach program to get pathimach */
10815: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
10816: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10817: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
10818: /* strcpy(pathimach,argv[0]); */
10819: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
10820: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
10821: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 10822: #ifdef WIN32
10823: _chdir(path); /* Can be a relative path */
10824: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
10825: #else
1.126 brouard 10826: chdir(path); /* Can be a relative path */
1.184 brouard 10827: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
10828: #endif
10829: printf("Current directory %s!\n",pathcd);
1.126 brouard 10830: strcpy(command,"mkdir ");
10831: strcat(command,optionfilefiname);
10832: if((outcmd=system(command)) != 0){
1.169 brouard 10833: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 10834: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
10835: /* fclose(ficlog); */
10836: /* exit(1); */
10837: }
10838: /* if((imk=mkdir(optionfilefiname))<0){ */
10839: /* perror("mkdir"); */
10840: /* } */
10841:
10842: /*-------- arguments in the command line --------*/
10843:
1.186 brouard 10844: /* Main Log file */
1.126 brouard 10845: strcat(filelog, optionfilefiname);
10846: strcat(filelog,".log"); /* */
10847: if((ficlog=fopen(filelog,"w"))==NULL) {
10848: printf("Problem with logfile %s\n",filelog);
10849: goto end;
10850: }
10851: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 10852: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 10853: fprintf(ficlog,"\nEnter the parameter file name: \n");
10854: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
10855: path=%s \n\
10856: optionfile=%s\n\
10857: optionfilext=%s\n\
1.156 brouard 10858: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 10859:
1.197 brouard 10860: syscompilerinfo(1);
1.167 brouard 10861:
1.126 brouard 10862: printf("Local time (at start):%s",strstart);
10863: fprintf(ficlog,"Local time (at start): %s",strstart);
10864: fflush(ficlog);
10865: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 10866: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 10867:
10868: /* */
10869: strcpy(fileres,"r");
10870: strcat(fileres, optionfilefiname);
1.201 brouard 10871: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 10872: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 10873: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 10874:
1.186 brouard 10875: /* Main ---------arguments file --------*/
1.126 brouard 10876:
10877: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 10878: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
10879: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 10880: fflush(ficlog);
1.149 brouard 10881: /* goto end; */
10882: exit(70);
1.126 brouard 10883: }
10884:
10885: strcpy(filereso,"o");
1.201 brouard 10886: strcat(filereso,fileresu);
1.126 brouard 10887: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
10888: printf("Problem with Output resultfile: %s\n", filereso);
10889: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
10890: fflush(ficlog);
10891: goto end;
10892: }
1.278 brouard 10893: /*-------- Rewriting parameter file ----------*/
10894: strcpy(rfileres,"r"); /* "Rparameterfile */
10895: strcat(rfileres,optionfilefiname); /* Parameter file first name */
10896: strcat(rfileres,"."); /* */
10897: strcat(rfileres,optionfilext); /* Other files have txt extension */
10898: if((ficres =fopen(rfileres,"w"))==NULL) {
10899: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
10900: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
10901: fflush(ficlog);
10902: goto end;
10903: }
10904: fprintf(ficres,"#IMaCh %s\n",version);
1.126 brouard 10905:
1.278 brouard 10906:
1.126 brouard 10907: /* Reads comments: lines beginning with '#' */
10908: numlinepar=0;
1.277 brouard 10909: /* Is it a BOM UTF-8 Windows file? */
10910: /* First parameter line */
1.197 brouard 10911: while(fgets(line, MAXLINE, ficpar)) {
1.277 brouard 10912: noffset=0;
10913: if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
10914: {
10915: noffset=noffset+3;
10916: printf("# File is an UTF8 Bom.\n"); // 0xBF
10917: }
10918: else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
10919: {
10920: noffset=noffset+2;
10921: printf("# File is an UTF16BE BOM file\n");
10922: }
10923: else if( line[0] == 0 && line[1] == 0)
10924: {
10925: if( line[2] == (char)0xFE && line[3] == (char)0xFF){
10926: noffset=noffset+4;
10927: printf("# File is an UTF16BE BOM file\n");
10928: }
10929: } else{
10930: ;/*printf(" Not a BOM file\n");*/
10931: }
10932:
1.197 brouard 10933: /* If line starts with a # it is a comment */
1.277 brouard 10934: if (line[noffset] == '#') {
1.197 brouard 10935: numlinepar++;
10936: fputs(line,stdout);
10937: fputs(line,ficparo);
1.278 brouard 10938: fputs(line,ficres);
1.197 brouard 10939: fputs(line,ficlog);
10940: continue;
10941: }else
10942: break;
10943: }
10944: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
10945: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
10946: if (num_filled != 5) {
10947: printf("Should be 5 parameters\n");
10948: }
1.126 brouard 10949: numlinepar++;
1.197 brouard 10950: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
10951: }
10952: /* Second parameter line */
10953: while(fgets(line, MAXLINE, ficpar)) {
10954: /* If line starts with a # it is a comment */
10955: if (line[0] == '#') {
10956: numlinepar++;
10957: fputs(line,stdout);
10958: fputs(line,ficparo);
1.278 brouard 10959: fputs(line,ficres);
1.197 brouard 10960: fputs(line,ficlog);
10961: continue;
10962: }else
10963: break;
10964: }
1.223 brouard 10965: 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", \
10966: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
10967: if (num_filled != 11) {
10968: 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 10969: printf("but line=%s\n",line);
1.197 brouard 10970: }
1.223 brouard 10971: 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);
1.126 brouard 10972: }
1.203 brouard 10973: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 10974: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 10975: /* Third parameter line */
10976: while(fgets(line, MAXLINE, ficpar)) {
10977: /* If line starts with a # it is a comment */
10978: if (line[0] == '#') {
10979: numlinepar++;
10980: fputs(line,stdout);
10981: fputs(line,ficparo);
1.278 brouard 10982: fputs(line,ficres);
1.197 brouard 10983: fputs(line,ficlog);
10984: continue;
10985: }else
10986: break;
10987: }
1.201 brouard 10988: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
1.279 brouard 10989: if (num_filled != 1){
10990: printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
10991: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
1.197 brouard 10992: model[0]='\0';
10993: goto end;
10994: }
10995: else{
10996: if (model[0]=='+'){
10997: for(i=1; i<=strlen(model);i++)
10998: modeltemp[i-1]=model[i];
1.201 brouard 10999: strcpy(model,modeltemp);
1.197 brouard 11000: }
11001: }
1.199 brouard 11002: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 11003: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 11004: }
11005: /* 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); */
11006: /* numlinepar=numlinepar+3; /\* In general *\/ */
11007: /* 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); */
1.223 brouard 11008: 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);
11009: 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 11010: fflush(ficlog);
1.190 brouard 11011: /* if(model[0]=='#'|| model[0]== '\0'){ */
11012: if(model[0]=='#'){
1.279 brouard 11013: printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
11014: 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
11015: 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
1.187 brouard 11016: if(mle != -1){
1.279 brouard 11017: 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 11018: exit(1);
11019: }
11020: }
1.126 brouard 11021: while((c=getc(ficpar))=='#' && c!= EOF){
11022: ungetc(c,ficpar);
11023: fgets(line, MAXLINE, ficpar);
11024: numlinepar++;
1.195 brouard 11025: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
11026: z[0]=line[1];
11027: }
11028: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 11029: fputs(line, stdout);
11030: //puts(line);
1.126 brouard 11031: fputs(line,ficparo);
11032: fputs(line,ficlog);
11033: }
11034: ungetc(c,ficpar);
11035:
11036:
1.145 brouard 11037: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.268 brouard 11038: if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
11039: if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
11040: if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.136 brouard 11041: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
11042: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
11043: v1+v2*age+v2*v3 makes cptcovn = 3
11044: */
11045: if (strlen(model)>1)
1.187 brouard 11046: 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 11047: else
1.187 brouard 11048: ncovmodel=2; /* Constant and age */
1.133 brouard 11049: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
11050: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 11051: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
11052: 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);
11053: 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);
11054: fflush(stdout);
11055: fclose (ficlog);
11056: goto end;
11057: }
1.126 brouard 11058: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11059: delti=delti3[1][1];
11060: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
11061: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 11062: /* We could also provide initial parameters values giving by simple logistic regression
11063: * only one way, that is without matrix product. We will have nlstate maximizations */
11064: /* for(i=1;i<nlstate;i++){ */
11065: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11066: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11067: /* } */
1.126 brouard 11068: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 11069: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
11070: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11071: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11072: fclose (ficparo);
11073: fclose (ficlog);
11074: goto end;
11075: exit(0);
1.220 brouard 11076: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 11077: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 11078: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
11079: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 11080: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
11081: matcov=matrix(1,npar,1,npar);
1.203 brouard 11082: hess=matrix(1,npar,1,npar);
1.220 brouard 11083: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 11084: /* Read guessed parameters */
1.126 brouard 11085: /* Reads comments: lines beginning with '#' */
11086: while((c=getc(ficpar))=='#' && c!= EOF){
11087: ungetc(c,ficpar);
11088: fgets(line, MAXLINE, ficpar);
11089: numlinepar++;
1.141 brouard 11090: fputs(line,stdout);
1.126 brouard 11091: fputs(line,ficparo);
11092: fputs(line,ficlog);
11093: }
11094: ungetc(c,ficpar);
11095:
11096: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 11097: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 11098: for(i=1; i <=nlstate; i++){
1.234 brouard 11099: j=0;
1.126 brouard 11100: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 11101: if(jj==i) continue;
11102: j++;
11103: fscanf(ficpar,"%1d%1d",&i1,&j1);
11104: if ((i1 != i) || (j1 != jj)){
11105: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 11106: It might be a problem of design; if ncovcol and the model are correct\n \
11107: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 11108: exit(1);
11109: }
11110: fprintf(ficparo,"%1d%1d",i1,j1);
11111: if(mle==1)
11112: printf("%1d%1d",i,jj);
11113: fprintf(ficlog,"%1d%1d",i,jj);
11114: for(k=1; k<=ncovmodel;k++){
11115: fscanf(ficpar," %lf",¶m[i][j][k]);
11116: if(mle==1){
11117: printf(" %lf",param[i][j][k]);
11118: fprintf(ficlog," %lf",param[i][j][k]);
11119: }
11120: else
11121: fprintf(ficlog," %lf",param[i][j][k]);
11122: fprintf(ficparo," %lf",param[i][j][k]);
11123: }
11124: fscanf(ficpar,"\n");
11125: numlinepar++;
11126: if(mle==1)
11127: printf("\n");
11128: fprintf(ficlog,"\n");
11129: fprintf(ficparo,"\n");
1.126 brouard 11130: }
11131: }
11132: fflush(ficlog);
1.234 brouard 11133:
1.251 brouard 11134: /* Reads parameters values */
1.126 brouard 11135: p=param[1][1];
1.251 brouard 11136: pstart=paramstart[1][1];
1.126 brouard 11137:
11138: /* Reads comments: lines beginning with '#' */
11139: while((c=getc(ficpar))=='#' && c!= EOF){
11140: ungetc(c,ficpar);
11141: fgets(line, MAXLINE, ficpar);
11142: numlinepar++;
1.141 brouard 11143: fputs(line,stdout);
1.126 brouard 11144: fputs(line,ficparo);
11145: fputs(line,ficlog);
11146: }
11147: ungetc(c,ficpar);
11148:
11149: for(i=1; i <=nlstate; i++){
11150: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 11151: fscanf(ficpar,"%1d%1d",&i1,&j1);
11152: if ( (i1-i) * (j1-j) != 0){
11153: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
11154: exit(1);
11155: }
11156: printf("%1d%1d",i,j);
11157: fprintf(ficparo,"%1d%1d",i1,j1);
11158: fprintf(ficlog,"%1d%1d",i1,j1);
11159: for(k=1; k<=ncovmodel;k++){
11160: fscanf(ficpar,"%le",&delti3[i][j][k]);
11161: printf(" %le",delti3[i][j][k]);
11162: fprintf(ficparo," %le",delti3[i][j][k]);
11163: fprintf(ficlog," %le",delti3[i][j][k]);
11164: }
11165: fscanf(ficpar,"\n");
11166: numlinepar++;
11167: printf("\n");
11168: fprintf(ficparo,"\n");
11169: fprintf(ficlog,"\n");
1.126 brouard 11170: }
11171: }
11172: fflush(ficlog);
1.234 brouard 11173:
1.145 brouard 11174: /* Reads covariance matrix */
1.126 brouard 11175: delti=delti3[1][1];
1.220 brouard 11176:
11177:
1.126 brouard 11178: /* 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 11179:
1.126 brouard 11180: /* Reads comments: lines beginning with '#' */
11181: while((c=getc(ficpar))=='#' && c!= EOF){
11182: ungetc(c,ficpar);
11183: fgets(line, MAXLINE, ficpar);
11184: numlinepar++;
1.141 brouard 11185: fputs(line,stdout);
1.126 brouard 11186: fputs(line,ficparo);
11187: fputs(line,ficlog);
11188: }
11189: ungetc(c,ficpar);
1.220 brouard 11190:
1.126 brouard 11191: matcov=matrix(1,npar,1,npar);
1.203 brouard 11192: hess=matrix(1,npar,1,npar);
1.131 brouard 11193: for(i=1; i <=npar; i++)
11194: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 11195:
1.194 brouard 11196: /* Scans npar lines */
1.126 brouard 11197: for(i=1; i <=npar; i++){
1.226 brouard 11198: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 11199: if(count != 3){
1.226 brouard 11200: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11201: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11202: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11203: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 11204: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
11205: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 11206: exit(1);
1.220 brouard 11207: }else{
1.226 brouard 11208: if(mle==1)
11209: printf("%1d%1d%d",i1,j1,jk);
11210: }
11211: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
11212: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 11213: for(j=1; j <=i; j++){
1.226 brouard 11214: fscanf(ficpar," %le",&matcov[i][j]);
11215: if(mle==1){
11216: printf(" %.5le",matcov[i][j]);
11217: }
11218: fprintf(ficlog," %.5le",matcov[i][j]);
11219: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 11220: }
11221: fscanf(ficpar,"\n");
11222: numlinepar++;
11223: if(mle==1)
1.220 brouard 11224: printf("\n");
1.126 brouard 11225: fprintf(ficlog,"\n");
11226: fprintf(ficparo,"\n");
11227: }
1.194 brouard 11228: /* End of read covariance matrix npar lines */
1.126 brouard 11229: for(i=1; i <=npar; i++)
11230: for(j=i+1;j<=npar;j++)
1.226 brouard 11231: matcov[i][j]=matcov[j][i];
1.126 brouard 11232:
11233: if(mle==1)
11234: printf("\n");
11235: fprintf(ficlog,"\n");
11236:
11237: fflush(ficlog);
11238:
11239: } /* End of mle != -3 */
1.218 brouard 11240:
1.186 brouard 11241: /* Main data
11242: */
1.126 brouard 11243: n= lastobs;
11244: num=lvector(1,n);
11245: moisnais=vector(1,n);
11246: annais=vector(1,n);
11247: moisdc=vector(1,n);
11248: andc=vector(1,n);
1.220 brouard 11249: weight=vector(1,n);
1.126 brouard 11250: agedc=vector(1,n);
11251: cod=ivector(1,n);
1.220 brouard 11252: for(i=1;i<=n;i++){
1.234 brouard 11253: num[i]=0;
11254: moisnais[i]=0;
11255: annais[i]=0;
11256: moisdc[i]=0;
11257: andc[i]=0;
11258: agedc[i]=0;
11259: cod[i]=0;
11260: weight[i]=1.0; /* Equal weights, 1 by default */
11261: }
1.126 brouard 11262: mint=matrix(1,maxwav,1,n);
11263: anint=matrix(1,maxwav,1,n);
1.131 brouard 11264: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 11265: tab=ivector(1,NCOVMAX);
1.144 brouard 11266: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 11267: 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 11268:
1.136 brouard 11269: /* Reads data from file datafile */
11270: if (readdata(datafile, firstobs, lastobs, &imx)==1)
11271: goto end;
11272:
11273: /* Calculation of the number of parameters from char model */
1.234 brouard 11274: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 11275: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
11276: k=3 V4 Tvar[k=3]= 4 (from V4)
11277: k=2 V1 Tvar[k=2]= 1 (from V1)
11278: k=1 Tvar[1]=2 (from V2)
1.234 brouard 11279: */
11280:
11281: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
11282: TvarsDind=ivector(1,NCOVMAX); /* */
11283: TvarsD=ivector(1,NCOVMAX); /* */
11284: TvarsQind=ivector(1,NCOVMAX); /* */
11285: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 11286: TvarF=ivector(1,NCOVMAX); /* */
11287: TvarFind=ivector(1,NCOVMAX); /* */
11288: TvarV=ivector(1,NCOVMAX); /* */
11289: TvarVind=ivector(1,NCOVMAX); /* */
11290: TvarA=ivector(1,NCOVMAX); /* */
11291: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 11292: TvarFD=ivector(1,NCOVMAX); /* */
11293: TvarFDind=ivector(1,NCOVMAX); /* */
11294: TvarFQ=ivector(1,NCOVMAX); /* */
11295: TvarFQind=ivector(1,NCOVMAX); /* */
11296: TvarVD=ivector(1,NCOVMAX); /* */
11297: TvarVDind=ivector(1,NCOVMAX); /* */
11298: TvarVQ=ivector(1,NCOVMAX); /* */
11299: TvarVQind=ivector(1,NCOVMAX); /* */
11300:
1.230 brouard 11301: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 11302: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 11303: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
11304: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
11305: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 11306: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
11307: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
11308: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
11309: */
11310: /* For model-covariate k tells which data-covariate to use but
11311: because this model-covariate is a construction we invent a new column
11312: ncovcol + k1
11313: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
11314: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 11315: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
11316: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 11317: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
11318: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 11319: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 11320: */
1.145 brouard 11321: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
11322: 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 11323: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
11324: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 11325: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 11326: 4 covariates (3 plus signs)
11327: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
11328: */
1.230 brouard 11329: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 11330: * individual dummy, fixed or varying:
11331: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
11332: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 11333: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
11334: * V1 df, V2 qf, V3 & V4 dv, V5 qv
11335: * Tmodelind[1]@9={9,0,3,2,}*/
11336: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
11337: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 11338: * individual quantitative, fixed or varying:
11339: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
11340: * 3, 1, 0, 0, 0, 0, 0, 0},
11341: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 11342: /* Main decodemodel */
11343:
1.187 brouard 11344:
1.223 brouard 11345: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 11346: goto end;
11347:
1.137 brouard 11348: if((double)(lastobs-imx)/(double)imx > 1.10){
11349: nbwarn++;
11350: 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);
11351: 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);
11352: }
1.136 brouard 11353: /* if(mle==1){*/
1.137 brouard 11354: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
11355: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 11356: }
11357:
11358: /*-calculation of age at interview from date of interview and age at death -*/
11359: agev=matrix(1,maxwav,1,imx);
11360:
11361: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
11362: goto end;
11363:
1.126 brouard 11364:
1.136 brouard 11365: agegomp=(int)agemin;
11366: free_vector(moisnais,1,n);
11367: free_vector(annais,1,n);
1.126 brouard 11368: /* free_matrix(mint,1,maxwav,1,n);
11369: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 11370: /* free_vector(moisdc,1,n); */
11371: /* free_vector(andc,1,n); */
1.145 brouard 11372: /* */
11373:
1.126 brouard 11374: wav=ivector(1,imx);
1.214 brouard 11375: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
11376: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
11377: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
11378: 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.*/
11379: bh=imatrix(1,lastpass-firstpass+2,1,imx);
11380: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 11381:
11382: /* Concatenates waves */
1.214 brouard 11383: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
11384: Death is a valid wave (if date is known).
11385: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
11386: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
11387: and mw[mi+1][i]. dh depends on stepm.
11388: */
11389:
1.126 brouard 11390: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 11391: /* Concatenates waves */
1.145 brouard 11392:
1.215 brouard 11393: free_vector(moisdc,1,n);
11394: free_vector(andc,1,n);
11395:
1.126 brouard 11396: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
11397: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
11398: ncodemax[1]=1;
1.145 brouard 11399: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 11400: cptcoveff=0;
1.220 brouard 11401: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
11402: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 11403: }
11404:
11405: ncovcombmax=pow(2,cptcoveff);
11406: invalidvarcomb=ivector(1, ncovcombmax);
11407: for(i=1;i<ncovcombmax;i++)
11408: invalidvarcomb[i]=0;
11409:
1.211 brouard 11410: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 11411: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 11412: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 11413:
1.200 brouard 11414: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 11415: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 11416: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 11417: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
11418: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
11419: * (currently 0 or 1) in the data.
11420: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
11421: * corresponding modality (h,j).
11422: */
11423:
1.145 brouard 11424: h=0;
11425: /*if (cptcovn > 0) */
1.126 brouard 11426: m=pow(2,cptcoveff);
11427:
1.144 brouard 11428: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 11429: * For k=4 covariates, h goes from 1 to m=2**k
11430: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
11431: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 11432: * h\k 1 2 3 4
1.143 brouard 11433: *______________________________
11434: * 1 i=1 1 i=1 1 i=1 1 i=1 1
11435: * 2 2 1 1 1
11436: * 3 i=2 1 2 1 1
11437: * 4 2 2 1 1
11438: * 5 i=3 1 i=2 1 2 1
11439: * 6 2 1 2 1
11440: * 7 i=4 1 2 2 1
11441: * 8 2 2 2 1
1.197 brouard 11442: * 9 i=5 1 i=3 1 i=2 1 2
11443: * 10 2 1 1 2
11444: * 11 i=6 1 2 1 2
11445: * 12 2 2 1 2
11446: * 13 i=7 1 i=4 1 2 2
11447: * 14 2 1 2 2
11448: * 15 i=8 1 2 2 2
11449: * 16 2 2 2 2
1.143 brouard 11450: */
1.212 brouard 11451: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 11452: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
11453: * and the value of each covariate?
11454: * V1=1, V2=1, V3=2, V4=1 ?
11455: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
11456: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
11457: * In order to get the real value in the data, we use nbcode
11458: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
11459: * We are keeping this crazy system in order to be able (in the future?)
11460: * to have more than 2 values (0 or 1) for a covariate.
11461: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
11462: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
11463: * bbbbbbbb
11464: * 76543210
11465: * h-1 00000101 (6-1=5)
1.219 brouard 11466: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 11467: * &
11468: * 1 00000001 (1)
1.219 brouard 11469: * 00000000 = 1 & ((h-1) >> (k-1))
11470: * +1= 00000001 =1
1.211 brouard 11471: *
11472: * h=14, k=3 => h'=h-1=13, k'=k-1=2
11473: * h' 1101 =2^3+2^2+0x2^1+2^0
11474: * >>k' 11
11475: * & 00000001
11476: * = 00000001
11477: * +1 = 00000010=2 = codtabm(14,3)
11478: * Reverse h=6 and m=16?
11479: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
11480: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
11481: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
11482: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
11483: * V3=decodtabm(14,3,2**4)=2
11484: * h'=13 1101 =2^3+2^2+0x2^1+2^0
11485: *(h-1) >> (j-1) 0011 =13 >> 2
11486: * &1 000000001
11487: * = 000000001
11488: * +1= 000000010 =2
11489: * 2211
11490: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
11491: * V3=2
1.220 brouard 11492: * codtabm and decodtabm are identical
1.211 brouard 11493: */
11494:
1.145 brouard 11495:
11496: free_ivector(Ndum,-1,NCOVMAX);
11497:
11498:
1.126 brouard 11499:
1.186 brouard 11500: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 11501: strcpy(optionfilegnuplot,optionfilefiname);
11502: if(mle==-3)
1.201 brouard 11503: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 11504: strcat(optionfilegnuplot,".gp");
11505:
11506: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
11507: printf("Problem with file %s",optionfilegnuplot);
11508: }
11509: else{
1.204 brouard 11510: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 11511: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 11512: //fprintf(ficgp,"set missing 'NaNq'\n");
11513: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 11514: }
11515: /* fclose(ficgp);*/
1.186 brouard 11516:
11517:
11518: /* Initialisation of --------- index.htm --------*/
1.126 brouard 11519:
11520: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
11521: if(mle==-3)
1.201 brouard 11522: strcat(optionfilehtm,"-MORT_");
1.126 brouard 11523: strcat(optionfilehtm,".htm");
11524: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 11525: printf("Problem with %s \n",optionfilehtm);
11526: exit(0);
1.126 brouard 11527: }
11528:
11529: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
11530: strcat(optionfilehtmcov,"-cov.htm");
11531: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
11532: printf("Problem with %s \n",optionfilehtmcov), exit(0);
11533: }
11534: else{
11535: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
11536: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11537: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 11538: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
11539: }
11540:
1.213 brouard 11541: 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 11542: <hr size=\"2\" color=\"#EC5E5E\"> \n\
11543: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 11544: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 11545: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 11546: \n\
11547: <hr size=\"2\" color=\"#EC5E5E\">\
11548: <ul><li><h4>Parameter files</h4>\n\
11549: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
11550: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
11551: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
11552: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
11553: - Date and time at start: %s</ul>\n",\
11554: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
11555: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
11556: fileres,fileres,\
11557: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
11558: fflush(fichtm);
11559:
11560: strcpy(pathr,path);
11561: strcat(pathr,optionfilefiname);
1.184 brouard 11562: #ifdef WIN32
11563: _chdir(optionfilefiname); /* Move to directory named optionfile */
11564: #else
1.126 brouard 11565: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 11566: #endif
11567:
1.126 brouard 11568:
1.220 brouard 11569: /* Calculates basic frequencies. Computes observed prevalence at single age
11570: and for any valid combination of covariates
1.126 brouard 11571: and prints on file fileres'p'. */
1.251 brouard 11572: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 11573: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 11574:
11575: fprintf(fichtm,"\n");
1.274 brouard 11576: 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",\
11577: ftol, stepm);
11578: fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
11579: ncurrv=1;
11580: for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
11581: fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
11582: ncurrv=i;
11583: for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
11584: fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);
11585: ncurrv=i;
11586: for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
11587: fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);
11588: ncurrv=i;
11589: for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
11590: 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", \
11591: nlstate, ndeath, maxwav, mle, weightopt);
11592:
11593: fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
11594: <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
11595:
11596:
11597: fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
1.126 brouard 11598: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
11599: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
1.274 brouard 11600: imx,agemin,agemax,jmin,jmax,jmean);
1.126 brouard 11601: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.268 brouard 11602: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11603: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11604: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
11605: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 11606:
1.126 brouard 11607: /* For Powell, parameters are in a vector p[] starting at p[1]
11608: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
11609: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
11610:
11611: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 11612: /* For mortality only */
1.126 brouard 11613: if (mle==-3){
1.136 brouard 11614: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 11615: for(i=1;i<=NDIM;i++)
11616: for(j=1;j<=NDIM;j++)
11617: ximort[i][j]=0.;
1.186 brouard 11618: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 11619: cens=ivector(1,n);
11620: ageexmed=vector(1,n);
11621: agecens=vector(1,n);
11622: dcwave=ivector(1,n);
1.223 brouard 11623:
1.126 brouard 11624: for (i=1; i<=imx; i++){
11625: dcwave[i]=-1;
11626: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 11627: if (s[m][i]>nlstate) {
11628: dcwave[i]=m;
11629: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
11630: break;
11631: }
1.126 brouard 11632: }
1.226 brouard 11633:
1.126 brouard 11634: for (i=1; i<=imx; i++) {
11635: if (wav[i]>0){
1.226 brouard 11636: ageexmed[i]=agev[mw[1][i]][i];
11637: j=wav[i];
11638: agecens[i]=1.;
11639:
11640: if (ageexmed[i]> 1 && wav[i] > 0){
11641: agecens[i]=agev[mw[j][i]][i];
11642: cens[i]= 1;
11643: }else if (ageexmed[i]< 1)
11644: cens[i]= -1;
11645: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
11646: cens[i]=0 ;
1.126 brouard 11647: }
11648: else cens[i]=-1;
11649: }
11650:
11651: for (i=1;i<=NDIM;i++) {
11652: for (j=1;j<=NDIM;j++)
1.226 brouard 11653: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 11654: }
11655:
1.145 brouard 11656: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 11657: /*printf("%lf %lf", p[1], p[2]);*/
11658:
11659:
1.136 brouard 11660: #ifdef GSL
11661: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 11662: #else
1.126 brouard 11663: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 11664: #endif
1.201 brouard 11665: strcpy(filerespow,"POW-MORT_");
11666: strcat(filerespow,fileresu);
1.126 brouard 11667: if((ficrespow=fopen(filerespow,"w"))==NULL) {
11668: printf("Problem with resultfile: %s\n", filerespow);
11669: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
11670: }
1.136 brouard 11671: #ifdef GSL
11672: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 11673: #else
1.126 brouard 11674: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 11675: #endif
1.126 brouard 11676: /* for (i=1;i<=nlstate;i++)
11677: for(j=1;j<=nlstate+ndeath;j++)
11678: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
11679: */
11680: fprintf(ficrespow,"\n");
1.136 brouard 11681: #ifdef GSL
11682: /* gsl starts here */
11683: T = gsl_multimin_fminimizer_nmsimplex;
11684: gsl_multimin_fminimizer *sfm = NULL;
11685: gsl_vector *ss, *x;
11686: gsl_multimin_function minex_func;
11687:
11688: /* Initial vertex size vector */
11689: ss = gsl_vector_alloc (NDIM);
11690:
11691: if (ss == NULL){
11692: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
11693: }
11694: /* Set all step sizes to 1 */
11695: gsl_vector_set_all (ss, 0.001);
11696:
11697: /* Starting point */
1.126 brouard 11698:
1.136 brouard 11699: x = gsl_vector_alloc (NDIM);
11700:
11701: if (x == NULL){
11702: gsl_vector_free(ss);
11703: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
11704: }
11705:
11706: /* Initialize method and iterate */
11707: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 11708: /* gsl_vector_set(x, 0, 0.0268); */
11709: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 11710: gsl_vector_set(x, 0, p[1]);
11711: gsl_vector_set(x, 1, p[2]);
11712:
11713: minex_func.f = &gompertz_f;
11714: minex_func.n = NDIM;
11715: minex_func.params = (void *)&p; /* ??? */
11716:
11717: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
11718: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
11719:
11720: printf("Iterations beginning .....\n\n");
11721: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
11722:
11723: iteri=0;
11724: while (rval == GSL_CONTINUE){
11725: iteri++;
11726: status = gsl_multimin_fminimizer_iterate(sfm);
11727:
11728: if (status) printf("error: %s\n", gsl_strerror (status));
11729: fflush(0);
11730:
11731: if (status)
11732: break;
11733:
11734: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
11735: ssval = gsl_multimin_fminimizer_size (sfm);
11736:
11737: if (rval == GSL_SUCCESS)
11738: printf ("converged to a local maximum at\n");
11739:
11740: printf("%5d ", iteri);
11741: for (it = 0; it < NDIM; it++){
11742: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
11743: }
11744: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
11745: }
11746:
11747: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
11748:
11749: gsl_vector_free(x); /* initial values */
11750: gsl_vector_free(ss); /* inital step size */
11751: for (it=0; it<NDIM; it++){
11752: p[it+1]=gsl_vector_get(sfm->x,it);
11753: fprintf(ficrespow," %.12lf", p[it]);
11754: }
11755: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
11756: #endif
11757: #ifdef POWELL
11758: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
11759: #endif
1.126 brouard 11760: fclose(ficrespow);
11761:
1.203 brouard 11762: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 11763:
11764: for(i=1; i <=NDIM; i++)
11765: for(j=i+1;j<=NDIM;j++)
1.220 brouard 11766: matcov[i][j]=matcov[j][i];
1.126 brouard 11767:
11768: printf("\nCovariance matrix\n ");
1.203 brouard 11769: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 11770: for(i=1; i <=NDIM; i++) {
11771: for(j=1;j<=NDIM;j++){
1.220 brouard 11772: printf("%f ",matcov[i][j]);
11773: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 11774: }
1.203 brouard 11775: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 11776: }
11777:
11778: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 11779: for (i=1;i<=NDIM;i++) {
1.126 brouard 11780: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 11781: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
11782: }
1.126 brouard 11783: lsurv=vector(1,AGESUP);
11784: lpop=vector(1,AGESUP);
11785: tpop=vector(1,AGESUP);
11786: lsurv[agegomp]=100000;
11787:
11788: for (k=agegomp;k<=AGESUP;k++) {
11789: agemortsup=k;
11790: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
11791: }
11792:
11793: for (k=agegomp;k<agemortsup;k++)
11794: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
11795:
11796: for (k=agegomp;k<agemortsup;k++){
11797: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
11798: sumlpop=sumlpop+lpop[k];
11799: }
11800:
11801: tpop[agegomp]=sumlpop;
11802: for (k=agegomp;k<(agemortsup-3);k++){
11803: /* tpop[k+1]=2;*/
11804: tpop[k+1]=tpop[k]-lpop[k];
11805: }
11806:
11807:
11808: printf("\nAge lx qx dx Lx Tx e(x)\n");
11809: for (k=agegomp;k<(agemortsup-2);k++)
11810: 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]);
11811:
11812:
11813: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 11814: ageminpar=50;
11815: agemaxpar=100;
1.194 brouard 11816: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
11817: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11818: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11819: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
11820: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
11821: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11822: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 11823: }else{
11824: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
11825: 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 11826: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 11827: }
1.201 brouard 11828: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 11829: stepm, weightopt,\
11830: model,imx,p,matcov,agemortsup);
11831:
11832: free_vector(lsurv,1,AGESUP);
11833: free_vector(lpop,1,AGESUP);
11834: free_vector(tpop,1,AGESUP);
1.220 brouard 11835: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 11836: free_ivector(cens,1,n);
11837: free_vector(agecens,1,n);
11838: free_ivector(dcwave,1,n);
1.220 brouard 11839: #ifdef GSL
1.136 brouard 11840: #endif
1.186 brouard 11841: } /* Endof if mle==-3 mortality only */
1.205 brouard 11842: /* Standard */
11843: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
11844: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11845: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 11846: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 11847: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11848: for (k=1; k<=npar;k++)
11849: printf(" %d %8.5f",k,p[k]);
11850: printf("\n");
1.205 brouard 11851: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
11852: /* mlikeli uses func not funcone */
1.247 brouard 11853: /* for(i=1;i<nlstate;i++){ */
11854: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
11855: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
11856: /* } */
1.205 brouard 11857: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
11858: }
11859: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
11860: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
11861: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
11862: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11863: }
11864: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 11865: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
11866: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
11867: for (k=1; k<=npar;k++)
11868: printf(" %d %8.5f",k,p[k]);
11869: printf("\n");
11870:
11871: /*--------- results files --------------*/
1.224 brouard 11872: 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 11873:
11874:
11875: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11876: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11877: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
11878: for(i=1,jk=1; i <=nlstate; i++){
11879: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 11880: if (k != i) {
11881: printf("%d%d ",i,k);
11882: fprintf(ficlog,"%d%d ",i,k);
11883: fprintf(ficres,"%1d%1d ",i,k);
11884: for(j=1; j <=ncovmodel; j++){
11885: printf("%12.7f ",p[jk]);
11886: fprintf(ficlog,"%12.7f ",p[jk]);
11887: fprintf(ficres,"%12.7f ",p[jk]);
11888: jk++;
11889: }
11890: printf("\n");
11891: fprintf(ficlog,"\n");
11892: fprintf(ficres,"\n");
11893: }
1.126 brouard 11894: }
11895: }
1.203 brouard 11896: if(mle != 0){
11897: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 11898: ftolhess=ftol; /* Usually correct */
1.203 brouard 11899: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
11900: 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");
11901: 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");
11902: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 11903: for(k=1; k <=(nlstate+ndeath); k++){
11904: if (k != i) {
11905: printf("%d%d ",i,k);
11906: fprintf(ficlog,"%d%d ",i,k);
11907: for(j=1; j <=ncovmodel; j++){
11908: 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]));
11909: 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]));
11910: jk++;
11911: }
11912: printf("\n");
11913: fprintf(ficlog,"\n");
11914: }
11915: }
1.193 brouard 11916: }
1.203 brouard 11917: } /* end of hesscov and Wald tests */
1.225 brouard 11918:
1.203 brouard 11919: /* */
1.126 brouard 11920: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
11921: printf("# Scales (for hessian or gradient estimation)\n");
11922: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
11923: for(i=1,jk=1; i <=nlstate; i++){
11924: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 11925: if (j!=i) {
11926: fprintf(ficres,"%1d%1d",i,j);
11927: printf("%1d%1d",i,j);
11928: fprintf(ficlog,"%1d%1d",i,j);
11929: for(k=1; k<=ncovmodel;k++){
11930: printf(" %.5e",delti[jk]);
11931: fprintf(ficlog," %.5e",delti[jk]);
11932: fprintf(ficres," %.5e",delti[jk]);
11933: jk++;
11934: }
11935: printf("\n");
11936: fprintf(ficlog,"\n");
11937: fprintf(ficres,"\n");
11938: }
1.126 brouard 11939: }
11940: }
11941:
11942: 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 11943: if(mle >= 1) /* To big for the screen */
1.126 brouard 11944: 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");
11945: 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");
11946: /* # 121 Var(a12)\n\ */
11947: /* # 122 Cov(b12,a12) Var(b12)\n\ */
11948: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
11949: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
11950: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
11951: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
11952: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
11953: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
11954:
11955:
11956: /* Just to have a covariance matrix which will be more understandable
11957: even is we still don't want to manage dictionary of variables
11958: */
11959: for(itimes=1;itimes<=2;itimes++){
11960: jj=0;
11961: for(i=1; i <=nlstate; i++){
1.225 brouard 11962: for(j=1; j <=nlstate+ndeath; j++){
11963: if(j==i) continue;
11964: for(k=1; k<=ncovmodel;k++){
11965: jj++;
11966: ca[0]= k+'a'-1;ca[1]='\0';
11967: if(itimes==1){
11968: if(mle>=1)
11969: printf("#%1d%1d%d",i,j,k);
11970: fprintf(ficlog,"#%1d%1d%d",i,j,k);
11971: fprintf(ficres,"#%1d%1d%d",i,j,k);
11972: }else{
11973: if(mle>=1)
11974: printf("%1d%1d%d",i,j,k);
11975: fprintf(ficlog,"%1d%1d%d",i,j,k);
11976: fprintf(ficres,"%1d%1d%d",i,j,k);
11977: }
11978: ll=0;
11979: for(li=1;li <=nlstate; li++){
11980: for(lj=1;lj <=nlstate+ndeath; lj++){
11981: if(lj==li) continue;
11982: for(lk=1;lk<=ncovmodel;lk++){
11983: ll++;
11984: if(ll<=jj){
11985: cb[0]= lk +'a'-1;cb[1]='\0';
11986: if(ll<jj){
11987: if(itimes==1){
11988: if(mle>=1)
11989: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11990: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11991: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11992: }else{
11993: if(mle>=1)
11994: printf(" %.5e",matcov[jj][ll]);
11995: fprintf(ficlog," %.5e",matcov[jj][ll]);
11996: fprintf(ficres," %.5e",matcov[jj][ll]);
11997: }
11998: }else{
11999: if(itimes==1){
12000: if(mle>=1)
12001: printf(" Var(%s%1d%1d)",ca,i,j);
12002: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
12003: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
12004: }else{
12005: if(mle>=1)
12006: printf(" %.7e",matcov[jj][ll]);
12007: fprintf(ficlog," %.7e",matcov[jj][ll]);
12008: fprintf(ficres," %.7e",matcov[jj][ll]);
12009: }
12010: }
12011: }
12012: } /* end lk */
12013: } /* end lj */
12014: } /* end li */
12015: if(mle>=1)
12016: printf("\n");
12017: fprintf(ficlog,"\n");
12018: fprintf(ficres,"\n");
12019: numlinepar++;
12020: } /* end k*/
12021: } /*end j */
1.126 brouard 12022: } /* end i */
12023: } /* end itimes */
12024:
12025: fflush(ficlog);
12026: fflush(ficres);
1.225 brouard 12027: while(fgets(line, MAXLINE, ficpar)) {
12028: /* If line starts with a # it is a comment */
12029: if (line[0] == '#') {
12030: numlinepar++;
12031: fputs(line,stdout);
12032: fputs(line,ficparo);
12033: fputs(line,ficlog);
12034: continue;
12035: }else
12036: break;
12037: }
12038:
1.209 brouard 12039: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
12040: /* ungetc(c,ficpar); */
12041: /* fgets(line, MAXLINE, ficpar); */
12042: /* fputs(line,stdout); */
12043: /* fputs(line,ficparo); */
12044: /* } */
12045: /* ungetc(c,ficpar); */
1.126 brouard 12046:
12047: estepm=0;
1.209 brouard 12048: 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 12049:
12050: if (num_filled != 6) {
12051: 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);
12052: 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);
12053: goto end;
12054: }
12055: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
12056: }
12057: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
12058: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
12059:
1.209 brouard 12060: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 12061: if (estepm==0 || estepm < stepm) estepm=stepm;
12062: if (fage <= 2) {
12063: bage = ageminpar;
12064: fage = agemaxpar;
12065: }
12066:
12067: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 12068: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
12069: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 12070:
1.186 brouard 12071: /* Other stuffs, more or less useful */
1.254 brouard 12072: while(fgets(line, MAXLINE, ficpar)) {
12073: /* If line starts with a # it is a comment */
12074: if (line[0] == '#') {
12075: numlinepar++;
12076: fputs(line,stdout);
12077: fputs(line,ficparo);
12078: fputs(line,ficlog);
12079: continue;
12080: }else
12081: break;
12082: }
12083:
12084: 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){
12085:
12086: if (num_filled != 7) {
12087: 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);
12088: 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);
12089: goto end;
12090: }
12091: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
12092: 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);
12093: 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);
12094: 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 12095: }
1.254 brouard 12096:
12097: while(fgets(line, MAXLINE, ficpar)) {
12098: /* If line starts with a # it is a comment */
12099: if (line[0] == '#') {
12100: numlinepar++;
12101: fputs(line,stdout);
12102: fputs(line,ficparo);
12103: fputs(line,ficlog);
12104: continue;
12105: }else
12106: break;
1.126 brouard 12107: }
12108:
12109:
12110: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
12111: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
12112:
1.254 brouard 12113: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
12114: if (num_filled != 1) {
12115: 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);
12116: 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);
12117: goto end;
12118: }
12119: printf("pop_based=%d\n",popbased);
12120: fprintf(ficlog,"pop_based=%d\n",popbased);
12121: fprintf(ficparo,"pop_based=%d\n",popbased);
12122: fprintf(ficres,"pop_based=%d\n",popbased);
12123: }
12124:
1.258 brouard 12125: /* Results */
12126: nresult=0;
12127: do{
12128: if(!fgets(line, MAXLINE, ficpar)){
12129: endishere=1;
12130: parameterline=14;
12131: }else if (line[0] == '#') {
12132: /* If line starts with a # it is a comment */
1.254 brouard 12133: numlinepar++;
12134: fputs(line,stdout);
12135: fputs(line,ficparo);
12136: fputs(line,ficlog);
12137: continue;
1.258 brouard 12138: }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
12139: parameterline=11;
12140: else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
12141: parameterline=12;
12142: else if(sscanf(line,"result:%[^\n]\n",modeltemp))
12143: parameterline=13;
12144: else{
12145: parameterline=14;
1.254 brouard 12146: }
1.258 brouard 12147: switch (parameterline){
12148: case 11:
12149: 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){
12150: if (num_filled != 8) {
12151: 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);
12152: 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);
12153: goto end;
12154: }
12155: 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);
12156: 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);
12157: 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);
12158: 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);
12159: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12160: dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
12161: dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
12162:
1.258 brouard 12163: }
1.254 brouard 12164: break;
1.258 brouard 12165: case 12:
12166: /*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);*/
12167: 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){
12168: if (num_filled != 8) {
1.262 brouard 12169: 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);
12170: 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 12171: goto end;
12172: }
12173: 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);
12174: 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);
12175: 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);
12176: 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);
12177: /* day and month of proj2 are not used but only year anproj2.*/
1.273 brouard 12178: dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
12179: dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
1.258 brouard 12180: }
1.230 brouard 12181: break;
1.258 brouard 12182: case 13:
12183: if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
12184: if (num_filled == 0){
12185: resultline[0]='\0';
12186: printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
12187: 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);
12188: break;
12189: } else if (num_filled != 1){
12190: printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12191: fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
12192: }
12193: nresult++; /* Sum of resultlines */
12194: printf("Result %d: result=%s\n",nresult, resultline);
12195: if(nresult > MAXRESULTLINES){
12196: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12197: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
12198: goto end;
12199: }
12200: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
12201: fprintf(ficparo,"result: %s\n",resultline);
12202: fprintf(ficres,"result: %s\n",resultline);
12203: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 12204: break;
1.258 brouard 12205: case 14:
1.259 brouard 12206: if(ncovmodel >2 && nresult==0 ){
12207: printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
1.258 brouard 12208: goto end;
12209: }
1.259 brouard 12210: break;
1.258 brouard 12211: default:
12212: nresult=1;
12213: decoderesult(".",nresult ); /* No covariate */
12214: }
12215: } /* End switch parameterline */
12216: }while(endishere==0); /* End do */
1.126 brouard 12217:
1.230 brouard 12218: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 12219: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 12220:
12221: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 12222: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 12223: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12224: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12225: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 12226: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 12227: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
12228: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 12229: }else{
1.270 brouard 12230: /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
12231: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
1.220 brouard 12232: }
12233: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.258 brouard 12234: model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
1.273 brouard 12235: jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
1.220 brouard 12236:
1.225 brouard 12237: /*------------ free_vector -------------*/
12238: /* chdir(path); */
1.220 brouard 12239:
1.215 brouard 12240: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
12241: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
12242: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
12243: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 12244: free_lvector(num,1,n);
12245: free_vector(agedc,1,n);
12246: /*free_matrix(covar,0,NCOVMAX,1,n);*/
12247: /*free_matrix(covar,1,NCOVMAX,1,n);*/
12248: fclose(ficparo);
12249: fclose(ficres);
1.220 brouard 12250:
12251:
1.186 brouard 12252: /* Other results (useful)*/
1.220 brouard 12253:
12254:
1.126 brouard 12255: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 12256: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
12257: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 12258: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 12259: fclose(ficrespl);
12260:
12261: /*------------- h Pij x at various ages ------------*/
1.180 brouard 12262: /*#include "hpijx.h"*/
12263: hPijx(p, bage, fage);
1.145 brouard 12264: fclose(ficrespij);
1.227 brouard 12265:
1.220 brouard 12266: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 12267: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 12268: k=1;
1.126 brouard 12269: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 12270:
1.269 brouard 12271: /* Prevalence for each covariate combination in probs[age][status][cov] */
12272: probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12273: for(i=AGEINF;i<=AGESUP;i++)
1.219 brouard 12274: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 12275: for(k=1;k<=ncovcombmax;k++)
12276: probs[i][j][k]=0.;
1.269 brouard 12277: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
12278: ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
1.219 brouard 12279: if (mobilav!=0 ||mobilavproj !=0 ) {
1.269 brouard 12280: mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
12281: for(i=AGEINF;i<=AGESUP;i++)
1.268 brouard 12282: for(j=1;j<=nlstate+ndeath;j++)
1.227 brouard 12283: for(k=1;k<=ncovcombmax;k++)
12284: mobaverages[i][j][k]=0.;
1.219 brouard 12285: mobaverage=mobaverages;
12286: if (mobilav!=0) {
1.235 brouard 12287: printf("Movingaveraging observed prevalence\n");
1.258 brouard 12288: fprintf(ficlog,"Movingaveraging observed prevalence\n");
1.227 brouard 12289: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
12290: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
12291: printf(" Error in movingaverage mobilav=%d\n",mobilav);
12292: }
1.269 brouard 12293: } else if (mobilavproj !=0) {
1.235 brouard 12294: printf("Movingaveraging projected observed prevalence\n");
1.258 brouard 12295: fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
1.227 brouard 12296: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
12297: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
12298: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
12299: }
1.269 brouard 12300: }else{
12301: printf("Internal error moving average\n");
12302: fflush(stdout);
12303: exit(1);
1.219 brouard 12304: }
12305: }/* end if moving average */
1.227 brouard 12306:
1.126 brouard 12307: /*---------- Forecasting ------------------*/
12308: if(prevfcast==1){
12309: /* if(stepm ==1){*/
1.269 brouard 12310: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 12311: }
1.269 brouard 12312:
12313: /* Backcasting */
1.217 brouard 12314: if(backcast==1){
1.219 brouard 12315: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12316: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12317: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
12318:
12319: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
12320:
12321: bprlim=matrix(1,nlstate,1,nlstate);
1.269 brouard 12322:
1.219 brouard 12323: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
12324: fclose(ficresplb);
12325:
1.222 brouard 12326: hBijx(p, bage, fage, mobaverage);
12327: fclose(ficrespijb);
1.219 brouard 12328:
1.269 brouard 12329: prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
12330: mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
12331: varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12332:
12333:
1.269 brouard 12334: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.219 brouard 12335: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12336: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
12337: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
1.269 brouard 12338: } /* end Backcasting */
1.268 brouard 12339:
1.186 brouard 12340:
12341: /* ------ Other prevalence ratios------------ */
1.126 brouard 12342:
1.215 brouard 12343: free_ivector(wav,1,imx);
12344: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
12345: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
12346: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 12347:
12348:
1.127 brouard 12349: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 12350:
1.201 brouard 12351: strcpy(filerese,"E_");
12352: strcat(filerese,fileresu);
1.126 brouard 12353: if((ficreseij=fopen(filerese,"w"))==NULL) {
12354: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12355: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
12356: }
1.208 brouard 12357: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
12358: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 12359:
12360: pstamp(ficreseij);
1.219 brouard 12361:
1.235 brouard 12362: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12363: if (cptcovn < 1){i1=1;}
12364:
12365: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12366: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12367: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12368: continue;
1.219 brouard 12369: fprintf(ficreseij,"\n#****** ");
1.235 brouard 12370: printf("\n#****** ");
1.225 brouard 12371: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12372: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12373: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12374: }
12375: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12376: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12377: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 12378: }
12379: fprintf(ficreseij,"******\n");
1.235 brouard 12380: printf("******\n");
1.219 brouard 12381:
12382: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12383: oldm=oldms;savm=savms;
1.235 brouard 12384: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 12385:
1.219 brouard 12386: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 12387: }
12388: fclose(ficreseij);
1.208 brouard 12389: printf("done evsij\n");fflush(stdout);
12390: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.269 brouard 12391:
1.218 brouard 12392:
1.227 brouard 12393: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 12394:
1.201 brouard 12395: strcpy(filerest,"T_");
12396: strcat(filerest,fileresu);
1.127 brouard 12397: if((ficrest=fopen(filerest,"w"))==NULL) {
12398: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
12399: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
12400: }
1.208 brouard 12401: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
12402: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.201 brouard 12403: strcpy(fileresstde,"STDE_");
12404: strcat(fileresstde,fileresu);
1.126 brouard 12405: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 12406: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
12407: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 12408: }
1.227 brouard 12409: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
12410: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 12411:
1.201 brouard 12412: strcpy(filerescve,"CVE_");
12413: strcat(filerescve,fileresu);
1.126 brouard 12414: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 12415: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
12416: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 12417: }
1.227 brouard 12418: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
12419: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 12420:
1.201 brouard 12421: strcpy(fileresv,"V_");
12422: strcat(fileresv,fileresu);
1.126 brouard 12423: if((ficresvij=fopen(fileresv,"w"))==NULL) {
12424: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
12425: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
12426: }
1.227 brouard 12427: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
12428: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 12429:
1.235 brouard 12430: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
12431: if (cptcovn < 1){i1=1;}
12432:
12433: for(nres=1; nres <= nresult; nres++) /* For each resultline */
12434: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 12435: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 12436: continue;
1.242 brouard 12437: printf("\n#****** Result for:");
12438: fprintf(ficrest,"\n#****** Result for:");
12439: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 12440: for(j=1;j<=cptcoveff;j++){
12441: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12442: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12443: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12444: }
1.235 brouard 12445: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12446: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12447: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12448: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12449: }
1.208 brouard 12450: fprintf(ficrest,"******\n");
1.227 brouard 12451: fprintf(ficlog,"******\n");
12452: printf("******\n");
1.208 brouard 12453:
12454: fprintf(ficresstdeij,"\n#****** ");
12455: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 12456: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 12457: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
12458: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 12459: }
1.235 brouard 12460: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12461: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12462: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12463: }
1.208 brouard 12464: fprintf(ficresstdeij,"******\n");
12465: fprintf(ficrescveij,"******\n");
12466:
12467: fprintf(ficresvij,"\n#****** ");
1.238 brouard 12468: /* pstamp(ficresvij); */
1.225 brouard 12469: for(j=1;j<=cptcoveff;j++)
1.227 brouard 12470: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 12471: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
12472: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
12473: }
1.208 brouard 12474: fprintf(ficresvij,"******\n");
12475:
12476: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12477: oldm=oldms;savm=savms;
1.235 brouard 12478: printf(" cvevsij ");
12479: fprintf(ficlog, " cvevsij ");
12480: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 12481: printf(" end cvevsij \n ");
12482: fprintf(ficlog, " end cvevsij \n ");
12483:
12484: /*
12485: */
12486: /* goto endfree; */
12487:
12488: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
12489: pstamp(ficrest);
12490:
1.269 brouard 12491: epj=vector(1,nlstate+1);
1.208 brouard 12492: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 12493: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
12494: cptcod= 0; /* To be deleted */
12495: printf("varevsij vpopbased=%d \n",vpopbased);
12496: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 12497: 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 12498: 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 ");
12499: if(vpopbased==1)
12500: 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);
12501: else
12502: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
12503: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
12504: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
12505: fprintf(ficrest,"\n");
12506: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
12507: printf("Computing age specific period (stable) prevalences in each health state \n");
12508: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
12509: for(age=bage; age <=fage ;age++){
1.235 brouard 12510: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 12511: if (vpopbased==1) {
12512: if(mobilav ==0){
12513: for(i=1; i<=nlstate;i++)
12514: prlim[i][i]=probs[(int)age][i][k];
12515: }else{ /* mobilav */
12516: for(i=1; i<=nlstate;i++)
12517: prlim[i][i]=mobaverage[(int)age][i][k];
12518: }
12519: }
1.219 brouard 12520:
1.227 brouard 12521: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
12522: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
12523: /* printf(" age %4.0f ",age); */
12524: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
12525: for(i=1, epj[j]=0.;i <=nlstate;i++) {
12526: epj[j] += prlim[i][i]*eij[i][j][(int)age];
12527: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
12528: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
12529: }
12530: epj[nlstate+1] +=epj[j];
12531: }
12532: /* printf(" age %4.0f \n",age); */
1.219 brouard 12533:
1.227 brouard 12534: for(i=1, vepp=0.;i <=nlstate;i++)
12535: for(j=1;j <=nlstate;j++)
12536: vepp += vareij[i][j][(int)age];
12537: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
12538: for(j=1;j <=nlstate;j++){
12539: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
12540: }
12541: fprintf(ficrest,"\n");
12542: }
1.208 brouard 12543: } /* End vpopbased */
1.269 brouard 12544: free_vector(epj,1,nlstate+1);
1.208 brouard 12545: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
12546: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.235 brouard 12547: printf("done selection\n");fflush(stdout);
12548: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 12549:
1.235 brouard 12550: } /* End k selection */
1.227 brouard 12551:
12552: printf("done State-specific expectancies\n");fflush(stdout);
12553: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
12554:
1.269 brouard 12555: /* variance-covariance of period prevalence*/
12556: varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
1.268 brouard 12557:
1.227 brouard 12558:
12559: free_vector(weight,1,n);
12560: free_imatrix(Tvard,1,NCOVMAX,1,2);
12561: free_imatrix(s,1,maxwav+1,1,n);
12562: free_matrix(anint,1,maxwav,1,n);
12563: free_matrix(mint,1,maxwav,1,n);
12564: free_ivector(cod,1,n);
12565: free_ivector(tab,1,NCOVMAX);
12566: fclose(ficresstdeij);
12567: fclose(ficrescveij);
12568: fclose(ficresvij);
12569: fclose(ficrest);
12570: fclose(ficpar);
12571:
12572:
1.126 brouard 12573: /*---------- End : free ----------------*/
1.219 brouard 12574: if (mobilav!=0 ||mobilavproj !=0)
1.269 brouard 12575: free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
12576: free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 12577: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
12578: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 12579: } /* mle==-3 arrives here for freeing */
1.227 brouard 12580: /* endfree:*/
12581: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
12582: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
12583: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
1.268 brouard 12584: if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
12585: if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
12586: if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
1.227 brouard 12587: free_matrix(covar,0,NCOVMAX,1,n);
12588: free_matrix(matcov,1,npar,1,npar);
12589: free_matrix(hess,1,npar,1,npar);
12590: /*free_vector(delti,1,npar);*/
12591: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12592: free_matrix(agev,1,maxwav,1,imx);
1.269 brouard 12593: free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
1.227 brouard 12594: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
12595:
12596: free_ivector(ncodemax,1,NCOVMAX);
12597: free_ivector(ncodemaxwundef,1,NCOVMAX);
12598: free_ivector(Dummy,-1,NCOVMAX);
12599: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 12600: free_ivector(DummyV,1,NCOVMAX);
12601: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 12602: free_ivector(Typevar,-1,NCOVMAX);
12603: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 12604: free_ivector(TvarsQ,1,NCOVMAX);
12605: free_ivector(TvarsQind,1,NCOVMAX);
12606: free_ivector(TvarsD,1,NCOVMAX);
12607: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 12608: free_ivector(TvarFD,1,NCOVMAX);
12609: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 12610: free_ivector(TvarF,1,NCOVMAX);
12611: free_ivector(TvarFind,1,NCOVMAX);
12612: free_ivector(TvarV,1,NCOVMAX);
12613: free_ivector(TvarVind,1,NCOVMAX);
12614: free_ivector(TvarA,1,NCOVMAX);
12615: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 12616: free_ivector(TvarFQ,1,NCOVMAX);
12617: free_ivector(TvarFQind,1,NCOVMAX);
12618: free_ivector(TvarVD,1,NCOVMAX);
12619: free_ivector(TvarVDind,1,NCOVMAX);
12620: free_ivector(TvarVQ,1,NCOVMAX);
12621: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 12622: free_ivector(Tvarsel,1,NCOVMAX);
12623: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 12624: free_ivector(Tposprod,1,NCOVMAX);
12625: free_ivector(Tprod,1,NCOVMAX);
12626: free_ivector(Tvaraff,1,NCOVMAX);
12627: free_ivector(invalidvarcomb,1,ncovcombmax);
12628: free_ivector(Tage,1,NCOVMAX);
12629: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 12630: free_ivector(TmodelInvind,1,NCOVMAX);
12631: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 12632:
12633: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
12634: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 12635: fflush(fichtm);
12636: fflush(ficgp);
12637:
1.227 brouard 12638:
1.126 brouard 12639: if((nberr >0) || (nbwarn>0)){
1.216 brouard 12640: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
12641: 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 12642: }else{
12643: printf("End of Imach\n");
12644: fprintf(ficlog,"End of Imach\n");
12645: }
12646: printf("See log file on %s\n",filelog);
12647: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 12648: /*(void) gettimeofday(&end_time,&tzp);*/
12649: rend_time = time(NULL);
12650: end_time = *localtime(&rend_time);
12651: /* tml = *localtime(&end_time.tm_sec); */
12652: strcpy(strtend,asctime(&end_time));
1.126 brouard 12653: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
12654: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 12655: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 12656:
1.157 brouard 12657: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
12658: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
12659: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 12660: /* printf("Total time was %d uSec.\n", total_usecs);*/
12661: /* if(fileappend(fichtm,optionfilehtm)){ */
12662: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12663: fclose(fichtm);
12664: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
12665: fclose(fichtmcov);
12666: fclose(ficgp);
12667: fclose(ficlog);
12668: /*------ End -----------*/
1.227 brouard 12669:
1.281 brouard 12670:
12671: /* Executes gnuplot */
1.227 brouard 12672:
12673: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 12674: #ifdef WIN32
1.227 brouard 12675: if (_chdir(pathcd) != 0)
12676: printf("Can't move to directory %s!\n",path);
12677: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 12678: #else
1.227 brouard 12679: if(chdir(pathcd) != 0)
12680: printf("Can't move to directory %s!\n", path);
12681: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 12682: #endif
1.126 brouard 12683: printf("Current directory %s!\n",pathcd);
12684: /*strcat(plotcmd,CHARSEPARATOR);*/
12685: sprintf(plotcmd,"gnuplot");
1.157 brouard 12686: #ifdef _WIN32
1.126 brouard 12687: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
12688: #endif
12689: if(!stat(plotcmd,&info)){
1.158 brouard 12690: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12691: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 12692: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 12693: }else
12694: strcpy(pplotcmd,plotcmd);
1.157 brouard 12695: #ifdef __unix
1.126 brouard 12696: strcpy(plotcmd,GNUPLOTPROGRAM);
12697: if(!stat(plotcmd,&info)){
1.158 brouard 12698: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 12699: }else
12700: strcpy(pplotcmd,plotcmd);
12701: #endif
12702: }else
12703: strcpy(pplotcmd,plotcmd);
12704:
12705: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 12706: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 12707:
1.126 brouard 12708: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 12709: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 12710: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 12711: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 12712: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 12713: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 12714: }
1.158 brouard 12715: printf(" Successful, please wait...");
1.126 brouard 12716: while (z[0] != 'q') {
12717: /* chdir(path); */
1.154 brouard 12718: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 12719: scanf("%s",z);
12720: /* if (z[0] == 'c') system("./imach"); */
12721: if (z[0] == 'e') {
1.158 brouard 12722: #ifdef __APPLE__
1.152 brouard 12723: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 12724: #elif __linux
12725: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 12726: #else
1.152 brouard 12727: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 12728: #endif
12729: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
12730: system(pplotcmd);
1.126 brouard 12731: }
12732: else if (z[0] == 'g') system(plotcmd);
12733: else if (z[0] == 'q') exit(0);
12734: }
1.227 brouard 12735: end:
1.126 brouard 12736: while (z[0] != 'q') {
1.195 brouard 12737: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 12738: scanf("%s",z);
12739: }
1.282 ! brouard 12740: exit(0);
1.126 brouard 12741: }
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