Annotation of imach/src/imach.c, revision 1.255
1.255 ! brouard 1: /* $Id: imach.c,v 1.254 2017/03/08 07:13:00 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.255 ! brouard 4: Revision 1.254 2017/03/08 07:13:00 brouard
! 5: Summary: Fixing data parameter line
! 6:
1.254 brouard 7: Revision 1.253 2016/12/15 11:59:41 brouard
8: Summary: 0.99 in progress
9:
1.253 brouard 10: Revision 1.252 2016/09/15 21:15:37 brouard
11: *** empty log message ***
12:
1.252 brouard 13: Revision 1.251 2016/09/15 15:01:13 brouard
14: Summary: not working
15:
1.251 brouard 16: Revision 1.250 2016/09/08 16:07:27 brouard
17: Summary: continue
18:
1.250 brouard 19: Revision 1.249 2016/09/07 17:14:18 brouard
20: Summary: Starting values from frequencies
21:
1.249 brouard 22: Revision 1.248 2016/09/07 14:10:18 brouard
23: *** empty log message ***
24:
1.248 brouard 25: Revision 1.247 2016/09/02 11:11:21 brouard
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27:
1.247 brouard 28: Revision 1.246 2016/09/02 08:49:22 brouard
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1.246 brouard 31: Revision 1.245 2016/09/02 07:25:01 brouard
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33:
1.245 brouard 34: Revision 1.244 2016/09/02 07:17:34 brouard
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36:
1.244 brouard 37: Revision 1.243 2016/09/02 06:45:35 brouard
38: *** empty log message ***
39:
1.243 brouard 40: Revision 1.242 2016/08/30 15:01:20 brouard
41: Summary: Fixing a lots
42:
1.242 brouard 43: Revision 1.241 2016/08/29 17:17:25 brouard
44: Summary: gnuplot problem in Back projection to fix
45:
1.241 brouard 46: Revision 1.240 2016/08/29 07:53:18 brouard
47: Summary: Better
48:
1.240 brouard 49: Revision 1.239 2016/08/26 15:51:03 brouard
50: Summary: Improvement in Powell output in order to copy and paste
51:
52: Author:
53:
1.239 brouard 54: Revision 1.238 2016/08/26 14:23:35 brouard
55: Summary: Starting tests of 0.99
56:
1.238 brouard 57: Revision 1.237 2016/08/26 09:20:19 brouard
58: Summary: to valgrind
59:
1.237 brouard 60: Revision 1.236 2016/08/25 10:50:18 brouard
61: *** empty log message ***
62:
1.236 brouard 63: Revision 1.235 2016/08/25 06:59:23 brouard
64: *** empty log message ***
65:
1.235 brouard 66: Revision 1.234 2016/08/23 16:51:20 brouard
67: *** empty log message ***
68:
1.234 brouard 69: Revision 1.233 2016/08/23 07:40:50 brouard
70: Summary: not working
71:
1.233 brouard 72: Revision 1.232 2016/08/22 14:20:21 brouard
73: Summary: not working
74:
1.232 brouard 75: Revision 1.231 2016/08/22 07:17:15 brouard
76: Summary: not working
77:
1.231 brouard 78: Revision 1.230 2016/08/22 06:55:53 brouard
79: Summary: Not working
80:
1.230 brouard 81: Revision 1.229 2016/07/23 09:45:53 brouard
82: Summary: Completing for func too
83:
1.229 brouard 84: Revision 1.228 2016/07/22 17:45:30 brouard
85: Summary: Fixing some arrays, still debugging
86:
1.227 brouard 87: Revision 1.226 2016/07/12 18:42:34 brouard
88: Summary: temp
89:
1.226 brouard 90: Revision 1.225 2016/07/12 08:40:03 brouard
91: Summary: saving but not running
92:
1.225 brouard 93: Revision 1.224 2016/07/01 13:16:01 brouard
94: Summary: Fixes
95:
1.224 brouard 96: Revision 1.223 2016/02/19 09:23:35 brouard
97: Summary: temporary
98:
1.223 brouard 99: Revision 1.222 2016/02/17 08:14:50 brouard
100: Summary: Probably last 0.98 stable version 0.98r6
101:
1.222 brouard 102: Revision 1.221 2016/02/15 23:35:36 brouard
103: Summary: minor bug
104:
1.220 brouard 105: Revision 1.219 2016/02/15 00:48:12 brouard
106: *** empty log message ***
107:
1.219 brouard 108: Revision 1.218 2016/02/12 11:29:23 brouard
109: Summary: 0.99 Back projections
110:
1.218 brouard 111: Revision 1.217 2015/12/23 17:18:31 brouard
112: Summary: Experimental backcast
113:
1.217 brouard 114: Revision 1.216 2015/12/18 17:32:11 brouard
115: Summary: 0.98r4 Warning and status=-2
116:
117: Version 0.98r4 is now:
118: - displaying an error when status is -1, date of interview unknown and date of death known;
119: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
120: Older changes concerning s=-2, dating from 2005 have been supersed.
121:
1.216 brouard 122: Revision 1.215 2015/12/16 08:52:24 brouard
123: Summary: 0.98r4 working
124:
1.215 brouard 125: Revision 1.214 2015/12/16 06:57:54 brouard
126: Summary: temporary not working
127:
1.214 brouard 128: Revision 1.213 2015/12/11 18:22:17 brouard
129: Summary: 0.98r4
130:
1.213 brouard 131: Revision 1.212 2015/11/21 12:47:24 brouard
132: Summary: minor typo
133:
1.212 brouard 134: Revision 1.211 2015/11/21 12:41:11 brouard
135: Summary: 0.98r3 with some graph of projected cross-sectional
136:
137: Author: Nicolas Brouard
138:
1.211 brouard 139: Revision 1.210 2015/11/18 17:41:20 brouard
1.252 brouard 140: Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard
1.210 brouard 141: Summary: Adding ftolpl parameter
142: Author: N Brouard
143:
144: We had difficulties to get smoothed confidence intervals. It was due
145: to the period prevalence which wasn't computed accurately. The inner
146: parameter ftolpl is now an outer parameter of the .imach parameter
147: file after estepm. If ftolpl is small 1.e-4 and estepm too,
148: computation are long.
149:
1.209 brouard 150: Revision 1.208 2015/11/17 14:31:57 brouard
151: Summary: temporary
152:
1.208 brouard 153: Revision 1.207 2015/10/27 17:36:57 brouard
154: *** empty log message ***
155:
1.207 brouard 156: Revision 1.206 2015/10/24 07:14:11 brouard
157: *** empty log message ***
158:
1.206 brouard 159: Revision 1.205 2015/10/23 15:50:53 brouard
160: Summary: 0.98r3 some clarification for graphs on likelihood contributions
161:
1.205 brouard 162: Revision 1.204 2015/10/01 16:20:26 brouard
163: Summary: Some new graphs of contribution to likelihood
164:
1.204 brouard 165: Revision 1.203 2015/09/30 17:45:14 brouard
166: Summary: looking at better estimation of the hessian
167:
168: Also a better criteria for convergence to the period prevalence And
169: therefore adding the number of years needed to converge. (The
170: prevalence in any alive state shold sum to one
171:
1.203 brouard 172: Revision 1.202 2015/09/22 19:45:16 brouard
173: Summary: Adding some overall graph on contribution to likelihood. Might change
174:
1.202 brouard 175: Revision 1.201 2015/09/15 17:34:58 brouard
176: Summary: 0.98r0
177:
178: - Some new graphs like suvival functions
179: - Some bugs fixed like model=1+age+V2.
180:
1.201 brouard 181: Revision 1.200 2015/09/09 16:53:55 brouard
182: Summary: Big bug thanks to Flavia
183:
184: Even model=1+age+V2. did not work anymore
185:
1.200 brouard 186: Revision 1.199 2015/09/07 14:09:23 brouard
187: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
188:
1.199 brouard 189: Revision 1.198 2015/09/03 07:14:39 brouard
190: Summary: 0.98q5 Flavia
191:
1.198 brouard 192: Revision 1.197 2015/09/01 18:24:39 brouard
193: *** empty log message ***
194:
1.197 brouard 195: Revision 1.196 2015/08/18 23:17:52 brouard
196: Summary: 0.98q5
197:
1.196 brouard 198: Revision 1.195 2015/08/18 16:28:39 brouard
199: Summary: Adding a hack for testing purpose
200:
201: After reading the title, ftol and model lines, if the comment line has
202: a q, starting with #q, the answer at the end of the run is quit. It
203: permits to run test files in batch with ctest. The former workaround was
204: $ echo q | imach foo.imach
205:
1.195 brouard 206: Revision 1.194 2015/08/18 13:32:00 brouard
207: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
208:
1.194 brouard 209: Revision 1.193 2015/08/04 07:17:42 brouard
210: Summary: 0.98q4
211:
1.193 brouard 212: Revision 1.192 2015/07/16 16:49:02 brouard
213: Summary: Fixing some outputs
214:
1.192 brouard 215: Revision 1.191 2015/07/14 10:00:33 brouard
216: Summary: Some fixes
217:
1.191 brouard 218: Revision 1.190 2015/05/05 08:51:13 brouard
219: Summary: Adding digits in output parameters (7 digits instead of 6)
220:
221: Fix 1+age+.
222:
1.190 brouard 223: Revision 1.189 2015/04/30 14:45:16 brouard
224: Summary: 0.98q2
225:
1.189 brouard 226: Revision 1.188 2015/04/30 08:27:53 brouard
227: *** empty log message ***
228:
1.188 brouard 229: Revision 1.187 2015/04/29 09:11:15 brouard
230: *** empty log message ***
231:
1.187 brouard 232: Revision 1.186 2015/04/23 12:01:52 brouard
233: Summary: V1*age is working now, version 0.98q1
234:
235: Some codes had been disabled in order to simplify and Vn*age was
236: working in the optimization phase, ie, giving correct MLE parameters,
237: but, as usual, outputs were not correct and program core dumped.
238:
1.186 brouard 239: Revision 1.185 2015/03/11 13:26:42 brouard
240: Summary: Inclusion of compile and links command line for Intel Compiler
241:
1.185 brouard 242: Revision 1.184 2015/03/11 11:52:39 brouard
243: Summary: Back from Windows 8. Intel Compiler
244:
1.184 brouard 245: Revision 1.183 2015/03/10 20:34:32 brouard
246: Summary: 0.98q0, trying with directest, mnbrak fixed
247:
248: We use directest instead of original Powell test; probably no
249: incidence on the results, but better justifications;
250: We fixed Numerical Recipes mnbrak routine which was wrong and gave
251: wrong results.
252:
1.183 brouard 253: Revision 1.182 2015/02/12 08:19:57 brouard
254: Summary: Trying to keep directest which seems simpler and more general
255: Author: Nicolas Brouard
256:
1.182 brouard 257: Revision 1.181 2015/02/11 23:22:24 brouard
258: Summary: Comments on Powell added
259:
260: Author:
261:
1.181 brouard 262: Revision 1.180 2015/02/11 17:33:45 brouard
263: Summary: Finishing move from main to function (hpijx and prevalence_limit)
264:
1.180 brouard 265: Revision 1.179 2015/01/04 09:57:06 brouard
266: Summary: back to OS/X
267:
1.179 brouard 268: Revision 1.178 2015/01/04 09:35:48 brouard
269: *** empty log message ***
270:
1.178 brouard 271: Revision 1.177 2015/01/03 18:40:56 brouard
272: Summary: Still testing ilc32 on OSX
273:
1.177 brouard 274: Revision 1.176 2015/01/03 16:45:04 brouard
275: *** empty log message ***
276:
1.176 brouard 277: Revision 1.175 2015/01/03 16:33:42 brouard
278: *** empty log message ***
279:
1.175 brouard 280: Revision 1.174 2015/01/03 16:15:49 brouard
281: Summary: Still in cross-compilation
282:
1.174 brouard 283: Revision 1.173 2015/01/03 12:06:26 brouard
284: Summary: trying to detect cross-compilation
285:
1.173 brouard 286: Revision 1.172 2014/12/27 12:07:47 brouard
287: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
288:
1.172 brouard 289: Revision 1.171 2014/12/23 13:26:59 brouard
290: Summary: Back from Visual C
291:
292: Still problem with utsname.h on Windows
293:
1.171 brouard 294: Revision 1.170 2014/12/23 11:17:12 brouard
295: Summary: Cleaning some \%% back to %%
296:
297: The escape was mandatory for a specific compiler (which one?), but too many warnings.
298:
1.170 brouard 299: Revision 1.169 2014/12/22 23:08:31 brouard
300: Summary: 0.98p
301:
302: Outputs some informations on compiler used, OS etc. Testing on different platforms.
303:
1.169 brouard 304: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 305: Summary: update
1.169 brouard 306:
1.168 brouard 307: Revision 1.167 2014/12/22 13:50:56 brouard
308: Summary: Testing uname and compiler version and if compiled 32 or 64
309:
310: Testing on Linux 64
311:
1.167 brouard 312: Revision 1.166 2014/12/22 11:40:47 brouard
313: *** empty log message ***
314:
1.166 brouard 315: Revision 1.165 2014/12/16 11:20:36 brouard
316: Summary: After compiling on Visual C
317:
318: * imach.c (Module): Merging 1.61 to 1.162
319:
1.165 brouard 320: Revision 1.164 2014/12/16 10:52:11 brouard
321: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
322:
323: * imach.c (Module): Merging 1.61 to 1.162
324:
1.164 brouard 325: Revision 1.163 2014/12/16 10:30:11 brouard
326: * imach.c (Module): Merging 1.61 to 1.162
327:
1.163 brouard 328: Revision 1.162 2014/09/25 11:43:39 brouard
329: Summary: temporary backup 0.99!
330:
1.162 brouard 331: Revision 1.1 2014/09/16 11:06:58 brouard
332: Summary: With some code (wrong) for nlopt
333:
334: Author:
335:
336: Revision 1.161 2014/09/15 20:41:41 brouard
337: Summary: Problem with macro SQR on Intel compiler
338:
1.161 brouard 339: Revision 1.160 2014/09/02 09:24:05 brouard
340: *** empty log message ***
341:
1.160 brouard 342: Revision 1.159 2014/09/01 10:34:10 brouard
343: Summary: WIN32
344: Author: Brouard
345:
1.159 brouard 346: Revision 1.158 2014/08/27 17:11:51 brouard
347: *** empty log message ***
348:
1.158 brouard 349: Revision 1.157 2014/08/27 16:26:55 brouard
350: Summary: Preparing windows Visual studio version
351: Author: Brouard
352:
353: In order to compile on Visual studio, time.h is now correct and time_t
354: and tm struct should be used. difftime should be used but sometimes I
355: just make the differences in raw time format (time(&now).
356: Trying to suppress #ifdef LINUX
357: Add xdg-open for __linux in order to open default browser.
358:
1.157 brouard 359: Revision 1.156 2014/08/25 20:10:10 brouard
360: *** empty log message ***
361:
1.156 brouard 362: Revision 1.155 2014/08/25 18:32:34 brouard
363: Summary: New compile, minor changes
364: Author: Brouard
365:
1.155 brouard 366: Revision 1.154 2014/06/20 17:32:08 brouard
367: Summary: Outputs now all graphs of convergence to period prevalence
368:
1.154 brouard 369: Revision 1.153 2014/06/20 16:45:46 brouard
370: Summary: If 3 live state, convergence to period prevalence on same graph
371: Author: Brouard
372:
1.153 brouard 373: Revision 1.152 2014/06/18 17:54:09 brouard
374: Summary: open browser, use gnuplot on same dir than imach if not found in the path
375:
1.152 brouard 376: Revision 1.151 2014/06/18 16:43:30 brouard
377: *** empty log message ***
378:
1.151 brouard 379: Revision 1.150 2014/06/18 16:42:35 brouard
380: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
381: Author: brouard
382:
1.150 brouard 383: Revision 1.149 2014/06/18 15:51:14 brouard
384: Summary: Some fixes in parameter files errors
385: Author: Nicolas Brouard
386:
1.149 brouard 387: Revision 1.148 2014/06/17 17:38:48 brouard
388: Summary: Nothing new
389: Author: Brouard
390:
391: Just a new packaging for OS/X version 0.98nS
392:
1.148 brouard 393: Revision 1.147 2014/06/16 10:33:11 brouard
394: *** empty log message ***
395:
1.147 brouard 396: Revision 1.146 2014/06/16 10:20:28 brouard
397: Summary: Merge
398: Author: Brouard
399:
400: Merge, before building revised version.
401:
1.146 brouard 402: Revision 1.145 2014/06/10 21:23:15 brouard
403: Summary: Debugging with valgrind
404: Author: Nicolas Brouard
405:
406: Lot of changes in order to output the results with some covariates
407: After the Edimburgh REVES conference 2014, it seems mandatory to
408: improve the code.
409: No more memory valgrind error but a lot has to be done in order to
410: continue the work of splitting the code into subroutines.
411: Also, decodemodel has been improved. Tricode is still not
412: optimal. nbcode should be improved. Documentation has been added in
413: the source code.
414:
1.144 brouard 415: Revision 1.143 2014/01/26 09:45:38 brouard
416: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
417:
418: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
419: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
420:
1.143 brouard 421: Revision 1.142 2014/01/26 03:57:36 brouard
422: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
423:
424: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
425:
1.142 brouard 426: Revision 1.141 2014/01/26 02:42:01 brouard
427: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
428:
1.141 brouard 429: Revision 1.140 2011/09/02 10:37:54 brouard
430: Summary: times.h is ok with mingw32 now.
431:
1.140 brouard 432: Revision 1.139 2010/06/14 07:50:17 brouard
433: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
434: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
435:
1.139 brouard 436: Revision 1.138 2010/04/30 18:19:40 brouard
437: *** empty log message ***
438:
1.138 brouard 439: Revision 1.137 2010/04/29 18:11:38 brouard
440: (Module): Checking covariates for more complex models
441: than V1+V2. A lot of change to be done. Unstable.
442:
1.137 brouard 443: Revision 1.136 2010/04/26 20:30:53 brouard
444: (Module): merging some libgsl code. Fixing computation
445: of likelione (using inter/intrapolation if mle = 0) in order to
446: get same likelihood as if mle=1.
447: Some cleaning of code and comments added.
448:
1.136 brouard 449: Revision 1.135 2009/10/29 15:33:14 brouard
450: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
451:
1.135 brouard 452: Revision 1.134 2009/10/29 13:18:53 brouard
453: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
454:
1.134 brouard 455: Revision 1.133 2009/07/06 10:21:25 brouard
456: just nforces
457:
1.133 brouard 458: Revision 1.132 2009/07/06 08:22:05 brouard
459: Many tings
460:
1.132 brouard 461: Revision 1.131 2009/06/20 16:22:47 brouard
462: Some dimensions resccaled
463:
1.131 brouard 464: Revision 1.130 2009/05/26 06:44:34 brouard
465: (Module): Max Covariate is now set to 20 instead of 8. A
466: lot of cleaning with variables initialized to 0. Trying to make
467: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
468:
1.130 brouard 469: Revision 1.129 2007/08/31 13:49:27 lievre
470: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
471:
1.129 lievre 472: Revision 1.128 2006/06/30 13:02:05 brouard
473: (Module): Clarifications on computing e.j
474:
1.128 brouard 475: Revision 1.127 2006/04/28 18:11:50 brouard
476: (Module): Yes the sum of survivors was wrong since
477: imach-114 because nhstepm was no more computed in the age
478: loop. Now we define nhstepma in the age loop.
479: (Module): In order to speed up (in case of numerous covariates) we
480: compute health expectancies (without variances) in a first step
481: and then all the health expectancies with variances or standard
482: deviation (needs data from the Hessian matrices) which slows the
483: computation.
484: In the future we should be able to stop the program is only health
485: expectancies and graph are needed without standard deviations.
486:
1.127 brouard 487: Revision 1.126 2006/04/28 17:23:28 brouard
488: (Module): Yes the sum of survivors was wrong since
489: imach-114 because nhstepm was no more computed in the age
490: loop. Now we define nhstepma in the age loop.
491: Version 0.98h
492:
1.126 brouard 493: Revision 1.125 2006/04/04 15:20:31 lievre
494: Errors in calculation of health expectancies. Age was not initialized.
495: Forecasting file added.
496:
497: Revision 1.124 2006/03/22 17:13:53 lievre
498: Parameters are printed with %lf instead of %f (more numbers after the comma).
499: The log-likelihood is printed in the log file
500:
501: Revision 1.123 2006/03/20 10:52:43 brouard
502: * imach.c (Module): <title> changed, corresponds to .htm file
503: name. <head> headers where missing.
504:
505: * imach.c (Module): Weights can have a decimal point as for
506: English (a comma might work with a correct LC_NUMERIC environment,
507: otherwise the weight is truncated).
508: Modification of warning when the covariates values are not 0 or
509: 1.
510: Version 0.98g
511:
512: Revision 1.122 2006/03/20 09:45:41 brouard
513: (Module): Weights can have a decimal point as for
514: English (a comma might work with a correct LC_NUMERIC environment,
515: otherwise the weight is truncated).
516: Modification of warning when the covariates values are not 0 or
517: 1.
518: Version 0.98g
519:
520: Revision 1.121 2006/03/16 17:45:01 lievre
521: * imach.c (Module): Comments concerning covariates added
522:
523: * imach.c (Module): refinements in the computation of lli if
524: status=-2 in order to have more reliable computation if stepm is
525: not 1 month. Version 0.98f
526:
527: Revision 1.120 2006/03/16 15:10:38 lievre
528: (Module): refinements in the computation of lli if
529: status=-2 in order to have more reliable computation if stepm is
530: not 1 month. Version 0.98f
531:
532: Revision 1.119 2006/03/15 17:42:26 brouard
533: (Module): Bug if status = -2, the loglikelihood was
534: computed as likelihood omitting the logarithm. Version O.98e
535:
536: Revision 1.118 2006/03/14 18:20:07 brouard
537: (Module): varevsij Comments added explaining the second
538: table of variances if popbased=1 .
539: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
540: (Module): Function pstamp added
541: (Module): Version 0.98d
542:
543: Revision 1.117 2006/03/14 17:16:22 brouard
544: (Module): varevsij Comments added explaining the second
545: table of variances if popbased=1 .
546: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
547: (Module): Function pstamp added
548: (Module): Version 0.98d
549:
550: Revision 1.116 2006/03/06 10:29:27 brouard
551: (Module): Variance-covariance wrong links and
552: varian-covariance of ej. is needed (Saito).
553:
554: Revision 1.115 2006/02/27 12:17:45 brouard
555: (Module): One freematrix added in mlikeli! 0.98c
556:
557: Revision 1.114 2006/02/26 12:57:58 brouard
558: (Module): Some improvements in processing parameter
559: filename with strsep.
560:
561: Revision 1.113 2006/02/24 14:20:24 brouard
562: (Module): Memory leaks checks with valgrind and:
563: datafile was not closed, some imatrix were not freed and on matrix
564: allocation too.
565:
566: Revision 1.112 2006/01/30 09:55:26 brouard
567: (Module): Back to gnuplot.exe instead of wgnuplot.exe
568:
569: Revision 1.111 2006/01/25 20:38:18 brouard
570: (Module): Lots of cleaning and bugs added (Gompertz)
571: (Module): Comments can be added in data file. Missing date values
572: can be a simple dot '.'.
573:
574: Revision 1.110 2006/01/25 00:51:50 brouard
575: (Module): Lots of cleaning and bugs added (Gompertz)
576:
577: Revision 1.109 2006/01/24 19:37:15 brouard
578: (Module): Comments (lines starting with a #) are allowed in data.
579:
580: Revision 1.108 2006/01/19 18:05:42 lievre
581: Gnuplot problem appeared...
582: To be fixed
583:
584: Revision 1.107 2006/01/19 16:20:37 brouard
585: Test existence of gnuplot in imach path
586:
587: Revision 1.106 2006/01/19 13:24:36 brouard
588: Some cleaning and links added in html output
589:
590: Revision 1.105 2006/01/05 20:23:19 lievre
591: *** empty log message ***
592:
593: Revision 1.104 2005/09/30 16:11:43 lievre
594: (Module): sump fixed, loop imx fixed, and simplifications.
595: (Module): If the status is missing at the last wave but we know
596: that the person is alive, then we can code his/her status as -2
597: (instead of missing=-1 in earlier versions) and his/her
598: contributions to the likelihood is 1 - Prob of dying from last
599: health status (= 1-p13= p11+p12 in the easiest case of somebody in
600: the healthy state at last known wave). Version is 0.98
601:
602: Revision 1.103 2005/09/30 15:54:49 lievre
603: (Module): sump fixed, loop imx fixed, and simplifications.
604:
605: Revision 1.102 2004/09/15 17:31:30 brouard
606: Add the possibility to read data file including tab characters.
607:
608: Revision 1.101 2004/09/15 10:38:38 brouard
609: Fix on curr_time
610:
611: Revision 1.100 2004/07/12 18:29:06 brouard
612: Add version for Mac OS X. Just define UNIX in Makefile
613:
614: Revision 1.99 2004/06/05 08:57:40 brouard
615: *** empty log message ***
616:
617: Revision 1.98 2004/05/16 15:05:56 brouard
618: New version 0.97 . First attempt to estimate force of mortality
619: directly from the data i.e. without the need of knowing the health
620: state at each age, but using a Gompertz model: log u =a + b*age .
621: This is the basic analysis of mortality and should be done before any
622: other analysis, in order to test if the mortality estimated from the
623: cross-longitudinal survey is different from the mortality estimated
624: from other sources like vital statistic data.
625:
626: The same imach parameter file can be used but the option for mle should be -3.
627:
1.133 brouard 628: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 629: former routines in order to include the new code within the former code.
630:
631: The output is very simple: only an estimate of the intercept and of
632: the slope with 95% confident intervals.
633:
634: Current limitations:
635: A) Even if you enter covariates, i.e. with the
636: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
637: B) There is no computation of Life Expectancy nor Life Table.
638:
639: Revision 1.97 2004/02/20 13:25:42 lievre
640: Version 0.96d. Population forecasting command line is (temporarily)
641: suppressed.
642:
643: Revision 1.96 2003/07/15 15:38:55 brouard
644: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
645: rewritten within the same printf. Workaround: many printfs.
646:
647: Revision 1.95 2003/07/08 07:54:34 brouard
648: * imach.c (Repository):
649: (Repository): Using imachwizard code to output a more meaningful covariance
650: matrix (cov(a12,c31) instead of numbers.
651:
652: Revision 1.94 2003/06/27 13:00:02 brouard
653: Just cleaning
654:
655: Revision 1.93 2003/06/25 16:33:55 brouard
656: (Module): On windows (cygwin) function asctime_r doesn't
657: exist so I changed back to asctime which exists.
658: (Module): Version 0.96b
659:
660: Revision 1.92 2003/06/25 16:30:45 brouard
661: (Module): On windows (cygwin) function asctime_r doesn't
662: exist so I changed back to asctime which exists.
663:
664: Revision 1.91 2003/06/25 15:30:29 brouard
665: * imach.c (Repository): Duplicated warning errors corrected.
666: (Repository): Elapsed time after each iteration is now output. It
667: helps to forecast when convergence will be reached. Elapsed time
668: is stamped in powell. We created a new html file for the graphs
669: concerning matrix of covariance. It has extension -cov.htm.
670:
671: Revision 1.90 2003/06/24 12:34:15 brouard
672: (Module): Some bugs corrected for windows. Also, when
673: mle=-1 a template is output in file "or"mypar.txt with the design
674: of the covariance matrix to be input.
675:
676: Revision 1.89 2003/06/24 12:30:52 brouard
677: (Module): Some bugs corrected for windows. Also, when
678: mle=-1 a template is output in file "or"mypar.txt with the design
679: of the covariance matrix to be input.
680:
681: Revision 1.88 2003/06/23 17:54:56 brouard
682: * 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.
683:
684: Revision 1.87 2003/06/18 12:26:01 brouard
685: Version 0.96
686:
687: Revision 1.86 2003/06/17 20:04:08 brouard
688: (Module): Change position of html and gnuplot routines and added
689: routine fileappend.
690:
691: Revision 1.85 2003/06/17 13:12:43 brouard
692: * imach.c (Repository): Check when date of death was earlier that
693: current date of interview. It may happen when the death was just
694: prior to the death. In this case, dh was negative and likelihood
695: was wrong (infinity). We still send an "Error" but patch by
696: assuming that the date of death was just one stepm after the
697: interview.
698: (Repository): Because some people have very long ID (first column)
699: we changed int to long in num[] and we added a new lvector for
700: memory allocation. But we also truncated to 8 characters (left
701: truncation)
702: (Repository): No more line truncation errors.
703:
704: Revision 1.84 2003/06/13 21:44:43 brouard
705: * imach.c (Repository): Replace "freqsummary" at a correct
706: place. It differs from routine "prevalence" which may be called
707: many times. Probs is memory consuming and must be used with
708: parcimony.
709: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
710:
711: Revision 1.83 2003/06/10 13:39:11 lievre
712: *** empty log message ***
713:
714: Revision 1.82 2003/06/05 15:57:20 brouard
715: Add log in imach.c and fullversion number is now printed.
716:
717: */
718: /*
719: Interpolated Markov Chain
720:
721: Short summary of the programme:
722:
1.227 brouard 723: This program computes Healthy Life Expectancies or State-specific
724: (if states aren't health statuses) Expectancies from
725: cross-longitudinal data. Cross-longitudinal data consist in:
726:
727: -1- a first survey ("cross") where individuals from different ages
728: are interviewed on their health status or degree of disability (in
729: the case of a health survey which is our main interest)
730:
731: -2- at least a second wave of interviews ("longitudinal") which
732: measure each change (if any) in individual health status. Health
733: expectancies are computed from the time spent in each health state
734: according to a model. More health states you consider, more time is
735: necessary to reach the Maximum Likelihood of the parameters involved
736: in the model. The simplest model is the multinomial logistic model
737: where pij is the probability to be observed in state j at the second
738: wave conditional to be observed in state i at the first
739: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
740: etc , where 'age' is age and 'sex' is a covariate. If you want to
741: have a more complex model than "constant and age", you should modify
742: the program where the markup *Covariates have to be included here
743: again* invites you to do it. More covariates you add, slower the
1.126 brouard 744: convergence.
745:
746: The advantage of this computer programme, compared to a simple
747: multinomial logistic model, is clear when the delay between waves is not
748: identical for each individual. Also, if a individual missed an
749: intermediate interview, the information is lost, but taken into
750: account using an interpolation or extrapolation.
751:
752: hPijx is the probability to be observed in state i at age x+h
753: conditional to the observed state i at age x. The delay 'h' can be
754: split into an exact number (nh*stepm) of unobserved intermediate
755: states. This elementary transition (by month, quarter,
756: semester or year) is modelled as a multinomial logistic. The hPx
757: matrix is simply the matrix product of nh*stepm elementary matrices
758: and the contribution of each individual to the likelihood is simply
759: hPijx.
760:
761: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 762: of the life expectancies. It also computes the period (stable) prevalence.
763:
764: Back prevalence and projections:
1.227 brouard 765:
766: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
767: double agemaxpar, double ftolpl, int *ncvyearp, double
768: dateprev1,double dateprev2, int firstpass, int lastpass, int
769: mobilavproj)
770:
771: Computes the back prevalence limit for any combination of
772: covariate values k at any age between ageminpar and agemaxpar and
773: returns it in **bprlim. In the loops,
774:
775: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
776: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
777:
778: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 779: Computes for any combination of covariates k and any age between bage and fage
780: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
781: oldm=oldms;savm=savms;
1.227 brouard 782:
783: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 784: Computes the transition matrix starting at age 'age' over
785: 'nhstepm*hstepm*stepm' months (i.e. until
786: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 787: nhstepm*hstepm matrices.
788:
789: Returns p3mat[i][j][h] after calling
790: p3mat[i][j][h]=matprod2(newm,
791: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
792: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
793: oldm);
1.226 brouard 794:
795: Important routines
796:
797: - func (or funcone), computes logit (pij) distinguishing
798: o fixed variables (single or product dummies or quantitative);
799: o varying variables by:
800: (1) wave (single, product dummies, quantitative),
801: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
802: % fixed dummy (treated) or quantitative (not done because time-consuming);
803: % varying dummy (not done) or quantitative (not done);
804: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
805: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
806: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
807: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
808: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 809:
1.226 brouard 810:
811:
1.133 brouard 812: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
813: Institut national d'études démographiques, Paris.
1.126 brouard 814: This software have been partly granted by Euro-REVES, a concerted action
815: from the European Union.
816: It is copyrighted identically to a GNU software product, ie programme and
817: software can be distributed freely for non commercial use. Latest version
818: can be accessed at http://euroreves.ined.fr/imach .
819:
820: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
821: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
822:
823: **********************************************************************/
824: /*
825: main
826: read parameterfile
827: read datafile
828: concatwav
829: freqsummary
830: if (mle >= 1)
831: mlikeli
832: print results files
833: if mle==1
834: computes hessian
835: read end of parameter file: agemin, agemax, bage, fage, estepm
836: begin-prev-date,...
837: open gnuplot file
838: open html file
1.145 brouard 839: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
840: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
841: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
842: freexexit2 possible for memory heap.
843:
844: h Pij x | pij_nom ficrestpij
845: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
846: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
847: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
848:
849: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
850: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
851: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
852: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
853: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
854:
1.126 brouard 855: forecasting if prevfcast==1 prevforecast call prevalence()
856: health expectancies
857: Variance-covariance of DFLE
858: prevalence()
859: movingaverage()
860: varevsij()
861: if popbased==1 varevsij(,popbased)
862: total life expectancies
863: Variance of period (stable) prevalence
864: end
865: */
866:
1.187 brouard 867: /* #define DEBUG */
868: /* #define DEBUGBRENT */
1.203 brouard 869: /* #define DEBUGLINMIN */
870: /* #define DEBUGHESS */
871: #define DEBUGHESSIJ
1.224 brouard 872: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 873: #define POWELL /* Instead of NLOPT */
1.224 brouard 874: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 875: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
876: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 877:
878: #include <math.h>
879: #include <stdio.h>
880: #include <stdlib.h>
881: #include <string.h>
1.226 brouard 882: #include <ctype.h>
1.159 brouard 883:
884: #ifdef _WIN32
885: #include <io.h>
1.172 brouard 886: #include <windows.h>
887: #include <tchar.h>
1.159 brouard 888: #else
1.126 brouard 889: #include <unistd.h>
1.159 brouard 890: #endif
1.126 brouard 891:
892: #include <limits.h>
893: #include <sys/types.h>
1.171 brouard 894:
895: #if defined(__GNUC__)
896: #include <sys/utsname.h> /* Doesn't work on Windows */
897: #endif
898:
1.126 brouard 899: #include <sys/stat.h>
900: #include <errno.h>
1.159 brouard 901: /* extern int errno; */
1.126 brouard 902:
1.157 brouard 903: /* #ifdef LINUX */
904: /* #include <time.h> */
905: /* #include "timeval.h" */
906: /* #else */
907: /* #include <sys/time.h> */
908: /* #endif */
909:
1.126 brouard 910: #include <time.h>
911:
1.136 brouard 912: #ifdef GSL
913: #include <gsl/gsl_errno.h>
914: #include <gsl/gsl_multimin.h>
915: #endif
916:
1.167 brouard 917:
1.162 brouard 918: #ifdef NLOPT
919: #include <nlopt.h>
920: typedef struct {
921: double (* function)(double [] );
922: } myfunc_data ;
923: #endif
924:
1.126 brouard 925: /* #include <libintl.h> */
926: /* #define _(String) gettext (String) */
927:
1.251 brouard 928: #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 929:
930: #define GNUPLOTPROGRAM "gnuplot"
931: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
932: #define FILENAMELENGTH 132
933:
934: #define GLOCK_ERROR_NOPATH -1 /* empty path */
935: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
936:
1.144 brouard 937: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
938: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 939:
940: #define NINTERVMAX 8
1.144 brouard 941: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
942: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
943: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 944: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 945: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
946: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 947: #define MAXN 20000
1.144 brouard 948: #define YEARM 12. /**< Number of months per year */
1.218 brouard 949: /* #define AGESUP 130 */
950: #define AGESUP 150
951: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 952: #define AGEBASE 40
1.194 brouard 953: #define AGEOVERFLOW 1.e20
1.164 brouard 954: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 955: #ifdef _WIN32
956: #define DIRSEPARATOR '\\'
957: #define CHARSEPARATOR "\\"
958: #define ODIRSEPARATOR '/'
959: #else
1.126 brouard 960: #define DIRSEPARATOR '/'
961: #define CHARSEPARATOR "/"
962: #define ODIRSEPARATOR '\\'
963: #endif
964:
1.255 ! brouard 965: /* $Id: imach.c,v 1.254 2017/03/08 07:13:00 brouard Exp $ */
1.126 brouard 966: /* $State: Exp $ */
1.196 brouard 967: #include "version.h"
968: char version[]=__IMACH_VERSION__;
1.224 brouard 969: 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";
1.255 ! brouard 970: char fullversion[]="$Revision: 1.254 $ $Date: 2017/03/08 07:13:00 $";
1.126 brouard 971: char strstart[80];
972: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 973: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 974: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 975: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
976: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
977: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 978: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
979: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 980: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
981: int cptcovprodnoage=0; /**< Number of covariate products without age */
982: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 983: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
984: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 985: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 986: int nsd=0; /**< Total number of single dummy variables (output) */
987: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 988: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 989: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 990: int ntveff=0; /**< ntveff number of effective time varying variables */
991: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 992: int cptcov=0; /* Working variable */
1.218 brouard 993: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 994: int npar=NPARMAX;
995: int nlstate=2; /* Number of live states */
996: int ndeath=1; /* Number of dead states */
1.130 brouard 997: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 998: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 999: int popbased=0;
1000:
1001: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 1002: int maxwav=0; /* Maxim number of waves */
1003: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
1004: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
1005: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 1006: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 1007: int mle=1, weightopt=0;
1.126 brouard 1008: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
1009: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
1010: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
1011: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 1012: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 1013: int selected(int kvar); /* Is covariate kvar selected for printing results */
1014:
1.130 brouard 1015: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 1016: double **matprod2(); /* test */
1.126 brouard 1017: double **oldm, **newm, **savm; /* Working pointers to matrices */
1018: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 1019: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
1020:
1.136 brouard 1021: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 1022: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 1023: FILE *ficlog, *ficrespow;
1.130 brouard 1024: int globpr=0; /* Global variable for printing or not */
1.126 brouard 1025: double fretone; /* Only one call to likelihood */
1.130 brouard 1026: long ipmx=0; /* Number of contributions */
1.126 brouard 1027: double sw; /* Sum of weights */
1028: char filerespow[FILENAMELENGTH];
1029: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
1030: FILE *ficresilk;
1031: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
1032: FILE *ficresprobmorprev;
1033: FILE *fichtm, *fichtmcov; /* Html File */
1034: FILE *ficreseij;
1035: char filerese[FILENAMELENGTH];
1036: FILE *ficresstdeij;
1037: char fileresstde[FILENAMELENGTH];
1038: FILE *ficrescveij;
1039: char filerescve[FILENAMELENGTH];
1040: FILE *ficresvij;
1041: char fileresv[FILENAMELENGTH];
1042: FILE *ficresvpl;
1043: char fileresvpl[FILENAMELENGTH];
1044: char title[MAXLINE];
1.234 brouard 1045: char model[MAXLINE]; /**< The model line */
1.217 brouard 1046: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1047: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1048: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1049: char command[FILENAMELENGTH];
1050: int outcmd=0;
1051:
1.217 brouard 1052: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1053: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1054: char filelog[FILENAMELENGTH]; /* Log file */
1055: char filerest[FILENAMELENGTH];
1056: char fileregp[FILENAMELENGTH];
1057: char popfile[FILENAMELENGTH];
1058:
1059: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1060:
1.157 brouard 1061: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1062: /* struct timezone tzp; */
1063: /* extern int gettimeofday(); */
1064: struct tm tml, *gmtime(), *localtime();
1065:
1066: extern time_t time();
1067:
1068: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1069: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1070: struct tm tm;
1071:
1.126 brouard 1072: char strcurr[80], strfor[80];
1073:
1074: char *endptr;
1075: long lval;
1076: double dval;
1077:
1078: #define NR_END 1
1079: #define FREE_ARG char*
1080: #define FTOL 1.0e-10
1081:
1082: #define NRANSI
1.240 brouard 1083: #define ITMAX 200
1084: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1085:
1086: #define TOL 2.0e-4
1087:
1088: #define CGOLD 0.3819660
1089: #define ZEPS 1.0e-10
1090: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1091:
1092: #define GOLD 1.618034
1093: #define GLIMIT 100.0
1094: #define TINY 1.0e-20
1095:
1096: static double maxarg1,maxarg2;
1097: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1098: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1099:
1100: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1101: #define rint(a) floor(a+0.5)
1.166 brouard 1102: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1103: #define mytinydouble 1.0e-16
1.166 brouard 1104: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1105: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1106: /* static double dsqrarg; */
1107: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1108: static double sqrarg;
1109: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1110: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1111: int agegomp= AGEGOMP;
1112:
1113: int imx;
1114: int stepm=1;
1115: /* Stepm, step in month: minimum step interpolation*/
1116:
1117: int estepm;
1118: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1119:
1120: int m,nb;
1121: long *num;
1.197 brouard 1122: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1123: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1124: covariate for which somebody answered excluding
1125: undefined. Usually 2: 0 and 1. */
1126: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1127: covariate for which somebody answered including
1128: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1129: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1130: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1131: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1132: double *ageexmed,*agecens;
1133: double dateintmean=0;
1134:
1135: double *weight;
1136: int **s; /* Status */
1.141 brouard 1137: double *agedc;
1.145 brouard 1138: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1139: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1140: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1141: double **coqvar; /* Fixed quantitative covariate iqv */
1142: double ***cotvar; /* Time varying covariate itv */
1143: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1144: double idx;
1145: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1146: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1147: /*k 1 2 3 4 5 6 7 8 9 */
1148: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1149: /* Tndvar[k] 1 2 3 4 5 */
1150: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1151: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1152: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1153: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1154: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1155: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1156: /* Tprod[i]=k 4 7 */
1157: /* Tage[i]=k 5 8 */
1158: /* */
1159: /* Type */
1160: /* V 1 2 3 4 5 */
1161: /* F F V V V */
1162: /* D Q D D Q */
1163: /* */
1164: int *TvarsD;
1165: int *TvarsDind;
1166: int *TvarsQ;
1167: int *TvarsQind;
1168:
1.235 brouard 1169: #define MAXRESULTLINES 10
1170: int nresult=0;
1171: int TKresult[MAXRESULTLINES];
1.237 brouard 1172: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1173: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1174: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1175: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1176: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1177: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1178:
1.234 brouard 1179: /* 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 1180: 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 */
1181: 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 */
1182: 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 */
1183: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1184: 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 */
1185: 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 1186: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1187: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1188: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1189: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1190: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1191: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1192: 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 */
1193: 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 */
1194:
1.230 brouard 1195: int *Tvarsel; /**< Selected covariates for output */
1196: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1197: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1198: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1199: 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 1200: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1201: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1202: int *Tage;
1.227 brouard 1203: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1204: 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 1205: 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*/
1206: 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 1207: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1208: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1209: int **Tvard;
1210: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1211: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1212: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1213: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1214: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1215: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1216: double *lsurv, *lpop, *tpop;
1217:
1.231 brouard 1218: #define FD 1; /* Fixed dummy covariate */
1219: #define FQ 2; /* Fixed quantitative covariate */
1220: #define FP 3; /* Fixed product covariate */
1221: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1222: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1223: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1224: #define VD 10; /* Varying dummy covariate */
1225: #define VQ 11; /* Varying quantitative covariate */
1226: #define VP 12; /* Varying product covariate */
1227: #define VPDD 13; /* Varying product dummy*dummy covariate */
1228: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1229: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1230: #define APFD 16; /* Age product * fixed dummy covariate */
1231: #define APFQ 17; /* Age product * fixed quantitative covariate */
1232: #define APVD 18; /* Age product * varying dummy covariate */
1233: #define APVQ 19; /* Age product * varying quantitative covariate */
1234:
1235: #define FTYPE 1; /* Fixed covariate */
1236: #define VTYPE 2; /* Varying covariate (loop in wave) */
1237: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1238:
1239: struct kmodel{
1240: int maintype; /* main type */
1241: int subtype; /* subtype */
1242: };
1243: struct kmodel modell[NCOVMAX];
1244:
1.143 brouard 1245: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1246: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1247:
1248: /**************** split *************************/
1249: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1250: {
1251: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1252: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1253: */
1254: char *ss; /* pointer */
1.186 brouard 1255: int l1=0, l2=0; /* length counters */
1.126 brouard 1256:
1257: l1 = strlen(path ); /* length of path */
1258: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1259: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1260: if ( ss == NULL ) { /* no directory, so determine current directory */
1261: strcpy( name, path ); /* we got the fullname name because no directory */
1262: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1263: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1264: /* get current working directory */
1265: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1266: #ifdef WIN32
1267: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1268: #else
1269: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1270: #endif
1.126 brouard 1271: return( GLOCK_ERROR_GETCWD );
1272: }
1273: /* got dirc from getcwd*/
1274: printf(" DIRC = %s \n",dirc);
1.205 brouard 1275: } else { /* strip directory from path */
1.126 brouard 1276: ss++; /* after this, the filename */
1277: l2 = strlen( ss ); /* length of filename */
1278: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1279: strcpy( name, ss ); /* save file name */
1280: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1281: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1282: printf(" DIRC2 = %s \n",dirc);
1283: }
1284: /* We add a separator at the end of dirc if not exists */
1285: l1 = strlen( dirc ); /* length of directory */
1286: if( dirc[l1-1] != DIRSEPARATOR ){
1287: dirc[l1] = DIRSEPARATOR;
1288: dirc[l1+1] = 0;
1289: printf(" DIRC3 = %s \n",dirc);
1290: }
1291: ss = strrchr( name, '.' ); /* find last / */
1292: if (ss >0){
1293: ss++;
1294: strcpy(ext,ss); /* save extension */
1295: l1= strlen( name);
1296: l2= strlen(ss)+1;
1297: strncpy( finame, name, l1-l2);
1298: finame[l1-l2]= 0;
1299: }
1300:
1301: return( 0 ); /* we're done */
1302: }
1303:
1304:
1305: /******************************************/
1306:
1307: void replace_back_to_slash(char *s, char*t)
1308: {
1309: int i;
1310: int lg=0;
1311: i=0;
1312: lg=strlen(t);
1313: for(i=0; i<= lg; i++) {
1314: (s[i] = t[i]);
1315: if (t[i]== '\\') s[i]='/';
1316: }
1317: }
1318:
1.132 brouard 1319: char *trimbb(char *out, char *in)
1.137 brouard 1320: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1321: char *s;
1322: s=out;
1323: while (*in != '\0'){
1.137 brouard 1324: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1325: in++;
1326: }
1327: *out++ = *in++;
1328: }
1329: *out='\0';
1330: return s;
1331: }
1332:
1.187 brouard 1333: /* char *substrchaine(char *out, char *in, char *chain) */
1334: /* { */
1335: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1336: /* char *s, *t; */
1337: /* t=in;s=out; */
1338: /* while ((*in != *chain) && (*in != '\0')){ */
1339: /* *out++ = *in++; */
1340: /* } */
1341:
1342: /* /\* *in matches *chain *\/ */
1343: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1344: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1345: /* } */
1346: /* in--; chain--; */
1347: /* while ( (*in != '\0')){ */
1348: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1349: /* *out++ = *in++; */
1350: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1351: /* } */
1352: /* *out='\0'; */
1353: /* out=s; */
1354: /* return out; */
1355: /* } */
1356: char *substrchaine(char *out, char *in, char *chain)
1357: {
1358: /* Substract chain 'chain' from 'in', return and output 'out' */
1359: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1360:
1361: char *strloc;
1362:
1363: strcpy (out, in);
1364: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1365: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1366: if(strloc != NULL){
1367: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1368: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1369: /* strcpy (strloc, strloc +strlen(chain));*/
1370: }
1371: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1372: return out;
1373: }
1374:
1375:
1.145 brouard 1376: char *cutl(char *blocc, char *alocc, char *in, char occ)
1377: {
1.187 brouard 1378: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1379: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1380: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1381: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1382: */
1.160 brouard 1383: char *s, *t;
1.145 brouard 1384: t=in;s=in;
1385: while ((*in != occ) && (*in != '\0')){
1386: *alocc++ = *in++;
1387: }
1388: if( *in == occ){
1389: *(alocc)='\0';
1390: s=++in;
1391: }
1392:
1393: if (s == t) {/* occ not found */
1394: *(alocc-(in-s))='\0';
1395: in=s;
1396: }
1397: while ( *in != '\0'){
1398: *blocc++ = *in++;
1399: }
1400:
1401: *blocc='\0';
1402: return t;
1403: }
1.137 brouard 1404: char *cutv(char *blocc, char *alocc, char *in, char occ)
1405: {
1.187 brouard 1406: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1407: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1408: gives blocc="abcdef2ghi" and alocc="j".
1409: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1410: */
1411: char *s, *t;
1412: t=in;s=in;
1413: while (*in != '\0'){
1414: while( *in == occ){
1415: *blocc++ = *in++;
1416: s=in;
1417: }
1418: *blocc++ = *in++;
1419: }
1420: if (s == t) /* occ not found */
1421: *(blocc-(in-s))='\0';
1422: else
1423: *(blocc-(in-s)-1)='\0';
1424: in=s;
1425: while ( *in != '\0'){
1426: *alocc++ = *in++;
1427: }
1428:
1429: *alocc='\0';
1430: return s;
1431: }
1432:
1.126 brouard 1433: int nbocc(char *s, char occ)
1434: {
1435: int i,j=0;
1436: int lg=20;
1437: i=0;
1438: lg=strlen(s);
1439: for(i=0; i<= lg; i++) {
1.234 brouard 1440: if (s[i] == occ ) j++;
1.126 brouard 1441: }
1442: return j;
1443: }
1444:
1.137 brouard 1445: /* void cutv(char *u,char *v, char*t, char occ) */
1446: /* { */
1447: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1448: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1449: /* gives u="abcdef2ghi" and v="j" *\/ */
1450: /* int i,lg,j,p=0; */
1451: /* i=0; */
1452: /* lg=strlen(t); */
1453: /* for(j=0; j<=lg-1; j++) { */
1454: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1455: /* } */
1.126 brouard 1456:
1.137 brouard 1457: /* for(j=0; j<p; j++) { */
1458: /* (u[j] = t[j]); */
1459: /* } */
1460: /* u[p]='\0'; */
1.126 brouard 1461:
1.137 brouard 1462: /* for(j=0; j<= lg; j++) { */
1463: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1464: /* } */
1465: /* } */
1.126 brouard 1466:
1.160 brouard 1467: #ifdef _WIN32
1468: char * strsep(char **pp, const char *delim)
1469: {
1470: char *p, *q;
1471:
1472: if ((p = *pp) == NULL)
1473: return 0;
1474: if ((q = strpbrk (p, delim)) != NULL)
1475: {
1476: *pp = q + 1;
1477: *q = '\0';
1478: }
1479: else
1480: *pp = 0;
1481: return p;
1482: }
1483: #endif
1484:
1.126 brouard 1485: /********************** nrerror ********************/
1486:
1487: void nrerror(char error_text[])
1488: {
1489: fprintf(stderr,"ERREUR ...\n");
1490: fprintf(stderr,"%s\n",error_text);
1491: exit(EXIT_FAILURE);
1492: }
1493: /*********************** vector *******************/
1494: double *vector(int nl, int nh)
1495: {
1496: double *v;
1497: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1498: if (!v) nrerror("allocation failure in vector");
1499: return v-nl+NR_END;
1500: }
1501:
1502: /************************ free vector ******************/
1503: void free_vector(double*v, int nl, int nh)
1504: {
1505: free((FREE_ARG)(v+nl-NR_END));
1506: }
1507:
1508: /************************ivector *******************************/
1509: int *ivector(long nl,long nh)
1510: {
1511: int *v;
1512: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1513: if (!v) nrerror("allocation failure in ivector");
1514: return v-nl+NR_END;
1515: }
1516:
1517: /******************free ivector **************************/
1518: void free_ivector(int *v, long nl, long nh)
1519: {
1520: free((FREE_ARG)(v+nl-NR_END));
1521: }
1522:
1523: /************************lvector *******************************/
1524: long *lvector(long nl,long nh)
1525: {
1526: long *v;
1527: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1528: if (!v) nrerror("allocation failure in ivector");
1529: return v-nl+NR_END;
1530: }
1531:
1532: /******************free lvector **************************/
1533: void free_lvector(long *v, long nl, long nh)
1534: {
1535: free((FREE_ARG)(v+nl-NR_END));
1536: }
1537:
1538: /******************* imatrix *******************************/
1539: int **imatrix(long nrl, long nrh, long ncl, long nch)
1540: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1541: {
1542: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1543: int **m;
1544:
1545: /* allocate pointers to rows */
1546: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1547: if (!m) nrerror("allocation failure 1 in matrix()");
1548: m += NR_END;
1549: m -= nrl;
1550:
1551:
1552: /* allocate rows and set pointers to them */
1553: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1554: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1555: m[nrl] += NR_END;
1556: m[nrl] -= ncl;
1557:
1558: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1559:
1560: /* return pointer to array of pointers to rows */
1561: return m;
1562: }
1563:
1564: /****************** free_imatrix *************************/
1565: void free_imatrix(m,nrl,nrh,ncl,nch)
1566: int **m;
1567: long nch,ncl,nrh,nrl;
1568: /* free an int matrix allocated by imatrix() */
1569: {
1570: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1571: free((FREE_ARG) (m+nrl-NR_END));
1572: }
1573:
1574: /******************* matrix *******************************/
1575: double **matrix(long nrl, long nrh, long ncl, long nch)
1576: {
1577: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1578: double **m;
1579:
1580: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1581: if (!m) nrerror("allocation failure 1 in matrix()");
1582: m += NR_END;
1583: m -= nrl;
1584:
1585: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1586: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1587: m[nrl] += NR_END;
1588: m[nrl] -= ncl;
1589:
1590: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1591: return m;
1.145 brouard 1592: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1593: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1594: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1595: */
1596: }
1597:
1598: /*************************free matrix ************************/
1599: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1600: {
1601: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1602: free((FREE_ARG)(m+nrl-NR_END));
1603: }
1604:
1605: /******************* ma3x *******************************/
1606: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1607: {
1608: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1609: double ***m;
1610:
1611: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1612: if (!m) nrerror("allocation failure 1 in matrix()");
1613: m += NR_END;
1614: m -= nrl;
1615:
1616: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1617: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1618: m[nrl] += NR_END;
1619: m[nrl] -= ncl;
1620:
1621: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1622:
1623: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1624: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1625: m[nrl][ncl] += NR_END;
1626: m[nrl][ncl] -= nll;
1627: for (j=ncl+1; j<=nch; j++)
1628: m[nrl][j]=m[nrl][j-1]+nlay;
1629:
1630: for (i=nrl+1; i<=nrh; i++) {
1631: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1632: for (j=ncl+1; j<=nch; j++)
1633: m[i][j]=m[i][j-1]+nlay;
1634: }
1635: return m;
1636: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1637: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1638: */
1639: }
1640:
1641: /*************************free ma3x ************************/
1642: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1643: {
1644: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1645: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1646: free((FREE_ARG)(m+nrl-NR_END));
1647: }
1648:
1649: /*************** function subdirf ***********/
1650: char *subdirf(char fileres[])
1651: {
1652: /* Caution optionfilefiname is hidden */
1653: strcpy(tmpout,optionfilefiname);
1654: strcat(tmpout,"/"); /* Add to the right */
1655: strcat(tmpout,fileres);
1656: return tmpout;
1657: }
1658:
1659: /*************** function subdirf2 ***********/
1660: char *subdirf2(char fileres[], char *preop)
1661: {
1662:
1663: /* Caution optionfilefiname is hidden */
1664: strcpy(tmpout,optionfilefiname);
1665: strcat(tmpout,"/");
1666: strcat(tmpout,preop);
1667: strcat(tmpout,fileres);
1668: return tmpout;
1669: }
1670:
1671: /*************** function subdirf3 ***********/
1672: char *subdirf3(char fileres[], char *preop, char *preop2)
1673: {
1674:
1675: /* Caution optionfilefiname is hidden */
1676: strcpy(tmpout,optionfilefiname);
1677: strcat(tmpout,"/");
1678: strcat(tmpout,preop);
1679: strcat(tmpout,preop2);
1680: strcat(tmpout,fileres);
1681: return tmpout;
1682: }
1.213 brouard 1683:
1684: /*************** function subdirfext ***********/
1685: char *subdirfext(char fileres[], char *preop, char *postop)
1686: {
1687:
1688: strcpy(tmpout,preop);
1689: strcat(tmpout,fileres);
1690: strcat(tmpout,postop);
1691: return tmpout;
1692: }
1.126 brouard 1693:
1.213 brouard 1694: /*************** function subdirfext3 ***********/
1695: char *subdirfext3(char fileres[], char *preop, char *postop)
1696: {
1697:
1698: /* Caution optionfilefiname is hidden */
1699: strcpy(tmpout,optionfilefiname);
1700: strcat(tmpout,"/");
1701: strcat(tmpout,preop);
1702: strcat(tmpout,fileres);
1703: strcat(tmpout,postop);
1704: return tmpout;
1705: }
1706:
1.162 brouard 1707: char *asc_diff_time(long time_sec, char ascdiff[])
1708: {
1709: long sec_left, days, hours, minutes;
1710: days = (time_sec) / (60*60*24);
1711: sec_left = (time_sec) % (60*60*24);
1712: hours = (sec_left) / (60*60) ;
1713: sec_left = (sec_left) %(60*60);
1714: minutes = (sec_left) /60;
1715: sec_left = (sec_left) % (60);
1716: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1717: return ascdiff;
1718: }
1719:
1.126 brouard 1720: /***************** f1dim *************************/
1721: extern int ncom;
1722: extern double *pcom,*xicom;
1723: extern double (*nrfunc)(double []);
1724:
1725: double f1dim(double x)
1726: {
1727: int j;
1728: double f;
1729: double *xt;
1730:
1731: xt=vector(1,ncom);
1732: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1733: f=(*nrfunc)(xt);
1734: free_vector(xt,1,ncom);
1735: return f;
1736: }
1737:
1738: /*****************brent *************************/
1739: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1740: {
1741: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1742: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1743: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1744: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1745: * returned function value.
1746: */
1.126 brouard 1747: int iter;
1748: double a,b,d,etemp;
1.159 brouard 1749: double fu=0,fv,fw,fx;
1.164 brouard 1750: double ftemp=0.;
1.126 brouard 1751: double p,q,r,tol1,tol2,u,v,w,x,xm;
1752: double e=0.0;
1753:
1754: a=(ax < cx ? ax : cx);
1755: b=(ax > cx ? ax : cx);
1756: x=w=v=bx;
1757: fw=fv=fx=(*f)(x);
1758: for (iter=1;iter<=ITMAX;iter++) {
1759: xm=0.5*(a+b);
1760: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1761: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1762: printf(".");fflush(stdout);
1763: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1764: #ifdef DEBUGBRENT
1.126 brouard 1765: 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);
1766: 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);
1767: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1768: #endif
1769: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1770: *xmin=x;
1771: return fx;
1772: }
1773: ftemp=fu;
1774: if (fabs(e) > tol1) {
1775: r=(x-w)*(fx-fv);
1776: q=(x-v)*(fx-fw);
1777: p=(x-v)*q-(x-w)*r;
1778: q=2.0*(q-r);
1779: if (q > 0.0) p = -p;
1780: q=fabs(q);
1781: etemp=e;
1782: e=d;
1783: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1784: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1785: else {
1.224 brouard 1786: d=p/q;
1787: u=x+d;
1788: if (u-a < tol2 || b-u < tol2)
1789: d=SIGN(tol1,xm-x);
1.126 brouard 1790: }
1791: } else {
1792: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1793: }
1794: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1795: fu=(*f)(u);
1796: if (fu <= fx) {
1797: if (u >= x) a=x; else b=x;
1798: SHFT(v,w,x,u)
1.183 brouard 1799: SHFT(fv,fw,fx,fu)
1800: } else {
1801: if (u < x) a=u; else b=u;
1802: if (fu <= fw || w == x) {
1.224 brouard 1803: v=w;
1804: w=u;
1805: fv=fw;
1806: fw=fu;
1.183 brouard 1807: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1808: v=u;
1809: fv=fu;
1.183 brouard 1810: }
1811: }
1.126 brouard 1812: }
1813: nrerror("Too many iterations in brent");
1814: *xmin=x;
1815: return fx;
1816: }
1817:
1818: /****************** mnbrak ***********************/
1819:
1820: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1821: double (*func)(double))
1.183 brouard 1822: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1823: the downhill direction (defined by the function as evaluated at the initial points) and returns
1824: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1825: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1826: */
1.126 brouard 1827: double ulim,u,r,q, dum;
1828: double fu;
1.187 brouard 1829:
1830: double scale=10.;
1831: int iterscale=0;
1832:
1833: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1834: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1835:
1836:
1837: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1838: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1839: /* *bx = *ax - (*ax - *bx)/scale; */
1840: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1841: /* } */
1842:
1.126 brouard 1843: if (*fb > *fa) {
1844: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1845: SHFT(dum,*fb,*fa,dum)
1846: }
1.126 brouard 1847: *cx=(*bx)+GOLD*(*bx-*ax);
1848: *fc=(*func)(*cx);
1.183 brouard 1849: #ifdef DEBUG
1.224 brouard 1850: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1851: 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 1852: #endif
1.224 brouard 1853: 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 1854: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1855: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1856: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1857: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1858: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1859: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1860: fu=(*func)(u);
1.163 brouard 1861: #ifdef DEBUG
1862: /* f(x)=A(x-u)**2+f(u) */
1863: double A, fparabu;
1864: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1865: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1866: 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);
1867: 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 1868: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1869: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1870: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1871: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1872: #endif
1.184 brouard 1873: #ifdef MNBRAKORIGINAL
1.183 brouard 1874: #else
1.191 brouard 1875: /* if (fu > *fc) { */
1876: /* #ifdef DEBUG */
1877: /* printf("mnbrak4 fu > fc \n"); */
1878: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1879: /* #endif */
1880: /* /\* 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 *\\/ *\/ */
1881: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1882: /* dum=u; /\* Shifting c and u *\/ */
1883: /* u = *cx; */
1884: /* *cx = dum; */
1885: /* dum = fu; */
1886: /* fu = *fc; */
1887: /* *fc =dum; */
1888: /* } else { /\* end *\/ */
1889: /* #ifdef DEBUG */
1890: /* printf("mnbrak3 fu < fc \n"); */
1891: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1892: /* #endif */
1893: /* dum=u; /\* Shifting c and u *\/ */
1894: /* u = *cx; */
1895: /* *cx = dum; */
1896: /* dum = fu; */
1897: /* fu = *fc; */
1898: /* *fc =dum; */
1899: /* } */
1.224 brouard 1900: #ifdef DEBUGMNBRAK
1901: double A, fparabu;
1902: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1903: fparabu= *fa - A*(*ax-u)*(*ax-u);
1904: 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);
1905: 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 1906: #endif
1.191 brouard 1907: dum=u; /* Shifting c and u */
1908: u = *cx;
1909: *cx = dum;
1910: dum = fu;
1911: fu = *fc;
1912: *fc =dum;
1.183 brouard 1913: #endif
1.162 brouard 1914: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1915: #ifdef DEBUG
1.224 brouard 1916: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1917: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1918: #endif
1.126 brouard 1919: fu=(*func)(u);
1920: if (fu < *fc) {
1.183 brouard 1921: #ifdef DEBUG
1.224 brouard 1922: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1923: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1924: #endif
1925: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1926: SHFT(*fb,*fc,fu,(*func)(u))
1927: #ifdef DEBUG
1928: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1929: #endif
1930: }
1.162 brouard 1931: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1932: #ifdef DEBUG
1.224 brouard 1933: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1934: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1935: #endif
1.126 brouard 1936: u=ulim;
1937: fu=(*func)(u);
1.183 brouard 1938: } else { /* u could be left to b (if r > q parabola has a maximum) */
1939: #ifdef DEBUG
1.224 brouard 1940: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1941: 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 1942: #endif
1.126 brouard 1943: u=(*cx)+GOLD*(*cx-*bx);
1944: fu=(*func)(u);
1.224 brouard 1945: #ifdef DEBUG
1946: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1947: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1948: #endif
1.183 brouard 1949: } /* end tests */
1.126 brouard 1950: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1951: SHFT(*fa,*fb,*fc,fu)
1952: #ifdef DEBUG
1.224 brouard 1953: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1954: 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 1955: #endif
1956: } /* 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 1957: }
1958:
1959: /*************** linmin ************************/
1.162 brouard 1960: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1961: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1962: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1963: the value of func at the returned location p . This is actually all accomplished by calling the
1964: routines mnbrak and brent .*/
1.126 brouard 1965: int ncom;
1966: double *pcom,*xicom;
1967: double (*nrfunc)(double []);
1968:
1.224 brouard 1969: #ifdef LINMINORIGINAL
1.126 brouard 1970: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1971: #else
1972: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1973: #endif
1.126 brouard 1974: {
1975: double brent(double ax, double bx, double cx,
1976: double (*f)(double), double tol, double *xmin);
1977: double f1dim(double x);
1978: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1979: double *fc, double (*func)(double));
1980: int j;
1981: double xx,xmin,bx,ax;
1982: double fx,fb,fa;
1.187 brouard 1983:
1.203 brouard 1984: #ifdef LINMINORIGINAL
1985: #else
1986: double scale=10., axs, xxs; /* Scale added for infinity */
1987: #endif
1988:
1.126 brouard 1989: ncom=n;
1990: pcom=vector(1,n);
1991: xicom=vector(1,n);
1992: nrfunc=func;
1993: for (j=1;j<=n;j++) {
1994: pcom[j]=p[j];
1.202 brouard 1995: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1996: }
1.187 brouard 1997:
1.203 brouard 1998: #ifdef LINMINORIGINAL
1999: xx=1.;
2000: #else
2001: axs=0.0;
2002: xxs=1.;
2003: do{
2004: xx= xxs;
2005: #endif
1.187 brouard 2006: ax=0.;
2007: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
2008: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
2009: /* 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)) */
2010: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
2011: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
2012: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
2013: /* 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 2014: #ifdef LINMINORIGINAL
2015: #else
2016: if (fx != fx){
1.224 brouard 2017: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
2018: printf("|");
2019: fprintf(ficlog,"|");
1.203 brouard 2020: #ifdef DEBUGLINMIN
1.224 brouard 2021: 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 2022: #endif
2023: }
1.224 brouard 2024: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 2025: #endif
2026:
1.191 brouard 2027: #ifdef DEBUGLINMIN
2028: 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 2029: 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 2030: #endif
1.224 brouard 2031: #ifdef LINMINORIGINAL
2032: #else
2033: if(fb == fx){ /* Flat function in the direction */
2034: xmin=xx;
2035: *flat=1;
2036: }else{
2037: *flat=0;
2038: #endif
2039: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 2040: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
2041: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
2042: /* fmin = f(p[j] + xmin * xi[j]) */
2043: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2044: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2045: #ifdef DEBUG
1.224 brouard 2046: 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);
2047: 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);
2048: #endif
2049: #ifdef LINMINORIGINAL
2050: #else
2051: }
1.126 brouard 2052: #endif
1.191 brouard 2053: #ifdef DEBUGLINMIN
2054: printf("linmin end ");
1.202 brouard 2055: fprintf(ficlog,"linmin end ");
1.191 brouard 2056: #endif
1.126 brouard 2057: for (j=1;j<=n;j++) {
1.203 brouard 2058: #ifdef LINMINORIGINAL
2059: xi[j] *= xmin;
2060: #else
2061: #ifdef DEBUGLINMIN
2062: if(xxs <1.0)
2063: printf(" before xi[%d]=%12.8f", j,xi[j]);
2064: #endif
2065: 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) */
2066: #ifdef DEBUGLINMIN
2067: if(xxs <1.0)
2068: 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 );
2069: #endif
2070: #endif
1.187 brouard 2071: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2072: }
1.191 brouard 2073: #ifdef DEBUGLINMIN
1.203 brouard 2074: printf("\n");
1.191 brouard 2075: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2076: 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 2077: for (j=1;j<=n;j++) {
1.202 brouard 2078: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2079: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2080: if(j % ncovmodel == 0){
1.191 brouard 2081: printf("\n");
1.202 brouard 2082: fprintf(ficlog,"\n");
2083: }
1.191 brouard 2084: }
1.203 brouard 2085: #else
1.191 brouard 2086: #endif
1.126 brouard 2087: free_vector(xicom,1,n);
2088: free_vector(pcom,1,n);
2089: }
2090:
2091:
2092: /*************** powell ************************/
1.162 brouard 2093: /*
2094: Minimization of a function func of n variables. Input consists of an initial starting point
2095: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2096: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2097: such that failure to decrease by more than this amount on one iteration signals doneness. On
2098: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2099: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2100: */
1.224 brouard 2101: #ifdef LINMINORIGINAL
2102: #else
2103: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2104: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2105: #endif
1.126 brouard 2106: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2107: double (*func)(double []))
2108: {
1.224 brouard 2109: #ifdef LINMINORIGINAL
2110: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2111: double (*func)(double []));
1.224 brouard 2112: #else
1.241 brouard 2113: void linmin(double p[], double xi[], int n, double *fret,
2114: double (*func)(double []),int *flat);
1.224 brouard 2115: #endif
1.239 brouard 2116: int i,ibig,j,jk,k;
1.126 brouard 2117: double del,t,*pt,*ptt,*xit;
1.181 brouard 2118: double directest;
1.126 brouard 2119: double fp,fptt;
2120: double *xits;
2121: int niterf, itmp;
1.224 brouard 2122: #ifdef LINMINORIGINAL
2123: #else
2124:
2125: flatdir=ivector(1,n);
2126: for (j=1;j<=n;j++) flatdir[j]=0;
2127: #endif
1.126 brouard 2128:
2129: pt=vector(1,n);
2130: ptt=vector(1,n);
2131: xit=vector(1,n);
2132: xits=vector(1,n);
2133: *fret=(*func)(p);
2134: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2135: rcurr_time = time(NULL);
1.126 brouard 2136: for (*iter=1;;++(*iter)) {
1.187 brouard 2137: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2138: ibig=0;
2139: del=0.0;
1.157 brouard 2140: rlast_time=rcurr_time;
2141: /* (void) gettimeofday(&curr_time,&tzp); */
2142: rcurr_time = time(NULL);
2143: curr_time = *localtime(&rcurr_time);
2144: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2145: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2146: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2147: for (i=1;i<=n;i++) {
1.126 brouard 2148: fprintf(ficrespow," %.12lf", p[i]);
2149: }
1.239 brouard 2150: fprintf(ficrespow,"\n");fflush(ficrespow);
2151: printf("\n#model= 1 + age ");
2152: fprintf(ficlog,"\n#model= 1 + age ");
2153: if(nagesqr==1){
1.241 brouard 2154: printf(" + age*age ");
2155: fprintf(ficlog," + age*age ");
1.239 brouard 2156: }
2157: for(j=1;j <=ncovmodel-2;j++){
2158: if(Typevar[j]==0) {
2159: printf(" + V%d ",Tvar[j]);
2160: fprintf(ficlog," + V%d ",Tvar[j]);
2161: }else if(Typevar[j]==1) {
2162: printf(" + V%d*age ",Tvar[j]);
2163: fprintf(ficlog," + V%d*age ",Tvar[j]);
2164: }else if(Typevar[j]==2) {
2165: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2166: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2167: }
2168: }
1.126 brouard 2169: printf("\n");
1.239 brouard 2170: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2171: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2172: fprintf(ficlog,"\n");
1.239 brouard 2173: for(i=1,jk=1; i <=nlstate; i++){
2174: for(k=1; k <=(nlstate+ndeath); k++){
2175: if (k != i) {
2176: printf("%d%d ",i,k);
2177: fprintf(ficlog,"%d%d ",i,k);
2178: for(j=1; j <=ncovmodel; j++){
2179: printf("%12.7f ",p[jk]);
2180: fprintf(ficlog,"%12.7f ",p[jk]);
2181: jk++;
2182: }
2183: printf("\n");
2184: fprintf(ficlog,"\n");
2185: }
2186: }
2187: }
1.241 brouard 2188: if(*iter <=3 && *iter >1){
1.157 brouard 2189: tml = *localtime(&rcurr_time);
2190: strcpy(strcurr,asctime(&tml));
2191: rforecast_time=rcurr_time;
1.126 brouard 2192: itmp = strlen(strcurr);
2193: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.241 brouard 2194: strcurr[itmp-1]='\0';
1.162 brouard 2195: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2196: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2197: for(niterf=10;niterf<=30;niterf+=10){
1.241 brouard 2198: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2199: forecast_time = *localtime(&rforecast_time);
2200: strcpy(strfor,asctime(&forecast_time));
2201: itmp = strlen(strfor);
2202: if(strfor[itmp-1]=='\n')
2203: strfor[itmp-1]='\0';
2204: 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);
2205: 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 2206: }
2207: }
1.187 brouard 2208: for (i=1;i<=n;i++) { /* For each direction i */
2209: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2210: fptt=(*fret);
2211: #ifdef DEBUG
1.203 brouard 2212: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2213: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2214: #endif
1.203 brouard 2215: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2216: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2217: #ifdef LINMINORIGINAL
1.188 brouard 2218: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2219: #else
2220: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2221: flatdir[i]=flat; /* Function is vanishing in that direction i */
2222: #endif
2223: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2224: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2225: /* because that direction will be replaced unless the gain del is small */
2226: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2227: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2228: /* with the new direction. */
2229: del=fabs(fptt-(*fret));
2230: ibig=i;
1.126 brouard 2231: }
2232: #ifdef DEBUG
2233: printf("%d %.12e",i,(*fret));
2234: fprintf(ficlog,"%d %.12e",i,(*fret));
2235: for (j=1;j<=n;j++) {
1.224 brouard 2236: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2237: printf(" x(%d)=%.12e",j,xit[j]);
2238: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2239: }
2240: for(j=1;j<=n;j++) {
1.225 brouard 2241: printf(" p(%d)=%.12e",j,p[j]);
2242: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2243: }
2244: printf("\n");
2245: fprintf(ficlog,"\n");
2246: #endif
1.187 brouard 2247: } /* end loop on each direction i */
2248: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2249: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2250: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2251: for(j=1;j<=n;j++) {
1.225 brouard 2252: if(flatdir[j] >0){
2253: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2254: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2255: }
2256: /* printf("\n"); */
2257: /* fprintf(ficlog,"\n"); */
2258: }
1.243 brouard 2259: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
2260: if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
1.188 brouard 2261: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2262: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2263: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2264: /* decreased of more than 3.84 */
2265: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2266: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2267: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2268:
1.188 brouard 2269: /* Starting the program with initial values given by a former maximization will simply change */
2270: /* the scales of the directions and the directions, because the are reset to canonical directions */
2271: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2272: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2273: #ifdef DEBUG
2274: int k[2],l;
2275: k[0]=1;
2276: k[1]=-1;
2277: printf("Max: %.12e",(*func)(p));
2278: fprintf(ficlog,"Max: %.12e",(*func)(p));
2279: for (j=1;j<=n;j++) {
2280: printf(" %.12e",p[j]);
2281: fprintf(ficlog," %.12e",p[j]);
2282: }
2283: printf("\n");
2284: fprintf(ficlog,"\n");
2285: for(l=0;l<=1;l++) {
2286: for (j=1;j<=n;j++) {
2287: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2288: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2289: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2290: }
2291: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2292: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2293: }
2294: #endif
2295:
1.224 brouard 2296: #ifdef LINMINORIGINAL
2297: #else
2298: free_ivector(flatdir,1,n);
2299: #endif
1.126 brouard 2300: free_vector(xit,1,n);
2301: free_vector(xits,1,n);
2302: free_vector(ptt,1,n);
2303: free_vector(pt,1,n);
2304: return;
1.192 brouard 2305: } /* enough precision */
1.240 brouard 2306: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2307: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2308: ptt[j]=2.0*p[j]-pt[j];
2309: xit[j]=p[j]-pt[j];
2310: pt[j]=p[j];
2311: }
1.181 brouard 2312: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2313: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2314: if (*iter <=4) {
1.225 brouard 2315: #else
2316: #endif
1.224 brouard 2317: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2318: #else
1.161 brouard 2319: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2320: #endif
1.162 brouard 2321: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2322: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2323: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2324: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2325: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2326: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2327: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2328: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2329: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2330: /* Even if f3 <f1, directest can be negative and t >0 */
2331: /* mu² and del² are equal when f3=f1 */
2332: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2333: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2334: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2335: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2336: #ifdef NRCORIGINAL
2337: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2338: #else
2339: 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 2340: t= t- del*SQR(fp-fptt);
1.183 brouard 2341: #endif
1.202 brouard 2342: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2343: #ifdef DEBUG
1.181 brouard 2344: 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);
2345: 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 2346: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2347: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2348: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2349: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2350: 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);
2351: 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);
2352: #endif
1.183 brouard 2353: #ifdef POWELLORIGINAL
2354: if (t < 0.0) { /* Then we use it for new direction */
2355: #else
1.182 brouard 2356: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2357: 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 2358: 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 2359: 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 2360: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2361: }
1.181 brouard 2362: if (directest < 0.0) { /* Then we use it for new direction */
2363: #endif
1.191 brouard 2364: #ifdef DEBUGLINMIN
1.234 brouard 2365: printf("Before linmin in direction P%d-P0\n",n);
2366: for (j=1;j<=n;j++) {
2367: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2368: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2369: if(j % ncovmodel == 0){
2370: printf("\n");
2371: fprintf(ficlog,"\n");
2372: }
2373: }
1.224 brouard 2374: #endif
2375: #ifdef LINMINORIGINAL
1.234 brouard 2376: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2377: #else
1.234 brouard 2378: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2379: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2380: #endif
1.234 brouard 2381:
1.191 brouard 2382: #ifdef DEBUGLINMIN
1.234 brouard 2383: for (j=1;j<=n;j++) {
2384: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2385: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2386: if(j % ncovmodel == 0){
2387: printf("\n");
2388: fprintf(ficlog,"\n");
2389: }
2390: }
1.224 brouard 2391: #endif
1.234 brouard 2392: for (j=1;j<=n;j++) {
2393: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2394: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2395: }
1.224 brouard 2396: #ifdef LINMINORIGINAL
2397: #else
1.234 brouard 2398: for (j=1, flatd=0;j<=n;j++) {
2399: if(flatdir[j]>0)
2400: flatd++;
2401: }
2402: if(flatd >0){
1.255 ! brouard 2403: printf("%d flat directions: ",flatd);
! 2404: fprintf(ficlog,"%d flat directions :",flatd);
1.234 brouard 2405: for (j=1;j<=n;j++) {
2406: if(flatdir[j]>0){
2407: printf("%d ",j);
2408: fprintf(ficlog,"%d ",j);
2409: }
2410: }
2411: printf("\n");
2412: fprintf(ficlog,"\n");
2413: }
1.191 brouard 2414: #endif
1.234 brouard 2415: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2416: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2417:
1.126 brouard 2418: #ifdef DEBUG
1.234 brouard 2419: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2420: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2421: for(j=1;j<=n;j++){
2422: printf(" %lf",xit[j]);
2423: fprintf(ficlog," %lf",xit[j]);
2424: }
2425: printf("\n");
2426: fprintf(ficlog,"\n");
1.126 brouard 2427: #endif
1.192 brouard 2428: } /* end of t or directest negative */
1.224 brouard 2429: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2430: #else
1.234 brouard 2431: } /* end if (fptt < fp) */
1.192 brouard 2432: #endif
1.225 brouard 2433: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2434: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2435: #else
1.224 brouard 2436: #endif
1.234 brouard 2437: } /* loop iteration */
1.126 brouard 2438: }
1.234 brouard 2439:
1.126 brouard 2440: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2441:
1.235 brouard 2442: 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 2443: {
1.235 brouard 2444: /* Computes the prevalence limit in each live state at age x and for covariate combination ij
2445: (and selected quantitative values in nres)
2446: by left multiplying the unit
1.234 brouard 2447: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2448: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2449: /* Wx is row vector: population in state 1, population in state 2, population dead */
2450: /* or prevalence in state 1, prevalence in state 2, 0 */
2451: /* newm is the matrix after multiplications, its rows are identical at a factor */
2452: /* Initial matrix pimij */
2453: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2454: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2455: /* 0, 0 , 1} */
2456: /*
2457: * and after some iteration: */
2458: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2459: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2460: /* 0, 0 , 1} */
2461: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2462: /* {0.51571254859325999, 0.4842874514067399, */
2463: /* 0.51326036147820708, 0.48673963852179264} */
2464: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2465:
1.126 brouard 2466: int i, ii,j,k;
1.209 brouard 2467: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2468: /* double **matprod2(); */ /* test */
1.218 brouard 2469: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2470: double **newm;
1.209 brouard 2471: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2472: int ncvloop=0;
1.169 brouard 2473:
1.209 brouard 2474: min=vector(1,nlstate);
2475: max=vector(1,nlstate);
2476: meandiff=vector(1,nlstate);
2477:
1.218 brouard 2478: /* Starting with matrix unity */
1.126 brouard 2479: for (ii=1;ii<=nlstate+ndeath;ii++)
2480: for (j=1;j<=nlstate+ndeath;j++){
2481: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2482: }
1.169 brouard 2483:
2484: cov[1]=1.;
2485:
2486: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2487: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2488: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2489: ncvloop++;
1.126 brouard 2490: newm=savm;
2491: /* Covariates have to be included here again */
1.138 brouard 2492: cov[2]=agefin;
1.187 brouard 2493: if(nagesqr==1)
2494: cov[3]= agefin*agefin;;
1.234 brouard 2495: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2496: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2497: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2498: /* 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 2499: }
2500: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2501: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2502: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2503: /* 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 2504: }
1.237 brouard 2505: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2506: if(Dummy[Tvar[Tage[k]]]){
2507: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2508: } else{
1.235 brouard 2509: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2510: }
1.235 brouard 2511: /* 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 2512: }
1.237 brouard 2513: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2514: /* 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 2515: if(Dummy[Tvard[k][1]==0]){
2516: if(Dummy[Tvard[k][2]==0]){
2517: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2518: }else{
2519: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2520: }
2521: }else{
2522: if(Dummy[Tvard[k][2]==0]){
2523: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2524: }else{
2525: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2526: }
2527: }
1.234 brouard 2528: }
1.138 brouard 2529: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2530: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2531: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2532: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2533: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2534: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2535: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2536:
1.126 brouard 2537: savm=oldm;
2538: oldm=newm;
1.209 brouard 2539:
2540: for(j=1; j<=nlstate; j++){
2541: max[j]=0.;
2542: min[j]=1.;
2543: }
2544: for(i=1;i<=nlstate;i++){
2545: sumnew=0;
2546: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2547: for(j=1; j<=nlstate; j++){
2548: prlim[i][j]= newm[i][j]/(1-sumnew);
2549: max[j]=FMAX(max[j],prlim[i][j]);
2550: min[j]=FMIN(min[j],prlim[i][j]);
2551: }
2552: }
2553:
1.126 brouard 2554: maxmax=0.;
1.209 brouard 2555: for(j=1; j<=nlstate; j++){
2556: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2557: maxmax=FMAX(maxmax,meandiff[j]);
2558: /* 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 2559: } /* j loop */
1.203 brouard 2560: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2561: /* 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 2562: if(maxmax < ftolpl){
1.209 brouard 2563: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2564: free_vector(min,1,nlstate);
2565: free_vector(max,1,nlstate);
2566: free_vector(meandiff,1,nlstate);
1.126 brouard 2567: return prlim;
2568: }
1.169 brouard 2569: } /* age loop */
1.208 brouard 2570: /* After some age loop it doesn't converge */
1.209 brouard 2571: 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 2572: 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 2573: /* 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); */
2574: free_vector(min,1,nlstate);
2575: free_vector(max,1,nlstate);
2576: free_vector(meandiff,1,nlstate);
1.208 brouard 2577:
1.169 brouard 2578: return prlim; /* should not reach here */
1.126 brouard 2579: }
2580:
1.217 brouard 2581:
2582: /**** Back Prevalence limit (stable or period prevalence) ****************/
2583:
1.218 brouard 2584: /* 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) */
2585: /* 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 2586: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
1.217 brouard 2587: {
1.218 brouard 2588: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2589: matrix by transitions matrix until convergence is reached with precision ftolpl */
2590: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2591: /* Wx is row vector: population in state 1, population in state 2, population dead */
2592: /* or prevalence in state 1, prevalence in state 2, 0 */
2593: /* newm is the matrix after multiplications, its rows are identical at a factor */
2594: /* Initial matrix pimij */
2595: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2596: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2597: /* 0, 0 , 1} */
2598: /*
2599: * and after some iteration: */
2600: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2601: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2602: /* 0, 0 , 1} */
2603: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2604: /* {0.51571254859325999, 0.4842874514067399, */
2605: /* 0.51326036147820708, 0.48673963852179264} */
2606: /* If we start from prlim again, prlim tends to a constant matrix */
2607:
2608: int i, ii,j,k;
1.247 brouard 2609: int first=0;
1.217 brouard 2610: double *min, *max, *meandiff, maxmax,sumnew=0.;
2611: /* double **matprod2(); */ /* test */
2612: double **out, cov[NCOVMAX+1], **bmij();
2613: double **newm;
1.218 brouard 2614: double **dnewm, **doldm, **dsavm; /* for use */
2615: double **oldm, **savm; /* for use */
2616:
1.217 brouard 2617: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2618: int ncvloop=0;
2619:
2620: min=vector(1,nlstate);
2621: max=vector(1,nlstate);
2622: meandiff=vector(1,nlstate);
2623:
1.218 brouard 2624: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2625: oldm=oldms; savm=savms;
2626:
2627: /* Starting with matrix unity */
2628: for (ii=1;ii<=nlstate+ndeath;ii++)
2629: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2630: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2631: }
2632:
2633: cov[1]=1.;
2634:
2635: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2636: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2637: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2638: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2639: ncvloop++;
1.218 brouard 2640: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2641: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2642: /* Covariates have to be included here again */
2643: cov[2]=agefin;
2644: if(nagesqr==1)
2645: cov[3]= agefin*agefin;;
1.242 brouard 2646: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2647: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2648: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
2649: /* printf("bprevalim 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)); */
2650: }
2651: /* for (k=1; k<=cptcovn;k++) { */
2652: /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
2653: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2654: /* /\* 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])]); *\/ */
2655: /* } */
2656: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2657: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2658: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2659: /* 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]); */
2660: }
2661: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
2662: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
2663: /* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
2664: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
2665: for (k=1; k<=cptcovage;k++){ /* For product with age */
2666: if(Dummy[Tvar[Tage[k]]]){
2667: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2668: } else{
2669: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2670: }
2671: /* 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]); */
2672: }
2673: for (k=1; k<=cptcovprod;k++){ /* For product without age */
2674: /* 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]); */
2675: if(Dummy[Tvard[k][1]==0]){
2676: if(Dummy[Tvard[k][2]==0]){
2677: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2678: }else{
2679: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2680: }
2681: }else{
2682: if(Dummy[Tvard[k][2]==0]){
2683: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2684: }else{
2685: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2686: }
2687: }
1.217 brouard 2688: }
2689:
2690: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2691: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2692: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2693: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2694: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2695: /* ij should be linked to the correct index of cov */
2696: /* age and covariate values ij are in 'cov', but we need to pass
2697: * ij for the observed prevalence at age and status and covariate
2698: * number: prevacurrent[(int)agefin][ii][ij]
2699: */
2700: /* 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 *\/ */
2701: /* 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 *\/ */
2702: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
1.217 brouard 2703: savm=oldm;
2704: oldm=newm;
2705: for(j=1; j<=nlstate; j++){
2706: max[j]=0.;
2707: min[j]=1.;
2708: }
2709: for(j=1; j<=nlstate; j++){
2710: for(i=1;i<=nlstate;i++){
1.234 brouard 2711: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2712: bprlim[i][j]= newm[i][j];
2713: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2714: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2715: }
2716: }
1.218 brouard 2717:
1.217 brouard 2718: maxmax=0.;
2719: for(i=1; i<=nlstate; i++){
2720: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2721: maxmax=FMAX(maxmax,meandiff[i]);
2722: /* 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); */
2723: } /* j loop */
2724: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2725: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2726: if(maxmax < ftolpl){
1.220 brouard 2727: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2728: free_vector(min,1,nlstate);
2729: free_vector(max,1,nlstate);
2730: free_vector(meandiff,1,nlstate);
2731: return bprlim;
2732: }
2733: } /* age loop */
2734: /* After some age loop it doesn't converge */
1.247 brouard 2735: if(first){
2736: first=1;
2737: 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\
2738: 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);
2739: }
2740: 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 2741: 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);
2742: /* 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); */
2743: free_vector(min,1,nlstate);
2744: free_vector(max,1,nlstate);
2745: free_vector(meandiff,1,nlstate);
2746:
2747: return bprlim; /* should not reach here */
2748: }
2749:
1.126 brouard 2750: /*************** transition probabilities ***************/
2751:
2752: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2753: {
1.138 brouard 2754: /* According to parameters values stored in x and the covariate's values stored in cov,
2755: computes the probability to be observed in state j being in state i by appying the
2756: model to the ncovmodel covariates (including constant and age).
2757: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2758: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2759: ncth covariate in the global vector x is given by the formula:
2760: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2761: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2762: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2763: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2764: Outputs ps[i][j] the probability to be observed in j being in j according to
2765: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2766: */
2767: double s1, lnpijopii;
1.126 brouard 2768: /*double t34;*/
1.164 brouard 2769: int i,j, nc, ii, jj;
1.126 brouard 2770:
1.223 brouard 2771: for(i=1; i<= nlstate; i++){
2772: for(j=1; j<i;j++){
2773: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2774: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2775: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2776: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2777: }
2778: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2779: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2780: }
2781: for(j=i+1; j<=nlstate+ndeath;j++){
2782: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2783: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2784: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2785: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2786: }
2787: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2788: }
2789: }
1.218 brouard 2790:
1.223 brouard 2791: for(i=1; i<= nlstate; i++){
2792: s1=0;
2793: for(j=1; j<i; j++){
2794: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2795: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2796: }
2797: for(j=i+1; j<=nlstate+ndeath; j++){
2798: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2799: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2800: }
2801: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2802: ps[i][i]=1./(s1+1.);
2803: /* Computing other pijs */
2804: for(j=1; j<i; j++)
2805: ps[i][j]= exp(ps[i][j])*ps[i][i];
2806: for(j=i+1; j<=nlstate+ndeath; j++)
2807: ps[i][j]= exp(ps[i][j])*ps[i][i];
2808: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2809: } /* end i */
1.218 brouard 2810:
1.223 brouard 2811: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2812: for(jj=1; jj<= nlstate+ndeath; jj++){
2813: ps[ii][jj]=0;
2814: ps[ii][ii]=1;
2815: }
2816: }
1.218 brouard 2817:
2818:
1.223 brouard 2819: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2820: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2821: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2822: /* } */
2823: /* printf("\n "); */
2824: /* } */
2825: /* printf("\n ");printf("%lf ",cov[2]);*/
2826: /*
2827: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2828: goto end;*/
1.223 brouard 2829: return ps;
1.126 brouard 2830: }
2831:
1.218 brouard 2832: /*************** backward transition probabilities ***************/
2833:
2834: /* 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 ) */
2835: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2836: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2837: {
1.222 brouard 2838: /* Computes the backward probability at age agefin and covariate ij
2839: * and returns in **ps as well as **bmij.
2840: */
1.218 brouard 2841: int i, ii, j,k;
1.222 brouard 2842:
2843: double **out, **pmij();
2844: double sumnew=0.;
1.218 brouard 2845: double agefin;
1.222 brouard 2846:
2847: double **dnewm, **dsavm, **doldm;
2848: double **bbmij;
2849:
1.218 brouard 2850: doldm=ddoldms; /* global pointers */
1.222 brouard 2851: dnewm=ddnewms;
2852: dsavm=ddsavms;
2853:
2854: agefin=cov[2];
2855: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2856: the observed prevalence (with this covariate ij) */
2857: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2858: /* We do have the matrix Px in savm and we need pij */
2859: for (j=1;j<=nlstate+ndeath;j++){
2860: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2861: for (ii=1;ii<=nlstate;ii++){
2862: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2863: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2864: for (ii=1;ii<=nlstate+ndeath;ii++){
2865: if(sumnew >= 1.e-10){
2866: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2867: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2868: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2869: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2870: /* }else */
2871: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2872: }else{
1.242 brouard 2873: ;
2874: /* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
1.222 brouard 2875: }
2876: } /*End ii */
2877: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2878: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2879: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2880: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2881: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2882: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2883: /* left Product of this matrix by diag matrix of prevalences (savm) */
2884: for (j=1;j<=nlstate+ndeath;j++){
2885: for (ii=1;ii<=nlstate+ndeath;ii++){
2886: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2887: }
2888: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2889: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2890: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2891: /* end bmij */
2892: return ps;
1.218 brouard 2893: }
1.217 brouard 2894: /*************** transition probabilities ***************/
2895:
1.218 brouard 2896: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2897: {
2898: /* According to parameters values stored in x and the covariate's values stored in cov,
2899: computes the probability to be observed in state j being in state i by appying the
2900: model to the ncovmodel covariates (including constant and age).
2901: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2902: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2903: ncth covariate in the global vector x is given by the formula:
2904: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2905: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2906: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2907: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2908: Outputs ps[i][j] the probability to be observed in j being in j according to
2909: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2910: */
2911: double s1, lnpijopii;
2912: /*double t34;*/
2913: int i,j, nc, ii, jj;
2914:
1.234 brouard 2915: for(i=1; i<= nlstate; i++){
2916: for(j=1; j<i;j++){
2917: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2918: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2919: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2920: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2921: }
2922: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2923: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2924: }
2925: for(j=i+1; j<=nlstate+ndeath;j++){
2926: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2927: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2928: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2929: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2930: }
2931: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2932: }
2933: }
2934:
2935: for(i=1; i<= nlstate; i++){
2936: s1=0;
2937: for(j=1; j<i; j++){
2938: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2939: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2940: }
2941: for(j=i+1; j<=nlstate+ndeath; j++){
2942: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2943: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2944: }
2945: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2946: ps[i][i]=1./(s1+1.);
2947: /* Computing other pijs */
2948: for(j=1; j<i; j++)
2949: ps[i][j]= exp(ps[i][j])*ps[i][i];
2950: for(j=i+1; j<=nlstate+ndeath; j++)
2951: ps[i][j]= exp(ps[i][j])*ps[i][i];
2952: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2953: } /* end i */
2954:
2955: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2956: for(jj=1; jj<= nlstate+ndeath; jj++){
2957: ps[ii][jj]=0;
2958: ps[ii][ii]=1;
2959: }
2960: }
2961: /* Added for backcast */ /* Transposed matrix too */
2962: for(jj=1; jj<= nlstate+ndeath; jj++){
2963: s1=0.;
2964: for(ii=1; ii<= nlstate+ndeath; ii++){
2965: s1+=ps[ii][jj];
2966: }
2967: for(ii=1; ii<= nlstate; ii++){
2968: ps[ii][jj]=ps[ii][jj]/s1;
2969: }
2970: }
2971: /* Transposition */
2972: for(jj=1; jj<= nlstate+ndeath; jj++){
2973: for(ii=jj; ii<= nlstate+ndeath; ii++){
2974: s1=ps[ii][jj];
2975: ps[ii][jj]=ps[jj][ii];
2976: ps[jj][ii]=s1;
2977: }
2978: }
2979: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2980: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2981: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2982: /* } */
2983: /* printf("\n "); */
2984: /* } */
2985: /* printf("\n ");printf("%lf ",cov[2]);*/
2986: /*
2987: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2988: goto end;*/
2989: return ps;
1.217 brouard 2990: }
2991:
2992:
1.126 brouard 2993: /**************** Product of 2 matrices ******************/
2994:
1.145 brouard 2995: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2996: {
2997: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2998: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2999: /* in, b, out are matrice of pointers which should have been initialized
3000: before: only the contents of out is modified. The function returns
3001: a pointer to pointers identical to out */
1.145 brouard 3002: int i, j, k;
1.126 brouard 3003: for(i=nrl; i<= nrh; i++)
1.145 brouard 3004: for(k=ncolol; k<=ncoloh; k++){
3005: out[i][k]=0.;
3006: for(j=ncl; j<=nch; j++)
3007: out[i][k] +=in[i][j]*b[j][k];
3008: }
1.126 brouard 3009: return out;
3010: }
3011:
3012:
3013: /************* Higher Matrix Product ***************/
3014:
1.235 brouard 3015: 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 3016: {
1.218 brouard 3017: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 3018: 'nhstepm*hstepm*stepm' months (i.e. until
3019: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3020: nhstepm*hstepm matrices.
3021: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3022: (typically every 2 years instead of every month which is too big
3023: for the memory).
3024: Model is determined by parameters x and covariates have to be
3025: included manually here.
3026:
3027: */
3028:
3029: int i, j, d, h, k;
1.131 brouard 3030: double **out, cov[NCOVMAX+1];
1.126 brouard 3031: double **newm;
1.187 brouard 3032: double agexact;
1.214 brouard 3033: double agebegin, ageend;
1.126 brouard 3034:
3035: /* Hstepm could be zero and should return the unit matrix */
3036: for (i=1;i<=nlstate+ndeath;i++)
3037: for (j=1;j<=nlstate+ndeath;j++){
3038: oldm[i][j]=(i==j ? 1.0 : 0.0);
3039: po[i][j][0]=(i==j ? 1.0 : 0.0);
3040: }
3041: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3042: for(h=1; h <=nhstepm; h++){
3043: for(d=1; d <=hstepm; d++){
3044: newm=savm;
3045: /* Covariates have to be included here again */
3046: cov[1]=1.;
1.214 brouard 3047: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 3048: cov[2]=agexact;
3049: if(nagesqr==1)
1.227 brouard 3050: cov[3]= agexact*agexact;
1.235 brouard 3051: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
3052: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
3053: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
3054: /* 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)); */
3055: }
3056: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
3057: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
3058: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
3059: /* 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]); */
3060: }
3061: for (k=1; k<=cptcovage;k++){
3062: if(Dummy[Tvar[Tage[k]]]){
3063: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3064: } else{
3065: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
3066: }
3067: /* 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]); */
3068: }
3069: for (k=1; k<=cptcovprod;k++){ /* */
3070: /* 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]); */
3071: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
3072: }
3073: /* for (k=1; k<=cptcovn;k++) */
3074: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
3075: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
3076: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
3077: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
3078: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 3079:
3080:
1.126 brouard 3081: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3082: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3083: /* right multiplication of oldm by the current matrix */
1.126 brouard 3084: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3085: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3086: /* if((int)age == 70){ */
3087: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3088: /* for(i=1; i<=nlstate+ndeath; i++) { */
3089: /* printf("%d pmmij ",i); */
3090: /* for(j=1;j<=nlstate+ndeath;j++) { */
3091: /* printf("%f ",pmmij[i][j]); */
3092: /* } */
3093: /* printf(" oldm "); */
3094: /* for(j=1;j<=nlstate+ndeath;j++) { */
3095: /* printf("%f ",oldm[i][j]); */
3096: /* } */
3097: /* printf("\n"); */
3098: /* } */
3099: /* } */
1.126 brouard 3100: savm=oldm;
3101: oldm=newm;
3102: }
3103: for(i=1; i<=nlstate+ndeath; i++)
3104: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 3105: po[i][j][h]=newm[i][j];
3106: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3107: }
1.128 brouard 3108: /*printf("h=%d ",h);*/
1.126 brouard 3109: } /* end h */
1.218 brouard 3110: /* printf("\n H=%d \n",h); */
1.126 brouard 3111: return po;
3112: }
3113:
1.217 brouard 3114: /************* Higher Back Matrix Product ***************/
1.218 brouard 3115: /* 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 ) */
1.222 brouard 3116: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 3117: {
1.218 brouard 3118: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 3119: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3120: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3121: nhstepm*hstepm matrices.
3122: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3123: (typically every 2 years instead of every month which is too big
1.217 brouard 3124: for the memory).
1.218 brouard 3125: Model is determined by parameters x and covariates have to be
3126: included manually here.
1.217 brouard 3127:
1.222 brouard 3128: */
1.217 brouard 3129:
3130: int i, j, d, h, k;
3131: double **out, cov[NCOVMAX+1];
3132: double **newm;
3133: double agexact;
3134: double agebegin, ageend;
1.222 brouard 3135: double **oldm, **savm;
1.217 brouard 3136:
1.222 brouard 3137: oldm=oldms;savm=savms;
1.217 brouard 3138: /* Hstepm could be zero and should return the unit matrix */
3139: for (i=1;i<=nlstate+ndeath;i++)
3140: for (j=1;j<=nlstate+ndeath;j++){
3141: oldm[i][j]=(i==j ? 1.0 : 0.0);
3142: po[i][j][0]=(i==j ? 1.0 : 0.0);
3143: }
3144: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3145: for(h=1; h <=nhstepm; h++){
3146: for(d=1; d <=hstepm; d++){
3147: newm=savm;
3148: /* Covariates have to be included here again */
3149: cov[1]=1.;
3150: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
3151: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3152: cov[2]=agexact;
3153: if(nagesqr==1)
1.222 brouard 3154: cov[3]= agexact*agexact;
1.218 brouard 3155: for (k=1; k<=cptcovn;k++)
1.222 brouard 3156: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
3157: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 3158: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 3159: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
3160: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3161: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 3162: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 3163: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
3164: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.218 brouard 3165:
3166:
1.217 brouard 3167: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3168: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3169: /* Careful transposed matrix */
1.222 brouard 3170: /* age is in cov[2] */
1.218 brouard 3171: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3172: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3173: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3174: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3175: /* if((int)age == 70){ */
3176: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3177: /* for(i=1; i<=nlstate+ndeath; i++) { */
3178: /* printf("%d pmmij ",i); */
3179: /* for(j=1;j<=nlstate+ndeath;j++) { */
3180: /* printf("%f ",pmmij[i][j]); */
3181: /* } */
3182: /* printf(" oldm "); */
3183: /* for(j=1;j<=nlstate+ndeath;j++) { */
3184: /* printf("%f ",oldm[i][j]); */
3185: /* } */
3186: /* printf("\n"); */
3187: /* } */
3188: /* } */
3189: savm=oldm;
3190: oldm=newm;
3191: }
3192: for(i=1; i<=nlstate+ndeath; i++)
3193: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3194: po[i][j][h]=newm[i][j];
3195: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 3196: }
3197: /*printf("h=%d ",h);*/
3198: } /* end h */
1.222 brouard 3199: /* printf("\n H=%d \n",h); */
1.217 brouard 3200: return po;
3201: }
3202:
3203:
1.162 brouard 3204: #ifdef NLOPT
3205: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3206: double fret;
3207: double *xt;
3208: int j;
3209: myfunc_data *d2 = (myfunc_data *) pd;
3210: /* xt = (p1-1); */
3211: xt=vector(1,n);
3212: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3213:
3214: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3215: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3216: printf("Function = %.12lf ",fret);
3217: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3218: printf("\n");
3219: free_vector(xt,1,n);
3220: return fret;
3221: }
3222: #endif
1.126 brouard 3223:
3224: /*************** log-likelihood *************/
3225: double func( double *x)
3226: {
1.226 brouard 3227: int i, ii, j, k, mi, d, kk;
3228: int ioffset=0;
3229: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3230: double **out;
3231: double lli; /* Individual log likelihood */
3232: int s1, s2;
1.228 brouard 3233: 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 3234: double bbh, survp;
3235: long ipmx;
3236: double agexact;
3237: /*extern weight */
3238: /* We are differentiating ll according to initial status */
3239: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3240: /*for(i=1;i<imx;i++)
3241: printf(" %d\n",s[4][i]);
3242: */
1.162 brouard 3243:
1.226 brouard 3244: ++countcallfunc;
1.162 brouard 3245:
1.226 brouard 3246: cov[1]=1.;
1.126 brouard 3247:
1.226 brouard 3248: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3249: ioffset=0;
1.226 brouard 3250: if(mle==1){
3251: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3252: /* Computes the values of the ncovmodel covariates of the model
3253: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3254: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3255: to be observed in j being in i according to the model.
3256: */
1.243 brouard 3257: ioffset=2+nagesqr ;
1.233 brouard 3258: /* Fixed */
1.234 brouard 3259: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3260: 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)*/
3261: }
1.226 brouard 3262: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3263: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3264: has been calculated etc */
3265: /* For an individual i, wav[i] gives the number of effective waves */
3266: /* We compute the contribution to Likelihood of each effective transition
3267: mw[mi][i] is real wave of the mi th effectve wave */
3268: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3269: s2=s[mw[mi+1][i]][i];
3270: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3271: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3272: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3273: */
3274: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3275: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3276: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3277: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
1.234 brouard 3278: }
3279: for (ii=1;ii<=nlstate+ndeath;ii++)
3280: for (j=1;j<=nlstate+ndeath;j++){
3281: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3282: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3283: }
3284: for(d=0; d<dh[mi][i]; d++){
3285: newm=savm;
3286: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3287: cov[2]=agexact;
3288: if(nagesqr==1)
3289: cov[3]= agexact*agexact; /* Should be changed here */
3290: for (kk=1; kk<=cptcovage;kk++) {
1.242 brouard 3291: if(!FixedV[Tvar[Tage[kk]]])
1.234 brouard 3292: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.242 brouard 3293: else
3294: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
1.234 brouard 3295: }
3296: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3297: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3298: savm=oldm;
3299: oldm=newm;
3300: } /* end mult */
3301:
3302: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3303: /* But now since version 0.9 we anticipate for bias at large stepm.
3304: * If stepm is larger than one month (smallest stepm) and if the exact delay
3305: * (in months) between two waves is not a multiple of stepm, we rounded to
3306: * the nearest (and in case of equal distance, to the lowest) interval but now
3307: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3308: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3309: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3310: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3311: * -stepm/2 to stepm/2 .
3312: * For stepm=1 the results are the same as for previous versions of Imach.
3313: * For stepm > 1 the results are less biased than in previous versions.
3314: */
1.234 brouard 3315: s1=s[mw[mi][i]][i];
3316: s2=s[mw[mi+1][i]][i];
3317: bbh=(double)bh[mi][i]/(double)stepm;
3318: /* bias bh is positive if real duration
3319: * is higher than the multiple of stepm and negative otherwise.
3320: */
3321: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3322: if( s2 > nlstate){
3323: /* i.e. if s2 is a death state and if the date of death is known
3324: then the contribution to the likelihood is the probability to
3325: die between last step unit time and current step unit time,
3326: which is also equal to probability to die before dh
3327: minus probability to die before dh-stepm .
3328: In version up to 0.92 likelihood was computed
3329: as if date of death was unknown. Death was treated as any other
3330: health state: the date of the interview describes the actual state
3331: and not the date of a change in health state. The former idea was
3332: to consider that at each interview the state was recorded
3333: (healthy, disable or death) and IMaCh was corrected; but when we
3334: introduced the exact date of death then we should have modified
3335: the contribution of an exact death to the likelihood. This new
3336: contribution is smaller and very dependent of the step unit
3337: stepm. It is no more the probability to die between last interview
3338: and month of death but the probability to survive from last
3339: interview up to one month before death multiplied by the
3340: probability to die within a month. Thanks to Chris
3341: Jackson for correcting this bug. Former versions increased
3342: mortality artificially. The bad side is that we add another loop
3343: which slows down the processing. The difference can be up to 10%
3344: lower mortality.
3345: */
3346: /* If, at the beginning of the maximization mostly, the
3347: cumulative probability or probability to be dead is
3348: constant (ie = 1) over time d, the difference is equal to
3349: 0. out[s1][3] = savm[s1][3]: probability, being at state
3350: s1 at precedent wave, to be dead a month before current
3351: wave is equal to probability, being at state s1 at
3352: precedent wave, to be dead at mont of the current
3353: wave. Then the observed probability (that this person died)
3354: is null according to current estimated parameter. In fact,
3355: it should be very low but not zero otherwise the log go to
3356: infinity.
3357: */
1.183 brouard 3358: /* #ifdef INFINITYORIGINAL */
3359: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3360: /* #else */
3361: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3362: /* lli=log(mytinydouble); */
3363: /* else */
3364: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3365: /* #endif */
1.226 brouard 3366: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3367:
1.226 brouard 3368: } else if ( s2==-1 ) { /* alive */
3369: for (j=1,survp=0. ; j<=nlstate; j++)
3370: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3371: /*survp += out[s1][j]; */
3372: lli= log(survp);
3373: }
3374: else if (s2==-4) {
3375: for (j=3,survp=0. ; j<=nlstate; j++)
3376: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3377: lli= log(survp);
3378: }
3379: else if (s2==-5) {
3380: for (j=1,survp=0. ; j<=2; j++)
3381: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3382: lli= log(survp);
3383: }
3384: else{
3385: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3386: /* 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 */
3387: }
3388: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3389: /*if(lli ==000.0)*/
3390: /*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); */
3391: ipmx +=1;
3392: sw += weight[i];
3393: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3394: /* if (lli < log(mytinydouble)){ */
3395: /* 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); */
3396: /* 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]); */
3397: /* } */
3398: } /* end of wave */
3399: } /* end of individual */
3400: } else if(mle==2){
3401: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3402: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3403: for(mi=1; mi<= wav[i]-1; mi++){
3404: for (ii=1;ii<=nlstate+ndeath;ii++)
3405: for (j=1;j<=nlstate+ndeath;j++){
3406: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3407: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3408: }
3409: for(d=0; d<=dh[mi][i]; d++){
3410: newm=savm;
3411: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3412: cov[2]=agexact;
3413: if(nagesqr==1)
3414: cov[3]= agexact*agexact;
3415: for (kk=1; kk<=cptcovage;kk++) {
3416: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3417: }
3418: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3419: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3420: savm=oldm;
3421: oldm=newm;
3422: } /* end mult */
3423:
3424: s1=s[mw[mi][i]][i];
3425: s2=s[mw[mi+1][i]][i];
3426: bbh=(double)bh[mi][i]/(double)stepm;
3427: 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 */
3428: ipmx +=1;
3429: sw += weight[i];
3430: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3431: } /* end of wave */
3432: } /* end of individual */
3433: } else if(mle==3){ /* exponential inter-extrapolation */
3434: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3435: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3436: for(mi=1; mi<= wav[i]-1; mi++){
3437: for (ii=1;ii<=nlstate+ndeath;ii++)
3438: for (j=1;j<=nlstate+ndeath;j++){
3439: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3440: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3441: }
3442: for(d=0; d<dh[mi][i]; d++){
3443: newm=savm;
3444: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3445: cov[2]=agexact;
3446: if(nagesqr==1)
3447: cov[3]= agexact*agexact;
3448: for (kk=1; kk<=cptcovage;kk++) {
3449: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3450: }
3451: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3452: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3453: savm=oldm;
3454: oldm=newm;
3455: } /* end mult */
3456:
3457: s1=s[mw[mi][i]][i];
3458: s2=s[mw[mi+1][i]][i];
3459: bbh=(double)bh[mi][i]/(double)stepm;
3460: 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 */
3461: ipmx +=1;
3462: sw += weight[i];
3463: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3464: } /* end of wave */
3465: } /* end of individual */
3466: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3467: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3468: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3469: for(mi=1; mi<= wav[i]-1; mi++){
3470: for (ii=1;ii<=nlstate+ndeath;ii++)
3471: for (j=1;j<=nlstate+ndeath;j++){
3472: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3473: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3474: }
3475: for(d=0; d<dh[mi][i]; d++){
3476: newm=savm;
3477: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3478: cov[2]=agexact;
3479: if(nagesqr==1)
3480: cov[3]= agexact*agexact;
3481: for (kk=1; kk<=cptcovage;kk++) {
3482: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3483: }
1.126 brouard 3484:
1.226 brouard 3485: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3486: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3487: savm=oldm;
3488: oldm=newm;
3489: } /* end mult */
3490:
3491: s1=s[mw[mi][i]][i];
3492: s2=s[mw[mi+1][i]][i];
3493: if( s2 > nlstate){
3494: lli=log(out[s1][s2] - savm[s1][s2]);
3495: } else if ( s2==-1 ) { /* alive */
3496: for (j=1,survp=0. ; j<=nlstate; j++)
3497: survp += out[s1][j];
3498: lli= log(survp);
3499: }else{
3500: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3501: }
3502: ipmx +=1;
3503: sw += weight[i];
3504: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3505: /* 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 3506: } /* end of wave */
3507: } /* end of individual */
3508: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3509: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3510: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3511: for(mi=1; mi<= wav[i]-1; mi++){
3512: for (ii=1;ii<=nlstate+ndeath;ii++)
3513: for (j=1;j<=nlstate+ndeath;j++){
3514: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3515: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3516: }
3517: for(d=0; d<dh[mi][i]; d++){
3518: newm=savm;
3519: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3520: cov[2]=agexact;
3521: if(nagesqr==1)
3522: cov[3]= agexact*agexact;
3523: for (kk=1; kk<=cptcovage;kk++) {
3524: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3525: }
1.126 brouard 3526:
1.226 brouard 3527: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3528: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3529: savm=oldm;
3530: oldm=newm;
3531: } /* end mult */
3532:
3533: s1=s[mw[mi][i]][i];
3534: s2=s[mw[mi+1][i]][i];
3535: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3536: ipmx +=1;
3537: sw += weight[i];
3538: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3539: /*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]);*/
3540: } /* end of wave */
3541: } /* end of individual */
3542: } /* End of if */
3543: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3544: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3545: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3546: return -l;
1.126 brouard 3547: }
3548:
3549: /*************** log-likelihood *************/
3550: double funcone( double *x)
3551: {
1.228 brouard 3552: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3553: int i, ii, j, k, mi, d, kk;
1.228 brouard 3554: int ioffset=0;
1.131 brouard 3555: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3556: double **out;
3557: double lli; /* Individual log likelihood */
3558: double llt;
3559: int s1, s2;
1.228 brouard 3560: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3561:
1.126 brouard 3562: double bbh, survp;
1.187 brouard 3563: double agexact;
1.214 brouard 3564: double agebegin, ageend;
1.126 brouard 3565: /*extern weight */
3566: /* We are differentiating ll according to initial status */
3567: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3568: /*for(i=1;i<imx;i++)
3569: printf(" %d\n",s[4][i]);
3570: */
3571: cov[1]=1.;
3572:
3573: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3574: ioffset=0;
3575: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.243 brouard 3576: /* ioffset=2+nagesqr+cptcovage; */
3577: ioffset=2+nagesqr;
1.232 brouard 3578: /* Fixed */
1.224 brouard 3579: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3580: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3581: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3582: 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)*/
3583: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3584: /* cov[2+6]=covar[Tvar[6]][i]; */
3585: /* cov[2+6]=covar[2][i]; V2 */
3586: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3587: /* cov[2+7]=covar[Tvar[7]][i]; */
3588: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3589: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3590: /* cov[2+9]=covar[Tvar[9]][i]; */
3591: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3592: }
1.232 brouard 3593: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3594: /* 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?)*\/ */
3595: /* } */
1.231 brouard 3596: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3597: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3598: /* } */
1.225 brouard 3599:
1.233 brouard 3600:
3601: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3602: /* Wave varying (but not age varying) */
3603: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.242 brouard 3604: /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
3605: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
3606: }
1.232 brouard 3607: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.242 brouard 3608: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3609: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
3610: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3611: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
3612: /* 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 3613: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
1.242 brouard 3614: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3615: /* /\* 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]); *\/ */
3616: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
1.232 brouard 3617: /* } */
1.126 brouard 3618: for (ii=1;ii<=nlstate+ndeath;ii++)
1.242 brouard 3619: for (j=1;j<=nlstate+ndeath;j++){
3620: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3621: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3622: }
1.214 brouard 3623:
3624: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3625: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3626: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.247 brouard 3627: /* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up*\/ */
1.242 brouard 3628: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3629: and mw[mi+1][i]. dh depends on stepm.*/
3630: newm=savm;
1.247 brouard 3631: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM; /* Here d is needed */
1.242 brouard 3632: cov[2]=agexact;
3633: if(nagesqr==1)
3634: cov[3]= agexact*agexact;
3635: for (kk=1; kk<=cptcovage;kk++) {
3636: if(!FixedV[Tvar[Tage[kk]]])
3637: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3638: else
3639: cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
3640: }
3641: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3642: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3643: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3644: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3645: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3646: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3647: savm=oldm;
3648: oldm=newm;
1.126 brouard 3649: } /* end mult */
3650:
3651: s1=s[mw[mi][i]][i];
3652: s2=s[mw[mi+1][i]][i];
1.217 brouard 3653: /* if(s2==-1){ */
3654: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3655: /* /\* exit(1); *\/ */
3656: /* } */
1.126 brouard 3657: bbh=(double)bh[mi][i]/(double)stepm;
3658: /* bias is positive if real duration
3659: * is higher than the multiple of stepm and negative otherwise.
3660: */
3661: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.242 brouard 3662: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3663: } else if ( s2==-1 ) { /* alive */
1.242 brouard 3664: for (j=1,survp=0. ; j<=nlstate; j++)
3665: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3666: lli= log(survp);
1.126 brouard 3667: }else if (mle==1){
1.242 brouard 3668: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3669: } else if(mle==2){
1.242 brouard 3670: 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 3671: } else if(mle==3){ /* exponential inter-extrapolation */
1.242 brouard 3672: 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 3673: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.242 brouard 3674: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3675: } else{ /* mle=0 back to 1 */
1.242 brouard 3676: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3677: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3678: } /* End of if */
3679: ipmx +=1;
3680: sw += weight[i];
3681: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3682: /*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 3683: if(globpr){
1.246 brouard 3684: fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3685: %11.6f %11.6f %11.6f ", \
1.242 brouard 3686: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3687: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3688: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3689: llt +=ll[k]*gipmx/gsw;
3690: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3691: }
3692: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3693: }
1.232 brouard 3694: } /* end of wave */
3695: } /* end of individual */
3696: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3697: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3698: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3699: if(globpr==0){ /* First time we count the contributions and weights */
3700: gipmx=ipmx;
3701: gsw=sw;
3702: }
3703: return -l;
1.126 brouard 3704: }
3705:
3706:
3707: /*************** function likelione ***********/
3708: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3709: {
3710: /* This routine should help understanding what is done with
3711: the selection of individuals/waves and
3712: to check the exact contribution to the likelihood.
3713: Plotting could be done.
3714: */
3715: int k;
3716:
3717: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3718: strcpy(fileresilk,"ILK_");
1.202 brouard 3719: strcat(fileresilk,fileresu);
1.126 brouard 3720: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3721: printf("Problem with resultfile: %s\n", fileresilk);
3722: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3723: }
1.214 brouard 3724: 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");
3725: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3726: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3727: for(k=1; k<=nlstate; k++)
3728: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3729: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3730: }
3731:
3732: *fretone=(*funcone)(p);
3733: if(*globpri !=0){
3734: fclose(ficresilk);
1.205 brouard 3735: if (mle ==0)
3736: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3737: else if(mle >=1)
3738: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3739: 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));
1.207 brouard 3740:
1.208 brouard 3741:
3742: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3743: 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 3744: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3745: }
1.207 brouard 3746: 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 3747: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3748: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3749: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3750: fflush(fichtm);
1.205 brouard 3751: }
1.126 brouard 3752: return;
3753: }
3754:
3755:
3756: /*********** Maximum Likelihood Estimation ***************/
3757:
3758: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3759: {
1.165 brouard 3760: int i,j, iter=0;
1.126 brouard 3761: double **xi;
3762: double fret;
3763: double fretone; /* Only one call to likelihood */
3764: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3765:
3766: #ifdef NLOPT
3767: int creturn;
3768: nlopt_opt opt;
3769: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3770: double *lb;
3771: double minf; /* the minimum objective value, upon return */
3772: double * p1; /* Shifted parameters from 0 instead of 1 */
3773: myfunc_data dinst, *d = &dinst;
3774: #endif
3775:
3776:
1.126 brouard 3777: xi=matrix(1,npar,1,npar);
3778: for (i=1;i<=npar;i++)
3779: for (j=1;j<=npar;j++)
3780: xi[i][j]=(i==j ? 1.0 : 0.0);
3781: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3782: strcpy(filerespow,"POW_");
1.126 brouard 3783: strcat(filerespow,fileres);
3784: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3785: printf("Problem with resultfile: %s\n", filerespow);
3786: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3787: }
3788: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3789: for (i=1;i<=nlstate;i++)
3790: for(j=1;j<=nlstate+ndeath;j++)
3791: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3792: fprintf(ficrespow,"\n");
1.162 brouard 3793: #ifdef POWELL
1.126 brouard 3794: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3795: #endif
1.126 brouard 3796:
1.162 brouard 3797: #ifdef NLOPT
3798: #ifdef NEWUOA
3799: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3800: #else
3801: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3802: #endif
3803: lb=vector(0,npar-1);
3804: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3805: nlopt_set_lower_bounds(opt, lb);
3806: nlopt_set_initial_step1(opt, 0.1);
3807:
3808: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3809: d->function = func;
3810: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3811: nlopt_set_min_objective(opt, myfunc, d);
3812: nlopt_set_xtol_rel(opt, ftol);
3813: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3814: printf("nlopt failed! %d\n",creturn);
3815: }
3816: else {
3817: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3818: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3819: iter=1; /* not equal */
3820: }
3821: nlopt_destroy(opt);
3822: #endif
1.126 brouard 3823: free_matrix(xi,1,npar,1,npar);
3824: fclose(ficrespow);
1.203 brouard 3825: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3826: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3827: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3828:
3829: }
3830:
3831: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3832: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3833: {
3834: double **a,**y,*x,pd;
1.203 brouard 3835: /* double **hess; */
1.164 brouard 3836: int i, j;
1.126 brouard 3837: int *indx;
3838:
3839: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3840: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3841: void lubksb(double **a, int npar, int *indx, double b[]) ;
3842: void ludcmp(double **a, int npar, int *indx, double *d) ;
3843: double gompertz(double p[]);
1.203 brouard 3844: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3845:
3846: printf("\nCalculation of the hessian matrix. Wait...\n");
3847: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3848: for (i=1;i<=npar;i++){
1.203 brouard 3849: printf("%d-",i);fflush(stdout);
3850: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3851:
3852: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3853:
3854: /* printf(" %f ",p[i]);
3855: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3856: }
3857:
3858: for (i=1;i<=npar;i++) {
3859: for (j=1;j<=npar;j++) {
3860: if (j>i) {
1.203 brouard 3861: printf(".%d-%d",i,j);fflush(stdout);
3862: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3863: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3864:
3865: hess[j][i]=hess[i][j];
3866: /*printf(" %lf ",hess[i][j]);*/
3867: }
3868: }
3869: }
3870: printf("\n");
3871: fprintf(ficlog,"\n");
3872:
3873: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3874: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3875:
3876: a=matrix(1,npar,1,npar);
3877: y=matrix(1,npar,1,npar);
3878: x=vector(1,npar);
3879: indx=ivector(1,npar);
3880: for (i=1;i<=npar;i++)
3881: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3882: ludcmp(a,npar,indx,&pd);
3883:
3884: for (j=1;j<=npar;j++) {
3885: for (i=1;i<=npar;i++) x[i]=0;
3886: x[j]=1;
3887: lubksb(a,npar,indx,x);
3888: for (i=1;i<=npar;i++){
3889: matcov[i][j]=x[i];
3890: }
3891: }
3892:
3893: printf("\n#Hessian matrix#\n");
3894: fprintf(ficlog,"\n#Hessian matrix#\n");
3895: for (i=1;i<=npar;i++) {
3896: for (j=1;j<=npar;j++) {
1.203 brouard 3897: printf("%.6e ",hess[i][j]);
3898: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3899: }
3900: printf("\n");
3901: fprintf(ficlog,"\n");
3902: }
3903:
1.203 brouard 3904: /* printf("\n#Covariance matrix#\n"); */
3905: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3906: /* for (i=1;i<=npar;i++) { */
3907: /* for (j=1;j<=npar;j++) { */
3908: /* printf("%.6e ",matcov[i][j]); */
3909: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3910: /* } */
3911: /* printf("\n"); */
3912: /* fprintf(ficlog,"\n"); */
3913: /* } */
3914:
1.126 brouard 3915: /* Recompute Inverse */
1.203 brouard 3916: /* for (i=1;i<=npar;i++) */
3917: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3918: /* ludcmp(a,npar,indx,&pd); */
3919:
3920: /* printf("\n#Hessian matrix recomputed#\n"); */
3921:
3922: /* for (j=1;j<=npar;j++) { */
3923: /* for (i=1;i<=npar;i++) x[i]=0; */
3924: /* x[j]=1; */
3925: /* lubksb(a,npar,indx,x); */
3926: /* for (i=1;i<=npar;i++){ */
3927: /* y[i][j]=x[i]; */
3928: /* printf("%.3e ",y[i][j]); */
3929: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3930: /* } */
3931: /* printf("\n"); */
3932: /* fprintf(ficlog,"\n"); */
3933: /* } */
3934:
3935: /* Verifying the inverse matrix */
3936: #ifdef DEBUGHESS
3937: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3938:
1.203 brouard 3939: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3940: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3941:
3942: for (j=1;j<=npar;j++) {
3943: for (i=1;i<=npar;i++){
1.203 brouard 3944: printf("%.2f ",y[i][j]);
3945: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3946: }
3947: printf("\n");
3948: fprintf(ficlog,"\n");
3949: }
1.203 brouard 3950: #endif
1.126 brouard 3951:
3952: free_matrix(a,1,npar,1,npar);
3953: free_matrix(y,1,npar,1,npar);
3954: free_vector(x,1,npar);
3955: free_ivector(indx,1,npar);
1.203 brouard 3956: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3957:
3958:
3959: }
3960:
3961: /*************** hessian matrix ****************/
3962: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3963: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3964: int i;
3965: int l=1, lmax=20;
1.203 brouard 3966: double k1,k2, res, fx;
1.132 brouard 3967: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3968: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3969: int k=0,kmax=10;
3970: double l1;
3971:
3972: fx=func(x);
3973: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3974: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3975: l1=pow(10,l);
3976: delts=delt;
3977: for(k=1 ; k <kmax; k=k+1){
3978: delt = delta*(l1*k);
3979: p2[theta]=x[theta] +delt;
1.145 brouard 3980: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3981: p2[theta]=x[theta]-delt;
3982: k2=func(p2)-fx;
3983: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3984: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3985:
1.203 brouard 3986: #ifdef DEBUGHESSII
1.126 brouard 3987: 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);
3988: 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);
3989: #endif
3990: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3991: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3992: k=kmax;
3993: }
3994: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3995: k=kmax; l=lmax*10;
1.126 brouard 3996: }
3997: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3998: delts=delt;
3999: }
1.203 brouard 4000: } /* End loop k */
1.126 brouard 4001: }
4002: delti[theta]=delts;
4003: return res;
4004:
4005: }
4006:
1.203 brouard 4007: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 4008: {
4009: int i;
1.164 brouard 4010: int l=1, lmax=20;
1.126 brouard 4011: double k1,k2,k3,k4,res,fx;
1.132 brouard 4012: double p2[MAXPARM+1];
1.203 brouard 4013: int k, kmax=1;
4014: double v1, v2, cv12, lc1, lc2;
1.208 brouard 4015:
4016: int firstime=0;
1.203 brouard 4017:
1.126 brouard 4018: fx=func(x);
1.203 brouard 4019: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 4020: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 4021: p2[thetai]=x[thetai]+delti[thetai]*k;
4022: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4023: k1=func(p2)-fx;
4024:
1.203 brouard 4025: p2[thetai]=x[thetai]+delti[thetai]*k;
4026: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4027: k2=func(p2)-fx;
4028:
1.203 brouard 4029: p2[thetai]=x[thetai]-delti[thetai]*k;
4030: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 4031: k3=func(p2)-fx;
4032:
1.203 brouard 4033: p2[thetai]=x[thetai]-delti[thetai]*k;
4034: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 4035: k4=func(p2)-fx;
1.203 brouard 4036: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
4037: if(k1*k2*k3*k4 <0.){
1.208 brouard 4038: firstime=1;
1.203 brouard 4039: kmax=kmax+10;
1.208 brouard 4040: }
4041: if(kmax >=10 || firstime ==1){
1.246 brouard 4042: 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);
4043: 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 4044: 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);
4045: 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);
4046: }
4047: #ifdef DEBUGHESSIJ
4048: v1=hess[thetai][thetai];
4049: v2=hess[thetaj][thetaj];
4050: cv12=res;
4051: /* Computing eigen value of Hessian matrix */
4052: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4053: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4054: if ((lc2 <0) || (lc1 <0) ){
4055: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4056: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
4057: 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);
4058: 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);
4059: }
1.126 brouard 4060: #endif
4061: }
4062: return res;
4063: }
4064:
1.203 brouard 4065: /* Not done yet: Was supposed to fix if not exactly at the maximum */
4066: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
4067: /* { */
4068: /* int i; */
4069: /* int l=1, lmax=20; */
4070: /* double k1,k2,k3,k4,res,fx; */
4071: /* double p2[MAXPARM+1]; */
4072: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
4073: /* int k=0,kmax=10; */
4074: /* double l1; */
4075:
4076: /* fx=func(x); */
4077: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
4078: /* l1=pow(10,l); */
4079: /* delts=delt; */
4080: /* for(k=1 ; k <kmax; k=k+1){ */
4081: /* delt = delti*(l1*k); */
4082: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
4083: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4084: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4085: /* k1=func(p2)-fx; */
4086:
4087: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
4088: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4089: /* k2=func(p2)-fx; */
4090:
4091: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4092: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
4093: /* k3=func(p2)-fx; */
4094:
4095: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4096: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4097: /* k4=func(p2)-fx; */
4098: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4099: /* #ifdef DEBUGHESSIJ */
4100: /* 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); */
4101: /* 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); */
4102: /* #endif */
4103: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4104: /* k=kmax; */
4105: /* } */
4106: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4107: /* k=kmax; l=lmax*10; */
4108: /* } */
4109: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4110: /* delts=delt; */
4111: /* } */
4112: /* } /\* End loop k *\/ */
4113: /* } */
4114: /* delti[theta]=delts; */
4115: /* return res; */
4116: /* } */
4117:
4118:
1.126 brouard 4119: /************** Inverse of matrix **************/
4120: void ludcmp(double **a, int n, int *indx, double *d)
4121: {
4122: int i,imax,j,k;
4123: double big,dum,sum,temp;
4124: double *vv;
4125:
4126: vv=vector(1,n);
4127: *d=1.0;
4128: for (i=1;i<=n;i++) {
4129: big=0.0;
4130: for (j=1;j<=n;j++)
4131: if ((temp=fabs(a[i][j])) > big) big=temp;
4132: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
4133: vv[i]=1.0/big;
4134: }
4135: for (j=1;j<=n;j++) {
4136: for (i=1;i<j;i++) {
4137: sum=a[i][j];
4138: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4139: a[i][j]=sum;
4140: }
4141: big=0.0;
4142: for (i=j;i<=n;i++) {
4143: sum=a[i][j];
4144: for (k=1;k<j;k++)
4145: sum -= a[i][k]*a[k][j];
4146: a[i][j]=sum;
4147: if ( (dum=vv[i]*fabs(sum)) >= big) {
4148: big=dum;
4149: imax=i;
4150: }
4151: }
4152: if (j != imax) {
4153: for (k=1;k<=n;k++) {
4154: dum=a[imax][k];
4155: a[imax][k]=a[j][k];
4156: a[j][k]=dum;
4157: }
4158: *d = -(*d);
4159: vv[imax]=vv[j];
4160: }
4161: indx[j]=imax;
4162: if (a[j][j] == 0.0) a[j][j]=TINY;
4163: if (j != n) {
4164: dum=1.0/(a[j][j]);
4165: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4166: }
4167: }
4168: free_vector(vv,1,n); /* Doesn't work */
4169: ;
4170: }
4171:
4172: void lubksb(double **a, int n, int *indx, double b[])
4173: {
4174: int i,ii=0,ip,j;
4175: double sum;
4176:
4177: for (i=1;i<=n;i++) {
4178: ip=indx[i];
4179: sum=b[ip];
4180: b[ip]=b[i];
4181: if (ii)
4182: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4183: else if (sum) ii=i;
4184: b[i]=sum;
4185: }
4186: for (i=n;i>=1;i--) {
4187: sum=b[i];
4188: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4189: b[i]=sum/a[i][i];
4190: }
4191: }
4192:
4193: void pstamp(FILE *fichier)
4194: {
1.196 brouard 4195: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4196: }
4197:
1.253 brouard 4198: int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
4199:
4200: /* y=a+bx regression */
4201: double sumx = 0.0; /* sum of x */
4202: double sumx2 = 0.0; /* sum of x**2 */
4203: double sumxy = 0.0; /* sum of x * y */
4204: double sumy = 0.0; /* sum of y */
4205: double sumy2 = 0.0; /* sum of y**2 */
4206: double sume2; /* sum of square or residuals */
4207: double yhat;
4208:
4209: double denom=0;
4210: int i;
4211: int ne=*no;
4212:
4213: for ( i=ifi, ne=0;i<=ila;i++) {
4214: if(!isfinite(x[i]) || !isfinite(y[i])){
4215: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4216: continue;
4217: }
4218: ne=ne+1;
4219: sumx += x[i];
4220: sumx2 += x[i]*x[i];
4221: sumxy += x[i] * y[i];
4222: sumy += y[i];
4223: sumy2 += y[i]*y[i];
4224: denom = (ne * sumx2 - sumx*sumx);
4225: /* 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); */
4226: }
4227:
4228: denom = (ne * sumx2 - sumx*sumx);
4229: if (denom == 0) {
4230: // vertical, slope m is infinity
4231: *b = INFINITY;
4232: *a = 0;
4233: if (r) *r = 0;
4234: return 1;
4235: }
4236:
4237: *b = (ne * sumxy - sumx * sumy) / denom;
4238: *a = (sumy * sumx2 - sumx * sumxy) / denom;
4239: if (r!=NULL) {
4240: *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
4241: sqrt((sumx2 - sumx*sumx/ne) *
4242: (sumy2 - sumy*sumy/ne));
4243: }
4244: *no=ne;
4245: for ( i=ifi, ne=0;i<=ila;i++) {
4246: if(!isfinite(x[i]) || !isfinite(y[i])){
4247: /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
4248: continue;
4249: }
4250: ne=ne+1;
4251: yhat = y[i] - *a -*b* x[i];
4252: sume2 += yhat * yhat ;
4253:
4254: denom = (ne * sumx2 - sumx*sumx);
4255: /* 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); */
4256: }
4257: *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne));
4258: *sa= *sb * sqrt(sumx2/ne);
4259:
4260: return 0;
4261: }
4262:
1.126 brouard 4263: /************ Frequencies ********************/
1.251 brouard 4264: void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
1.226 brouard 4265: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4266: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.250 brouard 4267: { /* Some frequencies as well as proposing some starting values */
1.226 brouard 4268:
1.253 brouard 4269: int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;
1.226 brouard 4270: int iind=0, iage=0;
4271: int mi; /* Effective wave */
4272: int first;
4273: double ***freq; /* Frequencies */
1.253 brouard 4274: double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */
4275: int no;
1.226 brouard 4276: double *meanq;
4277: double **meanqt;
4278: double *pp, **prop, *posprop, *pospropt;
4279: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4280: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4281: double agebegin, ageend;
4282:
4283: pp=vector(1,nlstate);
1.251 brouard 4284: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4285: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4286: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4287: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4288: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
4289: meanqt=matrix(1,lastpass,1,nqtveff);
4290: strcpy(fileresp,"P_");
4291: strcat(fileresp,fileresu);
4292: /*strcat(fileresphtm,fileresu);*/
4293: if((ficresp=fopen(fileresp,"w"))==NULL) {
4294: printf("Problem with prevalence resultfile: %s\n", fileresp);
4295: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4296: exit(0);
4297: }
1.240 brouard 4298:
1.226 brouard 4299: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4300: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4301: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4302: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4303: fflush(ficlog);
4304: exit(70);
4305: }
4306: else{
4307: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 brouard 4308: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4309: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4310: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4311: }
1.237 brouard 4312: 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 4313:
1.226 brouard 4314: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4315: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4316: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4317: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4318: fflush(ficlog);
4319: exit(70);
1.240 brouard 4320: } else{
1.226 brouard 4321: 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 4322: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4323: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4324: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4325: }
1.240 brouard 4326: 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);
4327:
1.253 brouard 4328: y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
4329: x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.251 brouard 4330: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.226 brouard 4331: j1=0;
1.126 brouard 4332:
1.227 brouard 4333: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4334: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4335: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 brouard 4336:
4337:
1.226 brouard 4338: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4339: reference=low_education V1=0,V2=0
4340: med_educ V1=1 V2=0,
4341: high_educ V1=0 V2=1
4342: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4343: */
1.249 brouard 4344: dateintsum=0;
4345: k2cpt=0;
4346:
1.253 brouard 4347: if(cptcoveff == 0 )
4348: nl=1; /* Constant model only */
4349: else
4350: nl=2;
4351: for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
4352: if(nj==1)
4353: j=0; /* First pass for the constant */
4354: else
4355: j=cptcoveff; /* Other passes for the covariate values */
1.251 brouard 4356: first=1;
4357: for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
4358: posproptt=0.;
4359: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4360: scanf("%d", i);*/
4361: for (i=-5; i<=nlstate+ndeath; i++)
4362: for (jk=-5; jk<=nlstate+ndeath; jk++)
4363: for(m=iagemin; m <= iagemax+3; m++)
4364: freq[i][jk][m]=0;
4365:
4366: for (i=1; i<=nlstate; i++) {
1.240 brouard 4367: for(m=iagemin; m <= iagemax+3; m++)
1.251 brouard 4368: prop[i][m]=0;
4369: posprop[i]=0;
4370: pospropt[i]=0;
4371: }
4372: /* for (z1=1; z1<= nqfveff; z1++) { */
4373: /* meanq[z1]+=0.; */
4374: /* for(m=1;m<=lastpass;m++){ */
4375: /* meanqt[m][z1]=0.; */
4376: /* } */
4377: /* } */
4378:
4379: /* dateintsum=0; */
4380: /* k2cpt=0; */
4381:
4382: /* For that combination of covariate j1, we count and print the frequencies in one pass */
4383: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4384: bool=1;
4385: if(j !=0){
4386: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4387: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4388: /* for (z1=1; z1<= nqfveff; z1++) { */
4389: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4390: /* } */
4391: for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
4392: /* if(Tvaraff[z1] ==-20){ */
4393: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4394: /* }else if(Tvaraff[z1] ==-10){ */
4395: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4396: /* }else */
4397: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
4398: /* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */
4399: bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
4400: /* 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",
4401: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4402: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4403: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4404: } /* Onlyf fixed */
4405: } /* end z1 */
4406: } /* cptcovn > 0 */
4407: } /* end any */
4408: }/* end j==0 */
4409: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
4410: /* for(m=firstpass; m<=lastpass; m++){ */
4411: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4412: m=mw[mi][iind];
4413: if(j!=0){
4414: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4415: for (z1=1; z1<=cptcoveff; z1++) {
4416: if( Fixed[Tmodelind[z1]]==1){
4417: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4418: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
4419: value is -1, we don't select. It differs from the
4420: constant and age model which counts them. */
4421: bool=0; /* not selected */
4422: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4423: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4424: bool=0;
4425: }
4426: }
4427: }
4428: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4429: } /* end j==0 */
4430: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4431: if(bool==1){
4432: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4433: and mw[mi+1][iind]. dh depends on stepm. */
4434: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4435: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4436: if(m >=firstpass && m <=lastpass){
4437: k2=anint[m][iind]+(mint[m][iind]/12.);
4438: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4439: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4440: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4441: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4442: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4443: if (m<lastpass) {
4444: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4445: /* 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]); */
4446: if(s[m][iind]==-1)
4447: 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.));
4448: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4449: /* if((int)agev[m][iind] == 55) */
4450: /* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
4451: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4452: 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 4453: }
1.251 brouard 4454: } /* end if between passes */
4455: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
4456: dateintsum=dateintsum+k2; /* on all covariates ?*/
4457: k2cpt++;
4458: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.234 brouard 4459: }
1.251 brouard 4460: }else{
4461: bool=1;
4462: }/* end bool 2 */
4463: } /* end m */
4464: } /* end bool */
4465: } /* end iind = 1 to imx */
4466: /* prop[s][age] is feeded for any initial and valid live state as well as
4467: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4468:
4469:
4470: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4471: pstamp(ficresp);
4472: if (cptcoveff>0 && j!=0){
4473: printf( "\n#********** Variable ");
4474: fprintf(ficresp, "\n#********** Variable ");
4475: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4476: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
4477: fprintf(ficlog, "\n#********** Variable ");
4478: for (z1=1; z1<=cptcoveff; z1++){
4479: if(!FixedV[Tvaraff[z1]]){
4480: printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4481: fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4482: fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4483: fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4484: fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.250 brouard 4485: }else{
1.251 brouard 4486: printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4487: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4488: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4489: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4490: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4491: }
4492: }
4493: printf( "**********\n#");
4494: fprintf(ficresp, "**********\n#");
4495: fprintf(ficresphtm, "**********</h3>\n");
4496: fprintf(ficresphtmfr, "**********</h3>\n");
4497: fprintf(ficlog, "**********\n");
4498: }
4499: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4500: for(i=1; i<=nlstate;i++) {
4501: fprintf(ficresp, " Age Prev(%d) N(%d) N ",i,i);
4502: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4503: }
4504: fprintf(ficresp, "\n");
4505: fprintf(ficresphtm, "\n");
4506:
4507: /* Header of frequency table by age */
4508: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4509: fprintf(ficresphtmfr,"<th>Age</th> ");
4510: for(jk=-1; jk <=nlstate+ndeath; jk++){
4511: for(m=-1; m <=nlstate+ndeath; m++){
4512: if(jk!=0 && m!=0)
4513: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
1.240 brouard 4514: }
1.226 brouard 4515: }
1.251 brouard 4516: fprintf(ficresphtmfr, "\n");
4517:
4518: /* For each age */
4519: for(iage=iagemin; iage <= iagemax+3; iage++){
4520: fprintf(ficresphtm,"<tr>");
4521: if(iage==iagemax+1){
4522: fprintf(ficlog,"1");
4523: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4524: }else if(iage==iagemax+2){
4525: fprintf(ficlog,"0");
4526: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4527: }else if(iage==iagemax+3){
4528: fprintf(ficlog,"Total");
4529: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4530: }else{
1.240 brouard 4531: if(first==1){
1.251 brouard 4532: first=0;
4533: printf("See log file for details...\n");
4534: }
4535: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4536: fprintf(ficlog,"Age %d", iage);
4537: }
4538: for(jk=1; jk <=nlstate ; jk++){
4539: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4540: pp[jk] += freq[jk][m][iage];
4541: }
4542: for(jk=1; jk <=nlstate ; jk++){
4543: for(m=-1, pos=0; m <=0 ; m++)
4544: pos += freq[jk][m][iage];
4545: if(pp[jk]>=1.e-10){
4546: if(first==1){
4547: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4548: }
4549: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4550: }else{
4551: if(first==1)
4552: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4553: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1.240 brouard 4554: }
4555: }
4556:
1.251 brouard 4557: for(jk=1; jk <=nlstate ; jk++){
4558: /* posprop[jk]=0; */
4559: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4560: pp[jk] += freq[jk][m][iage];
4561: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4562:
4563: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4564: pos += pp[jk]; /* pos is the total number of transitions until this age */
4565: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4566: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4567: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
1.240 brouard 4568: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4569: }
1.251 brouard 4570: for(jk=1; jk <=nlstate ; jk++){
1.240 brouard 4571: if(pos>=1.e-5){
1.251 brouard 4572: if(first==1)
4573: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4574: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4575: }else{
4576: if(first==1)
4577: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4578: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4579: }
4580: if( iage <= iagemax){
4581: if(pos>=1.e-5){
4582: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4583: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4584: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4585: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4586: }
4587: else{
4588: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4589: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4590: }
1.240 brouard 4591: }
1.251 brouard 4592: pospropt[jk] +=posprop[jk];
4593: } /* end loop jk */
4594: /* pospropt=0.; */
4595: for(jk=-1; jk <=nlstate+ndeath; jk++){
4596: for(m=-1; m <=nlstate+ndeath; m++){
4597: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4598: if(first==1){
4599: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4600: }
1.253 brouard 4601: /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); */
1.251 brouard 4602: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4603: }
4604: if(jk!=0 && m!=0)
4605: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
1.240 brouard 4606: }
1.251 brouard 4607: } /* end loop jk */
4608: posproptt=0.;
4609: for(jk=1; jk <=nlstate; jk++){
4610: posproptt += pospropt[jk];
4611: }
4612: fprintf(ficresphtmfr,"</tr>\n ");
4613: if(iage <= iagemax){
4614: fprintf(ficresp,"\n");
4615: fprintf(ficresphtm,"</tr>\n");
1.240 brouard 4616: }
1.251 brouard 4617: if(first==1)
4618: printf("Others in log...\n");
4619: fprintf(ficlog,"\n");
4620: } /* end loop age iage */
4621: fprintf(ficresphtm,"<tr><th>Tot</th>");
4622: for(jk=1; jk <=nlstate ; jk++){
4623: if(posproptt < 1.e-5){
4624: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4625: }else{
4626: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
1.240 brouard 4627: }
1.226 brouard 4628: }
1.251 brouard 4629: fprintf(ficresphtm,"</tr>\n");
4630: fprintf(ficresphtm,"</table>\n");
4631: fprintf(ficresphtmfr,"</table>\n");
1.226 brouard 4632: if(posproptt < 1.e-5){
1.251 brouard 4633: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4634: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4635: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4636: invalidvarcomb[j1]=1;
1.226 brouard 4637: }else{
1.251 brouard 4638: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4639: invalidvarcomb[j1]=0;
1.226 brouard 4640: }
1.251 brouard 4641: fprintf(ficresphtmfr,"</table>\n");
4642: fprintf(ficlog,"\n");
4643: if(j!=0){
4644: printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
4645: for(i=1,jk=1; i <=nlstate; i++){
4646: for(k=1; k <=(nlstate+ndeath); k++){
4647: if (k != i) {
4648: for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */
1.253 brouard 4649: if(jj==1){ /* Constant case (in fact cste + age) */
1.251 brouard 4650: if(j1==1){ /* All dummy covariates to zero */
4651: freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
4652: freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
1.252 brouard 4653: printf("%d%d ",i,k);
4654: fprintf(ficlog,"%d%d ",i,k);
4655: printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],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]));
4656: fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
4657: pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4658: }
1.253 brouard 4659: }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
4660: for(iage=iagemin; iage <= iagemax+3; iage++){
4661: x[iage]= (double)iage;
4662: y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
4663: /* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */
4664: }
4665: linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
4666: pstart[jk]=b;
4667: pstart[jk-1]=a;
1.252 brouard 4668: }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 */
4669: 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]);
4670: 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]);
1.251 brouard 4671: pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
1.252 brouard 4672: printf("%d%d ",i,k);
4673: fprintf(ficlog,"%d%d ",i,k);
1.251 brouard 4674: printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],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]));
4675: }else{ /* Other cases, like quantitative fixed or varying covariates */
4676: ;
4677: }
4678: /* printf("%12.7f )", param[i][jj][k]); */
4679: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
4680: jk++;
4681: } /* end jj */
4682: } /* end k!= i */
4683: } /* end k */
4684: } /* end i, jk */
4685: } /* end j !=0 */
4686: } /* end selected combination of covariate j1 */
4687: if(j==0){ /* We can estimate starting values from the occurences in each case */
4688: printf("#Freqsummary: Starting values for the constants:\n");
4689: fprintf(ficlog,"\n");
4690: for(i=1,jk=1; i <=nlstate; i++){
4691: for(k=1; k <=(nlstate+ndeath); k++){
4692: if (k != i) {
4693: printf("%d%d ",i,k);
4694: fprintf(ficlog,"%d%d ",i,k);
4695: for(jj=1; jj <=ncovmodel; jj++){
1.253 brouard 4696: pstart[jk]=p[jk]; /* Setting pstart to p values by default */
4697: if(jj==1){ /* Age has to be done */
4698: pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
1.251 brouard 4699: printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
4700: fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
4701: }
4702: /* printf("%12.7f )", param[i][jj][k]); */
4703: /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
4704: jk++;
1.250 brouard 4705: }
1.251 brouard 4706: printf("\n");
4707: fprintf(ficlog,"\n");
1.250 brouard 4708: }
4709: }
4710: }
1.251 brouard 4711: printf("#Freqsummary\n");
4712: fprintf(ficlog,"\n");
4713: for(jk=-1; jk <=nlstate+ndeath; jk++){
4714: for(m=-1; m <=nlstate+ndeath; m++){
4715: /* param[i]|j][k]= freq[jk][m][iagemax+3] */
1.250 brouard 4716: printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
4717: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);
1.251 brouard 4718: /* if(freq[jk][m][iage] !=0 ) { /\* minimizing output *\/ */
4719: /* printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
4720: /* fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */
4721: /* } */
4722: }
4723: } /* end loop jk */
4724:
4725: printf("\n");
4726: fprintf(ficlog,"\n");
4727: } /* end j=0 */
1.249 brouard 4728: } /* end j */
1.252 brouard 4729:
1.253 brouard 4730: if(mle == -2){ /* We want to use these values as starting values */
1.252 brouard 4731: for(i=1, jk=1; i <=nlstate; i++){
4732: for(j=1; j <=nlstate+ndeath; j++){
4733: if(j!=i){
4734: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4735: printf("%1d%1d",i,j);
4736: fprintf(ficparo,"%1d%1d",i,j);
4737: for(k=1; k<=ncovmodel;k++){
4738: /* printf(" %lf",param[i][j][k]); */
4739: /* fprintf(ficparo," %lf",param[i][j][k]); */
4740: p[jk]=pstart[jk];
4741: printf(" %f ",pstart[jk]);
4742: fprintf(ficparo," %f ",pstart[jk]);
4743: jk++;
4744: }
4745: printf("\n");
4746: fprintf(ficparo,"\n");
4747: }
4748: }
4749: }
4750: } /* end mle=-2 */
1.226 brouard 4751: dateintmean=dateintsum/k2cpt;
1.240 brouard 4752:
1.226 brouard 4753: fclose(ficresp);
4754: fclose(ficresphtm);
4755: fclose(ficresphtmfr);
4756: free_vector(meanq,1,nqfveff);
4757: free_matrix(meanqt,1,lastpass,1,nqtveff);
1.253 brouard 4758: free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
4759: free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.251 brouard 4760: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4761: free_vector(pospropt,1,nlstate);
4762: free_vector(posprop,1,nlstate);
1.251 brouard 4763: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
1.226 brouard 4764: free_vector(pp,1,nlstate);
4765: /* End of freqsummary */
4766: }
1.126 brouard 4767:
4768: /************ Prevalence ********************/
1.227 brouard 4769: 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)
4770: {
4771: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4772: in each health status at the date of interview (if between dateprev1 and dateprev2).
4773: We still use firstpass and lastpass as another selection.
4774: */
1.126 brouard 4775:
1.227 brouard 4776: int i, m, jk, j1, bool, z1,j, iv;
4777: int mi; /* Effective wave */
4778: int iage;
4779: double agebegin, ageend;
4780:
4781: double **prop;
4782: double posprop;
4783: double y2; /* in fractional years */
4784: int iagemin, iagemax;
4785: int first; /** to stop verbosity which is redirected to log file */
4786:
4787: iagemin= (int) agemin;
4788: iagemax= (int) agemax;
4789: /*pp=vector(1,nlstate);*/
1.251 brouard 4790: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 4791: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4792: j1=0;
1.222 brouard 4793:
1.227 brouard 4794: /*j=cptcoveff;*/
4795: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4796:
1.227 brouard 4797: first=1;
4798: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4799: for (i=1; i<=nlstate; i++)
1.251 brouard 4800: for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
1.227 brouard 4801: prop[i][iage]=0.0;
4802: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4803: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4804: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4805:
4806: for (i=1; i<=imx; i++) { /* Each individual */
4807: bool=1;
4808: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4809: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4810: m=mw[mi][i];
4811: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4812: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4813: for (z1=1; z1<=cptcoveff; z1++){
4814: if( Fixed[Tmodelind[z1]]==1){
4815: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4816: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4817: bool=0;
4818: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4819: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4820: bool=0;
4821: }
4822: }
4823: if(bool==1){ /* Otherwise we skip that wave/person */
4824: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4825: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4826: if(m >=firstpass && m <=lastpass){
4827: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4828: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4829: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4830: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1.251 brouard 4831: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
1.227 brouard 4832: 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);
4833: exit(1);
4834: }
4835: if (s[m][i]>0 && s[m][i]<=nlstate) {
4836: /*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]]);*/
4837: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4838: prop[s[m][i]][iagemax+3] += weight[i];
4839: } /* end valid statuses */
4840: } /* end selection of dates */
4841: } /* end selection of waves */
4842: } /* end bool */
4843: } /* end wave */
4844: } /* end individual */
4845: for(i=iagemin; i <= iagemax+3; i++){
4846: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4847: posprop += prop[jk][i];
4848: }
4849:
4850: for(jk=1; jk <=nlstate ; jk++){
4851: if( i <= iagemax){
4852: if(posprop>=1.e-5){
4853: probs[i][jk][j1]= prop[jk][i]/posprop;
4854: } else{
4855: if(first==1){
4856: first=0;
4857: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);
4858: }
4859: }
4860: }
4861: }/* end jk */
4862: }/* end i */
1.222 brouard 4863: /*} *//* end i1 */
1.227 brouard 4864: } /* end j1 */
1.222 brouard 4865:
1.227 brouard 4866: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4867: /*free_vector(pp,1,nlstate);*/
1.251 brouard 4868: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
1.227 brouard 4869: } /* End of prevalence */
1.126 brouard 4870:
4871: /************* Waves Concatenation ***************/
4872:
4873: 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)
4874: {
4875: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4876: Death is a valid wave (if date is known).
4877: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4878: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4879: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4880: */
1.126 brouard 4881:
1.224 brouard 4882: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4883: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4884: double sum=0., jmean=0.;*/
1.224 brouard 4885: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4886: int j, k=0,jk, ju, jl;
4887: double sum=0.;
4888: first=0;
1.214 brouard 4889: firstwo=0;
1.217 brouard 4890: firsthree=0;
1.218 brouard 4891: firstfour=0;
1.164 brouard 4892: jmin=100000;
1.126 brouard 4893: jmax=-1;
4894: jmean=0.;
1.224 brouard 4895:
4896: /* Treating live states */
1.214 brouard 4897: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4898: mi=0; /* First valid wave */
1.227 brouard 4899: mli=0; /* Last valid wave */
1.126 brouard 4900: m=firstpass;
1.214 brouard 4901: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4902: 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 */
4903: mli=m-1;/* mw[++mi][i]=m-1; */
4904: }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 */
4905: mw[++mi][i]=m;
4906: mli=m;
1.224 brouard 4907: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4908: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4909: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4910: }
1.227 brouard 4911: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4912: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4913: break;
1.224 brouard 4914: #else
1.227 brouard 4915: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4916: if(firsthree == 0){
4917: 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 pi. .\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);
4918: firsthree=1;
4919: }
4920: 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 pi. .\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);
4921: mw[++mi][i]=m;
4922: mli=m;
4923: }
4924: if(s[m][i]==-2){ /* Vital status is really unknown */
4925: nbwarn++;
4926: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4927: 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);
4928: 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);
4929: }
4930: break;
4931: }
4932: break;
1.224 brouard 4933: #endif
1.227 brouard 4934: }/* End m >= lastpass */
1.126 brouard 4935: }/* end while */
1.224 brouard 4936:
1.227 brouard 4937: /* 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 4938: /* After last pass */
1.224 brouard 4939: /* Treating death states */
1.214 brouard 4940: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4941: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4942: /* } */
1.126 brouard 4943: mi++; /* Death is another wave */
4944: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4945: /* Only death is a correct wave */
1.126 brouard 4946: mw[mi][i]=m;
1.224 brouard 4947: }
4948: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4949: else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
1.216 brouard 4950: /* m++; */
4951: /* mi++; */
4952: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4953: /* mw[mi][i]=m; */
1.218 brouard 4954: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4955: 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 */
4956: nbwarn++;
4957: if(firstfiv==0){
4958: 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 );
4959: firstfiv=1;
4960: }else{
4961: 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 );
4962: }
4963: }else{ /* Death occured afer last wave potential bias */
4964: nberr++;
4965: if(firstwo==0){
4966: 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.\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 );
4967: firstwo=1;
4968: }
4969: 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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
4970: }
1.218 brouard 4971: }else{ /* end date of interview is known */
1.227 brouard 4972: /* death is known but not confirmed by death status at any wave */
4973: if(firstfour==0){
4974: 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 );
4975: firstfour=1;
4976: }
4977: 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 4978: }
1.224 brouard 4979: } /* end if date of death is known */
4980: #endif
4981: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4982: /* wav[i]=mw[mi][i]; */
1.126 brouard 4983: if(mi==0){
4984: nbwarn++;
4985: if(first==0){
1.227 brouard 4986: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4987: first=1;
1.126 brouard 4988: }
4989: if(first==1){
1.227 brouard 4990: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4991: }
4992: } /* end mi==0 */
4993: } /* End individuals */
1.214 brouard 4994: /* wav and mw are no more changed */
1.223 brouard 4995:
1.214 brouard 4996:
1.126 brouard 4997: for(i=1; i<=imx; i++){
4998: for(mi=1; mi<wav[i];mi++){
4999: if (stepm <=0)
1.227 brouard 5000: dh[mi][i]=1;
1.126 brouard 5001: else{
1.227 brouard 5002: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
5003: if (agedc[i] < 2*AGESUP) {
5004: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
5005: if(j==0) j=1; /* Survives at least one month after exam */
5006: else if(j<0){
5007: nberr++;
5008: 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]);
5009: j=1; /* Temporary Dangerous patch */
5010: 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);
5011: 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]);
5012: 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);
5013: }
5014: k=k+1;
5015: if (j >= jmax){
5016: jmax=j;
5017: ijmax=i;
5018: }
5019: if (j <= jmin){
5020: jmin=j;
5021: ijmin=i;
5022: }
5023: sum=sum+j;
5024: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
5025: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
5026: }
5027: }
5028: else{
5029: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 5030: /* 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 5031:
1.227 brouard 5032: k=k+1;
5033: if (j >= jmax) {
5034: jmax=j;
5035: ijmax=i;
5036: }
5037: else if (j <= jmin){
5038: jmin=j;
5039: ijmin=i;
5040: }
5041: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
5042: /*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]);*/
5043: if(j<0){
5044: nberr++;
5045: 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]);
5046: 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]);
5047: }
5048: sum=sum+j;
5049: }
5050: jk= j/stepm;
5051: jl= j -jk*stepm;
5052: ju= j -(jk+1)*stepm;
5053: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
5054: if(jl==0){
5055: dh[mi][i]=jk;
5056: bh[mi][i]=0;
5057: }else{ /* We want a negative bias in order to only have interpolation ie
5058: * to avoid the price of an extra matrix product in likelihood */
5059: dh[mi][i]=jk+1;
5060: bh[mi][i]=ju;
5061: }
5062: }else{
5063: if(jl <= -ju){
5064: dh[mi][i]=jk;
5065: bh[mi][i]=jl; /* bias is positive if real duration
5066: * is higher than the multiple of stepm and negative otherwise.
5067: */
5068: }
5069: else{
5070: dh[mi][i]=jk+1;
5071: bh[mi][i]=ju;
5072: }
5073: if(dh[mi][i]==0){
5074: dh[mi][i]=1; /* At least one step */
5075: bh[mi][i]=ju; /* At least one step */
5076: /* 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);*/
5077: }
5078: } /* end if mle */
1.126 brouard 5079: }
5080: } /* end wave */
5081: }
5082: jmean=sum/k;
5083: 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 5084: 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 5085: }
1.126 brouard 5086:
5087: /*********** Tricode ****************************/
1.220 brouard 5088: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.242 brouard 5089: {
5090: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
5091: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
5092: * Boring subroutine which should only output nbcode[Tvar[j]][k]
5093: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
5094: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
5095: */
1.130 brouard 5096:
1.242 brouard 5097: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
5098: int modmaxcovj=0; /* Modality max of covariates j */
5099: int cptcode=0; /* Modality max of covariates j */
5100: int modmincovj=0; /* Modality min of covariates j */
1.145 brouard 5101:
5102:
1.242 brouard 5103: /* cptcoveff=0; */
5104: /* *cptcov=0; */
1.126 brouard 5105:
1.242 brouard 5106: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 5107:
1.242 brouard 5108: /* Loop on covariates without age and products and no quantitative variable */
5109: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
5110: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
5111: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
5112: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
5113: switch(Fixed[k]) {
5114: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
5115: 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*/
5116: ij=(int)(covar[Tvar[k]][i]);
5117: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
5118: * If product of Vn*Vm, still boolean *:
5119: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
5120: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
5121: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
5122: modality of the nth covariate of individual i. */
5123: if (ij > modmaxcovj)
5124: modmaxcovj=ij;
5125: else if (ij < modmincovj)
5126: modmincovj=ij;
5127: if ((ij < -1) && (ij > NCOVMAX)){
5128: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
5129: exit(1);
5130: }else
5131: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
5132: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
5133: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
5134: /* getting the maximum value of the modality of the covariate
5135: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
5136: female ies 1, then modmaxcovj=1.
5137: */
5138: } /* end for loop on individuals i */
5139: printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5140: fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
5141: cptcode=modmaxcovj;
5142: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
5143: /*for (i=0; i<=cptcode; i++) {*/
5144: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
5145: printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5146: fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
5147: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
5148: if( j != -1){
5149: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
5150: covariate for which somebody answered excluding
5151: undefined. Usually 2: 0 and 1. */
5152: }
5153: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
5154: covariate for which somebody answered including
5155: undefined. Usually 3: -1, 0 and 1. */
5156: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
5157: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
5158: } /* Ndum[-1] number of undefined modalities */
1.231 brouard 5159:
1.242 brouard 5160: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
5161: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
5162: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
5163: /* modmincovj=3; modmaxcovj = 7; */
5164: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
5165: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
5166: /* defining two dummy variables: variables V1_1 and V1_2.*/
5167: /* nbcode[Tvar[j]][ij]=k; */
5168: /* nbcode[Tvar[j]][1]=0; */
5169: /* nbcode[Tvar[j]][2]=1; */
5170: /* nbcode[Tvar[j]][3]=2; */
5171: /* To be continued (not working yet). */
5172: ij=0; /* ij is similar to i but can jump over null modalities */
5173: 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*/
5174: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
5175: break;
5176: }
5177: ij++;
5178: 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*/
5179: cptcode = ij; /* New max modality for covar j */
5180: } /* end of loop on modality i=-1 to 1 or more */
5181: break;
5182: case 1: /* Testing on varying covariate, could be simple and
5183: * should look at waves or product of fixed *
5184: * varying. No time to test -1, assuming 0 and 1 only */
5185: ij=0;
5186: for(i=0; i<=1;i++){
5187: nbcode[Tvar[k]][++ij]=i;
5188: }
5189: break;
5190: default:
5191: break;
5192: } /* end switch */
5193: } /* end dummy test */
5194:
5195: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
5196: /* /\*recode from 0 *\/ */
5197: /* k is a modality. If we have model=V1+V1*sex */
5198: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
5199: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
5200: /* } */
5201: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
5202: /* if (ij > ncodemax[j]) { */
5203: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5204: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
5205: /* break; */
5206: /* } */
5207: /* } /\* end of loop on modality k *\/ */
5208: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
5209:
5210: for (k=-1; k< maxncov; k++) Ndum[k]=0;
5211: /* Look at fixed dummy (single or product) covariates to check empty modalities */
5212: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
5213: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
5214: 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 */
5215: 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 */
5216: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
5217: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
5218:
5219: ij=0;
5220: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
5221: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
5222: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
5223: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
5224: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
5225: /* If product not in single variable we don't print results */
5226: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
5227: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
5228: 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*/
5229: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
5230: 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 */
5231: if(Fixed[k]!=0)
5232: anyvaryingduminmodel=1;
5233: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
5234: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
5235: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
5236: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
5237: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
5238: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
5239: }
5240: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
5241: /* ij--; */
5242: /* cptcoveff=ij; /\*Number of total covariates*\/ */
5243: *cptcov=ij; /*Number of total real effective covariates: effective
5244: * because they can be excluded from the model and real
5245: * if in the model but excluded because missing values, but how to get k from ij?*/
5246: for(j=ij+1; j<= cptcovt; j++){
5247: Tvaraff[j]=0;
5248: Tmodelind[j]=0;
5249: }
5250: for(j=ntveff+1; j<= cptcovt; j++){
5251: TmodelInvind[j]=0;
5252: }
5253: /* To be sorted */
5254: ;
5255: }
1.126 brouard 5256:
1.145 brouard 5257:
1.126 brouard 5258: /*********** Health Expectancies ****************/
5259:
1.235 brouard 5260: 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 5261:
5262: {
5263: /* Health expectancies, no variances */
1.164 brouard 5264: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 5265: int nhstepma, nstepma; /* Decreasing with age */
5266: double age, agelim, hf;
5267: double ***p3mat;
5268: double eip;
5269:
1.238 brouard 5270: /* pstamp(ficreseij); */
1.126 brouard 5271: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
5272: fprintf(ficreseij,"# Age");
5273: for(i=1; i<=nlstate;i++){
5274: for(j=1; j<=nlstate;j++){
5275: fprintf(ficreseij," e%1d%1d ",i,j);
5276: }
5277: fprintf(ficreseij," e%1d. ",i);
5278: }
5279: fprintf(ficreseij,"\n");
5280:
5281:
5282: if(estepm < stepm){
5283: printf ("Problem %d lower than %d\n",estepm, stepm);
5284: }
5285: else hstepm=estepm;
5286: /* We compute the life expectancy from trapezoids spaced every estepm months
5287: * This is mainly to measure the difference between two models: for example
5288: * if stepm=24 months pijx are given only every 2 years and by summing them
5289: * we are calculating an estimate of the Life Expectancy assuming a linear
5290: * progression in between and thus overestimating or underestimating according
5291: * to the curvature of the survival function. If, for the same date, we
5292: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5293: * to compare the new estimate of Life expectancy with the same linear
5294: * hypothesis. A more precise result, taking into account a more precise
5295: * curvature will be obtained if estepm is as small as stepm. */
5296:
5297: /* For example we decided to compute the life expectancy with the smallest unit */
5298: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5299: nhstepm is the number of hstepm from age to agelim
5300: nstepm is the number of stepm from age to agelin.
5301: Look at hpijx to understand the reason of that which relies in memory size
5302: and note for a fixed period like estepm months */
5303: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5304: survival function given by stepm (the optimization length). Unfortunately it
5305: means that if the survival funtion is printed only each two years of age and if
5306: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5307: results. So we changed our mind and took the option of the best precision.
5308: */
5309: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5310:
5311: agelim=AGESUP;
5312: /* If stepm=6 months */
5313: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5314: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5315:
5316: /* nhstepm age range expressed in number of stepm */
5317: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5318: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5319: /* if (stepm >= YEARM) hstepm=1;*/
5320: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5321: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5322:
5323: for (age=bage; age<=fage; age ++){
5324: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5325: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5326: /* if (stepm >= YEARM) hstepm=1;*/
5327: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5328:
5329: /* If stepm=6 months */
5330: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5331: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5332:
1.235 brouard 5333: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5334:
5335: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5336:
5337: printf("%d|",(int)age);fflush(stdout);
5338: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5339:
5340: /* Computing expectancies */
5341: for(i=1; i<=nlstate;i++)
5342: for(j=1; j<=nlstate;j++)
5343: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5344: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5345:
5346: /* 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]);*/
5347:
5348: }
5349:
5350: fprintf(ficreseij,"%3.0f",age );
5351: for(i=1; i<=nlstate;i++){
5352: eip=0;
5353: for(j=1; j<=nlstate;j++){
5354: eip +=eij[i][j][(int)age];
5355: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5356: }
5357: fprintf(ficreseij,"%9.4f", eip );
5358: }
5359: fprintf(ficreseij,"\n");
5360:
5361: }
5362: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5363: printf("\n");
5364: fprintf(ficlog,"\n");
5365:
5366: }
5367:
1.235 brouard 5368: 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 5369:
5370: {
5371: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5372: to initial status i, ei. .
1.126 brouard 5373: */
5374: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5375: int nhstepma, nstepma; /* Decreasing with age */
5376: double age, agelim, hf;
5377: double ***p3matp, ***p3matm, ***varhe;
5378: double **dnewm,**doldm;
5379: double *xp, *xm;
5380: double **gp, **gm;
5381: double ***gradg, ***trgradg;
5382: int theta;
5383:
5384: double eip, vip;
5385:
5386: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5387: xp=vector(1,npar);
5388: xm=vector(1,npar);
5389: dnewm=matrix(1,nlstate*nlstate,1,npar);
5390: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5391:
5392: pstamp(ficresstdeij);
5393: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5394: fprintf(ficresstdeij,"# Age");
5395: for(i=1; i<=nlstate;i++){
5396: for(j=1; j<=nlstate;j++)
5397: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5398: fprintf(ficresstdeij," e%1d. ",i);
5399: }
5400: fprintf(ficresstdeij,"\n");
5401:
5402: pstamp(ficrescveij);
5403: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5404: fprintf(ficrescveij,"# Age");
5405: for(i=1; i<=nlstate;i++)
5406: for(j=1; j<=nlstate;j++){
5407: cptj= (j-1)*nlstate+i;
5408: for(i2=1; i2<=nlstate;i2++)
5409: for(j2=1; j2<=nlstate;j2++){
5410: cptj2= (j2-1)*nlstate+i2;
5411: if(cptj2 <= cptj)
5412: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5413: }
5414: }
5415: fprintf(ficrescveij,"\n");
5416:
5417: if(estepm < stepm){
5418: printf ("Problem %d lower than %d\n",estepm, stepm);
5419: }
5420: else hstepm=estepm;
5421: /* We compute the life expectancy from trapezoids spaced every estepm months
5422: * This is mainly to measure the difference between two models: for example
5423: * if stepm=24 months pijx are given only every 2 years and by summing them
5424: * we are calculating an estimate of the Life Expectancy assuming a linear
5425: * progression in between and thus overestimating or underestimating according
5426: * to the curvature of the survival function. If, for the same date, we
5427: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5428: * to compare the new estimate of Life expectancy with the same linear
5429: * hypothesis. A more precise result, taking into account a more precise
5430: * curvature will be obtained if estepm is as small as stepm. */
5431:
5432: /* For example we decided to compute the life expectancy with the smallest unit */
5433: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5434: nhstepm is the number of hstepm from age to agelim
5435: nstepm is the number of stepm from age to agelin.
5436: Look at hpijx to understand the reason of that which relies in memory size
5437: and note for a fixed period like estepm months */
5438: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5439: survival function given by stepm (the optimization length). Unfortunately it
5440: means that if the survival funtion is printed only each two years of age and if
5441: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5442: results. So we changed our mind and took the option of the best precision.
5443: */
5444: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5445:
5446: /* If stepm=6 months */
5447: /* nhstepm age range expressed in number of stepm */
5448: agelim=AGESUP;
5449: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5450: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5451: /* if (stepm >= YEARM) hstepm=1;*/
5452: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5453:
5454: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5455: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5456: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5457: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5458: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5459: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5460:
5461: for (age=bage; age<=fage; age ++){
5462: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5463: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5464: /* if (stepm >= YEARM) hstepm=1;*/
5465: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5466:
1.126 brouard 5467: /* If stepm=6 months */
5468: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5469: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5470:
5471: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5472:
1.126 brouard 5473: /* Computing Variances of health expectancies */
5474: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5475: decrease memory allocation */
5476: for(theta=1; theta <=npar; theta++){
5477: for(i=1; i<=npar; i++){
1.222 brouard 5478: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5479: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5480: }
1.235 brouard 5481: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5482: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5483:
1.126 brouard 5484: for(j=1; j<= nlstate; j++){
1.222 brouard 5485: for(i=1; i<=nlstate; i++){
5486: for(h=0; h<=nhstepm-1; h++){
5487: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5488: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5489: }
5490: }
1.126 brouard 5491: }
1.218 brouard 5492:
1.126 brouard 5493: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5494: for(h=0; h<=nhstepm-1; h++){
5495: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5496: }
1.126 brouard 5497: }/* End theta */
5498:
5499:
5500: for(h=0; h<=nhstepm-1; h++)
5501: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5502: for(theta=1; theta <=npar; theta++)
5503: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5504:
1.218 brouard 5505:
1.222 brouard 5506: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5507: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5508: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5509:
1.222 brouard 5510: printf("%d|",(int)age);fflush(stdout);
5511: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5512: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5513: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5514: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5515: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5516: for(ij=1;ij<=nlstate*nlstate;ij++)
5517: for(ji=1;ji<=nlstate*nlstate;ji++)
5518: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5519: }
5520: }
1.218 brouard 5521:
1.126 brouard 5522: /* Computing expectancies */
1.235 brouard 5523: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5524: for(i=1; i<=nlstate;i++)
5525: for(j=1; j<=nlstate;j++)
1.222 brouard 5526: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5527: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5528:
1.222 brouard 5529: /* 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 5530:
1.222 brouard 5531: }
1.218 brouard 5532:
1.126 brouard 5533: fprintf(ficresstdeij,"%3.0f",age );
5534: for(i=1; i<=nlstate;i++){
5535: eip=0.;
5536: vip=0.;
5537: for(j=1; j<=nlstate;j++){
1.222 brouard 5538: eip += eij[i][j][(int)age];
5539: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5540: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5541: 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 5542: }
5543: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5544: }
5545: fprintf(ficresstdeij,"\n");
1.218 brouard 5546:
1.126 brouard 5547: fprintf(ficrescveij,"%3.0f",age );
5548: for(i=1; i<=nlstate;i++)
5549: for(j=1; j<=nlstate;j++){
1.222 brouard 5550: cptj= (j-1)*nlstate+i;
5551: for(i2=1; i2<=nlstate;i2++)
5552: for(j2=1; j2<=nlstate;j2++){
5553: cptj2= (j2-1)*nlstate+i2;
5554: if(cptj2 <= cptj)
5555: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5556: }
1.126 brouard 5557: }
5558: fprintf(ficrescveij,"\n");
1.218 brouard 5559:
1.126 brouard 5560: }
5561: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5562: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5563: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5564: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5565: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5566: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5567: printf("\n");
5568: fprintf(ficlog,"\n");
1.218 brouard 5569:
1.126 brouard 5570: free_vector(xm,1,npar);
5571: free_vector(xp,1,npar);
5572: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5573: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5574: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5575: }
1.218 brouard 5576:
1.126 brouard 5577: /************ Variance ******************/
1.235 brouard 5578: 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 5579: {
5580: /* Variance of health expectancies */
5581: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5582: /* double **newm;*/
5583: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5584:
5585: /* int movingaverage(); */
5586: double **dnewm,**doldm;
5587: double **dnewmp,**doldmp;
5588: int i, j, nhstepm, hstepm, h, nstepm ;
5589: int k;
5590: double *xp;
5591: double **gp, **gm; /* for var eij */
5592: double ***gradg, ***trgradg; /*for var eij */
5593: double **gradgp, **trgradgp; /* for var p point j */
5594: double *gpp, *gmp; /* for var p point j */
5595: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5596: double ***p3mat;
5597: double age,agelim, hf;
5598: /* double ***mobaverage; */
5599: int theta;
5600: char digit[4];
5601: char digitp[25];
5602:
5603: char fileresprobmorprev[FILENAMELENGTH];
5604:
5605: if(popbased==1){
5606: if(mobilav!=0)
5607: strcpy(digitp,"-POPULBASED-MOBILAV_");
5608: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5609: }
5610: else
5611: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5612:
1.218 brouard 5613: /* if (mobilav!=0) { */
5614: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5615: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5616: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5617: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5618: /* } */
5619: /* } */
5620:
5621: strcpy(fileresprobmorprev,"PRMORPREV-");
5622: sprintf(digit,"%-d",ij);
5623: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5624: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5625: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5626: strcat(fileresprobmorprev,fileresu);
5627: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5628: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5629: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5630: }
5631: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5632: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5633: pstamp(ficresprobmorprev);
5634: 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 5635: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5636: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5637: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5638: }
5639: for(j=1;j<=cptcoveff;j++)
5640: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5641: fprintf(ficresprobmorprev,"\n");
5642:
1.218 brouard 5643: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5644: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5645: fprintf(ficresprobmorprev," p.%-d SE",j);
5646: for(i=1; i<=nlstate;i++)
5647: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5648: }
5649: fprintf(ficresprobmorprev,"\n");
5650:
5651: fprintf(ficgp,"\n# Routine varevsij");
5652: fprintf(ficgp,"\nunset title \n");
5653: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5654: 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");
5655: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5656: /* } */
5657: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5658: pstamp(ficresvij);
5659: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5660: if(popbased==1)
5661: 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);
5662: else
5663: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5664: fprintf(ficresvij,"# Age");
5665: for(i=1; i<=nlstate;i++)
5666: for(j=1; j<=nlstate;j++)
5667: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5668: fprintf(ficresvij,"\n");
5669:
5670: xp=vector(1,npar);
5671: dnewm=matrix(1,nlstate,1,npar);
5672: doldm=matrix(1,nlstate,1,nlstate);
5673: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5674: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5675:
5676: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5677: gpp=vector(nlstate+1,nlstate+ndeath);
5678: gmp=vector(nlstate+1,nlstate+ndeath);
5679: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5680:
1.218 brouard 5681: if(estepm < stepm){
5682: printf ("Problem %d lower than %d\n",estepm, stepm);
5683: }
5684: else hstepm=estepm;
5685: /* For example we decided to compute the life expectancy with the smallest unit */
5686: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5687: nhstepm is the number of hstepm from age to agelim
5688: nstepm is the number of stepm from age to agelim.
5689: Look at function hpijx to understand why because of memory size limitations,
5690: we decided (b) to get a life expectancy respecting the most precise curvature of the
5691: survival function given by stepm (the optimization length). Unfortunately it
5692: means that if the survival funtion is printed every two years of age and if
5693: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5694: results. So we changed our mind and took the option of the best precision.
5695: */
5696: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5697: agelim = AGESUP;
5698: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5699: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5700: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5701: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5702: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5703: gp=matrix(0,nhstepm,1,nlstate);
5704: gm=matrix(0,nhstepm,1,nlstate);
5705:
5706:
5707: for(theta=1; theta <=npar; theta++){
5708: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5709: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5710: }
5711:
1.242 brouard 5712: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 5713:
5714: if (popbased==1) {
5715: if(mobilav ==0){
5716: for(i=1; i<=nlstate;i++)
5717: prlim[i][i]=probs[(int)age][i][ij];
5718: }else{ /* mobilav */
5719: for(i=1; i<=nlstate;i++)
5720: prlim[i][i]=mobaverage[(int)age][i][ij];
5721: }
5722: }
5723:
1.235 brouard 5724: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.218 brouard 5725: for(j=1; j<= nlstate; j++){
5726: for(h=0; h<=nhstepm; h++){
5727: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5728: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5729: }
5730: }
5731: /* Next for computing probability of death (h=1 means
5732: computed over hstepm matrices product = hstepm*stepm months)
5733: as a weighted average of prlim.
5734: */
5735: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5736: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5737: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5738: }
5739: /* end probability of death */
5740:
5741: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5742: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5743:
1.242 brouard 5744: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
1.218 brouard 5745:
5746: if (popbased==1) {
5747: if(mobilav ==0){
5748: for(i=1; i<=nlstate;i++)
5749: prlim[i][i]=probs[(int)age][i][ij];
5750: }else{ /* mobilav */
5751: for(i=1; i<=nlstate;i++)
5752: prlim[i][i]=mobaverage[(int)age][i][ij];
5753: }
5754: }
5755:
1.235 brouard 5756: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 5757:
5758: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5759: for(h=0; h<=nhstepm; h++){
5760: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5761: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5762: }
5763: }
5764: /* This for computing probability of death (h=1 means
5765: computed over hstepm matrices product = hstepm*stepm months)
5766: as a weighted average of prlim.
5767: */
5768: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5769: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5770: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5771: }
5772: /* end probability of death */
5773:
5774: for(j=1; j<= nlstate; j++) /* vareij */
5775: for(h=0; h<=nhstepm; h++){
5776: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5777: }
5778:
5779: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5780: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5781: }
5782:
5783: } /* End theta */
5784:
5785: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5786:
5787: for(h=0; h<=nhstepm; h++) /* veij */
5788: for(j=1; j<=nlstate;j++)
5789: for(theta=1; theta <=npar; theta++)
5790: trgradg[h][j][theta]=gradg[h][theta][j];
5791:
5792: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5793: for(theta=1; theta <=npar; theta++)
5794: trgradgp[j][theta]=gradgp[theta][j];
5795:
5796:
5797: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5798: for(i=1;i<=nlstate;i++)
5799: for(j=1;j<=nlstate;j++)
5800: vareij[i][j][(int)age] =0.;
5801:
5802: for(h=0;h<=nhstepm;h++){
5803: for(k=0;k<=nhstepm;k++){
5804: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5805: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5806: for(i=1;i<=nlstate;i++)
5807: for(j=1;j<=nlstate;j++)
5808: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5809: }
5810: }
5811:
5812: /* pptj */
5813: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5814: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5815: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5816: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5817: varppt[j][i]=doldmp[j][i];
5818: /* end ppptj */
5819: /* x centered again */
5820:
1.242 brouard 5821: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
1.218 brouard 5822:
5823: if (popbased==1) {
5824: if(mobilav ==0){
5825: for(i=1; i<=nlstate;i++)
5826: prlim[i][i]=probs[(int)age][i][ij];
5827: }else{ /* mobilav */
5828: for(i=1; i<=nlstate;i++)
5829: prlim[i][i]=mobaverage[(int)age][i][ij];
5830: }
5831: }
5832:
5833: /* This for computing probability of death (h=1 means
5834: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5835: as a weighted average of prlim.
5836: */
1.235 brouard 5837: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 5838: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5839: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5840: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5841: }
5842: /* end probability of death */
5843:
5844: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5845: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5846: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5847: for(i=1; i<=nlstate;i++){
5848: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5849: }
5850: }
5851: fprintf(ficresprobmorprev,"\n");
5852:
5853: fprintf(ficresvij,"%.0f ",age );
5854: for(i=1; i<=nlstate;i++)
5855: for(j=1; j<=nlstate;j++){
5856: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5857: }
5858: fprintf(ficresvij,"\n");
5859: free_matrix(gp,0,nhstepm,1,nlstate);
5860: free_matrix(gm,0,nhstepm,1,nlstate);
5861: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5862: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5863: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5864: } /* End age */
5865: free_vector(gpp,nlstate+1,nlstate+ndeath);
5866: free_vector(gmp,nlstate+1,nlstate+ndeath);
5867: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5868: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5869: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5870: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5871: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5872: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5873: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5874: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5875: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5876: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5877: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5878: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5879: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5880: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5881: 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);
5882: /* 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 5883: */
1.218 brouard 5884: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5885: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5886:
1.218 brouard 5887: free_vector(xp,1,npar);
5888: free_matrix(doldm,1,nlstate,1,nlstate);
5889: free_matrix(dnewm,1,nlstate,1,npar);
5890: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5891: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5892: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5893: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5894: fclose(ficresprobmorprev);
5895: fflush(ficgp);
5896: fflush(fichtm);
5897: } /* end varevsij */
1.126 brouard 5898:
5899: /************ Variance of prevlim ******************/
1.235 brouard 5900: void varprevlim(char fileres[], 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 5901: {
1.205 brouard 5902: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5903: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5904:
1.126 brouard 5905: double **dnewm,**doldm;
5906: int i, j, nhstepm, hstepm;
5907: double *xp;
5908: double *gp, *gm;
5909: double **gradg, **trgradg;
1.208 brouard 5910: double **mgm, **mgp;
1.126 brouard 5911: double age,agelim;
5912: int theta;
5913:
5914: pstamp(ficresvpl);
5915: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
1.241 brouard 5916: fprintf(ficresvpl,"# Age ");
5917: if(nresult >=1)
5918: fprintf(ficresvpl," Result# ");
1.126 brouard 5919: for(i=1; i<=nlstate;i++)
5920: fprintf(ficresvpl," %1d-%1d",i,i);
5921: fprintf(ficresvpl,"\n");
5922:
5923: xp=vector(1,npar);
5924: dnewm=matrix(1,nlstate,1,npar);
5925: doldm=matrix(1,nlstate,1,nlstate);
5926:
5927: hstepm=1*YEARM; /* Every year of age */
5928: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5929: agelim = AGESUP;
5930: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5931: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5932: if (stepm >= YEARM) hstepm=1;
5933: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5934: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5935: mgp=matrix(1,npar,1,nlstate);
5936: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5937: gp=vector(1,nlstate);
5938: gm=vector(1,nlstate);
5939:
5940: for(theta=1; theta <=npar; theta++){
5941: for(i=1; i<=npar; i++){ /* Computes gradient */
5942: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5943: }
1.209 brouard 5944: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 5945: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5946: else
1.235 brouard 5947: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5948: for(i=1;i<=nlstate;i++){
1.126 brouard 5949: gp[i] = prlim[i][i];
1.208 brouard 5950: mgp[theta][i] = prlim[i][i];
5951: }
1.126 brouard 5952: for(i=1; i<=npar; i++) /* Computes gradient */
5953: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5954: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 5955: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5956: else
1.235 brouard 5957: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5958: for(i=1;i<=nlstate;i++){
1.126 brouard 5959: gm[i] = prlim[i][i];
1.208 brouard 5960: mgm[theta][i] = prlim[i][i];
5961: }
1.126 brouard 5962: for(i=1;i<=nlstate;i++)
5963: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5964: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5965: } /* End theta */
5966:
5967: trgradg =matrix(1,nlstate,1,npar);
5968:
5969: for(j=1; j<=nlstate;j++)
5970: for(theta=1; theta <=npar; theta++)
5971: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5972: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5973: /* printf("\nmgm mgp %d ",(int)age); */
5974: /* for(j=1; j<=nlstate;j++){ */
5975: /* printf(" %d ",j); */
5976: /* for(theta=1; theta <=npar; theta++) */
5977: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5978: /* printf("\n "); */
5979: /* } */
5980: /* } */
5981: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5982: /* printf("\n gradg %d ",(int)age); */
5983: /* for(j=1; j<=nlstate;j++){ */
5984: /* printf("%d ",j); */
5985: /* for(theta=1; theta <=npar; theta++) */
5986: /* printf("%d %lf ",theta,gradg[theta][j]); */
5987: /* printf("\n "); */
5988: /* } */
5989: /* } */
1.126 brouard 5990:
5991: for(i=1;i<=nlstate;i++)
5992: varpl[i][(int)age] =0.;
1.209 brouard 5993: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5994: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5995: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5996: }else{
1.126 brouard 5997: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5998: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5999: }
1.126 brouard 6000: for(i=1;i<=nlstate;i++)
6001: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
6002:
6003: fprintf(ficresvpl,"%.0f ",age );
1.241 brouard 6004: if(nresult >=1)
6005: fprintf(ficresvpl,"%d ",nres );
1.126 brouard 6006: for(i=1; i<=nlstate;i++)
6007: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
6008: fprintf(ficresvpl,"\n");
6009: free_vector(gp,1,nlstate);
6010: free_vector(gm,1,nlstate);
1.208 brouard 6011: free_matrix(mgm,1,npar,1,nlstate);
6012: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 6013: free_matrix(gradg,1,npar,1,nlstate);
6014: free_matrix(trgradg,1,nlstate,1,npar);
6015: } /* End age */
6016:
6017: free_vector(xp,1,npar);
6018: free_matrix(doldm,1,nlstate,1,npar);
6019: free_matrix(dnewm,1,nlstate,1,nlstate);
6020:
6021: }
6022:
6023: /************ Variance of one-step probabilities ******************/
6024: 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 6025: {
6026: int i, j=0, k1, l1, tj;
6027: int k2, l2, j1, z1;
6028: int k=0, l;
6029: int first=1, first1, first2;
6030: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
6031: double **dnewm,**doldm;
6032: double *xp;
6033: double *gp, *gm;
6034: double **gradg, **trgradg;
6035: double **mu;
6036: double age, cov[NCOVMAX+1];
6037: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
6038: int theta;
6039: char fileresprob[FILENAMELENGTH];
6040: char fileresprobcov[FILENAMELENGTH];
6041: char fileresprobcor[FILENAMELENGTH];
6042: double ***varpij;
6043:
6044: strcpy(fileresprob,"PROB_");
6045: strcat(fileresprob,fileres);
6046: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
6047: printf("Problem with resultfile: %s\n", fileresprob);
6048: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
6049: }
6050: strcpy(fileresprobcov,"PROBCOV_");
6051: strcat(fileresprobcov,fileresu);
6052: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
6053: printf("Problem with resultfile: %s\n", fileresprobcov);
6054: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
6055: }
6056: strcpy(fileresprobcor,"PROBCOR_");
6057: strcat(fileresprobcor,fileresu);
6058: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
6059: printf("Problem with resultfile: %s\n", fileresprobcor);
6060: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
6061: }
6062: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6063: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
6064: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6065: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
6066: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6067: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
6068: pstamp(ficresprob);
6069: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
6070: fprintf(ficresprob,"# Age");
6071: pstamp(ficresprobcov);
6072: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
6073: fprintf(ficresprobcov,"# Age");
6074: pstamp(ficresprobcor);
6075: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
6076: fprintf(ficresprobcor,"# Age");
1.126 brouard 6077:
6078:
1.222 brouard 6079: for(i=1; i<=nlstate;i++)
6080: for(j=1; j<=(nlstate+ndeath);j++){
6081: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
6082: fprintf(ficresprobcov," p%1d-%1d ",i,j);
6083: fprintf(ficresprobcor," p%1d-%1d ",i,j);
6084: }
6085: /* fprintf(ficresprob,"\n");
6086: fprintf(ficresprobcov,"\n");
6087: fprintf(ficresprobcor,"\n");
6088: */
6089: xp=vector(1,npar);
6090: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6091: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6092: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
6093: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
6094: first=1;
6095: fprintf(ficgp,"\n# Routine varprob");
6096: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
6097: fprintf(fichtm,"\n");
6098:
6099: 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.</li>\n",optionfilehtmcov);
6100: 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);
6101: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 6102: and drawn. It helps understanding how is the covariance between two incidences.\
6103: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 6104: 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 6105: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
6106: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
6107: standard deviations wide on each axis. <br>\
6108: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
6109: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
6110: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
6111:
1.222 brouard 6112: cov[1]=1;
6113: /* tj=cptcoveff; */
1.225 brouard 6114: tj = (int) pow(2,cptcoveff);
1.222 brouard 6115: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
6116: j1=0;
1.224 brouard 6117: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 6118: if (cptcovn>0) {
6119: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 6120: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6121: fprintf(ficresprob, "**********\n#\n");
6122: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 6123: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6124: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 6125:
1.222 brouard 6126: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 6127: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6128: fprintf(ficgp, "**********\n#\n");
1.220 brouard 6129:
6130:
1.222 brouard 6131: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 6132: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6133: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6134:
1.222 brouard 6135: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 6136: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 6137: fprintf(ficresprobcor, "**********\n#");
6138: if(invalidvarcomb[j1]){
6139: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
6140: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
6141: continue;
6142: }
6143: }
6144: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
6145: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
6146: gp=vector(1,(nlstate)*(nlstate+ndeath));
6147: gm=vector(1,(nlstate)*(nlstate+ndeath));
6148: for (age=bage; age<=fage; age ++){
6149: cov[2]=age;
6150: if(nagesqr==1)
6151: cov[3]= age*age;
6152: for (k=1; k<=cptcovn;k++) {
6153: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
6154: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
6155: * 1 1 1 1 1
6156: * 2 2 1 1 1
6157: * 3 1 2 1 1
6158: */
6159: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
6160: }
6161: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
6162: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
6163: for (k=1; k<=cptcovprod;k++)
6164: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 6165:
6166:
1.222 brouard 6167: for(theta=1; theta <=npar; theta++){
6168: for(i=1; i<=npar; i++)
6169: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 6170:
1.222 brouard 6171: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 6172:
1.222 brouard 6173: k=0;
6174: for(i=1; i<= (nlstate); i++){
6175: for(j=1; j<=(nlstate+ndeath);j++){
6176: k=k+1;
6177: gp[k]=pmmij[i][j];
6178: }
6179: }
1.220 brouard 6180:
1.222 brouard 6181: for(i=1; i<=npar; i++)
6182: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 6183:
1.222 brouard 6184: pmij(pmmij,cov,ncovmodel,xp,nlstate);
6185: k=0;
6186: for(i=1; i<=(nlstate); i++){
6187: for(j=1; j<=(nlstate+ndeath);j++){
6188: k=k+1;
6189: gm[k]=pmmij[i][j];
6190: }
6191: }
1.220 brouard 6192:
1.222 brouard 6193: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
6194: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
6195: }
1.126 brouard 6196:
1.222 brouard 6197: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
6198: for(theta=1; theta <=npar; theta++)
6199: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 6200:
1.222 brouard 6201: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
6202: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 6203:
1.222 brouard 6204: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 6205:
1.222 brouard 6206: k=0;
6207: for(i=1; i<=(nlstate); i++){
6208: for(j=1; j<=(nlstate+ndeath);j++){
6209: k=k+1;
6210: mu[k][(int) age]=pmmij[i][j];
6211: }
6212: }
6213: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
6214: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
6215: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 6216:
1.222 brouard 6217: /*printf("\n%d ",(int)age);
6218: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6219: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6220: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
6221: }*/
1.220 brouard 6222:
1.222 brouard 6223: fprintf(ficresprob,"\n%d ",(int)age);
6224: fprintf(ficresprobcov,"\n%d ",(int)age);
6225: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 6226:
1.222 brouard 6227: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
6228: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
6229: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
6230: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
6231: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
6232: }
6233: i=0;
6234: for (k=1; k<=(nlstate);k++){
6235: for (l=1; l<=(nlstate+ndeath);l++){
6236: i++;
6237: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
6238: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
6239: for (j=1; j<=i;j++){
6240: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
6241: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
6242: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
6243: }
6244: }
6245: }/* end of loop for state */
6246: } /* end of loop for age */
6247: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
6248: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
6249: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6250: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
6251:
6252: /* Confidence intervalle of pij */
6253: /*
6254: fprintf(ficgp,"\nunset parametric;unset label");
6255: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
6256: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
6257: 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);
6258: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
6259: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
6260: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
6261: */
6262:
6263: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
6264: first1=1;first2=2;
6265: for (k2=1; k2<=(nlstate);k2++){
6266: for (l2=1; l2<=(nlstate+ndeath);l2++){
6267: if(l2==k2) continue;
6268: j=(k2-1)*(nlstate+ndeath)+l2;
6269: for (k1=1; k1<=(nlstate);k1++){
6270: for (l1=1; l1<=(nlstate+ndeath);l1++){
6271: if(l1==k1) continue;
6272: i=(k1-1)*(nlstate+ndeath)+l1;
6273: if(i<=j) continue;
6274: for (age=bage; age<=fage; age ++){
6275: if ((int)age %5==0){
6276: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
6277: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
6278: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
6279: mu1=mu[i][(int) age]/stepm*YEARM ;
6280: mu2=mu[j][(int) age]/stepm*YEARM;
6281: c12=cv12/sqrt(v1*v2);
6282: /* Computing eigen value of matrix of covariance */
6283: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6284: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
6285: if ((lc2 <0) || (lc1 <0) ){
6286: if(first2==1){
6287: first1=0;
6288: 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);
6289: }
6290: 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);
6291: /* lc1=fabs(lc1); */ /* If we want to have them positive */
6292: /* lc2=fabs(lc2); */
6293: }
1.220 brouard 6294:
1.222 brouard 6295: /* Eigen vectors */
6296: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
6297: /*v21=sqrt(1.-v11*v11); *//* error */
6298: v21=(lc1-v1)/cv12*v11;
6299: v12=-v21;
6300: v22=v11;
6301: tnalp=v21/v11;
6302: if(first1==1){
6303: first1=0;
6304: 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);
6305: }
6306: 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);
6307: /*printf(fignu*/
6308: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6309: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6310: if(first==1){
6311: first=0;
6312: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6313: fprintf(ficgp,"\nset parametric;unset label");
6314: 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);
6315: fprintf(ficgp,"\nset ter svg size 640, 480");
6316: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6317: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6318: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6319: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6320: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6321: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6322: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6323: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6324: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6325: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6326: 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", \
6327: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
6328: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
6329: }else{
6330: first=0;
6331: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6332: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6333: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6334: 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", \
6335: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
6336: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
6337: }/* if first */
6338: } /* age mod 5 */
6339: } /* end loop age */
6340: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6341: first=1;
6342: } /*l12 */
6343: } /* k12 */
6344: } /*l1 */
6345: }/* k1 */
6346: } /* loop on combination of covariates j1 */
6347: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6348: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6349: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6350: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6351: free_vector(xp,1,npar);
6352: fclose(ficresprob);
6353: fclose(ficresprobcov);
6354: fclose(ficresprobcor);
6355: fflush(ficgp);
6356: fflush(fichtmcov);
6357: }
1.126 brouard 6358:
6359:
6360: /******************* Printing html file ***********/
1.201 brouard 6361: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6362: int lastpass, int stepm, int weightopt, char model[],\
6363: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 6364: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 6365: double jprev1, double mprev1,double anprev1, double dateprev1, \
6366: double jprev2, double mprev2,double anprev2, double dateprev2){
1.237 brouard 6367: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6368:
6369: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6370: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6371: </ul>");
1.237 brouard 6372: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6373: </ul>", model);
1.214 brouard 6374: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6375: 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",
6376: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6377: 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 6378: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6379: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6380: fprintf(fichtm,"\
6381: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6382: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6383: fprintf(fichtm,"\
1.217 brouard 6384: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6385: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6386: fprintf(fichtm,"\
1.126 brouard 6387: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6388: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6389: fprintf(fichtm,"\
1.217 brouard 6390: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6391: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6392: fprintf(fichtm,"\
1.211 brouard 6393: - (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 6394: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6395: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6396: if(prevfcast==1){
6397: fprintf(fichtm,"\
6398: - Prevalence projections by age and states: \
1.201 brouard 6399: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6400: }
1.126 brouard 6401:
1.222 brouard 6402: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 6403:
1.225 brouard 6404: m=pow(2,cptcoveff);
1.222 brouard 6405: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6406:
1.222 brouard 6407: jj1=0;
1.237 brouard 6408:
6409: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.241 brouard 6410: for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
1.253 brouard 6411: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6412: continue;
1.220 brouard 6413:
1.222 brouard 6414: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6415: jj1++;
6416: if (cptcovn > 0) {
6417: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6418: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6419: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6420: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6421: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6422: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6423: }
1.237 brouard 6424: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6425: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6426: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6427: }
6428:
1.230 brouard 6429: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6430: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6431: if(invalidvarcomb[k1]){
6432: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6433: printf("\nCombination (%d) ignored because no cases \n",k1);
6434: continue;
6435: }
6436: }
6437: /* aij, bij */
1.241 brouard 6438: fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
6439: <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 6440: /* Pij */
1.241 brouard 6441: 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> \
6442: <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 6443: /* Quasi-incidences */
6444: 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 6445: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6446: 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 6447: 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> \
6448: <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 6449: /* Survival functions (period) in state j */
6450: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6451: 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> \
6452: <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 6453: }
6454: /* State specific survival functions (period) */
6455: for(cpt=1; cpt<=nlstate;cpt++){
6456: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6457: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.241 brouard 6458: <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 6459: }
6460: /* Period (stable) prevalence in each health state */
6461: for(cpt=1; cpt<=nlstate;cpt++){
1.255 ! brouard 6462: fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d some years earlier, knowing that we will be in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
1.241 brouard 6463: <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.222 brouard 6464: }
6465: if(backcast==1){
6466: /* Period (stable) back prevalence in each health state */
6467: for(cpt=1; cpt<=nlstate;cpt++){
1.255 ! brouard 6468: fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability to be in state %d at a younger age, knowing that we will be 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 6469: <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 6470: }
1.217 brouard 6471: }
1.222 brouard 6472: if(prevfcast==1){
6473: /* Projection of prevalence up to period (stable) prevalence in each health state */
6474: for(cpt=1; cpt<=nlstate;cpt++){
1.241 brouard 6475: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be 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> \
6476: <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.222 brouard 6477: }
6478: }
1.220 brouard 6479:
1.222 brouard 6480: for(cpt=1; cpt<=nlstate;cpt++) {
1.241 brouard 6481: 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> \
6482: <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 6483: }
6484: /* } /\* end i1 *\/ */
6485: }/* End k1 */
6486: fprintf(fichtm,"</ul>");
1.126 brouard 6487:
1.222 brouard 6488: fprintf(fichtm,"\
1.126 brouard 6489: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6490: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6491: - 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 6492: But because parameters are usually highly correlated (a higher incidence of disability \
6493: and a higher incidence of recovery can give very close observed transition) it might \
6494: be very useful to look not only at linear confidence intervals estimated from the \
6495: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6496: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6497: covariance matrix of the one-step probabilities. \
6498: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6499:
1.222 brouard 6500: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6501: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6502: fprintf(fichtm,"\
1.126 brouard 6503: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6504: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6505:
1.222 brouard 6506: fprintf(fichtm,"\
1.126 brouard 6507: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6508: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6509: fprintf(fichtm,"\
1.126 brouard 6510: - 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): \
6511: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6512: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6513: fprintf(fichtm,"\
1.126 brouard 6514: - (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): \
6515: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6516: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6517: fprintf(fichtm,"\
1.128 brouard 6518: - 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 6519: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6520: fprintf(fichtm,"\
1.128 brouard 6521: - 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 6522: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6523: fprintf(fichtm,"\
1.126 brouard 6524: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6525: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6526:
6527: /* if(popforecast==1) fprintf(fichtm,"\n */
6528: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6529: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6530: /* <br>",fileres,fileres,fileres,fileres); */
6531: /* else */
6532: /* 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 6533: fflush(fichtm);
6534: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6535:
1.225 brouard 6536: m=pow(2,cptcoveff);
1.222 brouard 6537: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6538:
1.222 brouard 6539: jj1=0;
1.237 brouard 6540:
1.241 brouard 6541: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.222 brouard 6542: for(k1=1; k1<=m;k1++){
1.253 brouard 6543: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6544: continue;
1.222 brouard 6545: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6546: jj1++;
1.126 brouard 6547: if (cptcovn > 0) {
6548: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6549: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 6550: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
6551: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6552: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6553: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6554: }
6555:
1.126 brouard 6556: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6557:
1.222 brouard 6558: if(invalidvarcomb[k1]){
6559: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6560: continue;
6561: }
1.126 brouard 6562: }
6563: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6564: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
1.241 brouard 6565: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
6566: <img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
1.126 brouard 6567: }
6568: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6569: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6570: true period expectancies (those weighted with period prevalences are also\
6571: drawn in addition to the population based expectancies computed using\
1.241 brouard 6572: observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
6573: <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
1.222 brouard 6574: /* } /\* end i1 *\/ */
6575: }/* End k1 */
1.241 brouard 6576: }/* End nres */
1.222 brouard 6577: fprintf(fichtm,"</ul>");
6578: fflush(fichtm);
1.126 brouard 6579: }
6580:
6581: /******************* Gnuplot file **************/
1.223 brouard 6582: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6583:
6584: char dirfileres[132],optfileres[132];
1.223 brouard 6585: char gplotcondition[132];
1.237 brouard 6586: 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 6587: int lv=0, vlv=0, kl=0;
1.130 brouard 6588: int ng=0;
1.201 brouard 6589: int vpopbased;
1.223 brouard 6590: int ioffset; /* variable offset for columns */
1.235 brouard 6591: int nres=0; /* Index of resultline */
1.219 brouard 6592:
1.126 brouard 6593: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6594: /* printf("Problem with file %s",optionfilegnuplot); */
6595: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6596: /* } */
6597:
6598: /*#ifdef windows */
6599: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6600: /*#endif */
1.225 brouard 6601: m=pow(2,cptcoveff);
1.126 brouard 6602:
1.202 brouard 6603: /* Contribution to likelihood */
6604: /* Plot the probability implied in the likelihood */
1.223 brouard 6605: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6606: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6607: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6608: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6609: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6610: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6611: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6612: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6613: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6614: 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));
6615: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6616: 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));
6617: for (i=1; i<= nlstate ; i ++) {
6618: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6619: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6620: 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);
6621: for (j=2; j<= nlstate+ndeath ; j ++) {
6622: 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);
6623: }
6624: fprintf(ficgp,";\nset out; unset ylabel;\n");
6625: }
6626: /* 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 */
6627: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6628: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6629: fprintf(ficgp,"\nset out;unset log\n");
6630: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6631:
1.126 brouard 6632: strcpy(dirfileres,optionfilefiname);
6633: strcpy(optfileres,"vpl");
1.223 brouard 6634: /* 1eme*/
1.238 brouard 6635: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
6636: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 6637: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 6638: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.253 brouard 6639: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 6640: continue;
6641: /* We are interested in selected combination by the resultline */
1.246 brouard 6642: /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
1.238 brouard 6643: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
6644: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6645: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
6646: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6647: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6648: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6649: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6650: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.246 brouard 6651: /* printf(" V%d=%d ",Tvaraff[k],vlv); */
1.238 brouard 6652: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6653: }
6654: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.246 brouard 6655: /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
1.238 brouard 6656: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6657: }
1.246 brouard 6658: /* printf("\n#\n"); */
1.238 brouard 6659: fprintf(ficgp,"\n#\n");
6660: if(invalidvarcomb[k1]){
6661: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6662: continue;
6663: }
1.235 brouard 6664:
1.241 brouard 6665: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
6666: fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
6667: 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);
1.235 brouard 6668:
1.238 brouard 6669: for (i=1; i<= nlstate ; i ++) {
6670: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6671: else fprintf(ficgp," %%*lf (%%*lf)");
6672: }
1.242 brouard 6673: 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_"),k1-1,k1-1,nres);
1.238 brouard 6674: for (i=1; i<= nlstate ; i ++) {
6675: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6676: else fprintf(ficgp," %%*lf (%%*lf)");
6677: }
1.242 brouard 6678: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
1.238 brouard 6679: for (i=1; i<= nlstate ; i ++) {
6680: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6681: else fprintf(ficgp," %%*lf (%%*lf)");
6682: }
6683: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6684: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6685: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
1.242 brouard 6686: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
1.238 brouard 6687: if(cptcoveff ==0){
1.245 brouard 6688: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
1.238 brouard 6689: }else{
6690: kl=0;
6691: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6692: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6693: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6694: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6695: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6696: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 6697: kl++;
1.238 brouard 6698: /* 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 *\/ */
6699: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6700: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6701: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
6702: if(k==cptcoveff){
1.245 brouard 6703: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
1.242 brouard 6704: 2+cptcoveff*2+(cpt-1), cpt ); /* 4 or 6 ?*/
1.238 brouard 6705: }else{
6706: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6707: kl++;
6708: }
6709: } /* end covariate */
6710: } /* end if no covariate */
6711: } /* end if backcast */
6712: fprintf(ficgp,"\nset out \n");
6713: } /* nres */
1.201 brouard 6714: } /* k1 */
6715: } /* cpt */
1.235 brouard 6716:
6717:
1.126 brouard 6718: /*2 eme*/
1.238 brouard 6719: for (k1=1; k1<= m ; k1 ++){
6720: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6721: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 6722: continue;
6723: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
6724: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 6725: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6726: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6727: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6728: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6729: vlv= nbcode[Tvaraff[k]][lv];
6730: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6731: }
1.237 brouard 6732: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 6733: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 6734: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 6735: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 6736: }
1.211 brouard 6737: fprintf(ficgp,"\n#\n");
1.223 brouard 6738: if(invalidvarcomb[k1]){
6739: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6740: continue;
6741: }
1.219 brouard 6742:
1.241 brouard 6743: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
1.238 brouard 6744: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6745: if(vpopbased==0)
6746: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6747: else
6748: fprintf(ficgp,"\nreplot ");
6749: for (i=1; i<= nlstate+1 ; i ++) {
6750: k=2*i;
6751: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
6752: for (j=1; j<= nlstate+1 ; j ++) {
6753: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6754: else fprintf(ficgp," %%*lf (%%*lf)");
6755: }
6756: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6757: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6758: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6759: for (j=1; j<= nlstate+1 ; j ++) {
6760: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6761: else fprintf(ficgp," %%*lf (%%*lf)");
6762: }
6763: fprintf(ficgp,"\" t\"\" w l lt 0,");
6764: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6765: for (j=1; j<= nlstate+1 ; j ++) {
6766: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6767: else fprintf(ficgp," %%*lf (%%*lf)");
6768: }
6769: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6770: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6771: } /* state */
6772: } /* vpopbased */
1.244 brouard 6773: fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
1.238 brouard 6774: } /* end nres */
6775: } /* k1 end 2 eme*/
6776:
6777:
6778: /*3eme*/
6779: for (k1=1; k1<= m ; k1 ++){
6780: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6781: if(m != 1 && TKresult[nres]!= k1)
1.238 brouard 6782: continue;
6783:
6784: for (cpt=1; cpt<= nlstate ; cpt ++) {
6785: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
6786: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6787: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6788: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6789: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6790: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6791: vlv= nbcode[Tvaraff[k]][lv];
6792: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6793: }
6794: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6795: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6796: }
6797: fprintf(ficgp,"\n#\n");
6798: if(invalidvarcomb[k1]){
6799: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6800: continue;
6801: }
6802:
6803: /* k=2+nlstate*(2*cpt-2); */
6804: k=2+(nlstate+1)*(cpt-1);
1.241 brouard 6805: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
1.238 brouard 6806: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6807: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.238 brouard 6808: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6809: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6810: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6811: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6812: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6813: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6814:
1.238 brouard 6815: */
6816: for (i=1; i< nlstate ; i ++) {
6817: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
6818: /* 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 6819:
1.238 brouard 6820: }
6821: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
6822: }
6823: } /* end nres */
6824: } /* end kl 3eme */
1.126 brouard 6825:
1.223 brouard 6826: /* 4eme */
1.201 brouard 6827: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 6828: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
6829: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6830: if(m != 1 && TKresult[nres]!= k1)
1.223 brouard 6831: continue;
1.238 brouard 6832: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
6833: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
6834: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6835: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6836: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6837: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6838: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6839: vlv= nbcode[Tvaraff[k]][lv];
6840: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6841: }
6842: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6843: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6844: }
6845: fprintf(ficgp,"\n#\n");
6846: if(invalidvarcomb[k1]){
6847: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6848: continue;
1.223 brouard 6849: }
1.238 brouard 6850:
1.241 brouard 6851: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
1.238 brouard 6852: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
6853: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
6854: k=3;
6855: for (i=1; i<= nlstate ; i ++){
6856: if(i==1){
6857: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6858: }else{
6859: fprintf(ficgp,", '' ");
6860: }
6861: l=(nlstate+ndeath)*(i-1)+1;
6862: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6863: for (j=2; j<= nlstate+ndeath ; j ++)
6864: fprintf(ficgp,"+$%d",k+l+j-1);
6865: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
6866: } /* nlstate */
6867: fprintf(ficgp,"\nset out\n");
6868: } /* end cpt state*/
6869: } /* end nres */
6870: } /* end covariate k1 */
6871:
1.220 brouard 6872: /* 5eme */
1.201 brouard 6873: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 6874: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
6875: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6876: if(m != 1 && TKresult[nres]!= k1)
1.227 brouard 6877: continue;
1.238 brouard 6878: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
6879: 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);
6880: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6881: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6882: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6883: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6884: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6885: vlv= nbcode[Tvaraff[k]][lv];
6886: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6887: }
6888: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6889: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6890: }
6891: fprintf(ficgp,"\n#\n");
6892: if(invalidvarcomb[k1]){
6893: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6894: continue;
6895: }
1.227 brouard 6896:
1.241 brouard 6897: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
1.238 brouard 6898: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
6899: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
6900: k=3;
6901: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
6902: if(j==1)
6903: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6904: else
6905: fprintf(ficgp,", '' ");
6906: l=(nlstate+ndeath)*(cpt-1) +j;
6907: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6908: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6909: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6910: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
6911: } /* nlstate */
6912: fprintf(ficgp,", '' ");
6913: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6914: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
6915: l=(nlstate+ndeath)*(cpt-1) +j;
6916: if(j < nlstate)
6917: fprintf(ficgp,"$%d +",k+l);
6918: else
6919: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
6920: }
6921: fprintf(ficgp,"\nset out\n");
6922: } /* end cpt state*/
6923: } /* end covariate */
6924: } /* end nres */
1.227 brouard 6925:
1.220 brouard 6926: /* 6eme */
1.202 brouard 6927: /* CV preval stable (period) for each covariate */
1.237 brouard 6928: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
6929: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6930: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6931: continue;
1.255 ! brouard 6932: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
1.227 brouard 6933:
1.211 brouard 6934: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6935: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6936: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6937: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6938: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6939: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6940: vlv= nbcode[Tvaraff[k]][lv];
6941: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6942: }
1.237 brouard 6943: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6944: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6945: }
1.211 brouard 6946: fprintf(ficgp,"\n#\n");
1.223 brouard 6947: if(invalidvarcomb[k1]){
1.227 brouard 6948: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6949: continue;
1.223 brouard 6950: }
1.227 brouard 6951:
1.241 brouard 6952: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
1.126 brouard 6953: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 6954: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6955: k=3; /* Offset */
1.255 ! brouard 6956: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 6957: if(i==1)
6958: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6959: else
6960: fprintf(ficgp,", '' ");
1.255 ! brouard 6961: l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 6962: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6963: for (j=2; j<= nlstate ; j ++)
6964: fprintf(ficgp,"+$%d",k+l+j-1);
6965: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6966: } /* nlstate */
1.201 brouard 6967: fprintf(ficgp,"\nset out\n");
1.153 brouard 6968: } /* end cpt state*/
6969: } /* end covariate */
1.227 brouard 6970:
6971:
1.220 brouard 6972: /* 7eme */
1.218 brouard 6973: if(backcast == 1){
1.217 brouard 6974: /* CV back preval stable (period) for each covariate */
1.237 brouard 6975: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
6976: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 6977: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 6978: continue;
1.255 ! brouard 6979: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */
! 6980: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
1.227 brouard 6981: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6982: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6983: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6984: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6985: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6986: vlv= nbcode[Tvaraff[k]][lv];
6987: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6988: }
1.237 brouard 6989: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6990: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6991: }
1.227 brouard 6992: fprintf(ficgp,"\n#\n");
6993: if(invalidvarcomb[k1]){
6994: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6995: continue;
6996: }
6997:
1.241 brouard 6998: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
1.227 brouard 6999: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 7000: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7001: k=3; /* Offset */
1.255 ! brouard 7002: for (i=1; i<= nlstate ; i ++){ /* State of origin */
1.227 brouard 7003: if(i==1)
7004: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
7005: else
7006: fprintf(ficgp,", '' ");
7007: /* l=(nlstate+ndeath)*(i-1)+1; */
1.255 ! brouard 7008: l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
1.227 brouard 7009: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
7010: /* 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 7011: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
1.227 brouard 7012: /* for (j=2; j<= nlstate ; j ++) */
7013: /* fprintf(ficgp,"+$%d",k+l+j-1); */
7014: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
7015: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
7016: } /* nlstate */
7017: fprintf(ficgp,"\nset out\n");
1.218 brouard 7018: } /* end cpt state*/
7019: } /* end covariate */
7020: } /* End if backcast */
7021:
1.223 brouard 7022: /* 8eme */
1.218 brouard 7023: if(prevfcast==1){
7024: /* Projection from cross-sectional to stable (period) for each covariate */
7025:
1.237 brouard 7026: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
7027: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7028: if(m != 1 && TKresult[nres]!= k1)
1.237 brouard 7029: continue;
1.211 brouard 7030: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 7031: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
7032: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
7033: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
7034: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7035: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7036: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7037: vlv= nbcode[Tvaraff[k]][lv];
7038: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
7039: }
1.237 brouard 7040: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7041: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7042: }
1.227 brouard 7043: fprintf(ficgp,"\n#\n");
7044: if(invalidvarcomb[k1]){
7045: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
7046: continue;
7047: }
7048:
7049: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
1.241 brouard 7050: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
1.227 brouard 7051: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 7052: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 7053: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
7054: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7055: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7056: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7057: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7058: if(i==1){
7059: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
7060: }else{
7061: fprintf(ficgp,",\\\n '' ");
7062: }
7063: if(cptcoveff ==0){ /* No covariate */
7064: ioffset=2; /* Age is in 2 */
7065: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7066: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7067: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
7068: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
7069: fprintf(ficgp," u %d:(", ioffset);
7070: if(i==nlstate+1)
7071: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
7072: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7073: else
7074: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
7075: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7076: }else{ /* more than 2 covariates */
7077: if(cptcoveff ==1){
7078: ioffset=4; /* Age is in 4 */
7079: }else{
7080: ioffset=6; /* Age is in 6 */
7081: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
7082: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
7083: }
7084: fprintf(ficgp," u %d:(",ioffset);
7085: kl=0;
7086: strcpy(gplotcondition,"(");
7087: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
7088: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
7089: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
7090: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
7091: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
7092: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
7093: kl++;
7094: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
7095: kl++;
7096: if(k <cptcoveff && cptcoveff>1)
7097: sprintf(gplotcondition+strlen(gplotcondition)," && ");
7098: }
7099: strcpy(gplotcondition+strlen(gplotcondition),")");
7100: /* 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 *\/ */
7101: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
7102: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
7103: /* '' 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*/
7104: if(i==nlstate+1){
7105: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
7106: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
7107: }else{
7108: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
7109: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
7110: }
7111: } /* end if covariate */
7112: } /* nlstate */
7113: fprintf(ficgp,"\nset out\n");
1.223 brouard 7114: } /* end cpt state*/
7115: } /* end covariate */
7116: } /* End if prevfcast */
1.227 brouard 7117:
7118:
1.238 brouard 7119: /* 9eme writing MLE parameters */
7120: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 7121: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 7122: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 7123: for(k=1; k <=(nlstate+ndeath); k++){
7124: if (k != i) {
1.227 brouard 7125: fprintf(ficgp,"# current state %d\n",k);
7126: for(j=1; j <=ncovmodel; j++){
7127: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
7128: jk++;
7129: }
7130: fprintf(ficgp,"\n");
1.126 brouard 7131: }
7132: }
1.223 brouard 7133: }
1.187 brouard 7134: fprintf(ficgp,"##############\n#\n");
1.227 brouard 7135:
1.145 brouard 7136: /*goto avoid;*/
1.238 brouard 7137: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
7138: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 7139: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
7140: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
7141: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
7142: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
7143: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7144: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7145: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7146: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
7147: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
7148: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
7149: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
7150: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
7151: fprintf(ficgp,"#\n");
1.223 brouard 7152: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 7153: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 7154: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 7155: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.237 brouard 7156: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
7157: for(jk=1; jk <=m; jk++) /* For each combination of covariate */
7158: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 7159: if(m != 1 && TKresult[nres]!= jk)
1.237 brouard 7160: continue;
7161: fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);
7162: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
7163: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
7164: }
7165: fprintf(ficgp,"\n#\n");
1.241 brouard 7166: fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
1.223 brouard 7167: fprintf(ficgp,"\nset ter svg size 640, 480 ");
7168: if (ng==1){
7169: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
7170: fprintf(ficgp,"\nunset log y");
7171: }else if (ng==2){
7172: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
7173: fprintf(ficgp,"\nset log y");
7174: }else if (ng==3){
7175: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
7176: fprintf(ficgp,"\nset log y");
7177: }else
7178: fprintf(ficgp,"\nunset title ");
7179: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
7180: i=1;
7181: for(k2=1; k2<=nlstate; k2++) {
7182: k3=i;
7183: for(k=1; k<=(nlstate+ndeath); k++) {
7184: if (k != k2){
7185: switch( ng) {
7186: case 1:
7187: if(nagesqr==0)
7188: fprintf(ficgp," p%d+p%d*x",i,i+1);
7189: else /* nagesqr =1 */
7190: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7191: break;
7192: case 2: /* ng=2 */
7193: if(nagesqr==0)
7194: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
7195: else /* nagesqr =1 */
7196: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
7197: break;
7198: case 3:
7199: if(nagesqr==0)
7200: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
7201: else /* nagesqr =1 */
7202: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
7203: break;
7204: }
7205: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 7206: ijp=1; /* product no age */
7207: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
7208: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 7209: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.237 brouard 7210: if(j==Tage[ij]) { /* Product by age */
7211: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
1.238 brouard 7212: if(DummyV[j]==0){
1.237 brouard 7213: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
7214: }else{ /* quantitative */
7215: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
7216: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
7217: }
7218: ij++;
7219: }
7220: }else if(j==Tprod[ijp]) { /* */
7221: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
7222: if(ijp <=cptcovprod) { /* Product */
1.238 brouard 7223: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
7224: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
1.237 brouard 7225: /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
7226: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
7227: }else{ /* Vn is dummy and Vm is quanti */
7228: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
7229: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7230: }
7231: }else{ /* Vn*Vm Vn is quanti */
1.238 brouard 7232: if(DummyV[Tvard[ijp][2]]==0){
1.237 brouard 7233: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
7234: }else{ /* Both quanti */
7235: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
7236: }
7237: }
1.238 brouard 7238: ijp++;
1.237 brouard 7239: }
7240: } else{ /* simple covariate */
7241: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
7242: if(Dummy[j]==0){
7243: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
7244: }else{ /* quantitative */
7245: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.223 brouard 7246: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
7247: }
1.237 brouard 7248: } /* end simple */
7249: } /* end j */
1.223 brouard 7250: }else{
7251: i=i-ncovmodel;
7252: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
7253: fprintf(ficgp," (1.");
7254: }
1.227 brouard 7255:
1.223 brouard 7256: if(ng != 1){
7257: fprintf(ficgp,")/(1");
1.227 brouard 7258:
1.223 brouard 7259: for(k1=1; k1 <=nlstate; k1++){
7260: if(nagesqr==0)
7261: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
7262: else /* nagesqr =1 */
7263: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
1.217 brouard 7264:
1.223 brouard 7265: ij=1;
7266: for(j=3; j <=ncovmodel-nagesqr; j++){
1.237 brouard 7267: if((j-2)==Tage[ij]) { /* Bug valgrind */
7268: if(ij <=cptcovage) { /* Bug valgrind */
1.223 brouard 7269: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
7270: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
7271: ij++;
7272: }
7273: }
7274: else
1.225 brouard 7275: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */
1.223 brouard 7276: }
7277: fprintf(ficgp,")");
7278: }
7279: fprintf(ficgp,")");
7280: if(ng ==2)
7281: fprintf(ficgp," t \"p%d%d\" ", k2,k);
7282: else /* ng= 3 */
7283: fprintf(ficgp," t \"i%d%d\" ", k2,k);
7284: }else{ /* end ng <> 1 */
7285: if( k !=k2) /* logit p11 is hard to draw */
7286: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
7287: }
7288: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
7289: fprintf(ficgp,",");
7290: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
7291: fprintf(ficgp,",");
7292: i=i+ncovmodel;
7293: } /* end k */
7294: } /* end k2 */
7295: fprintf(ficgp,"\n set out\n");
7296: } /* end jk */
7297: } /* end ng */
7298: /* avoid: */
7299: fflush(ficgp);
1.126 brouard 7300: } /* end gnuplot */
7301:
7302:
7303: /*************** Moving average **************/
1.219 brouard 7304: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 7305: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 7306:
1.222 brouard 7307: int i, cpt, cptcod;
7308: int modcovmax =1;
7309: int mobilavrange, mob;
7310: int iage=0;
7311:
7312: double sum=0.;
7313: double age;
7314: double *sumnewp, *sumnewm;
7315: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
7316:
7317:
1.225 brouard 7318: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 7319: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
7320:
7321: sumnewp = vector(1,ncovcombmax);
7322: sumnewm = vector(1,ncovcombmax);
7323: agemingood = vector(1,ncovcombmax);
7324: agemaxgood = vector(1,ncovcombmax);
7325:
7326: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7327: sumnewm[cptcod]=0.;
7328: sumnewp[cptcod]=0.;
7329: agemingood[cptcod]=0;
7330: agemaxgood[cptcod]=0;
7331: }
7332: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
7333:
7334: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
7335: if(mobilav==1) mobilavrange=5; /* default */
7336: else mobilavrange=mobilav;
7337: for (age=bage; age<=fage; age++)
7338: for (i=1; i<=nlstate;i++)
7339: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
7340: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
7341: /* We keep the original values on the extreme ages bage, fage and for
7342: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
7343: we use a 5 terms etc. until the borders are no more concerned.
7344: */
7345: for (mob=3;mob <=mobilavrange;mob=mob+2){
7346: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
7347: for (i=1; i<=nlstate;i++){
7348: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7349: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
7350: for (cpt=1;cpt<=(mob-1)/2;cpt++){
7351: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
7352: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
7353: }
7354: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
7355: }
7356: }
7357: }/* end age */
7358: }/* end mob */
7359: }else
7360: return -1;
7361: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7362: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
7363: if(invalidvarcomb[cptcod]){
7364: printf("\nCombination (%d) ignored because no cases \n",cptcod);
7365: continue;
7366: }
1.219 brouard 7367:
1.222 brouard 7368: agemingood[cptcod]=fage-(mob-1)/2;
7369: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
7370: sumnewm[cptcod]=0.;
7371: for (i=1; i<=nlstate;i++){
7372: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7373: }
7374: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
7375: agemingood[cptcod]=age;
7376: }else{ /* bad */
7377: for (i=1; i<=nlstate;i++){
7378: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7379: } /* i */
7380: } /* end bad */
7381: }/* age */
7382: sum=0.;
7383: for (i=1; i<=nlstate;i++){
7384: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7385: }
7386: if(fabs(sum - 1.) > 1.e-3) { /* bad */
7387: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
7388: /* for (i=1; i<=nlstate;i++){ */
7389: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
7390: /* } /\* i *\/ */
7391: } /* end bad */
7392: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
7393: /* From youngest, finding the oldest wrong */
7394: agemaxgood[cptcod]=bage+(mob-1)/2;
7395: for (age=bage+(mob-1)/2; age<=fage; age++){
7396: sumnewm[cptcod]=0.;
7397: for (i=1; i<=nlstate;i++){
7398: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7399: }
7400: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
7401: agemaxgood[cptcod]=age;
7402: }else{ /* bad */
7403: for (i=1; i<=nlstate;i++){
7404: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7405: } /* i */
7406: } /* end bad */
7407: }/* age */
7408: sum=0.;
7409: for (i=1; i<=nlstate;i++){
7410: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7411: }
7412: if(fabs(sum - 1.) > 1.e-3) { /* bad */
7413: printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);
7414: /* for (i=1; i<=nlstate;i++){ */
7415: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
7416: /* } /\* i *\/ */
7417: } /* end bad */
7418:
7419: for (age=bage; age<=fage; age++){
1.235 brouard 7420: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 7421: sumnewp[cptcod]=0.;
7422: sumnewm[cptcod]=0.;
7423: for (i=1; i<=nlstate;i++){
7424: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
7425: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7426: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
7427: }
7428: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
7429: }
7430: /* printf("\n"); */
7431: /* } */
7432: /* brutal averaging */
7433: for (i=1; i<=nlstate;i++){
7434: for (age=1; age<=bage; age++){
7435: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7436: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
7437: }
7438: for (age=fage; age<=AGESUP; age++){
7439: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7440: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
7441: }
7442: } /* end i status */
7443: for (i=nlstate+1; i<=nlstate+ndeath;i++){
7444: for (age=1; age<=AGESUP; age++){
7445: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
7446: mobaverage[(int)age][i][cptcod]=0.;
7447: }
7448: }
7449: }/* end cptcod */
7450: free_vector(sumnewm,1, ncovcombmax);
7451: free_vector(sumnewp,1, ncovcombmax);
7452: free_vector(agemaxgood,1, ncovcombmax);
7453: free_vector(agemingood,1, ncovcombmax);
7454: return 0;
7455: }/* End movingaverage */
1.218 brouard 7456:
1.126 brouard 7457:
7458: /************** Forecasting ******************/
1.235 brouard 7459: void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
1.126 brouard 7460: /* proj1, year, month, day of starting projection
7461: agemin, agemax range of age
7462: dateprev1 dateprev2 range of dates during which prevalence is computed
7463: anproj2 year of en of projection (same day and month as proj1).
7464: */
1.235 brouard 7465: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 7466: double agec; /* generic age */
7467: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
7468: double *popeffectif,*popcount;
7469: double ***p3mat;
1.218 brouard 7470: /* double ***mobaverage; */
1.126 brouard 7471: char fileresf[FILENAMELENGTH];
7472:
7473: agelim=AGESUP;
1.211 brouard 7474: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
7475: in each health status at the date of interview (if between dateprev1 and dateprev2).
7476: We still use firstpass and lastpass as another selection.
7477: */
1.214 brouard 7478: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
7479: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 7480:
1.201 brouard 7481: strcpy(fileresf,"F_");
7482: strcat(fileresf,fileresu);
1.126 brouard 7483: if((ficresf=fopen(fileresf,"w"))==NULL) {
7484: printf("Problem with forecast resultfile: %s\n", fileresf);
7485: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
7486: }
1.235 brouard 7487: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
7488: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 7489:
1.225 brouard 7490: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 7491:
7492:
7493: stepsize=(int) (stepm+YEARM-1)/YEARM;
7494: if (stepm<=12) stepsize=1;
7495: if(estepm < stepm){
7496: printf ("Problem %d lower than %d\n",estepm, stepm);
7497: }
7498: else hstepm=estepm;
7499:
7500: hstepm=hstepm/stepm;
7501: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
7502: fractional in yp1 */
7503: anprojmean=yp;
7504: yp2=modf((yp1*12),&yp);
7505: mprojmean=yp;
7506: yp1=modf((yp2*30.5),&yp);
7507: jprojmean=yp;
7508: if(jprojmean==0) jprojmean=1;
7509: if(mprojmean==0) jprojmean=1;
7510:
1.227 brouard 7511: i1=pow(2,cptcoveff);
1.126 brouard 7512: if (cptcovn < 1){i1=1;}
7513:
7514: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
7515:
7516: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 7517:
1.126 brouard 7518: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 7519: for(nres=1; nres <= nresult; nres++) /* For each resultline */
7520: for(k=1; k<=i1;k++){
1.253 brouard 7521: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 7522: continue;
1.227 brouard 7523: if(invalidvarcomb[k]){
7524: printf("\nCombination (%d) projection ignored because no cases \n",k);
7525: continue;
7526: }
7527: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
7528: for(j=1;j<=cptcoveff;j++) {
7529: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7530: }
1.235 brouard 7531: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7532: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 7533: }
1.227 brouard 7534: fprintf(ficresf," yearproj age");
7535: for(j=1; j<=nlstate+ndeath;j++){
7536: for(i=1; i<=nlstate;i++)
7537: fprintf(ficresf," p%d%d",i,j);
7538: fprintf(ficresf," wp.%d",j);
7539: }
7540: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
7541: fprintf(ficresf,"\n");
7542: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
7543: for (agec=fage; agec>=(ageminpar-1); agec--){
7544: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
7545: nhstepm = nhstepm/hstepm;
7546: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7547: oldm=oldms;savm=savms;
1.235 brouard 7548: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.227 brouard 7549:
7550: for (h=0; h<=nhstepm; h++){
7551: if (h*hstepm/YEARM*stepm ==yearp) {
7552: fprintf(ficresf,"\n");
7553: for(j=1;j<=cptcoveff;j++)
7554: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7555: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
7556: }
7557: for(j=1; j<=nlstate+ndeath;j++) {
7558: ppij=0.;
7559: for(i=1; i<=nlstate;i++) {
7560: if (mobilav==1)
7561: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
7562: else {
7563: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
7564: }
7565: if (h*hstepm/YEARM*stepm== yearp) {
7566: fprintf(ficresf," %.3f", p3mat[i][j][h]);
7567: }
7568: } /* end i */
7569: if (h*hstepm/YEARM*stepm==yearp) {
7570: fprintf(ficresf," %.3f", ppij);
7571: }
7572: }/* end j */
7573: } /* end h */
7574: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7575: } /* end agec */
7576: } /* end yearp */
7577: } /* end k */
1.219 brouard 7578:
1.126 brouard 7579: fclose(ficresf);
1.215 brouard 7580: printf("End of Computing forecasting \n");
7581: fprintf(ficlog,"End of Computing forecasting\n");
7582:
1.126 brouard 7583: }
7584:
1.218 brouard 7585: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 7586: /* void prevbackforecast(char fileres[], 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){ */
1.218 brouard 7587: /* /\* back1, year, month, day of starting backection */
7588: /* agemin, agemax range of age */
7589: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
7590: /* anback2 year of en of backection (same day and month as back1). */
7591: /* *\/ */
7592: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
7593: /* double agec; /\* generic age *\/ */
7594: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
7595: /* double *popeffectif,*popcount; */
7596: /* double ***p3mat; */
7597: /* /\* double ***mobaverage; *\/ */
7598: /* char fileresfb[FILENAMELENGTH]; */
7599:
7600: /* agelim=AGESUP; */
7601: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
7602: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
7603: /* We still use firstpass and lastpass as another selection. */
7604: /* *\/ */
7605: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
7606: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
7607: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
7608:
7609: /* strcpy(fileresfb,"FB_"); */
7610: /* strcat(fileresfb,fileresu); */
7611: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
7612: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
7613: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
7614: /* } */
7615: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7616: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7617:
1.225 brouard 7618: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 7619:
7620: /* /\* if (mobilav!=0) { *\/ */
7621: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7622: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7623: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7624: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7625: /* /\* } *\/ */
7626: /* /\* } *\/ */
7627:
7628: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7629: /* if (stepm<=12) stepsize=1; */
7630: /* if(estepm < stepm){ */
7631: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
7632: /* } */
7633: /* else hstepm=estepm; */
7634:
7635: /* hstepm=hstepm/stepm; */
7636: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7637: /* fractional in yp1 *\/ */
7638: /* anprojmean=yp; */
7639: /* yp2=modf((yp1*12),&yp); */
7640: /* mprojmean=yp; */
7641: /* yp1=modf((yp2*30.5),&yp); */
7642: /* jprojmean=yp; */
7643: /* if(jprojmean==0) jprojmean=1; */
7644: /* if(mprojmean==0) jprojmean=1; */
7645:
1.225 brouard 7646: /* i1=cptcoveff; */
1.218 brouard 7647: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7648:
1.218 brouard 7649: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7650:
1.218 brouard 7651: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7652:
7653: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7654: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7655: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7656: /* k=k+1; */
7657: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7658: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7659: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7660: /* } */
7661: /* fprintf(ficresfb," yearbproj age"); */
7662: /* for(j=1; j<=nlstate+ndeath;j++){ */
7663: /* for(i=1; i<=nlstate;i++) */
7664: /* fprintf(ficresfb," p%d%d",i,j); */
7665: /* fprintf(ficresfb," p.%d",j); */
7666: /* } */
7667: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7668: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7669: /* fprintf(ficresfb,"\n"); */
7670: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7671: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7672: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7673: /* nhstepm = nhstepm/hstepm; */
7674: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7675: /* oldm=oldms;savm=savms; */
7676: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7677: /* for (h=0; h<=nhstepm; h++){ */
7678: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7679: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7680: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7681: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7682: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7683: /* } */
7684: /* for(j=1; j<=nlstate+ndeath;j++) { */
7685: /* ppij=0.; */
7686: /* for(i=1; i<=nlstate;i++) { */
7687: /* if (mobilav==1) */
7688: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7689: /* else { */
7690: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7691: /* } */
7692: /* if (h*hstepm/YEARM*stepm== yearp) { */
7693: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7694: /* } */
7695: /* } /\* end i *\/ */
7696: /* if (h*hstepm/YEARM*stepm==yearp) { */
7697: /* fprintf(ficresfb," %.3f", ppij); */
7698: /* } */
7699: /* }/\* end j *\/ */
7700: /* } /\* end h *\/ */
7701: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7702: /* } /\* end agec *\/ */
7703: /* } /\* end yearp *\/ */
7704: /* } /\* end cptcod *\/ */
7705: /* } /\* end cptcov *\/ */
7706:
7707: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7708:
7709: /* fclose(ficresfb); */
7710: /* printf("End of Computing Back forecasting \n"); */
7711: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7712:
1.218 brouard 7713: /* } */
1.217 brouard 7714:
1.126 brouard 7715: /************** Forecasting *****not tested NB*************/
1.227 brouard 7716: /* 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 7717:
1.227 brouard 7718: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7719: /* int *popage; */
7720: /* double calagedatem, agelim, kk1, kk2; */
7721: /* double *popeffectif,*popcount; */
7722: /* double ***p3mat,***tabpop,***tabpopprev; */
7723: /* /\* double ***mobaverage; *\/ */
7724: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7725:
1.227 brouard 7726: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7727: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7728: /* agelim=AGESUP; */
7729: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7730:
1.227 brouard 7731: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7732:
7733:
1.227 brouard 7734: /* strcpy(filerespop,"POP_"); */
7735: /* strcat(filerespop,fileresu); */
7736: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7737: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7738: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7739: /* } */
7740: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7741: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7742:
1.227 brouard 7743: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7744:
1.227 brouard 7745: /* /\* if (mobilav!=0) { *\/ */
7746: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7747: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7748: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7749: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7750: /* /\* } *\/ */
7751: /* /\* } *\/ */
1.126 brouard 7752:
1.227 brouard 7753: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7754: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7755:
1.227 brouard 7756: /* agelim=AGESUP; */
1.126 brouard 7757:
1.227 brouard 7758: /* hstepm=1; */
7759: /* hstepm=hstepm/stepm; */
1.218 brouard 7760:
1.227 brouard 7761: /* if (popforecast==1) { */
7762: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7763: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7764: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7765: /* } */
7766: /* popage=ivector(0,AGESUP); */
7767: /* popeffectif=vector(0,AGESUP); */
7768: /* popcount=vector(0,AGESUP); */
1.126 brouard 7769:
1.227 brouard 7770: /* i=1; */
7771: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7772:
1.227 brouard 7773: /* imx=i; */
7774: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7775: /* } */
1.218 brouard 7776:
1.227 brouard 7777: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7778: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7779: /* k=k+1; */
7780: /* fprintf(ficrespop,"\n#******"); */
7781: /* for(j=1;j<=cptcoveff;j++) { */
7782: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7783: /* } */
7784: /* fprintf(ficrespop,"******\n"); */
7785: /* fprintf(ficrespop,"# Age"); */
7786: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7787: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7788:
1.227 brouard 7789: /* for (cpt=0; cpt<=0;cpt++) { */
7790: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7791:
1.227 brouard 7792: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7793: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7794: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7795:
1.227 brouard 7796: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7797: /* oldm=oldms;savm=savms; */
7798: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7799:
1.227 brouard 7800: /* for (h=0; h<=nhstepm; h++){ */
7801: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7802: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7803: /* } */
7804: /* for(j=1; j<=nlstate+ndeath;j++) { */
7805: /* kk1=0.;kk2=0; */
7806: /* for(i=1; i<=nlstate;i++) { */
7807: /* if (mobilav==1) */
7808: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7809: /* else { */
7810: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7811: /* } */
7812: /* } */
7813: /* if (h==(int)(calagedatem+12*cpt)){ */
7814: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7815: /* /\*fprintf(ficrespop," %.3f", kk1); */
7816: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7817: /* } */
7818: /* } */
7819: /* for(i=1; i<=nlstate;i++){ */
7820: /* kk1=0.; */
7821: /* for(j=1; j<=nlstate;j++){ */
7822: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7823: /* } */
7824: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7825: /* } */
1.218 brouard 7826:
1.227 brouard 7827: /* if (h==(int)(calagedatem+12*cpt)) */
7828: /* for(j=1; j<=nlstate;j++) */
7829: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7830: /* } */
7831: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7832: /* } */
7833: /* } */
1.218 brouard 7834:
1.227 brouard 7835: /* /\******\/ */
1.218 brouard 7836:
1.227 brouard 7837: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7838: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7839: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7840: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7841: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7842:
1.227 brouard 7843: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7844: /* oldm=oldms;savm=savms; */
7845: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7846: /* for (h=0; h<=nhstepm; h++){ */
7847: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7848: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7849: /* } */
7850: /* for(j=1; j<=nlstate+ndeath;j++) { */
7851: /* kk1=0.;kk2=0; */
7852: /* for(i=1; i<=nlstate;i++) { */
7853: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7854: /* } */
7855: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7856: /* } */
7857: /* } */
7858: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7859: /* } */
7860: /* } */
7861: /* } */
7862: /* } */
1.218 brouard 7863:
1.227 brouard 7864: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7865:
1.227 brouard 7866: /* if (popforecast==1) { */
7867: /* free_ivector(popage,0,AGESUP); */
7868: /* free_vector(popeffectif,0,AGESUP); */
7869: /* free_vector(popcount,0,AGESUP); */
7870: /* } */
7871: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7872: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7873: /* fclose(ficrespop); */
7874: /* } /\* End of popforecast *\/ */
1.218 brouard 7875:
1.126 brouard 7876: int fileappend(FILE *fichier, char *optionfich)
7877: {
7878: if((fichier=fopen(optionfich,"a"))==NULL) {
7879: printf("Problem with file: %s\n", optionfich);
7880: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7881: return (0);
7882: }
7883: fflush(fichier);
7884: return (1);
7885: }
7886:
7887:
7888: /**************** function prwizard **********************/
7889: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7890: {
7891:
7892: /* Wizard to print covariance matrix template */
7893:
1.164 brouard 7894: char ca[32], cb[32];
7895: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7896: int numlinepar;
7897:
7898: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7899: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7900: for(i=1; i <=nlstate; i++){
7901: jj=0;
7902: for(j=1; j <=nlstate+ndeath; j++){
7903: if(j==i) continue;
7904: jj++;
7905: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7906: printf("%1d%1d",i,j);
7907: fprintf(ficparo,"%1d%1d",i,j);
7908: for(k=1; k<=ncovmodel;k++){
7909: /* printf(" %lf",param[i][j][k]); */
7910: /* fprintf(ficparo," %lf",param[i][j][k]); */
7911: printf(" 0.");
7912: fprintf(ficparo," 0.");
7913: }
7914: printf("\n");
7915: fprintf(ficparo,"\n");
7916: }
7917: }
7918: printf("# Scales (for hessian or gradient estimation)\n");
7919: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7920: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7921: for(i=1; i <=nlstate; i++){
7922: jj=0;
7923: for(j=1; j <=nlstate+ndeath; j++){
7924: if(j==i) continue;
7925: jj++;
7926: fprintf(ficparo,"%1d%1d",i,j);
7927: printf("%1d%1d",i,j);
7928: fflush(stdout);
7929: for(k=1; k<=ncovmodel;k++){
7930: /* printf(" %le",delti3[i][j][k]); */
7931: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7932: printf(" 0.");
7933: fprintf(ficparo," 0.");
7934: }
7935: numlinepar++;
7936: printf("\n");
7937: fprintf(ficparo,"\n");
7938: }
7939: }
7940: printf("# Covariance matrix\n");
7941: /* # 121 Var(a12)\n\ */
7942: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7943: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7944: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7945: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7946: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7947: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7948: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7949: fflush(stdout);
7950: fprintf(ficparo,"# Covariance matrix\n");
7951: /* # 121 Var(a12)\n\ */
7952: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7953: /* # ...\n\ */
7954: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7955:
7956: for(itimes=1;itimes<=2;itimes++){
7957: jj=0;
7958: for(i=1; i <=nlstate; i++){
7959: for(j=1; j <=nlstate+ndeath; j++){
7960: if(j==i) continue;
7961: for(k=1; k<=ncovmodel;k++){
7962: jj++;
7963: ca[0]= k+'a'-1;ca[1]='\0';
7964: if(itimes==1){
7965: printf("#%1d%1d%d",i,j,k);
7966: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7967: }else{
7968: printf("%1d%1d%d",i,j,k);
7969: fprintf(ficparo,"%1d%1d%d",i,j,k);
7970: /* printf(" %.5le",matcov[i][j]); */
7971: }
7972: ll=0;
7973: for(li=1;li <=nlstate; li++){
7974: for(lj=1;lj <=nlstate+ndeath; lj++){
7975: if(lj==li) continue;
7976: for(lk=1;lk<=ncovmodel;lk++){
7977: ll++;
7978: if(ll<=jj){
7979: cb[0]= lk +'a'-1;cb[1]='\0';
7980: if(ll<jj){
7981: if(itimes==1){
7982: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7983: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7984: }else{
7985: printf(" 0.");
7986: fprintf(ficparo," 0.");
7987: }
7988: }else{
7989: if(itimes==1){
7990: printf(" Var(%s%1d%1d)",ca,i,j);
7991: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7992: }else{
7993: printf(" 0.");
7994: fprintf(ficparo," 0.");
7995: }
7996: }
7997: }
7998: } /* end lk */
7999: } /* end lj */
8000: } /* end li */
8001: printf("\n");
8002: fprintf(ficparo,"\n");
8003: numlinepar++;
8004: } /* end k*/
8005: } /*end j */
8006: } /* end i */
8007: } /* end itimes */
8008:
8009: } /* end of prwizard */
8010: /******************* Gompertz Likelihood ******************************/
8011: double gompertz(double x[])
8012: {
8013: double A,B,L=0.0,sump=0.,num=0.;
8014: int i,n=0; /* n is the size of the sample */
8015:
1.220 brouard 8016: for (i=1;i<=imx ; i++) {
1.126 brouard 8017: sump=sump+weight[i];
8018: /* sump=sump+1;*/
8019: num=num+1;
8020: }
8021:
8022:
8023: /* for (i=0; i<=imx; i++)
8024: 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]);*/
8025:
8026: for (i=1;i<=imx ; i++)
8027: {
8028: if (cens[i] == 1 && wav[i]>1)
8029: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
8030:
8031: if (cens[i] == 0 && wav[i]>1)
8032: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
8033: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
8034:
8035: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8036: if (wav[i] > 1 ) { /* ??? */
8037: L=L+A*weight[i];
8038: /* 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]);*/
8039: }
8040: }
8041:
8042: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8043:
8044: return -2*L*num/sump;
8045: }
8046:
1.136 brouard 8047: #ifdef GSL
8048: /******************* Gompertz_f Likelihood ******************************/
8049: double gompertz_f(const gsl_vector *v, void *params)
8050: {
8051: double A,B,LL=0.0,sump=0.,num=0.;
8052: double *x= (double *) v->data;
8053: int i,n=0; /* n is the size of the sample */
8054:
8055: for (i=0;i<=imx-1 ; i++) {
8056: sump=sump+weight[i];
8057: /* sump=sump+1;*/
8058: num=num+1;
8059: }
8060:
8061:
8062: /* for (i=0; i<=imx; i++)
8063: 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]);*/
8064: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
8065: for (i=1;i<=imx ; i++)
8066: {
8067: if (cens[i] == 1 && wav[i]>1)
8068: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
8069:
8070: if (cens[i] == 0 && wav[i]>1)
8071: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
8072: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
8073:
8074: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
8075: if (wav[i] > 1 ) { /* ??? */
8076: LL=LL+A*weight[i];
8077: /* 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]);*/
8078: }
8079: }
8080:
8081: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
8082: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
8083:
8084: return -2*LL*num/sump;
8085: }
8086: #endif
8087:
1.126 brouard 8088: /******************* Printing html file ***********/
1.201 brouard 8089: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 8090: int lastpass, int stepm, int weightopt, char model[],\
8091: int imx, double p[],double **matcov,double agemortsup){
8092: int i,k;
8093:
8094: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
8095: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
8096: for (i=1;i<=2;i++)
8097: 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 8098: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 8099: fprintf(fichtm,"</ul>");
8100:
8101: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
8102:
8103: 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>");
8104:
8105: for (k=agegomp;k<(agemortsup-2);k++)
8106: 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]);
8107:
8108:
8109: fflush(fichtm);
8110: }
8111:
8112: /******************* Gnuplot file **************/
1.201 brouard 8113: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 8114:
8115: char dirfileres[132],optfileres[132];
1.164 brouard 8116:
1.126 brouard 8117: int ng;
8118:
8119:
8120: /*#ifdef windows */
8121: fprintf(ficgp,"cd \"%s\" \n",pathc);
8122: /*#endif */
8123:
8124:
8125: strcpy(dirfileres,optionfilefiname);
8126: strcpy(optfileres,"vpl");
1.199 brouard 8127: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 8128: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 8129: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 8130: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 8131: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
8132:
8133: }
8134:
1.136 brouard 8135: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
8136: {
1.126 brouard 8137:
1.136 brouard 8138: /*-------- data file ----------*/
8139: FILE *fic;
8140: char dummy[]=" ";
1.240 brouard 8141: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 8142: int lstra;
1.136 brouard 8143: int linei, month, year,iout;
8144: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 8145: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 8146: char *stratrunc;
1.223 brouard 8147:
1.240 brouard 8148: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
8149: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 8150:
1.240 brouard 8151: for(v=1; v <=ncovcol;v++){
8152: DummyV[v]=0;
8153: FixedV[v]=0;
8154: }
8155: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
8156: DummyV[v]=1;
8157: FixedV[v]=0;
8158: }
8159: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
8160: DummyV[v]=0;
8161: FixedV[v]=1;
8162: }
8163: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
8164: DummyV[v]=1;
8165: FixedV[v]=1;
8166: }
8167: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
8168: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
8169: 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]);
8170: }
1.126 brouard 8171:
1.136 brouard 8172: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 8173: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
8174: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 8175: }
1.126 brouard 8176:
1.136 brouard 8177: i=1;
8178: linei=0;
8179: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
8180: linei=linei+1;
8181: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
8182: if(line[j] == '\t')
8183: line[j] = ' ';
8184: }
8185: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
8186: ;
8187: };
8188: line[j+1]=0; /* Trims blanks at end of line */
8189: if(line[0]=='#'){
8190: fprintf(ficlog,"Comment line\n%s\n",line);
8191: printf("Comment line\n%s\n",line);
8192: continue;
8193: }
8194: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 8195: strcpy(line, linetmp);
1.223 brouard 8196:
8197: /* Loops on waves */
8198: for (j=maxwav;j>=1;j--){
8199: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 8200: cutv(stra, strb, line, ' ');
8201: if(strb[0]=='.') { /* Missing value */
8202: lval=-1;
8203: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
8204: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
8205: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
8206: 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);
8207: 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);
8208: return 1;
8209: }
8210: }else{
8211: errno=0;
8212: /* what_kind_of_number(strb); */
8213: dval=strtod(strb,&endptr);
8214: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
8215: /* if(strb != endptr && *endptr == '\0') */
8216: /* dval=dlval; */
8217: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
8218: if( strb[0]=='\0' || (*endptr != '\0')){
8219: 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);
8220: 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);
8221: return 1;
8222: }
8223: cotqvar[j][iv][i]=dval;
8224: cotvar[j][ntv+iv][i]=dval;
8225: }
8226: strcpy(line,stra);
1.223 brouard 8227: }/* end loop ntqv */
1.225 brouard 8228:
1.223 brouard 8229: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 8230: cutv(stra, strb, line, ' ');
8231: if(strb[0]=='.') { /* Missing value */
8232: lval=-1;
8233: }else{
8234: errno=0;
8235: lval=strtol(strb,&endptr,10);
8236: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
8237: if( strb[0]=='\0' || (*endptr != '\0')){
8238: 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);
8239: 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);
8240: return 1;
8241: }
8242: }
8243: if(lval <-1 || lval >1){
8244: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 8245: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8246: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 8247: For example, for multinomial values like 1, 2 and 3,\n \
8248: build V1=0 V2=0 for the reference value (1),\n \
8249: V1=1 V2=0 for (2) \n \
1.223 brouard 8250: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 8251: output of IMaCh is often meaningless.\n \
1.223 brouard 8252: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 8253: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 8254: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8255: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 8256: For example, for multinomial values like 1, 2 and 3,\n \
8257: build V1=0 V2=0 for the reference value (1),\n \
8258: V1=1 V2=0 for (2) \n \
1.223 brouard 8259: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 8260: output of IMaCh is often meaningless.\n \
1.223 brouard 8261: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 8262: return 1;
8263: }
8264: cotvar[j][iv][i]=(double)(lval);
8265: strcpy(line,stra);
1.223 brouard 8266: }/* end loop ntv */
1.225 brouard 8267:
1.223 brouard 8268: /* Statuses at wave */
1.137 brouard 8269: cutv(stra, strb, line, ' ');
1.223 brouard 8270: if(strb[0]=='.') { /* Missing value */
1.238 brouard 8271: lval=-1;
1.136 brouard 8272: }else{
1.238 brouard 8273: errno=0;
8274: lval=strtol(strb,&endptr,10);
8275: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
8276: if( strb[0]=='\0' || (*endptr != '\0')){
8277: 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);
8278: 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);
8279: return 1;
8280: }
1.136 brouard 8281: }
1.225 brouard 8282:
1.136 brouard 8283: s[j][i]=lval;
1.225 brouard 8284:
1.223 brouard 8285: /* Date of Interview */
1.136 brouard 8286: strcpy(line,stra);
8287: cutv(stra, strb,line,' ');
1.169 brouard 8288: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 8289: }
1.169 brouard 8290: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 8291: month=99;
8292: year=9999;
1.136 brouard 8293: }else{
1.225 brouard 8294: 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);
8295: 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);
8296: return 1;
1.136 brouard 8297: }
8298: anint[j][i]= (double) year;
8299: mint[j][i]= (double)month;
8300: strcpy(line,stra);
1.223 brouard 8301: } /* End loop on waves */
1.225 brouard 8302:
1.223 brouard 8303: /* Date of death */
1.136 brouard 8304: cutv(stra, strb,line,' ');
1.169 brouard 8305: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 8306: }
1.169 brouard 8307: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 8308: month=99;
8309: year=9999;
8310: }else{
1.141 brouard 8311: 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 8312: 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);
8313: return 1;
1.136 brouard 8314: }
8315: andc[i]=(double) year;
8316: moisdc[i]=(double) month;
8317: strcpy(line,stra);
8318:
1.223 brouard 8319: /* Date of birth */
1.136 brouard 8320: cutv(stra, strb,line,' ');
1.169 brouard 8321: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 8322: }
1.169 brouard 8323: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 8324: month=99;
8325: year=9999;
8326: }else{
1.141 brouard 8327: 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);
8328: 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 8329: return 1;
1.136 brouard 8330: }
8331: if (year==9999) {
1.141 brouard 8332: 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);
8333: 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 8334: return 1;
8335:
1.136 brouard 8336: }
8337: annais[i]=(double)(year);
8338: moisnais[i]=(double)(month);
8339: strcpy(line,stra);
1.225 brouard 8340:
1.223 brouard 8341: /* Sample weight */
1.136 brouard 8342: cutv(stra, strb,line,' ');
8343: errno=0;
8344: dval=strtod(strb,&endptr);
8345: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 8346: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
8347: 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 8348: fflush(ficlog);
8349: return 1;
8350: }
8351: weight[i]=dval;
8352: strcpy(line,stra);
1.225 brouard 8353:
1.223 brouard 8354: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
8355: cutv(stra, strb, line, ' ');
8356: if(strb[0]=='.') { /* Missing value */
1.225 brouard 8357: lval=-1;
1.223 brouard 8358: }else{
1.225 brouard 8359: errno=0;
8360: /* what_kind_of_number(strb); */
8361: dval=strtod(strb,&endptr);
8362: /* if(strb != endptr && *endptr == '\0') */
8363: /* dval=dlval; */
8364: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
8365: if( strb[0]=='\0' || (*endptr != '\0')){
8366: 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);
8367: 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);
8368: return 1;
8369: }
8370: coqvar[iv][i]=dval;
1.226 brouard 8371: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 8372: }
8373: strcpy(line,stra);
8374: }/* end loop nqv */
1.136 brouard 8375:
1.223 brouard 8376: /* Covariate values */
1.136 brouard 8377: for (j=ncovcol;j>=1;j--){
8378: cutv(stra, strb,line,' ');
1.223 brouard 8379: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 8380: lval=-1;
1.136 brouard 8381: }else{
1.225 brouard 8382: errno=0;
8383: lval=strtol(strb,&endptr,10);
8384: if( strb[0]=='\0' || (*endptr != '\0')){
8385: 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);
8386: 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);
8387: return 1;
8388: }
1.136 brouard 8389: }
8390: if(lval <-1 || lval >1){
1.225 brouard 8391: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 8392: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8393: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 8394: For example, for multinomial values like 1, 2 and 3,\n \
8395: build V1=0 V2=0 for the reference value (1),\n \
8396: V1=1 V2=0 for (2) \n \
1.136 brouard 8397: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 8398: output of IMaCh is often meaningless.\n \
1.136 brouard 8399: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 8400: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 8401: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8402: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 8403: For example, for multinomial values like 1, 2 and 3,\n \
8404: build V1=0 V2=0 for the reference value (1),\n \
8405: V1=1 V2=0 for (2) \n \
1.136 brouard 8406: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 8407: output of IMaCh is often meaningless.\n \
1.136 brouard 8408: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 8409: return 1;
1.136 brouard 8410: }
8411: covar[j][i]=(double)(lval);
8412: strcpy(line,stra);
8413: }
8414: lstra=strlen(stra);
1.225 brouard 8415:
1.136 brouard 8416: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
8417: stratrunc = &(stra[lstra-9]);
8418: num[i]=atol(stratrunc);
8419: }
8420: else
8421: num[i]=atol(stra);
8422: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
8423: 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;}*/
8424:
8425: i=i+1;
8426: } /* End loop reading data */
1.225 brouard 8427:
1.136 brouard 8428: *imax=i-1; /* Number of individuals */
8429: fclose(fic);
1.225 brouard 8430:
1.136 brouard 8431: return (0);
1.164 brouard 8432: /* endread: */
1.225 brouard 8433: printf("Exiting readdata: ");
8434: fclose(fic);
8435: return (1);
1.223 brouard 8436: }
1.126 brouard 8437:
1.234 brouard 8438: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 8439: char *p1 = *stri, *p2 = *stri;
1.235 brouard 8440: while (*p2 == ' ')
1.234 brouard 8441: p2++;
8442: /* while ((*p1++ = *p2++) !=0) */
8443: /* ; */
8444: /* do */
8445: /* while (*p2 == ' ') */
8446: /* p2++; */
8447: /* while (*p1++ == *p2++); */
8448: *stri=p2;
1.145 brouard 8449: }
8450:
1.235 brouard 8451: int decoderesult ( char resultline[], int nres)
1.230 brouard 8452: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
8453: {
1.235 brouard 8454: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 8455: char resultsav[MAXLINE];
1.234 brouard 8456: int resultmodel[MAXLINE];
8457: int modelresult[MAXLINE];
1.230 brouard 8458: char stra[80], strb[80], strc[80], strd[80],stre[80];
8459:
1.234 brouard 8460: removefirstspace(&resultline);
1.233 brouard 8461: printf("decoderesult:%s\n",resultline);
1.230 brouard 8462:
8463: if (strstr(resultline,"v") !=0){
8464: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
8465: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
8466: return 1;
8467: }
8468: trimbb(resultsav, resultline);
8469: if (strlen(resultsav) >1){
8470: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
8471: }
1.253 brouard 8472: if(j == 0){ /* Resultline but no = */
8473: TKresult[nres]=0; /* Combination for the nresult and the model */
8474: return (0);
8475: }
8476:
1.234 brouard 8477: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
8478: 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);
8479: 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);
8480: }
8481: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
8482: if(nbocc(resultsav,'=') >1){
8483: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
8484: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
8485: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
8486: }else
8487: cutl(strc,strd,resultsav,'=');
1.230 brouard 8488: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 8489:
1.230 brouard 8490: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
8491: Tvarsel[k]=atoi(strc);
8492: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
8493: /* cptcovsel++; */
8494: if (nbocc(stra,'=') >0)
8495: strcpy(resultsav,stra); /* and analyzes it */
8496: }
1.235 brouard 8497: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 8498: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8499: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 8500: match=0;
1.236 brouard 8501: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 8502: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 8503: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 8504: match=1;
8505: break;
8506: }
8507: }
8508: if(match == 0){
8509: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8510: }
8511: }
8512: }
1.235 brouard 8513: /* Checking for missing or useless values in comparison of current model needs */
8514: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 8515: match=0;
1.235 brouard 8516: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8517: if(Typevar[k1]==0){ /* Single */
1.237 brouard 8518: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 8519: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 8520: ++match;
8521: }
8522: }
8523: }
8524: if(match == 0){
8525: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8526: }else if(match > 1){
8527: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
8528: }
8529: }
1.235 brouard 8530:
1.234 brouard 8531: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 8532: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8533: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
8534: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
8535: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
8536: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
8537: /* 1 0 0 0 */
8538: /* 2 1 0 0 */
8539: /* 3 0 1 0 */
8540: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
8541: /* 5 0 0 1 */
8542: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
8543: /* 7 0 1 1 */
8544: /* 8 1 1 1 */
1.237 brouard 8545: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
8546: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
8547: /* V5*age V5 known which value for nres? */
8548: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 8549: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
8550: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 8551: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 8552: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
8553: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 8554: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
8555: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
8556: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 8557: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
8558: k4++;;
8559: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
8560: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
8561: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 8562: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
8563: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
8564: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 8565: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
8566: k4q++;;
8567: }
8568: }
1.234 brouard 8569:
1.235 brouard 8570: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 8571: return (0);
8572: }
1.235 brouard 8573:
1.230 brouard 8574: int decodemodel( char model[], int lastobs)
8575: /**< This routine decodes the model and returns:
1.224 brouard 8576: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
8577: * - nagesqr = 1 if age*age in the model, otherwise 0.
8578: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
8579: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
8580: * - cptcovage number of covariates with age*products =2
8581: * - cptcovs number of simple covariates
8582: * - 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
8583: * which is a new column after the 9 (ncovcol) variables.
8584: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
8585: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
8586: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
8587: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
8588: */
1.136 brouard 8589: {
1.238 brouard 8590: int i, j, k, ks, v;
1.227 brouard 8591: int j1, k1, k2, k3, k4;
1.136 brouard 8592: char modelsav[80];
1.145 brouard 8593: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 8594: char *strpt;
1.136 brouard 8595:
1.145 brouard 8596: /*removespace(model);*/
1.136 brouard 8597: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 8598: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 8599: if (strstr(model,"AGE") !=0){
1.192 brouard 8600: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
8601: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 8602: return 1;
8603: }
1.141 brouard 8604: if (strstr(model,"v") !=0){
8605: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
8606: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
8607: return 1;
8608: }
1.187 brouard 8609: strcpy(modelsav,model);
8610: if ((strpt=strstr(model,"age*age")) !=0){
8611: printf(" strpt=%s, model=%s\n",strpt, model);
8612: if(strpt != model){
1.234 brouard 8613: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8614: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8615: corresponding column of parameters.\n",model);
1.234 brouard 8616: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8617: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8618: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 8619: return 1;
1.225 brouard 8620: }
1.187 brouard 8621: nagesqr=1;
8622: if (strstr(model,"+age*age") !=0)
1.234 brouard 8623: substrchaine(modelsav, model, "+age*age");
1.187 brouard 8624: else if (strstr(model,"age*age+") !=0)
1.234 brouard 8625: substrchaine(modelsav, model, "age*age+");
1.187 brouard 8626: else
1.234 brouard 8627: substrchaine(modelsav, model, "age*age");
1.187 brouard 8628: }else
8629: nagesqr=0;
8630: if (strlen(modelsav) >1){
8631: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
8632: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 8633: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 8634: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 8635: * cst, age and age*age
8636: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
8637: /* including age products which are counted in cptcovage.
8638: * but the covariates which are products must be treated
8639: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 8640: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
8641: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 8642:
8643:
1.187 brouard 8644: /* Design
8645: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
8646: * < ncovcol=8 >
8647: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
8648: * k= 1 2 3 4 5 6 7 8
8649: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
8650: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 8651: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
8652: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 8653: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
8654: * Tage[++cptcovage]=k
8655: * if products, new covar are created after ncovcol with k1
8656: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
8657: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
8658: * 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
8659: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
8660: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
8661: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
8662: * < ncovcol=8 >
8663: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
8664: * k= 1 2 3 4 5 6 7 8 9 10 11 12
8665: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
8666: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8667: * p Tprod[1]@2={ 6, 5}
8668: *p Tvard[1][1]@4= {7, 8, 5, 6}
8669: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
8670: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
8671: *How to reorganize?
8672: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
8673: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8674: * {2, 1, 4, 8, 5, 6, 3, 7}
8675: * Struct []
8676: */
1.225 brouard 8677:
1.187 brouard 8678: /* This loop fills the array Tvar from the string 'model'.*/
8679: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
8680: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
8681: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
8682: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
8683: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
8684: /* k=1 Tvar[1]=2 (from V2) */
8685: /* k=5 Tvar[5] */
8686: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 8687: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 8688: /* } */
1.198 brouard 8689: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 8690: /*
8691: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 8692: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
8693: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
8694: }
1.187 brouard 8695: cptcovage=0;
8696: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 8697: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 8698: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 8699: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
8700: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
8701: /*scanf("%d",i);*/
8702: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
8703: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
8704: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
8705: /* covar is not filled and then is empty */
8706: cptcovprod--;
8707: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
8708: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
8709: Typevar[k]=1; /* 1 for age product */
8710: cptcovage++; /* Sums the number of covariates which include age as a product */
8711: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
8712: /*printf("stre=%s ", stre);*/
8713: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
8714: cptcovprod--;
8715: cutl(stre,strb,strc,'V');
8716: Tvar[k]=atoi(stre);
8717: Typevar[k]=1; /* 1 for age product */
8718: cptcovage++;
8719: Tage[cptcovage]=k;
8720: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
8721: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
8722: cptcovn++;
8723: cptcovprodnoage++;k1++;
8724: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
8725: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
8726: because this model-covariate is a construction we invent a new column
8727: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
8728: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
8729: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
8730: Typevar[k]=2; /* 2 for double fixed dummy covariates */
8731: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
8732: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
8733: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
8734: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
8735: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
8736: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
8737: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
8738: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 8739: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 8740: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
8741: for (i=1; i<=lastobs;i++){
8742: /* Computes the new covariate which is a product of
8743: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
8744: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
8745: }
8746: } /* End age is not in the model */
8747: } /* End if model includes a product */
8748: else { /* no more sum */
8749: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
8750: /* scanf("%d",i);*/
8751: cutl(strd,strc,strb,'V');
8752: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
8753: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
8754: Tvar[k]=atoi(strd);
8755: Typevar[k]=0; /* 0 for simple covariates */
8756: }
8757: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 8758: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 8759: scanf("%d",i);*/
1.187 brouard 8760: } /* end of loop + on total covariates */
8761: } /* end if strlen(modelsave == 0) age*age might exist */
8762: } /* end if strlen(model == 0) */
1.136 brouard 8763:
8764: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
8765: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 8766:
1.136 brouard 8767: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 8768: printf("cptcovprod=%d ", cptcovprod);
8769: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
8770: scanf("%d ",i);*/
8771:
8772:
1.230 brouard 8773: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
8774: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 8775: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
8776: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
8777: k = 1 2 3 4 5 6 7 8 9
8778: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
8779: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 8780: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
8781: Dummy[k] 1 0 0 0 3 1 1 2 3
8782: Tmodelind[combination of covar]=k;
1.225 brouard 8783: */
8784: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 8785: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 8786: /* 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 8787: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8788: printf("Model=%s\n\
8789: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8790: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8791: 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);
8792: fprintf(ficlog,"Model=%s\n\
8793: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8794: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8795: 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 8796: for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 8797: 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 */
8798: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 8799: Fixed[k]= 0;
8800: Dummy[k]= 0;
1.225 brouard 8801: ncoveff++;
1.232 brouard 8802: ncovf++;
1.234 brouard 8803: nsd++;
8804: modell[k].maintype= FTYPE;
8805: TvarsD[nsd]=Tvar[k];
8806: TvarsDind[nsd]=k;
8807: TvarF[ncovf]=Tvar[k];
8808: TvarFind[ncovf]=k;
8809: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8810: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8811: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
8812: Fixed[k]= 0;
8813: Dummy[k]= 0;
8814: ncoveff++;
8815: ncovf++;
8816: modell[k].maintype= FTYPE;
8817: TvarF[ncovf]=Tvar[k];
8818: TvarFind[ncovf]=k;
1.230 brouard 8819: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 8820: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 brouard 8821: }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 8822: Fixed[k]= 0;
8823: Dummy[k]= 1;
1.230 brouard 8824: nqfveff++;
1.234 brouard 8825: modell[k].maintype= FTYPE;
8826: modell[k].subtype= FQ;
8827: nsq++;
8828: TvarsQ[nsq]=Tvar[k];
8829: TvarsQind[nsq]=k;
1.232 brouard 8830: ncovf++;
1.234 brouard 8831: TvarF[ncovf]=Tvar[k];
8832: TvarFind[ncovf]=k;
1.231 brouard 8833: 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 8834: 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 8835: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
1.227 brouard 8836: Fixed[k]= 1;
8837: Dummy[k]= 0;
1.225 brouard 8838: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 8839: modell[k].maintype= VTYPE;
8840: modell[k].subtype= VD;
8841: nsd++;
8842: TvarsD[nsd]=Tvar[k];
8843: TvarsDind[nsd]=k;
8844: ncovv++; /* Only simple time varying variables */
8845: TvarV[ncovv]=Tvar[k];
1.242 brouard 8846: 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 8847: 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 */
8848: 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 8849: 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);
8850: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 8851: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 8852: Fixed[k]= 1;
8853: Dummy[k]= 1;
8854: nqtveff++;
8855: modell[k].maintype= VTYPE;
8856: modell[k].subtype= VQ;
8857: ncovv++; /* Only simple time varying variables */
8858: nsq++;
8859: TvarsQ[nsq]=Tvar[k];
8860: TvarsQind[nsq]=k;
8861: TvarV[ncovv]=Tvar[k];
1.242 brouard 8862: 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 8863: 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 */
8864: 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 8865: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8866: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8867: 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 8868: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8869: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 8870: ncova++;
8871: TvarA[ncova]=Tvar[k];
8872: TvarAind[ncova]=k;
1.231 brouard 8873: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 brouard 8874: Fixed[k]= 2;
8875: Dummy[k]= 2;
8876: modell[k].maintype= ATYPE;
8877: modell[k].subtype= APFD;
8878: /* ncoveff++; */
1.227 brouard 8879: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 brouard 8880: Fixed[k]= 2;
8881: Dummy[k]= 3;
8882: modell[k].maintype= ATYPE;
8883: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
8884: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 8885: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 brouard 8886: Fixed[k]= 3;
8887: Dummy[k]= 2;
8888: modell[k].maintype= ATYPE;
8889: modell[k].subtype= APVD; /* Product age * varying dummy */
8890: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 8891: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 8892: Fixed[k]= 3;
8893: Dummy[k]= 3;
8894: modell[k].maintype= ATYPE;
8895: modell[k].subtype= APVQ; /* Product age * varying quantitative */
8896: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 8897: }
8898: }else if (Typevar[k] == 2) { /* product without age */
8899: k1=Tposprod[k];
8900: if(Tvard[k1][1] <=ncovcol){
1.240 brouard 8901: if(Tvard[k1][2] <=ncovcol){
8902: Fixed[k]= 1;
8903: Dummy[k]= 0;
8904: modell[k].maintype= FTYPE;
8905: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
8906: ncovf++; /* Fixed variables without age */
8907: TvarF[ncovf]=Tvar[k];
8908: TvarFind[ncovf]=k;
8909: }else if(Tvard[k1][2] <=ncovcol+nqv){
8910: Fixed[k]= 0; /* or 2 ?*/
8911: Dummy[k]= 1;
8912: modell[k].maintype= FTYPE;
8913: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
8914: ncovf++; /* Varying variables without age */
8915: TvarF[ncovf]=Tvar[k];
8916: TvarFind[ncovf]=k;
8917: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8918: Fixed[k]= 1;
8919: Dummy[k]= 0;
8920: modell[k].maintype= VTYPE;
8921: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
8922: ncovv++; /* Varying variables without age */
8923: TvarV[ncovv]=Tvar[k];
8924: TvarVind[ncovv]=k;
8925: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8926: Fixed[k]= 1;
8927: Dummy[k]= 1;
8928: modell[k].maintype= VTYPE;
8929: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
8930: ncovv++; /* Varying variables without age */
8931: TvarV[ncovv]=Tvar[k];
8932: TvarVind[ncovv]=k;
8933: }
1.227 brouard 8934: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 brouard 8935: if(Tvard[k1][2] <=ncovcol){
8936: Fixed[k]= 0; /* or 2 ?*/
8937: Dummy[k]= 1;
8938: modell[k].maintype= FTYPE;
8939: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
8940: ncovf++; /* Fixed variables without age */
8941: TvarF[ncovf]=Tvar[k];
8942: TvarFind[ncovf]=k;
8943: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8944: Fixed[k]= 1;
8945: Dummy[k]= 1;
8946: modell[k].maintype= VTYPE;
8947: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
8948: ncovv++; /* Varying variables without age */
8949: TvarV[ncovv]=Tvar[k];
8950: TvarVind[ncovv]=k;
8951: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8952: Fixed[k]= 1;
8953: Dummy[k]= 1;
8954: modell[k].maintype= VTYPE;
8955: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
8956: ncovv++; /* Varying variables without age */
8957: TvarV[ncovv]=Tvar[k];
8958: TvarVind[ncovv]=k;
8959: ncovv++; /* Varying variables without age */
8960: TvarV[ncovv]=Tvar[k];
8961: TvarVind[ncovv]=k;
8962: }
1.227 brouard 8963: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 brouard 8964: if(Tvard[k1][2] <=ncovcol){
8965: Fixed[k]= 1;
8966: Dummy[k]= 1;
8967: modell[k].maintype= VTYPE;
8968: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
8969: ncovv++; /* Varying variables without age */
8970: TvarV[ncovv]=Tvar[k];
8971: TvarVind[ncovv]=k;
8972: }else if(Tvard[k1][2] <=ncovcol+nqv){
8973: Fixed[k]= 1;
8974: Dummy[k]= 1;
8975: modell[k].maintype= VTYPE;
8976: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
8977: ncovv++; /* Varying variables without age */
8978: TvarV[ncovv]=Tvar[k];
8979: TvarVind[ncovv]=k;
8980: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8981: Fixed[k]= 1;
8982: Dummy[k]= 0;
8983: modell[k].maintype= VTYPE;
8984: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
8985: ncovv++; /* Varying variables without age */
8986: TvarV[ncovv]=Tvar[k];
8987: TvarVind[ncovv]=k;
8988: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8989: Fixed[k]= 1;
8990: Dummy[k]= 1;
8991: modell[k].maintype= VTYPE;
8992: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
8993: ncovv++; /* Varying variables without age */
8994: TvarV[ncovv]=Tvar[k];
8995: TvarVind[ncovv]=k;
8996: }
1.227 brouard 8997: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 brouard 8998: if(Tvard[k1][2] <=ncovcol){
8999: Fixed[k]= 1;
9000: Dummy[k]= 1;
9001: modell[k].maintype= VTYPE;
9002: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
9003: ncovv++; /* Varying variables without age */
9004: TvarV[ncovv]=Tvar[k];
9005: TvarVind[ncovv]=k;
9006: }else if(Tvard[k1][2] <=ncovcol+nqv){
9007: Fixed[k]= 1;
9008: Dummy[k]= 1;
9009: modell[k].maintype= VTYPE;
9010: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
9011: ncovv++; /* Varying variables without age */
9012: TvarV[ncovv]=Tvar[k];
9013: TvarVind[ncovv]=k;
9014: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
9015: Fixed[k]= 1;
9016: Dummy[k]= 1;
9017: modell[k].maintype= VTYPE;
9018: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
9019: ncovv++; /* Varying variables without age */
9020: TvarV[ncovv]=Tvar[k];
9021: TvarVind[ncovv]=k;
9022: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
9023: Fixed[k]= 1;
9024: Dummy[k]= 1;
9025: modell[k].maintype= VTYPE;
9026: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
9027: ncovv++; /* Varying variables without age */
9028: TvarV[ncovv]=Tvar[k];
9029: TvarVind[ncovv]=k;
9030: }
1.227 brouard 9031: }else{
1.240 brouard 9032: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9033: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
9034: } /*end k1*/
1.225 brouard 9035: }else{
1.226 brouard 9036: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
9037: 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 9038: }
1.227 brouard 9039: 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 9040: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 9041: 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]);
9042: }
9043: /* Searching for doublons in the model */
9044: for(k1=1; k1<= cptcovt;k1++){
9045: for(k2=1; k2 <k1;k2++){
9046: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234 brouard 9047: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
9048: if(Tvar[k1]==Tvar[k2]){
9049: 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]]);
9050: 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);
9051: return(1);
9052: }
9053: }else if (Typevar[k1] ==2){
9054: k3=Tposprod[k1];
9055: k4=Tposprod[k2];
9056: 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])) ){
9057: 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]]);
9058: 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);
9059: return(1);
9060: }
9061: }
1.227 brouard 9062: }
9063: }
1.225 brouard 9064: }
9065: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
9066: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 9067: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
9068: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 9069: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 9070: /*endread:*/
1.225 brouard 9071: printf("Exiting decodemodel: ");
9072: return (1);
1.136 brouard 9073: }
9074:
1.169 brouard 9075: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.248 brouard 9076: {/* Check ages at death */
1.136 brouard 9077: int i, m;
1.218 brouard 9078: int firstone=0;
9079:
1.136 brouard 9080: for (i=1; i<=imx; i++) {
9081: for(m=2; (m<= maxwav); m++) {
9082: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
9083: anint[m][i]=9999;
1.216 brouard 9084: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
9085: s[m][i]=-1;
1.136 brouard 9086: }
9087: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 9088: *nberr = *nberr + 1;
1.218 brouard 9089: if(firstone == 0){
9090: firstone=1;
9091: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
9092: }
9093: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);
1.136 brouard 9094: s[m][i]=-1;
9095: }
9096: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 9097: (*nberr)++;
1.136 brouard 9098: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
9099: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
9100: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
9101: }
9102: }
9103: }
9104:
9105: for (i=1; i<=imx; i++) {
9106: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
9107: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 9108: 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 9109: if (s[m][i] >= nlstate+1) {
1.169 brouard 9110: if(agedc[i]>0){
9111: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 9112: agev[m][i]=agedc[i];
1.214 brouard 9113: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 9114: }else {
1.136 brouard 9115: if ((int)andc[i]!=9999){
9116: nbwarn++;
9117: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
9118: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
9119: agev[m][i]=-1;
9120: }
9121: }
1.169 brouard 9122: } /* agedc > 0 */
1.214 brouard 9123: } /* end if */
1.136 brouard 9124: else if(s[m][i] !=9){ /* Standard case, age in fractional
9125: years but with the precision of a month */
9126: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
9127: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
9128: agev[m][i]=1;
9129: else if(agev[m][i] < *agemin){
9130: *agemin=agev[m][i];
9131: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
9132: }
9133: else if(agev[m][i] >*agemax){
9134: *agemax=agev[m][i];
1.156 brouard 9135: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 9136: }
9137: /*agev[m][i]=anint[m][i]-annais[i];*/
9138: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 9139: } /* en if 9*/
1.136 brouard 9140: else { /* =9 */
1.214 brouard 9141: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 9142: agev[m][i]=1;
9143: s[m][i]=-1;
9144: }
9145: }
1.214 brouard 9146: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 9147: agev[m][i]=1;
1.214 brouard 9148: else{
9149: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
9150: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
9151: agev[m][i]=0;
9152: }
9153: } /* End for lastpass */
9154: }
1.136 brouard 9155:
9156: for (i=1; i<=imx; i++) {
9157: for(m=firstpass; (m<=lastpass); m++){
9158: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 9159: (*nberr)++;
1.136 brouard 9160: 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);
9161: 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);
9162: return 1;
9163: }
9164: }
9165: }
9166:
9167: /*for (i=1; i<=imx; i++){
9168: for (m=firstpass; (m<lastpass); m++){
9169: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
9170: }
9171:
9172: }*/
9173:
9174:
1.139 brouard 9175: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
9176: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 9177:
9178: return (0);
1.164 brouard 9179: /* endread:*/
1.136 brouard 9180: printf("Exiting calandcheckages: ");
9181: return (1);
9182: }
9183:
1.172 brouard 9184: #if defined(_MSC_VER)
9185: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
9186: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
9187: //#include "stdafx.h"
9188: //#include <stdio.h>
9189: //#include <tchar.h>
9190: //#include <windows.h>
9191: //#include <iostream>
9192: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
9193:
9194: LPFN_ISWOW64PROCESS fnIsWow64Process;
9195:
9196: BOOL IsWow64()
9197: {
9198: BOOL bIsWow64 = FALSE;
9199:
9200: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
9201: // (HANDLE, PBOOL);
9202:
9203: //LPFN_ISWOW64PROCESS fnIsWow64Process;
9204:
9205: HMODULE module = GetModuleHandle(_T("kernel32"));
9206: const char funcName[] = "IsWow64Process";
9207: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
9208: GetProcAddress(module, funcName);
9209:
9210: if (NULL != fnIsWow64Process)
9211: {
9212: if (!fnIsWow64Process(GetCurrentProcess(),
9213: &bIsWow64))
9214: //throw std::exception("Unknown error");
9215: printf("Unknown error\n");
9216: }
9217: return bIsWow64 != FALSE;
9218: }
9219: #endif
1.177 brouard 9220:
1.191 brouard 9221: void syscompilerinfo(int logged)
1.167 brouard 9222: {
9223: /* #include "syscompilerinfo.h"*/
1.185 brouard 9224: /* command line Intel compiler 32bit windows, XP compatible:*/
9225: /* /GS /W3 /Gy
9226: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
9227: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
9228: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 9229: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
9230: */
9231: /* 64 bits */
1.185 brouard 9232: /*
9233: /GS /W3 /Gy
9234: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
9235: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
9236: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
9237: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
9238: /* Optimization are useless and O3 is slower than O2 */
9239: /*
9240: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
9241: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
9242: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
9243: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
9244: */
1.186 brouard 9245: /* Link is */ /* /OUT:"visual studio
1.185 brouard 9246: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
9247: /PDB:"visual studio
9248: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
9249: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
9250: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
9251: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
9252: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
9253: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
9254: uiAccess='false'"
9255: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
9256: /NOLOGO /TLBID:1
9257: */
1.177 brouard 9258: #if defined __INTEL_COMPILER
1.178 brouard 9259: #if defined(__GNUC__)
9260: struct utsname sysInfo; /* For Intel on Linux and OS/X */
9261: #endif
1.177 brouard 9262: #elif defined(__GNUC__)
1.179 brouard 9263: #ifndef __APPLE__
1.174 brouard 9264: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 9265: #endif
1.177 brouard 9266: struct utsname sysInfo;
1.178 brouard 9267: int cross = CROSS;
9268: if (cross){
9269: printf("Cross-");
1.191 brouard 9270: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 9271: }
1.174 brouard 9272: #endif
9273:
1.171 brouard 9274: #include <stdint.h>
1.178 brouard 9275:
1.191 brouard 9276: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 9277: #if defined(__clang__)
1.191 brouard 9278: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 9279: #endif
9280: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 9281: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 9282: #endif
9283: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 9284: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 9285: #endif
9286: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 9287: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 9288: #endif
9289: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 9290: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 9291: #endif
9292: #if defined(_MSC_VER)
1.191 brouard 9293: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 9294: #endif
9295: #if defined(__PGI)
1.191 brouard 9296: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 9297: #endif
9298: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 9299: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 9300: #endif
1.191 brouard 9301: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 9302:
1.167 brouard 9303: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
9304: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
9305: // Windows (x64 and x86)
1.191 brouard 9306: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 9307: #elif __unix__ // all unices, not all compilers
9308: // Unix
1.191 brouard 9309: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 9310: #elif __linux__
9311: // linux
1.191 brouard 9312: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 9313: #elif __APPLE__
1.174 brouard 9314: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 9315: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 9316: #endif
9317:
9318: /* __MINGW32__ */
9319: /* __CYGWIN__ */
9320: /* __MINGW64__ */
9321: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
9322: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
9323: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
9324: /* _WIN64 // Defined for applications for Win64. */
9325: /* _M_X64 // Defined for compilations that target x64 processors. */
9326: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 9327:
1.167 brouard 9328: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 9329: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 9330: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 9331: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 9332: #else
1.191 brouard 9333: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 9334: #endif
9335:
1.169 brouard 9336: #if defined(__GNUC__)
9337: # if defined(__GNUC_PATCHLEVEL__)
9338: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
9339: + __GNUC_MINOR__ * 100 \
9340: + __GNUC_PATCHLEVEL__)
9341: # else
9342: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
9343: + __GNUC_MINOR__ * 100)
9344: # endif
1.174 brouard 9345: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 9346: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 9347:
9348: if (uname(&sysInfo) != -1) {
9349: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 9350: 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 9351: }
9352: else
9353: perror("uname() error");
1.179 brouard 9354: //#ifndef __INTEL_COMPILER
9355: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 9356: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 9357: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 9358: #endif
1.169 brouard 9359: #endif
1.172 brouard 9360:
9361: // void main()
9362: // {
1.169 brouard 9363: #if defined(_MSC_VER)
1.174 brouard 9364: if (IsWow64()){
1.191 brouard 9365: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
9366: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 9367: }
9368: else{
1.191 brouard 9369: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
9370: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 9371: }
1.172 brouard 9372: // printf("\nPress Enter to continue...");
9373: // getchar();
9374: // }
9375:
1.169 brouard 9376: #endif
9377:
1.167 brouard 9378:
1.219 brouard 9379: }
1.136 brouard 9380:
1.219 brouard 9381: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 9382: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 brouard 9383: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 9384: /* double ftolpl = 1.e-10; */
1.180 brouard 9385: double age, agebase, agelim;
1.203 brouard 9386: double tot;
1.180 brouard 9387:
1.202 brouard 9388: strcpy(filerespl,"PL_");
9389: strcat(filerespl,fileresu);
9390: if((ficrespl=fopen(filerespl,"w"))==NULL) {
9391: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
9392: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
9393: }
1.227 brouard 9394: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
9395: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 9396: pstamp(ficrespl);
1.203 brouard 9397: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 9398: fprintf(ficrespl,"#Age ");
9399: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
9400: fprintf(ficrespl,"\n");
1.180 brouard 9401:
1.219 brouard 9402: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 9403:
1.219 brouard 9404: agebase=ageminpar;
9405: agelim=agemaxpar;
1.180 brouard 9406:
1.227 brouard 9407: /* i1=pow(2,ncoveff); */
1.234 brouard 9408: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 9409: if (cptcovn < 1){i1=1;}
1.180 brouard 9410:
1.238 brouard 9411: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
9412: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.253 brouard 9413: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 9414: continue;
1.235 brouard 9415:
1.238 brouard 9416: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9417: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
9418: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
9419: /* k=k+1; */
9420: /* to clean */
9421: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
9422: fprintf(ficrespl,"#******");
9423: printf("#******");
9424: fprintf(ficlog,"#******");
9425: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
9426: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
9427: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9428: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9429: }
9430: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
9431: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9432: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9433: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9434: }
9435: fprintf(ficrespl,"******\n");
9436: printf("******\n");
9437: fprintf(ficlog,"******\n");
9438: if(invalidvarcomb[k]){
9439: printf("\nCombination (%d) ignored because no case \n",k);
9440: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
9441: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
9442: continue;
9443: }
1.219 brouard 9444:
1.238 brouard 9445: fprintf(ficrespl,"#Age ");
9446: for(j=1;j<=cptcoveff;j++) {
9447: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9448: }
9449: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
9450: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 9451:
1.238 brouard 9452: for (age=agebase; age<=agelim; age++){
9453: /* for (age=agebase; age<=agebase; age++){ */
9454: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
9455: fprintf(ficrespl,"%.0f ",age );
9456: for(j=1;j<=cptcoveff;j++)
9457: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9458: tot=0.;
9459: for(i=1; i<=nlstate;i++){
9460: tot += prlim[i][i];
9461: fprintf(ficrespl," %.5f", prlim[i][i]);
9462: }
9463: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
9464: } /* Age */
9465: /* was end of cptcod */
9466: } /* cptcov */
9467: } /* nres */
1.219 brouard 9468: return 0;
1.180 brouard 9469: }
9470:
1.218 brouard 9471: 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){
9472: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9473:
9474: /* Computes the back prevalence limit for any combination of covariate values
9475: * at any age between ageminpar and agemaxpar
9476: */
1.235 brouard 9477: int i, j, k, i1, nres=0 ;
1.217 brouard 9478: /* double ftolpl = 1.e-10; */
9479: double age, agebase, agelim;
9480: double tot;
1.218 brouard 9481: /* double ***mobaverage; */
9482: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 9483:
9484: strcpy(fileresplb,"PLB_");
9485: strcat(fileresplb,fileresu);
9486: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
9487: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
9488: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
9489: }
9490: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
9491: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
9492: pstamp(ficresplb);
9493: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
9494: fprintf(ficresplb,"#Age ");
9495: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
9496: fprintf(ficresplb,"\n");
9497:
1.218 brouard 9498:
9499: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
9500:
9501: agebase=ageminpar;
9502: agelim=agemaxpar;
9503:
9504:
1.227 brouard 9505: i1=pow(2,cptcoveff);
1.218 brouard 9506: if (cptcovn < 1){i1=1;}
1.227 brouard 9507:
1.238 brouard 9508: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
9509: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 9510: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 9511: continue;
9512: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
9513: fprintf(ficresplb,"#******");
9514: printf("#******");
9515: fprintf(ficlog,"#******");
9516: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
9517: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9518: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9519: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9520: }
9521: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9522: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9523: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9524: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9525: }
9526: fprintf(ficresplb,"******\n");
9527: printf("******\n");
9528: fprintf(ficlog,"******\n");
9529: if(invalidvarcomb[k]){
9530: printf("\nCombination (%d) ignored because no cases \n",k);
9531: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
9532: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
9533: continue;
9534: }
1.218 brouard 9535:
1.238 brouard 9536: fprintf(ficresplb,"#Age ");
9537: for(j=1;j<=cptcoveff;j++) {
9538: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9539: }
9540: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
9541: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 9542:
9543:
1.238 brouard 9544: for (age=agebase; age<=agelim; age++){
9545: /* for (age=agebase; age<=agebase; age++){ */
9546: if(mobilavproj > 0){
9547: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
9548: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 9549: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
1.238 brouard 9550: }else if (mobilavproj == 0){
9551: 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);
9552: 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);
9553: exit(1);
9554: }else{
9555: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.242 brouard 9556: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
1.238 brouard 9557: }
9558: fprintf(ficresplb,"%.0f ",age );
9559: for(j=1;j<=cptcoveff;j++)
9560: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9561: tot=0.;
9562: for(i=1; i<=nlstate;i++){
9563: tot += bprlim[i][i];
9564: fprintf(ficresplb," %.5f", bprlim[i][i]);
9565: }
9566: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
9567: } /* Age */
9568: /* was end of cptcod */
1.255 ! brouard 9569: /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
1.238 brouard 9570: } /* end of any combination */
9571: } /* end of nres */
1.218 brouard 9572: /* hBijx(p, bage, fage); */
9573: /* fclose(ficrespijb); */
9574:
9575: return 0;
1.217 brouard 9576: }
1.218 brouard 9577:
1.180 brouard 9578: int hPijx(double *p, int bage, int fage){
9579: /*------------- h Pij x at various ages ------------*/
9580:
9581: int stepsize;
9582: int agelim;
9583: int hstepm;
9584: int nhstepm;
1.235 brouard 9585: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 9586:
9587: double agedeb;
9588: double ***p3mat;
9589:
1.201 brouard 9590: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 9591: if((ficrespij=fopen(filerespij,"w"))==NULL) {
9592: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
9593: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
9594: }
9595: printf("Computing pij: result on file '%s' \n", filerespij);
9596: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
9597:
9598: stepsize=(int) (stepm+YEARM-1)/YEARM;
9599: /*if (stepm<=24) stepsize=2;*/
9600:
9601: agelim=AGESUP;
9602: hstepm=stepsize*YEARM; /* Every year of age */
9603: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 9604:
1.180 brouard 9605: /* hstepm=1; aff par mois*/
9606: pstamp(ficrespij);
9607: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 9608: i1= pow(2,cptcoveff);
1.218 brouard 9609: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9610: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9611: /* k=k+1; */
1.235 brouard 9612: for(nres=1; nres <= nresult; nres++) /* For each resultline */
9613: for(k=1; k<=i1;k++){
1.253 brouard 9614: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 9615: continue;
1.183 brouard 9616: fprintf(ficrespij,"\n#****** ");
1.227 brouard 9617: for(j=1;j<=cptcoveff;j++)
1.198 brouard 9618: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 9619: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
9620: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9621: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9622: }
1.183 brouard 9623: fprintf(ficrespij,"******\n");
9624:
9625: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
9626: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9627: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
9628:
9629: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 9630:
1.183 brouard 9631: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9632: oldm=oldms;savm=savms;
1.235 brouard 9633: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 9634: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
9635: for(i=1; i<=nlstate;i++)
9636: for(j=1; j<=nlstate+ndeath;j++)
9637: fprintf(ficrespij," %1d-%1d",i,j);
9638: fprintf(ficrespij,"\n");
9639: for (h=0; h<=nhstepm; h++){
9640: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9641: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 9642: for(i=1; i<=nlstate;i++)
9643: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 9644: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 9645: fprintf(ficrespij,"\n");
9646: }
1.183 brouard 9647: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9648: fprintf(ficrespij,"\n");
9649: }
1.180 brouard 9650: /*}*/
9651: }
1.218 brouard 9652: return 0;
1.180 brouard 9653: }
1.218 brouard 9654:
9655: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 9656: /*------------- h Bij x at various ages ------------*/
9657:
9658: int stepsize;
1.218 brouard 9659: /* int agelim; */
9660: int ageminl;
1.217 brouard 9661: int hstepm;
9662: int nhstepm;
1.238 brouard 9663: int h, i, i1, j, k, nres;
1.218 brouard 9664:
1.217 brouard 9665: double agedeb;
9666: double ***p3mat;
1.218 brouard 9667:
9668: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
9669: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
9670: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9671: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9672: }
9673: printf("Computing pij back: result on file '%s' \n", filerespijb);
9674: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
9675:
9676: stepsize=(int) (stepm+YEARM-1)/YEARM;
9677: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 9678:
1.218 brouard 9679: /* agelim=AGESUP; */
9680: ageminl=30;
9681: hstepm=stepsize*YEARM; /* Every year of age */
9682: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
9683:
9684: /* hstepm=1; aff par mois*/
9685: pstamp(ficrespijb);
1.255 ! brouard 9686: 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 9687: i1= pow(2,cptcoveff);
1.218 brouard 9688: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9689: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9690: /* k=k+1; */
1.238 brouard 9691: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
9692: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 9693: if(i1 != 1 && TKresult[nres]!= k)
1.238 brouard 9694: continue;
9695: fprintf(ficrespijb,"\n#****** ");
9696: for(j=1;j<=cptcoveff;j++)
9697: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9698: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9699: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9700: }
9701: fprintf(ficrespijb,"******\n");
9702: if(invalidvarcomb[k]){
9703: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
9704: continue;
9705: }
9706:
9707: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
9708: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
9709: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
9710: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9711: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
9712:
9713: /* nhstepm=nhstepm*YEARM; aff par mois*/
9714:
9715: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9716: /* oldm=oldms;savm=savms; */
9717: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
9718: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
9719: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
1.255 ! brouard 9720: fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
1.217 brouard 9721: for(i=1; i<=nlstate;i++)
9722: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 9723: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 9724: fprintf(ficrespijb,"\n");
1.238 brouard 9725: for (h=0; h<=nhstepm; h++){
9726: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9727: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
9728: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
9729: for(i=1; i<=nlstate;i++)
9730: for(j=1; j<=nlstate+ndeath;j++)
9731: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
9732: fprintf(ficrespijb,"\n");
9733: }
9734: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9735: fprintf(ficrespijb,"\n");
9736: } /* end age deb */
9737: } /* end combination */
9738: } /* end nres */
1.218 brouard 9739: return 0;
9740: } /* hBijx */
1.217 brouard 9741:
1.180 brouard 9742:
1.136 brouard 9743: /***********************************************/
9744: /**************** Main Program *****************/
9745: /***********************************************/
9746:
9747: int main(int argc, char *argv[])
9748: {
9749: #ifdef GSL
9750: const gsl_multimin_fminimizer_type *T;
9751: size_t iteri = 0, it;
9752: int rval = GSL_CONTINUE;
9753: int status = GSL_SUCCESS;
9754: double ssval;
9755: #endif
9756: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 9757: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 9758: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 9759: int jj, ll, li, lj, lk;
1.136 brouard 9760: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 9761: int num_filled;
1.136 brouard 9762: int itimes;
9763: int NDIM=2;
9764: int vpopbased=0;
1.235 brouard 9765: int nres=0;
1.136 brouard 9766:
1.164 brouard 9767: char ca[32], cb[32];
1.136 brouard 9768: /* FILE *fichtm; *//* Html File */
9769: /* FILE *ficgp;*/ /*Gnuplot File */
9770: struct stat info;
1.191 brouard 9771: double agedeb=0.;
1.194 brouard 9772:
9773: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 9774: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 9775:
1.165 brouard 9776: double fret;
1.191 brouard 9777: double dum=0.; /* Dummy variable */
1.136 brouard 9778: double ***p3mat;
1.218 brouard 9779: /* double ***mobaverage; */
1.164 brouard 9780:
9781: char line[MAXLINE];
1.197 brouard 9782: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
9783:
1.234 brouard 9784: char modeltemp[MAXLINE];
1.230 brouard 9785: char resultline[MAXLINE];
9786:
1.136 brouard 9787: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 9788: char *tok, *val; /* pathtot */
1.136 brouard 9789: int firstobs=1, lastobs=10;
1.195 brouard 9790: int c, h , cpt, c2;
1.191 brouard 9791: int jl=0;
9792: int i1, j1, jk, stepsize=0;
1.194 brouard 9793: int count=0;
9794:
1.164 brouard 9795: int *tab;
1.136 brouard 9796: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 9797: int backcast=0;
1.136 brouard 9798: int mobilav=0,popforecast=0;
1.191 brouard 9799: int hstepm=0, nhstepm=0;
1.136 brouard 9800: int agemortsup;
9801: float sumlpop=0.;
9802: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
9803: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
9804:
1.191 brouard 9805: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 9806: double ftolpl=FTOL;
9807: double **prlim;
1.217 brouard 9808: double **bprlim;
1.136 brouard 9809: double ***param; /* Matrix of parameters */
1.251 brouard 9810: double ***paramstart; /* Matrix of starting parameter values */
9811: double *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
1.136 brouard 9812: double **matcov; /* Matrix of covariance */
1.203 brouard 9813: double **hess; /* Hessian matrix */
1.136 brouard 9814: double ***delti3; /* Scale */
9815: double *delti; /* Scale */
9816: double ***eij, ***vareij;
9817: double **varpl; /* Variances of prevalence limits by age */
9818: double *epj, vepp;
1.164 brouard 9819:
1.136 brouard 9820: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 9821: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
9822:
1.136 brouard 9823: double **ximort;
1.145 brouard 9824: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 9825: int *dcwave;
9826:
1.164 brouard 9827: char z[1]="c";
1.136 brouard 9828:
9829: /*char *strt;*/
9830: char strtend[80];
1.126 brouard 9831:
1.164 brouard 9832:
1.126 brouard 9833: /* setlocale (LC_ALL, ""); */
9834: /* bindtextdomain (PACKAGE, LOCALEDIR); */
9835: /* textdomain (PACKAGE); */
9836: /* setlocale (LC_CTYPE, ""); */
9837: /* setlocale (LC_MESSAGES, ""); */
9838:
9839: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 9840: rstart_time = time(NULL);
9841: /* (void) gettimeofday(&start_time,&tzp);*/
9842: start_time = *localtime(&rstart_time);
1.126 brouard 9843: curr_time=start_time;
1.157 brouard 9844: /*tml = *localtime(&start_time.tm_sec);*/
9845: /* strcpy(strstart,asctime(&tml)); */
9846: strcpy(strstart,asctime(&start_time));
1.126 brouard 9847:
9848: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 9849: /* tp.tm_sec = tp.tm_sec +86400; */
9850: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 9851: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
9852: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
9853: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 9854: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 9855: /* strt=asctime(&tmg); */
9856: /* printf("Time(after) =%s",strstart); */
9857: /* (void) time (&time_value);
9858: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
9859: * tm = *localtime(&time_value);
9860: * strstart=asctime(&tm);
9861: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
9862: */
9863:
9864: nberr=0; /* Number of errors and warnings */
9865: nbwarn=0;
1.184 brouard 9866: #ifdef WIN32
9867: _getcwd(pathcd, size);
9868: #else
1.126 brouard 9869: getcwd(pathcd, size);
1.184 brouard 9870: #endif
1.191 brouard 9871: syscompilerinfo(0);
1.196 brouard 9872: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 9873: if(argc <=1){
9874: printf("\nEnter the parameter file name: ");
1.205 brouard 9875: if(!fgets(pathr,FILENAMELENGTH,stdin)){
9876: printf("ERROR Empty parameter file name\n");
9877: goto end;
9878: }
1.126 brouard 9879: i=strlen(pathr);
9880: if(pathr[i-1]=='\n')
9881: pathr[i-1]='\0';
1.156 brouard 9882: i=strlen(pathr);
1.205 brouard 9883: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 9884: pathr[i-1]='\0';
1.205 brouard 9885: }
9886: i=strlen(pathr);
9887: if( i==0 ){
9888: printf("ERROR Empty parameter file name\n");
9889: goto end;
9890: }
9891: for (tok = pathr; tok != NULL; ){
1.126 brouard 9892: printf("Pathr |%s|\n",pathr);
9893: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
9894: printf("val= |%s| pathr=%s\n",val,pathr);
9895: strcpy (pathtot, val);
9896: if(pathr[0] == '\0') break; /* Dirty */
9897: }
9898: }
9899: else{
9900: strcpy(pathtot,argv[1]);
9901: }
9902: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
9903: /*cygwin_split_path(pathtot,path,optionfile);
9904: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
9905: /* cutv(path,optionfile,pathtot,'\\');*/
9906:
9907: /* Split argv[0], imach program to get pathimach */
9908: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
9909: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9910: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9911: /* strcpy(pathimach,argv[0]); */
9912: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
9913: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
9914: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 9915: #ifdef WIN32
9916: _chdir(path); /* Can be a relative path */
9917: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
9918: #else
1.126 brouard 9919: chdir(path); /* Can be a relative path */
1.184 brouard 9920: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
9921: #endif
9922: printf("Current directory %s!\n",pathcd);
1.126 brouard 9923: strcpy(command,"mkdir ");
9924: strcat(command,optionfilefiname);
9925: if((outcmd=system(command)) != 0){
1.169 brouard 9926: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 9927: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
9928: /* fclose(ficlog); */
9929: /* exit(1); */
9930: }
9931: /* if((imk=mkdir(optionfilefiname))<0){ */
9932: /* perror("mkdir"); */
9933: /* } */
9934:
9935: /*-------- arguments in the command line --------*/
9936:
1.186 brouard 9937: /* Main Log file */
1.126 brouard 9938: strcat(filelog, optionfilefiname);
9939: strcat(filelog,".log"); /* */
9940: if((ficlog=fopen(filelog,"w"))==NULL) {
9941: printf("Problem with logfile %s\n",filelog);
9942: goto end;
9943: }
9944: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 9945: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 9946: fprintf(ficlog,"\nEnter the parameter file name: \n");
9947: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
9948: path=%s \n\
9949: optionfile=%s\n\
9950: optionfilext=%s\n\
1.156 brouard 9951: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 9952:
1.197 brouard 9953: syscompilerinfo(1);
1.167 brouard 9954:
1.126 brouard 9955: printf("Local time (at start):%s",strstart);
9956: fprintf(ficlog,"Local time (at start): %s",strstart);
9957: fflush(ficlog);
9958: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 9959: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 9960:
9961: /* */
9962: strcpy(fileres,"r");
9963: strcat(fileres, optionfilefiname);
1.201 brouard 9964: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9965: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9966: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9967:
1.186 brouard 9968: /* Main ---------arguments file --------*/
1.126 brouard 9969:
9970: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9971: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9972: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9973: fflush(ficlog);
1.149 brouard 9974: /* goto end; */
9975: exit(70);
1.126 brouard 9976: }
9977:
9978:
9979:
9980: strcpy(filereso,"o");
1.201 brouard 9981: strcat(filereso,fileresu);
1.126 brouard 9982: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9983: printf("Problem with Output resultfile: %s\n", filereso);
9984: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9985: fflush(ficlog);
9986: goto end;
9987: }
9988:
9989: /* Reads comments: lines beginning with '#' */
9990: numlinepar=0;
1.197 brouard 9991:
9992: /* First parameter line */
9993: while(fgets(line, MAXLINE, ficpar)) {
9994: /* If line starts with a # it is a comment */
9995: if (line[0] == '#') {
9996: numlinepar++;
9997: fputs(line,stdout);
9998: fputs(line,ficparo);
9999: fputs(line,ficlog);
10000: continue;
10001: }else
10002: break;
10003: }
10004: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
10005: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
10006: if (num_filled != 5) {
10007: printf("Should be 5 parameters\n");
10008: }
1.126 brouard 10009: numlinepar++;
1.197 brouard 10010: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
10011: }
10012: /* Second parameter line */
10013: while(fgets(line, MAXLINE, ficpar)) {
10014: /* If line starts with a # it is a comment */
10015: if (line[0] == '#') {
10016: numlinepar++;
10017: fputs(line,stdout);
10018: fputs(line,ficparo);
10019: fputs(line,ficlog);
10020: continue;
10021: }else
10022: break;
10023: }
1.223 brouard 10024: 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", \
10025: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
10026: if (num_filled != 11) {
10027: 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 10028: printf("but line=%s\n",line);
1.197 brouard 10029: }
1.223 brouard 10030: 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 10031: }
1.203 brouard 10032: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 10033: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 10034: /* Third parameter line */
10035: while(fgets(line, MAXLINE, ficpar)) {
10036: /* If line starts with a # it is a comment */
10037: if (line[0] == '#') {
10038: numlinepar++;
10039: fputs(line,stdout);
10040: fputs(line,ficparo);
10041: fputs(line,ficlog);
10042: continue;
10043: }else
10044: break;
10045: }
1.201 brouard 10046: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
10047: if (num_filled == 0)
10048: model[0]='\0';
10049: else if (num_filled != 1){
1.197 brouard 10050: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
10051: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
10052: model[0]='\0';
10053: goto end;
10054: }
10055: else{
10056: if (model[0]=='+'){
10057: for(i=1; i<=strlen(model);i++)
10058: modeltemp[i-1]=model[i];
1.201 brouard 10059: strcpy(model,modeltemp);
1.197 brouard 10060: }
10061: }
1.199 brouard 10062: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 10063: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 10064: }
10065: /* 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); */
10066: /* numlinepar=numlinepar+3; /\* In general *\/ */
10067: /* 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 10068: 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);
10069: 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 10070: fflush(ficlog);
1.190 brouard 10071: /* if(model[0]=='#'|| model[0]== '\0'){ */
10072: if(model[0]=='#'){
1.187 brouard 10073: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
10074: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
10075: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
10076: if(mle != -1){
10077: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
10078: exit(1);
10079: }
10080: }
1.126 brouard 10081: while((c=getc(ficpar))=='#' && c!= EOF){
10082: ungetc(c,ficpar);
10083: fgets(line, MAXLINE, ficpar);
10084: numlinepar++;
1.195 brouard 10085: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
10086: z[0]=line[1];
10087: }
10088: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 10089: fputs(line, stdout);
10090: //puts(line);
1.126 brouard 10091: fputs(line,ficparo);
10092: fputs(line,ficlog);
10093: }
10094: ungetc(c,ficpar);
10095:
10096:
1.145 brouard 10097: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 10098: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
1.233 brouard 10099: cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.225 brouard 10100: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 10101: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
10102: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
10103: v1+v2*age+v2*v3 makes cptcovn = 3
10104: */
10105: if (strlen(model)>1)
1.187 brouard 10106: 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 10107: else
1.187 brouard 10108: ncovmodel=2; /* Constant and age */
1.133 brouard 10109: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
10110: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 10111: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
10112: 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);
10113: 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);
10114: fflush(stdout);
10115: fclose (ficlog);
10116: goto end;
10117: }
1.126 brouard 10118: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
10119: delti=delti3[1][1];
10120: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
10121: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
1.247 brouard 10122: /* We could also provide initial parameters values giving by simple logistic regression
10123: * only one way, that is without matrix product. We will have nlstate maximizations */
10124: /* for(i=1;i<nlstate;i++){ */
10125: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
10126: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
10127: /* } */
1.126 brouard 10128: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 10129: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
10130: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 10131: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10132: fclose (ficparo);
10133: fclose (ficlog);
10134: goto end;
10135: exit(0);
1.220 brouard 10136: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 10137: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 10138: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
10139: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 10140: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
10141: matcov=matrix(1,npar,1,npar);
1.203 brouard 10142: hess=matrix(1,npar,1,npar);
1.220 brouard 10143: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 10144: /* Read guessed parameters */
1.126 brouard 10145: /* Reads comments: lines beginning with '#' */
10146: while((c=getc(ficpar))=='#' && c!= EOF){
10147: ungetc(c,ficpar);
10148: fgets(line, MAXLINE, ficpar);
10149: numlinepar++;
1.141 brouard 10150: fputs(line,stdout);
1.126 brouard 10151: fputs(line,ficparo);
10152: fputs(line,ficlog);
10153: }
10154: ungetc(c,ficpar);
10155:
10156: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.251 brouard 10157: paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
1.126 brouard 10158: for(i=1; i <=nlstate; i++){
1.234 brouard 10159: j=0;
1.126 brouard 10160: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 10161: if(jj==i) continue;
10162: j++;
10163: fscanf(ficpar,"%1d%1d",&i1,&j1);
10164: if ((i1 != i) || (j1 != jj)){
10165: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 10166: It might be a problem of design; if ncovcol and the model are correct\n \
10167: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 10168: exit(1);
10169: }
10170: fprintf(ficparo,"%1d%1d",i1,j1);
10171: if(mle==1)
10172: printf("%1d%1d",i,jj);
10173: fprintf(ficlog,"%1d%1d",i,jj);
10174: for(k=1; k<=ncovmodel;k++){
10175: fscanf(ficpar," %lf",¶m[i][j][k]);
10176: if(mle==1){
10177: printf(" %lf",param[i][j][k]);
10178: fprintf(ficlog," %lf",param[i][j][k]);
10179: }
10180: else
10181: fprintf(ficlog," %lf",param[i][j][k]);
10182: fprintf(ficparo," %lf",param[i][j][k]);
10183: }
10184: fscanf(ficpar,"\n");
10185: numlinepar++;
10186: if(mle==1)
10187: printf("\n");
10188: fprintf(ficlog,"\n");
10189: fprintf(ficparo,"\n");
1.126 brouard 10190: }
10191: }
10192: fflush(ficlog);
1.234 brouard 10193:
1.251 brouard 10194: /* Reads parameters values */
1.126 brouard 10195: p=param[1][1];
1.251 brouard 10196: pstart=paramstart[1][1];
1.126 brouard 10197:
10198: /* Reads comments: lines beginning with '#' */
10199: while((c=getc(ficpar))=='#' && c!= EOF){
10200: ungetc(c,ficpar);
10201: fgets(line, MAXLINE, ficpar);
10202: numlinepar++;
1.141 brouard 10203: fputs(line,stdout);
1.126 brouard 10204: fputs(line,ficparo);
10205: fputs(line,ficlog);
10206: }
10207: ungetc(c,ficpar);
10208:
10209: for(i=1; i <=nlstate; i++){
10210: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 10211: fscanf(ficpar,"%1d%1d",&i1,&j1);
10212: if ( (i1-i) * (j1-j) != 0){
10213: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
10214: exit(1);
10215: }
10216: printf("%1d%1d",i,j);
10217: fprintf(ficparo,"%1d%1d",i1,j1);
10218: fprintf(ficlog,"%1d%1d",i1,j1);
10219: for(k=1; k<=ncovmodel;k++){
10220: fscanf(ficpar,"%le",&delti3[i][j][k]);
10221: printf(" %le",delti3[i][j][k]);
10222: fprintf(ficparo," %le",delti3[i][j][k]);
10223: fprintf(ficlog," %le",delti3[i][j][k]);
10224: }
10225: fscanf(ficpar,"\n");
10226: numlinepar++;
10227: printf("\n");
10228: fprintf(ficparo,"\n");
10229: fprintf(ficlog,"\n");
1.126 brouard 10230: }
10231: }
10232: fflush(ficlog);
1.234 brouard 10233:
1.145 brouard 10234: /* Reads covariance matrix */
1.126 brouard 10235: delti=delti3[1][1];
1.220 brouard 10236:
10237:
1.126 brouard 10238: /* 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 10239:
1.126 brouard 10240: /* Reads comments: lines beginning with '#' */
10241: while((c=getc(ficpar))=='#' && c!= EOF){
10242: ungetc(c,ficpar);
10243: fgets(line, MAXLINE, ficpar);
10244: numlinepar++;
1.141 brouard 10245: fputs(line,stdout);
1.126 brouard 10246: fputs(line,ficparo);
10247: fputs(line,ficlog);
10248: }
10249: ungetc(c,ficpar);
1.220 brouard 10250:
1.126 brouard 10251: matcov=matrix(1,npar,1,npar);
1.203 brouard 10252: hess=matrix(1,npar,1,npar);
1.131 brouard 10253: for(i=1; i <=npar; i++)
10254: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 10255:
1.194 brouard 10256: /* Scans npar lines */
1.126 brouard 10257: for(i=1; i <=npar; i++){
1.226 brouard 10258: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 10259: if(count != 3){
1.226 brouard 10260: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 10261: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
10262: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 10263: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 10264: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
10265: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 10266: exit(1);
1.220 brouard 10267: }else{
1.226 brouard 10268: if(mle==1)
10269: printf("%1d%1d%d",i1,j1,jk);
10270: }
10271: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
10272: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 10273: for(j=1; j <=i; j++){
1.226 brouard 10274: fscanf(ficpar," %le",&matcov[i][j]);
10275: if(mle==1){
10276: printf(" %.5le",matcov[i][j]);
10277: }
10278: fprintf(ficlog," %.5le",matcov[i][j]);
10279: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 10280: }
10281: fscanf(ficpar,"\n");
10282: numlinepar++;
10283: if(mle==1)
1.220 brouard 10284: printf("\n");
1.126 brouard 10285: fprintf(ficlog,"\n");
10286: fprintf(ficparo,"\n");
10287: }
1.194 brouard 10288: /* End of read covariance matrix npar lines */
1.126 brouard 10289: for(i=1; i <=npar; i++)
10290: for(j=i+1;j<=npar;j++)
1.226 brouard 10291: matcov[i][j]=matcov[j][i];
1.126 brouard 10292:
10293: if(mle==1)
10294: printf("\n");
10295: fprintf(ficlog,"\n");
10296:
10297: fflush(ficlog);
10298:
10299: /*-------- Rewriting parameter file ----------*/
10300: strcpy(rfileres,"r"); /* "Rparameterfile */
10301: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
10302: strcat(rfileres,"."); /* */
10303: strcat(rfileres,optionfilext); /* Other files have txt extension */
10304: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 10305: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
10306: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 10307: }
10308: fprintf(ficres,"#%s\n",version);
10309: } /* End of mle != -3 */
1.218 brouard 10310:
1.186 brouard 10311: /* Main data
10312: */
1.126 brouard 10313: n= lastobs;
10314: num=lvector(1,n);
10315: moisnais=vector(1,n);
10316: annais=vector(1,n);
10317: moisdc=vector(1,n);
10318: andc=vector(1,n);
1.220 brouard 10319: weight=vector(1,n);
1.126 brouard 10320: agedc=vector(1,n);
10321: cod=ivector(1,n);
1.220 brouard 10322: for(i=1;i<=n;i++){
1.234 brouard 10323: num[i]=0;
10324: moisnais[i]=0;
10325: annais[i]=0;
10326: moisdc[i]=0;
10327: andc[i]=0;
10328: agedc[i]=0;
10329: cod[i]=0;
10330: weight[i]=1.0; /* Equal weights, 1 by default */
10331: }
1.126 brouard 10332: mint=matrix(1,maxwav,1,n);
10333: anint=matrix(1,maxwav,1,n);
1.131 brouard 10334: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 10335: tab=ivector(1,NCOVMAX);
1.144 brouard 10336: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 10337: 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 10338:
1.136 brouard 10339: /* Reads data from file datafile */
10340: if (readdata(datafile, firstobs, lastobs, &imx)==1)
10341: goto end;
10342:
10343: /* Calculation of the number of parameters from char model */
1.234 brouard 10344: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 10345: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
10346: k=3 V4 Tvar[k=3]= 4 (from V4)
10347: k=2 V1 Tvar[k=2]= 1 (from V1)
10348: k=1 Tvar[1]=2 (from V2)
1.234 brouard 10349: */
10350:
10351: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
10352: TvarsDind=ivector(1,NCOVMAX); /* */
10353: TvarsD=ivector(1,NCOVMAX); /* */
10354: TvarsQind=ivector(1,NCOVMAX); /* */
10355: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 10356: TvarF=ivector(1,NCOVMAX); /* */
10357: TvarFind=ivector(1,NCOVMAX); /* */
10358: TvarV=ivector(1,NCOVMAX); /* */
10359: TvarVind=ivector(1,NCOVMAX); /* */
10360: TvarA=ivector(1,NCOVMAX); /* */
10361: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 10362: TvarFD=ivector(1,NCOVMAX); /* */
10363: TvarFDind=ivector(1,NCOVMAX); /* */
10364: TvarFQ=ivector(1,NCOVMAX); /* */
10365: TvarFQind=ivector(1,NCOVMAX); /* */
10366: TvarVD=ivector(1,NCOVMAX); /* */
10367: TvarVDind=ivector(1,NCOVMAX); /* */
10368: TvarVQ=ivector(1,NCOVMAX); /* */
10369: TvarVQind=ivector(1,NCOVMAX); /* */
10370:
1.230 brouard 10371: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 10372: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 10373: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
10374: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
10375: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 10376: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
10377: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
10378: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
10379: */
10380: /* For model-covariate k tells which data-covariate to use but
10381: because this model-covariate is a construction we invent a new column
10382: ncovcol + k1
10383: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
10384: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 10385: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
10386: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 10387: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
10388: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 10389: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 10390: */
1.145 brouard 10391: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
10392: 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 10393: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
10394: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 10395: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 10396: 4 covariates (3 plus signs)
10397: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
10398: */
1.230 brouard 10399: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 10400: * individual dummy, fixed or varying:
10401: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
10402: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 10403: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
10404: * V1 df, V2 qf, V3 & V4 dv, V5 qv
10405: * Tmodelind[1]@9={9,0,3,2,}*/
10406: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
10407: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 10408: * individual quantitative, fixed or varying:
10409: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
10410: * 3, 1, 0, 0, 0, 0, 0, 0},
10411: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 10412: /* Main decodemodel */
10413:
1.187 brouard 10414:
1.223 brouard 10415: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 10416: goto end;
10417:
1.137 brouard 10418: if((double)(lastobs-imx)/(double)imx > 1.10){
10419: nbwarn++;
10420: 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);
10421: 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);
10422: }
1.136 brouard 10423: /* if(mle==1){*/
1.137 brouard 10424: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
10425: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 10426: }
10427:
10428: /*-calculation of age at interview from date of interview and age at death -*/
10429: agev=matrix(1,maxwav,1,imx);
10430:
10431: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
10432: goto end;
10433:
1.126 brouard 10434:
1.136 brouard 10435: agegomp=(int)agemin;
10436: free_vector(moisnais,1,n);
10437: free_vector(annais,1,n);
1.126 brouard 10438: /* free_matrix(mint,1,maxwav,1,n);
10439: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 10440: /* free_vector(moisdc,1,n); */
10441: /* free_vector(andc,1,n); */
1.145 brouard 10442: /* */
10443:
1.126 brouard 10444: wav=ivector(1,imx);
1.214 brouard 10445: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
10446: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
10447: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
10448: 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.*/
10449: bh=imatrix(1,lastpass-firstpass+2,1,imx);
10450: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 10451:
10452: /* Concatenates waves */
1.214 brouard 10453: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
10454: Death is a valid wave (if date is known).
10455: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
10456: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
10457: and mw[mi+1][i]. dh depends on stepm.
10458: */
10459:
1.126 brouard 10460: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.248 brouard 10461: /* Concatenates waves */
1.145 brouard 10462:
1.215 brouard 10463: free_vector(moisdc,1,n);
10464: free_vector(andc,1,n);
10465:
1.126 brouard 10466: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
10467: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
10468: ncodemax[1]=1;
1.145 brouard 10469: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 10470: cptcoveff=0;
1.220 brouard 10471: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
10472: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 10473: }
10474:
10475: ncovcombmax=pow(2,cptcoveff);
10476: invalidvarcomb=ivector(1, ncovcombmax);
10477: for(i=1;i<ncovcombmax;i++)
10478: invalidvarcomb[i]=0;
10479:
1.211 brouard 10480: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 10481: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 10482: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 10483:
1.200 brouard 10484: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 10485: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 10486: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 10487: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
10488: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
10489: * (currently 0 or 1) in the data.
10490: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
10491: * corresponding modality (h,j).
10492: */
10493:
1.145 brouard 10494: h=0;
10495: /*if (cptcovn > 0) */
1.126 brouard 10496: m=pow(2,cptcoveff);
10497:
1.144 brouard 10498: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 10499: * For k=4 covariates, h goes from 1 to m=2**k
10500: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
10501: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 10502: * h\k 1 2 3 4
1.143 brouard 10503: *______________________________
10504: * 1 i=1 1 i=1 1 i=1 1 i=1 1
10505: * 2 2 1 1 1
10506: * 3 i=2 1 2 1 1
10507: * 4 2 2 1 1
10508: * 5 i=3 1 i=2 1 2 1
10509: * 6 2 1 2 1
10510: * 7 i=4 1 2 2 1
10511: * 8 2 2 2 1
1.197 brouard 10512: * 9 i=5 1 i=3 1 i=2 1 2
10513: * 10 2 1 1 2
10514: * 11 i=6 1 2 1 2
10515: * 12 2 2 1 2
10516: * 13 i=7 1 i=4 1 2 2
10517: * 14 2 1 2 2
10518: * 15 i=8 1 2 2 2
10519: * 16 2 2 2 2
1.143 brouard 10520: */
1.212 brouard 10521: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 10522: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
10523: * and the value of each covariate?
10524: * V1=1, V2=1, V3=2, V4=1 ?
10525: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
10526: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
10527: * In order to get the real value in the data, we use nbcode
10528: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
10529: * We are keeping this crazy system in order to be able (in the future?)
10530: * to have more than 2 values (0 or 1) for a covariate.
10531: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
10532: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
10533: * bbbbbbbb
10534: * 76543210
10535: * h-1 00000101 (6-1=5)
1.219 brouard 10536: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 10537: * &
10538: * 1 00000001 (1)
1.219 brouard 10539: * 00000000 = 1 & ((h-1) >> (k-1))
10540: * +1= 00000001 =1
1.211 brouard 10541: *
10542: * h=14, k=3 => h'=h-1=13, k'=k-1=2
10543: * h' 1101 =2^3+2^2+0x2^1+2^0
10544: * >>k' 11
10545: * & 00000001
10546: * = 00000001
10547: * +1 = 00000010=2 = codtabm(14,3)
10548: * Reverse h=6 and m=16?
10549: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
10550: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
10551: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
10552: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
10553: * V3=decodtabm(14,3,2**4)=2
10554: * h'=13 1101 =2^3+2^2+0x2^1+2^0
10555: *(h-1) >> (j-1) 0011 =13 >> 2
10556: * &1 000000001
10557: * = 000000001
10558: * +1= 000000010 =2
10559: * 2211
10560: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
10561: * V3=2
1.220 brouard 10562: * codtabm and decodtabm are identical
1.211 brouard 10563: */
10564:
1.145 brouard 10565:
10566: free_ivector(Ndum,-1,NCOVMAX);
10567:
10568:
1.126 brouard 10569:
1.186 brouard 10570: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 10571: strcpy(optionfilegnuplot,optionfilefiname);
10572: if(mle==-3)
1.201 brouard 10573: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 10574: strcat(optionfilegnuplot,".gp");
10575:
10576: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
10577: printf("Problem with file %s",optionfilegnuplot);
10578: }
10579: else{
1.204 brouard 10580: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 10581: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 10582: //fprintf(ficgp,"set missing 'NaNq'\n");
10583: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 10584: }
10585: /* fclose(ficgp);*/
1.186 brouard 10586:
10587:
10588: /* Initialisation of --------- index.htm --------*/
1.126 brouard 10589:
10590: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
10591: if(mle==-3)
1.201 brouard 10592: strcat(optionfilehtm,"-MORT_");
1.126 brouard 10593: strcat(optionfilehtm,".htm");
10594: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 10595: printf("Problem with %s \n",optionfilehtm);
10596: exit(0);
1.126 brouard 10597: }
10598:
10599: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
10600: strcat(optionfilehtmcov,"-cov.htm");
10601: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
10602: printf("Problem with %s \n",optionfilehtmcov), exit(0);
10603: }
10604: else{
10605: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
10606: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10607: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 10608: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
10609: }
10610:
1.213 brouard 10611: 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 10612: <hr size=\"2\" color=\"#EC5E5E\"> \n\
10613: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 10614: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10615: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 10616: \n\
10617: <hr size=\"2\" color=\"#EC5E5E\">\
10618: <ul><li><h4>Parameter files</h4>\n\
10619: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
10620: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
10621: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
10622: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
10623: - Date and time at start: %s</ul>\n",\
10624: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
10625: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
10626: fileres,fileres,\
10627: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
10628: fflush(fichtm);
10629:
10630: strcpy(pathr,path);
10631: strcat(pathr,optionfilefiname);
1.184 brouard 10632: #ifdef WIN32
10633: _chdir(optionfilefiname); /* Move to directory named optionfile */
10634: #else
1.126 brouard 10635: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 10636: #endif
10637:
1.126 brouard 10638:
1.220 brouard 10639: /* Calculates basic frequencies. Computes observed prevalence at single age
10640: and for any valid combination of covariates
1.126 brouard 10641: and prints on file fileres'p'. */
1.251 brouard 10642: freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.227 brouard 10643: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 10644:
10645: fprintf(fichtm,"\n");
10646: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
10647: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
10648: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
10649: imx,agemin,agemax,jmin,jmax,jmean);
10650: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 10651: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10652: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10653: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10654: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 10655:
1.126 brouard 10656: /* For Powell, parameters are in a vector p[] starting at p[1]
10657: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
10658: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
10659:
10660: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 10661: /* For mortality only */
1.126 brouard 10662: if (mle==-3){
1.136 brouard 10663: ximort=matrix(1,NDIM,1,NDIM);
1.248 brouard 10664: for(i=1;i<=NDIM;i++)
10665: for(j=1;j<=NDIM;j++)
10666: ximort[i][j]=0.;
1.186 brouard 10667: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 10668: cens=ivector(1,n);
10669: ageexmed=vector(1,n);
10670: agecens=vector(1,n);
10671: dcwave=ivector(1,n);
1.223 brouard 10672:
1.126 brouard 10673: for (i=1; i<=imx; i++){
10674: dcwave[i]=-1;
10675: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 10676: if (s[m][i]>nlstate) {
10677: dcwave[i]=m;
10678: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
10679: break;
10680: }
1.126 brouard 10681: }
1.226 brouard 10682:
1.126 brouard 10683: for (i=1; i<=imx; i++) {
10684: if (wav[i]>0){
1.226 brouard 10685: ageexmed[i]=agev[mw[1][i]][i];
10686: j=wav[i];
10687: agecens[i]=1.;
10688:
10689: if (ageexmed[i]> 1 && wav[i] > 0){
10690: agecens[i]=agev[mw[j][i]][i];
10691: cens[i]= 1;
10692: }else if (ageexmed[i]< 1)
10693: cens[i]= -1;
10694: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
10695: cens[i]=0 ;
1.126 brouard 10696: }
10697: else cens[i]=-1;
10698: }
10699:
10700: for (i=1;i<=NDIM;i++) {
10701: for (j=1;j<=NDIM;j++)
1.226 brouard 10702: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 10703: }
10704:
1.145 brouard 10705: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 10706: /*printf("%lf %lf", p[1], p[2]);*/
10707:
10708:
1.136 brouard 10709: #ifdef GSL
10710: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 10711: #else
1.126 brouard 10712: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 10713: #endif
1.201 brouard 10714: strcpy(filerespow,"POW-MORT_");
10715: strcat(filerespow,fileresu);
1.126 brouard 10716: if((ficrespow=fopen(filerespow,"w"))==NULL) {
10717: printf("Problem with resultfile: %s\n", filerespow);
10718: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
10719: }
1.136 brouard 10720: #ifdef GSL
10721: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 10722: #else
1.126 brouard 10723: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 10724: #endif
1.126 brouard 10725: /* for (i=1;i<=nlstate;i++)
10726: for(j=1;j<=nlstate+ndeath;j++)
10727: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
10728: */
10729: fprintf(ficrespow,"\n");
1.136 brouard 10730: #ifdef GSL
10731: /* gsl starts here */
10732: T = gsl_multimin_fminimizer_nmsimplex;
10733: gsl_multimin_fminimizer *sfm = NULL;
10734: gsl_vector *ss, *x;
10735: gsl_multimin_function minex_func;
10736:
10737: /* Initial vertex size vector */
10738: ss = gsl_vector_alloc (NDIM);
10739:
10740: if (ss == NULL){
10741: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
10742: }
10743: /* Set all step sizes to 1 */
10744: gsl_vector_set_all (ss, 0.001);
10745:
10746: /* Starting point */
1.126 brouard 10747:
1.136 brouard 10748: x = gsl_vector_alloc (NDIM);
10749:
10750: if (x == NULL){
10751: gsl_vector_free(ss);
10752: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
10753: }
10754:
10755: /* Initialize method and iterate */
10756: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 10757: /* gsl_vector_set(x, 0, 0.0268); */
10758: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 10759: gsl_vector_set(x, 0, p[1]);
10760: gsl_vector_set(x, 1, p[2]);
10761:
10762: minex_func.f = &gompertz_f;
10763: minex_func.n = NDIM;
10764: minex_func.params = (void *)&p; /* ??? */
10765:
10766: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
10767: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
10768:
10769: printf("Iterations beginning .....\n\n");
10770: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
10771:
10772: iteri=0;
10773: while (rval == GSL_CONTINUE){
10774: iteri++;
10775: status = gsl_multimin_fminimizer_iterate(sfm);
10776:
10777: if (status) printf("error: %s\n", gsl_strerror (status));
10778: fflush(0);
10779:
10780: if (status)
10781: break;
10782:
10783: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
10784: ssval = gsl_multimin_fminimizer_size (sfm);
10785:
10786: if (rval == GSL_SUCCESS)
10787: printf ("converged to a local maximum at\n");
10788:
10789: printf("%5d ", iteri);
10790: for (it = 0; it < NDIM; it++){
10791: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
10792: }
10793: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
10794: }
10795:
10796: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
10797:
10798: gsl_vector_free(x); /* initial values */
10799: gsl_vector_free(ss); /* inital step size */
10800: for (it=0; it<NDIM; it++){
10801: p[it+1]=gsl_vector_get(sfm->x,it);
10802: fprintf(ficrespow," %.12lf", p[it]);
10803: }
10804: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
10805: #endif
10806: #ifdef POWELL
10807: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
10808: #endif
1.126 brouard 10809: fclose(ficrespow);
10810:
1.203 brouard 10811: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 10812:
10813: for(i=1; i <=NDIM; i++)
10814: for(j=i+1;j<=NDIM;j++)
1.220 brouard 10815: matcov[i][j]=matcov[j][i];
1.126 brouard 10816:
10817: printf("\nCovariance matrix\n ");
1.203 brouard 10818: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 10819: for(i=1; i <=NDIM; i++) {
10820: for(j=1;j<=NDIM;j++){
1.220 brouard 10821: printf("%f ",matcov[i][j]);
10822: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 10823: }
1.203 brouard 10824: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 10825: }
10826:
10827: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 10828: for (i=1;i<=NDIM;i++) {
1.126 brouard 10829: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 10830: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
10831: }
1.126 brouard 10832: lsurv=vector(1,AGESUP);
10833: lpop=vector(1,AGESUP);
10834: tpop=vector(1,AGESUP);
10835: lsurv[agegomp]=100000;
10836:
10837: for (k=agegomp;k<=AGESUP;k++) {
10838: agemortsup=k;
10839: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
10840: }
10841:
10842: for (k=agegomp;k<agemortsup;k++)
10843: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
10844:
10845: for (k=agegomp;k<agemortsup;k++){
10846: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
10847: sumlpop=sumlpop+lpop[k];
10848: }
10849:
10850: tpop[agegomp]=sumlpop;
10851: for (k=agegomp;k<(agemortsup-3);k++){
10852: /* tpop[k+1]=2;*/
10853: tpop[k+1]=tpop[k]-lpop[k];
10854: }
10855:
10856:
10857: printf("\nAge lx qx dx Lx Tx e(x)\n");
10858: for (k=agegomp;k<(agemortsup-2);k++)
10859: 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]);
10860:
10861:
10862: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 10863: ageminpar=50;
10864: agemaxpar=100;
1.194 brouard 10865: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
10866: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10867: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10868: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
10869: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10870: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10871: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10872: }else{
10873: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
10874: 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 10875: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 10876: }
1.201 brouard 10877: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 10878: stepm, weightopt,\
10879: model,imx,p,matcov,agemortsup);
10880:
10881: free_vector(lsurv,1,AGESUP);
10882: free_vector(lpop,1,AGESUP);
10883: free_vector(tpop,1,AGESUP);
1.220 brouard 10884: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 10885: free_ivector(cens,1,n);
10886: free_vector(agecens,1,n);
10887: free_ivector(dcwave,1,n);
1.220 brouard 10888: #ifdef GSL
1.136 brouard 10889: #endif
1.186 brouard 10890: } /* Endof if mle==-3 mortality only */
1.205 brouard 10891: /* Standard */
10892: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
10893: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10894: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 10895: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 10896: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10897: for (k=1; k<=npar;k++)
10898: printf(" %d %8.5f",k,p[k]);
10899: printf("\n");
1.205 brouard 10900: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
10901: /* mlikeli uses func not funcone */
1.247 brouard 10902: /* for(i=1;i<nlstate;i++){ */
10903: /* /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
10904: /* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
10905: /* } */
1.205 brouard 10906: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
10907: }
10908: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
10909: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10910: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
10911: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10912: }
10913: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 10914: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10915: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10916: for (k=1; k<=npar;k++)
10917: printf(" %d %8.5f",k,p[k]);
10918: printf("\n");
10919:
10920: /*--------- results files --------------*/
1.224 brouard 10921: 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 10922:
10923:
10924: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10925: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10926: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10927: for(i=1,jk=1; i <=nlstate; i++){
10928: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 10929: if (k != i) {
10930: printf("%d%d ",i,k);
10931: fprintf(ficlog,"%d%d ",i,k);
10932: fprintf(ficres,"%1d%1d ",i,k);
10933: for(j=1; j <=ncovmodel; j++){
10934: printf("%12.7f ",p[jk]);
10935: fprintf(ficlog,"%12.7f ",p[jk]);
10936: fprintf(ficres,"%12.7f ",p[jk]);
10937: jk++;
10938: }
10939: printf("\n");
10940: fprintf(ficlog,"\n");
10941: fprintf(ficres,"\n");
10942: }
1.126 brouard 10943: }
10944: }
1.203 brouard 10945: if(mle != 0){
10946: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 10947: ftolhess=ftol; /* Usually correct */
1.203 brouard 10948: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
10949: 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");
10950: 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");
10951: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 10952: for(k=1; k <=(nlstate+ndeath); k++){
10953: if (k != i) {
10954: printf("%d%d ",i,k);
10955: fprintf(ficlog,"%d%d ",i,k);
10956: for(j=1; j <=ncovmodel; j++){
10957: 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]));
10958: 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]));
10959: jk++;
10960: }
10961: printf("\n");
10962: fprintf(ficlog,"\n");
10963: }
10964: }
1.193 brouard 10965: }
1.203 brouard 10966: } /* end of hesscov and Wald tests */
1.225 brouard 10967:
1.203 brouard 10968: /* */
1.126 brouard 10969: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
10970: printf("# Scales (for hessian or gradient estimation)\n");
10971: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
10972: for(i=1,jk=1; i <=nlstate; i++){
10973: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 10974: if (j!=i) {
10975: fprintf(ficres,"%1d%1d",i,j);
10976: printf("%1d%1d",i,j);
10977: fprintf(ficlog,"%1d%1d",i,j);
10978: for(k=1; k<=ncovmodel;k++){
10979: printf(" %.5e",delti[jk]);
10980: fprintf(ficlog," %.5e",delti[jk]);
10981: fprintf(ficres," %.5e",delti[jk]);
10982: jk++;
10983: }
10984: printf("\n");
10985: fprintf(ficlog,"\n");
10986: fprintf(ficres,"\n");
10987: }
1.126 brouard 10988: }
10989: }
10990:
10991: 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 10992: if(mle >= 1) /* To big for the screen */
1.126 brouard 10993: 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");
10994: 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");
10995: /* # 121 Var(a12)\n\ */
10996: /* # 122 Cov(b12,a12) Var(b12)\n\ */
10997: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10998: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10999: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
11000: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
11001: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
11002: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
11003:
11004:
11005: /* Just to have a covariance matrix which will be more understandable
11006: even is we still don't want to manage dictionary of variables
11007: */
11008: for(itimes=1;itimes<=2;itimes++){
11009: jj=0;
11010: for(i=1; i <=nlstate; i++){
1.225 brouard 11011: for(j=1; j <=nlstate+ndeath; j++){
11012: if(j==i) continue;
11013: for(k=1; k<=ncovmodel;k++){
11014: jj++;
11015: ca[0]= k+'a'-1;ca[1]='\0';
11016: if(itimes==1){
11017: if(mle>=1)
11018: printf("#%1d%1d%d",i,j,k);
11019: fprintf(ficlog,"#%1d%1d%d",i,j,k);
11020: fprintf(ficres,"#%1d%1d%d",i,j,k);
11021: }else{
11022: if(mle>=1)
11023: printf("%1d%1d%d",i,j,k);
11024: fprintf(ficlog,"%1d%1d%d",i,j,k);
11025: fprintf(ficres,"%1d%1d%d",i,j,k);
11026: }
11027: ll=0;
11028: for(li=1;li <=nlstate; li++){
11029: for(lj=1;lj <=nlstate+ndeath; lj++){
11030: if(lj==li) continue;
11031: for(lk=1;lk<=ncovmodel;lk++){
11032: ll++;
11033: if(ll<=jj){
11034: cb[0]= lk +'a'-1;cb[1]='\0';
11035: if(ll<jj){
11036: if(itimes==1){
11037: if(mle>=1)
11038: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11039: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11040: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
11041: }else{
11042: if(mle>=1)
11043: printf(" %.5e",matcov[jj][ll]);
11044: fprintf(ficlog," %.5e",matcov[jj][ll]);
11045: fprintf(ficres," %.5e",matcov[jj][ll]);
11046: }
11047: }else{
11048: if(itimes==1){
11049: if(mle>=1)
11050: printf(" Var(%s%1d%1d)",ca,i,j);
11051: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
11052: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
11053: }else{
11054: if(mle>=1)
11055: printf(" %.7e",matcov[jj][ll]);
11056: fprintf(ficlog," %.7e",matcov[jj][ll]);
11057: fprintf(ficres," %.7e",matcov[jj][ll]);
11058: }
11059: }
11060: }
11061: } /* end lk */
11062: } /* end lj */
11063: } /* end li */
11064: if(mle>=1)
11065: printf("\n");
11066: fprintf(ficlog,"\n");
11067: fprintf(ficres,"\n");
11068: numlinepar++;
11069: } /* end k*/
11070: } /*end j */
1.126 brouard 11071: } /* end i */
11072: } /* end itimes */
11073:
11074: fflush(ficlog);
11075: fflush(ficres);
1.225 brouard 11076: while(fgets(line, MAXLINE, ficpar)) {
11077: /* If line starts with a # it is a comment */
11078: if (line[0] == '#') {
11079: numlinepar++;
11080: fputs(line,stdout);
11081: fputs(line,ficparo);
11082: fputs(line,ficlog);
11083: continue;
11084: }else
11085: break;
11086: }
11087:
1.209 brouard 11088: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
11089: /* ungetc(c,ficpar); */
11090: /* fgets(line, MAXLINE, ficpar); */
11091: /* fputs(line,stdout); */
11092: /* fputs(line,ficparo); */
11093: /* } */
11094: /* ungetc(c,ficpar); */
1.126 brouard 11095:
11096: estepm=0;
1.209 brouard 11097: 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 11098:
11099: if (num_filled != 6) {
11100: 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);
11101: 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);
11102: goto end;
11103: }
11104: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
11105: }
11106: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
11107: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
11108:
1.209 brouard 11109: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 11110: if (estepm==0 || estepm < stepm) estepm=stepm;
11111: if (fage <= 2) {
11112: bage = ageminpar;
11113: fage = agemaxpar;
11114: }
11115:
11116: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 11117: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
11118: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 11119:
1.186 brouard 11120: /* Other stuffs, more or less useful */
1.254 brouard 11121: while(fgets(line, MAXLINE, ficpar)) {
11122: /* If line starts with a # it is a comment */
11123: if (line[0] == '#') {
11124: numlinepar++;
11125: fputs(line,stdout);
11126: fputs(line,ficparo);
11127: fputs(line,ficlog);
11128: continue;
11129: }else
11130: break;
11131: }
11132:
11133: 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){
11134:
11135: if (num_filled != 7) {
11136: 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);
11137: 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);
11138: goto end;
11139: }
11140: /* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */
11141: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
11142: 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);
11143: 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);
11144: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
11145: 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 11146: }
1.254 brouard 11147:
11148: while(fgets(line, MAXLINE, ficpar)) {
11149: /* If line starts with a # it is a comment */
11150: if (line[0] == '#') {
11151: numlinepar++;
11152: fputs(line,stdout);
11153: fputs(line,ficparo);
11154: fputs(line,ficlog);
11155: continue;
11156: }else
11157: break;
1.126 brouard 11158: }
11159:
11160:
11161: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
11162: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
11163:
1.254 brouard 11164: if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
11165: if (num_filled != 1) {
11166: 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);
11167: 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);
11168: goto end;
11169: }
11170: printf("pop_based=%d\n",popbased);
11171: fprintf(ficlog,"pop_based=%d\n",popbased);
11172: fprintf(ficparo,"pop_based=%d\n",popbased);
11173: fprintf(ficres,"pop_based=%d\n",popbased);
11174: }
11175:
11176: while(fgets(line, MAXLINE, ficpar)) {
11177: /* If line starts with a # it is a comment */
11178: if (line[0] == '#') {
11179: numlinepar++;
11180: fputs(line,stdout);
11181: fputs(line,ficparo);
11182: fputs(line,ficlog);
11183: continue;
11184: }else
11185: break;
1.126 brouard 11186: }
1.254 brouard 11187: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
11188: /* ungetc(c,ficpar); */
11189: /* fgets(line, MAXLINE, ficpar); */
11190: /* fputs(line,stdout); */
11191: /* fputs(line,ficres); */
11192: /* fputs(line,ficparo); */
11193: /* } */
11194: /* ungetc(c,ficpar); */
11195:
11196: /* fscanf(ficpar,"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); */
11197: 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){
11198: if (num_filled != 8) {
11199: 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);
11200: 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);
11201: goto end;
11202: }
11203: 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);
11204: 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);
11205: 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);
11206: 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);
1.126 brouard 11207: /* day and month of proj2 are not used but only year anproj2.*/
1.217 brouard 11208: }
1.254 brouard 11209: while(fgets(line, MAXLINE, ficpar)) {
11210: /* If line starts with a # it is a comment */
11211: if (line[0] == '#') {
11212: numlinepar++;
11213: fputs(line,stdout);
11214: fputs(line,ficparo);
11215: fputs(line,ficlog);
11216: continue;
11217: }else
11218: break;
11219: }
11220: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
11221: /* ungetc(c,ficpar); */
11222: /* fgets(line, MAXLINE, ficpar); */
11223: /* fputs(line,stdout); */
11224: /* fputs(line,ficparo); */
11225: /* fputs(line,ficres); */
11226: /* } */
11227: /* ungetc(c,ficpar); */
1.217 brouard 11228:
11229: 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);
1.254 brouard 11230: 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){
11231: if (num_filled != 8) {
11232: printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
11233: fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
11234: goto end;
11235: }
11236: 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);
11237: 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);
11238: 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);
11239: 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);
1.217 brouard 11240: /* day and month of proj2 are not used but only year anproj2.*/
1.254 brouard 11241: }
1.230 brouard 11242: /* Results */
1.235 brouard 11243: nresult=0;
1.230 brouard 11244: while(fgets(line, MAXLINE, ficpar)) {
11245: /* If line starts with a # it is a comment */
11246: if (line[0] == '#') {
11247: numlinepar++;
11248: fputs(line,stdout);
11249: fputs(line,ficparo);
11250: fputs(line,ficlog);
1.238 brouard 11251: fputs(line,ficres);
1.230 brouard 11252: continue;
11253: }else
11254: break;
11255: }
1.240 brouard 11256: if (!feof(ficpar))
1.230 brouard 11257: while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
1.240 brouard 11258: if (num_filled == 0){
1.230 brouard 11259: resultline[0]='\0';
1.253 brouard 11260: printf("Warning %d: no result line should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
1.240 brouard 11261: break;
11262: } else if (num_filled != 1){
1.253 brouard 11263: printf("ERROR %d: result line should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
1.230 brouard 11264: }
1.235 brouard 11265: nresult++; /* Sum of resultlines */
11266: printf("Result %d: result=%s\n",nresult, resultline);
11267: if(nresult > MAXRESULTLINES){
11268: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
11269: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
11270: goto end;
11271: }
11272: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.238 brouard 11273: fprintf(ficparo,"result: %s\n",resultline);
11274: fprintf(ficres,"result: %s\n",resultline);
11275: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 11276: while(fgets(line, MAXLINE, ficpar)) {
11277: /* If line starts with a # it is a comment */
11278: if (line[0] == '#') {
11279: numlinepar++;
11280: fputs(line,stdout);
11281: fputs(line,ficparo);
1.238 brouard 11282: fputs(line,ficres);
1.230 brouard 11283: fputs(line,ficlog);
11284: continue;
11285: }else
11286: break;
11287: }
11288: if (feof(ficpar))
11289: break;
11290: else{ /* Processess output results for this combination of covariate values */
11291: }
1.240 brouard 11292: } /* end while */
1.230 brouard 11293:
11294:
1.126 brouard 11295:
1.230 brouard 11296: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 11297: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 11298:
11299: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 11300: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 11301: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 11302: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11303: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 11304: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 11305: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
11306: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 11307: }else{
1.218 brouard 11308: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 11309: }
11310: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 11311: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
11312: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 11313:
1.225 brouard 11314: /*------------ free_vector -------------*/
11315: /* chdir(path); */
1.220 brouard 11316:
1.215 brouard 11317: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
11318: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
11319: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
11320: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 11321: free_lvector(num,1,n);
11322: free_vector(agedc,1,n);
11323: /*free_matrix(covar,0,NCOVMAX,1,n);*/
11324: /*free_matrix(covar,1,NCOVMAX,1,n);*/
11325: fclose(ficparo);
11326: fclose(ficres);
1.220 brouard 11327:
11328:
1.186 brouard 11329: /* Other results (useful)*/
1.220 brouard 11330:
11331:
1.126 brouard 11332: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 11333: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
11334: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 11335: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 11336: fclose(ficrespl);
11337:
11338: /*------------- h Pij x at various ages ------------*/
1.180 brouard 11339: /*#include "hpijx.h"*/
11340: hPijx(p, bage, fage);
1.145 brouard 11341: fclose(ficrespij);
1.227 brouard 11342:
1.220 brouard 11343: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 11344: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 11345: k=1;
1.126 brouard 11346: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 11347:
1.219 brouard 11348: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 11349: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 11350: for(i=1;i<=AGESUP;i++)
1.219 brouard 11351: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 11352: for(k=1;k<=ncovcombmax;k++)
11353: probs[i][j][k]=0.;
1.219 brouard 11354: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
11355: if (mobilav!=0 ||mobilavproj !=0 ) {
11356: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 11357: for(i=1;i<=AGESUP;i++)
11358: for(j=1;j<=nlstate;j++)
11359: for(k=1;k<=ncovcombmax;k++)
11360: mobaverages[i][j][k]=0.;
1.219 brouard 11361: mobaverage=mobaverages;
11362: if (mobilav!=0) {
1.235 brouard 11363: printf("Movingaveraging observed prevalence\n");
1.227 brouard 11364: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
11365: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
11366: printf(" Error in movingaverage mobilav=%d\n",mobilav);
11367: }
1.219 brouard 11368: }
11369: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
11370: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
11371: else if (mobilavproj !=0) {
1.235 brouard 11372: printf("Movingaveraging projected observed prevalence\n");
1.227 brouard 11373: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
11374: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
11375: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
11376: }
1.219 brouard 11377: }
11378: }/* end if moving average */
1.227 brouard 11379:
1.126 brouard 11380: /*---------- Forecasting ------------------*/
11381: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
11382: if(prevfcast==1){
11383: /* if(stepm ==1){*/
1.225 brouard 11384: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 11385: }
1.217 brouard 11386: if(backcast==1){
1.219 brouard 11387: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11388: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11389: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11390:
11391: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
11392:
11393: bprlim=matrix(1,nlstate,1,nlstate);
11394: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
11395: fclose(ficresplb);
11396:
1.222 brouard 11397: hBijx(p, bage, fage, mobaverage);
11398: fclose(ficrespijb);
1.219 brouard 11399: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
11400:
11401: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 11402: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 11403: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11404: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11405: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11406: }
1.217 brouard 11407:
1.186 brouard 11408:
11409: /* ------ Other prevalence ratios------------ */
1.126 brouard 11410:
1.215 brouard 11411: free_ivector(wav,1,imx);
11412: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
11413: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
11414: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 11415:
11416:
1.127 brouard 11417: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 11418:
1.201 brouard 11419: strcpy(filerese,"E_");
11420: strcat(filerese,fileresu);
1.126 brouard 11421: if((ficreseij=fopen(filerese,"w"))==NULL) {
11422: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
11423: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
11424: }
1.208 brouard 11425: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
11426: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 11427:
11428: pstamp(ficreseij);
1.219 brouard 11429:
1.235 brouard 11430: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
11431: if (cptcovn < 1){i1=1;}
11432:
11433: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11434: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 11435: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 11436: continue;
1.219 brouard 11437: fprintf(ficreseij,"\n#****** ");
1.235 brouard 11438: printf("\n#****** ");
1.225 brouard 11439: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 11440: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 11441: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11442: }
11443: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11444: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11445: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 11446: }
11447: fprintf(ficreseij,"******\n");
1.235 brouard 11448: printf("******\n");
1.219 brouard 11449:
11450: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11451: oldm=oldms;savm=savms;
1.235 brouard 11452: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 11453:
1.219 brouard 11454: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 11455: }
11456: fclose(ficreseij);
1.208 brouard 11457: printf("done evsij\n");fflush(stdout);
11458: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 11459:
1.227 brouard 11460: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 11461:
11462:
1.201 brouard 11463: strcpy(filerest,"T_");
11464: strcat(filerest,fileresu);
1.127 brouard 11465: if((ficrest=fopen(filerest,"w"))==NULL) {
11466: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
11467: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
11468: }
1.208 brouard 11469: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
11470: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 11471:
1.126 brouard 11472:
1.201 brouard 11473: strcpy(fileresstde,"STDE_");
11474: strcat(fileresstde,fileresu);
1.126 brouard 11475: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 11476: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
11477: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 11478: }
1.227 brouard 11479: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
11480: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 11481:
1.201 brouard 11482: strcpy(filerescve,"CVE_");
11483: strcat(filerescve,fileresu);
1.126 brouard 11484: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 11485: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
11486: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 11487: }
1.227 brouard 11488: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
11489: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 11490:
1.201 brouard 11491: strcpy(fileresv,"V_");
11492: strcat(fileresv,fileresu);
1.126 brouard 11493: if((ficresvij=fopen(fileresv,"w"))==NULL) {
11494: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
11495: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
11496: }
1.227 brouard 11497: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
11498: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 11499:
1.145 brouard 11500: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
11501: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
11502:
1.235 brouard 11503: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
11504: if (cptcovn < 1){i1=1;}
11505:
11506: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11507: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
1.253 brouard 11508: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 11509: continue;
1.242 brouard 11510: printf("\n#****** Result for:");
11511: fprintf(ficrest,"\n#****** Result for:");
11512: fprintf(ficlog,"\n#****** Result for:");
1.227 brouard 11513: for(j=1;j<=cptcoveff;j++){
11514: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11515: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11516: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11517: }
1.235 brouard 11518: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11519: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11520: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11521: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11522: }
1.208 brouard 11523: fprintf(ficrest,"******\n");
1.227 brouard 11524: fprintf(ficlog,"******\n");
11525: printf("******\n");
1.208 brouard 11526:
11527: fprintf(ficresstdeij,"\n#****** ");
11528: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 11529: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 11530: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11531: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 11532: }
1.235 brouard 11533: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11534: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11535: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11536: }
1.208 brouard 11537: fprintf(ficresstdeij,"******\n");
11538: fprintf(ficrescveij,"******\n");
11539:
11540: fprintf(ficresvij,"\n#****** ");
1.238 brouard 11541: /* pstamp(ficresvij); */
1.225 brouard 11542: for(j=1;j<=cptcoveff;j++)
1.227 brouard 11543: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 11544: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11545: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11546: }
1.208 brouard 11547: fprintf(ficresvij,"******\n");
11548:
11549: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11550: oldm=oldms;savm=savms;
1.235 brouard 11551: printf(" cvevsij ");
11552: fprintf(ficlog, " cvevsij ");
11553: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 11554: printf(" end cvevsij \n ");
11555: fprintf(ficlog, " end cvevsij \n ");
11556:
11557: /*
11558: */
11559: /* goto endfree; */
11560:
11561: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11562: pstamp(ficrest);
11563:
11564:
11565: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 11566: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
11567: cptcod= 0; /* To be deleted */
11568: printf("varevsij vpopbased=%d \n",vpopbased);
11569: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 11570: 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 11571: 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 ");
11572: if(vpopbased==1)
11573: 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);
11574: else
11575: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
11576: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
11577: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
11578: fprintf(ficrest,"\n");
11579: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
11580: epj=vector(1,nlstate+1);
11581: printf("Computing age specific period (stable) prevalences in each health state \n");
11582: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
11583: for(age=bage; age <=fage ;age++){
1.235 brouard 11584: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 11585: if (vpopbased==1) {
11586: if(mobilav ==0){
11587: for(i=1; i<=nlstate;i++)
11588: prlim[i][i]=probs[(int)age][i][k];
11589: }else{ /* mobilav */
11590: for(i=1; i<=nlstate;i++)
11591: prlim[i][i]=mobaverage[(int)age][i][k];
11592: }
11593: }
1.219 brouard 11594:
1.227 brouard 11595: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
11596: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
11597: /* printf(" age %4.0f ",age); */
11598: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
11599: for(i=1, epj[j]=0.;i <=nlstate;i++) {
11600: epj[j] += prlim[i][i]*eij[i][j][(int)age];
11601: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
11602: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
11603: }
11604: epj[nlstate+1] +=epj[j];
11605: }
11606: /* printf(" age %4.0f \n",age); */
1.219 brouard 11607:
1.227 brouard 11608: for(i=1, vepp=0.;i <=nlstate;i++)
11609: for(j=1;j <=nlstate;j++)
11610: vepp += vareij[i][j][(int)age];
11611: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
11612: for(j=1;j <=nlstate;j++){
11613: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
11614: }
11615: fprintf(ficrest,"\n");
11616: }
1.208 brouard 11617: } /* End vpopbased */
11618: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11619: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11620: free_vector(epj,1,nlstate+1);
1.235 brouard 11621: printf("done selection\n");fflush(stdout);
11622: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 11623:
1.145 brouard 11624: /*}*/
1.235 brouard 11625: } /* End k selection */
1.227 brouard 11626:
11627: printf("done State-specific expectancies\n");fflush(stdout);
11628: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
11629:
1.126 brouard 11630: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 11631:
1.201 brouard 11632: strcpy(fileresvpl,"VPL_");
11633: strcat(fileresvpl,fileresu);
1.126 brouard 11634: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
11635: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
11636: exit(0);
11637: }
1.208 brouard 11638: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
11639: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 11640:
1.145 brouard 11641: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
11642: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 11643:
1.235 brouard 11644: i1=pow(2,cptcoveff);
11645: if (cptcovn < 1){i1=1;}
11646:
11647: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11648: for(k=1; k<=i1;k++){
1.253 brouard 11649: if(i1 != 1 && TKresult[nres]!= k)
1.235 brouard 11650: continue;
1.227 brouard 11651: fprintf(ficresvpl,"\n#****** ");
11652: printf("\n#****** ");
11653: fprintf(ficlog,"\n#****** ");
11654: for(j=1;j<=cptcoveff;j++) {
11655: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11656: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11657: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11658: }
1.235 brouard 11659: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11660: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11661: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11662: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11663: }
1.227 brouard 11664: fprintf(ficresvpl,"******\n");
11665: printf("******\n");
11666: fprintf(ficlog,"******\n");
11667:
11668: varpl=matrix(1,nlstate,(int) bage, (int) fage);
11669: oldm=oldms;savm=savms;
1.235 brouard 11670: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
1.227 brouard 11671: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 11672: /*}*/
1.126 brouard 11673: }
1.227 brouard 11674:
1.126 brouard 11675: fclose(ficresvpl);
1.208 brouard 11676: printf("done variance-covariance of period prevalence\n");fflush(stdout);
11677: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 11678:
11679: free_vector(weight,1,n);
11680: free_imatrix(Tvard,1,NCOVMAX,1,2);
11681: free_imatrix(s,1,maxwav+1,1,n);
11682: free_matrix(anint,1,maxwav,1,n);
11683: free_matrix(mint,1,maxwav,1,n);
11684: free_ivector(cod,1,n);
11685: free_ivector(tab,1,NCOVMAX);
11686: fclose(ficresstdeij);
11687: fclose(ficrescveij);
11688: fclose(ficresvij);
11689: fclose(ficrest);
11690: fclose(ficpar);
11691:
11692:
1.126 brouard 11693: /*---------- End : free ----------------*/
1.219 brouard 11694: if (mobilav!=0 ||mobilavproj !=0)
11695: free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
1.218 brouard 11696: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 11697: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
11698: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 11699: } /* mle==-3 arrives here for freeing */
1.227 brouard 11700: /* endfree:*/
11701: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
11702: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
11703: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
11704: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
1.233 brouard 11705: free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
1.227 brouard 11706: free_matrix(coqvar,1,maxwav,1,n);
11707: free_matrix(covar,0,NCOVMAX,1,n);
11708: free_matrix(matcov,1,npar,1,npar);
11709: free_matrix(hess,1,npar,1,npar);
11710: /*free_vector(delti,1,npar);*/
11711: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11712: free_matrix(agev,1,maxwav,1,imx);
11713: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11714:
11715: free_ivector(ncodemax,1,NCOVMAX);
11716: free_ivector(ncodemaxwundef,1,NCOVMAX);
11717: free_ivector(Dummy,-1,NCOVMAX);
11718: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 11719: free_ivector(DummyV,1,NCOVMAX);
11720: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 11721: free_ivector(Typevar,-1,NCOVMAX);
11722: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 11723: free_ivector(TvarsQ,1,NCOVMAX);
11724: free_ivector(TvarsQind,1,NCOVMAX);
11725: free_ivector(TvarsD,1,NCOVMAX);
11726: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 11727: free_ivector(TvarFD,1,NCOVMAX);
11728: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 11729: free_ivector(TvarF,1,NCOVMAX);
11730: free_ivector(TvarFind,1,NCOVMAX);
11731: free_ivector(TvarV,1,NCOVMAX);
11732: free_ivector(TvarVind,1,NCOVMAX);
11733: free_ivector(TvarA,1,NCOVMAX);
11734: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 11735: free_ivector(TvarFQ,1,NCOVMAX);
11736: free_ivector(TvarFQind,1,NCOVMAX);
11737: free_ivector(TvarVD,1,NCOVMAX);
11738: free_ivector(TvarVDind,1,NCOVMAX);
11739: free_ivector(TvarVQ,1,NCOVMAX);
11740: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 11741: free_ivector(Tvarsel,1,NCOVMAX);
11742: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 11743: free_ivector(Tposprod,1,NCOVMAX);
11744: free_ivector(Tprod,1,NCOVMAX);
11745: free_ivector(Tvaraff,1,NCOVMAX);
11746: free_ivector(invalidvarcomb,1,ncovcombmax);
11747: free_ivector(Tage,1,NCOVMAX);
11748: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 11749: free_ivector(TmodelInvind,1,NCOVMAX);
11750: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 11751:
11752: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
11753: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 11754: fflush(fichtm);
11755: fflush(ficgp);
11756:
1.227 brouard 11757:
1.126 brouard 11758: if((nberr >0) || (nbwarn>0)){
1.216 brouard 11759: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
11760: 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 11761: }else{
11762: printf("End of Imach\n");
11763: fprintf(ficlog,"End of Imach\n");
11764: }
11765: printf("See log file on %s\n",filelog);
11766: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 11767: /*(void) gettimeofday(&end_time,&tzp);*/
11768: rend_time = time(NULL);
11769: end_time = *localtime(&rend_time);
11770: /* tml = *localtime(&end_time.tm_sec); */
11771: strcpy(strtend,asctime(&end_time));
1.126 brouard 11772: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
11773: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 11774: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 11775:
1.157 brouard 11776: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
11777: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
11778: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 11779: /* printf("Total time was %d uSec.\n", total_usecs);*/
11780: /* if(fileappend(fichtm,optionfilehtm)){ */
11781: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11782: fclose(fichtm);
11783: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11784: fclose(fichtmcov);
11785: fclose(ficgp);
11786: fclose(ficlog);
11787: /*------ End -----------*/
1.227 brouard 11788:
11789:
11790: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 11791: #ifdef WIN32
1.227 brouard 11792: if (_chdir(pathcd) != 0)
11793: printf("Can't move to directory %s!\n",path);
11794: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 11795: #else
1.227 brouard 11796: if(chdir(pathcd) != 0)
11797: printf("Can't move to directory %s!\n", path);
11798: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 11799: #endif
1.126 brouard 11800: printf("Current directory %s!\n",pathcd);
11801: /*strcat(plotcmd,CHARSEPARATOR);*/
11802: sprintf(plotcmd,"gnuplot");
1.157 brouard 11803: #ifdef _WIN32
1.126 brouard 11804: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
11805: #endif
11806: if(!stat(plotcmd,&info)){
1.158 brouard 11807: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11808: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 11809: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 11810: }else
11811: strcpy(pplotcmd,plotcmd);
1.157 brouard 11812: #ifdef __unix
1.126 brouard 11813: strcpy(plotcmd,GNUPLOTPROGRAM);
11814: if(!stat(plotcmd,&info)){
1.158 brouard 11815: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11816: }else
11817: strcpy(pplotcmd,plotcmd);
11818: #endif
11819: }else
11820: strcpy(pplotcmd,plotcmd);
11821:
11822: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 11823: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 11824:
1.126 brouard 11825: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 11826: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 11827: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 11828: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 11829: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 11830: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 11831: }
1.158 brouard 11832: printf(" Successful, please wait...");
1.126 brouard 11833: while (z[0] != 'q') {
11834: /* chdir(path); */
1.154 brouard 11835: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 11836: scanf("%s",z);
11837: /* if (z[0] == 'c') system("./imach"); */
11838: if (z[0] == 'e') {
1.158 brouard 11839: #ifdef __APPLE__
1.152 brouard 11840: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 11841: #elif __linux
11842: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 11843: #else
1.152 brouard 11844: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 11845: #endif
11846: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
11847: system(pplotcmd);
1.126 brouard 11848: }
11849: else if (z[0] == 'g') system(plotcmd);
11850: else if (z[0] == 'q') exit(0);
11851: }
1.227 brouard 11852: end:
1.126 brouard 11853: while (z[0] != 'q') {
1.195 brouard 11854: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 11855: scanf("%s",z);
11856: }
11857: }
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