Annotation of imach/src/imach.c, revision 1.240
1.240 ! brouard 1: /* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.240 ! brouard 4: Revision 1.239 2016/08/26 15:51:03 brouard
! 5: Summary: Improvement in Powell output in order to copy and paste
! 6:
! 7: Author:
! 8:
1.239 brouard 9: Revision 1.238 2016/08/26 14:23:35 brouard
10: Summary: Starting tests of 0.99
11:
1.238 brouard 12: Revision 1.237 2016/08/26 09:20:19 brouard
13: Summary: to valgrind
14:
1.237 brouard 15: Revision 1.236 2016/08/25 10:50:18 brouard
16: *** empty log message ***
17:
1.236 brouard 18: Revision 1.235 2016/08/25 06:59:23 brouard
19: *** empty log message ***
20:
1.235 brouard 21: Revision 1.234 2016/08/23 16:51:20 brouard
22: *** empty log message ***
23:
1.234 brouard 24: Revision 1.233 2016/08/23 07:40:50 brouard
25: Summary: not working
26:
1.233 brouard 27: Revision 1.232 2016/08/22 14:20:21 brouard
28: Summary: not working
29:
1.232 brouard 30: Revision 1.231 2016/08/22 07:17:15 brouard
31: Summary: not working
32:
1.231 brouard 33: Revision 1.230 2016/08/22 06:55:53 brouard
34: Summary: Not working
35:
1.230 brouard 36: Revision 1.229 2016/07/23 09:45:53 brouard
37: Summary: Completing for func too
38:
1.229 brouard 39: Revision 1.228 2016/07/22 17:45:30 brouard
40: Summary: Fixing some arrays, still debugging
41:
1.227 brouard 42: Revision 1.226 2016/07/12 18:42:34 brouard
43: Summary: temp
44:
1.226 brouard 45: Revision 1.225 2016/07/12 08:40:03 brouard
46: Summary: saving but not running
47:
1.225 brouard 48: Revision 1.224 2016/07/01 13:16:01 brouard
49: Summary: Fixes
50:
1.224 brouard 51: Revision 1.223 2016/02/19 09:23:35 brouard
52: Summary: temporary
53:
1.223 brouard 54: Revision 1.222 2016/02/17 08:14:50 brouard
55: Summary: Probably last 0.98 stable version 0.98r6
56:
1.222 brouard 57: Revision 1.221 2016/02/15 23:35:36 brouard
58: Summary: minor bug
59:
1.220 brouard 60: Revision 1.219 2016/02/15 00:48:12 brouard
61: *** empty log message ***
62:
1.219 brouard 63: Revision 1.218 2016/02/12 11:29:23 brouard
64: Summary: 0.99 Back projections
65:
1.218 brouard 66: Revision 1.217 2015/12/23 17:18:31 brouard
67: Summary: Experimental backcast
68:
1.217 brouard 69: Revision 1.216 2015/12/18 17:32:11 brouard
70: Summary: 0.98r4 Warning and status=-2
71:
72: Version 0.98r4 is now:
73: - displaying an error when status is -1, date of interview unknown and date of death known;
74: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
75: Older changes concerning s=-2, dating from 2005 have been supersed.
76:
1.216 brouard 77: Revision 1.215 2015/12/16 08:52:24 brouard
78: Summary: 0.98r4 working
79:
1.215 brouard 80: Revision 1.214 2015/12/16 06:57:54 brouard
81: Summary: temporary not working
82:
1.214 brouard 83: Revision 1.213 2015/12/11 18:22:17 brouard
84: Summary: 0.98r4
85:
1.213 brouard 86: Revision 1.212 2015/11/21 12:47:24 brouard
87: Summary: minor typo
88:
1.212 brouard 89: Revision 1.211 2015/11/21 12:41:11 brouard
90: Summary: 0.98r3 with some graph of projected cross-sectional
91:
92: Author: Nicolas Brouard
93:
1.211 brouard 94: Revision 1.210 2015/11/18 17:41:20 brouard
95: Summary: Start working on projected prevalences
96:
1.210 brouard 97: Revision 1.209 2015/11/17 22:12:03 brouard
98: Summary: Adding ftolpl parameter
99: Author: N Brouard
100:
101: We had difficulties to get smoothed confidence intervals. It was due
102: to the period prevalence which wasn't computed accurately. The inner
103: parameter ftolpl is now an outer parameter of the .imach parameter
104: file after estepm. If ftolpl is small 1.e-4 and estepm too,
105: computation are long.
106:
1.209 brouard 107: Revision 1.208 2015/11/17 14:31:57 brouard
108: Summary: temporary
109:
1.208 brouard 110: Revision 1.207 2015/10/27 17:36:57 brouard
111: *** empty log message ***
112:
1.207 brouard 113: Revision 1.206 2015/10/24 07:14:11 brouard
114: *** empty log message ***
115:
1.206 brouard 116: Revision 1.205 2015/10/23 15:50:53 brouard
117: Summary: 0.98r3 some clarification for graphs on likelihood contributions
118:
1.205 brouard 119: Revision 1.204 2015/10/01 16:20:26 brouard
120: Summary: Some new graphs of contribution to likelihood
121:
1.204 brouard 122: Revision 1.203 2015/09/30 17:45:14 brouard
123: Summary: looking at better estimation of the hessian
124:
125: Also a better criteria for convergence to the period prevalence And
126: therefore adding the number of years needed to converge. (The
127: prevalence in any alive state shold sum to one
128:
1.203 brouard 129: Revision 1.202 2015/09/22 19:45:16 brouard
130: Summary: Adding some overall graph on contribution to likelihood. Might change
131:
1.202 brouard 132: Revision 1.201 2015/09/15 17:34:58 brouard
133: Summary: 0.98r0
134:
135: - Some new graphs like suvival functions
136: - Some bugs fixed like model=1+age+V2.
137:
1.201 brouard 138: Revision 1.200 2015/09/09 16:53:55 brouard
139: Summary: Big bug thanks to Flavia
140:
141: Even model=1+age+V2. did not work anymore
142:
1.200 brouard 143: Revision 1.199 2015/09/07 14:09:23 brouard
144: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
145:
1.199 brouard 146: Revision 1.198 2015/09/03 07:14:39 brouard
147: Summary: 0.98q5 Flavia
148:
1.198 brouard 149: Revision 1.197 2015/09/01 18:24:39 brouard
150: *** empty log message ***
151:
1.197 brouard 152: Revision 1.196 2015/08/18 23:17:52 brouard
153: Summary: 0.98q5
154:
1.196 brouard 155: Revision 1.195 2015/08/18 16:28:39 brouard
156: Summary: Adding a hack for testing purpose
157:
158: After reading the title, ftol and model lines, if the comment line has
159: a q, starting with #q, the answer at the end of the run is quit. It
160: permits to run test files in batch with ctest. The former workaround was
161: $ echo q | imach foo.imach
162:
1.195 brouard 163: Revision 1.194 2015/08/18 13:32:00 brouard
164: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
165:
1.194 brouard 166: Revision 1.193 2015/08/04 07:17:42 brouard
167: Summary: 0.98q4
168:
1.193 brouard 169: Revision 1.192 2015/07/16 16:49:02 brouard
170: Summary: Fixing some outputs
171:
1.192 brouard 172: Revision 1.191 2015/07/14 10:00:33 brouard
173: Summary: Some fixes
174:
1.191 brouard 175: Revision 1.190 2015/05/05 08:51:13 brouard
176: Summary: Adding digits in output parameters (7 digits instead of 6)
177:
178: Fix 1+age+.
179:
1.190 brouard 180: Revision 1.189 2015/04/30 14:45:16 brouard
181: Summary: 0.98q2
182:
1.189 brouard 183: Revision 1.188 2015/04/30 08:27:53 brouard
184: *** empty log message ***
185:
1.188 brouard 186: Revision 1.187 2015/04/29 09:11:15 brouard
187: *** empty log message ***
188:
1.187 brouard 189: Revision 1.186 2015/04/23 12:01:52 brouard
190: Summary: V1*age is working now, version 0.98q1
191:
192: Some codes had been disabled in order to simplify and Vn*age was
193: working in the optimization phase, ie, giving correct MLE parameters,
194: but, as usual, outputs were not correct and program core dumped.
195:
1.186 brouard 196: Revision 1.185 2015/03/11 13:26:42 brouard
197: Summary: Inclusion of compile and links command line for Intel Compiler
198:
1.185 brouard 199: Revision 1.184 2015/03/11 11:52:39 brouard
200: Summary: Back from Windows 8. Intel Compiler
201:
1.184 brouard 202: Revision 1.183 2015/03/10 20:34:32 brouard
203: Summary: 0.98q0, trying with directest, mnbrak fixed
204:
205: We use directest instead of original Powell test; probably no
206: incidence on the results, but better justifications;
207: We fixed Numerical Recipes mnbrak routine which was wrong and gave
208: wrong results.
209:
1.183 brouard 210: Revision 1.182 2015/02/12 08:19:57 brouard
211: Summary: Trying to keep directest which seems simpler and more general
212: Author: Nicolas Brouard
213:
1.182 brouard 214: Revision 1.181 2015/02/11 23:22:24 brouard
215: Summary: Comments on Powell added
216:
217: Author:
218:
1.181 brouard 219: Revision 1.180 2015/02/11 17:33:45 brouard
220: Summary: Finishing move from main to function (hpijx and prevalence_limit)
221:
1.180 brouard 222: Revision 1.179 2015/01/04 09:57:06 brouard
223: Summary: back to OS/X
224:
1.179 brouard 225: Revision 1.178 2015/01/04 09:35:48 brouard
226: *** empty log message ***
227:
1.178 brouard 228: Revision 1.177 2015/01/03 18:40:56 brouard
229: Summary: Still testing ilc32 on OSX
230:
1.177 brouard 231: Revision 1.176 2015/01/03 16:45:04 brouard
232: *** empty log message ***
233:
1.176 brouard 234: Revision 1.175 2015/01/03 16:33:42 brouard
235: *** empty log message ***
236:
1.175 brouard 237: Revision 1.174 2015/01/03 16:15:49 brouard
238: Summary: Still in cross-compilation
239:
1.174 brouard 240: Revision 1.173 2015/01/03 12:06:26 brouard
241: Summary: trying to detect cross-compilation
242:
1.173 brouard 243: Revision 1.172 2014/12/27 12:07:47 brouard
244: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
245:
1.172 brouard 246: Revision 1.171 2014/12/23 13:26:59 brouard
247: Summary: Back from Visual C
248:
249: Still problem with utsname.h on Windows
250:
1.171 brouard 251: Revision 1.170 2014/12/23 11:17:12 brouard
252: Summary: Cleaning some \%% back to %%
253:
254: The escape was mandatory for a specific compiler (which one?), but too many warnings.
255:
1.170 brouard 256: Revision 1.169 2014/12/22 23:08:31 brouard
257: Summary: 0.98p
258:
259: Outputs some informations on compiler used, OS etc. Testing on different platforms.
260:
1.169 brouard 261: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 262: Summary: update
1.169 brouard 263:
1.168 brouard 264: Revision 1.167 2014/12/22 13:50:56 brouard
265: Summary: Testing uname and compiler version and if compiled 32 or 64
266:
267: Testing on Linux 64
268:
1.167 brouard 269: Revision 1.166 2014/12/22 11:40:47 brouard
270: *** empty log message ***
271:
1.166 brouard 272: Revision 1.165 2014/12/16 11:20:36 brouard
273: Summary: After compiling on Visual C
274:
275: * imach.c (Module): Merging 1.61 to 1.162
276:
1.165 brouard 277: Revision 1.164 2014/12/16 10:52:11 brouard
278: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
279:
280: * imach.c (Module): Merging 1.61 to 1.162
281:
1.164 brouard 282: Revision 1.163 2014/12/16 10:30:11 brouard
283: * imach.c (Module): Merging 1.61 to 1.162
284:
1.163 brouard 285: Revision 1.162 2014/09/25 11:43:39 brouard
286: Summary: temporary backup 0.99!
287:
1.162 brouard 288: Revision 1.1 2014/09/16 11:06:58 brouard
289: Summary: With some code (wrong) for nlopt
290:
291: Author:
292:
293: Revision 1.161 2014/09/15 20:41:41 brouard
294: Summary: Problem with macro SQR on Intel compiler
295:
1.161 brouard 296: Revision 1.160 2014/09/02 09:24:05 brouard
297: *** empty log message ***
298:
1.160 brouard 299: Revision 1.159 2014/09/01 10:34:10 brouard
300: Summary: WIN32
301: Author: Brouard
302:
1.159 brouard 303: Revision 1.158 2014/08/27 17:11:51 brouard
304: *** empty log message ***
305:
1.158 brouard 306: Revision 1.157 2014/08/27 16:26:55 brouard
307: Summary: Preparing windows Visual studio version
308: Author: Brouard
309:
310: In order to compile on Visual studio, time.h is now correct and time_t
311: and tm struct should be used. difftime should be used but sometimes I
312: just make the differences in raw time format (time(&now).
313: Trying to suppress #ifdef LINUX
314: Add xdg-open for __linux in order to open default browser.
315:
1.157 brouard 316: Revision 1.156 2014/08/25 20:10:10 brouard
317: *** empty log message ***
318:
1.156 brouard 319: Revision 1.155 2014/08/25 18:32:34 brouard
320: Summary: New compile, minor changes
321: Author: Brouard
322:
1.155 brouard 323: Revision 1.154 2014/06/20 17:32:08 brouard
324: Summary: Outputs now all graphs of convergence to period prevalence
325:
1.154 brouard 326: Revision 1.153 2014/06/20 16:45:46 brouard
327: Summary: If 3 live state, convergence to period prevalence on same graph
328: Author: Brouard
329:
1.153 brouard 330: Revision 1.152 2014/06/18 17:54:09 brouard
331: Summary: open browser, use gnuplot on same dir than imach if not found in the path
332:
1.152 brouard 333: Revision 1.151 2014/06/18 16:43:30 brouard
334: *** empty log message ***
335:
1.151 brouard 336: Revision 1.150 2014/06/18 16:42:35 brouard
337: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
338: Author: brouard
339:
1.150 brouard 340: Revision 1.149 2014/06/18 15:51:14 brouard
341: Summary: Some fixes in parameter files errors
342: Author: Nicolas Brouard
343:
1.149 brouard 344: Revision 1.148 2014/06/17 17:38:48 brouard
345: Summary: Nothing new
346: Author: Brouard
347:
348: Just a new packaging for OS/X version 0.98nS
349:
1.148 brouard 350: Revision 1.147 2014/06/16 10:33:11 brouard
351: *** empty log message ***
352:
1.147 brouard 353: Revision 1.146 2014/06/16 10:20:28 brouard
354: Summary: Merge
355: Author: Brouard
356:
357: Merge, before building revised version.
358:
1.146 brouard 359: Revision 1.145 2014/06/10 21:23:15 brouard
360: Summary: Debugging with valgrind
361: Author: Nicolas Brouard
362:
363: Lot of changes in order to output the results with some covariates
364: After the Edimburgh REVES conference 2014, it seems mandatory to
365: improve the code.
366: No more memory valgrind error but a lot has to be done in order to
367: continue the work of splitting the code into subroutines.
368: Also, decodemodel has been improved. Tricode is still not
369: optimal. nbcode should be improved. Documentation has been added in
370: the source code.
371:
1.144 brouard 372: Revision 1.143 2014/01/26 09:45:38 brouard
373: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
374:
375: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
376: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
377:
1.143 brouard 378: Revision 1.142 2014/01/26 03:57:36 brouard
379: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
380:
381: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
382:
1.142 brouard 383: Revision 1.141 2014/01/26 02:42:01 brouard
384: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
385:
1.141 brouard 386: Revision 1.140 2011/09/02 10:37:54 brouard
387: Summary: times.h is ok with mingw32 now.
388:
1.140 brouard 389: Revision 1.139 2010/06/14 07:50:17 brouard
390: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
391: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
392:
1.139 brouard 393: Revision 1.138 2010/04/30 18:19:40 brouard
394: *** empty log message ***
395:
1.138 brouard 396: Revision 1.137 2010/04/29 18:11:38 brouard
397: (Module): Checking covariates for more complex models
398: than V1+V2. A lot of change to be done. Unstable.
399:
1.137 brouard 400: Revision 1.136 2010/04/26 20:30:53 brouard
401: (Module): merging some libgsl code. Fixing computation
402: of likelione (using inter/intrapolation if mle = 0) in order to
403: get same likelihood as if mle=1.
404: Some cleaning of code and comments added.
405:
1.136 brouard 406: Revision 1.135 2009/10/29 15:33:14 brouard
407: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
408:
1.135 brouard 409: Revision 1.134 2009/10/29 13:18:53 brouard
410: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
411:
1.134 brouard 412: Revision 1.133 2009/07/06 10:21:25 brouard
413: just nforces
414:
1.133 brouard 415: Revision 1.132 2009/07/06 08:22:05 brouard
416: Many tings
417:
1.132 brouard 418: Revision 1.131 2009/06/20 16:22:47 brouard
419: Some dimensions resccaled
420:
1.131 brouard 421: Revision 1.130 2009/05/26 06:44:34 brouard
422: (Module): Max Covariate is now set to 20 instead of 8. A
423: lot of cleaning with variables initialized to 0. Trying to make
424: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
425:
1.130 brouard 426: Revision 1.129 2007/08/31 13:49:27 lievre
427: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
428:
1.129 lievre 429: Revision 1.128 2006/06/30 13:02:05 brouard
430: (Module): Clarifications on computing e.j
431:
1.128 brouard 432: Revision 1.127 2006/04/28 18:11:50 brouard
433: (Module): Yes the sum of survivors was wrong since
434: imach-114 because nhstepm was no more computed in the age
435: loop. Now we define nhstepma in the age loop.
436: (Module): In order to speed up (in case of numerous covariates) we
437: compute health expectancies (without variances) in a first step
438: and then all the health expectancies with variances or standard
439: deviation (needs data from the Hessian matrices) which slows the
440: computation.
441: In the future we should be able to stop the program is only health
442: expectancies and graph are needed without standard deviations.
443:
1.127 brouard 444: Revision 1.126 2006/04/28 17:23:28 brouard
445: (Module): Yes the sum of survivors was wrong since
446: imach-114 because nhstepm was no more computed in the age
447: loop. Now we define nhstepma in the age loop.
448: Version 0.98h
449:
1.126 brouard 450: Revision 1.125 2006/04/04 15:20:31 lievre
451: Errors in calculation of health expectancies. Age was not initialized.
452: Forecasting file added.
453:
454: Revision 1.124 2006/03/22 17:13:53 lievre
455: Parameters are printed with %lf instead of %f (more numbers after the comma).
456: The log-likelihood is printed in the log file
457:
458: Revision 1.123 2006/03/20 10:52:43 brouard
459: * imach.c (Module): <title> changed, corresponds to .htm file
460: name. <head> headers where missing.
461:
462: * imach.c (Module): Weights can have a decimal point as for
463: English (a comma might work with a correct LC_NUMERIC environment,
464: otherwise the weight is truncated).
465: Modification of warning when the covariates values are not 0 or
466: 1.
467: Version 0.98g
468:
469: Revision 1.122 2006/03/20 09:45:41 brouard
470: (Module): Weights can have a decimal point as for
471: English (a comma might work with a correct LC_NUMERIC environment,
472: otherwise the weight is truncated).
473: Modification of warning when the covariates values are not 0 or
474: 1.
475: Version 0.98g
476:
477: Revision 1.121 2006/03/16 17:45:01 lievre
478: * imach.c (Module): Comments concerning covariates added
479:
480: * imach.c (Module): refinements in the computation of lli if
481: status=-2 in order to have more reliable computation if stepm is
482: not 1 month. Version 0.98f
483:
484: Revision 1.120 2006/03/16 15:10:38 lievre
485: (Module): refinements in the computation of lli if
486: status=-2 in order to have more reliable computation if stepm is
487: not 1 month. Version 0.98f
488:
489: Revision 1.119 2006/03/15 17:42:26 brouard
490: (Module): Bug if status = -2, the loglikelihood was
491: computed as likelihood omitting the logarithm. Version O.98e
492:
493: Revision 1.118 2006/03/14 18:20:07 brouard
494: (Module): varevsij Comments added explaining the second
495: table of variances if popbased=1 .
496: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
497: (Module): Function pstamp added
498: (Module): Version 0.98d
499:
500: Revision 1.117 2006/03/14 17:16:22 brouard
501: (Module): varevsij Comments added explaining the second
502: table of variances if popbased=1 .
503: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
504: (Module): Function pstamp added
505: (Module): Version 0.98d
506:
507: Revision 1.116 2006/03/06 10:29:27 brouard
508: (Module): Variance-covariance wrong links and
509: varian-covariance of ej. is needed (Saito).
510:
511: Revision 1.115 2006/02/27 12:17:45 brouard
512: (Module): One freematrix added in mlikeli! 0.98c
513:
514: Revision 1.114 2006/02/26 12:57:58 brouard
515: (Module): Some improvements in processing parameter
516: filename with strsep.
517:
518: Revision 1.113 2006/02/24 14:20:24 brouard
519: (Module): Memory leaks checks with valgrind and:
520: datafile was not closed, some imatrix were not freed and on matrix
521: allocation too.
522:
523: Revision 1.112 2006/01/30 09:55:26 brouard
524: (Module): Back to gnuplot.exe instead of wgnuplot.exe
525:
526: Revision 1.111 2006/01/25 20:38:18 brouard
527: (Module): Lots of cleaning and bugs added (Gompertz)
528: (Module): Comments can be added in data file. Missing date values
529: can be a simple dot '.'.
530:
531: Revision 1.110 2006/01/25 00:51:50 brouard
532: (Module): Lots of cleaning and bugs added (Gompertz)
533:
534: Revision 1.109 2006/01/24 19:37:15 brouard
535: (Module): Comments (lines starting with a #) are allowed in data.
536:
537: Revision 1.108 2006/01/19 18:05:42 lievre
538: Gnuplot problem appeared...
539: To be fixed
540:
541: Revision 1.107 2006/01/19 16:20:37 brouard
542: Test existence of gnuplot in imach path
543:
544: Revision 1.106 2006/01/19 13:24:36 brouard
545: Some cleaning and links added in html output
546:
547: Revision 1.105 2006/01/05 20:23:19 lievre
548: *** empty log message ***
549:
550: Revision 1.104 2005/09/30 16:11:43 lievre
551: (Module): sump fixed, loop imx fixed, and simplifications.
552: (Module): If the status is missing at the last wave but we know
553: that the person is alive, then we can code his/her status as -2
554: (instead of missing=-1 in earlier versions) and his/her
555: contributions to the likelihood is 1 - Prob of dying from last
556: health status (= 1-p13= p11+p12 in the easiest case of somebody in
557: the healthy state at last known wave). Version is 0.98
558:
559: Revision 1.103 2005/09/30 15:54:49 lievre
560: (Module): sump fixed, loop imx fixed, and simplifications.
561:
562: Revision 1.102 2004/09/15 17:31:30 brouard
563: Add the possibility to read data file including tab characters.
564:
565: Revision 1.101 2004/09/15 10:38:38 brouard
566: Fix on curr_time
567:
568: Revision 1.100 2004/07/12 18:29:06 brouard
569: Add version for Mac OS X. Just define UNIX in Makefile
570:
571: Revision 1.99 2004/06/05 08:57:40 brouard
572: *** empty log message ***
573:
574: Revision 1.98 2004/05/16 15:05:56 brouard
575: New version 0.97 . First attempt to estimate force of mortality
576: directly from the data i.e. without the need of knowing the health
577: state at each age, but using a Gompertz model: log u =a + b*age .
578: This is the basic analysis of mortality and should be done before any
579: other analysis, in order to test if the mortality estimated from the
580: cross-longitudinal survey is different from the mortality estimated
581: from other sources like vital statistic data.
582:
583: The same imach parameter file can be used but the option for mle should be -3.
584:
1.133 brouard 585: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 586: former routines in order to include the new code within the former code.
587:
588: The output is very simple: only an estimate of the intercept and of
589: the slope with 95% confident intervals.
590:
591: Current limitations:
592: A) Even if you enter covariates, i.e. with the
593: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
594: B) There is no computation of Life Expectancy nor Life Table.
595:
596: Revision 1.97 2004/02/20 13:25:42 lievre
597: Version 0.96d. Population forecasting command line is (temporarily)
598: suppressed.
599:
600: Revision 1.96 2003/07/15 15:38:55 brouard
601: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
602: rewritten within the same printf. Workaround: many printfs.
603:
604: Revision 1.95 2003/07/08 07:54:34 brouard
605: * imach.c (Repository):
606: (Repository): Using imachwizard code to output a more meaningful covariance
607: matrix (cov(a12,c31) instead of numbers.
608:
609: Revision 1.94 2003/06/27 13:00:02 brouard
610: Just cleaning
611:
612: Revision 1.93 2003/06/25 16:33:55 brouard
613: (Module): On windows (cygwin) function asctime_r doesn't
614: exist so I changed back to asctime which exists.
615: (Module): Version 0.96b
616:
617: Revision 1.92 2003/06/25 16:30:45 brouard
618: (Module): On windows (cygwin) function asctime_r doesn't
619: exist so I changed back to asctime which exists.
620:
621: Revision 1.91 2003/06/25 15:30:29 brouard
622: * imach.c (Repository): Duplicated warning errors corrected.
623: (Repository): Elapsed time after each iteration is now output. It
624: helps to forecast when convergence will be reached. Elapsed time
625: is stamped in powell. We created a new html file for the graphs
626: concerning matrix of covariance. It has extension -cov.htm.
627:
628: Revision 1.90 2003/06/24 12:34:15 brouard
629: (Module): Some bugs corrected for windows. Also, when
630: mle=-1 a template is output in file "or"mypar.txt with the design
631: of the covariance matrix to be input.
632:
633: Revision 1.89 2003/06/24 12:30:52 brouard
634: (Module): Some bugs corrected for windows. Also, when
635: mle=-1 a template is output in file "or"mypar.txt with the design
636: of the covariance matrix to be input.
637:
638: Revision 1.88 2003/06/23 17:54:56 brouard
639: * 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.
640:
641: Revision 1.87 2003/06/18 12:26:01 brouard
642: Version 0.96
643:
644: Revision 1.86 2003/06/17 20:04:08 brouard
645: (Module): Change position of html and gnuplot routines and added
646: routine fileappend.
647:
648: Revision 1.85 2003/06/17 13:12:43 brouard
649: * imach.c (Repository): Check when date of death was earlier that
650: current date of interview. It may happen when the death was just
651: prior to the death. In this case, dh was negative and likelihood
652: was wrong (infinity). We still send an "Error" but patch by
653: assuming that the date of death was just one stepm after the
654: interview.
655: (Repository): Because some people have very long ID (first column)
656: we changed int to long in num[] and we added a new lvector for
657: memory allocation. But we also truncated to 8 characters (left
658: truncation)
659: (Repository): No more line truncation errors.
660:
661: Revision 1.84 2003/06/13 21:44:43 brouard
662: * imach.c (Repository): Replace "freqsummary" at a correct
663: place. It differs from routine "prevalence" which may be called
664: many times. Probs is memory consuming and must be used with
665: parcimony.
666: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
667:
668: Revision 1.83 2003/06/10 13:39:11 lievre
669: *** empty log message ***
670:
671: Revision 1.82 2003/06/05 15:57:20 brouard
672: Add log in imach.c and fullversion number is now printed.
673:
674: */
675: /*
676: Interpolated Markov Chain
677:
678: Short summary of the programme:
679:
1.227 brouard 680: This program computes Healthy Life Expectancies or State-specific
681: (if states aren't health statuses) Expectancies from
682: cross-longitudinal data. Cross-longitudinal data consist in:
683:
684: -1- a first survey ("cross") where individuals from different ages
685: are interviewed on their health status or degree of disability (in
686: the case of a health survey which is our main interest)
687:
688: -2- at least a second wave of interviews ("longitudinal") which
689: measure each change (if any) in individual health status. Health
690: expectancies are computed from the time spent in each health state
691: according to a model. More health states you consider, more time is
692: necessary to reach the Maximum Likelihood of the parameters involved
693: in the model. The simplest model is the multinomial logistic model
694: where pij is the probability to be observed in state j at the second
695: wave conditional to be observed in state i at the first
696: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
697: etc , where 'age' is age and 'sex' is a covariate. If you want to
698: have a more complex model than "constant and age", you should modify
699: the program where the markup *Covariates have to be included here
700: again* invites you to do it. More covariates you add, slower the
1.126 brouard 701: convergence.
702:
703: The advantage of this computer programme, compared to a simple
704: multinomial logistic model, is clear when the delay between waves is not
705: identical for each individual. Also, if a individual missed an
706: intermediate interview, the information is lost, but taken into
707: account using an interpolation or extrapolation.
708:
709: hPijx is the probability to be observed in state i at age x+h
710: conditional to the observed state i at age x. The delay 'h' can be
711: split into an exact number (nh*stepm) of unobserved intermediate
712: states. This elementary transition (by month, quarter,
713: semester or year) is modelled as a multinomial logistic. The hPx
714: matrix is simply the matrix product of nh*stepm elementary matrices
715: and the contribution of each individual to the likelihood is simply
716: hPijx.
717:
718: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 719: of the life expectancies. It also computes the period (stable) prevalence.
720:
721: Back prevalence and projections:
1.227 brouard 722:
723: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
724: double agemaxpar, double ftolpl, int *ncvyearp, double
725: dateprev1,double dateprev2, int firstpass, int lastpass, int
726: mobilavproj)
727:
728: Computes the back prevalence limit for any combination of
729: covariate values k at any age between ageminpar and agemaxpar and
730: returns it in **bprlim. In the loops,
731:
732: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
733: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
734:
735: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 736: Computes for any combination of covariates k and any age between bage and fage
737: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
738: oldm=oldms;savm=savms;
1.227 brouard 739:
740: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 741: Computes the transition matrix starting at age 'age' over
742: 'nhstepm*hstepm*stepm' months (i.e. until
743: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 744: nhstepm*hstepm matrices.
745:
746: Returns p3mat[i][j][h] after calling
747: p3mat[i][j][h]=matprod2(newm,
748: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
749: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
750: oldm);
1.226 brouard 751:
752: Important routines
753:
754: - func (or funcone), computes logit (pij) distinguishing
755: o fixed variables (single or product dummies or quantitative);
756: o varying variables by:
757: (1) wave (single, product dummies, quantitative),
758: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
759: % fixed dummy (treated) or quantitative (not done because time-consuming);
760: % varying dummy (not done) or quantitative (not done);
761: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
762: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
763: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
764: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
765: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 766:
1.226 brouard 767:
768:
1.133 brouard 769: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
770: Institut national d'études démographiques, Paris.
1.126 brouard 771: This software have been partly granted by Euro-REVES, a concerted action
772: from the European Union.
773: It is copyrighted identically to a GNU software product, ie programme and
774: software can be distributed freely for non commercial use. Latest version
775: can be accessed at http://euroreves.ined.fr/imach .
776:
777: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
778: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
779:
780: **********************************************************************/
781: /*
782: main
783: read parameterfile
784: read datafile
785: concatwav
786: freqsummary
787: if (mle >= 1)
788: mlikeli
789: print results files
790: if mle==1
791: computes hessian
792: read end of parameter file: agemin, agemax, bage, fage, estepm
793: begin-prev-date,...
794: open gnuplot file
795: open html file
1.145 brouard 796: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
797: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
798: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
799: freexexit2 possible for memory heap.
800:
801: h Pij x | pij_nom ficrestpij
802: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
803: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
804: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
805:
806: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
807: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
808: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
809: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
810: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
811:
1.126 brouard 812: forecasting if prevfcast==1 prevforecast call prevalence()
813: health expectancies
814: Variance-covariance of DFLE
815: prevalence()
816: movingaverage()
817: varevsij()
818: if popbased==1 varevsij(,popbased)
819: total life expectancies
820: Variance of period (stable) prevalence
821: end
822: */
823:
1.187 brouard 824: /* #define DEBUG */
825: /* #define DEBUGBRENT */
1.203 brouard 826: /* #define DEBUGLINMIN */
827: /* #define DEBUGHESS */
828: #define DEBUGHESSIJ
1.224 brouard 829: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 830: #define POWELL /* Instead of NLOPT */
1.224 brouard 831: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 832: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
833: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 834:
835: #include <math.h>
836: #include <stdio.h>
837: #include <stdlib.h>
838: #include <string.h>
1.226 brouard 839: #include <ctype.h>
1.159 brouard 840:
841: #ifdef _WIN32
842: #include <io.h>
1.172 brouard 843: #include <windows.h>
844: #include <tchar.h>
1.159 brouard 845: #else
1.126 brouard 846: #include <unistd.h>
1.159 brouard 847: #endif
1.126 brouard 848:
849: #include <limits.h>
850: #include <sys/types.h>
1.171 brouard 851:
852: #if defined(__GNUC__)
853: #include <sys/utsname.h> /* Doesn't work on Windows */
854: #endif
855:
1.126 brouard 856: #include <sys/stat.h>
857: #include <errno.h>
1.159 brouard 858: /* extern int errno; */
1.126 brouard 859:
1.157 brouard 860: /* #ifdef LINUX */
861: /* #include <time.h> */
862: /* #include "timeval.h" */
863: /* #else */
864: /* #include <sys/time.h> */
865: /* #endif */
866:
1.126 brouard 867: #include <time.h>
868:
1.136 brouard 869: #ifdef GSL
870: #include <gsl/gsl_errno.h>
871: #include <gsl/gsl_multimin.h>
872: #endif
873:
1.167 brouard 874:
1.162 brouard 875: #ifdef NLOPT
876: #include <nlopt.h>
877: typedef struct {
878: double (* function)(double [] );
879: } myfunc_data ;
880: #endif
881:
1.126 brouard 882: /* #include <libintl.h> */
883: /* #define _(String) gettext (String) */
884:
1.141 brouard 885: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 886:
887: #define GNUPLOTPROGRAM "gnuplot"
888: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
889: #define FILENAMELENGTH 132
890:
891: #define GLOCK_ERROR_NOPATH -1 /* empty path */
892: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
893:
1.144 brouard 894: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
895: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 896:
897: #define NINTERVMAX 8
1.144 brouard 898: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
899: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
900: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 901: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 902: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
903: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 904: #define MAXN 20000
1.144 brouard 905: #define YEARM 12. /**< Number of months per year */
1.218 brouard 906: /* #define AGESUP 130 */
907: #define AGESUP 150
908: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 909: #define AGEBASE 40
1.194 brouard 910: #define AGEOVERFLOW 1.e20
1.164 brouard 911: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 912: #ifdef _WIN32
913: #define DIRSEPARATOR '\\'
914: #define CHARSEPARATOR "\\"
915: #define ODIRSEPARATOR '/'
916: #else
1.126 brouard 917: #define DIRSEPARATOR '/'
918: #define CHARSEPARATOR "/"
919: #define ODIRSEPARATOR '\\'
920: #endif
921:
1.240 ! brouard 922: /* $Id: imach.c,v 1.239 2016/08/26 15:51:03 brouard Exp $ */
1.126 brouard 923: /* $State: Exp $ */
1.196 brouard 924: #include "version.h"
925: char version[]=__IMACH_VERSION__;
1.224 brouard 926: 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";
1.240 ! brouard 927: char fullversion[]="$Revision: 1.239 $ $Date: 2016/08/26 15:51:03 $";
1.126 brouard 928: char strstart[80];
929: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 930: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 931: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 932: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
933: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
934: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 935: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
936: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 937: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
938: int cptcovprodnoage=0; /**< Number of covariate products without age */
939: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.233 brouard 940: int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
941: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
1.232 brouard 942: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
1.234 brouard 943: int nsd=0; /**< Total number of single dummy variables (output) */
944: int nsq=0; /**< Total number of single quantitative variables (output) */
1.232 brouard 945: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 946: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 947: int ntveff=0; /**< ntveff number of effective time varying variables */
948: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 949: int cptcov=0; /* Working variable */
1.218 brouard 950: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 951: int npar=NPARMAX;
952: int nlstate=2; /* Number of live states */
953: int ndeath=1; /* Number of dead states */
1.130 brouard 954: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 955: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 956: int popbased=0;
957:
958: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 959: int maxwav=0; /* Maxim number of waves */
960: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
961: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
962: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 963: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 964: int mle=1, weightopt=0;
1.126 brouard 965: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
966: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
967: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
968: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 969: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 970: int selected(int kvar); /* Is covariate kvar selected for printing results */
971:
1.130 brouard 972: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 973: double **matprod2(); /* test */
1.126 brouard 974: double **oldm, **newm, **savm; /* Working pointers to matrices */
975: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 976: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
977:
1.136 brouard 978: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 979: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 980: FILE *ficlog, *ficrespow;
1.130 brouard 981: int globpr=0; /* Global variable for printing or not */
1.126 brouard 982: double fretone; /* Only one call to likelihood */
1.130 brouard 983: long ipmx=0; /* Number of contributions */
1.126 brouard 984: double sw; /* Sum of weights */
985: char filerespow[FILENAMELENGTH];
986: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
987: FILE *ficresilk;
988: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
989: FILE *ficresprobmorprev;
990: FILE *fichtm, *fichtmcov; /* Html File */
991: FILE *ficreseij;
992: char filerese[FILENAMELENGTH];
993: FILE *ficresstdeij;
994: char fileresstde[FILENAMELENGTH];
995: FILE *ficrescveij;
996: char filerescve[FILENAMELENGTH];
997: FILE *ficresvij;
998: char fileresv[FILENAMELENGTH];
999: FILE *ficresvpl;
1000: char fileresvpl[FILENAMELENGTH];
1001: char title[MAXLINE];
1.234 brouard 1002: char model[MAXLINE]; /**< The model line */
1.217 brouard 1003: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 1004: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
1005: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
1006: char command[FILENAMELENGTH];
1007: int outcmd=0;
1008:
1.217 brouard 1009: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 1010: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 1011: char filelog[FILENAMELENGTH]; /* Log file */
1012: char filerest[FILENAMELENGTH];
1013: char fileregp[FILENAMELENGTH];
1014: char popfile[FILENAMELENGTH];
1015:
1016: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
1017:
1.157 brouard 1018: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
1019: /* struct timezone tzp; */
1020: /* extern int gettimeofday(); */
1021: struct tm tml, *gmtime(), *localtime();
1022:
1023: extern time_t time();
1024:
1025: struct tm start_time, end_time, curr_time, last_time, forecast_time;
1026: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
1027: struct tm tm;
1028:
1.126 brouard 1029: char strcurr[80], strfor[80];
1030:
1031: char *endptr;
1032: long lval;
1033: double dval;
1034:
1035: #define NR_END 1
1036: #define FREE_ARG char*
1037: #define FTOL 1.0e-10
1038:
1039: #define NRANSI
1.240 ! brouard 1040: #define ITMAX 200
! 1041: #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */
1.126 brouard 1042:
1043: #define TOL 2.0e-4
1044:
1045: #define CGOLD 0.3819660
1046: #define ZEPS 1.0e-10
1047: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1048:
1049: #define GOLD 1.618034
1050: #define GLIMIT 100.0
1051: #define TINY 1.0e-20
1052:
1053: static double maxarg1,maxarg2;
1054: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1055: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1056:
1057: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1058: #define rint(a) floor(a+0.5)
1.166 brouard 1059: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1060: #define mytinydouble 1.0e-16
1.166 brouard 1061: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1062: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1063: /* static double dsqrarg; */
1064: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1065: static double sqrarg;
1066: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1067: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1068: int agegomp= AGEGOMP;
1069:
1070: int imx;
1071: int stepm=1;
1072: /* Stepm, step in month: minimum step interpolation*/
1073:
1074: int estepm;
1075: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1076:
1077: int m,nb;
1078: long *num;
1.197 brouard 1079: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1080: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1081: covariate for which somebody answered excluding
1082: undefined. Usually 2: 0 and 1. */
1083: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1084: covariate for which somebody answered including
1085: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1086: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1087: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1088: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1089: double *ageexmed,*agecens;
1090: double dateintmean=0;
1091:
1092: double *weight;
1093: int **s; /* Status */
1.141 brouard 1094: double *agedc;
1.145 brouard 1095: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1096: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1097: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1098: double **coqvar; /* Fixed quantitative covariate iqv */
1099: double ***cotvar; /* Time varying covariate itv */
1100: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1101: double idx;
1102: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.234 brouard 1103: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1104: /*k 1 2 3 4 5 6 7 8 9 */
1105: /*Tvar[k]= 5 4 3 6 5 2 7 1 1 */
1106: /* Tndvar[k] 1 2 3 4 5 */
1107: /*TDvar 4 3 6 7 1 */ /* For outputs only; combination of dummies fixed or varying */
1108: /* Tns[k] 1 2 2 4 5 */ /* Number of single cova */
1109: /* TvarsD[k] 1 2 3 */ /* Number of single dummy cova */
1110: /* TvarsDind 2 3 9 */ /* position K of single dummy cova */
1111: /* TvarsQ[k] 1 2 */ /* Number of single quantitative cova */
1112: /* TvarsQind 1 6 */ /* position K of single quantitative cova */
1113: /* Tprod[i]=k 4 7 */
1114: /* Tage[i]=k 5 8 */
1115: /* */
1116: /* Type */
1117: /* V 1 2 3 4 5 */
1118: /* F F V V V */
1119: /* D Q D D Q */
1120: /* */
1121: int *TvarsD;
1122: int *TvarsDind;
1123: int *TvarsQ;
1124: int *TvarsQind;
1125:
1.235 brouard 1126: #define MAXRESULTLINES 10
1127: int nresult=0;
1128: int TKresult[MAXRESULTLINES];
1.237 brouard 1129: int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1130: int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
1.235 brouard 1131: int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
1132: double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.237 brouard 1133: double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
1.235 brouard 1134: int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
1135:
1.234 brouard 1136: /* 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 1137: 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 */
1138: 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 */
1139: 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 */
1140: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1141: 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 */
1142: 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 1143: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1144: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1145: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1146: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1147: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1148: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1149: 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 */
1150: 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 */
1151:
1.230 brouard 1152: int *Tvarsel; /**< Selected covariates for output */
1153: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1154: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1155: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1156: 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 1157: int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
1158: int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
1.197 brouard 1159: int *Tage;
1.227 brouard 1160: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1161: 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 1162: 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*/
1163: 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 1164: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1165: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1166: int **Tvard;
1167: int *Tprod;/**< Gives the k position of the k1 product */
1.238 brouard 1168: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3 */
1.227 brouard 1169: int *Tposprod; /**< Gives the k1 product from the k position */
1.238 brouard 1170: /* if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2) */
1171: /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
1.227 brouard 1172: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1173: double *lsurv, *lpop, *tpop;
1174:
1.231 brouard 1175: #define FD 1; /* Fixed dummy covariate */
1176: #define FQ 2; /* Fixed quantitative covariate */
1177: #define FP 3; /* Fixed product covariate */
1178: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1179: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1180: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1181: #define VD 10; /* Varying dummy covariate */
1182: #define VQ 11; /* Varying quantitative covariate */
1183: #define VP 12; /* Varying product covariate */
1184: #define VPDD 13; /* Varying product dummy*dummy covariate */
1185: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1186: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1187: #define APFD 16; /* Age product * fixed dummy covariate */
1188: #define APFQ 17; /* Age product * fixed quantitative covariate */
1189: #define APVD 18; /* Age product * varying dummy covariate */
1190: #define APVQ 19; /* Age product * varying quantitative covariate */
1191:
1192: #define FTYPE 1; /* Fixed covariate */
1193: #define VTYPE 2; /* Varying covariate (loop in wave) */
1194: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1195:
1196: struct kmodel{
1197: int maintype; /* main type */
1198: int subtype; /* subtype */
1199: };
1200: struct kmodel modell[NCOVMAX];
1201:
1.143 brouard 1202: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1203: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1204:
1205: /**************** split *************************/
1206: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1207: {
1208: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1209: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1210: */
1211: char *ss; /* pointer */
1.186 brouard 1212: int l1=0, l2=0; /* length counters */
1.126 brouard 1213:
1214: l1 = strlen(path ); /* length of path */
1215: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1216: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1217: if ( ss == NULL ) { /* no directory, so determine current directory */
1218: strcpy( name, path ); /* we got the fullname name because no directory */
1219: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1220: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1221: /* get current working directory */
1222: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1223: #ifdef WIN32
1224: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1225: #else
1226: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1227: #endif
1.126 brouard 1228: return( GLOCK_ERROR_GETCWD );
1229: }
1230: /* got dirc from getcwd*/
1231: printf(" DIRC = %s \n",dirc);
1.205 brouard 1232: } else { /* strip directory from path */
1.126 brouard 1233: ss++; /* after this, the filename */
1234: l2 = strlen( ss ); /* length of filename */
1235: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1236: strcpy( name, ss ); /* save file name */
1237: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1238: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1239: printf(" DIRC2 = %s \n",dirc);
1240: }
1241: /* We add a separator at the end of dirc if not exists */
1242: l1 = strlen( dirc ); /* length of directory */
1243: if( dirc[l1-1] != DIRSEPARATOR ){
1244: dirc[l1] = DIRSEPARATOR;
1245: dirc[l1+1] = 0;
1246: printf(" DIRC3 = %s \n",dirc);
1247: }
1248: ss = strrchr( name, '.' ); /* find last / */
1249: if (ss >0){
1250: ss++;
1251: strcpy(ext,ss); /* save extension */
1252: l1= strlen( name);
1253: l2= strlen(ss)+1;
1254: strncpy( finame, name, l1-l2);
1255: finame[l1-l2]= 0;
1256: }
1257:
1258: return( 0 ); /* we're done */
1259: }
1260:
1261:
1262: /******************************************/
1263:
1264: void replace_back_to_slash(char *s, char*t)
1265: {
1266: int i;
1267: int lg=0;
1268: i=0;
1269: lg=strlen(t);
1270: for(i=0; i<= lg; i++) {
1271: (s[i] = t[i]);
1272: if (t[i]== '\\') s[i]='/';
1273: }
1274: }
1275:
1.132 brouard 1276: char *trimbb(char *out, char *in)
1.137 brouard 1277: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1278: char *s;
1279: s=out;
1280: while (*in != '\0'){
1.137 brouard 1281: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1282: in++;
1283: }
1284: *out++ = *in++;
1285: }
1286: *out='\0';
1287: return s;
1288: }
1289:
1.187 brouard 1290: /* char *substrchaine(char *out, char *in, char *chain) */
1291: /* { */
1292: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1293: /* char *s, *t; */
1294: /* t=in;s=out; */
1295: /* while ((*in != *chain) && (*in != '\0')){ */
1296: /* *out++ = *in++; */
1297: /* } */
1298:
1299: /* /\* *in matches *chain *\/ */
1300: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1301: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1302: /* } */
1303: /* in--; chain--; */
1304: /* while ( (*in != '\0')){ */
1305: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1306: /* *out++ = *in++; */
1307: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1308: /* } */
1309: /* *out='\0'; */
1310: /* out=s; */
1311: /* return out; */
1312: /* } */
1313: char *substrchaine(char *out, char *in, char *chain)
1314: {
1315: /* Substract chain 'chain' from 'in', return and output 'out' */
1316: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1317:
1318: char *strloc;
1319:
1320: strcpy (out, in);
1321: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1322: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1323: if(strloc != NULL){
1324: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1325: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1326: /* strcpy (strloc, strloc +strlen(chain));*/
1327: }
1328: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1329: return out;
1330: }
1331:
1332:
1.145 brouard 1333: char *cutl(char *blocc, char *alocc, char *in, char occ)
1334: {
1.187 brouard 1335: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1336: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1337: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1338: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1339: */
1.160 brouard 1340: char *s, *t;
1.145 brouard 1341: t=in;s=in;
1342: while ((*in != occ) && (*in != '\0')){
1343: *alocc++ = *in++;
1344: }
1345: if( *in == occ){
1346: *(alocc)='\0';
1347: s=++in;
1348: }
1349:
1350: if (s == t) {/* occ not found */
1351: *(alocc-(in-s))='\0';
1352: in=s;
1353: }
1354: while ( *in != '\0'){
1355: *blocc++ = *in++;
1356: }
1357:
1358: *blocc='\0';
1359: return t;
1360: }
1.137 brouard 1361: char *cutv(char *blocc, char *alocc, char *in, char occ)
1362: {
1.187 brouard 1363: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1364: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1365: gives blocc="abcdef2ghi" and alocc="j".
1366: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1367: */
1368: char *s, *t;
1369: t=in;s=in;
1370: while (*in != '\0'){
1371: while( *in == occ){
1372: *blocc++ = *in++;
1373: s=in;
1374: }
1375: *blocc++ = *in++;
1376: }
1377: if (s == t) /* occ not found */
1378: *(blocc-(in-s))='\0';
1379: else
1380: *(blocc-(in-s)-1)='\0';
1381: in=s;
1382: while ( *in != '\0'){
1383: *alocc++ = *in++;
1384: }
1385:
1386: *alocc='\0';
1387: return s;
1388: }
1389:
1.126 brouard 1390: int nbocc(char *s, char occ)
1391: {
1392: int i,j=0;
1393: int lg=20;
1394: i=0;
1395: lg=strlen(s);
1396: for(i=0; i<= lg; i++) {
1.234 brouard 1397: if (s[i] == occ ) j++;
1.126 brouard 1398: }
1399: return j;
1400: }
1401:
1.137 brouard 1402: /* void cutv(char *u,char *v, char*t, char occ) */
1403: /* { */
1404: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1405: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1406: /* gives u="abcdef2ghi" and v="j" *\/ */
1407: /* int i,lg,j,p=0; */
1408: /* i=0; */
1409: /* lg=strlen(t); */
1410: /* for(j=0; j<=lg-1; j++) { */
1411: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1412: /* } */
1.126 brouard 1413:
1.137 brouard 1414: /* for(j=0; j<p; j++) { */
1415: /* (u[j] = t[j]); */
1416: /* } */
1417: /* u[p]='\0'; */
1.126 brouard 1418:
1.137 brouard 1419: /* for(j=0; j<= lg; j++) { */
1420: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1421: /* } */
1422: /* } */
1.126 brouard 1423:
1.160 brouard 1424: #ifdef _WIN32
1425: char * strsep(char **pp, const char *delim)
1426: {
1427: char *p, *q;
1428:
1429: if ((p = *pp) == NULL)
1430: return 0;
1431: if ((q = strpbrk (p, delim)) != NULL)
1432: {
1433: *pp = q + 1;
1434: *q = '\0';
1435: }
1436: else
1437: *pp = 0;
1438: return p;
1439: }
1440: #endif
1441:
1.126 brouard 1442: /********************** nrerror ********************/
1443:
1444: void nrerror(char error_text[])
1445: {
1446: fprintf(stderr,"ERREUR ...\n");
1447: fprintf(stderr,"%s\n",error_text);
1448: exit(EXIT_FAILURE);
1449: }
1450: /*********************** vector *******************/
1451: double *vector(int nl, int nh)
1452: {
1453: double *v;
1454: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1455: if (!v) nrerror("allocation failure in vector");
1456: return v-nl+NR_END;
1457: }
1458:
1459: /************************ free vector ******************/
1460: void free_vector(double*v, int nl, int nh)
1461: {
1462: free((FREE_ARG)(v+nl-NR_END));
1463: }
1464:
1465: /************************ivector *******************************/
1466: int *ivector(long nl,long nh)
1467: {
1468: int *v;
1469: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1470: if (!v) nrerror("allocation failure in ivector");
1471: return v-nl+NR_END;
1472: }
1473:
1474: /******************free ivector **************************/
1475: void free_ivector(int *v, long nl, long nh)
1476: {
1477: free((FREE_ARG)(v+nl-NR_END));
1478: }
1479:
1480: /************************lvector *******************************/
1481: long *lvector(long nl,long nh)
1482: {
1483: long *v;
1484: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1485: if (!v) nrerror("allocation failure in ivector");
1486: return v-nl+NR_END;
1487: }
1488:
1489: /******************free lvector **************************/
1490: void free_lvector(long *v, long nl, long nh)
1491: {
1492: free((FREE_ARG)(v+nl-NR_END));
1493: }
1494:
1495: /******************* imatrix *******************************/
1496: int **imatrix(long nrl, long nrh, long ncl, long nch)
1497: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1498: {
1499: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1500: int **m;
1501:
1502: /* allocate pointers to rows */
1503: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1504: if (!m) nrerror("allocation failure 1 in matrix()");
1505: m += NR_END;
1506: m -= nrl;
1507:
1508:
1509: /* allocate rows and set pointers to them */
1510: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1511: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1512: m[nrl] += NR_END;
1513: m[nrl] -= ncl;
1514:
1515: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1516:
1517: /* return pointer to array of pointers to rows */
1518: return m;
1519: }
1520:
1521: /****************** free_imatrix *************************/
1522: void free_imatrix(m,nrl,nrh,ncl,nch)
1523: int **m;
1524: long nch,ncl,nrh,nrl;
1525: /* free an int matrix allocated by imatrix() */
1526: {
1527: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1528: free((FREE_ARG) (m+nrl-NR_END));
1529: }
1530:
1531: /******************* matrix *******************************/
1532: double **matrix(long nrl, long nrh, long ncl, long nch)
1533: {
1534: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1535: double **m;
1536:
1537: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1538: if (!m) nrerror("allocation failure 1 in matrix()");
1539: m += NR_END;
1540: m -= nrl;
1541:
1542: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1543: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1544: m[nrl] += NR_END;
1545: m[nrl] -= ncl;
1546:
1547: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1548: return m;
1.145 brouard 1549: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1550: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1551: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1552: */
1553: }
1554:
1555: /*************************free matrix ************************/
1556: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1557: {
1558: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1559: free((FREE_ARG)(m+nrl-NR_END));
1560: }
1561:
1562: /******************* ma3x *******************************/
1563: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1564: {
1565: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1566: double ***m;
1567:
1568: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1569: if (!m) nrerror("allocation failure 1 in matrix()");
1570: m += NR_END;
1571: m -= nrl;
1572:
1573: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1574: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1575: m[nrl] += NR_END;
1576: m[nrl] -= ncl;
1577:
1578: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1579:
1580: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1581: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1582: m[nrl][ncl] += NR_END;
1583: m[nrl][ncl] -= nll;
1584: for (j=ncl+1; j<=nch; j++)
1585: m[nrl][j]=m[nrl][j-1]+nlay;
1586:
1587: for (i=nrl+1; i<=nrh; i++) {
1588: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1589: for (j=ncl+1; j<=nch; j++)
1590: m[i][j]=m[i][j-1]+nlay;
1591: }
1592: return m;
1593: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1594: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1595: */
1596: }
1597:
1598: /*************************free ma3x ************************/
1599: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1600: {
1601: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1602: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1603: free((FREE_ARG)(m+nrl-NR_END));
1604: }
1605:
1606: /*************** function subdirf ***********/
1607: char *subdirf(char fileres[])
1608: {
1609: /* Caution optionfilefiname is hidden */
1610: strcpy(tmpout,optionfilefiname);
1611: strcat(tmpout,"/"); /* Add to the right */
1612: strcat(tmpout,fileres);
1613: return tmpout;
1614: }
1615:
1616: /*************** function subdirf2 ***********/
1617: char *subdirf2(char fileres[], char *preop)
1618: {
1619:
1620: /* Caution optionfilefiname is hidden */
1621: strcpy(tmpout,optionfilefiname);
1622: strcat(tmpout,"/");
1623: strcat(tmpout,preop);
1624: strcat(tmpout,fileres);
1625: return tmpout;
1626: }
1627:
1628: /*************** function subdirf3 ***********/
1629: char *subdirf3(char fileres[], char *preop, char *preop2)
1630: {
1631:
1632: /* Caution optionfilefiname is hidden */
1633: strcpy(tmpout,optionfilefiname);
1634: strcat(tmpout,"/");
1635: strcat(tmpout,preop);
1636: strcat(tmpout,preop2);
1637: strcat(tmpout,fileres);
1638: return tmpout;
1639: }
1.213 brouard 1640:
1641: /*************** function subdirfext ***********/
1642: char *subdirfext(char fileres[], char *preop, char *postop)
1643: {
1644:
1645: strcpy(tmpout,preop);
1646: strcat(tmpout,fileres);
1647: strcat(tmpout,postop);
1648: return tmpout;
1649: }
1.126 brouard 1650:
1.213 brouard 1651: /*************** function subdirfext3 ***********/
1652: char *subdirfext3(char fileres[], char *preop, char *postop)
1653: {
1654:
1655: /* Caution optionfilefiname is hidden */
1656: strcpy(tmpout,optionfilefiname);
1657: strcat(tmpout,"/");
1658: strcat(tmpout,preop);
1659: strcat(tmpout,fileres);
1660: strcat(tmpout,postop);
1661: return tmpout;
1662: }
1663:
1.162 brouard 1664: char *asc_diff_time(long time_sec, char ascdiff[])
1665: {
1666: long sec_left, days, hours, minutes;
1667: days = (time_sec) / (60*60*24);
1668: sec_left = (time_sec) % (60*60*24);
1669: hours = (sec_left) / (60*60) ;
1670: sec_left = (sec_left) %(60*60);
1671: minutes = (sec_left) /60;
1672: sec_left = (sec_left) % (60);
1673: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1674: return ascdiff;
1675: }
1676:
1.126 brouard 1677: /***************** f1dim *************************/
1678: extern int ncom;
1679: extern double *pcom,*xicom;
1680: extern double (*nrfunc)(double []);
1681:
1682: double f1dim(double x)
1683: {
1684: int j;
1685: double f;
1686: double *xt;
1687:
1688: xt=vector(1,ncom);
1689: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1690: f=(*nrfunc)(xt);
1691: free_vector(xt,1,ncom);
1692: return f;
1693: }
1694:
1695: /*****************brent *************************/
1696: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1697: {
1698: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1699: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1700: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1701: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1702: * returned function value.
1703: */
1.126 brouard 1704: int iter;
1705: double a,b,d,etemp;
1.159 brouard 1706: double fu=0,fv,fw,fx;
1.164 brouard 1707: double ftemp=0.;
1.126 brouard 1708: double p,q,r,tol1,tol2,u,v,w,x,xm;
1709: double e=0.0;
1710:
1711: a=(ax < cx ? ax : cx);
1712: b=(ax > cx ? ax : cx);
1713: x=w=v=bx;
1714: fw=fv=fx=(*f)(x);
1715: for (iter=1;iter<=ITMAX;iter++) {
1716: xm=0.5*(a+b);
1717: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1718: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1719: printf(".");fflush(stdout);
1720: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1721: #ifdef DEBUGBRENT
1.126 brouard 1722: 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);
1723: 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);
1724: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1725: #endif
1726: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1727: *xmin=x;
1728: return fx;
1729: }
1730: ftemp=fu;
1731: if (fabs(e) > tol1) {
1732: r=(x-w)*(fx-fv);
1733: q=(x-v)*(fx-fw);
1734: p=(x-v)*q-(x-w)*r;
1735: q=2.0*(q-r);
1736: if (q > 0.0) p = -p;
1737: q=fabs(q);
1738: etemp=e;
1739: e=d;
1740: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1741: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1742: else {
1.224 brouard 1743: d=p/q;
1744: u=x+d;
1745: if (u-a < tol2 || b-u < tol2)
1746: d=SIGN(tol1,xm-x);
1.126 brouard 1747: }
1748: } else {
1749: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1750: }
1751: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1752: fu=(*f)(u);
1753: if (fu <= fx) {
1754: if (u >= x) a=x; else b=x;
1755: SHFT(v,w,x,u)
1.183 brouard 1756: SHFT(fv,fw,fx,fu)
1757: } else {
1758: if (u < x) a=u; else b=u;
1759: if (fu <= fw || w == x) {
1.224 brouard 1760: v=w;
1761: w=u;
1762: fv=fw;
1763: fw=fu;
1.183 brouard 1764: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1765: v=u;
1766: fv=fu;
1.183 brouard 1767: }
1768: }
1.126 brouard 1769: }
1770: nrerror("Too many iterations in brent");
1771: *xmin=x;
1772: return fx;
1773: }
1774:
1775: /****************** mnbrak ***********************/
1776:
1777: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1778: double (*func)(double))
1.183 brouard 1779: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1780: the downhill direction (defined by the function as evaluated at the initial points) and returns
1781: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1782: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1783: */
1.126 brouard 1784: double ulim,u,r,q, dum;
1785: double fu;
1.187 brouard 1786:
1787: double scale=10.;
1788: int iterscale=0;
1789:
1790: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1791: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1792:
1793:
1794: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1795: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1796: /* *bx = *ax - (*ax - *bx)/scale; */
1797: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1798: /* } */
1799:
1.126 brouard 1800: if (*fb > *fa) {
1801: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1802: SHFT(dum,*fb,*fa,dum)
1803: }
1.126 brouard 1804: *cx=(*bx)+GOLD*(*bx-*ax);
1805: *fc=(*func)(*cx);
1.183 brouard 1806: #ifdef DEBUG
1.224 brouard 1807: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1808: 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 1809: #endif
1.224 brouard 1810: 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 1811: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1812: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1813: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1814: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1815: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1816: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1817: fu=(*func)(u);
1.163 brouard 1818: #ifdef DEBUG
1819: /* f(x)=A(x-u)**2+f(u) */
1820: double A, fparabu;
1821: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1822: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1823: 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);
1824: 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 1825: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1826: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1827: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1828: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1829: #endif
1.184 brouard 1830: #ifdef MNBRAKORIGINAL
1.183 brouard 1831: #else
1.191 brouard 1832: /* if (fu > *fc) { */
1833: /* #ifdef DEBUG */
1834: /* printf("mnbrak4 fu > fc \n"); */
1835: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1836: /* #endif */
1837: /* /\* 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 *\\/ *\/ */
1838: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1839: /* dum=u; /\* Shifting c and u *\/ */
1840: /* u = *cx; */
1841: /* *cx = dum; */
1842: /* dum = fu; */
1843: /* fu = *fc; */
1844: /* *fc =dum; */
1845: /* } else { /\* end *\/ */
1846: /* #ifdef DEBUG */
1847: /* printf("mnbrak3 fu < fc \n"); */
1848: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1849: /* #endif */
1850: /* dum=u; /\* Shifting c and u *\/ */
1851: /* u = *cx; */
1852: /* *cx = dum; */
1853: /* dum = fu; */
1854: /* fu = *fc; */
1855: /* *fc =dum; */
1856: /* } */
1.224 brouard 1857: #ifdef DEBUGMNBRAK
1858: double A, fparabu;
1859: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1860: fparabu= *fa - A*(*ax-u)*(*ax-u);
1861: 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);
1862: 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 1863: #endif
1.191 brouard 1864: dum=u; /* Shifting c and u */
1865: u = *cx;
1866: *cx = dum;
1867: dum = fu;
1868: fu = *fc;
1869: *fc =dum;
1.183 brouard 1870: #endif
1.162 brouard 1871: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1872: #ifdef DEBUG
1.224 brouard 1873: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1874: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1875: #endif
1.126 brouard 1876: fu=(*func)(u);
1877: if (fu < *fc) {
1.183 brouard 1878: #ifdef DEBUG
1.224 brouard 1879: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1880: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1881: #endif
1882: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1883: SHFT(*fb,*fc,fu,(*func)(u))
1884: #ifdef DEBUG
1885: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1886: #endif
1887: }
1.162 brouard 1888: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1889: #ifdef DEBUG
1.224 brouard 1890: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1891: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1892: #endif
1.126 brouard 1893: u=ulim;
1894: fu=(*func)(u);
1.183 brouard 1895: } else { /* u could be left to b (if r > q parabola has a maximum) */
1896: #ifdef DEBUG
1.224 brouard 1897: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1898: 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 1899: #endif
1.126 brouard 1900: u=(*cx)+GOLD*(*cx-*bx);
1901: fu=(*func)(u);
1.224 brouard 1902: #ifdef DEBUG
1903: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1904: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1905: #endif
1.183 brouard 1906: } /* end tests */
1.126 brouard 1907: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1908: SHFT(*fa,*fb,*fc,fu)
1909: #ifdef DEBUG
1.224 brouard 1910: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1911: 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 1912: #endif
1913: } /* 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 1914: }
1915:
1916: /*************** linmin ************************/
1.162 brouard 1917: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1918: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1919: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1920: the value of func at the returned location p . This is actually all accomplished by calling the
1921: routines mnbrak and brent .*/
1.126 brouard 1922: int ncom;
1923: double *pcom,*xicom;
1924: double (*nrfunc)(double []);
1925:
1.224 brouard 1926: #ifdef LINMINORIGINAL
1.126 brouard 1927: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1928: #else
1929: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1930: #endif
1.126 brouard 1931: {
1932: double brent(double ax, double bx, double cx,
1933: double (*f)(double), double tol, double *xmin);
1934: double f1dim(double x);
1935: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1936: double *fc, double (*func)(double));
1937: int j;
1938: double xx,xmin,bx,ax;
1939: double fx,fb,fa;
1.187 brouard 1940:
1.203 brouard 1941: #ifdef LINMINORIGINAL
1942: #else
1943: double scale=10., axs, xxs; /* Scale added for infinity */
1944: #endif
1945:
1.126 brouard 1946: ncom=n;
1947: pcom=vector(1,n);
1948: xicom=vector(1,n);
1949: nrfunc=func;
1950: for (j=1;j<=n;j++) {
1951: pcom[j]=p[j];
1.202 brouard 1952: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1953: }
1.187 brouard 1954:
1.203 brouard 1955: #ifdef LINMINORIGINAL
1956: xx=1.;
1957: #else
1958: axs=0.0;
1959: xxs=1.;
1960: do{
1961: xx= xxs;
1962: #endif
1.187 brouard 1963: ax=0.;
1964: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1965: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1966: /* 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)) */
1967: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1968: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1969: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1970: /* 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 1971: #ifdef LINMINORIGINAL
1972: #else
1973: if (fx != fx){
1.224 brouard 1974: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1975: printf("|");
1976: fprintf(ficlog,"|");
1.203 brouard 1977: #ifdef DEBUGLINMIN
1.224 brouard 1978: 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 1979: #endif
1980: }
1.224 brouard 1981: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1982: #endif
1983:
1.191 brouard 1984: #ifdef DEBUGLINMIN
1985: 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 1986: 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 1987: #endif
1.224 brouard 1988: #ifdef LINMINORIGINAL
1989: #else
1990: if(fb == fx){ /* Flat function in the direction */
1991: xmin=xx;
1992: *flat=1;
1993: }else{
1994: *flat=0;
1995: #endif
1996: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1997: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1998: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1999: /* fmin = f(p[j] + xmin * xi[j]) */
2000: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
2001: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 2002: #ifdef DEBUG
1.224 brouard 2003: 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);
2004: 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);
2005: #endif
2006: #ifdef LINMINORIGINAL
2007: #else
2008: }
1.126 brouard 2009: #endif
1.191 brouard 2010: #ifdef DEBUGLINMIN
2011: printf("linmin end ");
1.202 brouard 2012: fprintf(ficlog,"linmin end ");
1.191 brouard 2013: #endif
1.126 brouard 2014: for (j=1;j<=n;j++) {
1.203 brouard 2015: #ifdef LINMINORIGINAL
2016: xi[j] *= xmin;
2017: #else
2018: #ifdef DEBUGLINMIN
2019: if(xxs <1.0)
2020: printf(" before xi[%d]=%12.8f", j,xi[j]);
2021: #endif
2022: 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) */
2023: #ifdef DEBUGLINMIN
2024: if(xxs <1.0)
2025: 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 );
2026: #endif
2027: #endif
1.187 brouard 2028: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 2029: }
1.191 brouard 2030: #ifdef DEBUGLINMIN
1.203 brouard 2031: printf("\n");
1.191 brouard 2032: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 2033: 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 2034: for (j=1;j<=n;j++) {
1.202 brouard 2035: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2036: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
2037: if(j % ncovmodel == 0){
1.191 brouard 2038: printf("\n");
1.202 brouard 2039: fprintf(ficlog,"\n");
2040: }
1.191 brouard 2041: }
1.203 brouard 2042: #else
1.191 brouard 2043: #endif
1.126 brouard 2044: free_vector(xicom,1,n);
2045: free_vector(pcom,1,n);
2046: }
2047:
2048:
2049: /*************** powell ************************/
1.162 brouard 2050: /*
2051: Minimization of a function func of n variables. Input consists of an initial starting point
2052: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
2053: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
2054: such that failure to decrease by more than this amount on one iteration signals doneness. On
2055: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
2056: function value at p , and iter is the number of iterations taken. The routine linmin is used.
2057: */
1.224 brouard 2058: #ifdef LINMINORIGINAL
2059: #else
2060: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 2061: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 2062: #endif
1.126 brouard 2063: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2064: double (*func)(double []))
2065: {
1.224 brouard 2066: #ifdef LINMINORIGINAL
2067: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2068: double (*func)(double []));
1.224 brouard 2069: #else
2070: void linmin(double p[], double xi[], int n, double *fret,
2071: double (*func)(double []),int *flat);
2072: #endif
1.239 brouard 2073: int i,ibig,j,jk,k;
1.126 brouard 2074: double del,t,*pt,*ptt,*xit;
1.181 brouard 2075: double directest;
1.126 brouard 2076: double fp,fptt;
2077: double *xits;
2078: int niterf, itmp;
1.224 brouard 2079: #ifdef LINMINORIGINAL
2080: #else
2081:
2082: flatdir=ivector(1,n);
2083: for (j=1;j<=n;j++) flatdir[j]=0;
2084: #endif
1.126 brouard 2085:
2086: pt=vector(1,n);
2087: ptt=vector(1,n);
2088: xit=vector(1,n);
2089: xits=vector(1,n);
2090: *fret=(*func)(p);
2091: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2092: rcurr_time = time(NULL);
1.126 brouard 2093: for (*iter=1;;++(*iter)) {
1.187 brouard 2094: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2095: ibig=0;
2096: del=0.0;
1.157 brouard 2097: rlast_time=rcurr_time;
2098: /* (void) gettimeofday(&curr_time,&tzp); */
2099: rcurr_time = time(NULL);
2100: curr_time = *localtime(&rcurr_time);
2101: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2102: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2103: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2104: for (i=1;i<=n;i++) {
1.126 brouard 2105: fprintf(ficrespow," %.12lf", p[i]);
2106: }
1.239 brouard 2107: fprintf(ficrespow,"\n");fflush(ficrespow);
2108: printf("\n#model= 1 + age ");
2109: fprintf(ficlog,"\n#model= 1 + age ");
2110: if(nagesqr==1){
2111: printf(" + age*age ",Tvar[j]);
2112: fprintf(ficlog," + age*age ",Tvar[j]);
2113: }
2114: for(j=1;j <=ncovmodel-2;j++){
2115: if(Typevar[j]==0) {
2116: printf(" + V%d ",Tvar[j]);
2117: fprintf(ficlog," + V%d ",Tvar[j]);
2118: }else if(Typevar[j]==1) {
2119: printf(" + V%d*age ",Tvar[j]);
2120: fprintf(ficlog," + V%d*age ",Tvar[j]);
2121: }else if(Typevar[j]==2) {
2122: printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2123: fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
2124: }
2125: }
1.126 brouard 2126: printf("\n");
1.239 brouard 2127: /* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
2128: /* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
1.126 brouard 2129: fprintf(ficlog,"\n");
1.239 brouard 2130: for(i=1,jk=1; i <=nlstate; i++){
2131: for(k=1; k <=(nlstate+ndeath); k++){
2132: if (k != i) {
2133: printf("%d%d ",i,k);
2134: fprintf(ficlog,"%d%d ",i,k);
2135: for(j=1; j <=ncovmodel; j++){
2136: printf("%12.7f ",p[jk]);
2137: fprintf(ficlog,"%12.7f ",p[jk]);
2138: jk++;
2139: }
2140: printf("\n");
2141: fprintf(ficlog,"\n");
2142: }
2143: }
2144: }
1.126 brouard 2145: if(*iter <=3){
1.157 brouard 2146: tml = *localtime(&rcurr_time);
2147: strcpy(strcurr,asctime(&tml));
2148: rforecast_time=rcurr_time;
1.126 brouard 2149: itmp = strlen(strcurr);
2150: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 2151: strcurr[itmp-1]='\0';
1.162 brouard 2152: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2153: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2154: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 2155: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2156: forecast_time = *localtime(&rforecast_time);
2157: strcpy(strfor,asctime(&forecast_time));
2158: itmp = strlen(strfor);
2159: if(strfor[itmp-1]=='\n')
2160: strfor[itmp-1]='\0';
2161: 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);
2162: 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 2163: }
2164: }
1.187 brouard 2165: for (i=1;i<=n;i++) { /* For each direction i */
2166: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2167: fptt=(*fret);
2168: #ifdef DEBUG
1.203 brouard 2169: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2170: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2171: #endif
1.203 brouard 2172: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2173: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2174: #ifdef LINMINORIGINAL
1.188 brouard 2175: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2176: #else
2177: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2178: flatdir[i]=flat; /* Function is vanishing in that direction i */
2179: #endif
2180: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2181: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2182: /* because that direction will be replaced unless the gain del is small */
2183: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2184: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2185: /* with the new direction. */
2186: del=fabs(fptt-(*fret));
2187: ibig=i;
1.126 brouard 2188: }
2189: #ifdef DEBUG
2190: printf("%d %.12e",i,(*fret));
2191: fprintf(ficlog,"%d %.12e",i,(*fret));
2192: for (j=1;j<=n;j++) {
1.224 brouard 2193: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2194: printf(" x(%d)=%.12e",j,xit[j]);
2195: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2196: }
2197: for(j=1;j<=n;j++) {
1.225 brouard 2198: printf(" p(%d)=%.12e",j,p[j]);
2199: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2200: }
2201: printf("\n");
2202: fprintf(ficlog,"\n");
2203: #endif
1.187 brouard 2204: } /* end loop on each direction i */
2205: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2206: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2207: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2208: for(j=1;j<=n;j++) {
1.225 brouard 2209: if(flatdir[j] >0){
2210: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2211: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2212: }
2213: /* printf("\n"); */
2214: /* fprintf(ficlog,"\n"); */
2215: }
1.182 brouard 2216: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2217: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2218: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2219: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2220: /* decreased of more than 3.84 */
2221: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2222: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2223: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2224:
1.188 brouard 2225: /* Starting the program with initial values given by a former maximization will simply change */
2226: /* the scales of the directions and the directions, because the are reset to canonical directions */
2227: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2228: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2229: #ifdef DEBUG
2230: int k[2],l;
2231: k[0]=1;
2232: k[1]=-1;
2233: printf("Max: %.12e",(*func)(p));
2234: fprintf(ficlog,"Max: %.12e",(*func)(p));
2235: for (j=1;j<=n;j++) {
2236: printf(" %.12e",p[j]);
2237: fprintf(ficlog," %.12e",p[j]);
2238: }
2239: printf("\n");
2240: fprintf(ficlog,"\n");
2241: for(l=0;l<=1;l++) {
2242: for (j=1;j<=n;j++) {
2243: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2244: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2245: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2246: }
2247: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2248: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2249: }
2250: #endif
2251:
1.224 brouard 2252: #ifdef LINMINORIGINAL
2253: #else
2254: free_ivector(flatdir,1,n);
2255: #endif
1.126 brouard 2256: free_vector(xit,1,n);
2257: free_vector(xits,1,n);
2258: free_vector(ptt,1,n);
2259: free_vector(pt,1,n);
2260: return;
1.192 brouard 2261: } /* enough precision */
1.240 ! brouard 2262: if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2263: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2264: ptt[j]=2.0*p[j]-pt[j];
2265: xit[j]=p[j]-pt[j];
2266: pt[j]=p[j];
2267: }
1.181 brouard 2268: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2269: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2270: if (*iter <=4) {
1.225 brouard 2271: #else
2272: #endif
1.224 brouard 2273: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2274: #else
1.161 brouard 2275: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2276: #endif
1.162 brouard 2277: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2278: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2279: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2280: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2281: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2282: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2283: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2284: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2285: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2286: /* Even if f3 <f1, directest can be negative and t >0 */
2287: /* mu² and del² are equal when f3=f1 */
2288: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2289: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2290: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2291: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2292: #ifdef NRCORIGINAL
2293: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2294: #else
2295: 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 2296: t= t- del*SQR(fp-fptt);
1.183 brouard 2297: #endif
1.202 brouard 2298: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2299: #ifdef DEBUG
1.181 brouard 2300: 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);
2301: 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 2302: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2303: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2304: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2305: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2306: 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);
2307: 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);
2308: #endif
1.183 brouard 2309: #ifdef POWELLORIGINAL
2310: if (t < 0.0) { /* Then we use it for new direction */
2311: #else
1.182 brouard 2312: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2313: 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 2314: 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 2315: 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 2316: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2317: }
1.181 brouard 2318: if (directest < 0.0) { /* Then we use it for new direction */
2319: #endif
1.191 brouard 2320: #ifdef DEBUGLINMIN
1.234 brouard 2321: printf("Before linmin in direction P%d-P0\n",n);
2322: for (j=1;j<=n;j++) {
2323: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2324: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2325: if(j % ncovmodel == 0){
2326: printf("\n");
2327: fprintf(ficlog,"\n");
2328: }
2329: }
1.224 brouard 2330: #endif
2331: #ifdef LINMINORIGINAL
1.234 brouard 2332: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.224 brouard 2333: #else
1.234 brouard 2334: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2335: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2336: #endif
1.234 brouard 2337:
1.191 brouard 2338: #ifdef DEBUGLINMIN
1.234 brouard 2339: for (j=1;j<=n;j++) {
2340: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2341: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2342: if(j % ncovmodel == 0){
2343: printf("\n");
2344: fprintf(ficlog,"\n");
2345: }
2346: }
1.224 brouard 2347: #endif
1.234 brouard 2348: for (j=1;j<=n;j++) {
2349: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2350: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2351: }
1.224 brouard 2352: #ifdef LINMINORIGINAL
2353: #else
1.234 brouard 2354: for (j=1, flatd=0;j<=n;j++) {
2355: if(flatdir[j]>0)
2356: flatd++;
2357: }
2358: if(flatd >0){
2359: printf("%d flat directions\n",flatd);
2360: fprintf(ficlog,"%d flat directions\n",flatd);
2361: for (j=1;j<=n;j++) {
2362: if(flatdir[j]>0){
2363: printf("%d ",j);
2364: fprintf(ficlog,"%d ",j);
2365: }
2366: }
2367: printf("\n");
2368: fprintf(ficlog,"\n");
2369: }
1.191 brouard 2370: #endif
1.234 brouard 2371: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2372: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2373:
1.126 brouard 2374: #ifdef DEBUG
1.234 brouard 2375: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2376: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2377: for(j=1;j<=n;j++){
2378: printf(" %lf",xit[j]);
2379: fprintf(ficlog," %lf",xit[j]);
2380: }
2381: printf("\n");
2382: fprintf(ficlog,"\n");
1.126 brouard 2383: #endif
1.192 brouard 2384: } /* end of t or directest negative */
1.224 brouard 2385: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2386: #else
1.234 brouard 2387: } /* end if (fptt < fp) */
1.192 brouard 2388: #endif
1.225 brouard 2389: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.234 brouard 2390: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2391: #else
1.224 brouard 2392: #endif
1.234 brouard 2393: } /* loop iteration */
1.126 brouard 2394: }
1.234 brouard 2395:
1.126 brouard 2396: /**** Prevalence limit (stable or period prevalence) ****************/
1.234 brouard 2397:
1.235 brouard 2398: 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 2399: {
1.235 brouard 2400: /* Computes the prevalence limit in each live state at age x and for covariate combination ij
2401: (and selected quantitative values in nres)
2402: by left multiplying the unit
1.234 brouard 2403: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2404: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2405: /* Wx is row vector: population in state 1, population in state 2, population dead */
2406: /* or prevalence in state 1, prevalence in state 2, 0 */
2407: /* newm is the matrix after multiplications, its rows are identical at a factor */
2408: /* Initial matrix pimij */
2409: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2410: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2411: /* 0, 0 , 1} */
2412: /*
2413: * and after some iteration: */
2414: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2415: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2416: /* 0, 0 , 1} */
2417: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2418: /* {0.51571254859325999, 0.4842874514067399, */
2419: /* 0.51326036147820708, 0.48673963852179264} */
2420: /* If we start from prlim again, prlim tends to a constant matrix */
1.234 brouard 2421:
1.126 brouard 2422: int i, ii,j,k;
1.209 brouard 2423: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2424: /* double **matprod2(); */ /* test */
1.218 brouard 2425: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2426: double **newm;
1.209 brouard 2427: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2428: int ncvloop=0;
1.169 brouard 2429:
1.209 brouard 2430: min=vector(1,nlstate);
2431: max=vector(1,nlstate);
2432: meandiff=vector(1,nlstate);
2433:
1.218 brouard 2434: /* Starting with matrix unity */
1.126 brouard 2435: for (ii=1;ii<=nlstate+ndeath;ii++)
2436: for (j=1;j<=nlstate+ndeath;j++){
2437: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2438: }
1.169 brouard 2439:
2440: cov[1]=1.;
2441:
2442: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2443: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2444: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2445: ncvloop++;
1.126 brouard 2446: newm=savm;
2447: /* Covariates have to be included here again */
1.138 brouard 2448: cov[2]=agefin;
1.187 brouard 2449: if(nagesqr==1)
2450: cov[3]= agefin*agefin;;
1.234 brouard 2451: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2452: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2453: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
1.235 brouard 2454: /* 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 2455: }
2456: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2457: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
1.235 brouard 2458: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2459: /* 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 2460: }
1.237 brouard 2461: for (k=1; k<=cptcovage;k++){ /* For product with age */
1.234 brouard 2462: if(Dummy[Tvar[Tage[k]]]){
2463: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2464: } else{
1.235 brouard 2465: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
1.234 brouard 2466: }
1.235 brouard 2467: /* 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 2468: }
1.237 brouard 2469: for (k=1; k<=cptcovprod;k++){ /* For product without age */
1.235 brouard 2470: /* 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 2471: if(Dummy[Tvard[k][1]==0]){
2472: if(Dummy[Tvard[k][2]==0]){
2473: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2474: }else{
2475: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
2476: }
2477: }else{
2478: if(Dummy[Tvard[k][2]==0]){
2479: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
2480: }else{
2481: cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
2482: }
2483: }
1.234 brouard 2484: }
1.138 brouard 2485: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2486: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2487: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2488: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2489: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2490: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2491: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2492:
1.126 brouard 2493: savm=oldm;
2494: oldm=newm;
1.209 brouard 2495:
2496: for(j=1; j<=nlstate; j++){
2497: max[j]=0.;
2498: min[j]=1.;
2499: }
2500: for(i=1;i<=nlstate;i++){
2501: sumnew=0;
2502: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2503: for(j=1; j<=nlstate; j++){
2504: prlim[i][j]= newm[i][j]/(1-sumnew);
2505: max[j]=FMAX(max[j],prlim[i][j]);
2506: min[j]=FMIN(min[j],prlim[i][j]);
2507: }
2508: }
2509:
1.126 brouard 2510: maxmax=0.;
1.209 brouard 2511: for(j=1; j<=nlstate; j++){
2512: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2513: maxmax=FMAX(maxmax,meandiff[j]);
2514: /* 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 2515: } /* j loop */
1.203 brouard 2516: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2517: /* 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 2518: if(maxmax < ftolpl){
1.209 brouard 2519: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2520: free_vector(min,1,nlstate);
2521: free_vector(max,1,nlstate);
2522: free_vector(meandiff,1,nlstate);
1.126 brouard 2523: return prlim;
2524: }
1.169 brouard 2525: } /* age loop */
1.208 brouard 2526: /* After some age loop it doesn't converge */
1.209 brouard 2527: 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 2528: 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 2529: /* 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); */
2530: free_vector(min,1,nlstate);
2531: free_vector(max,1,nlstate);
2532: free_vector(meandiff,1,nlstate);
1.208 brouard 2533:
1.169 brouard 2534: return prlim; /* should not reach here */
1.126 brouard 2535: }
2536:
1.217 brouard 2537:
2538: /**** Back Prevalence limit (stable or period prevalence) ****************/
2539:
1.218 brouard 2540: /* 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) */
2541: /* 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) */
2542: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2543: {
1.218 brouard 2544: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2545: matrix by transitions matrix until convergence is reached with precision ftolpl */
2546: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2547: /* Wx is row vector: population in state 1, population in state 2, population dead */
2548: /* or prevalence in state 1, prevalence in state 2, 0 */
2549: /* newm is the matrix after multiplications, its rows are identical at a factor */
2550: /* Initial matrix pimij */
2551: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2552: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2553: /* 0, 0 , 1} */
2554: /*
2555: * and after some iteration: */
2556: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2557: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2558: /* 0, 0 , 1} */
2559: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2560: /* {0.51571254859325999, 0.4842874514067399, */
2561: /* 0.51326036147820708, 0.48673963852179264} */
2562: /* If we start from prlim again, prlim tends to a constant matrix */
2563:
2564: int i, ii,j,k;
2565: double *min, *max, *meandiff, maxmax,sumnew=0.;
2566: /* double **matprod2(); */ /* test */
2567: double **out, cov[NCOVMAX+1], **bmij();
2568: double **newm;
1.218 brouard 2569: double **dnewm, **doldm, **dsavm; /* for use */
2570: double **oldm, **savm; /* for use */
2571:
1.217 brouard 2572: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2573: int ncvloop=0;
2574:
2575: min=vector(1,nlstate);
2576: max=vector(1,nlstate);
2577: meandiff=vector(1,nlstate);
2578:
1.218 brouard 2579: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2580: oldm=oldms; savm=savms;
2581:
2582: /* Starting with matrix unity */
2583: for (ii=1;ii<=nlstate+ndeath;ii++)
2584: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2585: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2586: }
2587:
2588: cov[1]=1.;
2589:
2590: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2591: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2592: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2593: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2594: ncvloop++;
1.218 brouard 2595: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2596: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2597: /* Covariates have to be included here again */
2598: cov[2]=agefin;
2599: if(nagesqr==1)
2600: cov[3]= agefin*agefin;;
2601: for (k=1; k<=cptcovn;k++) {
2602: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2603: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2604: /* 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])]); */
2605: }
2606: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2607: for (k=1; k<=cptcovprod;k++) /* Useless */
2608: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2609: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2610:
2611: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2612: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2613: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2614: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2615: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2616: /* ij should be linked to the correct index of cov */
2617: /* age and covariate values ij are in 'cov', but we need to pass
2618: * ij for the observed prevalence at age and status and covariate
2619: * number: prevacurrent[(int)agefin][ii][ij]
2620: */
2621: /* 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 *\/ */
2622: /* 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 *\/ */
2623: 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 2624: savm=oldm;
2625: oldm=newm;
2626: for(j=1; j<=nlstate; j++){
2627: max[j]=0.;
2628: min[j]=1.;
2629: }
2630: for(j=1; j<=nlstate; j++){
2631: for(i=1;i<=nlstate;i++){
1.234 brouard 2632: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2633: bprlim[i][j]= newm[i][j];
2634: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2635: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2636: }
2637: }
1.218 brouard 2638:
1.217 brouard 2639: maxmax=0.;
2640: for(i=1; i<=nlstate; i++){
2641: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2642: maxmax=FMAX(maxmax,meandiff[i]);
2643: /* 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); */
2644: } /* j loop */
2645: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2646: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2647: if(maxmax < ftolpl){
1.220 brouard 2648: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2649: free_vector(min,1,nlstate);
2650: free_vector(max,1,nlstate);
2651: free_vector(meandiff,1,nlstate);
2652: return bprlim;
2653: }
2654: } /* age loop */
2655: /* After some age loop it doesn't converge */
2656: 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'. \n\
2657: 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);
2658: /* 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); */
2659: free_vector(min,1,nlstate);
2660: free_vector(max,1,nlstate);
2661: free_vector(meandiff,1,nlstate);
2662:
2663: return bprlim; /* should not reach here */
2664: }
2665:
1.126 brouard 2666: /*************** transition probabilities ***************/
2667:
2668: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2669: {
1.138 brouard 2670: /* According to parameters values stored in x and the covariate's values stored in cov,
2671: computes the probability to be observed in state j being in state i by appying the
2672: model to the ncovmodel covariates (including constant and age).
2673: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2674: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2675: ncth covariate in the global vector x is given by the formula:
2676: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2677: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2678: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2679: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2680: Outputs ps[i][j] the probability to be observed in j being in j according to
2681: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2682: */
2683: double s1, lnpijopii;
1.126 brouard 2684: /*double t34;*/
1.164 brouard 2685: int i,j, nc, ii, jj;
1.126 brouard 2686:
1.223 brouard 2687: for(i=1; i<= nlstate; i++){
2688: for(j=1; j<i;j++){
2689: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2690: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2691: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2692: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2693: }
2694: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2695: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2696: }
2697: for(j=i+1; j<=nlstate+ndeath;j++){
2698: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2699: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2700: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2701: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2702: }
2703: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2704: }
2705: }
1.218 brouard 2706:
1.223 brouard 2707: for(i=1; i<= nlstate; i++){
2708: s1=0;
2709: for(j=1; j<i; j++){
2710: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2711: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2712: }
2713: for(j=i+1; j<=nlstate+ndeath; j++){
2714: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2715: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2716: }
2717: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2718: ps[i][i]=1./(s1+1.);
2719: /* Computing other pijs */
2720: for(j=1; j<i; j++)
2721: ps[i][j]= exp(ps[i][j])*ps[i][i];
2722: for(j=i+1; j<=nlstate+ndeath; j++)
2723: ps[i][j]= exp(ps[i][j])*ps[i][i];
2724: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2725: } /* end i */
1.218 brouard 2726:
1.223 brouard 2727: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2728: for(jj=1; jj<= nlstate+ndeath; jj++){
2729: ps[ii][jj]=0;
2730: ps[ii][ii]=1;
2731: }
2732: }
1.218 brouard 2733:
2734:
1.223 brouard 2735: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2736: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2737: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2738: /* } */
2739: /* printf("\n "); */
2740: /* } */
2741: /* printf("\n ");printf("%lf ",cov[2]);*/
2742: /*
2743: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2744: goto end;*/
1.223 brouard 2745: return ps;
1.126 brouard 2746: }
2747:
1.218 brouard 2748: /*************** backward transition probabilities ***************/
2749:
2750: /* 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 ) */
2751: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2752: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2753: {
1.222 brouard 2754: /* Computes the backward probability at age agefin and covariate ij
2755: * and returns in **ps as well as **bmij.
2756: */
1.218 brouard 2757: int i, ii, j,k;
1.222 brouard 2758:
2759: double **out, **pmij();
2760: double sumnew=0.;
1.218 brouard 2761: double agefin;
1.222 brouard 2762:
2763: double **dnewm, **dsavm, **doldm;
2764: double **bbmij;
2765:
1.218 brouard 2766: doldm=ddoldms; /* global pointers */
1.222 brouard 2767: dnewm=ddnewms;
2768: dsavm=ddsavms;
2769:
2770: agefin=cov[2];
2771: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2772: the observed prevalence (with this covariate ij) */
2773: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2774: /* We do have the matrix Px in savm and we need pij */
2775: for (j=1;j<=nlstate+ndeath;j++){
2776: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2777: for (ii=1;ii<=nlstate;ii++){
2778: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2779: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2780: for (ii=1;ii<=nlstate+ndeath;ii++){
2781: if(sumnew >= 1.e-10){
2782: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2783: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2784: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2785: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2786: /* }else */
2787: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2788: }else{
2789: 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);
2790: }
2791: } /*End ii */
2792: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2793: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2794: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2795: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2796: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2797: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2798: /* left Product of this matrix by diag matrix of prevalences (savm) */
2799: for (j=1;j<=nlstate+ndeath;j++){
2800: for (ii=1;ii<=nlstate+ndeath;ii++){
2801: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2802: }
2803: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2804: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2805: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2806: /* end bmij */
2807: return ps;
1.218 brouard 2808: }
1.217 brouard 2809: /*************** transition probabilities ***************/
2810:
1.218 brouard 2811: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2812: {
2813: /* According to parameters values stored in x and the covariate's values stored in cov,
2814: computes the probability to be observed in state j being in state i by appying the
2815: model to the ncovmodel covariates (including constant and age).
2816: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2817: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2818: ncth covariate in the global vector x is given by the formula:
2819: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2820: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2821: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2822: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2823: Outputs ps[i][j] the probability to be observed in j being in j according to
2824: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2825: */
2826: double s1, lnpijopii;
2827: /*double t34;*/
2828: int i,j, nc, ii, jj;
2829:
1.234 brouard 2830: for(i=1; i<= nlstate; i++){
2831: for(j=1; j<i;j++){
2832: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2833: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2834: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2835: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2836: }
2837: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2838: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2839: }
2840: for(j=i+1; j<=nlstate+ndeath;j++){
2841: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2842: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2843: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2844: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2845: }
2846: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2847: }
2848: }
2849:
2850: for(i=1; i<= nlstate; i++){
2851: s1=0;
2852: for(j=1; j<i; j++){
2853: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2854: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2855: }
2856: for(j=i+1; j<=nlstate+ndeath; j++){
2857: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2858: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2859: }
2860: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2861: ps[i][i]=1./(s1+1.);
2862: /* Computing other pijs */
2863: for(j=1; j<i; j++)
2864: ps[i][j]= exp(ps[i][j])*ps[i][i];
2865: for(j=i+1; j<=nlstate+ndeath; j++)
2866: ps[i][j]= exp(ps[i][j])*ps[i][i];
2867: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2868: } /* end i */
2869:
2870: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2871: for(jj=1; jj<= nlstate+ndeath; jj++){
2872: ps[ii][jj]=0;
2873: ps[ii][ii]=1;
2874: }
2875: }
2876: /* Added for backcast */ /* Transposed matrix too */
2877: for(jj=1; jj<= nlstate+ndeath; jj++){
2878: s1=0.;
2879: for(ii=1; ii<= nlstate+ndeath; ii++){
2880: s1+=ps[ii][jj];
2881: }
2882: for(ii=1; ii<= nlstate; ii++){
2883: ps[ii][jj]=ps[ii][jj]/s1;
2884: }
2885: }
2886: /* Transposition */
2887: for(jj=1; jj<= nlstate+ndeath; jj++){
2888: for(ii=jj; ii<= nlstate+ndeath; ii++){
2889: s1=ps[ii][jj];
2890: ps[ii][jj]=ps[jj][ii];
2891: ps[jj][ii]=s1;
2892: }
2893: }
2894: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2895: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2896: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2897: /* } */
2898: /* printf("\n "); */
2899: /* } */
2900: /* printf("\n ");printf("%lf ",cov[2]);*/
2901: /*
2902: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2903: goto end;*/
2904: return ps;
1.217 brouard 2905: }
2906:
2907:
1.126 brouard 2908: /**************** Product of 2 matrices ******************/
2909:
1.145 brouard 2910: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2911: {
2912: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2913: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2914: /* in, b, out are matrice of pointers which should have been initialized
2915: before: only the contents of out is modified. The function returns
2916: a pointer to pointers identical to out */
1.145 brouard 2917: int i, j, k;
1.126 brouard 2918: for(i=nrl; i<= nrh; i++)
1.145 brouard 2919: for(k=ncolol; k<=ncoloh; k++){
2920: out[i][k]=0.;
2921: for(j=ncl; j<=nch; j++)
2922: out[i][k] +=in[i][j]*b[j][k];
2923: }
1.126 brouard 2924: return out;
2925: }
2926:
2927:
2928: /************* Higher Matrix Product ***************/
2929:
1.235 brouard 2930: 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 2931: {
1.218 brouard 2932: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2933: 'nhstepm*hstepm*stepm' months (i.e. until
2934: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2935: nhstepm*hstepm matrices.
2936: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2937: (typically every 2 years instead of every month which is too big
2938: for the memory).
2939: Model is determined by parameters x and covariates have to be
2940: included manually here.
2941:
2942: */
2943:
2944: int i, j, d, h, k;
1.131 brouard 2945: double **out, cov[NCOVMAX+1];
1.126 brouard 2946: double **newm;
1.187 brouard 2947: double agexact;
1.214 brouard 2948: double agebegin, ageend;
1.126 brouard 2949:
2950: /* Hstepm could be zero and should return the unit matrix */
2951: for (i=1;i<=nlstate+ndeath;i++)
2952: for (j=1;j<=nlstate+ndeath;j++){
2953: oldm[i][j]=(i==j ? 1.0 : 0.0);
2954: po[i][j][0]=(i==j ? 1.0 : 0.0);
2955: }
2956: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2957: for(h=1; h <=nhstepm; h++){
2958: for(d=1; d <=hstepm; d++){
2959: newm=savm;
2960: /* Covariates have to be included here again */
2961: cov[1]=1.;
1.214 brouard 2962: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2963: cov[2]=agexact;
2964: if(nagesqr==1)
1.227 brouard 2965: cov[3]= agexact*agexact;
1.235 brouard 2966: for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
2967: /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
2968: cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
2969: /* 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)); */
2970: }
2971: for (k=1; k<=nsq;k++) { /* For single varying covariates only */
2972: /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
2973: cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
2974: /* 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]); */
2975: }
2976: for (k=1; k<=cptcovage;k++){
2977: if(Dummy[Tvar[Tage[k]]]){
2978: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2979: } else{
2980: cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
2981: }
2982: /* 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]); */
2983: }
2984: for (k=1; k<=cptcovprod;k++){ /* */
2985: /* 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]); */
2986: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2987: }
2988: /* for (k=1; k<=cptcovn;k++) */
2989: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
2990: /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
2991: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
2992: /* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn *\/ */
2993: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */
1.227 brouard 2994:
2995:
1.126 brouard 2996: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2997: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2998: /* right multiplication of oldm by the current matrix */
1.126 brouard 2999: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
3000: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 3001: /* if((int)age == 70){ */
3002: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3003: /* for(i=1; i<=nlstate+ndeath; i++) { */
3004: /* printf("%d pmmij ",i); */
3005: /* for(j=1;j<=nlstate+ndeath;j++) { */
3006: /* printf("%f ",pmmij[i][j]); */
3007: /* } */
3008: /* printf(" oldm "); */
3009: /* for(j=1;j<=nlstate+ndeath;j++) { */
3010: /* printf("%f ",oldm[i][j]); */
3011: /* } */
3012: /* printf("\n"); */
3013: /* } */
3014: /* } */
1.126 brouard 3015: savm=oldm;
3016: oldm=newm;
3017: }
3018: for(i=1; i<=nlstate+ndeath; i++)
3019: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 3020: po[i][j][h]=newm[i][j];
3021: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 3022: }
1.128 brouard 3023: /*printf("h=%d ",h);*/
1.126 brouard 3024: } /* end h */
1.218 brouard 3025: /* printf("\n H=%d \n",h); */
1.126 brouard 3026: return po;
3027: }
3028:
1.217 brouard 3029: /************* Higher Back Matrix Product ***************/
1.218 brouard 3030: /* 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 3031: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 3032: {
1.218 brouard 3033: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 3034: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 3035: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
3036: nhstepm*hstepm matrices.
3037: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
3038: (typically every 2 years instead of every month which is too big
1.217 brouard 3039: for the memory).
1.218 brouard 3040: Model is determined by parameters x and covariates have to be
3041: included manually here.
1.217 brouard 3042:
1.222 brouard 3043: */
1.217 brouard 3044:
3045: int i, j, d, h, k;
3046: double **out, cov[NCOVMAX+1];
3047: double **newm;
3048: double agexact;
3049: double agebegin, ageend;
1.222 brouard 3050: double **oldm, **savm;
1.217 brouard 3051:
1.222 brouard 3052: oldm=oldms;savm=savms;
1.217 brouard 3053: /* Hstepm could be zero and should return the unit matrix */
3054: for (i=1;i<=nlstate+ndeath;i++)
3055: for (j=1;j<=nlstate+ndeath;j++){
3056: oldm[i][j]=(i==j ? 1.0 : 0.0);
3057: po[i][j][0]=(i==j ? 1.0 : 0.0);
3058: }
3059: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
3060: for(h=1; h <=nhstepm; h++){
3061: for(d=1; d <=hstepm; d++){
3062: newm=savm;
3063: /* Covariates have to be included here again */
3064: cov[1]=1.;
3065: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
3066: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
3067: cov[2]=agexact;
3068: if(nagesqr==1)
1.222 brouard 3069: cov[3]= agexact*agexact;
1.218 brouard 3070: for (k=1; k<=cptcovn;k++)
1.222 brouard 3071: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
3072: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 3073: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 3074: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
3075: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
3076: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 3077: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 3078: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
3079: /* 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 3080:
3081:
1.217 brouard 3082: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
3083: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 3084: /* Careful transposed matrix */
1.222 brouard 3085: /* age is in cov[2] */
1.218 brouard 3086: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 3087: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 3088: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 3089: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 3090: /* if((int)age == 70){ */
3091: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
3092: /* for(i=1; i<=nlstate+ndeath; i++) { */
3093: /* printf("%d pmmij ",i); */
3094: /* for(j=1;j<=nlstate+ndeath;j++) { */
3095: /* printf("%f ",pmmij[i][j]); */
3096: /* } */
3097: /* printf(" oldm "); */
3098: /* for(j=1;j<=nlstate+ndeath;j++) { */
3099: /* printf("%f ",oldm[i][j]); */
3100: /* } */
3101: /* printf("\n"); */
3102: /* } */
3103: /* } */
3104: savm=oldm;
3105: oldm=newm;
3106: }
3107: for(i=1; i<=nlstate+ndeath; i++)
3108: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 3109: po[i][j][h]=newm[i][j];
3110: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 3111: }
3112: /*printf("h=%d ",h);*/
3113: } /* end h */
1.222 brouard 3114: /* printf("\n H=%d \n",h); */
1.217 brouard 3115: return po;
3116: }
3117:
3118:
1.162 brouard 3119: #ifdef NLOPT
3120: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
3121: double fret;
3122: double *xt;
3123: int j;
3124: myfunc_data *d2 = (myfunc_data *) pd;
3125: /* xt = (p1-1); */
3126: xt=vector(1,n);
3127: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
3128:
3129: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
3130: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
3131: printf("Function = %.12lf ",fret);
3132: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
3133: printf("\n");
3134: free_vector(xt,1,n);
3135: return fret;
3136: }
3137: #endif
1.126 brouard 3138:
3139: /*************** log-likelihood *************/
3140: double func( double *x)
3141: {
1.226 brouard 3142: int i, ii, j, k, mi, d, kk;
3143: int ioffset=0;
3144: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3145: double **out;
3146: double lli; /* Individual log likelihood */
3147: int s1, s2;
1.228 brouard 3148: 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 3149: double bbh, survp;
3150: long ipmx;
3151: double agexact;
3152: /*extern weight */
3153: /* We are differentiating ll according to initial status */
3154: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3155: /*for(i=1;i<imx;i++)
3156: printf(" %d\n",s[4][i]);
3157: */
1.162 brouard 3158:
1.226 brouard 3159: ++countcallfunc;
1.162 brouard 3160:
1.226 brouard 3161: cov[1]=1.;
1.126 brouard 3162:
1.226 brouard 3163: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3164: ioffset=0;
1.226 brouard 3165: if(mle==1){
3166: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3167: /* Computes the values of the ncovmodel covariates of the model
3168: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3169: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3170: to be observed in j being in i according to the model.
3171: */
3172: ioffset=2+nagesqr+cptcovage;
1.233 brouard 3173: /* Fixed */
1.234 brouard 3174: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3175: 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)*/
3176: }
1.226 brouard 3177: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3178: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3179: has been calculated etc */
3180: /* For an individual i, wav[i] gives the number of effective waves */
3181: /* We compute the contribution to Likelihood of each effective transition
3182: mw[mi][i] is real wave of the mi th effectve wave */
3183: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3184: s2=s[mw[mi+1][i]][i];
3185: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3186: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3187: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3188: */
3189: for(mi=1; mi<= wav[i]-1; mi++){
1.234 brouard 3190: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
3191: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
3192: }
3193: for (ii=1;ii<=nlstate+ndeath;ii++)
3194: for (j=1;j<=nlstate+ndeath;j++){
3195: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3196: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3197: }
3198: for(d=0; d<dh[mi][i]; d++){
3199: newm=savm;
3200: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3201: cov[2]=agexact;
3202: if(nagesqr==1)
3203: cov[3]= agexact*agexact; /* Should be changed here */
3204: for (kk=1; kk<=cptcovage;kk++) {
3205: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3206: }
3207: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3208: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3209: savm=oldm;
3210: oldm=newm;
3211: } /* end mult */
3212:
3213: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3214: /* But now since version 0.9 we anticipate for bias at large stepm.
3215: * If stepm is larger than one month (smallest stepm) and if the exact delay
3216: * (in months) between two waves is not a multiple of stepm, we rounded to
3217: * the nearest (and in case of equal distance, to the lowest) interval but now
3218: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3219: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3220: * probability in order to take into account the bias as a fraction of the way
1.231 brouard 3221: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3222: * -stepm/2 to stepm/2 .
3223: * For stepm=1 the results are the same as for previous versions of Imach.
3224: * For stepm > 1 the results are less biased than in previous versions.
3225: */
1.234 brouard 3226: s1=s[mw[mi][i]][i];
3227: s2=s[mw[mi+1][i]][i];
3228: bbh=(double)bh[mi][i]/(double)stepm;
3229: /* bias bh is positive if real duration
3230: * is higher than the multiple of stepm and negative otherwise.
3231: */
3232: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3233: if( s2 > nlstate){
3234: /* i.e. if s2 is a death state and if the date of death is known
3235: then the contribution to the likelihood is the probability to
3236: die between last step unit time and current step unit time,
3237: which is also equal to probability to die before dh
3238: minus probability to die before dh-stepm .
3239: In version up to 0.92 likelihood was computed
3240: as if date of death was unknown. Death was treated as any other
3241: health state: the date of the interview describes the actual state
3242: and not the date of a change in health state. The former idea was
3243: to consider that at each interview the state was recorded
3244: (healthy, disable or death) and IMaCh was corrected; but when we
3245: introduced the exact date of death then we should have modified
3246: the contribution of an exact death to the likelihood. This new
3247: contribution is smaller and very dependent of the step unit
3248: stepm. It is no more the probability to die between last interview
3249: and month of death but the probability to survive from last
3250: interview up to one month before death multiplied by the
3251: probability to die within a month. Thanks to Chris
3252: Jackson for correcting this bug. Former versions increased
3253: mortality artificially. The bad side is that we add another loop
3254: which slows down the processing. The difference can be up to 10%
3255: lower mortality.
3256: */
3257: /* If, at the beginning of the maximization mostly, the
3258: cumulative probability or probability to be dead is
3259: constant (ie = 1) over time d, the difference is equal to
3260: 0. out[s1][3] = savm[s1][3]: probability, being at state
3261: s1 at precedent wave, to be dead a month before current
3262: wave is equal to probability, being at state s1 at
3263: precedent wave, to be dead at mont of the current
3264: wave. Then the observed probability (that this person died)
3265: is null according to current estimated parameter. In fact,
3266: it should be very low but not zero otherwise the log go to
3267: infinity.
3268: */
1.183 brouard 3269: /* #ifdef INFINITYORIGINAL */
3270: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3271: /* #else */
3272: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3273: /* lli=log(mytinydouble); */
3274: /* else */
3275: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3276: /* #endif */
1.226 brouard 3277: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3278:
1.226 brouard 3279: } else if ( s2==-1 ) { /* alive */
3280: for (j=1,survp=0. ; j<=nlstate; j++)
3281: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3282: /*survp += out[s1][j]; */
3283: lli= log(survp);
3284: }
3285: else if (s2==-4) {
3286: for (j=3,survp=0. ; j<=nlstate; j++)
3287: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3288: lli= log(survp);
3289: }
3290: else if (s2==-5) {
3291: for (j=1,survp=0. ; j<=2; j++)
3292: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3293: lli= log(survp);
3294: }
3295: else{
3296: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3297: /* 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 */
3298: }
3299: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3300: /*if(lli ==000.0)*/
3301: /*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); */
3302: ipmx +=1;
3303: sw += weight[i];
3304: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3305: /* if (lli < log(mytinydouble)){ */
3306: /* 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); */
3307: /* 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]); */
3308: /* } */
3309: } /* end of wave */
3310: } /* end of individual */
3311: } else if(mle==2){
3312: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3313: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3314: for(mi=1; mi<= wav[i]-1; mi++){
3315: for (ii=1;ii<=nlstate+ndeath;ii++)
3316: for (j=1;j<=nlstate+ndeath;j++){
3317: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3318: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3319: }
3320: for(d=0; d<=dh[mi][i]; d++){
3321: newm=savm;
3322: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3323: cov[2]=agexact;
3324: if(nagesqr==1)
3325: cov[3]= agexact*agexact;
3326: for (kk=1; kk<=cptcovage;kk++) {
3327: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3328: }
3329: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3330: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3331: savm=oldm;
3332: oldm=newm;
3333: } /* end mult */
3334:
3335: s1=s[mw[mi][i]][i];
3336: s2=s[mw[mi+1][i]][i];
3337: bbh=(double)bh[mi][i]/(double)stepm;
3338: 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 */
3339: ipmx +=1;
3340: sw += weight[i];
3341: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3342: } /* end of wave */
3343: } /* end of individual */
3344: } else if(mle==3){ /* exponential inter-extrapolation */
3345: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3346: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3347: for(mi=1; mi<= wav[i]-1; mi++){
3348: for (ii=1;ii<=nlstate+ndeath;ii++)
3349: for (j=1;j<=nlstate+ndeath;j++){
3350: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3351: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3352: }
3353: for(d=0; d<dh[mi][i]; d++){
3354: newm=savm;
3355: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3356: cov[2]=agexact;
3357: if(nagesqr==1)
3358: cov[3]= agexact*agexact;
3359: for (kk=1; kk<=cptcovage;kk++) {
3360: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3361: }
3362: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3363: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3364: savm=oldm;
3365: oldm=newm;
3366: } /* end mult */
3367:
3368: s1=s[mw[mi][i]][i];
3369: s2=s[mw[mi+1][i]][i];
3370: bbh=(double)bh[mi][i]/(double)stepm;
3371: 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 */
3372: ipmx +=1;
3373: sw += weight[i];
3374: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3375: } /* end of wave */
3376: } /* end of individual */
3377: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3378: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3379: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3380: for(mi=1; mi<= wav[i]-1; mi++){
3381: for (ii=1;ii<=nlstate+ndeath;ii++)
3382: for (j=1;j<=nlstate+ndeath;j++){
3383: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3384: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3385: }
3386: for(d=0; d<dh[mi][i]; d++){
3387: newm=savm;
3388: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3389: cov[2]=agexact;
3390: if(nagesqr==1)
3391: cov[3]= agexact*agexact;
3392: for (kk=1; kk<=cptcovage;kk++) {
3393: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3394: }
1.126 brouard 3395:
1.226 brouard 3396: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3397: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3398: savm=oldm;
3399: oldm=newm;
3400: } /* end mult */
3401:
3402: s1=s[mw[mi][i]][i];
3403: s2=s[mw[mi+1][i]][i];
3404: if( s2 > nlstate){
3405: lli=log(out[s1][s2] - savm[s1][s2]);
3406: } else if ( s2==-1 ) { /* alive */
3407: for (j=1,survp=0. ; j<=nlstate; j++)
3408: survp += out[s1][j];
3409: lli= log(survp);
3410: }else{
3411: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3412: }
3413: ipmx +=1;
3414: sw += weight[i];
3415: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3416: /* 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 3417: } /* end of wave */
3418: } /* end of individual */
3419: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3420: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3421: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3422: for(mi=1; mi<= wav[i]-1; mi++){
3423: for (ii=1;ii<=nlstate+ndeath;ii++)
3424: for (j=1;j<=nlstate+ndeath;j++){
3425: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3426: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3427: }
3428: for(d=0; d<dh[mi][i]; d++){
3429: newm=savm;
3430: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3431: cov[2]=agexact;
3432: if(nagesqr==1)
3433: cov[3]= agexact*agexact;
3434: for (kk=1; kk<=cptcovage;kk++) {
3435: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3436: }
1.126 brouard 3437:
1.226 brouard 3438: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3439: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3440: savm=oldm;
3441: oldm=newm;
3442: } /* end mult */
3443:
3444: s1=s[mw[mi][i]][i];
3445: s2=s[mw[mi+1][i]][i];
3446: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3447: ipmx +=1;
3448: sw += weight[i];
3449: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3450: /*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]);*/
3451: } /* end of wave */
3452: } /* end of individual */
3453: } /* End of if */
3454: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3455: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3456: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3457: return -l;
1.126 brouard 3458: }
3459:
3460: /*************** log-likelihood *************/
3461: double funcone( double *x)
3462: {
1.228 brouard 3463: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3464: int i, ii, j, k, mi, d, kk;
1.228 brouard 3465: int ioffset=0;
1.131 brouard 3466: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3467: double **out;
3468: double lli; /* Individual log likelihood */
3469: double llt;
3470: int s1, s2;
1.228 brouard 3471: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3472:
1.126 brouard 3473: double bbh, survp;
1.187 brouard 3474: double agexact;
1.214 brouard 3475: double agebegin, ageend;
1.126 brouard 3476: /*extern weight */
3477: /* We are differentiating ll according to initial status */
3478: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3479: /*for(i=1;i<imx;i++)
3480: printf(" %d\n",s[4][i]);
3481: */
3482: cov[1]=1.;
3483:
3484: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3485: ioffset=0;
3486: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3487: ioffset=2+nagesqr+cptcovage;
1.232 brouard 3488: /* Fixed */
1.224 brouard 3489: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 brouard 3490: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
3491: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
3492: 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)*/
3493: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
3494: /* cov[2+6]=covar[Tvar[6]][i]; */
3495: /* cov[2+6]=covar[2][i]; V2 */
3496: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
3497: /* cov[2+7]=covar[Tvar[7]][i]; */
3498: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
3499: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
3500: /* cov[2+9]=covar[Tvar[9]][i]; */
3501: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3502: }
1.232 brouard 3503: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
3504: /* 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?)*\/ */
3505: /* } */
1.231 brouard 3506: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3507: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3508: /* } */
1.225 brouard 3509:
1.233 brouard 3510:
3511: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 brouard 3512: /* Wave varying (but not age varying) */
3513: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
1.233 brouard 3514: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
1.232 brouard 3515: }
3516: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.231 brouard 3517: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3518: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
1.232 brouard 3519: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
3520: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
1.231 brouard 3521: /* 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 3522: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
3523: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3524: /* /\* 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]); *\/ */
3525: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
3526: /* } */
1.126 brouard 3527: for (ii=1;ii<=nlstate+ndeath;ii++)
1.231 brouard 3528: for (j=1;j<=nlstate+ndeath;j++){
3529: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3530: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3531: }
1.214 brouard 3532:
3533: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3534: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3535: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.231 brouard 3536: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3537: and mw[mi+1][i]. dh depends on stepm.*/
3538: newm=savm;
3539: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3540: cov[2]=agexact;
3541: if(nagesqr==1)
3542: cov[3]= agexact*agexact;
3543: for (kk=1; kk<=cptcovage;kk++) {
3544: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3545: }
3546: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3547: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3548: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3549: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3550: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3551: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3552: savm=oldm;
3553: oldm=newm;
1.126 brouard 3554: } /* end mult */
3555:
3556: s1=s[mw[mi][i]][i];
3557: s2=s[mw[mi+1][i]][i];
1.217 brouard 3558: /* if(s2==-1){ */
3559: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3560: /* /\* exit(1); *\/ */
3561: /* } */
1.126 brouard 3562: bbh=(double)bh[mi][i]/(double)stepm;
3563: /* bias is positive if real duration
3564: * is higher than the multiple of stepm and negative otherwise.
3565: */
3566: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.232 brouard 3567: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3568: } else if ( s2==-1 ) { /* alive */
1.232 brouard 3569: for (j=1,survp=0. ; j<=nlstate; j++)
3570: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3571: lli= log(survp);
1.126 brouard 3572: }else if (mle==1){
1.232 brouard 3573: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3574: } else if(mle==2){
1.232 brouard 3575: 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 3576: } else if(mle==3){ /* exponential inter-extrapolation */
1.232 brouard 3577: 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 3578: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.232 brouard 3579: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3580: } else{ /* mle=0 back to 1 */
1.232 brouard 3581: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3582: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3583: } /* End of if */
3584: ipmx +=1;
3585: sw += weight[i];
3586: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3587: /*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 3588: if(globpr){
1.232 brouard 3589: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3590: %11.6f %11.6f %11.6f ", \
1.232 brouard 3591: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3592: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3593: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3594: llt +=ll[k]*gipmx/gsw;
3595: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3596: }
3597: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3598: }
1.232 brouard 3599: } /* end of wave */
3600: } /* end of individual */
3601: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3602: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3603: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3604: if(globpr==0){ /* First time we count the contributions and weights */
3605: gipmx=ipmx;
3606: gsw=sw;
3607: }
3608: return -l;
1.126 brouard 3609: }
3610:
3611:
3612: /*************** function likelione ***********/
3613: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3614: {
3615: /* This routine should help understanding what is done with
3616: the selection of individuals/waves and
3617: to check the exact contribution to the likelihood.
3618: Plotting could be done.
3619: */
3620: int k;
3621:
3622: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3623: strcpy(fileresilk,"ILK_");
1.202 brouard 3624: strcat(fileresilk,fileresu);
1.126 brouard 3625: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3626: printf("Problem with resultfile: %s\n", fileresilk);
3627: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3628: }
1.214 brouard 3629: 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");
3630: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3631: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3632: for(k=1; k<=nlstate; k++)
3633: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3634: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3635: }
3636:
3637: *fretone=(*funcone)(p);
3638: if(*globpri !=0){
3639: fclose(ficresilk);
1.205 brouard 3640: if (mle ==0)
3641: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3642: else if(mle >=1)
3643: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3644: 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 3645:
1.208 brouard 3646:
3647: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3648: 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 3649: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3650: }
1.207 brouard 3651: 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 3652: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3653: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3654: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3655: fflush(fichtm);
1.205 brouard 3656: }
1.126 brouard 3657: return;
3658: }
3659:
3660:
3661: /*********** Maximum Likelihood Estimation ***************/
3662:
3663: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3664: {
1.165 brouard 3665: int i,j, iter=0;
1.126 brouard 3666: double **xi;
3667: double fret;
3668: double fretone; /* Only one call to likelihood */
3669: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3670:
3671: #ifdef NLOPT
3672: int creturn;
3673: nlopt_opt opt;
3674: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3675: double *lb;
3676: double minf; /* the minimum objective value, upon return */
3677: double * p1; /* Shifted parameters from 0 instead of 1 */
3678: myfunc_data dinst, *d = &dinst;
3679: #endif
3680:
3681:
1.126 brouard 3682: xi=matrix(1,npar,1,npar);
3683: for (i=1;i<=npar;i++)
3684: for (j=1;j<=npar;j++)
3685: xi[i][j]=(i==j ? 1.0 : 0.0);
3686: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3687: strcpy(filerespow,"POW_");
1.126 brouard 3688: strcat(filerespow,fileres);
3689: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3690: printf("Problem with resultfile: %s\n", filerespow);
3691: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3692: }
3693: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3694: for (i=1;i<=nlstate;i++)
3695: for(j=1;j<=nlstate+ndeath;j++)
3696: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3697: fprintf(ficrespow,"\n");
1.162 brouard 3698: #ifdef POWELL
1.126 brouard 3699: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3700: #endif
1.126 brouard 3701:
1.162 brouard 3702: #ifdef NLOPT
3703: #ifdef NEWUOA
3704: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3705: #else
3706: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3707: #endif
3708: lb=vector(0,npar-1);
3709: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3710: nlopt_set_lower_bounds(opt, lb);
3711: nlopt_set_initial_step1(opt, 0.1);
3712:
3713: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3714: d->function = func;
3715: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3716: nlopt_set_min_objective(opt, myfunc, d);
3717: nlopt_set_xtol_rel(opt, ftol);
3718: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3719: printf("nlopt failed! %d\n",creturn);
3720: }
3721: else {
3722: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3723: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3724: iter=1; /* not equal */
3725: }
3726: nlopt_destroy(opt);
3727: #endif
1.126 brouard 3728: free_matrix(xi,1,npar,1,npar);
3729: fclose(ficrespow);
1.203 brouard 3730: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3731: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3732: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3733:
3734: }
3735:
3736: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3737: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3738: {
3739: double **a,**y,*x,pd;
1.203 brouard 3740: /* double **hess; */
1.164 brouard 3741: int i, j;
1.126 brouard 3742: int *indx;
3743:
3744: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3745: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3746: void lubksb(double **a, int npar, int *indx, double b[]) ;
3747: void ludcmp(double **a, int npar, int *indx, double *d) ;
3748: double gompertz(double p[]);
1.203 brouard 3749: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3750:
3751: printf("\nCalculation of the hessian matrix. Wait...\n");
3752: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3753: for (i=1;i<=npar;i++){
1.203 brouard 3754: printf("%d-",i);fflush(stdout);
3755: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3756:
3757: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3758:
3759: /* printf(" %f ",p[i]);
3760: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3761: }
3762:
3763: for (i=1;i<=npar;i++) {
3764: for (j=1;j<=npar;j++) {
3765: if (j>i) {
1.203 brouard 3766: printf(".%d-%d",i,j);fflush(stdout);
3767: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3768: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3769:
3770: hess[j][i]=hess[i][j];
3771: /*printf(" %lf ",hess[i][j]);*/
3772: }
3773: }
3774: }
3775: printf("\n");
3776: fprintf(ficlog,"\n");
3777:
3778: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3779: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3780:
3781: a=matrix(1,npar,1,npar);
3782: y=matrix(1,npar,1,npar);
3783: x=vector(1,npar);
3784: indx=ivector(1,npar);
3785: for (i=1;i<=npar;i++)
3786: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3787: ludcmp(a,npar,indx,&pd);
3788:
3789: for (j=1;j<=npar;j++) {
3790: for (i=1;i<=npar;i++) x[i]=0;
3791: x[j]=1;
3792: lubksb(a,npar,indx,x);
3793: for (i=1;i<=npar;i++){
3794: matcov[i][j]=x[i];
3795: }
3796: }
3797:
3798: printf("\n#Hessian matrix#\n");
3799: fprintf(ficlog,"\n#Hessian matrix#\n");
3800: for (i=1;i<=npar;i++) {
3801: for (j=1;j<=npar;j++) {
1.203 brouard 3802: printf("%.6e ",hess[i][j]);
3803: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3804: }
3805: printf("\n");
3806: fprintf(ficlog,"\n");
3807: }
3808:
1.203 brouard 3809: /* printf("\n#Covariance matrix#\n"); */
3810: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3811: /* for (i=1;i<=npar;i++) { */
3812: /* for (j=1;j<=npar;j++) { */
3813: /* printf("%.6e ",matcov[i][j]); */
3814: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3815: /* } */
3816: /* printf("\n"); */
3817: /* fprintf(ficlog,"\n"); */
3818: /* } */
3819:
1.126 brouard 3820: /* Recompute Inverse */
1.203 brouard 3821: /* for (i=1;i<=npar;i++) */
3822: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3823: /* ludcmp(a,npar,indx,&pd); */
3824:
3825: /* printf("\n#Hessian matrix recomputed#\n"); */
3826:
3827: /* for (j=1;j<=npar;j++) { */
3828: /* for (i=1;i<=npar;i++) x[i]=0; */
3829: /* x[j]=1; */
3830: /* lubksb(a,npar,indx,x); */
3831: /* for (i=1;i<=npar;i++){ */
3832: /* y[i][j]=x[i]; */
3833: /* printf("%.3e ",y[i][j]); */
3834: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3835: /* } */
3836: /* printf("\n"); */
3837: /* fprintf(ficlog,"\n"); */
3838: /* } */
3839:
3840: /* Verifying the inverse matrix */
3841: #ifdef DEBUGHESS
3842: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3843:
1.203 brouard 3844: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3845: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3846:
3847: for (j=1;j<=npar;j++) {
3848: for (i=1;i<=npar;i++){
1.203 brouard 3849: printf("%.2f ",y[i][j]);
3850: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3851: }
3852: printf("\n");
3853: fprintf(ficlog,"\n");
3854: }
1.203 brouard 3855: #endif
1.126 brouard 3856:
3857: free_matrix(a,1,npar,1,npar);
3858: free_matrix(y,1,npar,1,npar);
3859: free_vector(x,1,npar);
3860: free_ivector(indx,1,npar);
1.203 brouard 3861: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3862:
3863:
3864: }
3865:
3866: /*************** hessian matrix ****************/
3867: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3868: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3869: int i;
3870: int l=1, lmax=20;
1.203 brouard 3871: double k1,k2, res, fx;
1.132 brouard 3872: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3873: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3874: int k=0,kmax=10;
3875: double l1;
3876:
3877: fx=func(x);
3878: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3879: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3880: l1=pow(10,l);
3881: delts=delt;
3882: for(k=1 ; k <kmax; k=k+1){
3883: delt = delta*(l1*k);
3884: p2[theta]=x[theta] +delt;
1.145 brouard 3885: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3886: p2[theta]=x[theta]-delt;
3887: k2=func(p2)-fx;
3888: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3889: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3890:
1.203 brouard 3891: #ifdef DEBUGHESSII
1.126 brouard 3892: 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);
3893: 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);
3894: #endif
3895: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3896: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3897: k=kmax;
3898: }
3899: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3900: k=kmax; l=lmax*10;
1.126 brouard 3901: }
3902: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3903: delts=delt;
3904: }
1.203 brouard 3905: } /* End loop k */
1.126 brouard 3906: }
3907: delti[theta]=delts;
3908: return res;
3909:
3910: }
3911:
1.203 brouard 3912: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3913: {
3914: int i;
1.164 brouard 3915: int l=1, lmax=20;
1.126 brouard 3916: double k1,k2,k3,k4,res,fx;
1.132 brouard 3917: double p2[MAXPARM+1];
1.203 brouard 3918: int k, kmax=1;
3919: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3920:
3921: int firstime=0;
1.203 brouard 3922:
1.126 brouard 3923: fx=func(x);
1.203 brouard 3924: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3925: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3926: p2[thetai]=x[thetai]+delti[thetai]*k;
3927: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3928: k1=func(p2)-fx;
3929:
1.203 brouard 3930: p2[thetai]=x[thetai]+delti[thetai]*k;
3931: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3932: k2=func(p2)-fx;
3933:
1.203 brouard 3934: p2[thetai]=x[thetai]-delti[thetai]*k;
3935: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3936: k3=func(p2)-fx;
3937:
1.203 brouard 3938: p2[thetai]=x[thetai]-delti[thetai]*k;
3939: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3940: k4=func(p2)-fx;
1.203 brouard 3941: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3942: if(k1*k2*k3*k4 <0.){
1.208 brouard 3943: firstime=1;
1.203 brouard 3944: kmax=kmax+10;
1.208 brouard 3945: }
3946: if(kmax >=10 || firstime ==1){
1.218 brouard 3947: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
3948: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);
1.203 brouard 3949: 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);
3950: 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);
3951: }
3952: #ifdef DEBUGHESSIJ
3953: v1=hess[thetai][thetai];
3954: v2=hess[thetaj][thetaj];
3955: cv12=res;
3956: /* Computing eigen value of Hessian matrix */
3957: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3958: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3959: if ((lc2 <0) || (lc1 <0) ){
3960: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3961: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3962: 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);
3963: 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);
3964: }
1.126 brouard 3965: #endif
3966: }
3967: return res;
3968: }
3969:
1.203 brouard 3970: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3971: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3972: /* { */
3973: /* int i; */
3974: /* int l=1, lmax=20; */
3975: /* double k1,k2,k3,k4,res,fx; */
3976: /* double p2[MAXPARM+1]; */
3977: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3978: /* int k=0,kmax=10; */
3979: /* double l1; */
3980:
3981: /* fx=func(x); */
3982: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3983: /* l1=pow(10,l); */
3984: /* delts=delt; */
3985: /* for(k=1 ; k <kmax; k=k+1){ */
3986: /* delt = delti*(l1*k); */
3987: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3988: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3989: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3990: /* k1=func(p2)-fx; */
3991:
3992: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3993: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3994: /* k2=func(p2)-fx; */
3995:
3996: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3997: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3998: /* k3=func(p2)-fx; */
3999:
4000: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
4001: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
4002: /* k4=func(p2)-fx; */
4003: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
4004: /* #ifdef DEBUGHESSIJ */
4005: /* 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); */
4006: /* 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); */
4007: /* #endif */
4008: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
4009: /* k=kmax; */
4010: /* } */
4011: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
4012: /* k=kmax; l=lmax*10; */
4013: /* } */
4014: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
4015: /* delts=delt; */
4016: /* } */
4017: /* } /\* End loop k *\/ */
4018: /* } */
4019: /* delti[theta]=delts; */
4020: /* return res; */
4021: /* } */
4022:
4023:
1.126 brouard 4024: /************** Inverse of matrix **************/
4025: void ludcmp(double **a, int n, int *indx, double *d)
4026: {
4027: int i,imax,j,k;
4028: double big,dum,sum,temp;
4029: double *vv;
4030:
4031: vv=vector(1,n);
4032: *d=1.0;
4033: for (i=1;i<=n;i++) {
4034: big=0.0;
4035: for (j=1;j<=n;j++)
4036: if ((temp=fabs(a[i][j])) > big) big=temp;
4037: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
4038: vv[i]=1.0/big;
4039: }
4040: for (j=1;j<=n;j++) {
4041: for (i=1;i<j;i++) {
4042: sum=a[i][j];
4043: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
4044: a[i][j]=sum;
4045: }
4046: big=0.0;
4047: for (i=j;i<=n;i++) {
4048: sum=a[i][j];
4049: for (k=1;k<j;k++)
4050: sum -= a[i][k]*a[k][j];
4051: a[i][j]=sum;
4052: if ( (dum=vv[i]*fabs(sum)) >= big) {
4053: big=dum;
4054: imax=i;
4055: }
4056: }
4057: if (j != imax) {
4058: for (k=1;k<=n;k++) {
4059: dum=a[imax][k];
4060: a[imax][k]=a[j][k];
4061: a[j][k]=dum;
4062: }
4063: *d = -(*d);
4064: vv[imax]=vv[j];
4065: }
4066: indx[j]=imax;
4067: if (a[j][j] == 0.0) a[j][j]=TINY;
4068: if (j != n) {
4069: dum=1.0/(a[j][j]);
4070: for (i=j+1;i<=n;i++) a[i][j] *= dum;
4071: }
4072: }
4073: free_vector(vv,1,n); /* Doesn't work */
4074: ;
4075: }
4076:
4077: void lubksb(double **a, int n, int *indx, double b[])
4078: {
4079: int i,ii=0,ip,j;
4080: double sum;
4081:
4082: for (i=1;i<=n;i++) {
4083: ip=indx[i];
4084: sum=b[ip];
4085: b[ip]=b[i];
4086: if (ii)
4087: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
4088: else if (sum) ii=i;
4089: b[i]=sum;
4090: }
4091: for (i=n;i>=1;i--) {
4092: sum=b[i];
4093: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
4094: b[i]=sum/a[i][i];
4095: }
4096: }
4097:
4098: void pstamp(FILE *fichier)
4099: {
1.196 brouard 4100: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 4101: }
4102:
4103: /************ Frequencies ********************/
1.226 brouard 4104: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
4105: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
4106: int firstpass, int lastpass, int stepm, int weightopt, char model[])
4107: { /* Some frequencies */
4108:
1.227 brouard 4109: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 4110: int iind=0, iage=0;
4111: int mi; /* Effective wave */
4112: int first;
4113: double ***freq; /* Frequencies */
4114: double *meanq;
4115: double **meanqt;
4116: double *pp, **prop, *posprop, *pospropt;
4117: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
4118: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
4119: double agebegin, ageend;
4120:
4121: pp=vector(1,nlstate);
4122: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4123: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4124: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4125: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4126: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
4127: meanqt=matrix(1,lastpass,1,nqtveff);
4128: strcpy(fileresp,"P_");
4129: strcat(fileresp,fileresu);
4130: /*strcat(fileresphtm,fileresu);*/
4131: if((ficresp=fopen(fileresp,"w"))==NULL) {
4132: printf("Problem with prevalence resultfile: %s\n", fileresp);
4133: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4134: exit(0);
4135: }
1.240 ! brouard 4136:
1.226 brouard 4137: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4138: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4139: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4140: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4141: fflush(ficlog);
4142: exit(70);
4143: }
4144: else{
4145: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.240 ! brouard 4146: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4147: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4148: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4149: }
1.237 brouard 4150: 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 4151:
1.226 brouard 4152: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4153: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4154: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4155: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4156: fflush(ficlog);
4157: exit(70);
1.240 ! brouard 4158: } else{
1.226 brouard 4159: 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 4160: <hr size=\"2\" color=\"#EC5E5E\"> \n \
1.214 brouard 4161: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4162: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4163: }
1.240 ! brouard 4164: 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);
! 4165:
1.226 brouard 4166: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4167: j1=0;
1.126 brouard 4168:
1.227 brouard 4169: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4170: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4171: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.240 ! brouard 4172:
1.226 brouard 4173: first=1;
1.240 ! brouard 4174:
1.226 brouard 4175: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4176: reference=low_education V1=0,V2=0
4177: med_educ V1=1 V2=0,
4178: high_educ V1=0 V2=1
4179: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4180: */
1.240 ! brouard 4181:
1.227 brouard 4182: 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 */
1.226 brouard 4183: posproptt=0.;
4184: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4185: scanf("%d", i);*/
4186: for (i=-5; i<=nlstate+ndeath; i++)
4187: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.240 ! brouard 4188: for(m=iagemin; m <= iagemax+3; m++)
! 4189: freq[i][jk][m]=0;
! 4190:
1.226 brouard 4191: for (i=1; i<=nlstate; i++) {
4192: for(m=iagemin; m <= iagemax+3; m++)
1.240 ! brouard 4193: prop[i][m]=0;
1.226 brouard 4194: posprop[i]=0;
4195: pospropt[i]=0;
4196: }
1.227 brouard 4197: /* for (z1=1; z1<= nqfveff; z1++) { */
4198: /* meanq[z1]+=0.; */
4199: /* for(m=1;m<=lastpass;m++){ */
4200: /* meanqt[m][z1]=0.; */
4201: /* } */
4202: /* } */
1.240 ! brouard 4203:
1.226 brouard 4204: dateintsum=0;
4205: k2cpt=0;
1.227 brouard 4206: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4207: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4208: bool=1;
1.227 brouard 4209: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
1.234 brouard 4210: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.227 brouard 4211: /* for (z1=1; z1<= nqfveff; z1++) { */
4212: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4213: /* } */
1.234 brouard 4214: for (z1=1; z1<=cptcoveff; z1++) {
4215: /* if(Tvaraff[z1] ==-20){ */
4216: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4217: /* }else if(Tvaraff[z1] ==-10){ */
4218: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4219: /* }else */
4220: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4221: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4222: bool=0;
4223: /* 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",
4224: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4225: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4226: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4227: } /* Onlyf fixed */
4228: } /* end z1 */
4229: } /* cptcovn > 0 */
1.227 brouard 4230: } /* end any */
4231: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.234 brouard 4232: /* for(m=firstpass; m<=lastpass; m++){ */
4233: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4234: m=mw[mi][iind];
4235: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4236: for (z1=1; z1<=cptcoveff; z1++) {
4237: if( Fixed[Tmodelind[z1]]==1){
4238: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4239: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4240: bool=0;
4241: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4242: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4243: bool=0;
4244: }
4245: }
4246: }
4247: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4248: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4249: if(bool==1){
4250: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4251: and mw[mi+1][iind]. dh depends on stepm. */
4252: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4253: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4254: if(m >=firstpass && m <=lastpass){
4255: k2=anint[m][iind]+(mint[m][iind]/12.);
4256: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4257: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4258: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4259: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4260: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4261: if (m<lastpass) {
4262: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4263: /* 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]); */
4264: if(s[m][iind]==-1)
4265: 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.));
4266: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4267: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4268: 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 */
4269: }
4270: } /* end if between passes */
4271: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4272: dateintsum=dateintsum+k2;
4273: k2cpt++;
4274: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
4275: }
4276: } /* end bool 2 */
4277: } /* end m */
1.226 brouard 4278: } /* end bool */
4279: } /* end iind = 1 to imx */
4280: /* prop[s][age] is feeded for any initial and valid live state as well as
4281: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
1.240 ! brouard 4282:
! 4283:
1.226 brouard 4284: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4285: pstamp(ficresp);
1.240 ! brouard 4286: if (cptcoveff>0){
1.226 brouard 4287: fprintf(ficresp, "\n#********** Variable ");
4288: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4289: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.240 ! brouard 4290: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4291: for (z1=1; z1<=cptcoveff; z1++){
1.240 ! brouard 4292: if(DummyV[z1]){
! 4293: fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4294: fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4295: fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4296: fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4297: }else{
! 4298: fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4299: fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4300: fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4301: fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
! 4302: }
1.226 brouard 4303: }
4304: fprintf(ficresp, "**********\n#");
4305: fprintf(ficresphtm, "**********</h3>\n");
4306: fprintf(ficresphtmfr, "**********</h3>\n");
4307: fprintf(ficlog, "**********\n");
4308: }
4309: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4310: for(i=1; i<=nlstate;i++) {
1.240 ! brouard 4311: fprintf(ficresp, " Age Prev(%d) N(%d) N ",i,i);
1.226 brouard 4312: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4313: }
4314: fprintf(ficresp, "\n");
4315: fprintf(ficresphtm, "\n");
1.240 ! brouard 4316:
1.226 brouard 4317: /* Header of frequency table by age */
4318: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4319: fprintf(ficresphtmfr,"<th>Age</th> ");
4320: for(jk=-1; jk <=nlstate+ndeath; jk++){
4321: for(m=-1; m <=nlstate+ndeath; m++){
1.234 brouard 4322: if(jk!=0 && m!=0)
4323: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
1.226 brouard 4324: }
4325: }
4326: fprintf(ficresphtmfr, "\n");
1.240 ! brouard 4327:
1.226 brouard 4328: /* For each age */
4329: for(iage=iagemin; iage <= iagemax+3; iage++){
4330: fprintf(ficresphtm,"<tr>");
4331: if(iage==iagemax+1){
1.240 ! brouard 4332: fprintf(ficlog,"1");
! 4333: fprintf(ficresphtmfr,"<tr><th>0</th> ");
1.226 brouard 4334: }else if(iage==iagemax+2){
1.240 ! brouard 4335: fprintf(ficlog,"0");
! 4336: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
1.226 brouard 4337: }else if(iage==iagemax+3){
1.240 ! brouard 4338: fprintf(ficlog,"Total");
! 4339: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.226 brouard 4340: }else{
1.240 ! brouard 4341: if(first==1){
! 4342: first=0;
! 4343: printf("See log file for details...\n");
! 4344: }
! 4345: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
! 4346: fprintf(ficlog,"Age %d", iage);
1.226 brouard 4347: }
4348: for(jk=1; jk <=nlstate ; jk++){
1.240 ! brouard 4349: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
! 4350: pp[jk] += freq[jk][m][iage];
1.226 brouard 4351: }
4352: for(jk=1; jk <=nlstate ; jk++){
1.240 ! brouard 4353: for(m=-1, pos=0; m <=0 ; m++)
! 4354: pos += freq[jk][m][iage];
! 4355: if(pp[jk]>=1.e-10){
! 4356: if(first==1){
! 4357: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 4358: }
! 4359: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
! 4360: }else{
! 4361: if(first==1)
! 4362: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 4363: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
! 4364: }
1.226 brouard 4365: }
1.240 ! brouard 4366:
1.226 brouard 4367: for(jk=1; jk <=nlstate ; jk++){
1.240 ! brouard 4368: /* posprop[jk]=0; */
! 4369: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
! 4370: pp[jk] += freq[jk][m][iage];
1.226 brouard 4371: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
1.240 ! brouard 4372:
1.226 brouard 4373: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
1.240 ! brouard 4374: pos += pp[jk]; /* pos is the total number of transitions until this age */
! 4375: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
! 4376: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
! 4377: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
! 4378: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
1.226 brouard 4379: }
4380: for(jk=1; jk <=nlstate ; jk++){
1.240 ! brouard 4381: if(pos>=1.e-5){
! 4382: if(first==1)
! 4383: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 4384: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
! 4385: }else{
! 4386: if(first==1)
! 4387: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 4388: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
! 4389: }
! 4390: if( iage <= iagemax){
! 4391: if(pos>=1.e-5){
! 4392: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
! 4393: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
! 4394: /*probs[iage][jk][j1]= pp[jk]/pos;*/
! 4395: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
! 4396: }
! 4397: else{
! 4398: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
! 4399: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
! 4400: }
! 4401: }
! 4402: pospropt[jk] +=posprop[jk];
1.226 brouard 4403: } /* end loop jk */
4404: /* pospropt=0.; */
4405: for(jk=-1; jk <=nlstate+ndeath; jk++){
1.240 ! brouard 4406: for(m=-1; m <=nlstate+ndeath; m++){
! 4407: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
! 4408: if(first==1){
! 4409: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
! 4410: }
! 4411: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
! 4412: }
! 4413: if(jk!=0 && m!=0)
! 4414: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
! 4415: }
1.226 brouard 4416: } /* end loop jk */
4417: posproptt=0.;
4418: for(jk=1; jk <=nlstate; jk++){
1.240 ! brouard 4419: posproptt += pospropt[jk];
1.226 brouard 4420: }
4421: fprintf(ficresphtmfr,"</tr>\n ");
4422: if(iage <= iagemax){
1.240 ! brouard 4423: fprintf(ficresp,"\n");
! 4424: fprintf(ficresphtm,"</tr>\n");
1.226 brouard 4425: }
4426: if(first==1)
1.240 ! brouard 4427: printf("Others in log...\n");
1.226 brouard 4428: fprintf(ficlog,"\n");
4429: } /* end loop age iage */
4430: fprintf(ficresphtm,"<tr><th>Tot</th>");
4431: for(jk=1; jk <=nlstate ; jk++){
4432: if(posproptt < 1.e-5){
1.240 ! brouard 4433: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
1.226 brouard 4434: }else{
1.240 ! brouard 4435: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
1.226 brouard 4436: }
4437: }
4438: fprintf(ficresphtm,"</tr>\n");
4439: fprintf(ficresphtm,"</table>\n");
4440: fprintf(ficresphtmfr,"</table>\n");
4441: if(posproptt < 1.e-5){
4442: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4443: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4444: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4445: invalidvarcomb[j1]=1;
4446: }else{
4447: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4448: invalidvarcomb[j1]=0;
4449: }
4450: fprintf(ficresphtmfr,"</table>\n");
4451: } /* end selected combination of covariate j1 */
4452: dateintmean=dateintsum/k2cpt;
1.240 ! brouard 4453:
1.226 brouard 4454: fclose(ficresp);
4455: fclose(ficresphtm);
4456: fclose(ficresphtmfr);
4457: free_vector(meanq,1,nqfveff);
4458: free_matrix(meanqt,1,lastpass,1,nqtveff);
4459: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4460: free_vector(pospropt,1,nlstate);
4461: free_vector(posprop,1,nlstate);
4462: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4463: free_vector(pp,1,nlstate);
4464: /* End of freqsummary */
4465: }
1.126 brouard 4466:
4467: /************ Prevalence ********************/
1.227 brouard 4468: 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)
4469: {
4470: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4471: in each health status at the date of interview (if between dateprev1 and dateprev2).
4472: We still use firstpass and lastpass as another selection.
4473: */
1.126 brouard 4474:
1.227 brouard 4475: int i, m, jk, j1, bool, z1,j, iv;
4476: int mi; /* Effective wave */
4477: int iage;
4478: double agebegin, ageend;
4479:
4480: double **prop;
4481: double posprop;
4482: double y2; /* in fractional years */
4483: int iagemin, iagemax;
4484: int first; /** to stop verbosity which is redirected to log file */
4485:
4486: iagemin= (int) agemin;
4487: iagemax= (int) agemax;
4488: /*pp=vector(1,nlstate);*/
4489: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4490: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4491: j1=0;
1.222 brouard 4492:
1.227 brouard 4493: /*j=cptcoveff;*/
4494: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4495:
1.227 brouard 4496: first=1;
4497: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4498: for (i=1; i<=nlstate; i++)
4499: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4500: prop[i][iage]=0.0;
4501: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4502: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4503: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4504:
4505: for (i=1; i<=imx; i++) { /* Each individual */
4506: bool=1;
4507: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4508: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4509: m=mw[mi][i];
4510: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4511: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4512: for (z1=1; z1<=cptcoveff; z1++){
4513: if( Fixed[Tmodelind[z1]]==1){
4514: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4515: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4516: bool=0;
4517: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4518: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4519: bool=0;
4520: }
4521: }
4522: if(bool==1){ /* Otherwise we skip that wave/person */
4523: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4524: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4525: if(m >=firstpass && m <=lastpass){
4526: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4527: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4528: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4529: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4530: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4531: 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);
4532: exit(1);
4533: }
4534: if (s[m][i]>0 && s[m][i]<=nlstate) {
4535: /*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]]);*/
4536: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4537: prop[s[m][i]][iagemax+3] += weight[i];
4538: } /* end valid statuses */
4539: } /* end selection of dates */
4540: } /* end selection of waves */
4541: } /* end bool */
4542: } /* end wave */
4543: } /* end individual */
4544: for(i=iagemin; i <= iagemax+3; i++){
4545: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4546: posprop += prop[jk][i];
4547: }
4548:
4549: for(jk=1; jk <=nlstate ; jk++){
4550: if( i <= iagemax){
4551: if(posprop>=1.e-5){
4552: probs[i][jk][j1]= prop[jk][i]/posprop;
4553: } else{
4554: if(first==1){
4555: first=0;
4556: 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]);
4557: }
4558: }
4559: }
4560: }/* end jk */
4561: }/* end i */
1.222 brouard 4562: /*} *//* end i1 */
1.227 brouard 4563: } /* end j1 */
1.222 brouard 4564:
1.227 brouard 4565: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4566: /*free_vector(pp,1,nlstate);*/
4567: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4568: } /* End of prevalence */
1.126 brouard 4569:
4570: /************* Waves Concatenation ***************/
4571:
4572: 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)
4573: {
4574: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4575: Death is a valid wave (if date is known).
4576: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4577: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4578: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4579: */
1.126 brouard 4580:
1.224 brouard 4581: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4582: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4583: double sum=0., jmean=0.;*/
1.224 brouard 4584: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4585: int j, k=0,jk, ju, jl;
4586: double sum=0.;
4587: first=0;
1.214 brouard 4588: firstwo=0;
1.217 brouard 4589: firsthree=0;
1.218 brouard 4590: firstfour=0;
1.164 brouard 4591: jmin=100000;
1.126 brouard 4592: jmax=-1;
4593: jmean=0.;
1.224 brouard 4594:
4595: /* Treating live states */
1.214 brouard 4596: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4597: mi=0; /* First valid wave */
1.227 brouard 4598: mli=0; /* Last valid wave */
1.126 brouard 4599: m=firstpass;
1.214 brouard 4600: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4601: 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 */
4602: mli=m-1;/* mw[++mi][i]=m-1; */
4603: }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 */
4604: mw[++mi][i]=m;
4605: mli=m;
1.224 brouard 4606: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4607: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4608: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4609: }
1.227 brouard 4610: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4611: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4612: break;
1.224 brouard 4613: #else
1.227 brouard 4614: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4615: if(firsthree == 0){
4616: 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);
4617: firsthree=1;
4618: }
4619: 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);
4620: mw[++mi][i]=m;
4621: mli=m;
4622: }
4623: if(s[m][i]==-2){ /* Vital status is really unknown */
4624: nbwarn++;
4625: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4626: 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);
4627: 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);
4628: }
4629: break;
4630: }
4631: break;
1.224 brouard 4632: #endif
1.227 brouard 4633: }/* End m >= lastpass */
1.126 brouard 4634: }/* end while */
1.224 brouard 4635:
1.227 brouard 4636: /* 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 4637: /* After last pass */
1.224 brouard 4638: /* Treating death states */
1.214 brouard 4639: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4640: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4641: /* } */
1.126 brouard 4642: mi++; /* Death is another wave */
4643: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4644: /* Only death is a correct wave */
1.126 brouard 4645: mw[mi][i]=m;
1.224 brouard 4646: }
4647: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4648: 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 4649: /* m++; */
4650: /* mi++; */
4651: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4652: /* mw[mi][i]=m; */
1.218 brouard 4653: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4654: 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 */
4655: nbwarn++;
4656: if(firstfiv==0){
4657: 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 );
4658: firstfiv=1;
4659: }else{
4660: 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 );
4661: }
4662: }else{ /* Death occured afer last wave potential bias */
4663: nberr++;
4664: if(firstwo==0){
4665: 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 );
4666: firstwo=1;
4667: }
4668: 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 );
4669: }
1.218 brouard 4670: }else{ /* end date of interview is known */
1.227 brouard 4671: /* death is known but not confirmed by death status at any wave */
4672: if(firstfour==0){
4673: 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 );
4674: firstfour=1;
4675: }
4676: 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 4677: }
1.224 brouard 4678: } /* end if date of death is known */
4679: #endif
4680: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4681: /* wav[i]=mw[mi][i]; */
1.126 brouard 4682: if(mi==0){
4683: nbwarn++;
4684: if(first==0){
1.227 brouard 4685: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4686: first=1;
1.126 brouard 4687: }
4688: if(first==1){
1.227 brouard 4689: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4690: }
4691: } /* end mi==0 */
4692: } /* End individuals */
1.214 brouard 4693: /* wav and mw are no more changed */
1.223 brouard 4694:
1.214 brouard 4695:
1.126 brouard 4696: for(i=1; i<=imx; i++){
4697: for(mi=1; mi<wav[i];mi++){
4698: if (stepm <=0)
1.227 brouard 4699: dh[mi][i]=1;
1.126 brouard 4700: else{
1.227 brouard 4701: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4702: if (agedc[i] < 2*AGESUP) {
4703: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4704: if(j==0) j=1; /* Survives at least one month after exam */
4705: else if(j<0){
4706: nberr++;
4707: 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]);
4708: j=1; /* Temporary Dangerous patch */
4709: 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);
4710: 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]);
4711: 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);
4712: }
4713: k=k+1;
4714: if (j >= jmax){
4715: jmax=j;
4716: ijmax=i;
4717: }
4718: if (j <= jmin){
4719: jmin=j;
4720: ijmin=i;
4721: }
4722: sum=sum+j;
4723: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4724: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4725: }
4726: }
4727: else{
4728: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4729: /* 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 4730:
1.227 brouard 4731: k=k+1;
4732: if (j >= jmax) {
4733: jmax=j;
4734: ijmax=i;
4735: }
4736: else if (j <= jmin){
4737: jmin=j;
4738: ijmin=i;
4739: }
4740: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4741: /*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]);*/
4742: if(j<0){
4743: nberr++;
4744: 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]);
4745: 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]);
4746: }
4747: sum=sum+j;
4748: }
4749: jk= j/stepm;
4750: jl= j -jk*stepm;
4751: ju= j -(jk+1)*stepm;
4752: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4753: if(jl==0){
4754: dh[mi][i]=jk;
4755: bh[mi][i]=0;
4756: }else{ /* We want a negative bias in order to only have interpolation ie
4757: * to avoid the price of an extra matrix product in likelihood */
4758: dh[mi][i]=jk+1;
4759: bh[mi][i]=ju;
4760: }
4761: }else{
4762: if(jl <= -ju){
4763: dh[mi][i]=jk;
4764: bh[mi][i]=jl; /* bias is positive if real duration
4765: * is higher than the multiple of stepm and negative otherwise.
4766: */
4767: }
4768: else{
4769: dh[mi][i]=jk+1;
4770: bh[mi][i]=ju;
4771: }
4772: if(dh[mi][i]==0){
4773: dh[mi][i]=1; /* At least one step */
4774: bh[mi][i]=ju; /* At least one step */
4775: /* 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);*/
4776: }
4777: } /* end if mle */
1.126 brouard 4778: }
4779: } /* end wave */
4780: }
4781: jmean=sum/k;
4782: 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 4783: 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 4784: }
1.126 brouard 4785:
4786: /*********** Tricode ****************************/
1.220 brouard 4787: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4788: {
1.144 brouard 4789: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4790: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 brouard 4791: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4792: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4793: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4794: */
1.130 brouard 4795:
1.145 brouard 4796: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4797: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4798: int cptcode=0; /* Modality max of covariates j */
4799: int modmincovj=0; /* Modality min of covariates j */
4800:
4801:
1.220 brouard 4802: /* cptcoveff=0; */
1.224 brouard 4803: /* *cptcov=0; */
1.126 brouard 4804:
1.144 brouard 4805: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4806:
1.224 brouard 4807: /* Loop on covariates without age and products and no quantitative variable */
4808: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4809: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4810: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4811: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4812: switch(Fixed[k]) {
4813: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.231 brouard 4814: 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*/
4815: ij=(int)(covar[Tvar[k]][i]);
4816: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4817: * If product of Vn*Vm, still boolean *:
4818: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4819: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4820: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4821: modality of the nth covariate of individual i. */
4822: if (ij > modmaxcovj)
4823: modmaxcovj=ij;
4824: else if (ij < modmincovj)
4825: modmincovj=ij;
4826: if ((ij < -1) && (ij > NCOVMAX)){
4827: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4828: exit(1);
4829: }else
4830: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4831: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4832: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4833: /* getting the maximum value of the modality of the covariate
4834: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4835: female ies 1, then modmaxcovj=1.
4836: */
4837: } /* end for loop on individuals i */
4838: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4839: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4840: cptcode=modmaxcovj;
4841: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4842: /*for (i=0; i<=cptcode; i++) {*/
4843: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4844: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4845: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4846: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4847: if( j != -1){
4848: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4849: covariate for which somebody answered excluding
4850: undefined. Usually 2: 0 and 1. */
4851: }
4852: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4853: covariate for which somebody answered including
4854: undefined. Usually 3: -1, 0 and 1. */
4855: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4856: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4857: } /* Ndum[-1] number of undefined modalities */
4858:
4859: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4860: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
4861: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
4862: /* modmincovj=3; modmaxcovj = 7; */
4863: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
4864: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
4865: /* defining two dummy variables: variables V1_1 and V1_2.*/
4866: /* nbcode[Tvar[j]][ij]=k; */
4867: /* nbcode[Tvar[j]][1]=0; */
4868: /* nbcode[Tvar[j]][2]=1; */
4869: /* nbcode[Tvar[j]][3]=2; */
4870: /* To be continued (not working yet). */
4871: ij=0; /* ij is similar to i but can jump over null modalities */
4872: 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*/
4873: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4874: break;
4875: }
4876: ij++;
4877: 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*/
4878: cptcode = ij; /* New max modality for covar j */
4879: } /* end of loop on modality i=-1 to 1 or more */
4880: break;
1.227 brouard 4881: case 1: /* Testing on varying covariate, could be simple and
4882: * should look at waves or product of fixed *
4883: * varying. No time to test -1, assuming 0 and 1 only */
1.231 brouard 4884: ij=0;
4885: for(i=0; i<=1;i++){
4886: nbcode[Tvar[k]][++ij]=i;
4887: }
4888: break;
1.227 brouard 4889: default:
1.231 brouard 4890: break;
1.227 brouard 4891: } /* end switch */
4892: } /* end dummy test */
1.225 brouard 4893:
1.192 brouard 4894: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4895: /* /\*recode from 0 *\/ */
4896: /* k is a modality. If we have model=V1+V1*sex */
4897: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4898: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4899: /* } */
4900: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4901: /* if (ij > ncodemax[j]) { */
4902: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4903: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4904: /* break; */
4905: /* } */
4906: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4907: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4908:
1.225 brouard 4909: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4910: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4911: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4912: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.227 brouard 4913: 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 */
4914: 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 */
4915: /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
1.225 brouard 4916: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4917:
4918: ij=0;
1.227 brouard 4919: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4920: for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
1.225 brouard 4921: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4922: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4923: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4924: /* If product not in single variable we don't print results */
1.225 brouard 4925: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.230 brouard 4926: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
4927: 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*/
4928: Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
1.231 brouard 4929: 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 */
1.227 brouard 4930: if(Fixed[k]!=0)
4931: anyvaryingduminmodel=1;
1.231 brouard 4932: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
4933: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
4934: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
4935: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
4936: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
4937: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
1.227 brouard 4938: }
1.225 brouard 4939: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4940: /* ij--; */
4941: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4942: *cptcov=ij; /*Number of total real effective covariates: effective
1.231 brouard 4943: * because they can be excluded from the model and real
4944: * if in the model but excluded because missing values, but how to get k from ij?*/
1.227 brouard 4945: for(j=ij+1; j<= cptcovt; j++){
4946: Tvaraff[j]=0;
4947: Tmodelind[j]=0;
4948: }
1.228 brouard 4949: for(j=ntveff+1; j<= cptcovt; j++){
4950: TmodelInvind[j]=0;
4951: }
1.227 brouard 4952: /* To be sorted */
4953: ;
1.126 brouard 4954: }
4955:
1.145 brouard 4956:
1.126 brouard 4957: /*********** Health Expectancies ****************/
4958:
1.235 brouard 4959: 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 4960:
4961: {
4962: /* Health expectancies, no variances */
1.164 brouard 4963: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4964: int nhstepma, nstepma; /* Decreasing with age */
4965: double age, agelim, hf;
4966: double ***p3mat;
4967: double eip;
4968:
1.238 brouard 4969: /* pstamp(ficreseij); */
1.126 brouard 4970: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4971: fprintf(ficreseij,"# Age");
4972: for(i=1; i<=nlstate;i++){
4973: for(j=1; j<=nlstate;j++){
4974: fprintf(ficreseij," e%1d%1d ",i,j);
4975: }
4976: fprintf(ficreseij," e%1d. ",i);
4977: }
4978: fprintf(ficreseij,"\n");
4979:
4980:
4981: if(estepm < stepm){
4982: printf ("Problem %d lower than %d\n",estepm, stepm);
4983: }
4984: else hstepm=estepm;
4985: /* We compute the life expectancy from trapezoids spaced every estepm months
4986: * This is mainly to measure the difference between two models: for example
4987: * if stepm=24 months pijx are given only every 2 years and by summing them
4988: * we are calculating an estimate of the Life Expectancy assuming a linear
4989: * progression in between and thus overestimating or underestimating according
4990: * to the curvature of the survival function. If, for the same date, we
4991: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4992: * to compare the new estimate of Life expectancy with the same linear
4993: * hypothesis. A more precise result, taking into account a more precise
4994: * curvature will be obtained if estepm is as small as stepm. */
4995:
4996: /* For example we decided to compute the life expectancy with the smallest unit */
4997: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4998: nhstepm is the number of hstepm from age to agelim
4999: nstepm is the number of stepm from age to agelin.
5000: Look at hpijx to understand the reason of that which relies in memory size
5001: and note for a fixed period like estepm months */
5002: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5003: survival function given by stepm (the optimization length). Unfortunately it
5004: means that if the survival funtion is printed only each two years of age and if
5005: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5006: results. So we changed our mind and took the option of the best precision.
5007: */
5008: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5009:
5010: agelim=AGESUP;
5011: /* If stepm=6 months */
5012: /* Computed by stepm unit matrices, product of hstepm matrices, stored
5013: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
5014:
5015: /* nhstepm age range expressed in number of stepm */
5016: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5017: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5018: /* if (stepm >= YEARM) hstepm=1;*/
5019: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5020: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5021:
5022: for (age=bage; age<=fage; age ++){
5023: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5024: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5025: /* if (stepm >= YEARM) hstepm=1;*/
5026: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
5027:
5028: /* If stepm=6 months */
5029: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5030: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5031:
1.235 brouard 5032: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);
1.126 brouard 5033:
5034: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5035:
5036: printf("%d|",(int)age);fflush(stdout);
5037: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5038:
5039: /* Computing expectancies */
5040: for(i=1; i<=nlstate;i++)
5041: for(j=1; j<=nlstate;j++)
5042: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5043: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
5044:
5045: /* 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]);*/
5046:
5047: }
5048:
5049: fprintf(ficreseij,"%3.0f",age );
5050: for(i=1; i<=nlstate;i++){
5051: eip=0;
5052: for(j=1; j<=nlstate;j++){
5053: eip +=eij[i][j][(int)age];
5054: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
5055: }
5056: fprintf(ficreseij,"%9.4f", eip );
5057: }
5058: fprintf(ficreseij,"\n");
5059:
5060: }
5061: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5062: printf("\n");
5063: fprintf(ficlog,"\n");
5064:
5065: }
5066:
1.235 brouard 5067: 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 5068:
5069: {
5070: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 5071: to initial status i, ei. .
1.126 brouard 5072: */
5073: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
5074: int nhstepma, nstepma; /* Decreasing with age */
5075: double age, agelim, hf;
5076: double ***p3matp, ***p3matm, ***varhe;
5077: double **dnewm,**doldm;
5078: double *xp, *xm;
5079: double **gp, **gm;
5080: double ***gradg, ***trgradg;
5081: int theta;
5082:
5083: double eip, vip;
5084:
5085: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
5086: xp=vector(1,npar);
5087: xm=vector(1,npar);
5088: dnewm=matrix(1,nlstate*nlstate,1,npar);
5089: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
5090:
5091: pstamp(ficresstdeij);
5092: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
5093: fprintf(ficresstdeij,"# Age");
5094: for(i=1; i<=nlstate;i++){
5095: for(j=1; j<=nlstate;j++)
5096: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
5097: fprintf(ficresstdeij," e%1d. ",i);
5098: }
5099: fprintf(ficresstdeij,"\n");
5100:
5101: pstamp(ficrescveij);
5102: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
5103: fprintf(ficrescveij,"# Age");
5104: for(i=1; i<=nlstate;i++)
5105: for(j=1; j<=nlstate;j++){
5106: cptj= (j-1)*nlstate+i;
5107: for(i2=1; i2<=nlstate;i2++)
5108: for(j2=1; j2<=nlstate;j2++){
5109: cptj2= (j2-1)*nlstate+i2;
5110: if(cptj2 <= cptj)
5111: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
5112: }
5113: }
5114: fprintf(ficrescveij,"\n");
5115:
5116: if(estepm < stepm){
5117: printf ("Problem %d lower than %d\n",estepm, stepm);
5118: }
5119: else hstepm=estepm;
5120: /* We compute the life expectancy from trapezoids spaced every estepm months
5121: * This is mainly to measure the difference between two models: for example
5122: * if stepm=24 months pijx are given only every 2 years and by summing them
5123: * we are calculating an estimate of the Life Expectancy assuming a linear
5124: * progression in between and thus overestimating or underestimating according
5125: * to the curvature of the survival function. If, for the same date, we
5126: * estimate the model with stepm=1 month, we can keep estepm to 24 months
5127: * to compare the new estimate of Life expectancy with the same linear
5128: * hypothesis. A more precise result, taking into account a more precise
5129: * curvature will be obtained if estepm is as small as stepm. */
5130:
5131: /* For example we decided to compute the life expectancy with the smallest unit */
5132: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5133: nhstepm is the number of hstepm from age to agelim
5134: nstepm is the number of stepm from age to agelin.
5135: Look at hpijx to understand the reason of that which relies in memory size
5136: and note for a fixed period like estepm months */
5137: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5138: survival function given by stepm (the optimization length). Unfortunately it
5139: means that if the survival funtion is printed only each two years of age and if
5140: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5141: results. So we changed our mind and took the option of the best precision.
5142: */
5143: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5144:
5145: /* If stepm=6 months */
5146: /* nhstepm age range expressed in number of stepm */
5147: agelim=AGESUP;
5148: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5149: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5150: /* if (stepm >= YEARM) hstepm=1;*/
5151: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5152:
5153: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5154: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5155: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5156: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5157: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5158: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5159:
5160: for (age=bage; age<=fage; age ++){
5161: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5162: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5163: /* if (stepm >= YEARM) hstepm=1;*/
5164: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5165:
1.126 brouard 5166: /* If stepm=6 months */
5167: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5168: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5169:
5170: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5171:
1.126 brouard 5172: /* Computing Variances of health expectancies */
5173: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5174: decrease memory allocation */
5175: for(theta=1; theta <=npar; theta++){
5176: for(i=1; i<=npar; i++){
1.222 brouard 5177: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5178: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5179: }
1.235 brouard 5180: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
5181: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);
1.218 brouard 5182:
1.126 brouard 5183: for(j=1; j<= nlstate; j++){
1.222 brouard 5184: for(i=1; i<=nlstate; i++){
5185: for(h=0; h<=nhstepm-1; h++){
5186: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5187: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5188: }
5189: }
1.126 brouard 5190: }
1.218 brouard 5191:
1.126 brouard 5192: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5193: for(h=0; h<=nhstepm-1; h++){
5194: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5195: }
1.126 brouard 5196: }/* End theta */
5197:
5198:
5199: for(h=0; h<=nhstepm-1; h++)
5200: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5201: for(theta=1; theta <=npar; theta++)
5202: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5203:
1.218 brouard 5204:
1.222 brouard 5205: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5206: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5207: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5208:
1.222 brouard 5209: printf("%d|",(int)age);fflush(stdout);
5210: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5211: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5212: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5213: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5214: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5215: for(ij=1;ij<=nlstate*nlstate;ij++)
5216: for(ji=1;ji<=nlstate*nlstate;ji++)
5217: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5218: }
5219: }
1.218 brouard 5220:
1.126 brouard 5221: /* Computing expectancies */
1.235 brouard 5222: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
1.126 brouard 5223: for(i=1; i<=nlstate;i++)
5224: for(j=1; j<=nlstate;j++)
1.222 brouard 5225: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5226: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5227:
1.222 brouard 5228: /* 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 5229:
1.222 brouard 5230: }
1.218 brouard 5231:
1.126 brouard 5232: fprintf(ficresstdeij,"%3.0f",age );
5233: for(i=1; i<=nlstate;i++){
5234: eip=0.;
5235: vip=0.;
5236: for(j=1; j<=nlstate;j++){
1.222 brouard 5237: eip += eij[i][j][(int)age];
5238: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5239: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5240: 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 5241: }
5242: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5243: }
5244: fprintf(ficresstdeij,"\n");
1.218 brouard 5245:
1.126 brouard 5246: fprintf(ficrescveij,"%3.0f",age );
5247: for(i=1; i<=nlstate;i++)
5248: for(j=1; j<=nlstate;j++){
1.222 brouard 5249: cptj= (j-1)*nlstate+i;
5250: for(i2=1; i2<=nlstate;i2++)
5251: for(j2=1; j2<=nlstate;j2++){
5252: cptj2= (j2-1)*nlstate+i2;
5253: if(cptj2 <= cptj)
5254: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5255: }
1.126 brouard 5256: }
5257: fprintf(ficrescveij,"\n");
1.218 brouard 5258:
1.126 brouard 5259: }
5260: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5261: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5262: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5263: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5264: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5265: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5266: printf("\n");
5267: fprintf(ficlog,"\n");
1.218 brouard 5268:
1.126 brouard 5269: free_vector(xm,1,npar);
5270: free_vector(xp,1,npar);
5271: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5272: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5273: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5274: }
1.218 brouard 5275:
1.126 brouard 5276: /************ Variance ******************/
1.235 brouard 5277: 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 5278: {
5279: /* Variance of health expectancies */
5280: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5281: /* double **newm;*/
5282: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5283:
5284: /* int movingaverage(); */
5285: double **dnewm,**doldm;
5286: double **dnewmp,**doldmp;
5287: int i, j, nhstepm, hstepm, h, nstepm ;
5288: int k;
5289: double *xp;
5290: double **gp, **gm; /* for var eij */
5291: double ***gradg, ***trgradg; /*for var eij */
5292: double **gradgp, **trgradgp; /* for var p point j */
5293: double *gpp, *gmp; /* for var p point j */
5294: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5295: double ***p3mat;
5296: double age,agelim, hf;
5297: /* double ***mobaverage; */
5298: int theta;
5299: char digit[4];
5300: char digitp[25];
5301:
5302: char fileresprobmorprev[FILENAMELENGTH];
5303:
5304: if(popbased==1){
5305: if(mobilav!=0)
5306: strcpy(digitp,"-POPULBASED-MOBILAV_");
5307: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5308: }
5309: else
5310: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5311:
1.218 brouard 5312: /* if (mobilav!=0) { */
5313: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5314: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5315: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5316: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5317: /* } */
5318: /* } */
5319:
5320: strcpy(fileresprobmorprev,"PRMORPREV-");
5321: sprintf(digit,"%-d",ij);
5322: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5323: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5324: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5325: strcat(fileresprobmorprev,fileresu);
5326: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5327: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5328: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5329: }
5330: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5331: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5332: pstamp(ficresprobmorprev);
5333: 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 5334: fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
5335: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
5336: fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
5337: }
5338: for(j=1;j<=cptcoveff;j++)
5339: fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
5340: fprintf(ficresprobmorprev,"\n");
5341:
1.218 brouard 5342: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5343: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5344: fprintf(ficresprobmorprev," p.%-d SE",j);
5345: for(i=1; i<=nlstate;i++)
5346: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5347: }
5348: fprintf(ficresprobmorprev,"\n");
5349:
5350: fprintf(ficgp,"\n# Routine varevsij");
5351: fprintf(ficgp,"\nunset title \n");
5352: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5353: 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");
5354: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5355: /* } */
5356: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5357: pstamp(ficresvij);
5358: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5359: if(popbased==1)
5360: 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);
5361: else
5362: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5363: fprintf(ficresvij,"# Age");
5364: for(i=1; i<=nlstate;i++)
5365: for(j=1; j<=nlstate;j++)
5366: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5367: fprintf(ficresvij,"\n");
5368:
5369: xp=vector(1,npar);
5370: dnewm=matrix(1,nlstate,1,npar);
5371: doldm=matrix(1,nlstate,1,nlstate);
5372: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5373: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5374:
5375: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5376: gpp=vector(nlstate+1,nlstate+ndeath);
5377: gmp=vector(nlstate+1,nlstate+ndeath);
5378: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5379:
1.218 brouard 5380: if(estepm < stepm){
5381: printf ("Problem %d lower than %d\n",estepm, stepm);
5382: }
5383: else hstepm=estepm;
5384: /* For example we decided to compute the life expectancy with the smallest unit */
5385: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5386: nhstepm is the number of hstepm from age to agelim
5387: nstepm is the number of stepm from age to agelim.
5388: Look at function hpijx to understand why because of memory size limitations,
5389: we decided (b) to get a life expectancy respecting the most precise curvature of the
5390: survival function given by stepm (the optimization length). Unfortunately it
5391: means that if the survival funtion is printed every two years of age and if
5392: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5393: results. So we changed our mind and took the option of the best precision.
5394: */
5395: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5396: agelim = AGESUP;
5397: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5398: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5399: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5400: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5401: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5402: gp=matrix(0,nhstepm,1,nlstate);
5403: gm=matrix(0,nhstepm,1,nlstate);
5404:
5405:
5406: for(theta=1; theta <=npar; theta++){
5407: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5408: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5409: }
5410:
1.235 brouard 5411: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
1.218 brouard 5412:
5413: if (popbased==1) {
5414: if(mobilav ==0){
5415: for(i=1; i<=nlstate;i++)
5416: prlim[i][i]=probs[(int)age][i][ij];
5417: }else{ /* mobilav */
5418: for(i=1; i<=nlstate;i++)
5419: prlim[i][i]=mobaverage[(int)age][i][ij];
5420: }
5421: }
5422:
1.235 brouard 5423: 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 5424: for(j=1; j<= nlstate; j++){
5425: for(h=0; h<=nhstepm; h++){
5426: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5427: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5428: }
5429: }
5430: /* Next for computing probability of death (h=1 means
5431: computed over hstepm matrices product = hstepm*stepm months)
5432: as a weighted average of prlim.
5433: */
5434: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5435: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5436: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5437: }
5438: /* end probability of death */
5439:
5440: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5441: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5442:
1.235 brouard 5443: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nresult);
1.218 brouard 5444:
5445: if (popbased==1) {
5446: if(mobilav ==0){
5447: for(i=1; i<=nlstate;i++)
5448: prlim[i][i]=probs[(int)age][i][ij];
5449: }else{ /* mobilav */
5450: for(i=1; i<=nlstate;i++)
5451: prlim[i][i]=mobaverage[(int)age][i][ij];
5452: }
5453: }
5454:
1.235 brouard 5455: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);
1.218 brouard 5456:
5457: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5458: for(h=0; h<=nhstepm; h++){
5459: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5460: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5461: }
5462: }
5463: /* This for computing probability of death (h=1 means
5464: computed over hstepm matrices product = hstepm*stepm months)
5465: as a weighted average of prlim.
5466: */
5467: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5468: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5469: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5470: }
5471: /* end probability of death */
5472:
5473: for(j=1; j<= nlstate; j++) /* vareij */
5474: for(h=0; h<=nhstepm; h++){
5475: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5476: }
5477:
5478: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5479: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5480: }
5481:
5482: } /* End theta */
5483:
5484: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5485:
5486: for(h=0; h<=nhstepm; h++) /* veij */
5487: for(j=1; j<=nlstate;j++)
5488: for(theta=1; theta <=npar; theta++)
5489: trgradg[h][j][theta]=gradg[h][theta][j];
5490:
5491: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5492: for(theta=1; theta <=npar; theta++)
5493: trgradgp[j][theta]=gradgp[theta][j];
5494:
5495:
5496: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5497: for(i=1;i<=nlstate;i++)
5498: for(j=1;j<=nlstate;j++)
5499: vareij[i][j][(int)age] =0.;
5500:
5501: for(h=0;h<=nhstepm;h++){
5502: for(k=0;k<=nhstepm;k++){
5503: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5504: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5505: for(i=1;i<=nlstate;i++)
5506: for(j=1;j<=nlstate;j++)
5507: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5508: }
5509: }
5510:
5511: /* pptj */
5512: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5513: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5514: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5515: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5516: varppt[j][i]=doldmp[j][i];
5517: /* end ppptj */
5518: /* x centered again */
5519:
1.235 brouard 5520: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);
1.218 brouard 5521:
5522: if (popbased==1) {
5523: if(mobilav ==0){
5524: for(i=1; i<=nlstate;i++)
5525: prlim[i][i]=probs[(int)age][i][ij];
5526: }else{ /* mobilav */
5527: for(i=1; i<=nlstate;i++)
5528: prlim[i][i]=mobaverage[(int)age][i][ij];
5529: }
5530: }
5531:
5532: /* This for computing probability of death (h=1 means
5533: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5534: as a weighted average of prlim.
5535: */
1.235 brouard 5536: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
1.218 brouard 5537: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5538: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5539: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5540: }
5541: /* end probability of death */
5542:
5543: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5544: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5545: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5546: for(i=1; i<=nlstate;i++){
5547: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5548: }
5549: }
5550: fprintf(ficresprobmorprev,"\n");
5551:
5552: fprintf(ficresvij,"%.0f ",age );
5553: for(i=1; i<=nlstate;i++)
5554: for(j=1; j<=nlstate;j++){
5555: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5556: }
5557: fprintf(ficresvij,"\n");
5558: free_matrix(gp,0,nhstepm,1,nlstate);
5559: free_matrix(gm,0,nhstepm,1,nlstate);
5560: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5561: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5562: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5563: } /* End age */
5564: free_vector(gpp,nlstate+1,nlstate+ndeath);
5565: free_vector(gmp,nlstate+1,nlstate+ndeath);
5566: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5567: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5568: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5569: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5570: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5571: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5572: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5573: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5574: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5575: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5576: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5577: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5578: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5579: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5580: 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);
5581: /* 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 5582: */
1.218 brouard 5583: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5584: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5585:
1.218 brouard 5586: free_vector(xp,1,npar);
5587: free_matrix(doldm,1,nlstate,1,nlstate);
5588: free_matrix(dnewm,1,nlstate,1,npar);
5589: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5590: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5591: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5592: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5593: fclose(ficresprobmorprev);
5594: fflush(ficgp);
5595: fflush(fichtm);
5596: } /* end varevsij */
1.126 brouard 5597:
5598: /************ Variance of prevlim ******************/
1.235 brouard 5599: 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 5600: {
1.205 brouard 5601: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5602: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5603:
1.126 brouard 5604: double **dnewm,**doldm;
5605: int i, j, nhstepm, hstepm;
5606: double *xp;
5607: double *gp, *gm;
5608: double **gradg, **trgradg;
1.208 brouard 5609: double **mgm, **mgp;
1.126 brouard 5610: double age,agelim;
5611: int theta;
5612:
5613: pstamp(ficresvpl);
5614: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5615: fprintf(ficresvpl,"# Age");
5616: for(i=1; i<=nlstate;i++)
5617: fprintf(ficresvpl," %1d-%1d",i,i);
5618: fprintf(ficresvpl,"\n");
5619:
5620: xp=vector(1,npar);
5621: dnewm=matrix(1,nlstate,1,npar);
5622: doldm=matrix(1,nlstate,1,nlstate);
5623:
5624: hstepm=1*YEARM; /* Every year of age */
5625: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5626: agelim = AGESUP;
5627: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5628: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5629: if (stepm >= YEARM) hstepm=1;
5630: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5631: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5632: mgp=matrix(1,npar,1,nlstate);
5633: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5634: gp=vector(1,nlstate);
5635: gm=vector(1,nlstate);
5636:
5637: for(theta=1; theta <=npar; theta++){
5638: for(i=1; i<=npar; i++){ /* Computes gradient */
5639: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5640: }
1.209 brouard 5641: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 5642: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5643: else
1.235 brouard 5644: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5645: for(i=1;i<=nlstate;i++){
1.126 brouard 5646: gp[i] = prlim[i][i];
1.208 brouard 5647: mgp[theta][i] = prlim[i][i];
5648: }
1.126 brouard 5649: for(i=1; i<=npar; i++) /* Computes gradient */
5650: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5651: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
1.235 brouard 5652: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.209 brouard 5653: else
1.235 brouard 5654: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
1.208 brouard 5655: for(i=1;i<=nlstate;i++){
1.126 brouard 5656: gm[i] = prlim[i][i];
1.208 brouard 5657: mgm[theta][i] = prlim[i][i];
5658: }
1.126 brouard 5659: for(i=1;i<=nlstate;i++)
5660: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5661: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5662: } /* End theta */
5663:
5664: trgradg =matrix(1,nlstate,1,npar);
5665:
5666: for(j=1; j<=nlstate;j++)
5667: for(theta=1; theta <=npar; theta++)
5668: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5669: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5670: /* printf("\nmgm mgp %d ",(int)age); */
5671: /* for(j=1; j<=nlstate;j++){ */
5672: /* printf(" %d ",j); */
5673: /* for(theta=1; theta <=npar; theta++) */
5674: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5675: /* printf("\n "); */
5676: /* } */
5677: /* } */
5678: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5679: /* printf("\n gradg %d ",(int)age); */
5680: /* for(j=1; j<=nlstate;j++){ */
5681: /* printf("%d ",j); */
5682: /* for(theta=1; theta <=npar; theta++) */
5683: /* printf("%d %lf ",theta,gradg[theta][j]); */
5684: /* printf("\n "); */
5685: /* } */
5686: /* } */
1.126 brouard 5687:
5688: for(i=1;i<=nlstate;i++)
5689: varpl[i][(int)age] =0.;
1.209 brouard 5690: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5691: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5692: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5693: }else{
1.126 brouard 5694: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5695: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5696: }
1.126 brouard 5697: for(i=1;i<=nlstate;i++)
5698: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5699:
5700: fprintf(ficresvpl,"%.0f ",age );
5701: for(i=1; i<=nlstate;i++)
5702: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5703: fprintf(ficresvpl,"\n");
5704: free_vector(gp,1,nlstate);
5705: free_vector(gm,1,nlstate);
1.208 brouard 5706: free_matrix(mgm,1,npar,1,nlstate);
5707: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5708: free_matrix(gradg,1,npar,1,nlstate);
5709: free_matrix(trgradg,1,nlstate,1,npar);
5710: } /* End age */
5711:
5712: free_vector(xp,1,npar);
5713: free_matrix(doldm,1,nlstate,1,npar);
5714: free_matrix(dnewm,1,nlstate,1,nlstate);
5715:
5716: }
5717:
5718: /************ Variance of one-step probabilities ******************/
5719: 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 5720: {
5721: int i, j=0, k1, l1, tj;
5722: int k2, l2, j1, z1;
5723: int k=0, l;
5724: int first=1, first1, first2;
5725: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5726: double **dnewm,**doldm;
5727: double *xp;
5728: double *gp, *gm;
5729: double **gradg, **trgradg;
5730: double **mu;
5731: double age, cov[NCOVMAX+1];
5732: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5733: int theta;
5734: char fileresprob[FILENAMELENGTH];
5735: char fileresprobcov[FILENAMELENGTH];
5736: char fileresprobcor[FILENAMELENGTH];
5737: double ***varpij;
5738:
5739: strcpy(fileresprob,"PROB_");
5740: strcat(fileresprob,fileres);
5741: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5742: printf("Problem with resultfile: %s\n", fileresprob);
5743: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5744: }
5745: strcpy(fileresprobcov,"PROBCOV_");
5746: strcat(fileresprobcov,fileresu);
5747: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5748: printf("Problem with resultfile: %s\n", fileresprobcov);
5749: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5750: }
5751: strcpy(fileresprobcor,"PROBCOR_");
5752: strcat(fileresprobcor,fileresu);
5753: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5754: printf("Problem with resultfile: %s\n", fileresprobcor);
5755: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5756: }
5757: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5758: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5759: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5760: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5761: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5762: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5763: pstamp(ficresprob);
5764: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5765: fprintf(ficresprob,"# Age");
5766: pstamp(ficresprobcov);
5767: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5768: fprintf(ficresprobcov,"# Age");
5769: pstamp(ficresprobcor);
5770: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5771: fprintf(ficresprobcor,"# Age");
1.126 brouard 5772:
5773:
1.222 brouard 5774: for(i=1; i<=nlstate;i++)
5775: for(j=1; j<=(nlstate+ndeath);j++){
5776: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5777: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5778: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5779: }
5780: /* fprintf(ficresprob,"\n");
5781: fprintf(ficresprobcov,"\n");
5782: fprintf(ficresprobcor,"\n");
5783: */
5784: xp=vector(1,npar);
5785: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5786: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5787: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5788: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5789: first=1;
5790: fprintf(ficgp,"\n# Routine varprob");
5791: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5792: fprintf(fichtm,"\n");
5793:
5794: 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);
5795: 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);
5796: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5797: and drawn. It helps understanding how is the covariance between two incidences.\
5798: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5799: 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 5800: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5801: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5802: standard deviations wide on each axis. <br>\
5803: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5804: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5805: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5806:
1.222 brouard 5807: cov[1]=1;
5808: /* tj=cptcoveff; */
1.225 brouard 5809: tj = (int) pow(2,cptcoveff);
1.222 brouard 5810: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5811: j1=0;
1.224 brouard 5812: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5813: if (cptcovn>0) {
5814: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5815: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5816: fprintf(ficresprob, "**********\n#\n");
5817: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5818: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5819: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5820:
1.222 brouard 5821: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5822: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5823: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5824:
5825:
1.222 brouard 5826: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5827: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5828: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5829:
1.222 brouard 5830: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5831: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5832: fprintf(ficresprobcor, "**********\n#");
5833: if(invalidvarcomb[j1]){
5834: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5835: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5836: continue;
5837: }
5838: }
5839: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5840: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5841: gp=vector(1,(nlstate)*(nlstate+ndeath));
5842: gm=vector(1,(nlstate)*(nlstate+ndeath));
5843: for (age=bage; age<=fage; age ++){
5844: cov[2]=age;
5845: if(nagesqr==1)
5846: cov[3]= age*age;
5847: for (k=1; k<=cptcovn;k++) {
5848: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5849: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5850: * 1 1 1 1 1
5851: * 2 2 1 1 1
5852: * 3 1 2 1 1
5853: */
5854: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5855: }
5856: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5857: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5858: for (k=1; k<=cptcovprod;k++)
5859: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5860:
5861:
1.222 brouard 5862: for(theta=1; theta <=npar; theta++){
5863: for(i=1; i<=npar; i++)
5864: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5865:
1.222 brouard 5866: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5867:
1.222 brouard 5868: k=0;
5869: for(i=1; i<= (nlstate); i++){
5870: for(j=1; j<=(nlstate+ndeath);j++){
5871: k=k+1;
5872: gp[k]=pmmij[i][j];
5873: }
5874: }
1.220 brouard 5875:
1.222 brouard 5876: for(i=1; i<=npar; i++)
5877: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5878:
1.222 brouard 5879: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5880: k=0;
5881: for(i=1; i<=(nlstate); i++){
5882: for(j=1; j<=(nlstate+ndeath);j++){
5883: k=k+1;
5884: gm[k]=pmmij[i][j];
5885: }
5886: }
1.220 brouard 5887:
1.222 brouard 5888: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5889: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5890: }
1.126 brouard 5891:
1.222 brouard 5892: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5893: for(theta=1; theta <=npar; theta++)
5894: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5895:
1.222 brouard 5896: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5897: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5898:
1.222 brouard 5899: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5900:
1.222 brouard 5901: k=0;
5902: for(i=1; i<=(nlstate); i++){
5903: for(j=1; j<=(nlstate+ndeath);j++){
5904: k=k+1;
5905: mu[k][(int) age]=pmmij[i][j];
5906: }
5907: }
5908: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5909: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5910: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5911:
1.222 brouard 5912: /*printf("\n%d ",(int)age);
5913: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5914: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5915: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5916: }*/
1.220 brouard 5917:
1.222 brouard 5918: fprintf(ficresprob,"\n%d ",(int)age);
5919: fprintf(ficresprobcov,"\n%d ",(int)age);
5920: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5921:
1.222 brouard 5922: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5923: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5924: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5925: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5926: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5927: }
5928: i=0;
5929: for (k=1; k<=(nlstate);k++){
5930: for (l=1; l<=(nlstate+ndeath);l++){
5931: i++;
5932: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5933: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5934: for (j=1; j<=i;j++){
5935: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5936: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5937: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5938: }
5939: }
5940: }/* end of loop for state */
5941: } /* end of loop for age */
5942: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5943: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5944: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5945: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5946:
5947: /* Confidence intervalle of pij */
5948: /*
5949: fprintf(ficgp,"\nunset parametric;unset label");
5950: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5951: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5952: 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);
5953: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5954: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5955: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5956: */
5957:
5958: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5959: first1=1;first2=2;
5960: for (k2=1; k2<=(nlstate);k2++){
5961: for (l2=1; l2<=(nlstate+ndeath);l2++){
5962: if(l2==k2) continue;
5963: j=(k2-1)*(nlstate+ndeath)+l2;
5964: for (k1=1; k1<=(nlstate);k1++){
5965: for (l1=1; l1<=(nlstate+ndeath);l1++){
5966: if(l1==k1) continue;
5967: i=(k1-1)*(nlstate+ndeath)+l1;
5968: if(i<=j) continue;
5969: for (age=bage; age<=fage; age ++){
5970: if ((int)age %5==0){
5971: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5972: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5973: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5974: mu1=mu[i][(int) age]/stepm*YEARM ;
5975: mu2=mu[j][(int) age]/stepm*YEARM;
5976: c12=cv12/sqrt(v1*v2);
5977: /* Computing eigen value of matrix of covariance */
5978: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5979: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5980: if ((lc2 <0) || (lc1 <0) ){
5981: if(first2==1){
5982: first1=0;
5983: 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);
5984: }
5985: 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);
5986: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5987: /* lc2=fabs(lc2); */
5988: }
1.220 brouard 5989:
1.222 brouard 5990: /* Eigen vectors */
5991: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5992: /*v21=sqrt(1.-v11*v11); *//* error */
5993: v21=(lc1-v1)/cv12*v11;
5994: v12=-v21;
5995: v22=v11;
5996: tnalp=v21/v11;
5997: if(first1==1){
5998: first1=0;
5999: 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);
6000: }
6001: 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);
6002: /*printf(fignu*/
6003: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
6004: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
6005: if(first==1){
6006: first=0;
6007: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
6008: fprintf(ficgp,"\nset parametric;unset label");
6009: 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);
6010: fprintf(ficgp,"\nset ter svg size 640, 480");
6011: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 6012: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 6013: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 6014: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
6015: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6016: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6017: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
6018: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6019: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6020: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6021: 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", \
6022: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
6023: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
6024: }else{
6025: first=0;
6026: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
6027: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
6028: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
6029: 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", \
6030: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
6031: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
6032: }/* if first */
6033: } /* age mod 5 */
6034: } /* end loop age */
6035: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
6036: first=1;
6037: } /*l12 */
6038: } /* k12 */
6039: } /*l1 */
6040: }/* k1 */
6041: } /* loop on combination of covariates j1 */
6042: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
6043: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
6044: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
6045: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
6046: free_vector(xp,1,npar);
6047: fclose(ficresprob);
6048: fclose(ficresprobcov);
6049: fclose(ficresprobcor);
6050: fflush(ficgp);
6051: fflush(fichtmcov);
6052: }
1.126 brouard 6053:
6054:
6055: /******************* Printing html file ***********/
1.201 brouard 6056: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6057: int lastpass, int stepm, int weightopt, char model[],\
6058: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 6059: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 6060: double jprev1, double mprev1,double anprev1, double dateprev1, \
6061: double jprev2, double mprev2,double anprev2, double dateprev2){
1.237 brouard 6062: int jj1, k1, i1, cpt, k4, nres;
1.126 brouard 6063:
6064: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
6065: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
6066: </ul>");
1.237 brouard 6067: fprintf(fichtm,"<ul><li> model=1+age+%s\n \
6068: </ul>", model);
1.214 brouard 6069: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
6070: 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",
6071: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
6072: 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 6073: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
6074: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 6075: fprintf(fichtm,"\
6076: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 6077: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 6078: fprintf(fichtm,"\
1.217 brouard 6079: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
6080: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
6081: fprintf(fichtm,"\
1.126 brouard 6082: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6083: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 6084: fprintf(fichtm,"\
1.217 brouard 6085: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
6086: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
6087: fprintf(fichtm,"\
1.211 brouard 6088: - (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 6089: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 6090: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 6091: if(prevfcast==1){
6092: fprintf(fichtm,"\
6093: - Prevalence projections by age and states: \
1.201 brouard 6094: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 6095: }
1.126 brouard 6096:
1.222 brouard 6097: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 6098:
1.225 brouard 6099: m=pow(2,cptcoveff);
1.222 brouard 6100: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6101:
1.222 brouard 6102: jj1=0;
1.237 brouard 6103:
6104: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.222 brouard 6105: for(k1=1; k1<=m;k1++){
1.237 brouard 6106: if(TKresult[nres]!= k1)
6107: continue;
1.220 brouard 6108:
1.222 brouard 6109: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6110: jj1++;
6111: if (cptcovn > 0) {
6112: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6113: for (cpt=1; cpt<=cptcoveff;cpt++){
1.237 brouard 6114: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
6115: printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
6116: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6117: /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
1.222 brouard 6118: }
1.237 brouard 6119: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6120: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6121: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
6122: }
6123:
1.230 brouard 6124: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 6125: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
6126: if(invalidvarcomb[k1]){
6127: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
6128: printf("\nCombination (%d) ignored because no cases \n",k1);
6129: continue;
6130: }
6131: }
6132: /* aij, bij */
6133: 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.svg\">%s_%d-1.svg</a><br> \
1.211 brouard 6134: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6135: /* Pij */
6136: 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.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 6137: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6138: /* Quasi-incidences */
6139: 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 6140: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 6141: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
6142: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
1.201 brouard 6143: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 6144: /* Survival functions (period) in state j */
6145: for(cpt=1; cpt<=nlstate;cpt++){
6146: 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.svg\">%s%d_%d.svg</a><br> \
1.201 brouard 6147: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
1.222 brouard 6148: }
6149: /* State specific survival functions (period) */
6150: for(cpt=1; cpt<=nlstate;cpt++){
6151: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6152: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 6153: <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
1.222 brouard 6154: }
6155: /* Period (stable) prevalence in each health state */
6156: for(cpt=1; cpt<=nlstate;cpt++){
6157: fprintf(fichtm,"<br>\n- Convergence 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.svg\">%s_%d-%d.svg</a><br> \
1.201 brouard 6158: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
1.222 brouard 6159: }
6160: if(backcast==1){
6161: /* Period (stable) back prevalence in each health state */
6162: for(cpt=1; cpt<=nlstate;cpt++){
6163: fprintf(fichtm,"<br>\n- Convergence to period (stable) back 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.svg\">%s_%d-%d.svg</a><br> \
1.217 brouard 6164: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
1.222 brouard 6165: }
1.217 brouard 6166: }
1.222 brouard 6167: if(prevfcast==1){
6168: /* Projection of prevalence up to period (stable) prevalence in each health state */
6169: for(cpt=1; cpt<=nlstate;cpt++){
6170: 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.svg\">%s%d_%d.svg</a><br> \
1.213 brouard 6171: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.222 brouard 6172: }
6173: }
1.220 brouard 6174:
1.222 brouard 6175: for(cpt=1; cpt<=nlstate;cpt++) {
6176: 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.svg\">%s_%d%d.svg</a> <br> \
1.201 brouard 6177: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.222 brouard 6178: }
6179: /* } /\* end i1 *\/ */
6180: }/* End k1 */
6181: fprintf(fichtm,"</ul>");
1.126 brouard 6182:
1.222 brouard 6183: fprintf(fichtm,"\
1.126 brouard 6184: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6185: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6186: - 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 6187: But because parameters are usually highly correlated (a higher incidence of disability \
6188: and a higher incidence of recovery can give very close observed transition) it might \
6189: be very useful to look not only at linear confidence intervals estimated from the \
6190: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6191: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6192: covariance matrix of the one-step probabilities. \
6193: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6194:
1.222 brouard 6195: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6196: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6197: fprintf(fichtm,"\
1.126 brouard 6198: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6199: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6200:
1.222 brouard 6201: fprintf(fichtm,"\
1.126 brouard 6202: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6203: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6204: fprintf(fichtm,"\
1.126 brouard 6205: - 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): \
6206: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6207: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6208: fprintf(fichtm,"\
1.126 brouard 6209: - (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): \
6210: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6211: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6212: fprintf(fichtm,"\
1.128 brouard 6213: - 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 6214: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6215: fprintf(fichtm,"\
1.128 brouard 6216: - 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 6217: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6218: fprintf(fichtm,"\
1.126 brouard 6219: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6220: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6221:
6222: /* if(popforecast==1) fprintf(fichtm,"\n */
6223: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6224: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6225: /* <br>",fileres,fileres,fileres,fileres); */
6226: /* else */
6227: /* 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 6228: fflush(fichtm);
6229: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6230:
1.225 brouard 6231: m=pow(2,cptcoveff);
1.222 brouard 6232: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6233:
1.222 brouard 6234: jj1=0;
1.237 brouard 6235:
6236: for(nres=1; nres <= nresult; nres++) /* For each resultline */
1.222 brouard 6237: for(k1=1; k1<=m;k1++){
1.237 brouard 6238: if(TKresult[nres]!= k1)
6239: continue;
1.222 brouard 6240: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6241: jj1++;
1.126 brouard 6242: if (cptcovn > 0) {
6243: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6244: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.237 brouard 6245: fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
6246: /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
6247: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6248: fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6249: }
6250:
1.126 brouard 6251: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6252:
1.222 brouard 6253: if(invalidvarcomb[k1]){
6254: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6255: continue;
6256: }
1.126 brouard 6257: }
6258: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6259: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6260: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6261: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 6262: }
6263: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6264: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6265: true period expectancies (those weighted with period prevalences are also\
6266: drawn in addition to the population based expectancies computed using\
1.218 brouard 6267: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6268: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6269: /* } /\* end i1 *\/ */
6270: }/* End k1 */
6271: fprintf(fichtm,"</ul>");
6272: fflush(fichtm);
1.126 brouard 6273: }
6274:
6275: /******************* Gnuplot file **************/
1.223 brouard 6276: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6277:
6278: char dirfileres[132],optfileres[132];
1.223 brouard 6279: char gplotcondition[132];
1.237 brouard 6280: 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 6281: int lv=0, vlv=0, kl=0;
1.130 brouard 6282: int ng=0;
1.201 brouard 6283: int vpopbased;
1.223 brouard 6284: int ioffset; /* variable offset for columns */
1.235 brouard 6285: int nres=0; /* Index of resultline */
1.219 brouard 6286:
1.126 brouard 6287: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6288: /* printf("Problem with file %s",optionfilegnuplot); */
6289: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6290: /* } */
6291:
6292: /*#ifdef windows */
6293: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6294: /*#endif */
1.225 brouard 6295: m=pow(2,cptcoveff);
1.126 brouard 6296:
1.202 brouard 6297: /* Contribution to likelihood */
6298: /* Plot the probability implied in the likelihood */
1.223 brouard 6299: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6300: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6301: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6302: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6303: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6304: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6305: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6306: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6307: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6308: 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));
6309: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6310: 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));
6311: for (i=1; i<= nlstate ; i ++) {
6312: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6313: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6314: 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);
6315: for (j=2; j<= nlstate+ndeath ; j ++) {
6316: 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);
6317: }
6318: fprintf(ficgp,";\nset out; unset ylabel;\n");
6319: }
6320: /* 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 */
6321: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6322: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6323: fprintf(ficgp,"\nset out;unset log\n");
6324: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6325:
1.126 brouard 6326: strcpy(dirfileres,optionfilefiname);
6327: strcpy(optfileres,"vpl");
1.223 brouard 6328: /* 1eme*/
1.238 brouard 6329: for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
6330: for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
1.236 brouard 6331: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.238 brouard 6332: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6333: if(TKresult[nres]!= k1)
6334: continue;
6335: /* We are interested in selected combination by the resultline */
6336: printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
6337: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
6338: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6339: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
6340: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6341: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6342: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6343: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6344: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6345: printf(" V%d=%d ",Tvaraff[k],vlv);
6346: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6347: }
6348: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6349: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6350: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6351: }
6352: printf("\n#\n");
6353: fprintf(ficgp,"\n#\n");
6354: if(invalidvarcomb[k1]){
6355: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6356: continue;
6357: }
1.235 brouard 6358:
1.238 brouard 6359: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6360: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.240 ! brouard 6361: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.235 brouard 6362:
1.238 brouard 6363: for (i=1; i<= nlstate ; i ++) {
6364: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6365: else fprintf(ficgp," %%*lf (%%*lf)");
6366: }
6367: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6368: for (i=1; i<= nlstate ; i ++) {
6369: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6370: else fprintf(ficgp," %%*lf (%%*lf)");
6371: }
6372: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6373: for (i=1; i<= nlstate ; i ++) {
6374: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6375: else fprintf(ficgp," %%*lf (%%*lf)");
6376: }
6377: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6378: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6379: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6380: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
6381: if(cptcoveff ==0){
6382: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6383: }else{
6384: kl=0;
6385: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6386: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6387: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6388: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6389: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6390: vlv= nbcode[Tvaraff[k]][lv];
1.223 brouard 6391: kl++;
1.238 brouard 6392: /* 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 *\/ */
6393: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6394: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6395: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
6396: if(k==cptcoveff){
6397: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6398: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
6399: }else{
6400: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6401: kl++;
6402: }
6403: } /* end covariate */
6404: } /* end if no covariate */
6405: } /* end if backcast */
6406: fprintf(ficgp,"\nset out \n");
6407: } /* nres */
1.201 brouard 6408: } /* k1 */
6409: } /* cpt */
1.235 brouard 6410:
6411:
1.126 brouard 6412: /*2 eme*/
1.238 brouard 6413: for (k1=1; k1<= m ; k1 ++){
6414: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6415: if(TKresult[nres]!= k1)
6416: continue;
6417: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
6418: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.225 brouard 6419: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6420: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6421: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6422: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6423: vlv= nbcode[Tvaraff[k]][lv];
6424: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6425: }
1.237 brouard 6426: /* for(k=1; k <= ncovds; k++){ */
1.236 brouard 6427: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 6428: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.236 brouard 6429: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.238 brouard 6430: }
1.211 brouard 6431: fprintf(ficgp,"\n#\n");
1.223 brouard 6432: if(invalidvarcomb[k1]){
6433: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6434: continue;
6435: }
1.219 brouard 6436:
1.238 brouard 6437: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6438: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6439: if(vpopbased==0)
6440: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6441: else
6442: fprintf(ficgp,"\nreplot ");
6443: for (i=1; i<= nlstate+1 ; i ++) {
6444: k=2*i;
6445: 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);
6446: for (j=1; j<= nlstate+1 ; j ++) {
6447: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6448: else fprintf(ficgp," %%*lf (%%*lf)");
6449: }
6450: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6451: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6452: 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);
6453: for (j=1; j<= nlstate+1 ; j ++) {
6454: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6455: else fprintf(ficgp," %%*lf (%%*lf)");
6456: }
6457: fprintf(ficgp,"\" t\"\" w l lt 0,");
6458: 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);
6459: for (j=1; j<= nlstate+1 ; j ++) {
6460: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6461: else fprintf(ficgp," %%*lf (%%*lf)");
6462: }
6463: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6464: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6465: } /* state */
6466: } /* vpopbased */
6467: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
6468: } /* end nres */
6469: } /* k1 end 2 eme*/
6470:
6471:
6472: /*3eme*/
6473: for (k1=1; k1<= m ; k1 ++){
6474: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
1.240 ! brouard 6475: if(TKresult[nres]!= k1)
1.238 brouard 6476: continue;
6477:
6478: for (cpt=1; cpt<= nlstate ; cpt ++) {
6479: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
6480: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6481: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6482: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6483: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6484: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6485: vlv= nbcode[Tvaraff[k]][lv];
6486: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6487: }
6488: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6489: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6490: }
6491: fprintf(ficgp,"\n#\n");
6492: if(invalidvarcomb[k1]){
6493: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6494: continue;
6495: }
6496:
6497: /* k=2+nlstate*(2*cpt-2); */
6498: k=2+(nlstate+1)*(cpt-1);
6499: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
6500: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6501: 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 6502: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6503: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6504: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6505: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6506: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6507: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6508:
1.238 brouard 6509: */
6510: for (i=1; i< nlstate ; i ++) {
6511: 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);
6512: /* 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 6513:
1.238 brouard 6514: }
6515: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
6516: }
6517: } /* end nres */
6518: } /* end kl 3eme */
1.126 brouard 6519:
1.223 brouard 6520: /* 4eme */
1.201 brouard 6521: /* Survival functions (period) from state i in state j by initial state i */
1.238 brouard 6522: for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
6523: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6524: if(TKresult[nres]!= k1)
1.223 brouard 6525: continue;
1.238 brouard 6526: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
6527: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
6528: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6529: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6530: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6531: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6532: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6533: vlv= nbcode[Tvaraff[k]][lv];
6534: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6535: }
6536: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6537: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6538: }
6539: fprintf(ficgp,"\n#\n");
6540: if(invalidvarcomb[k1]){
6541: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6542: continue;
1.223 brouard 6543: }
1.238 brouard 6544:
6545: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6546: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
6547: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
6548: k=3;
6549: for (i=1; i<= nlstate ; i ++){
6550: if(i==1){
6551: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6552: }else{
6553: fprintf(ficgp,", '' ");
6554: }
6555: l=(nlstate+ndeath)*(i-1)+1;
6556: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6557: for (j=2; j<= nlstate+ndeath ; j ++)
6558: fprintf(ficgp,"+$%d",k+l+j-1);
6559: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
6560: } /* nlstate */
6561: fprintf(ficgp,"\nset out\n");
6562: } /* end cpt state*/
6563: } /* end nres */
6564: } /* end covariate k1 */
6565:
1.220 brouard 6566: /* 5eme */
1.201 brouard 6567: /* Survival functions (period) from state i in state j by final state j */
1.238 brouard 6568: for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
6569: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6570: if(TKresult[nres]!= k1)
1.227 brouard 6571: continue;
1.238 brouard 6572: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
6573: 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);
6574: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6575: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6576: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6577: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6578: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6579: vlv= nbcode[Tvaraff[k]][lv];
6580: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6581: }
6582: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6583: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6584: }
6585: fprintf(ficgp,"\n#\n");
6586: if(invalidvarcomb[k1]){
6587: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6588: continue;
6589: }
1.227 brouard 6590:
1.238 brouard 6591: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6592: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
6593: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
6594: k=3;
6595: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
6596: if(j==1)
6597: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6598: else
6599: fprintf(ficgp,", '' ");
6600: l=(nlstate+ndeath)*(cpt-1) +j;
6601: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6602: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6603: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6604: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
6605: } /* nlstate */
6606: fprintf(ficgp,", '' ");
6607: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6608: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
6609: l=(nlstate+ndeath)*(cpt-1) +j;
6610: if(j < nlstate)
6611: fprintf(ficgp,"$%d +",k+l);
6612: else
6613: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
6614: }
6615: fprintf(ficgp,"\nset out\n");
6616: } /* end cpt state*/
6617: } /* end covariate */
6618: } /* end nres */
1.227 brouard 6619:
1.220 brouard 6620: /* 6eme */
1.202 brouard 6621: /* CV preval stable (period) for each covariate */
1.237 brouard 6622: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
6623: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6624: if(TKresult[nres]!= k1)
6625: continue;
1.153 brouard 6626: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6627:
1.211 brouard 6628: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6629: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6630: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6631: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6632: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6633: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6634: vlv= nbcode[Tvaraff[k]][lv];
6635: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6636: }
1.237 brouard 6637: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6638: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6639: }
1.211 brouard 6640: fprintf(ficgp,"\n#\n");
1.223 brouard 6641: if(invalidvarcomb[k1]){
1.227 brouard 6642: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6643: continue;
1.223 brouard 6644: }
1.227 brouard 6645:
1.201 brouard 6646: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6647: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 6648: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6649: k=3; /* Offset */
1.153 brouard 6650: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6651: if(i==1)
6652: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6653: else
6654: fprintf(ficgp,", '' ");
6655: l=(nlstate+ndeath)*(i-1)+1;
6656: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6657: for (j=2; j<= nlstate ; j ++)
6658: fprintf(ficgp,"+$%d",k+l+j-1);
6659: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6660: } /* nlstate */
1.201 brouard 6661: fprintf(ficgp,"\nset out\n");
1.153 brouard 6662: } /* end cpt state*/
6663: } /* end covariate */
1.227 brouard 6664:
6665:
1.220 brouard 6666: /* 7eme */
1.218 brouard 6667: if(backcast == 1){
1.217 brouard 6668: /* CV back preval stable (period) for each covariate */
1.237 brouard 6669: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
6670: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6671: if(TKresult[nres]!= k1)
6672: continue;
1.218 brouard 6673: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6674: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6675: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6676: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6677: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6678: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6679: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6680: vlv= nbcode[Tvaraff[k]][lv];
6681: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6682: }
1.237 brouard 6683: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6684: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6685: }
1.227 brouard 6686: fprintf(ficgp,"\n#\n");
6687: if(invalidvarcomb[k1]){
6688: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6689: continue;
6690: }
6691:
6692: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6693: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.238 brouard 6694: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6695: k=3; /* Offset */
6696: for (i=1; i<= nlstate ; i ++){
6697: if(i==1)
6698: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6699: else
6700: fprintf(ficgp,", '' ");
6701: /* l=(nlstate+ndeath)*(i-1)+1; */
6702: l=(nlstate+ndeath)*(cpt-1)+1;
6703: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6704: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6705: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6706: /* for (j=2; j<= nlstate ; j ++) */
6707: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6708: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6709: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6710: } /* nlstate */
6711: fprintf(ficgp,"\nset out\n");
1.218 brouard 6712: } /* end cpt state*/
6713: } /* end covariate */
6714: } /* End if backcast */
6715:
1.223 brouard 6716: /* 8eme */
1.218 brouard 6717: if(prevfcast==1){
6718: /* Projection from cross-sectional to stable (period) for each covariate */
6719:
1.237 brouard 6720: for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
6721: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6722: if(TKresult[nres]!= k1)
6723: continue;
1.211 brouard 6724: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6725: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6726: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6727: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6728: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6729: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6730: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6731: vlv= nbcode[Tvaraff[k]][lv];
6732: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6733: }
1.237 brouard 6734: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6735: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6736: }
1.227 brouard 6737: fprintf(ficgp,"\n#\n");
6738: if(invalidvarcomb[k1]){
6739: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6740: continue;
6741: }
6742:
6743: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6744: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6745: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
1.238 brouard 6746: set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6747: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6748: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6749: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6750: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6751: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6752: if(i==1){
6753: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6754: }else{
6755: fprintf(ficgp,",\\\n '' ");
6756: }
6757: if(cptcoveff ==0){ /* No covariate */
6758: ioffset=2; /* Age is in 2 */
6759: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6760: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6761: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6762: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6763: fprintf(ficgp," u %d:(", ioffset);
6764: if(i==nlstate+1)
6765: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6766: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6767: else
6768: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6769: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6770: }else{ /* more than 2 covariates */
6771: if(cptcoveff ==1){
6772: ioffset=4; /* Age is in 4 */
6773: }else{
6774: ioffset=6; /* Age is in 6 */
6775: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6776: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6777: }
6778: fprintf(ficgp," u %d:(",ioffset);
6779: kl=0;
6780: strcpy(gplotcondition,"(");
6781: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6782: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6783: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6784: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6785: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6786: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6787: kl++;
6788: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6789: kl++;
6790: if(k <cptcoveff && cptcoveff>1)
6791: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6792: }
6793: strcpy(gplotcondition+strlen(gplotcondition),")");
6794: /* 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 *\/ */
6795: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6796: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6797: /* '' 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*/
6798: if(i==nlstate+1){
6799: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6800: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6801: }else{
6802: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6803: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6804: }
6805: } /* end if covariate */
6806: } /* nlstate */
6807: fprintf(ficgp,"\nset out\n");
1.223 brouard 6808: } /* end cpt state*/
6809: } /* end covariate */
6810: } /* End if prevfcast */
1.227 brouard 6811:
6812:
1.238 brouard 6813: /* 9eme writing MLE parameters */
6814: fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
1.126 brouard 6815: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6816: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6817: for(k=1; k <=(nlstate+ndeath); k++){
6818: if (k != i) {
1.227 brouard 6819: fprintf(ficgp,"# current state %d\n",k);
6820: for(j=1; j <=ncovmodel; j++){
6821: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6822: jk++;
6823: }
6824: fprintf(ficgp,"\n");
1.126 brouard 6825: }
6826: }
1.223 brouard 6827: }
1.187 brouard 6828: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6829:
1.145 brouard 6830: /*goto avoid;*/
1.238 brouard 6831: /* 10eme Graphics of probabilities or incidences using written MLE parameters */
6832: fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6833: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6834: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6835: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6836: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6837: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6838: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6839: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6840: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6841: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6842: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6843: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6844: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6845: fprintf(ficgp,"#\n");
1.223 brouard 6846: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.238 brouard 6847: fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
1.237 brouard 6848: fprintf(ficgp,"#model=%s \n",model);
1.238 brouard 6849: fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
1.237 brouard 6850: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
6851: for(jk=1; jk <=m; jk++) /* For each combination of covariate */
6852: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
6853: if(TKresult[nres]!= jk)
6854: continue;
6855: fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);
6856: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
6857: fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
6858: }
6859: fprintf(ficgp,"\n#\n");
1.223 brouard 6860: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6861: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6862: if (ng==1){
6863: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6864: fprintf(ficgp,"\nunset log y");
6865: }else if (ng==2){
6866: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6867: fprintf(ficgp,"\nset log y");
6868: }else if (ng==3){
6869: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6870: fprintf(ficgp,"\nset log y");
6871: }else
6872: fprintf(ficgp,"\nunset title ");
6873: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6874: i=1;
6875: for(k2=1; k2<=nlstate; k2++) {
6876: k3=i;
6877: for(k=1; k<=(nlstate+ndeath); k++) {
6878: if (k != k2){
6879: switch( ng) {
6880: case 1:
6881: if(nagesqr==0)
6882: fprintf(ficgp," p%d+p%d*x",i,i+1);
6883: else /* nagesqr =1 */
6884: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6885: break;
6886: case 2: /* ng=2 */
6887: if(nagesqr==0)
6888: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6889: else /* nagesqr =1 */
6890: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6891: break;
6892: case 3:
6893: if(nagesqr==0)
6894: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6895: else /* nagesqr =1 */
6896: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6897: break;
6898: }
6899: ij=1;/* To be checked else nbcode[0][0] wrong */
1.237 brouard 6900: ijp=1; /* product no age */
6901: /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
6902: for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
1.223 brouard 6903: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
1.237 brouard 6904: if(j==Tage[ij]) { /* Product by age */
6905: if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
1.238 brouard 6906: if(DummyV[j]==0){
1.237 brouard 6907: fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
6908: }else{ /* quantitative */
6909: fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
6910: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6911: }
6912: ij++;
6913: }
6914: }else if(j==Tprod[ijp]) { /* */
6915: /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
6916: if(ijp <=cptcovprod) { /* Product */
1.238 brouard 6917: if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
6918: if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
1.237 brouard 6919: /* 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)]); */
6920: fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
6921: }else{ /* Vn is dummy and Vm is quanti */
6922: /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
6923: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
6924: }
6925: }else{ /* Vn*Vm Vn is quanti */
1.238 brouard 6926: if(DummyV[Tvard[ijp][2]]==0){
1.237 brouard 6927: fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
6928: }else{ /* Both quanti */
6929: fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
6930: }
6931: }
1.238 brouard 6932: ijp++;
1.237 brouard 6933: }
6934: } else{ /* simple covariate */
6935: /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\* Valgrind bug nbcode *\/ */
6936: if(Dummy[j]==0){
6937: fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /* */
6938: }else{ /* quantitative */
6939: fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
1.223 brouard 6940: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6941: }
1.237 brouard 6942: } /* end simple */
6943: } /* end j */
1.223 brouard 6944: }else{
6945: i=i-ncovmodel;
6946: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6947: fprintf(ficgp," (1.");
6948: }
1.227 brouard 6949:
1.223 brouard 6950: if(ng != 1){
6951: fprintf(ficgp,")/(1");
1.227 brouard 6952:
1.223 brouard 6953: for(k1=1; k1 <=nlstate; k1++){
6954: if(nagesqr==0)
6955: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6956: else /* nagesqr =1 */
6957: 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 6958:
1.223 brouard 6959: ij=1;
6960: for(j=3; j <=ncovmodel-nagesqr; j++){
1.237 brouard 6961: if((j-2)==Tage[ij]) { /* Bug valgrind */
6962: if(ij <=cptcovage) { /* Bug valgrind */
1.223 brouard 6963: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6964: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6965: ij++;
6966: }
6967: }
6968: else
1.225 brouard 6969: 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 6970: }
6971: fprintf(ficgp,")");
6972: }
6973: fprintf(ficgp,")");
6974: if(ng ==2)
6975: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6976: else /* ng= 3 */
6977: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6978: }else{ /* end ng <> 1 */
6979: if( k !=k2) /* logit p11 is hard to draw */
6980: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6981: }
6982: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6983: fprintf(ficgp,",");
6984: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6985: fprintf(ficgp,",");
6986: i=i+ncovmodel;
6987: } /* end k */
6988: } /* end k2 */
6989: fprintf(ficgp,"\n set out\n");
6990: } /* end jk */
6991: } /* end ng */
6992: /* avoid: */
6993: fflush(ficgp);
1.126 brouard 6994: } /* end gnuplot */
6995:
6996:
6997: /*************** Moving average **************/
1.219 brouard 6998: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6999: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 7000:
1.222 brouard 7001: int i, cpt, cptcod;
7002: int modcovmax =1;
7003: int mobilavrange, mob;
7004: int iage=0;
7005:
7006: double sum=0.;
7007: double age;
7008: double *sumnewp, *sumnewm;
7009: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
7010:
7011:
1.225 brouard 7012: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 7013: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
7014:
7015: sumnewp = vector(1,ncovcombmax);
7016: sumnewm = vector(1,ncovcombmax);
7017: agemingood = vector(1,ncovcombmax);
7018: agemaxgood = vector(1,ncovcombmax);
7019:
7020: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7021: sumnewm[cptcod]=0.;
7022: sumnewp[cptcod]=0.;
7023: agemingood[cptcod]=0;
7024: agemaxgood[cptcod]=0;
7025: }
7026: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
7027:
7028: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
7029: if(mobilav==1) mobilavrange=5; /* default */
7030: else mobilavrange=mobilav;
7031: for (age=bage; age<=fage; age++)
7032: for (i=1; i<=nlstate;i++)
7033: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
7034: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
7035: /* We keep the original values on the extreme ages bage, fage and for
7036: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
7037: we use a 5 terms etc. until the borders are no more concerned.
7038: */
7039: for (mob=3;mob <=mobilavrange;mob=mob+2){
7040: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
7041: for (i=1; i<=nlstate;i++){
7042: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7043: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
7044: for (cpt=1;cpt<=(mob-1)/2;cpt++){
7045: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
7046: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
7047: }
7048: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
7049: }
7050: }
7051: }/* end age */
7052: }/* end mob */
7053: }else
7054: return -1;
7055: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
7056: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
7057: if(invalidvarcomb[cptcod]){
7058: printf("\nCombination (%d) ignored because no cases \n",cptcod);
7059: continue;
7060: }
1.219 brouard 7061:
1.222 brouard 7062: agemingood[cptcod]=fage-(mob-1)/2;
7063: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
7064: sumnewm[cptcod]=0.;
7065: for (i=1; i<=nlstate;i++){
7066: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7067: }
7068: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
7069: agemingood[cptcod]=age;
7070: }else{ /* bad */
7071: for (i=1; i<=nlstate;i++){
7072: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7073: } /* i */
7074: } /* end bad */
7075: }/* age */
7076: sum=0.;
7077: for (i=1; i<=nlstate;i++){
7078: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7079: }
7080: if(fabs(sum - 1.) > 1.e-3) { /* bad */
7081: 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);
7082: /* for (i=1; i<=nlstate;i++){ */
7083: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
7084: /* } /\* i *\/ */
7085: } /* end bad */
7086: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
7087: /* From youngest, finding the oldest wrong */
7088: agemaxgood[cptcod]=bage+(mob-1)/2;
7089: for (age=bage+(mob-1)/2; age<=fage; age++){
7090: sumnewm[cptcod]=0.;
7091: for (i=1; i<=nlstate;i++){
7092: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7093: }
7094: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
7095: agemaxgood[cptcod]=age;
7096: }else{ /* bad */
7097: for (i=1; i<=nlstate;i++){
7098: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7099: } /* i */
7100: } /* end bad */
7101: }/* age */
7102: sum=0.;
7103: for (i=1; i<=nlstate;i++){
7104: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7105: }
7106: if(fabs(sum - 1.) > 1.e-3) { /* bad */
7107: 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);
7108: /* for (i=1; i<=nlstate;i++){ */
7109: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
7110: /* } /\* i *\/ */
7111: } /* end bad */
7112:
7113: for (age=bage; age<=fage; age++){
1.235 brouard 7114: /* printf("%d %d ", cptcod, (int)age); */
1.222 brouard 7115: sumnewp[cptcod]=0.;
7116: sumnewm[cptcod]=0.;
7117: for (i=1; i<=nlstate;i++){
7118: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
7119: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
7120: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
7121: }
7122: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
7123: }
7124: /* printf("\n"); */
7125: /* } */
7126: /* brutal averaging */
7127: for (i=1; i<=nlstate;i++){
7128: for (age=1; age<=bage; age++){
7129: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
7130: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
7131: }
7132: for (age=fage; age<=AGESUP; age++){
7133: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
7134: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
7135: }
7136: } /* end i status */
7137: for (i=nlstate+1; i<=nlstate+ndeath;i++){
7138: for (age=1; age<=AGESUP; age++){
7139: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
7140: mobaverage[(int)age][i][cptcod]=0.;
7141: }
7142: }
7143: }/* end cptcod */
7144: free_vector(sumnewm,1, ncovcombmax);
7145: free_vector(sumnewp,1, ncovcombmax);
7146: free_vector(agemaxgood,1, ncovcombmax);
7147: free_vector(agemingood,1, ncovcombmax);
7148: return 0;
7149: }/* End movingaverage */
1.218 brouard 7150:
1.126 brouard 7151:
7152: /************** Forecasting ******************/
1.235 brouard 7153: 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 7154: /* proj1, year, month, day of starting projection
7155: agemin, agemax range of age
7156: dateprev1 dateprev2 range of dates during which prevalence is computed
7157: anproj2 year of en of projection (same day and month as proj1).
7158: */
1.235 brouard 7159: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
1.126 brouard 7160: double agec; /* generic age */
7161: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
7162: double *popeffectif,*popcount;
7163: double ***p3mat;
1.218 brouard 7164: /* double ***mobaverage; */
1.126 brouard 7165: char fileresf[FILENAMELENGTH];
7166:
7167: agelim=AGESUP;
1.211 brouard 7168: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
7169: in each health status at the date of interview (if between dateprev1 and dateprev2).
7170: We still use firstpass and lastpass as another selection.
7171: */
1.214 brouard 7172: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
7173: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 7174:
1.201 brouard 7175: strcpy(fileresf,"F_");
7176: strcat(fileresf,fileresu);
1.126 brouard 7177: if((ficresf=fopen(fileresf,"w"))==NULL) {
7178: printf("Problem with forecast resultfile: %s\n", fileresf);
7179: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
7180: }
1.235 brouard 7181: printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
7182: fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 7183:
1.225 brouard 7184: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 7185:
7186:
7187: stepsize=(int) (stepm+YEARM-1)/YEARM;
7188: if (stepm<=12) stepsize=1;
7189: if(estepm < stepm){
7190: printf ("Problem %d lower than %d\n",estepm, stepm);
7191: }
7192: else hstepm=estepm;
7193:
7194: hstepm=hstepm/stepm;
7195: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
7196: fractional in yp1 */
7197: anprojmean=yp;
7198: yp2=modf((yp1*12),&yp);
7199: mprojmean=yp;
7200: yp1=modf((yp2*30.5),&yp);
7201: jprojmean=yp;
7202: if(jprojmean==0) jprojmean=1;
7203: if(mprojmean==0) jprojmean=1;
7204:
1.227 brouard 7205: i1=pow(2,cptcoveff);
1.126 brouard 7206: if (cptcovn < 1){i1=1;}
7207:
7208: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
7209:
7210: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 7211:
1.126 brouard 7212: /* if (h==(int)(YEARM*yearp)){ */
1.235 brouard 7213: for(nres=1; nres <= nresult; nres++) /* For each resultline */
7214: for(k=1; k<=i1;k++){
7215: if(TKresult[nres]!= k)
7216: continue;
1.227 brouard 7217: if(invalidvarcomb[k]){
7218: printf("\nCombination (%d) projection ignored because no cases \n",k);
7219: continue;
7220: }
7221: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
7222: for(j=1;j<=cptcoveff;j++) {
7223: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7224: }
1.235 brouard 7225: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
1.238 brouard 7226: fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
1.235 brouard 7227: }
1.227 brouard 7228: fprintf(ficresf," yearproj age");
7229: for(j=1; j<=nlstate+ndeath;j++){
7230: for(i=1; i<=nlstate;i++)
7231: fprintf(ficresf," p%d%d",i,j);
7232: fprintf(ficresf," wp.%d",j);
7233: }
7234: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
7235: fprintf(ficresf,"\n");
7236: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
7237: for (agec=fage; agec>=(ageminpar-1); agec--){
7238: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
7239: nhstepm = nhstepm/hstepm;
7240: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7241: oldm=oldms;savm=savms;
1.235 brouard 7242: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
1.227 brouard 7243:
7244: for (h=0; h<=nhstepm; h++){
7245: if (h*hstepm/YEARM*stepm ==yearp) {
7246: fprintf(ficresf,"\n");
7247: for(j=1;j<=cptcoveff;j++)
7248: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7249: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
7250: }
7251: for(j=1; j<=nlstate+ndeath;j++) {
7252: ppij=0.;
7253: for(i=1; i<=nlstate;i++) {
7254: if (mobilav==1)
7255: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
7256: else {
7257: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
7258: }
7259: if (h*hstepm/YEARM*stepm== yearp) {
7260: fprintf(ficresf," %.3f", p3mat[i][j][h]);
7261: }
7262: } /* end i */
7263: if (h*hstepm/YEARM*stepm==yearp) {
7264: fprintf(ficresf," %.3f", ppij);
7265: }
7266: }/* end j */
7267: } /* end h */
7268: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7269: } /* end agec */
7270: } /* end yearp */
7271: } /* end k */
1.219 brouard 7272:
1.126 brouard 7273: fclose(ficresf);
1.215 brouard 7274: printf("End of Computing forecasting \n");
7275: fprintf(ficlog,"End of Computing forecasting\n");
7276:
1.126 brouard 7277: }
7278:
1.218 brouard 7279: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 7280: /* 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 7281: /* /\* back1, year, month, day of starting backection */
7282: /* agemin, agemax range of age */
7283: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
7284: /* anback2 year of en of backection (same day and month as back1). */
7285: /* *\/ */
7286: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
7287: /* double agec; /\* generic age *\/ */
7288: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
7289: /* double *popeffectif,*popcount; */
7290: /* double ***p3mat; */
7291: /* /\* double ***mobaverage; *\/ */
7292: /* char fileresfb[FILENAMELENGTH]; */
7293:
7294: /* agelim=AGESUP; */
7295: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
7296: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
7297: /* We still use firstpass and lastpass as another selection. */
7298: /* *\/ */
7299: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
7300: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
7301: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
7302:
7303: /* strcpy(fileresfb,"FB_"); */
7304: /* strcat(fileresfb,fileresu); */
7305: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
7306: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
7307: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
7308: /* } */
7309: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7310: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7311:
1.225 brouard 7312: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 7313:
7314: /* /\* if (mobilav!=0) { *\/ */
7315: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7316: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7317: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7318: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7319: /* /\* } *\/ */
7320: /* /\* } *\/ */
7321:
7322: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7323: /* if (stepm<=12) stepsize=1; */
7324: /* if(estepm < stepm){ */
7325: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
7326: /* } */
7327: /* else hstepm=estepm; */
7328:
7329: /* hstepm=hstepm/stepm; */
7330: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7331: /* fractional in yp1 *\/ */
7332: /* anprojmean=yp; */
7333: /* yp2=modf((yp1*12),&yp); */
7334: /* mprojmean=yp; */
7335: /* yp1=modf((yp2*30.5),&yp); */
7336: /* jprojmean=yp; */
7337: /* if(jprojmean==0) jprojmean=1; */
7338: /* if(mprojmean==0) jprojmean=1; */
7339:
1.225 brouard 7340: /* i1=cptcoveff; */
1.218 brouard 7341: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7342:
1.218 brouard 7343: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7344:
1.218 brouard 7345: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7346:
7347: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7348: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7349: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7350: /* k=k+1; */
7351: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7352: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7353: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7354: /* } */
7355: /* fprintf(ficresfb," yearbproj age"); */
7356: /* for(j=1; j<=nlstate+ndeath;j++){ */
7357: /* for(i=1; i<=nlstate;i++) */
7358: /* fprintf(ficresfb," p%d%d",i,j); */
7359: /* fprintf(ficresfb," p.%d",j); */
7360: /* } */
7361: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7362: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7363: /* fprintf(ficresfb,"\n"); */
7364: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7365: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7366: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7367: /* nhstepm = nhstepm/hstepm; */
7368: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7369: /* oldm=oldms;savm=savms; */
7370: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7371: /* for (h=0; h<=nhstepm; h++){ */
7372: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7373: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7374: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7375: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7376: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7377: /* } */
7378: /* for(j=1; j<=nlstate+ndeath;j++) { */
7379: /* ppij=0.; */
7380: /* for(i=1; i<=nlstate;i++) { */
7381: /* if (mobilav==1) */
7382: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7383: /* else { */
7384: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7385: /* } */
7386: /* if (h*hstepm/YEARM*stepm== yearp) { */
7387: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7388: /* } */
7389: /* } /\* end i *\/ */
7390: /* if (h*hstepm/YEARM*stepm==yearp) { */
7391: /* fprintf(ficresfb," %.3f", ppij); */
7392: /* } */
7393: /* }/\* end j *\/ */
7394: /* } /\* end h *\/ */
7395: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7396: /* } /\* end agec *\/ */
7397: /* } /\* end yearp *\/ */
7398: /* } /\* end cptcod *\/ */
7399: /* } /\* end cptcov *\/ */
7400:
7401: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7402:
7403: /* fclose(ficresfb); */
7404: /* printf("End of Computing Back forecasting \n"); */
7405: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7406:
1.218 brouard 7407: /* } */
1.217 brouard 7408:
1.126 brouard 7409: /************** Forecasting *****not tested NB*************/
1.227 brouard 7410: /* 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 7411:
1.227 brouard 7412: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7413: /* int *popage; */
7414: /* double calagedatem, agelim, kk1, kk2; */
7415: /* double *popeffectif,*popcount; */
7416: /* double ***p3mat,***tabpop,***tabpopprev; */
7417: /* /\* double ***mobaverage; *\/ */
7418: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7419:
1.227 brouard 7420: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7421: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7422: /* agelim=AGESUP; */
7423: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7424:
1.227 brouard 7425: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7426:
7427:
1.227 brouard 7428: /* strcpy(filerespop,"POP_"); */
7429: /* strcat(filerespop,fileresu); */
7430: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7431: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7432: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7433: /* } */
7434: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7435: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7436:
1.227 brouard 7437: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7438:
1.227 brouard 7439: /* /\* if (mobilav!=0) { *\/ */
7440: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7441: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7442: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7443: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7444: /* /\* } *\/ */
7445: /* /\* } *\/ */
1.126 brouard 7446:
1.227 brouard 7447: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7448: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7449:
1.227 brouard 7450: /* agelim=AGESUP; */
1.126 brouard 7451:
1.227 brouard 7452: /* hstepm=1; */
7453: /* hstepm=hstepm/stepm; */
1.218 brouard 7454:
1.227 brouard 7455: /* if (popforecast==1) { */
7456: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7457: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7458: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7459: /* } */
7460: /* popage=ivector(0,AGESUP); */
7461: /* popeffectif=vector(0,AGESUP); */
7462: /* popcount=vector(0,AGESUP); */
1.126 brouard 7463:
1.227 brouard 7464: /* i=1; */
7465: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7466:
1.227 brouard 7467: /* imx=i; */
7468: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7469: /* } */
1.218 brouard 7470:
1.227 brouard 7471: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7472: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7473: /* k=k+1; */
7474: /* fprintf(ficrespop,"\n#******"); */
7475: /* for(j=1;j<=cptcoveff;j++) { */
7476: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7477: /* } */
7478: /* fprintf(ficrespop,"******\n"); */
7479: /* fprintf(ficrespop,"# Age"); */
7480: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7481: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7482:
1.227 brouard 7483: /* for (cpt=0; cpt<=0;cpt++) { */
7484: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7485:
1.227 brouard 7486: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7487: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7488: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7489:
1.227 brouard 7490: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7491: /* oldm=oldms;savm=savms; */
7492: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7493:
1.227 brouard 7494: /* for (h=0; h<=nhstepm; h++){ */
7495: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7496: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7497: /* } */
7498: /* for(j=1; j<=nlstate+ndeath;j++) { */
7499: /* kk1=0.;kk2=0; */
7500: /* for(i=1; i<=nlstate;i++) { */
7501: /* if (mobilav==1) */
7502: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7503: /* else { */
7504: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7505: /* } */
7506: /* } */
7507: /* if (h==(int)(calagedatem+12*cpt)){ */
7508: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7509: /* /\*fprintf(ficrespop," %.3f", kk1); */
7510: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7511: /* } */
7512: /* } */
7513: /* for(i=1; i<=nlstate;i++){ */
7514: /* kk1=0.; */
7515: /* for(j=1; j<=nlstate;j++){ */
7516: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7517: /* } */
7518: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7519: /* } */
1.218 brouard 7520:
1.227 brouard 7521: /* if (h==(int)(calagedatem+12*cpt)) */
7522: /* for(j=1; j<=nlstate;j++) */
7523: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7524: /* } */
7525: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7526: /* } */
7527: /* } */
1.218 brouard 7528:
1.227 brouard 7529: /* /\******\/ */
1.218 brouard 7530:
1.227 brouard 7531: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7532: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7533: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7534: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7535: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7536:
1.227 brouard 7537: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7538: /* oldm=oldms;savm=savms; */
7539: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7540: /* for (h=0; h<=nhstepm; h++){ */
7541: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7542: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7543: /* } */
7544: /* for(j=1; j<=nlstate+ndeath;j++) { */
7545: /* kk1=0.;kk2=0; */
7546: /* for(i=1; i<=nlstate;i++) { */
7547: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7548: /* } */
7549: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7550: /* } */
7551: /* } */
7552: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7553: /* } */
7554: /* } */
7555: /* } */
7556: /* } */
1.218 brouard 7557:
1.227 brouard 7558: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7559:
1.227 brouard 7560: /* if (popforecast==1) { */
7561: /* free_ivector(popage,0,AGESUP); */
7562: /* free_vector(popeffectif,0,AGESUP); */
7563: /* free_vector(popcount,0,AGESUP); */
7564: /* } */
7565: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7566: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7567: /* fclose(ficrespop); */
7568: /* } /\* End of popforecast *\/ */
1.218 brouard 7569:
1.126 brouard 7570: int fileappend(FILE *fichier, char *optionfich)
7571: {
7572: if((fichier=fopen(optionfich,"a"))==NULL) {
7573: printf("Problem with file: %s\n", optionfich);
7574: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7575: return (0);
7576: }
7577: fflush(fichier);
7578: return (1);
7579: }
7580:
7581:
7582: /**************** function prwizard **********************/
7583: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7584: {
7585:
7586: /* Wizard to print covariance matrix template */
7587:
1.164 brouard 7588: char ca[32], cb[32];
7589: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7590: int numlinepar;
7591:
7592: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7593: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7594: for(i=1; i <=nlstate; i++){
7595: jj=0;
7596: for(j=1; j <=nlstate+ndeath; j++){
7597: if(j==i) continue;
7598: jj++;
7599: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7600: printf("%1d%1d",i,j);
7601: fprintf(ficparo,"%1d%1d",i,j);
7602: for(k=1; k<=ncovmodel;k++){
7603: /* printf(" %lf",param[i][j][k]); */
7604: /* fprintf(ficparo," %lf",param[i][j][k]); */
7605: printf(" 0.");
7606: fprintf(ficparo," 0.");
7607: }
7608: printf("\n");
7609: fprintf(ficparo,"\n");
7610: }
7611: }
7612: printf("# Scales (for hessian or gradient estimation)\n");
7613: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7614: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7615: for(i=1; i <=nlstate; i++){
7616: jj=0;
7617: for(j=1; j <=nlstate+ndeath; j++){
7618: if(j==i) continue;
7619: jj++;
7620: fprintf(ficparo,"%1d%1d",i,j);
7621: printf("%1d%1d",i,j);
7622: fflush(stdout);
7623: for(k=1; k<=ncovmodel;k++){
7624: /* printf(" %le",delti3[i][j][k]); */
7625: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7626: printf(" 0.");
7627: fprintf(ficparo," 0.");
7628: }
7629: numlinepar++;
7630: printf("\n");
7631: fprintf(ficparo,"\n");
7632: }
7633: }
7634: printf("# Covariance matrix\n");
7635: /* # 121 Var(a12)\n\ */
7636: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7637: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7638: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7639: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7640: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7641: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7642: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7643: fflush(stdout);
7644: fprintf(ficparo,"# Covariance matrix\n");
7645: /* # 121 Var(a12)\n\ */
7646: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7647: /* # ...\n\ */
7648: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7649:
7650: for(itimes=1;itimes<=2;itimes++){
7651: jj=0;
7652: for(i=1; i <=nlstate; i++){
7653: for(j=1; j <=nlstate+ndeath; j++){
7654: if(j==i) continue;
7655: for(k=1; k<=ncovmodel;k++){
7656: jj++;
7657: ca[0]= k+'a'-1;ca[1]='\0';
7658: if(itimes==1){
7659: printf("#%1d%1d%d",i,j,k);
7660: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7661: }else{
7662: printf("%1d%1d%d",i,j,k);
7663: fprintf(ficparo,"%1d%1d%d",i,j,k);
7664: /* printf(" %.5le",matcov[i][j]); */
7665: }
7666: ll=0;
7667: for(li=1;li <=nlstate; li++){
7668: for(lj=1;lj <=nlstate+ndeath; lj++){
7669: if(lj==li) continue;
7670: for(lk=1;lk<=ncovmodel;lk++){
7671: ll++;
7672: if(ll<=jj){
7673: cb[0]= lk +'a'-1;cb[1]='\0';
7674: if(ll<jj){
7675: if(itimes==1){
7676: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7677: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7678: }else{
7679: printf(" 0.");
7680: fprintf(ficparo," 0.");
7681: }
7682: }else{
7683: if(itimes==1){
7684: printf(" Var(%s%1d%1d)",ca,i,j);
7685: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7686: }else{
7687: printf(" 0.");
7688: fprintf(ficparo," 0.");
7689: }
7690: }
7691: }
7692: } /* end lk */
7693: } /* end lj */
7694: } /* end li */
7695: printf("\n");
7696: fprintf(ficparo,"\n");
7697: numlinepar++;
7698: } /* end k*/
7699: } /*end j */
7700: } /* end i */
7701: } /* end itimes */
7702:
7703: } /* end of prwizard */
7704: /******************* Gompertz Likelihood ******************************/
7705: double gompertz(double x[])
7706: {
7707: double A,B,L=0.0,sump=0.,num=0.;
7708: int i,n=0; /* n is the size of the sample */
7709:
1.220 brouard 7710: for (i=1;i<=imx ; i++) {
1.126 brouard 7711: sump=sump+weight[i];
7712: /* sump=sump+1;*/
7713: num=num+1;
7714: }
7715:
7716:
7717: /* for (i=0; i<=imx; i++)
7718: 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]);*/
7719:
7720: for (i=1;i<=imx ; i++)
7721: {
7722: if (cens[i] == 1 && wav[i]>1)
7723: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7724:
7725: if (cens[i] == 0 && wav[i]>1)
7726: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7727: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7728:
7729: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7730: if (wav[i] > 1 ) { /* ??? */
7731: L=L+A*weight[i];
7732: /* 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]);*/
7733: }
7734: }
7735:
7736: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7737:
7738: return -2*L*num/sump;
7739: }
7740:
1.136 brouard 7741: #ifdef GSL
7742: /******************* Gompertz_f Likelihood ******************************/
7743: double gompertz_f(const gsl_vector *v, void *params)
7744: {
7745: double A,B,LL=0.0,sump=0.,num=0.;
7746: double *x= (double *) v->data;
7747: int i,n=0; /* n is the size of the sample */
7748:
7749: for (i=0;i<=imx-1 ; i++) {
7750: sump=sump+weight[i];
7751: /* sump=sump+1;*/
7752: num=num+1;
7753: }
7754:
7755:
7756: /* for (i=0; i<=imx; i++)
7757: 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]);*/
7758: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7759: for (i=1;i<=imx ; i++)
7760: {
7761: if (cens[i] == 1 && wav[i]>1)
7762: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7763:
7764: if (cens[i] == 0 && wav[i]>1)
7765: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7766: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7767:
7768: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7769: if (wav[i] > 1 ) { /* ??? */
7770: LL=LL+A*weight[i];
7771: /* 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]);*/
7772: }
7773: }
7774:
7775: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7776: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7777:
7778: return -2*LL*num/sump;
7779: }
7780: #endif
7781:
1.126 brouard 7782: /******************* Printing html file ***********/
1.201 brouard 7783: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7784: int lastpass, int stepm, int weightopt, char model[],\
7785: int imx, double p[],double **matcov,double agemortsup){
7786: int i,k;
7787:
7788: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7789: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7790: for (i=1;i<=2;i++)
7791: 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 7792: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7793: fprintf(fichtm,"</ul>");
7794:
7795: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7796:
7797: 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>");
7798:
7799: for (k=agegomp;k<(agemortsup-2);k++)
7800: 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]);
7801:
7802:
7803: fflush(fichtm);
7804: }
7805:
7806: /******************* Gnuplot file **************/
1.201 brouard 7807: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7808:
7809: char dirfileres[132],optfileres[132];
1.164 brouard 7810:
1.126 brouard 7811: int ng;
7812:
7813:
7814: /*#ifdef windows */
7815: fprintf(ficgp,"cd \"%s\" \n",pathc);
7816: /*#endif */
7817:
7818:
7819: strcpy(dirfileres,optionfilefiname);
7820: strcpy(optfileres,"vpl");
1.199 brouard 7821: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7822: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7823: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7824: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7825: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7826:
7827: }
7828:
1.136 brouard 7829: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7830: {
1.126 brouard 7831:
1.136 brouard 7832: /*-------- data file ----------*/
7833: FILE *fic;
7834: char dummy[]=" ";
1.240 ! brouard 7835: int i=0, j=0, n=0, iv=0, v;
1.223 brouard 7836: int lstra;
1.136 brouard 7837: int linei, month, year,iout;
7838: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7839: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7840: char *stratrunc;
1.223 brouard 7841:
1.240 ! brouard 7842: DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
! 7843: FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
1.126 brouard 7844:
1.240 ! brouard 7845: for(v=1; v <=ncovcol;v++){
! 7846: DummyV[v]=0;
! 7847: FixedV[v]=0;
! 7848: }
! 7849: for(v=ncovcol+1; v <=ncovcol+nqv;v++){
! 7850: DummyV[v]=1;
! 7851: FixedV[v]=0;
! 7852: }
! 7853: for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
! 7854: DummyV[v]=0;
! 7855: FixedV[v]=1;
! 7856: }
! 7857: for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
! 7858: DummyV[v]=1;
! 7859: FixedV[v]=1;
! 7860: }
! 7861: for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
! 7862: printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
! 7863: 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]);
! 7864: }
1.126 brouard 7865:
1.136 brouard 7866: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7867: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7868: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7869: }
1.126 brouard 7870:
1.136 brouard 7871: i=1;
7872: linei=0;
7873: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7874: linei=linei+1;
7875: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7876: if(line[j] == '\t')
7877: line[j] = ' ';
7878: }
7879: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7880: ;
7881: };
7882: line[j+1]=0; /* Trims blanks at end of line */
7883: if(line[0]=='#'){
7884: fprintf(ficlog,"Comment line\n%s\n",line);
7885: printf("Comment line\n%s\n",line);
7886: continue;
7887: }
7888: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7889: strcpy(line, linetmp);
1.223 brouard 7890:
7891: /* Loops on waves */
7892: for (j=maxwav;j>=1;j--){
7893: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.238 brouard 7894: cutv(stra, strb, line, ' ');
7895: if(strb[0]=='.') { /* Missing value */
7896: lval=-1;
7897: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7898: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
7899: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7900: 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);
7901: 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);
7902: return 1;
7903: }
7904: }else{
7905: errno=0;
7906: /* what_kind_of_number(strb); */
7907: dval=strtod(strb,&endptr);
7908: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7909: /* if(strb != endptr && *endptr == '\0') */
7910: /* dval=dlval; */
7911: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7912: if( strb[0]=='\0' || (*endptr != '\0')){
7913: 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);
7914: 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);
7915: return 1;
7916: }
7917: cotqvar[j][iv][i]=dval;
7918: cotvar[j][ntv+iv][i]=dval;
7919: }
7920: strcpy(line,stra);
1.223 brouard 7921: }/* end loop ntqv */
1.225 brouard 7922:
1.223 brouard 7923: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.238 brouard 7924: cutv(stra, strb, line, ' ');
7925: if(strb[0]=='.') { /* Missing value */
7926: lval=-1;
7927: }else{
7928: errno=0;
7929: lval=strtol(strb,&endptr,10);
7930: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7931: if( strb[0]=='\0' || (*endptr != '\0')){
7932: 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);
7933: 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);
7934: return 1;
7935: }
7936: }
7937: if(lval <-1 || lval >1){
7938: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7939: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7940: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 7941: For example, for multinomial values like 1, 2 and 3,\n \
7942: build V1=0 V2=0 for the reference value (1),\n \
7943: V1=1 V2=0 for (2) \n \
1.223 brouard 7944: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 7945: output of IMaCh is often meaningless.\n \
1.223 brouard 7946: Exiting.\n",lval,linei, i,line,j);
1.238 brouard 7947: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7948: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7949: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.238 brouard 7950: For example, for multinomial values like 1, 2 and 3,\n \
7951: build V1=0 V2=0 for the reference value (1),\n \
7952: V1=1 V2=0 for (2) \n \
1.223 brouard 7953: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.238 brouard 7954: output of IMaCh is often meaningless.\n \
1.223 brouard 7955: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.238 brouard 7956: return 1;
7957: }
7958: cotvar[j][iv][i]=(double)(lval);
7959: strcpy(line,stra);
1.223 brouard 7960: }/* end loop ntv */
1.225 brouard 7961:
1.223 brouard 7962: /* Statuses at wave */
1.137 brouard 7963: cutv(stra, strb, line, ' ');
1.223 brouard 7964: if(strb[0]=='.') { /* Missing value */
1.238 brouard 7965: lval=-1;
1.136 brouard 7966: }else{
1.238 brouard 7967: errno=0;
7968: lval=strtol(strb,&endptr,10);
7969: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7970: if( strb[0]=='\0' || (*endptr != '\0')){
7971: 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);
7972: 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);
7973: return 1;
7974: }
1.136 brouard 7975: }
1.225 brouard 7976:
1.136 brouard 7977: s[j][i]=lval;
1.225 brouard 7978:
1.223 brouard 7979: /* Date of Interview */
1.136 brouard 7980: strcpy(line,stra);
7981: cutv(stra, strb,line,' ');
1.169 brouard 7982: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7983: }
1.169 brouard 7984: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7985: month=99;
7986: year=9999;
1.136 brouard 7987: }else{
1.225 brouard 7988: 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);
7989: 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);
7990: return 1;
1.136 brouard 7991: }
7992: anint[j][i]= (double) year;
7993: mint[j][i]= (double)month;
7994: strcpy(line,stra);
1.223 brouard 7995: } /* End loop on waves */
1.225 brouard 7996:
1.223 brouard 7997: /* Date of death */
1.136 brouard 7998: cutv(stra, strb,line,' ');
1.169 brouard 7999: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 8000: }
1.169 brouard 8001: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 8002: month=99;
8003: year=9999;
8004: }else{
1.141 brouard 8005: 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 8006: 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);
8007: return 1;
1.136 brouard 8008: }
8009: andc[i]=(double) year;
8010: moisdc[i]=(double) month;
8011: strcpy(line,stra);
8012:
1.223 brouard 8013: /* Date of birth */
1.136 brouard 8014: cutv(stra, strb,line,' ');
1.169 brouard 8015: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 8016: }
1.169 brouard 8017: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 8018: month=99;
8019: year=9999;
8020: }else{
1.141 brouard 8021: 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);
8022: 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 8023: return 1;
1.136 brouard 8024: }
8025: if (year==9999) {
1.141 brouard 8026: 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);
8027: 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 8028: return 1;
8029:
1.136 brouard 8030: }
8031: annais[i]=(double)(year);
8032: moisnais[i]=(double)(month);
8033: strcpy(line,stra);
1.225 brouard 8034:
1.223 brouard 8035: /* Sample weight */
1.136 brouard 8036: cutv(stra, strb,line,' ');
8037: errno=0;
8038: dval=strtod(strb,&endptr);
8039: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 8040: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
8041: 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 8042: fflush(ficlog);
8043: return 1;
8044: }
8045: weight[i]=dval;
8046: strcpy(line,stra);
1.225 brouard 8047:
1.223 brouard 8048: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
8049: cutv(stra, strb, line, ' ');
8050: if(strb[0]=='.') { /* Missing value */
1.225 brouard 8051: lval=-1;
1.223 brouard 8052: }else{
1.225 brouard 8053: errno=0;
8054: /* what_kind_of_number(strb); */
8055: dval=strtod(strb,&endptr);
8056: /* if(strb != endptr && *endptr == '\0') */
8057: /* dval=dlval; */
8058: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
8059: if( strb[0]=='\0' || (*endptr != '\0')){
8060: 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);
8061: 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);
8062: return 1;
8063: }
8064: coqvar[iv][i]=dval;
1.226 brouard 8065: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 8066: }
8067: strcpy(line,stra);
8068: }/* end loop nqv */
1.136 brouard 8069:
1.223 brouard 8070: /* Covariate values */
1.136 brouard 8071: for (j=ncovcol;j>=1;j--){
8072: cutv(stra, strb,line,' ');
1.223 brouard 8073: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 8074: lval=-1;
1.136 brouard 8075: }else{
1.225 brouard 8076: errno=0;
8077: lval=strtol(strb,&endptr,10);
8078: if( strb[0]=='\0' || (*endptr != '\0')){
8079: 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);
8080: 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);
8081: return 1;
8082: }
1.136 brouard 8083: }
8084: if(lval <-1 || lval >1){
1.225 brouard 8085: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 8086: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8087: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 8088: For example, for multinomial values like 1, 2 and 3,\n \
8089: build V1=0 V2=0 for the reference value (1),\n \
8090: V1=1 V2=0 for (2) \n \
1.136 brouard 8091: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 8092: output of IMaCh is often meaningless.\n \
1.136 brouard 8093: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 8094: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 8095: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
8096: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 8097: For example, for multinomial values like 1, 2 and 3,\n \
8098: build V1=0 V2=0 for the reference value (1),\n \
8099: V1=1 V2=0 for (2) \n \
1.136 brouard 8100: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 8101: output of IMaCh is often meaningless.\n \
1.136 brouard 8102: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 8103: return 1;
1.136 brouard 8104: }
8105: covar[j][i]=(double)(lval);
8106: strcpy(line,stra);
8107: }
8108: lstra=strlen(stra);
1.225 brouard 8109:
1.136 brouard 8110: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
8111: stratrunc = &(stra[lstra-9]);
8112: num[i]=atol(stratrunc);
8113: }
8114: else
8115: num[i]=atol(stra);
8116: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
8117: 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;}*/
8118:
8119: i=i+1;
8120: } /* End loop reading data */
1.225 brouard 8121:
1.136 brouard 8122: *imax=i-1; /* Number of individuals */
8123: fclose(fic);
1.225 brouard 8124:
1.136 brouard 8125: return (0);
1.164 brouard 8126: /* endread: */
1.225 brouard 8127: printf("Exiting readdata: ");
8128: fclose(fic);
8129: return (1);
1.223 brouard 8130: }
1.126 brouard 8131:
1.234 brouard 8132: void removefirstspace(char **stri){/*, char stro[]) {*/
1.230 brouard 8133: char *p1 = *stri, *p2 = *stri;
1.235 brouard 8134: while (*p2 == ' ')
1.234 brouard 8135: p2++;
8136: /* while ((*p1++ = *p2++) !=0) */
8137: /* ; */
8138: /* do */
8139: /* while (*p2 == ' ') */
8140: /* p2++; */
8141: /* while (*p1++ == *p2++); */
8142: *stri=p2;
1.145 brouard 8143: }
8144:
1.235 brouard 8145: int decoderesult ( char resultline[], int nres)
1.230 brouard 8146: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
8147: {
1.235 brouard 8148: int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
1.230 brouard 8149: char resultsav[MAXLINE];
1.234 brouard 8150: int resultmodel[MAXLINE];
8151: int modelresult[MAXLINE];
1.230 brouard 8152: char stra[80], strb[80], strc[80], strd[80],stre[80];
8153:
1.234 brouard 8154: removefirstspace(&resultline);
1.233 brouard 8155: printf("decoderesult:%s\n",resultline);
1.230 brouard 8156:
8157: if (strstr(resultline,"v") !=0){
8158: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
8159: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
8160: return 1;
8161: }
8162: trimbb(resultsav, resultline);
8163: if (strlen(resultsav) >1){
8164: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
8165: }
1.234 brouard 8166: if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
8167: 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);
8168: 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);
8169: }
8170: for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
8171: if(nbocc(resultsav,'=') >1){
8172: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
8173: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
8174: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
8175: }else
8176: cutl(strc,strd,resultsav,'=');
1.230 brouard 8177: Tvalsel[k]=atof(strc); /* 1 */
1.234 brouard 8178:
1.230 brouard 8179: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
8180: Tvarsel[k]=atoi(strc);
8181: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
8182: /* cptcovsel++; */
8183: if (nbocc(stra,'=') >0)
8184: strcpy(resultsav,stra); /* and analyzes it */
8185: }
1.235 brouard 8186: /* Checking for missing or useless values in comparison of current model needs */
1.236 brouard 8187: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8188: if(Typevar[k1]==0){ /* Single covariate in model */
1.234 brouard 8189: match=0;
1.236 brouard 8190: for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.237 brouard 8191: if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
1.236 brouard 8192: modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
1.234 brouard 8193: match=1;
8194: break;
8195: }
8196: }
8197: if(match == 0){
8198: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8199: }
8200: }
8201: }
1.235 brouard 8202: /* Checking for missing or useless values in comparison of current model needs */
8203: for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
1.234 brouard 8204: match=0;
1.235 brouard 8205: for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8206: if(Typevar[k1]==0){ /* Single */
1.237 brouard 8207: if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
1.235 brouard 8208: resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
1.234 brouard 8209: ++match;
8210: }
8211: }
8212: }
8213: if(match == 0){
8214: printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
8215: }else if(match > 1){
8216: printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
8217: }
8218: }
1.235 brouard 8219:
1.234 brouard 8220: /* We need to deduce which combination number is chosen and save quantitative values */
1.235 brouard 8221: /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8222: /* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
8223: /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
8224: /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
8225: /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
8226: /* 1 0 0 0 */
8227: /* 2 1 0 0 */
8228: /* 3 0 1 0 */
8229: /* 4 1 1 0 */ /* V4=1, V3=1, V1=0 */
8230: /* 5 0 0 1 */
8231: /* 6 1 0 1 */ /* V4=1, V3=0, V1=1 */
8232: /* 7 0 1 1 */
8233: /* 8 1 1 1 */
1.237 brouard 8234: /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
8235: /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
8236: /* V5*age V5 known which value for nres? */
8237: /* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
1.235 brouard 8238: for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
8239: if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
1.237 brouard 8240: k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
1.235 brouard 8241: k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
8242: k+=Tvalsel[k3]*pow(2,k4); /* Tvalsel[1]=1 */
1.237 brouard 8243: Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
8244: Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
8245: Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
1.235 brouard 8246: printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
8247: k4++;;
8248: } else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
8249: k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
8250: k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
1.237 brouard 8251: Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
8252: Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
8253: Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
1.235 brouard 8254: printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
8255: k4q++;;
8256: }
8257: }
1.234 brouard 8258:
1.235 brouard 8259: TKresult[nres]=++k; /* Combination for the nresult and the model */
1.230 brouard 8260: return (0);
8261: }
1.235 brouard 8262:
1.230 brouard 8263: int decodemodel( char model[], int lastobs)
8264: /**< This routine decodes the model and returns:
1.224 brouard 8265: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
8266: * - nagesqr = 1 if age*age in the model, otherwise 0.
8267: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
8268: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
8269: * - cptcovage number of covariates with age*products =2
8270: * - cptcovs number of simple covariates
8271: * - 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
8272: * which is a new column after the 9 (ncovcol) variables.
8273: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
8274: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
8275: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
8276: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
8277: */
1.136 brouard 8278: {
1.238 brouard 8279: int i, j, k, ks, v;
1.227 brouard 8280: int j1, k1, k2, k3, k4;
1.136 brouard 8281: char modelsav[80];
1.145 brouard 8282: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 8283: char *strpt;
1.136 brouard 8284:
1.145 brouard 8285: /*removespace(model);*/
1.136 brouard 8286: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 8287: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 8288: if (strstr(model,"AGE") !=0){
1.192 brouard 8289: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
8290: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 8291: return 1;
8292: }
1.141 brouard 8293: if (strstr(model,"v") !=0){
8294: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
8295: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
8296: return 1;
8297: }
1.187 brouard 8298: strcpy(modelsav,model);
8299: if ((strpt=strstr(model,"age*age")) !=0){
8300: printf(" strpt=%s, model=%s\n",strpt, model);
8301: if(strpt != model){
1.234 brouard 8302: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8303: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8304: corresponding column of parameters.\n",model);
1.234 brouard 8305: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 8306: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 8307: corresponding column of parameters.\n",model); fflush(ficlog);
1.234 brouard 8308: return 1;
1.225 brouard 8309: }
1.187 brouard 8310: nagesqr=1;
8311: if (strstr(model,"+age*age") !=0)
1.234 brouard 8312: substrchaine(modelsav, model, "+age*age");
1.187 brouard 8313: else if (strstr(model,"age*age+") !=0)
1.234 brouard 8314: substrchaine(modelsav, model, "age*age+");
1.187 brouard 8315: else
1.234 brouard 8316: substrchaine(modelsav, model, "age*age");
1.187 brouard 8317: }else
8318: nagesqr=0;
8319: if (strlen(modelsav) >1){
8320: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
8321: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 8322: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 8323: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 8324: * cst, age and age*age
8325: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
8326: /* including age products which are counted in cptcovage.
8327: * but the covariates which are products must be treated
8328: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 8329: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
8330: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 8331:
8332:
1.187 brouard 8333: /* Design
8334: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
8335: * < ncovcol=8 >
8336: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
8337: * k= 1 2 3 4 5 6 7 8
8338: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
8339: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 8340: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
8341: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 8342: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
8343: * Tage[++cptcovage]=k
8344: * if products, new covar are created after ncovcol with k1
8345: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
8346: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
8347: * 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
8348: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
8349: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
8350: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
8351: * < ncovcol=8 >
8352: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
8353: * k= 1 2 3 4 5 6 7 8 9 10 11 12
8354: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
8355: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8356: * p Tprod[1]@2={ 6, 5}
8357: *p Tvard[1][1]@4= {7, 8, 5, 6}
8358: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
8359: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
8360: *How to reorganize?
8361: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
8362: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8363: * {2, 1, 4, 8, 5, 6, 3, 7}
8364: * Struct []
8365: */
1.225 brouard 8366:
1.187 brouard 8367: /* This loop fills the array Tvar from the string 'model'.*/
8368: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
8369: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
8370: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
8371: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
8372: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
8373: /* k=1 Tvar[1]=2 (from V2) */
8374: /* k=5 Tvar[5] */
8375: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 8376: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 8377: /* } */
1.198 brouard 8378: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 8379: /*
8380: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 8381: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
8382: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
8383: }
1.187 brouard 8384: cptcovage=0;
8385: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.234 brouard 8386: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 8387: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.234 brouard 8388: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
8389: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
8390: /*scanf("%d",i);*/
8391: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
8392: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
8393: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
8394: /* covar is not filled and then is empty */
8395: cptcovprod--;
8396: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
8397: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
8398: Typevar[k]=1; /* 1 for age product */
8399: cptcovage++; /* Sums the number of covariates which include age as a product */
8400: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
8401: /*printf("stre=%s ", stre);*/
8402: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
8403: cptcovprod--;
8404: cutl(stre,strb,strc,'V');
8405: Tvar[k]=atoi(stre);
8406: Typevar[k]=1; /* 1 for age product */
8407: cptcovage++;
8408: Tage[cptcovage]=k;
8409: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
8410: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
8411: cptcovn++;
8412: cptcovprodnoage++;k1++;
8413: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
8414: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
8415: because this model-covariate is a construction we invent a new column
8416: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
8417: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
8418: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
8419: Typevar[k]=2; /* 2 for double fixed dummy covariates */
8420: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
8421: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
8422: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
8423: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
8424: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
8425: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
8426: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
8427: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 8428: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.234 brouard 8429: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
8430: for (i=1; i<=lastobs;i++){
8431: /* Computes the new covariate which is a product of
8432: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
8433: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
8434: }
8435: } /* End age is not in the model */
8436: } /* End if model includes a product */
8437: else { /* no more sum */
8438: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
8439: /* scanf("%d",i);*/
8440: cutl(strd,strc,strb,'V');
8441: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
8442: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
8443: Tvar[k]=atoi(strd);
8444: Typevar[k]=0; /* 0 for simple covariates */
8445: }
8446: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 8447: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 8448: scanf("%d",i);*/
1.187 brouard 8449: } /* end of loop + on total covariates */
8450: } /* end if strlen(modelsave == 0) age*age might exist */
8451: } /* end if strlen(model == 0) */
1.136 brouard 8452:
8453: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
8454: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 8455:
1.136 brouard 8456: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 8457: printf("cptcovprod=%d ", cptcovprod);
8458: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
8459: scanf("%d ",i);*/
8460:
8461:
1.230 brouard 8462: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
8463: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 8464: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
8465: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
8466: k = 1 2 3 4 5 6 7 8 9
8467: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
8468: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 8469: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
8470: Dummy[k] 1 0 0 0 3 1 1 2 3
8471: Tmodelind[combination of covar]=k;
1.225 brouard 8472: */
8473: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 8474: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 8475: /* 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 8476: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8477: printf("Model=%s\n\
8478: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8479: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8480: 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);
8481: fprintf(ficlog,"Model=%s\n\
8482: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8483: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8484: 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 8485: for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
1.234 brouard 8486: 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 */
8487: if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
1.227 brouard 8488: Fixed[k]= 0;
8489: Dummy[k]= 0;
1.225 brouard 8490: ncoveff++;
1.232 brouard 8491: ncovf++;
1.234 brouard 8492: nsd++;
8493: modell[k].maintype= FTYPE;
8494: TvarsD[nsd]=Tvar[k];
8495: TvarsDind[nsd]=k;
8496: TvarF[ncovf]=Tvar[k];
8497: TvarFind[ncovf]=k;
8498: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8499: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8500: }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
8501: Fixed[k]= 0;
8502: Dummy[k]= 0;
8503: ncoveff++;
8504: ncovf++;
8505: modell[k].maintype= FTYPE;
8506: TvarF[ncovf]=Tvar[k];
8507: TvarFind[ncovf]=k;
1.230 brouard 8508: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 8509: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.240 ! brouard 8510: }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 8511: Fixed[k]= 0;
8512: Dummy[k]= 1;
1.230 brouard 8513: nqfveff++;
1.234 brouard 8514: modell[k].maintype= FTYPE;
8515: modell[k].subtype= FQ;
8516: nsq++;
8517: TvarsQ[nsq]=Tvar[k];
8518: TvarsQind[nsq]=k;
1.232 brouard 8519: ncovf++;
1.234 brouard 8520: TvarF[ncovf]=Tvar[k];
8521: TvarFind[ncovf]=k;
1.231 brouard 8522: 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 8523: 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 */
1.234 brouard 8524: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
1.227 brouard 8525: Fixed[k]= 1;
8526: Dummy[k]= 0;
1.225 brouard 8527: ntveff++; /* Only simple time varying dummy variable */
1.234 brouard 8528: modell[k].maintype= VTYPE;
8529: modell[k].subtype= VD;
8530: nsd++;
8531: TvarsD[nsd]=Tvar[k];
8532: TvarsDind[nsd]=k;
8533: ncovv++; /* Only simple time varying variables */
8534: TvarV[ncovv]=Tvar[k];
8535: TvarVind[ncovv]=k;
1.231 brouard 8536: 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 */
8537: 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 8538: 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);
8539: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 8540: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
1.234 brouard 8541: Fixed[k]= 1;
8542: Dummy[k]= 1;
8543: nqtveff++;
8544: modell[k].maintype= VTYPE;
8545: modell[k].subtype= VQ;
8546: ncovv++; /* Only simple time varying variables */
8547: nsq++;
8548: TvarsQ[nsq]=Tvar[k];
8549: TvarsQind[nsq]=k;
8550: TvarV[ncovv]=Tvar[k];
8551: TvarVind[ncovv]=k;
1.231 brouard 8552: 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 */
8553: 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 8554: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8555: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8556: 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 8557: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8558: }else if (Typevar[k] == 1) { /* product with age */
1.234 brouard 8559: ncova++;
8560: TvarA[ncova]=Tvar[k];
8561: TvarAind[ncova]=k;
1.231 brouard 8562: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
1.240 ! brouard 8563: Fixed[k]= 2;
! 8564: Dummy[k]= 2;
! 8565: modell[k].maintype= ATYPE;
! 8566: modell[k].subtype= APFD;
! 8567: /* ncoveff++; */
1.227 brouard 8568: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.240 ! brouard 8569: Fixed[k]= 2;
! 8570: Dummy[k]= 3;
! 8571: modell[k].maintype= ATYPE;
! 8572: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
! 8573: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 8574: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.240 ! brouard 8575: Fixed[k]= 3;
! 8576: Dummy[k]= 2;
! 8577: modell[k].maintype= ATYPE;
! 8578: modell[k].subtype= APVD; /* Product age * varying dummy */
! 8579: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 8580: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.240 ! brouard 8581: Fixed[k]= 3;
! 8582: Dummy[k]= 3;
! 8583: modell[k].maintype= ATYPE;
! 8584: modell[k].subtype= APVQ; /* Product age * varying quantitative */
! 8585: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 8586: }
8587: }else if (Typevar[k] == 2) { /* product without age */
8588: k1=Tposprod[k];
8589: if(Tvard[k1][1] <=ncovcol){
1.240 ! brouard 8590: if(Tvard[k1][2] <=ncovcol){
! 8591: Fixed[k]= 1;
! 8592: Dummy[k]= 0;
! 8593: modell[k].maintype= FTYPE;
! 8594: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
! 8595: ncovf++; /* Fixed variables without age */
! 8596: TvarF[ncovf]=Tvar[k];
! 8597: TvarFind[ncovf]=k;
! 8598: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8599: Fixed[k]= 0; /* or 2 ?*/
! 8600: Dummy[k]= 1;
! 8601: modell[k].maintype= FTYPE;
! 8602: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
! 8603: ncovf++; /* Varying variables without age */
! 8604: TvarF[ncovf]=Tvar[k];
! 8605: TvarFind[ncovf]=k;
! 8606: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8607: Fixed[k]= 1;
! 8608: Dummy[k]= 0;
! 8609: modell[k].maintype= VTYPE;
! 8610: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
! 8611: ncovv++; /* Varying variables without age */
! 8612: TvarV[ncovv]=Tvar[k];
! 8613: TvarVind[ncovv]=k;
! 8614: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8615: Fixed[k]= 1;
! 8616: Dummy[k]= 1;
! 8617: modell[k].maintype= VTYPE;
! 8618: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
! 8619: ncovv++; /* Varying variables without age */
! 8620: TvarV[ncovv]=Tvar[k];
! 8621: TvarVind[ncovv]=k;
! 8622: }
1.227 brouard 8623: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.240 ! brouard 8624: if(Tvard[k1][2] <=ncovcol){
! 8625: Fixed[k]= 0; /* or 2 ?*/
! 8626: Dummy[k]= 1;
! 8627: modell[k].maintype= FTYPE;
! 8628: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
! 8629: ncovf++; /* Fixed variables without age */
! 8630: TvarF[ncovf]=Tvar[k];
! 8631: TvarFind[ncovf]=k;
! 8632: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8633: Fixed[k]= 1;
! 8634: Dummy[k]= 1;
! 8635: modell[k].maintype= VTYPE;
! 8636: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
! 8637: ncovv++; /* Varying variables without age */
! 8638: TvarV[ncovv]=Tvar[k];
! 8639: TvarVind[ncovv]=k;
! 8640: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8641: Fixed[k]= 1;
! 8642: Dummy[k]= 1;
! 8643: modell[k].maintype= VTYPE;
! 8644: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
! 8645: ncovv++; /* Varying variables without age */
! 8646: TvarV[ncovv]=Tvar[k];
! 8647: TvarVind[ncovv]=k;
! 8648: ncovv++; /* Varying variables without age */
! 8649: TvarV[ncovv]=Tvar[k];
! 8650: TvarVind[ncovv]=k;
! 8651: }
1.227 brouard 8652: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.240 ! brouard 8653: if(Tvard[k1][2] <=ncovcol){
! 8654: Fixed[k]= 1;
! 8655: Dummy[k]= 1;
! 8656: modell[k].maintype= VTYPE;
! 8657: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
! 8658: ncovv++; /* Varying variables without age */
! 8659: TvarV[ncovv]=Tvar[k];
! 8660: TvarVind[ncovv]=k;
! 8661: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8662: Fixed[k]= 1;
! 8663: Dummy[k]= 1;
! 8664: modell[k].maintype= VTYPE;
! 8665: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
! 8666: ncovv++; /* Varying variables without age */
! 8667: TvarV[ncovv]=Tvar[k];
! 8668: TvarVind[ncovv]=k;
! 8669: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8670: Fixed[k]= 1;
! 8671: Dummy[k]= 0;
! 8672: modell[k].maintype= VTYPE;
! 8673: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
! 8674: ncovv++; /* Varying variables without age */
! 8675: TvarV[ncovv]=Tvar[k];
! 8676: TvarVind[ncovv]=k;
! 8677: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8678: Fixed[k]= 1;
! 8679: Dummy[k]= 1;
! 8680: modell[k].maintype= VTYPE;
! 8681: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
! 8682: ncovv++; /* Varying variables without age */
! 8683: TvarV[ncovv]=Tvar[k];
! 8684: TvarVind[ncovv]=k;
! 8685: }
1.227 brouard 8686: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.240 ! brouard 8687: if(Tvard[k1][2] <=ncovcol){
! 8688: Fixed[k]= 1;
! 8689: Dummy[k]= 1;
! 8690: modell[k].maintype= VTYPE;
! 8691: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
! 8692: ncovv++; /* Varying variables without age */
! 8693: TvarV[ncovv]=Tvar[k];
! 8694: TvarVind[ncovv]=k;
! 8695: }else if(Tvard[k1][2] <=ncovcol+nqv){
! 8696: Fixed[k]= 1;
! 8697: Dummy[k]= 1;
! 8698: modell[k].maintype= VTYPE;
! 8699: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
! 8700: ncovv++; /* Varying variables without age */
! 8701: TvarV[ncovv]=Tvar[k];
! 8702: TvarVind[ncovv]=k;
! 8703: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
! 8704: Fixed[k]= 1;
! 8705: Dummy[k]= 1;
! 8706: modell[k].maintype= VTYPE;
! 8707: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
! 8708: ncovv++; /* Varying variables without age */
! 8709: TvarV[ncovv]=Tvar[k];
! 8710: TvarVind[ncovv]=k;
! 8711: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
! 8712: Fixed[k]= 1;
! 8713: Dummy[k]= 1;
! 8714: modell[k].maintype= VTYPE;
! 8715: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
! 8716: ncovv++; /* Varying variables without age */
! 8717: TvarV[ncovv]=Tvar[k];
! 8718: TvarVind[ncovv]=k;
! 8719: }
1.227 brouard 8720: }else{
1.240 ! brouard 8721: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
! 8722: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
! 8723: } /*end k1*/
1.225 brouard 8724: }else{
1.226 brouard 8725: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8726: 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 8727: }
1.227 brouard 8728: 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 8729: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 8730: 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]);
8731: }
8732: /* Searching for doublons in the model */
8733: for(k1=1; k1<= cptcovt;k1++){
8734: for(k2=1; k2 <k1;k2++){
8735: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.234 brouard 8736: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8737: if(Tvar[k1]==Tvar[k2]){
8738: 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]]);
8739: 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);
8740: return(1);
8741: }
8742: }else if (Typevar[k1] ==2){
8743: k3=Tposprod[k1];
8744: k4=Tposprod[k2];
8745: 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])) ){
8746: 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]]);
8747: 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);
8748: return(1);
8749: }
8750: }
1.227 brouard 8751: }
8752: }
1.225 brouard 8753: }
8754: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8755: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.234 brouard 8756: printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
8757: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
1.137 brouard 8758: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8759: /*endread:*/
1.225 brouard 8760: printf("Exiting decodemodel: ");
8761: return (1);
1.136 brouard 8762: }
8763:
1.169 brouard 8764: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8765: {
8766: int i, m;
1.218 brouard 8767: int firstone=0;
8768:
1.136 brouard 8769: for (i=1; i<=imx; i++) {
8770: for(m=2; (m<= maxwav); m++) {
8771: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8772: anint[m][i]=9999;
1.216 brouard 8773: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8774: s[m][i]=-1;
1.136 brouard 8775: }
8776: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8777: *nberr = *nberr + 1;
1.218 brouard 8778: if(firstone == 0){
8779: firstone=1;
8780: 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);
8781: }
8782: 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 8783: s[m][i]=-1;
8784: }
8785: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8786: (*nberr)++;
1.136 brouard 8787: 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]);
8788: 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]);
8789: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8790: }
8791: }
8792: }
8793:
8794: for (i=1; i<=imx; i++) {
8795: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8796: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8797: 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 8798: if (s[m][i] >= nlstate+1) {
1.169 brouard 8799: if(agedc[i]>0){
8800: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8801: agev[m][i]=agedc[i];
1.214 brouard 8802: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8803: }else {
1.136 brouard 8804: if ((int)andc[i]!=9999){
8805: nbwarn++;
8806: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8807: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8808: agev[m][i]=-1;
8809: }
8810: }
1.169 brouard 8811: } /* agedc > 0 */
1.214 brouard 8812: } /* end if */
1.136 brouard 8813: else if(s[m][i] !=9){ /* Standard case, age in fractional
8814: years but with the precision of a month */
8815: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8816: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8817: agev[m][i]=1;
8818: else if(agev[m][i] < *agemin){
8819: *agemin=agev[m][i];
8820: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8821: }
8822: else if(agev[m][i] >*agemax){
8823: *agemax=agev[m][i];
1.156 brouard 8824: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8825: }
8826: /*agev[m][i]=anint[m][i]-annais[i];*/
8827: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8828: } /* en if 9*/
1.136 brouard 8829: else { /* =9 */
1.214 brouard 8830: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8831: agev[m][i]=1;
8832: s[m][i]=-1;
8833: }
8834: }
1.214 brouard 8835: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8836: agev[m][i]=1;
1.214 brouard 8837: else{
8838: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8839: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8840: agev[m][i]=0;
8841: }
8842: } /* End for lastpass */
8843: }
1.136 brouard 8844:
8845: for (i=1; i<=imx; i++) {
8846: for(m=firstpass; (m<=lastpass); m++){
8847: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8848: (*nberr)++;
1.136 brouard 8849: 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);
8850: 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);
8851: return 1;
8852: }
8853: }
8854: }
8855:
8856: /*for (i=1; i<=imx; i++){
8857: for (m=firstpass; (m<lastpass); m++){
8858: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8859: }
8860:
8861: }*/
8862:
8863:
1.139 brouard 8864: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8865: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8866:
8867: return (0);
1.164 brouard 8868: /* endread:*/
1.136 brouard 8869: printf("Exiting calandcheckages: ");
8870: return (1);
8871: }
8872:
1.172 brouard 8873: #if defined(_MSC_VER)
8874: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8875: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8876: //#include "stdafx.h"
8877: //#include <stdio.h>
8878: //#include <tchar.h>
8879: //#include <windows.h>
8880: //#include <iostream>
8881: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8882:
8883: LPFN_ISWOW64PROCESS fnIsWow64Process;
8884:
8885: BOOL IsWow64()
8886: {
8887: BOOL bIsWow64 = FALSE;
8888:
8889: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8890: // (HANDLE, PBOOL);
8891:
8892: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8893:
8894: HMODULE module = GetModuleHandle(_T("kernel32"));
8895: const char funcName[] = "IsWow64Process";
8896: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8897: GetProcAddress(module, funcName);
8898:
8899: if (NULL != fnIsWow64Process)
8900: {
8901: if (!fnIsWow64Process(GetCurrentProcess(),
8902: &bIsWow64))
8903: //throw std::exception("Unknown error");
8904: printf("Unknown error\n");
8905: }
8906: return bIsWow64 != FALSE;
8907: }
8908: #endif
1.177 brouard 8909:
1.191 brouard 8910: void syscompilerinfo(int logged)
1.167 brouard 8911: {
8912: /* #include "syscompilerinfo.h"*/
1.185 brouard 8913: /* command line Intel compiler 32bit windows, XP compatible:*/
8914: /* /GS /W3 /Gy
8915: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8916: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8917: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8918: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8919: */
8920: /* 64 bits */
1.185 brouard 8921: /*
8922: /GS /W3 /Gy
8923: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8924: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8925: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8926: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8927: /* Optimization are useless and O3 is slower than O2 */
8928: /*
8929: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8930: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8931: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8932: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8933: */
1.186 brouard 8934: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8935: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8936: /PDB:"visual studio
8937: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8938: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8939: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8940: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8941: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8942: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8943: uiAccess='false'"
8944: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8945: /NOLOGO /TLBID:1
8946: */
1.177 brouard 8947: #if defined __INTEL_COMPILER
1.178 brouard 8948: #if defined(__GNUC__)
8949: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8950: #endif
1.177 brouard 8951: #elif defined(__GNUC__)
1.179 brouard 8952: #ifndef __APPLE__
1.174 brouard 8953: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8954: #endif
1.177 brouard 8955: struct utsname sysInfo;
1.178 brouard 8956: int cross = CROSS;
8957: if (cross){
8958: printf("Cross-");
1.191 brouard 8959: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8960: }
1.174 brouard 8961: #endif
8962:
1.171 brouard 8963: #include <stdint.h>
1.178 brouard 8964:
1.191 brouard 8965: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8966: #if defined(__clang__)
1.191 brouard 8967: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8968: #endif
8969: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8970: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8971: #endif
8972: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8973: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8974: #endif
8975: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8976: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8977: #endif
8978: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8979: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8980: #endif
8981: #if defined(_MSC_VER)
1.191 brouard 8982: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8983: #endif
8984: #if defined(__PGI)
1.191 brouard 8985: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8986: #endif
8987: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8988: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8989: #endif
1.191 brouard 8990: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8991:
1.167 brouard 8992: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8993: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8994: // Windows (x64 and x86)
1.191 brouard 8995: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8996: #elif __unix__ // all unices, not all compilers
8997: // Unix
1.191 brouard 8998: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8999: #elif __linux__
9000: // linux
1.191 brouard 9001: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 9002: #elif __APPLE__
1.174 brouard 9003: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 9004: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 9005: #endif
9006:
9007: /* __MINGW32__ */
9008: /* __CYGWIN__ */
9009: /* __MINGW64__ */
9010: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
9011: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
9012: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
9013: /* _WIN64 // Defined for applications for Win64. */
9014: /* _M_X64 // Defined for compilations that target x64 processors. */
9015: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 9016:
1.167 brouard 9017: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 9018: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 9019: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 9020: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 9021: #else
1.191 brouard 9022: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 9023: #endif
9024:
1.169 brouard 9025: #if defined(__GNUC__)
9026: # if defined(__GNUC_PATCHLEVEL__)
9027: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
9028: + __GNUC_MINOR__ * 100 \
9029: + __GNUC_PATCHLEVEL__)
9030: # else
9031: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
9032: + __GNUC_MINOR__ * 100)
9033: # endif
1.174 brouard 9034: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 9035: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 9036:
9037: if (uname(&sysInfo) != -1) {
9038: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 9039: 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 9040: }
9041: else
9042: perror("uname() error");
1.179 brouard 9043: //#ifndef __INTEL_COMPILER
9044: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 9045: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 9046: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 9047: #endif
1.169 brouard 9048: #endif
1.172 brouard 9049:
9050: // void main()
9051: // {
1.169 brouard 9052: #if defined(_MSC_VER)
1.174 brouard 9053: if (IsWow64()){
1.191 brouard 9054: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
9055: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 9056: }
9057: else{
1.191 brouard 9058: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
9059: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 9060: }
1.172 brouard 9061: // printf("\nPress Enter to continue...");
9062: // getchar();
9063: // }
9064:
1.169 brouard 9065: #endif
9066:
1.167 brouard 9067:
1.219 brouard 9068: }
1.136 brouard 9069:
1.219 brouard 9070: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 9071: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.235 brouard 9072: int i, j, k, i1, k4=0, nres=0 ;
1.202 brouard 9073: /* double ftolpl = 1.e-10; */
1.180 brouard 9074: double age, agebase, agelim;
1.203 brouard 9075: double tot;
1.180 brouard 9076:
1.202 brouard 9077: strcpy(filerespl,"PL_");
9078: strcat(filerespl,fileresu);
9079: if((ficrespl=fopen(filerespl,"w"))==NULL) {
9080: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
9081: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
9082: }
1.227 brouard 9083: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
9084: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 9085: pstamp(ficrespl);
1.203 brouard 9086: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 9087: fprintf(ficrespl,"#Age ");
9088: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
9089: fprintf(ficrespl,"\n");
1.180 brouard 9090:
1.219 brouard 9091: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 9092:
1.219 brouard 9093: agebase=ageminpar;
9094: agelim=agemaxpar;
1.180 brouard 9095:
1.227 brouard 9096: /* i1=pow(2,ncoveff); */
1.234 brouard 9097: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
1.219 brouard 9098: if (cptcovn < 1){i1=1;}
1.180 brouard 9099:
1.238 brouard 9100: for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
9101: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
9102: if(TKresult[nres]!= k)
9103: continue;
1.235 brouard 9104:
1.238 brouard 9105: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9106: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
9107: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
9108: /* k=k+1; */
9109: /* to clean */
9110: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
9111: fprintf(ficrespl,"#******");
9112: printf("#******");
9113: fprintf(ficlog,"#******");
9114: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
9115: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
9116: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9117: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9118: }
9119: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
9120: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9121: fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9122: fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9123: }
9124: fprintf(ficrespl,"******\n");
9125: printf("******\n");
9126: fprintf(ficlog,"******\n");
9127: if(invalidvarcomb[k]){
9128: printf("\nCombination (%d) ignored because no case \n",k);
9129: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
9130: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
9131: continue;
9132: }
1.219 brouard 9133:
1.238 brouard 9134: fprintf(ficrespl,"#Age ");
9135: for(j=1;j<=cptcoveff;j++) {
9136: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9137: }
9138: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
9139: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 9140:
1.238 brouard 9141: for (age=agebase; age<=agelim; age++){
9142: /* for (age=agebase; age<=agebase; age++){ */
9143: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
9144: fprintf(ficrespl,"%.0f ",age );
9145: for(j=1;j<=cptcoveff;j++)
9146: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9147: tot=0.;
9148: for(i=1; i<=nlstate;i++){
9149: tot += prlim[i][i];
9150: fprintf(ficrespl," %.5f", prlim[i][i]);
9151: }
9152: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
9153: } /* Age */
9154: /* was end of cptcod */
9155: } /* cptcov */
9156: } /* nres */
1.219 brouard 9157: return 0;
1.180 brouard 9158: }
9159:
1.218 brouard 9160: 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){
9161: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9162:
9163: /* Computes the back prevalence limit for any combination of covariate values
9164: * at any age between ageminpar and agemaxpar
9165: */
1.235 brouard 9166: int i, j, k, i1, nres=0 ;
1.217 brouard 9167: /* double ftolpl = 1.e-10; */
9168: double age, agebase, agelim;
9169: double tot;
1.218 brouard 9170: /* double ***mobaverage; */
9171: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 9172:
9173: strcpy(fileresplb,"PLB_");
9174: strcat(fileresplb,fileresu);
9175: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
9176: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
9177: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
9178: }
9179: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
9180: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
9181: pstamp(ficresplb);
9182: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
9183: fprintf(ficresplb,"#Age ");
9184: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
9185: fprintf(ficresplb,"\n");
9186:
1.218 brouard 9187:
9188: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
9189:
9190: agebase=ageminpar;
9191: agelim=agemaxpar;
9192:
9193:
1.227 brouard 9194: i1=pow(2,cptcoveff);
1.218 brouard 9195: if (cptcovn < 1){i1=1;}
1.227 brouard 9196:
1.238 brouard 9197: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
9198: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
9199: if(TKresult[nres]!= k)
9200: continue;
9201: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
9202: fprintf(ficresplb,"#******");
9203: printf("#******");
9204: fprintf(ficlog,"#******");
9205: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
9206: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9207: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9208: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9209: }
9210: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9211: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9212: fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9213: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9214: }
9215: fprintf(ficresplb,"******\n");
9216: printf("******\n");
9217: fprintf(ficlog,"******\n");
9218: if(invalidvarcomb[k]){
9219: printf("\nCombination (%d) ignored because no cases \n",k);
9220: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
9221: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
9222: continue;
9223: }
1.218 brouard 9224:
1.238 brouard 9225: fprintf(ficresplb,"#Age ");
9226: for(j=1;j<=cptcoveff;j++) {
9227: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9228: }
9229: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
9230: fprintf(ficresplb,"Total Years_to_converge\n");
1.218 brouard 9231:
9232:
1.238 brouard 9233: for (age=agebase; age<=agelim; age++){
9234: /* for (age=agebase; age<=agebase; age++){ */
9235: if(mobilavproj > 0){
9236: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
9237: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
9238: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
9239: }else if (mobilavproj == 0){
9240: 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);
9241: 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);
9242: exit(1);
9243: }else{
9244: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
9245: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
9246: }
9247: fprintf(ficresplb,"%.0f ",age );
9248: for(j=1;j<=cptcoveff;j++)
9249: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9250: tot=0.;
9251: for(i=1; i<=nlstate;i++){
9252: tot += bprlim[i][i];
9253: fprintf(ficresplb," %.5f", bprlim[i][i]);
9254: }
9255: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
9256: } /* Age */
9257: /* was end of cptcod */
9258: } /* end of any combination */
9259: } /* end of nres */
1.218 brouard 9260: /* hBijx(p, bage, fage); */
9261: /* fclose(ficrespijb); */
9262:
9263: return 0;
1.217 brouard 9264: }
1.218 brouard 9265:
1.180 brouard 9266: int hPijx(double *p, int bage, int fage){
9267: /*------------- h Pij x at various ages ------------*/
9268:
9269: int stepsize;
9270: int agelim;
9271: int hstepm;
9272: int nhstepm;
1.235 brouard 9273: int h, i, i1, j, k, k4, nres=0;
1.180 brouard 9274:
9275: double agedeb;
9276: double ***p3mat;
9277:
1.201 brouard 9278: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 9279: if((ficrespij=fopen(filerespij,"w"))==NULL) {
9280: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
9281: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
9282: }
9283: printf("Computing pij: result on file '%s' \n", filerespij);
9284: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
9285:
9286: stepsize=(int) (stepm+YEARM-1)/YEARM;
9287: /*if (stepm<=24) stepsize=2;*/
9288:
9289: agelim=AGESUP;
9290: hstepm=stepsize*YEARM; /* Every year of age */
9291: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 9292:
1.180 brouard 9293: /* hstepm=1; aff par mois*/
9294: pstamp(ficrespij);
9295: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 9296: i1= pow(2,cptcoveff);
1.218 brouard 9297: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9298: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9299: /* k=k+1; */
1.235 brouard 9300: for(nres=1; nres <= nresult; nres++) /* For each resultline */
9301: for(k=1; k<=i1;k++){
9302: if(TKresult[nres]!= k)
9303: continue;
1.183 brouard 9304: fprintf(ficrespij,"\n#****** ");
1.227 brouard 9305: for(j=1;j<=cptcoveff;j++)
1.198 brouard 9306: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 9307: for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
9308: printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9309: fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
9310: }
1.183 brouard 9311: fprintf(ficrespij,"******\n");
9312:
9313: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
9314: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9315: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
9316:
9317: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 9318:
1.183 brouard 9319: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9320: oldm=oldms;savm=savms;
1.235 brouard 9321: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
1.183 brouard 9322: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
9323: for(i=1; i<=nlstate;i++)
9324: for(j=1; j<=nlstate+ndeath;j++)
9325: fprintf(ficrespij," %1d-%1d",i,j);
9326: fprintf(ficrespij,"\n");
9327: for (h=0; h<=nhstepm; h++){
9328: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9329: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 9330: for(i=1; i<=nlstate;i++)
9331: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 9332: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 9333: fprintf(ficrespij,"\n");
9334: }
1.183 brouard 9335: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9336: fprintf(ficrespij,"\n");
9337: }
1.180 brouard 9338: /*}*/
9339: }
1.218 brouard 9340: return 0;
1.180 brouard 9341: }
1.218 brouard 9342:
9343: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 9344: /*------------- h Bij x at various ages ------------*/
9345:
9346: int stepsize;
1.218 brouard 9347: /* int agelim; */
9348: int ageminl;
1.217 brouard 9349: int hstepm;
9350: int nhstepm;
1.238 brouard 9351: int h, i, i1, j, k, nres;
1.218 brouard 9352:
1.217 brouard 9353: double agedeb;
9354: double ***p3mat;
1.218 brouard 9355:
9356: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
9357: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
9358: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9359: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
9360: }
9361: printf("Computing pij back: result on file '%s' \n", filerespijb);
9362: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
9363:
9364: stepsize=(int) (stepm+YEARM-1)/YEARM;
9365: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 9366:
1.218 brouard 9367: /* agelim=AGESUP; */
9368: ageminl=30;
9369: hstepm=stepsize*YEARM; /* Every year of age */
9370: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
9371:
9372: /* hstepm=1; aff par mois*/
9373: pstamp(ficrespijb);
9374: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 9375: i1= pow(2,cptcoveff);
1.218 brouard 9376: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
9377: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
9378: /* k=k+1; */
1.238 brouard 9379: for(nres=1; nres <= nresult; nres++){ /* For each resultline */
9380: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
9381: if(TKresult[nres]!= k)
9382: continue;
9383: fprintf(ficrespijb,"\n#****** ");
9384: for(j=1;j<=cptcoveff;j++)
9385: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9386: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
9387: fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
9388: }
9389: fprintf(ficrespijb,"******\n");
9390: if(invalidvarcomb[k]){
9391: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
9392: continue;
9393: }
9394:
9395: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
9396: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
9397: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
9398: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
9399: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
9400:
9401: /* nhstepm=nhstepm*YEARM; aff par mois*/
9402:
9403: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9404: /* oldm=oldms;savm=savms; */
9405: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
9406: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
9407: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
9408: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
1.217 brouard 9409: for(i=1; i<=nlstate;i++)
9410: for(j=1; j<=nlstate+ndeath;j++)
1.238 brouard 9411: fprintf(ficrespijb," %1d-%1d",i,j);
1.217 brouard 9412: fprintf(ficrespijb,"\n");
1.238 brouard 9413: for (h=0; h<=nhstepm; h++){
9414: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
9415: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
9416: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
9417: for(i=1; i<=nlstate;i++)
9418: for(j=1; j<=nlstate+ndeath;j++)
9419: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
9420: fprintf(ficrespijb,"\n");
9421: }
9422: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
9423: fprintf(ficrespijb,"\n");
9424: } /* end age deb */
9425: } /* end combination */
9426: } /* end nres */
1.218 brouard 9427: return 0;
9428: } /* hBijx */
1.217 brouard 9429:
1.180 brouard 9430:
1.136 brouard 9431: /***********************************************/
9432: /**************** Main Program *****************/
9433: /***********************************************/
9434:
9435: int main(int argc, char *argv[])
9436: {
9437: #ifdef GSL
9438: const gsl_multimin_fminimizer_type *T;
9439: size_t iteri = 0, it;
9440: int rval = GSL_CONTINUE;
9441: int status = GSL_SUCCESS;
9442: double ssval;
9443: #endif
9444: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 9445: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 9446: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 9447: int jj, ll, li, lj, lk;
1.136 brouard 9448: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 9449: int num_filled;
1.136 brouard 9450: int itimes;
9451: int NDIM=2;
9452: int vpopbased=0;
1.235 brouard 9453: int nres=0;
1.136 brouard 9454:
1.164 brouard 9455: char ca[32], cb[32];
1.136 brouard 9456: /* FILE *fichtm; *//* Html File */
9457: /* FILE *ficgp;*/ /*Gnuplot File */
9458: struct stat info;
1.191 brouard 9459: double agedeb=0.;
1.194 brouard 9460:
9461: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 9462: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 9463:
1.165 brouard 9464: double fret;
1.191 brouard 9465: double dum=0.; /* Dummy variable */
1.136 brouard 9466: double ***p3mat;
1.218 brouard 9467: /* double ***mobaverage; */
1.164 brouard 9468:
9469: char line[MAXLINE];
1.197 brouard 9470: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
9471:
1.234 brouard 9472: char modeltemp[MAXLINE];
1.230 brouard 9473: char resultline[MAXLINE];
9474:
1.136 brouard 9475: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 9476: char *tok, *val; /* pathtot */
1.136 brouard 9477: int firstobs=1, lastobs=10;
1.195 brouard 9478: int c, h , cpt, c2;
1.191 brouard 9479: int jl=0;
9480: int i1, j1, jk, stepsize=0;
1.194 brouard 9481: int count=0;
9482:
1.164 brouard 9483: int *tab;
1.136 brouard 9484: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 9485: int backcast=0;
1.136 brouard 9486: int mobilav=0,popforecast=0;
1.191 brouard 9487: int hstepm=0, nhstepm=0;
1.136 brouard 9488: int agemortsup;
9489: float sumlpop=0.;
9490: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
9491: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
9492:
1.191 brouard 9493: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 9494: double ftolpl=FTOL;
9495: double **prlim;
1.217 brouard 9496: double **bprlim;
1.136 brouard 9497: double ***param; /* Matrix of parameters */
9498: double *p;
9499: double **matcov; /* Matrix of covariance */
1.203 brouard 9500: double **hess; /* Hessian matrix */
1.136 brouard 9501: double ***delti3; /* Scale */
9502: double *delti; /* Scale */
9503: double ***eij, ***vareij;
9504: double **varpl; /* Variances of prevalence limits by age */
9505: double *epj, vepp;
1.164 brouard 9506:
1.136 brouard 9507: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 9508: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
9509:
1.136 brouard 9510: double **ximort;
1.145 brouard 9511: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 9512: int *dcwave;
9513:
1.164 brouard 9514: char z[1]="c";
1.136 brouard 9515:
9516: /*char *strt;*/
9517: char strtend[80];
1.126 brouard 9518:
1.164 brouard 9519:
1.126 brouard 9520: /* setlocale (LC_ALL, ""); */
9521: /* bindtextdomain (PACKAGE, LOCALEDIR); */
9522: /* textdomain (PACKAGE); */
9523: /* setlocale (LC_CTYPE, ""); */
9524: /* setlocale (LC_MESSAGES, ""); */
9525:
9526: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 9527: rstart_time = time(NULL);
9528: /* (void) gettimeofday(&start_time,&tzp);*/
9529: start_time = *localtime(&rstart_time);
1.126 brouard 9530: curr_time=start_time;
1.157 brouard 9531: /*tml = *localtime(&start_time.tm_sec);*/
9532: /* strcpy(strstart,asctime(&tml)); */
9533: strcpy(strstart,asctime(&start_time));
1.126 brouard 9534:
9535: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 9536: /* tp.tm_sec = tp.tm_sec +86400; */
9537: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 9538: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
9539: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
9540: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 9541: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 9542: /* strt=asctime(&tmg); */
9543: /* printf("Time(after) =%s",strstart); */
9544: /* (void) time (&time_value);
9545: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
9546: * tm = *localtime(&time_value);
9547: * strstart=asctime(&tm);
9548: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
9549: */
9550:
9551: nberr=0; /* Number of errors and warnings */
9552: nbwarn=0;
1.184 brouard 9553: #ifdef WIN32
9554: _getcwd(pathcd, size);
9555: #else
1.126 brouard 9556: getcwd(pathcd, size);
1.184 brouard 9557: #endif
1.191 brouard 9558: syscompilerinfo(0);
1.196 brouard 9559: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 9560: if(argc <=1){
9561: printf("\nEnter the parameter file name: ");
1.205 brouard 9562: if(!fgets(pathr,FILENAMELENGTH,stdin)){
9563: printf("ERROR Empty parameter file name\n");
9564: goto end;
9565: }
1.126 brouard 9566: i=strlen(pathr);
9567: if(pathr[i-1]=='\n')
9568: pathr[i-1]='\0';
1.156 brouard 9569: i=strlen(pathr);
1.205 brouard 9570: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 9571: pathr[i-1]='\0';
1.205 brouard 9572: }
9573: i=strlen(pathr);
9574: if( i==0 ){
9575: printf("ERROR Empty parameter file name\n");
9576: goto end;
9577: }
9578: for (tok = pathr; tok != NULL; ){
1.126 brouard 9579: printf("Pathr |%s|\n",pathr);
9580: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
9581: printf("val= |%s| pathr=%s\n",val,pathr);
9582: strcpy (pathtot, val);
9583: if(pathr[0] == '\0') break; /* Dirty */
9584: }
9585: }
9586: else{
9587: strcpy(pathtot,argv[1]);
9588: }
9589: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
9590: /*cygwin_split_path(pathtot,path,optionfile);
9591: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
9592: /* cutv(path,optionfile,pathtot,'\\');*/
9593:
9594: /* Split argv[0], imach program to get pathimach */
9595: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
9596: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9597: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9598: /* strcpy(pathimach,argv[0]); */
9599: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
9600: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
9601: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 9602: #ifdef WIN32
9603: _chdir(path); /* Can be a relative path */
9604: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
9605: #else
1.126 brouard 9606: chdir(path); /* Can be a relative path */
1.184 brouard 9607: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
9608: #endif
9609: printf("Current directory %s!\n",pathcd);
1.126 brouard 9610: strcpy(command,"mkdir ");
9611: strcat(command,optionfilefiname);
9612: if((outcmd=system(command)) != 0){
1.169 brouard 9613: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 9614: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
9615: /* fclose(ficlog); */
9616: /* exit(1); */
9617: }
9618: /* if((imk=mkdir(optionfilefiname))<0){ */
9619: /* perror("mkdir"); */
9620: /* } */
9621:
9622: /*-------- arguments in the command line --------*/
9623:
1.186 brouard 9624: /* Main Log file */
1.126 brouard 9625: strcat(filelog, optionfilefiname);
9626: strcat(filelog,".log"); /* */
9627: if((ficlog=fopen(filelog,"w"))==NULL) {
9628: printf("Problem with logfile %s\n",filelog);
9629: goto end;
9630: }
9631: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 9632: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 9633: fprintf(ficlog,"\nEnter the parameter file name: \n");
9634: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
9635: path=%s \n\
9636: optionfile=%s\n\
9637: optionfilext=%s\n\
1.156 brouard 9638: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 9639:
1.197 brouard 9640: syscompilerinfo(1);
1.167 brouard 9641:
1.126 brouard 9642: printf("Local time (at start):%s",strstart);
9643: fprintf(ficlog,"Local time (at start): %s",strstart);
9644: fflush(ficlog);
9645: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 9646: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 9647:
9648: /* */
9649: strcpy(fileres,"r");
9650: strcat(fileres, optionfilefiname);
1.201 brouard 9651: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9652: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9653: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9654:
1.186 brouard 9655: /* Main ---------arguments file --------*/
1.126 brouard 9656:
9657: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9658: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9659: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9660: fflush(ficlog);
1.149 brouard 9661: /* goto end; */
9662: exit(70);
1.126 brouard 9663: }
9664:
9665:
9666:
9667: strcpy(filereso,"o");
1.201 brouard 9668: strcat(filereso,fileresu);
1.126 brouard 9669: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9670: printf("Problem with Output resultfile: %s\n", filereso);
9671: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9672: fflush(ficlog);
9673: goto end;
9674: }
9675:
9676: /* Reads comments: lines beginning with '#' */
9677: numlinepar=0;
1.197 brouard 9678:
9679: /* First parameter line */
9680: while(fgets(line, MAXLINE, ficpar)) {
9681: /* If line starts with a # it is a comment */
9682: if (line[0] == '#') {
9683: numlinepar++;
9684: fputs(line,stdout);
9685: fputs(line,ficparo);
9686: fputs(line,ficlog);
9687: continue;
9688: }else
9689: break;
9690: }
9691: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9692: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9693: if (num_filled != 5) {
9694: printf("Should be 5 parameters\n");
9695: }
1.126 brouard 9696: numlinepar++;
1.197 brouard 9697: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9698: }
9699: /* Second parameter line */
9700: while(fgets(line, MAXLINE, ficpar)) {
9701: /* If line starts with a # it is a comment */
9702: if (line[0] == '#') {
9703: numlinepar++;
9704: fputs(line,stdout);
9705: fputs(line,ficparo);
9706: fputs(line,ficlog);
9707: continue;
9708: }else
9709: break;
9710: }
1.223 brouard 9711: 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", \
9712: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9713: if (num_filled != 11) {
9714: 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 9715: printf("but line=%s\n",line);
1.197 brouard 9716: }
1.223 brouard 9717: 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 9718: }
1.203 brouard 9719: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9720: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9721: /* Third parameter line */
9722: while(fgets(line, MAXLINE, ficpar)) {
9723: /* If line starts with a # it is a comment */
9724: if (line[0] == '#') {
9725: numlinepar++;
9726: fputs(line,stdout);
9727: fputs(line,ficparo);
9728: fputs(line,ficlog);
9729: continue;
9730: }else
9731: break;
9732: }
1.201 brouard 9733: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9734: if (num_filled == 0)
9735: model[0]='\0';
9736: else if (num_filled != 1){
1.197 brouard 9737: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9738: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9739: model[0]='\0';
9740: goto end;
9741: }
9742: else{
9743: if (model[0]=='+'){
9744: for(i=1; i<=strlen(model);i++)
9745: modeltemp[i-1]=model[i];
1.201 brouard 9746: strcpy(model,modeltemp);
1.197 brouard 9747: }
9748: }
1.199 brouard 9749: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9750: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9751: }
9752: /* 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); */
9753: /* numlinepar=numlinepar+3; /\* In general *\/ */
9754: /* 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 9755: 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);
9756: 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 9757: fflush(ficlog);
1.190 brouard 9758: /* if(model[0]=='#'|| model[0]== '\0'){ */
9759: if(model[0]=='#'){
1.187 brouard 9760: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9761: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9762: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9763: if(mle != -1){
9764: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9765: exit(1);
9766: }
9767: }
1.126 brouard 9768: while((c=getc(ficpar))=='#' && c!= EOF){
9769: ungetc(c,ficpar);
9770: fgets(line, MAXLINE, ficpar);
9771: numlinepar++;
1.195 brouard 9772: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9773: z[0]=line[1];
9774: }
9775: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9776: fputs(line, stdout);
9777: //puts(line);
1.126 brouard 9778: fputs(line,ficparo);
9779: fputs(line,ficlog);
9780: }
9781: ungetc(c,ficpar);
9782:
9783:
1.145 brouard 9784: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9785: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
1.233 brouard 9786: cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
1.225 brouard 9787: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9788: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9789: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9790: v1+v2*age+v2*v3 makes cptcovn = 3
9791: */
9792: if (strlen(model)>1)
1.187 brouard 9793: 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 9794: else
1.187 brouard 9795: ncovmodel=2; /* Constant and age */
1.133 brouard 9796: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9797: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9798: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9799: 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);
9800: 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);
9801: fflush(stdout);
9802: fclose (ficlog);
9803: goto end;
9804: }
1.126 brouard 9805: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9806: delti=delti3[1][1];
9807: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9808: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9809: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9810: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9811: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9812: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9813: fclose (ficparo);
9814: fclose (ficlog);
9815: goto end;
9816: exit(0);
1.220 brouard 9817: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9818: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9819: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9820: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9821: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9822: matcov=matrix(1,npar,1,npar);
1.203 brouard 9823: hess=matrix(1,npar,1,npar);
1.220 brouard 9824: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9825: /* Read guessed parameters */
1.126 brouard 9826: /* Reads comments: lines beginning with '#' */
9827: while((c=getc(ficpar))=='#' && c!= EOF){
9828: ungetc(c,ficpar);
9829: fgets(line, MAXLINE, ficpar);
9830: numlinepar++;
1.141 brouard 9831: fputs(line,stdout);
1.126 brouard 9832: fputs(line,ficparo);
9833: fputs(line,ficlog);
9834: }
9835: ungetc(c,ficpar);
9836:
9837: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9838: for(i=1; i <=nlstate; i++){
1.234 brouard 9839: j=0;
1.126 brouard 9840: for(jj=1; jj <=nlstate+ndeath; jj++){
1.234 brouard 9841: if(jj==i) continue;
9842: j++;
9843: fscanf(ficpar,"%1d%1d",&i1,&j1);
9844: if ((i1 != i) || (j1 != jj)){
9845: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9846: It might be a problem of design; if ncovcol and the model are correct\n \
9847: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.234 brouard 9848: exit(1);
9849: }
9850: fprintf(ficparo,"%1d%1d",i1,j1);
9851: if(mle==1)
9852: printf("%1d%1d",i,jj);
9853: fprintf(ficlog,"%1d%1d",i,jj);
9854: for(k=1; k<=ncovmodel;k++){
9855: fscanf(ficpar," %lf",¶m[i][j][k]);
9856: if(mle==1){
9857: printf(" %lf",param[i][j][k]);
9858: fprintf(ficlog," %lf",param[i][j][k]);
9859: }
9860: else
9861: fprintf(ficlog," %lf",param[i][j][k]);
9862: fprintf(ficparo," %lf",param[i][j][k]);
9863: }
9864: fscanf(ficpar,"\n");
9865: numlinepar++;
9866: if(mle==1)
9867: printf("\n");
9868: fprintf(ficlog,"\n");
9869: fprintf(ficparo,"\n");
1.126 brouard 9870: }
9871: }
9872: fflush(ficlog);
1.234 brouard 9873:
1.145 brouard 9874: /* Reads scales values */
1.126 brouard 9875: p=param[1][1];
9876:
9877: /* Reads comments: lines beginning with '#' */
9878: while((c=getc(ficpar))=='#' && c!= EOF){
9879: ungetc(c,ficpar);
9880: fgets(line, MAXLINE, ficpar);
9881: numlinepar++;
1.141 brouard 9882: fputs(line,stdout);
1.126 brouard 9883: fputs(line,ficparo);
9884: fputs(line,ficlog);
9885: }
9886: ungetc(c,ficpar);
9887:
9888: for(i=1; i <=nlstate; i++){
9889: for(j=1; j <=nlstate+ndeath-1; j++){
1.234 brouard 9890: fscanf(ficpar,"%1d%1d",&i1,&j1);
9891: if ( (i1-i) * (j1-j) != 0){
9892: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9893: exit(1);
9894: }
9895: printf("%1d%1d",i,j);
9896: fprintf(ficparo,"%1d%1d",i1,j1);
9897: fprintf(ficlog,"%1d%1d",i1,j1);
9898: for(k=1; k<=ncovmodel;k++){
9899: fscanf(ficpar,"%le",&delti3[i][j][k]);
9900: printf(" %le",delti3[i][j][k]);
9901: fprintf(ficparo," %le",delti3[i][j][k]);
9902: fprintf(ficlog," %le",delti3[i][j][k]);
9903: }
9904: fscanf(ficpar,"\n");
9905: numlinepar++;
9906: printf("\n");
9907: fprintf(ficparo,"\n");
9908: fprintf(ficlog,"\n");
1.126 brouard 9909: }
9910: }
9911: fflush(ficlog);
1.234 brouard 9912:
1.145 brouard 9913: /* Reads covariance matrix */
1.126 brouard 9914: delti=delti3[1][1];
1.220 brouard 9915:
9916:
1.126 brouard 9917: /* 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 9918:
1.126 brouard 9919: /* Reads comments: lines beginning with '#' */
9920: while((c=getc(ficpar))=='#' && c!= EOF){
9921: ungetc(c,ficpar);
9922: fgets(line, MAXLINE, ficpar);
9923: numlinepar++;
1.141 brouard 9924: fputs(line,stdout);
1.126 brouard 9925: fputs(line,ficparo);
9926: fputs(line,ficlog);
9927: }
9928: ungetc(c,ficpar);
1.220 brouard 9929:
1.126 brouard 9930: matcov=matrix(1,npar,1,npar);
1.203 brouard 9931: hess=matrix(1,npar,1,npar);
1.131 brouard 9932: for(i=1; i <=npar; i++)
9933: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9934:
1.194 brouard 9935: /* Scans npar lines */
1.126 brouard 9936: for(i=1; i <=npar; i++){
1.226 brouard 9937: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9938: if(count != 3){
1.226 brouard 9939: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9940: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9941: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9942: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9943: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9944: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9945: exit(1);
1.220 brouard 9946: }else{
1.226 brouard 9947: if(mle==1)
9948: printf("%1d%1d%d",i1,j1,jk);
9949: }
9950: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9951: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9952: for(j=1; j <=i; j++){
1.226 brouard 9953: fscanf(ficpar," %le",&matcov[i][j]);
9954: if(mle==1){
9955: printf(" %.5le",matcov[i][j]);
9956: }
9957: fprintf(ficlog," %.5le",matcov[i][j]);
9958: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9959: }
9960: fscanf(ficpar,"\n");
9961: numlinepar++;
9962: if(mle==1)
1.220 brouard 9963: printf("\n");
1.126 brouard 9964: fprintf(ficlog,"\n");
9965: fprintf(ficparo,"\n");
9966: }
1.194 brouard 9967: /* End of read covariance matrix npar lines */
1.126 brouard 9968: for(i=1; i <=npar; i++)
9969: for(j=i+1;j<=npar;j++)
1.226 brouard 9970: matcov[i][j]=matcov[j][i];
1.126 brouard 9971:
9972: if(mle==1)
9973: printf("\n");
9974: fprintf(ficlog,"\n");
9975:
9976: fflush(ficlog);
9977:
9978: /*-------- Rewriting parameter file ----------*/
9979: strcpy(rfileres,"r"); /* "Rparameterfile */
9980: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9981: strcat(rfileres,"."); /* */
9982: strcat(rfileres,optionfilext); /* Other files have txt extension */
9983: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9984: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9985: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9986: }
9987: fprintf(ficres,"#%s\n",version);
9988: } /* End of mle != -3 */
1.218 brouard 9989:
1.186 brouard 9990: /* Main data
9991: */
1.126 brouard 9992: n= lastobs;
9993: num=lvector(1,n);
9994: moisnais=vector(1,n);
9995: annais=vector(1,n);
9996: moisdc=vector(1,n);
9997: andc=vector(1,n);
1.220 brouard 9998: weight=vector(1,n);
1.126 brouard 9999: agedc=vector(1,n);
10000: cod=ivector(1,n);
1.220 brouard 10001: for(i=1;i<=n;i++){
1.234 brouard 10002: num[i]=0;
10003: moisnais[i]=0;
10004: annais[i]=0;
10005: moisdc[i]=0;
10006: andc[i]=0;
10007: agedc[i]=0;
10008: cod[i]=0;
10009: weight[i]=1.0; /* Equal weights, 1 by default */
10010: }
1.126 brouard 10011: mint=matrix(1,maxwav,1,n);
10012: anint=matrix(1,maxwav,1,n);
1.131 brouard 10013: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 10014: tab=ivector(1,NCOVMAX);
1.144 brouard 10015: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 10016: 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 10017:
1.136 brouard 10018: /* Reads data from file datafile */
10019: if (readdata(datafile, firstobs, lastobs, &imx)==1)
10020: goto end;
10021:
10022: /* Calculation of the number of parameters from char model */
1.234 brouard 10023: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
1.137 brouard 10024: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
10025: k=3 V4 Tvar[k=3]= 4 (from V4)
10026: k=2 V1 Tvar[k=2]= 1 (from V1)
10027: k=1 Tvar[1]=2 (from V2)
1.234 brouard 10028: */
10029:
10030: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
10031: TvarsDind=ivector(1,NCOVMAX); /* */
10032: TvarsD=ivector(1,NCOVMAX); /* */
10033: TvarsQind=ivector(1,NCOVMAX); /* */
10034: TvarsQ=ivector(1,NCOVMAX); /* */
1.232 brouard 10035: TvarF=ivector(1,NCOVMAX); /* */
10036: TvarFind=ivector(1,NCOVMAX); /* */
10037: TvarV=ivector(1,NCOVMAX); /* */
10038: TvarVind=ivector(1,NCOVMAX); /* */
10039: TvarA=ivector(1,NCOVMAX); /* */
10040: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 10041: TvarFD=ivector(1,NCOVMAX); /* */
10042: TvarFDind=ivector(1,NCOVMAX); /* */
10043: TvarFQ=ivector(1,NCOVMAX); /* */
10044: TvarFQind=ivector(1,NCOVMAX); /* */
10045: TvarVD=ivector(1,NCOVMAX); /* */
10046: TvarVDind=ivector(1,NCOVMAX); /* */
10047: TvarVQ=ivector(1,NCOVMAX); /* */
10048: TvarVQind=ivector(1,NCOVMAX); /* */
10049:
1.230 brouard 10050: Tvalsel=vector(1,NCOVMAX); /* */
1.233 brouard 10051: Tvarsel=ivector(1,NCOVMAX); /* */
1.226 brouard 10052: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
10053: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
10054: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 10055: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
10056: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
10057: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
10058: */
10059: /* For model-covariate k tells which data-covariate to use but
10060: because this model-covariate is a construction we invent a new column
10061: ncovcol + k1
10062: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
10063: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 10064: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
10065: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 10066: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
10067: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 10068: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 10069: */
1.145 brouard 10070: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
10071: 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 10072: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
10073: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 10074: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 10075: 4 covariates (3 plus signs)
10076: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
10077: */
1.230 brouard 10078: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 10079: * individual dummy, fixed or varying:
10080: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
10081: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 10082: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
10083: * V1 df, V2 qf, V3 & V4 dv, V5 qv
10084: * Tmodelind[1]@9={9,0,3,2,}*/
10085: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
10086: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 10087: * individual quantitative, fixed or varying:
10088: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
10089: * 3, 1, 0, 0, 0, 0, 0, 0},
10090: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 10091: /* Main decodemodel */
10092:
1.187 brouard 10093:
1.223 brouard 10094: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 10095: goto end;
10096:
1.137 brouard 10097: if((double)(lastobs-imx)/(double)imx > 1.10){
10098: nbwarn++;
10099: 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);
10100: 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);
10101: }
1.136 brouard 10102: /* if(mle==1){*/
1.137 brouard 10103: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
10104: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 10105: }
10106:
10107: /*-calculation of age at interview from date of interview and age at death -*/
10108: agev=matrix(1,maxwav,1,imx);
10109:
10110: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
10111: goto end;
10112:
1.126 brouard 10113:
1.136 brouard 10114: agegomp=(int)agemin;
10115: free_vector(moisnais,1,n);
10116: free_vector(annais,1,n);
1.126 brouard 10117: /* free_matrix(mint,1,maxwav,1,n);
10118: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 10119: /* free_vector(moisdc,1,n); */
10120: /* free_vector(andc,1,n); */
1.145 brouard 10121: /* */
10122:
1.126 brouard 10123: wav=ivector(1,imx);
1.214 brouard 10124: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
10125: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
10126: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
10127: 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.*/
10128: bh=imatrix(1,lastpass-firstpass+2,1,imx);
10129: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 10130:
10131: /* Concatenates waves */
1.214 brouard 10132: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
10133: Death is a valid wave (if date is known).
10134: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
10135: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
10136: and mw[mi+1][i]. dh depends on stepm.
10137: */
10138:
1.126 brouard 10139: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 10140: /* */
10141:
1.215 brouard 10142: free_vector(moisdc,1,n);
10143: free_vector(andc,1,n);
10144:
1.126 brouard 10145: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
10146: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
10147: ncodemax[1]=1;
1.145 brouard 10148: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 10149: cptcoveff=0;
1.220 brouard 10150: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
10151: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 10152: }
10153:
10154: ncovcombmax=pow(2,cptcoveff);
10155: invalidvarcomb=ivector(1, ncovcombmax);
10156: for(i=1;i<ncovcombmax;i++)
10157: invalidvarcomb[i]=0;
10158:
1.211 brouard 10159: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 10160: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 10161: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 10162:
1.200 brouard 10163: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 10164: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 10165: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 10166: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
10167: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
10168: * (currently 0 or 1) in the data.
10169: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
10170: * corresponding modality (h,j).
10171: */
10172:
1.145 brouard 10173: h=0;
10174: /*if (cptcovn > 0) */
1.126 brouard 10175: m=pow(2,cptcoveff);
10176:
1.144 brouard 10177: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 10178: * For k=4 covariates, h goes from 1 to m=2**k
10179: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
10180: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 10181: * h\k 1 2 3 4
1.143 brouard 10182: *______________________________
10183: * 1 i=1 1 i=1 1 i=1 1 i=1 1
10184: * 2 2 1 1 1
10185: * 3 i=2 1 2 1 1
10186: * 4 2 2 1 1
10187: * 5 i=3 1 i=2 1 2 1
10188: * 6 2 1 2 1
10189: * 7 i=4 1 2 2 1
10190: * 8 2 2 2 1
1.197 brouard 10191: * 9 i=5 1 i=3 1 i=2 1 2
10192: * 10 2 1 1 2
10193: * 11 i=6 1 2 1 2
10194: * 12 2 2 1 2
10195: * 13 i=7 1 i=4 1 2 2
10196: * 14 2 1 2 2
10197: * 15 i=8 1 2 2 2
10198: * 16 2 2 2 2
1.143 brouard 10199: */
1.212 brouard 10200: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 10201: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
10202: * and the value of each covariate?
10203: * V1=1, V2=1, V3=2, V4=1 ?
10204: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
10205: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
10206: * In order to get the real value in the data, we use nbcode
10207: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
10208: * We are keeping this crazy system in order to be able (in the future?)
10209: * to have more than 2 values (0 or 1) for a covariate.
10210: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
10211: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
10212: * bbbbbbbb
10213: * 76543210
10214: * h-1 00000101 (6-1=5)
1.219 brouard 10215: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 10216: * &
10217: * 1 00000001 (1)
1.219 brouard 10218: * 00000000 = 1 & ((h-1) >> (k-1))
10219: * +1= 00000001 =1
1.211 brouard 10220: *
10221: * h=14, k=3 => h'=h-1=13, k'=k-1=2
10222: * h' 1101 =2^3+2^2+0x2^1+2^0
10223: * >>k' 11
10224: * & 00000001
10225: * = 00000001
10226: * +1 = 00000010=2 = codtabm(14,3)
10227: * Reverse h=6 and m=16?
10228: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
10229: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
10230: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
10231: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
10232: * V3=decodtabm(14,3,2**4)=2
10233: * h'=13 1101 =2^3+2^2+0x2^1+2^0
10234: *(h-1) >> (j-1) 0011 =13 >> 2
10235: * &1 000000001
10236: * = 000000001
10237: * +1= 000000010 =2
10238: * 2211
10239: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
10240: * V3=2
1.220 brouard 10241: * codtabm and decodtabm are identical
1.211 brouard 10242: */
10243:
1.145 brouard 10244:
10245: free_ivector(Ndum,-1,NCOVMAX);
10246:
10247:
1.126 brouard 10248:
1.186 brouard 10249: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 10250: strcpy(optionfilegnuplot,optionfilefiname);
10251: if(mle==-3)
1.201 brouard 10252: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 10253: strcat(optionfilegnuplot,".gp");
10254:
10255: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
10256: printf("Problem with file %s",optionfilegnuplot);
10257: }
10258: else{
1.204 brouard 10259: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 10260: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 10261: //fprintf(ficgp,"set missing 'NaNq'\n");
10262: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 10263: }
10264: /* fclose(ficgp);*/
1.186 brouard 10265:
10266:
10267: /* Initialisation of --------- index.htm --------*/
1.126 brouard 10268:
10269: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
10270: if(mle==-3)
1.201 brouard 10271: strcat(optionfilehtm,"-MORT_");
1.126 brouard 10272: strcat(optionfilehtm,".htm");
10273: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 10274: printf("Problem with %s \n",optionfilehtm);
10275: exit(0);
1.126 brouard 10276: }
10277:
10278: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
10279: strcat(optionfilehtmcov,"-cov.htm");
10280: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
10281: printf("Problem with %s \n",optionfilehtmcov), exit(0);
10282: }
10283: else{
10284: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
10285: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10286: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 10287: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
10288: }
10289:
1.213 brouard 10290: 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 10291: <hr size=\"2\" color=\"#EC5E5E\"> \n\
10292: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 10293: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 10294: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 10295: \n\
10296: <hr size=\"2\" color=\"#EC5E5E\">\
10297: <ul><li><h4>Parameter files</h4>\n\
10298: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
10299: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
10300: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
10301: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
10302: - Date and time at start: %s</ul>\n",\
10303: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
10304: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
10305: fileres,fileres,\
10306: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
10307: fflush(fichtm);
10308:
10309: strcpy(pathr,path);
10310: strcat(pathr,optionfilefiname);
1.184 brouard 10311: #ifdef WIN32
10312: _chdir(optionfilefiname); /* Move to directory named optionfile */
10313: #else
1.126 brouard 10314: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 10315: #endif
10316:
1.126 brouard 10317:
1.220 brouard 10318: /* Calculates basic frequencies. Computes observed prevalence at single age
10319: and for any valid combination of covariates
1.126 brouard 10320: and prints on file fileres'p'. */
1.227 brouard 10321: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
10322: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 10323:
10324: fprintf(fichtm,"\n");
10325: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
10326: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
10327: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
10328: imx,agemin,agemax,jmin,jmax,jmean);
10329: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 10330: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10331: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10332: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
10333: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 10334:
1.126 brouard 10335: /* For Powell, parameters are in a vector p[] starting at p[1]
10336: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
10337: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
10338:
10339: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 10340: /* For mortality only */
1.126 brouard 10341: if (mle==-3){
1.136 brouard 10342: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 10343: for(i=1;i<=NDIM;i++)
10344: for(j=1;j<=NDIM;j++)
10345: ximort[i][j]=0.;
1.186 brouard 10346: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 10347: cens=ivector(1,n);
10348: ageexmed=vector(1,n);
10349: agecens=vector(1,n);
10350: dcwave=ivector(1,n);
1.223 brouard 10351:
1.126 brouard 10352: for (i=1; i<=imx; i++){
10353: dcwave[i]=-1;
10354: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 10355: if (s[m][i]>nlstate) {
10356: dcwave[i]=m;
10357: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
10358: break;
10359: }
1.126 brouard 10360: }
1.226 brouard 10361:
1.126 brouard 10362: for (i=1; i<=imx; i++) {
10363: if (wav[i]>0){
1.226 brouard 10364: ageexmed[i]=agev[mw[1][i]][i];
10365: j=wav[i];
10366: agecens[i]=1.;
10367:
10368: if (ageexmed[i]> 1 && wav[i] > 0){
10369: agecens[i]=agev[mw[j][i]][i];
10370: cens[i]= 1;
10371: }else if (ageexmed[i]< 1)
10372: cens[i]= -1;
10373: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
10374: cens[i]=0 ;
1.126 brouard 10375: }
10376: else cens[i]=-1;
10377: }
10378:
10379: for (i=1;i<=NDIM;i++) {
10380: for (j=1;j<=NDIM;j++)
1.226 brouard 10381: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 10382: }
10383:
1.145 brouard 10384: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 10385: /*printf("%lf %lf", p[1], p[2]);*/
10386:
10387:
1.136 brouard 10388: #ifdef GSL
10389: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 10390: #else
1.126 brouard 10391: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 10392: #endif
1.201 brouard 10393: strcpy(filerespow,"POW-MORT_");
10394: strcat(filerespow,fileresu);
1.126 brouard 10395: if((ficrespow=fopen(filerespow,"w"))==NULL) {
10396: printf("Problem with resultfile: %s\n", filerespow);
10397: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
10398: }
1.136 brouard 10399: #ifdef GSL
10400: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 10401: #else
1.126 brouard 10402: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 10403: #endif
1.126 brouard 10404: /* for (i=1;i<=nlstate;i++)
10405: for(j=1;j<=nlstate+ndeath;j++)
10406: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
10407: */
10408: fprintf(ficrespow,"\n");
1.136 brouard 10409: #ifdef GSL
10410: /* gsl starts here */
10411: T = gsl_multimin_fminimizer_nmsimplex;
10412: gsl_multimin_fminimizer *sfm = NULL;
10413: gsl_vector *ss, *x;
10414: gsl_multimin_function minex_func;
10415:
10416: /* Initial vertex size vector */
10417: ss = gsl_vector_alloc (NDIM);
10418:
10419: if (ss == NULL){
10420: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
10421: }
10422: /* Set all step sizes to 1 */
10423: gsl_vector_set_all (ss, 0.001);
10424:
10425: /* Starting point */
1.126 brouard 10426:
1.136 brouard 10427: x = gsl_vector_alloc (NDIM);
10428:
10429: if (x == NULL){
10430: gsl_vector_free(ss);
10431: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
10432: }
10433:
10434: /* Initialize method and iterate */
10435: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 10436: /* gsl_vector_set(x, 0, 0.0268); */
10437: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 10438: gsl_vector_set(x, 0, p[1]);
10439: gsl_vector_set(x, 1, p[2]);
10440:
10441: minex_func.f = &gompertz_f;
10442: minex_func.n = NDIM;
10443: minex_func.params = (void *)&p; /* ??? */
10444:
10445: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
10446: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
10447:
10448: printf("Iterations beginning .....\n\n");
10449: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
10450:
10451: iteri=0;
10452: while (rval == GSL_CONTINUE){
10453: iteri++;
10454: status = gsl_multimin_fminimizer_iterate(sfm);
10455:
10456: if (status) printf("error: %s\n", gsl_strerror (status));
10457: fflush(0);
10458:
10459: if (status)
10460: break;
10461:
10462: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
10463: ssval = gsl_multimin_fminimizer_size (sfm);
10464:
10465: if (rval == GSL_SUCCESS)
10466: printf ("converged to a local maximum at\n");
10467:
10468: printf("%5d ", iteri);
10469: for (it = 0; it < NDIM; it++){
10470: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
10471: }
10472: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
10473: }
10474:
10475: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
10476:
10477: gsl_vector_free(x); /* initial values */
10478: gsl_vector_free(ss); /* inital step size */
10479: for (it=0; it<NDIM; it++){
10480: p[it+1]=gsl_vector_get(sfm->x,it);
10481: fprintf(ficrespow," %.12lf", p[it]);
10482: }
10483: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
10484: #endif
10485: #ifdef POWELL
10486: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
10487: #endif
1.126 brouard 10488: fclose(ficrespow);
10489:
1.203 brouard 10490: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 10491:
10492: for(i=1; i <=NDIM; i++)
10493: for(j=i+1;j<=NDIM;j++)
1.220 brouard 10494: matcov[i][j]=matcov[j][i];
1.126 brouard 10495:
10496: printf("\nCovariance matrix\n ");
1.203 brouard 10497: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 10498: for(i=1; i <=NDIM; i++) {
10499: for(j=1;j<=NDIM;j++){
1.220 brouard 10500: printf("%f ",matcov[i][j]);
10501: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 10502: }
1.203 brouard 10503: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 10504: }
10505:
10506: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 10507: for (i=1;i<=NDIM;i++) {
1.126 brouard 10508: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 10509: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
10510: }
1.126 brouard 10511: lsurv=vector(1,AGESUP);
10512: lpop=vector(1,AGESUP);
10513: tpop=vector(1,AGESUP);
10514: lsurv[agegomp]=100000;
10515:
10516: for (k=agegomp;k<=AGESUP;k++) {
10517: agemortsup=k;
10518: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
10519: }
10520:
10521: for (k=agegomp;k<agemortsup;k++)
10522: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
10523:
10524: for (k=agegomp;k<agemortsup;k++){
10525: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
10526: sumlpop=sumlpop+lpop[k];
10527: }
10528:
10529: tpop[agegomp]=sumlpop;
10530: for (k=agegomp;k<(agemortsup-3);k++){
10531: /* tpop[k+1]=2;*/
10532: tpop[k+1]=tpop[k]-lpop[k];
10533: }
10534:
10535:
10536: printf("\nAge lx qx dx Lx Tx e(x)\n");
10537: for (k=agegomp;k<(agemortsup-2);k++)
10538: 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]);
10539:
10540:
10541: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 10542: ageminpar=50;
10543: agemaxpar=100;
1.194 brouard 10544: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
10545: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10546: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10547: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
10548: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10549: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10550: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10551: }else{
10552: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
10553: 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 10554: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 10555: }
1.201 brouard 10556: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 10557: stepm, weightopt,\
10558: model,imx,p,matcov,agemortsup);
10559:
10560: free_vector(lsurv,1,AGESUP);
10561: free_vector(lpop,1,AGESUP);
10562: free_vector(tpop,1,AGESUP);
1.220 brouard 10563: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 10564: free_ivector(cens,1,n);
10565: free_vector(agecens,1,n);
10566: free_ivector(dcwave,1,n);
1.220 brouard 10567: #ifdef GSL
1.136 brouard 10568: #endif
1.186 brouard 10569: } /* Endof if mle==-3 mortality only */
1.205 brouard 10570: /* Standard */
10571: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
10572: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10573: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 10574: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 10575: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10576: for (k=1; k<=npar;k++)
10577: printf(" %d %8.5f",k,p[k]);
10578: printf("\n");
1.205 brouard 10579: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
10580: /* mlikeli uses func not funcone */
10581: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
10582: }
10583: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
10584: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10585: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
10586: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10587: }
10588: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 10589: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10590: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10591: for (k=1; k<=npar;k++)
10592: printf(" %d %8.5f",k,p[k]);
10593: printf("\n");
10594:
10595: /*--------- results files --------------*/
1.224 brouard 10596: 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 10597:
10598:
10599: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10600: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10601: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10602: for(i=1,jk=1; i <=nlstate; i++){
10603: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 10604: if (k != i) {
10605: printf("%d%d ",i,k);
10606: fprintf(ficlog,"%d%d ",i,k);
10607: fprintf(ficres,"%1d%1d ",i,k);
10608: for(j=1; j <=ncovmodel; j++){
10609: printf("%12.7f ",p[jk]);
10610: fprintf(ficlog,"%12.7f ",p[jk]);
10611: fprintf(ficres,"%12.7f ",p[jk]);
10612: jk++;
10613: }
10614: printf("\n");
10615: fprintf(ficlog,"\n");
10616: fprintf(ficres,"\n");
10617: }
1.126 brouard 10618: }
10619: }
1.203 brouard 10620: if(mle != 0){
10621: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 10622: ftolhess=ftol; /* Usually correct */
1.203 brouard 10623: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
10624: 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");
10625: 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");
10626: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 10627: for(k=1; k <=(nlstate+ndeath); k++){
10628: if (k != i) {
10629: printf("%d%d ",i,k);
10630: fprintf(ficlog,"%d%d ",i,k);
10631: for(j=1; j <=ncovmodel; j++){
10632: 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]));
10633: 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]));
10634: jk++;
10635: }
10636: printf("\n");
10637: fprintf(ficlog,"\n");
10638: }
10639: }
1.193 brouard 10640: }
1.203 brouard 10641: } /* end of hesscov and Wald tests */
1.225 brouard 10642:
1.203 brouard 10643: /* */
1.126 brouard 10644: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
10645: printf("# Scales (for hessian or gradient estimation)\n");
10646: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
10647: for(i=1,jk=1; i <=nlstate; i++){
10648: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 10649: if (j!=i) {
10650: fprintf(ficres,"%1d%1d",i,j);
10651: printf("%1d%1d",i,j);
10652: fprintf(ficlog,"%1d%1d",i,j);
10653: for(k=1; k<=ncovmodel;k++){
10654: printf(" %.5e",delti[jk]);
10655: fprintf(ficlog," %.5e",delti[jk]);
10656: fprintf(ficres," %.5e",delti[jk]);
10657: jk++;
10658: }
10659: printf("\n");
10660: fprintf(ficlog,"\n");
10661: fprintf(ficres,"\n");
10662: }
1.126 brouard 10663: }
10664: }
10665:
10666: 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 10667: if(mle >= 1) /* To big for the screen */
1.126 brouard 10668: 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");
10669: 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");
10670: /* # 121 Var(a12)\n\ */
10671: /* # 122 Cov(b12,a12) Var(b12)\n\ */
10672: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10673: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10674: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
10675: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
10676: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
10677: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10678:
10679:
10680: /* Just to have a covariance matrix which will be more understandable
10681: even is we still don't want to manage dictionary of variables
10682: */
10683: for(itimes=1;itimes<=2;itimes++){
10684: jj=0;
10685: for(i=1; i <=nlstate; i++){
1.225 brouard 10686: for(j=1; j <=nlstate+ndeath; j++){
10687: if(j==i) continue;
10688: for(k=1; k<=ncovmodel;k++){
10689: jj++;
10690: ca[0]= k+'a'-1;ca[1]='\0';
10691: if(itimes==1){
10692: if(mle>=1)
10693: printf("#%1d%1d%d",i,j,k);
10694: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10695: fprintf(ficres,"#%1d%1d%d",i,j,k);
10696: }else{
10697: if(mle>=1)
10698: printf("%1d%1d%d",i,j,k);
10699: fprintf(ficlog,"%1d%1d%d",i,j,k);
10700: fprintf(ficres,"%1d%1d%d",i,j,k);
10701: }
10702: ll=0;
10703: for(li=1;li <=nlstate; li++){
10704: for(lj=1;lj <=nlstate+ndeath; lj++){
10705: if(lj==li) continue;
10706: for(lk=1;lk<=ncovmodel;lk++){
10707: ll++;
10708: if(ll<=jj){
10709: cb[0]= lk +'a'-1;cb[1]='\0';
10710: if(ll<jj){
10711: if(itimes==1){
10712: if(mle>=1)
10713: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10714: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10715: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10716: }else{
10717: if(mle>=1)
10718: printf(" %.5e",matcov[jj][ll]);
10719: fprintf(ficlog," %.5e",matcov[jj][ll]);
10720: fprintf(ficres," %.5e",matcov[jj][ll]);
10721: }
10722: }else{
10723: if(itimes==1){
10724: if(mle>=1)
10725: printf(" Var(%s%1d%1d)",ca,i,j);
10726: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10727: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10728: }else{
10729: if(mle>=1)
10730: printf(" %.7e",matcov[jj][ll]);
10731: fprintf(ficlog," %.7e",matcov[jj][ll]);
10732: fprintf(ficres," %.7e",matcov[jj][ll]);
10733: }
10734: }
10735: }
10736: } /* end lk */
10737: } /* end lj */
10738: } /* end li */
10739: if(mle>=1)
10740: printf("\n");
10741: fprintf(ficlog,"\n");
10742: fprintf(ficres,"\n");
10743: numlinepar++;
10744: } /* end k*/
10745: } /*end j */
1.126 brouard 10746: } /* end i */
10747: } /* end itimes */
10748:
10749: fflush(ficlog);
10750: fflush(ficres);
1.225 brouard 10751: while(fgets(line, MAXLINE, ficpar)) {
10752: /* If line starts with a # it is a comment */
10753: if (line[0] == '#') {
10754: numlinepar++;
10755: fputs(line,stdout);
10756: fputs(line,ficparo);
10757: fputs(line,ficlog);
10758: continue;
10759: }else
10760: break;
10761: }
10762:
1.209 brouard 10763: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10764: /* ungetc(c,ficpar); */
10765: /* fgets(line, MAXLINE, ficpar); */
10766: /* fputs(line,stdout); */
10767: /* fputs(line,ficparo); */
10768: /* } */
10769: /* ungetc(c,ficpar); */
1.126 brouard 10770:
10771: estepm=0;
1.209 brouard 10772: 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 10773:
10774: if (num_filled != 6) {
10775: 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);
10776: 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);
10777: goto end;
10778: }
10779: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10780: }
10781: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10782: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10783:
1.209 brouard 10784: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10785: if (estepm==0 || estepm < stepm) estepm=stepm;
10786: if (fage <= 2) {
10787: bage = ageminpar;
10788: fage = agemaxpar;
10789: }
10790:
10791: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10792: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10793: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10794:
1.186 brouard 10795: /* Other stuffs, more or less useful */
1.126 brouard 10796: while((c=getc(ficpar))=='#' && c!= EOF){
10797: ungetc(c,ficpar);
10798: fgets(line, MAXLINE, ficpar);
1.141 brouard 10799: fputs(line,stdout);
1.126 brouard 10800: fputs(line,ficparo);
10801: }
10802: ungetc(c,ficpar);
10803:
10804: 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);
10805: 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);
10806: 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);
10807: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10808: 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);
10809:
10810: while((c=getc(ficpar))=='#' && c!= EOF){
10811: ungetc(c,ficpar);
10812: fgets(line, MAXLINE, ficpar);
1.141 brouard 10813: fputs(line,stdout);
1.126 brouard 10814: fputs(line,ficparo);
10815: }
10816: ungetc(c,ficpar);
10817:
10818:
10819: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10820: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10821:
10822: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10823: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10824: fprintf(ficparo,"pop_based=%d\n",popbased);
10825: fprintf(ficres,"pop_based=%d\n",popbased);
10826:
10827: while((c=getc(ficpar))=='#' && c!= EOF){
10828: ungetc(c,ficpar);
10829: fgets(line, MAXLINE, ficpar);
1.141 brouard 10830: fputs(line,stdout);
1.238 brouard 10831: fputs(line,ficres);
1.126 brouard 10832: fputs(line,ficparo);
10833: }
10834: ungetc(c,ficpar);
10835:
10836: 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);
10837: 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);
10838: 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);
10839: 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);
10840: 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);
10841: /* day and month of proj2 are not used but only year anproj2.*/
10842:
1.217 brouard 10843: while((c=getc(ficpar))=='#' && c!= EOF){
10844: ungetc(c,ficpar);
10845: fgets(line, MAXLINE, ficpar);
10846: fputs(line,stdout);
10847: fputs(line,ficparo);
1.238 brouard 10848: fputs(line,ficres);
1.217 brouard 10849: }
10850: ungetc(c,ficpar);
10851:
10852: 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);
1.223 brouard 10853: 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);
10854: 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);
10855: 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 10856: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10857:
1.230 brouard 10858: /* Results */
1.235 brouard 10859: nresult=0;
1.230 brouard 10860: while(fgets(line, MAXLINE, ficpar)) {
10861: /* If line starts with a # it is a comment */
10862: if (line[0] == '#') {
10863: numlinepar++;
10864: fputs(line,stdout);
10865: fputs(line,ficparo);
10866: fputs(line,ficlog);
1.238 brouard 10867: fputs(line,ficres);
1.230 brouard 10868: continue;
10869: }else
10870: break;
10871: }
1.240 ! brouard 10872: if (!feof(ficpar))
1.230 brouard 10873: while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
1.240 ! brouard 10874: if (num_filled == 0){
1.230 brouard 10875: resultline[0]='\0';
1.240 ! brouard 10876: break;
! 10877: } else if (num_filled != 1){
1.230 brouard 10878: printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
10879: }
1.235 brouard 10880: nresult++; /* Sum of resultlines */
10881: printf("Result %d: result=%s\n",nresult, resultline);
10882: if(nresult > MAXRESULTLINES){
10883: printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
10884: fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
10885: goto end;
10886: }
10887: decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
1.238 brouard 10888: fprintf(ficparo,"result: %s\n",resultline);
10889: fprintf(ficres,"result: %s\n",resultline);
10890: fprintf(ficlog,"result: %s\n",resultline);
1.230 brouard 10891: while(fgets(line, MAXLINE, ficpar)) {
10892: /* If line starts with a # it is a comment */
10893: if (line[0] == '#') {
10894: numlinepar++;
10895: fputs(line,stdout);
10896: fputs(line,ficparo);
1.238 brouard 10897: fputs(line,ficres);
1.230 brouard 10898: fputs(line,ficlog);
10899: continue;
10900: }else
10901: break;
10902: }
10903: if (feof(ficpar))
10904: break;
10905: else{ /* Processess output results for this combination of covariate values */
10906: }
1.240 ! brouard 10907: } /* end while */
1.230 brouard 10908:
10909:
1.126 brouard 10910:
1.230 brouard 10911: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10912: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10913:
10914: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10915: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 10916: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10917: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10918: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 10919: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10920: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10921: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10922: }else{
1.218 brouard 10923: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10924: }
10925: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10926: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10927: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10928:
1.225 brouard 10929: /*------------ free_vector -------------*/
10930: /* chdir(path); */
1.220 brouard 10931:
1.215 brouard 10932: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10933: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10934: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10935: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10936: free_lvector(num,1,n);
10937: free_vector(agedc,1,n);
10938: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10939: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10940: fclose(ficparo);
10941: fclose(ficres);
1.220 brouard 10942:
10943:
1.186 brouard 10944: /* Other results (useful)*/
1.220 brouard 10945:
10946:
1.126 brouard 10947: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10948: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10949: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10950: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10951: fclose(ficrespl);
10952:
10953: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10954: /*#include "hpijx.h"*/
10955: hPijx(p, bage, fage);
1.145 brouard 10956: fclose(ficrespij);
1.227 brouard 10957:
1.220 brouard 10958: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10959: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10960: k=1;
1.126 brouard 10961: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10962:
1.219 brouard 10963: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10964: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10965: for(i=1;i<=AGESUP;i++)
1.219 brouard 10966: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10967: for(k=1;k<=ncovcombmax;k++)
10968: probs[i][j][k]=0.;
1.219 brouard 10969: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10970: if (mobilav!=0 ||mobilavproj !=0 ) {
10971: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10972: for(i=1;i<=AGESUP;i++)
10973: for(j=1;j<=nlstate;j++)
10974: for(k=1;k<=ncovcombmax;k++)
10975: mobaverages[i][j][k]=0.;
1.219 brouard 10976: mobaverage=mobaverages;
10977: if (mobilav!=0) {
1.235 brouard 10978: printf("Movingaveraging observed prevalence\n");
1.227 brouard 10979: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10980: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10981: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10982: }
1.219 brouard 10983: }
10984: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10985: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10986: else if (mobilavproj !=0) {
1.235 brouard 10987: printf("Movingaveraging projected observed prevalence\n");
1.227 brouard 10988: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10989: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10990: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10991: }
1.219 brouard 10992: }
10993: }/* end if moving average */
1.227 brouard 10994:
1.126 brouard 10995: /*---------- Forecasting ------------------*/
10996: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10997: if(prevfcast==1){
10998: /* if(stepm ==1){*/
1.225 brouard 10999: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 11000: }
1.217 brouard 11001: if(backcast==1){
1.219 brouard 11002: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11003: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11004: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
11005:
11006: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
11007:
11008: bprlim=matrix(1,nlstate,1,nlstate);
11009: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
11010: fclose(ficresplb);
11011:
1.222 brouard 11012: hBijx(p, bage, fage, mobaverage);
11013: fclose(ficrespijb);
1.219 brouard 11014: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
11015:
11016: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 11017: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 11018: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11019: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11020: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
11021: }
1.217 brouard 11022:
1.186 brouard 11023:
11024: /* ------ Other prevalence ratios------------ */
1.126 brouard 11025:
1.215 brouard 11026: free_ivector(wav,1,imx);
11027: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
11028: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
11029: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 11030:
11031:
1.127 brouard 11032: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 11033:
1.201 brouard 11034: strcpy(filerese,"E_");
11035: strcat(filerese,fileresu);
1.126 brouard 11036: if((ficreseij=fopen(filerese,"w"))==NULL) {
11037: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
11038: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
11039: }
1.208 brouard 11040: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
11041: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.238 brouard 11042:
11043: pstamp(ficreseij);
1.219 brouard 11044:
1.235 brouard 11045: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
11046: if (cptcovn < 1){i1=1;}
11047:
11048: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11049: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
11050: if(TKresult[nres]!= k)
11051: continue;
1.219 brouard 11052: fprintf(ficreseij,"\n#****** ");
1.235 brouard 11053: printf("\n#****** ");
1.225 brouard 11054: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 11055: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 11056: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11057: }
11058: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11059: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11060: fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
1.219 brouard 11061: }
11062: fprintf(ficreseij,"******\n");
1.235 brouard 11063: printf("******\n");
1.219 brouard 11064:
11065: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11066: oldm=oldms;savm=savms;
1.235 brouard 11067: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);
1.127 brouard 11068:
1.219 brouard 11069: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 11070: }
11071: fclose(ficreseij);
1.208 brouard 11072: printf("done evsij\n");fflush(stdout);
11073: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 11074:
1.227 brouard 11075: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 11076:
11077:
1.201 brouard 11078: strcpy(filerest,"T_");
11079: strcat(filerest,fileresu);
1.127 brouard 11080: if((ficrest=fopen(filerest,"w"))==NULL) {
11081: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
11082: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
11083: }
1.208 brouard 11084: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
11085: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 11086:
1.126 brouard 11087:
1.201 brouard 11088: strcpy(fileresstde,"STDE_");
11089: strcat(fileresstde,fileresu);
1.126 brouard 11090: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 11091: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
11092: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 11093: }
1.227 brouard 11094: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
11095: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 11096:
1.201 brouard 11097: strcpy(filerescve,"CVE_");
11098: strcat(filerescve,fileresu);
1.126 brouard 11099: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 11100: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
11101: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 11102: }
1.227 brouard 11103: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
11104: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 11105:
1.201 brouard 11106: strcpy(fileresv,"V_");
11107: strcat(fileresv,fileresu);
1.126 brouard 11108: if((ficresvij=fopen(fileresv,"w"))==NULL) {
11109: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
11110: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
11111: }
1.227 brouard 11112: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
11113: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 11114:
1.145 brouard 11115: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
11116: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
11117:
1.235 brouard 11118: i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
11119: if (cptcovn < 1){i1=1;}
11120:
11121: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11122: for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
11123: if(TKresult[nres]!= k)
11124: continue;
11125: printf("\n#****** Selected:");
11126: fprintf(ficrest,"\n#****** Selected:");
11127: fprintf(ficlog,"\n#****** Selected:");
1.227 brouard 11128: for(j=1;j<=cptcoveff;j++){
11129: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11130: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11131: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11132: }
1.235 brouard 11133: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11134: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11135: fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11136: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11137: }
1.208 brouard 11138: fprintf(ficrest,"******\n");
1.227 brouard 11139: fprintf(ficlog,"******\n");
11140: printf("******\n");
1.208 brouard 11141:
11142: fprintf(ficresstdeij,"\n#****** ");
11143: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 11144: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 11145: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11146: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 11147: }
1.235 brouard 11148: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11149: fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11150: fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11151: }
1.208 brouard 11152: fprintf(ficresstdeij,"******\n");
11153: fprintf(ficrescveij,"******\n");
11154:
11155: fprintf(ficresvij,"\n#****** ");
1.238 brouard 11156: /* pstamp(ficresvij); */
1.225 brouard 11157: for(j=1;j<=cptcoveff;j++)
1.227 brouard 11158: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.235 brouard 11159: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11160: fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11161: }
1.208 brouard 11162: fprintf(ficresvij,"******\n");
11163:
11164: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11165: oldm=oldms;savm=savms;
1.235 brouard 11166: printf(" cvevsij ");
11167: fprintf(ficlog, " cvevsij ");
11168: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
1.208 brouard 11169: printf(" end cvevsij \n ");
11170: fprintf(ficlog, " end cvevsij \n ");
11171:
11172: /*
11173: */
11174: /* goto endfree; */
11175:
11176: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
11177: pstamp(ficrest);
11178:
11179:
11180: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 11181: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
11182: cptcod= 0; /* To be deleted */
11183: printf("varevsij vpopbased=%d \n",vpopbased);
11184: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
1.235 brouard 11185: 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 11186: 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 ");
11187: if(vpopbased==1)
11188: 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);
11189: else
11190: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
11191: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
11192: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
11193: fprintf(ficrest,"\n");
11194: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
11195: epj=vector(1,nlstate+1);
11196: printf("Computing age specific period (stable) prevalences in each health state \n");
11197: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
11198: for(age=bage; age <=fage ;age++){
1.235 brouard 11199: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
1.227 brouard 11200: if (vpopbased==1) {
11201: if(mobilav ==0){
11202: for(i=1; i<=nlstate;i++)
11203: prlim[i][i]=probs[(int)age][i][k];
11204: }else{ /* mobilav */
11205: for(i=1; i<=nlstate;i++)
11206: prlim[i][i]=mobaverage[(int)age][i][k];
11207: }
11208: }
1.219 brouard 11209:
1.227 brouard 11210: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
11211: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
11212: /* printf(" age %4.0f ",age); */
11213: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
11214: for(i=1, epj[j]=0.;i <=nlstate;i++) {
11215: epj[j] += prlim[i][i]*eij[i][j][(int)age];
11216: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
11217: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
11218: }
11219: epj[nlstate+1] +=epj[j];
11220: }
11221: /* printf(" age %4.0f \n",age); */
1.219 brouard 11222:
1.227 brouard 11223: for(i=1, vepp=0.;i <=nlstate;i++)
11224: for(j=1;j <=nlstate;j++)
11225: vepp += vareij[i][j][(int)age];
11226: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
11227: for(j=1;j <=nlstate;j++){
11228: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
11229: }
11230: fprintf(ficrest,"\n");
11231: }
1.208 brouard 11232: } /* End vpopbased */
11233: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11234: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
11235: free_vector(epj,1,nlstate+1);
1.235 brouard 11236: printf("done selection\n");fflush(stdout);
11237: fprintf(ficlog,"done selection\n");fflush(ficlog);
1.208 brouard 11238:
1.145 brouard 11239: /*}*/
1.235 brouard 11240: } /* End k selection */
1.227 brouard 11241:
11242: printf("done State-specific expectancies\n");fflush(stdout);
11243: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
11244:
1.126 brouard 11245: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 11246:
1.201 brouard 11247: strcpy(fileresvpl,"VPL_");
11248: strcat(fileresvpl,fileresu);
1.126 brouard 11249: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
11250: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
11251: exit(0);
11252: }
1.208 brouard 11253: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
11254: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 11255:
1.145 brouard 11256: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
11257: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 11258:
1.235 brouard 11259: i1=pow(2,cptcoveff);
11260: if (cptcovn < 1){i1=1;}
11261:
11262: for(nres=1; nres <= nresult; nres++) /* For each resultline */
11263: for(k=1; k<=i1;k++){
11264: if(TKresult[nres]!= k)
11265: continue;
1.227 brouard 11266: fprintf(ficresvpl,"\n#****** ");
11267: printf("\n#****** ");
11268: fprintf(ficlog,"\n#****** ");
11269: for(j=1;j<=cptcoveff;j++) {
11270: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11271: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11272: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
11273: }
1.235 brouard 11274: for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
11275: printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11276: fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11277: fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
11278: }
1.227 brouard 11279: fprintf(ficresvpl,"******\n");
11280: printf("******\n");
11281: fprintf(ficlog,"******\n");
11282:
11283: varpl=matrix(1,nlstate,(int) bage, (int) fage);
11284: oldm=oldms;savm=savms;
1.235 brouard 11285: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
1.227 brouard 11286: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 11287: /*}*/
1.126 brouard 11288: }
1.227 brouard 11289:
1.126 brouard 11290: fclose(ficresvpl);
1.208 brouard 11291: printf("done variance-covariance of period prevalence\n");fflush(stdout);
11292: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 11293:
11294: free_vector(weight,1,n);
11295: free_imatrix(Tvard,1,NCOVMAX,1,2);
11296: free_imatrix(s,1,maxwav+1,1,n);
11297: free_matrix(anint,1,maxwav,1,n);
11298: free_matrix(mint,1,maxwav,1,n);
11299: free_ivector(cod,1,n);
11300: free_ivector(tab,1,NCOVMAX);
11301: fclose(ficresstdeij);
11302: fclose(ficrescveij);
11303: fclose(ficresvij);
11304: fclose(ficrest);
11305: fclose(ficpar);
11306:
11307:
1.126 brouard 11308: /*---------- End : free ----------------*/
1.219 brouard 11309: if (mobilav!=0 ||mobilavproj !=0)
11310: 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 11311: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 11312: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
11313: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 11314: } /* mle==-3 arrives here for freeing */
1.227 brouard 11315: /* endfree:*/
11316: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
11317: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
11318: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
11319: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
1.233 brouard 11320: free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
1.227 brouard 11321: free_matrix(coqvar,1,maxwav,1,n);
11322: free_matrix(covar,0,NCOVMAX,1,n);
11323: free_matrix(matcov,1,npar,1,npar);
11324: free_matrix(hess,1,npar,1,npar);
11325: /*free_vector(delti,1,npar);*/
11326: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11327: free_matrix(agev,1,maxwav,1,imx);
11328: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
11329:
11330: free_ivector(ncodemax,1,NCOVMAX);
11331: free_ivector(ncodemaxwundef,1,NCOVMAX);
11332: free_ivector(Dummy,-1,NCOVMAX);
11333: free_ivector(Fixed,-1,NCOVMAX);
1.238 brouard 11334: free_ivector(DummyV,1,NCOVMAX);
11335: free_ivector(FixedV,1,NCOVMAX);
1.227 brouard 11336: free_ivector(Typevar,-1,NCOVMAX);
11337: free_ivector(Tvar,1,NCOVMAX);
1.234 brouard 11338: free_ivector(TvarsQ,1,NCOVMAX);
11339: free_ivector(TvarsQind,1,NCOVMAX);
11340: free_ivector(TvarsD,1,NCOVMAX);
11341: free_ivector(TvarsDind,1,NCOVMAX);
1.231 brouard 11342: free_ivector(TvarFD,1,NCOVMAX);
11343: free_ivector(TvarFDind,1,NCOVMAX);
1.232 brouard 11344: free_ivector(TvarF,1,NCOVMAX);
11345: free_ivector(TvarFind,1,NCOVMAX);
11346: free_ivector(TvarV,1,NCOVMAX);
11347: free_ivector(TvarVind,1,NCOVMAX);
11348: free_ivector(TvarA,1,NCOVMAX);
11349: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 11350: free_ivector(TvarFQ,1,NCOVMAX);
11351: free_ivector(TvarFQind,1,NCOVMAX);
11352: free_ivector(TvarVD,1,NCOVMAX);
11353: free_ivector(TvarVDind,1,NCOVMAX);
11354: free_ivector(TvarVQ,1,NCOVMAX);
11355: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 11356: free_ivector(Tvarsel,1,NCOVMAX);
11357: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 11358: free_ivector(Tposprod,1,NCOVMAX);
11359: free_ivector(Tprod,1,NCOVMAX);
11360: free_ivector(Tvaraff,1,NCOVMAX);
11361: free_ivector(invalidvarcomb,1,ncovcombmax);
11362: free_ivector(Tage,1,NCOVMAX);
11363: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 11364: free_ivector(TmodelInvind,1,NCOVMAX);
11365: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 11366:
11367: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
11368: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 11369: fflush(fichtm);
11370: fflush(ficgp);
11371:
1.227 brouard 11372:
1.126 brouard 11373: if((nberr >0) || (nbwarn>0)){
1.216 brouard 11374: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
11375: 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 11376: }else{
11377: printf("End of Imach\n");
11378: fprintf(ficlog,"End of Imach\n");
11379: }
11380: printf("See log file on %s\n",filelog);
11381: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 11382: /*(void) gettimeofday(&end_time,&tzp);*/
11383: rend_time = time(NULL);
11384: end_time = *localtime(&rend_time);
11385: /* tml = *localtime(&end_time.tm_sec); */
11386: strcpy(strtend,asctime(&end_time));
1.126 brouard 11387: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
11388: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 11389: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 11390:
1.157 brouard 11391: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
11392: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
11393: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 11394: /* printf("Total time was %d uSec.\n", total_usecs);*/
11395: /* if(fileappend(fichtm,optionfilehtm)){ */
11396: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11397: fclose(fichtm);
11398: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
11399: fclose(fichtmcov);
11400: fclose(ficgp);
11401: fclose(ficlog);
11402: /*------ End -----------*/
1.227 brouard 11403:
11404:
11405: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 11406: #ifdef WIN32
1.227 brouard 11407: if (_chdir(pathcd) != 0)
11408: printf("Can't move to directory %s!\n",path);
11409: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 11410: #else
1.227 brouard 11411: if(chdir(pathcd) != 0)
11412: printf("Can't move to directory %s!\n", path);
11413: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 11414: #endif
1.126 brouard 11415: printf("Current directory %s!\n",pathcd);
11416: /*strcat(plotcmd,CHARSEPARATOR);*/
11417: sprintf(plotcmd,"gnuplot");
1.157 brouard 11418: #ifdef _WIN32
1.126 brouard 11419: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
11420: #endif
11421: if(!stat(plotcmd,&info)){
1.158 brouard 11422: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11423: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 11424: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 11425: }else
11426: strcpy(pplotcmd,plotcmd);
1.157 brouard 11427: #ifdef __unix
1.126 brouard 11428: strcpy(plotcmd,GNUPLOTPROGRAM);
11429: if(!stat(plotcmd,&info)){
1.158 brouard 11430: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 11431: }else
11432: strcpy(pplotcmd,plotcmd);
11433: #endif
11434: }else
11435: strcpy(pplotcmd,plotcmd);
11436:
11437: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 11438: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 11439:
1.126 brouard 11440: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 11441: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 11442: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 11443: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 11444: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 11445: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 11446: }
1.158 brouard 11447: printf(" Successful, please wait...");
1.126 brouard 11448: while (z[0] != 'q') {
11449: /* chdir(path); */
1.154 brouard 11450: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 11451: scanf("%s",z);
11452: /* if (z[0] == 'c') system("./imach"); */
11453: if (z[0] == 'e') {
1.158 brouard 11454: #ifdef __APPLE__
1.152 brouard 11455: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 11456: #elif __linux
11457: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 11458: #else
1.152 brouard 11459: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 11460: #endif
11461: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
11462: system(pplotcmd);
1.126 brouard 11463: }
11464: else if (z[0] == 'g') system(plotcmd);
11465: else if (z[0] == 'q') exit(0);
11466: }
1.227 brouard 11467: end:
1.126 brouard 11468: while (z[0] != 'q') {
1.195 brouard 11469: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 11470: scanf("%s",z);
11471: }
11472: }
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