Annotation of imach/src/imach.c, revision 1.232
1.232 ! brouard 1: /* $Id: imach.c,v 1.231 2016/08/22 07:17:15 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.232 ! brouard 4: Revision 1.231 2016/08/22 07:17:15 brouard
! 5: Summary: not working
! 6:
1.231 brouard 7: Revision 1.230 2016/08/22 06:55:53 brouard
8: Summary: Not working
9:
1.230 brouard 10: Revision 1.229 2016/07/23 09:45:53 brouard
11: Summary: Completing for func too
12:
1.229 brouard 13: Revision 1.228 2016/07/22 17:45:30 brouard
14: Summary: Fixing some arrays, still debugging
15:
1.227 brouard 16: Revision 1.226 2016/07/12 18:42:34 brouard
17: Summary: temp
18:
1.226 brouard 19: Revision 1.225 2016/07/12 08:40:03 brouard
20: Summary: saving but not running
21:
1.225 brouard 22: Revision 1.224 2016/07/01 13:16:01 brouard
23: Summary: Fixes
24:
1.224 brouard 25: Revision 1.223 2016/02/19 09:23:35 brouard
26: Summary: temporary
27:
1.223 brouard 28: Revision 1.222 2016/02/17 08:14:50 brouard
29: Summary: Probably last 0.98 stable version 0.98r6
30:
1.222 brouard 31: Revision 1.221 2016/02/15 23:35:36 brouard
32: Summary: minor bug
33:
1.220 brouard 34: Revision 1.219 2016/02/15 00:48:12 brouard
35: *** empty log message ***
36:
1.219 brouard 37: Revision 1.218 2016/02/12 11:29:23 brouard
38: Summary: 0.99 Back projections
39:
1.218 brouard 40: Revision 1.217 2015/12/23 17:18:31 brouard
41: Summary: Experimental backcast
42:
1.217 brouard 43: Revision 1.216 2015/12/18 17:32:11 brouard
44: Summary: 0.98r4 Warning and status=-2
45:
46: Version 0.98r4 is now:
47: - displaying an error when status is -1, date of interview unknown and date of death known;
48: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
49: Older changes concerning s=-2, dating from 2005 have been supersed.
50:
1.216 brouard 51: Revision 1.215 2015/12/16 08:52:24 brouard
52: Summary: 0.98r4 working
53:
1.215 brouard 54: Revision 1.214 2015/12/16 06:57:54 brouard
55: Summary: temporary not working
56:
1.214 brouard 57: Revision 1.213 2015/12/11 18:22:17 brouard
58: Summary: 0.98r4
59:
1.213 brouard 60: Revision 1.212 2015/11/21 12:47:24 brouard
61: Summary: minor typo
62:
1.212 brouard 63: Revision 1.211 2015/11/21 12:41:11 brouard
64: Summary: 0.98r3 with some graph of projected cross-sectional
65:
66: Author: Nicolas Brouard
67:
1.211 brouard 68: Revision 1.210 2015/11/18 17:41:20 brouard
69: Summary: Start working on projected prevalences
70:
1.210 brouard 71: Revision 1.209 2015/11/17 22:12:03 brouard
72: Summary: Adding ftolpl parameter
73: Author: N Brouard
74:
75: We had difficulties to get smoothed confidence intervals. It was due
76: to the period prevalence which wasn't computed accurately. The inner
77: parameter ftolpl is now an outer parameter of the .imach parameter
78: file after estepm. If ftolpl is small 1.e-4 and estepm too,
79: computation are long.
80:
1.209 brouard 81: Revision 1.208 2015/11/17 14:31:57 brouard
82: Summary: temporary
83:
1.208 brouard 84: Revision 1.207 2015/10/27 17:36:57 brouard
85: *** empty log message ***
86:
1.207 brouard 87: Revision 1.206 2015/10/24 07:14:11 brouard
88: *** empty log message ***
89:
1.206 brouard 90: Revision 1.205 2015/10/23 15:50:53 brouard
91: Summary: 0.98r3 some clarification for graphs on likelihood contributions
92:
1.205 brouard 93: Revision 1.204 2015/10/01 16:20:26 brouard
94: Summary: Some new graphs of contribution to likelihood
95:
1.204 brouard 96: Revision 1.203 2015/09/30 17:45:14 brouard
97: Summary: looking at better estimation of the hessian
98:
99: Also a better criteria for convergence to the period prevalence And
100: therefore adding the number of years needed to converge. (The
101: prevalence in any alive state shold sum to one
102:
1.203 brouard 103: Revision 1.202 2015/09/22 19:45:16 brouard
104: Summary: Adding some overall graph on contribution to likelihood. Might change
105:
1.202 brouard 106: Revision 1.201 2015/09/15 17:34:58 brouard
107: Summary: 0.98r0
108:
109: - Some new graphs like suvival functions
110: - Some bugs fixed like model=1+age+V2.
111:
1.201 brouard 112: Revision 1.200 2015/09/09 16:53:55 brouard
113: Summary: Big bug thanks to Flavia
114:
115: Even model=1+age+V2. did not work anymore
116:
1.200 brouard 117: Revision 1.199 2015/09/07 14:09:23 brouard
118: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
119:
1.199 brouard 120: Revision 1.198 2015/09/03 07:14:39 brouard
121: Summary: 0.98q5 Flavia
122:
1.198 brouard 123: Revision 1.197 2015/09/01 18:24:39 brouard
124: *** empty log message ***
125:
1.197 brouard 126: Revision 1.196 2015/08/18 23:17:52 brouard
127: Summary: 0.98q5
128:
1.196 brouard 129: Revision 1.195 2015/08/18 16:28:39 brouard
130: Summary: Adding a hack for testing purpose
131:
132: After reading the title, ftol and model lines, if the comment line has
133: a q, starting with #q, the answer at the end of the run is quit. It
134: permits to run test files in batch with ctest. The former workaround was
135: $ echo q | imach foo.imach
136:
1.195 brouard 137: Revision 1.194 2015/08/18 13:32:00 brouard
138: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
139:
1.194 brouard 140: Revision 1.193 2015/08/04 07:17:42 brouard
141: Summary: 0.98q4
142:
1.193 brouard 143: Revision 1.192 2015/07/16 16:49:02 brouard
144: Summary: Fixing some outputs
145:
1.192 brouard 146: Revision 1.191 2015/07/14 10:00:33 brouard
147: Summary: Some fixes
148:
1.191 brouard 149: Revision 1.190 2015/05/05 08:51:13 brouard
150: Summary: Adding digits in output parameters (7 digits instead of 6)
151:
152: Fix 1+age+.
153:
1.190 brouard 154: Revision 1.189 2015/04/30 14:45:16 brouard
155: Summary: 0.98q2
156:
1.189 brouard 157: Revision 1.188 2015/04/30 08:27:53 brouard
158: *** empty log message ***
159:
1.188 brouard 160: Revision 1.187 2015/04/29 09:11:15 brouard
161: *** empty log message ***
162:
1.187 brouard 163: Revision 1.186 2015/04/23 12:01:52 brouard
164: Summary: V1*age is working now, version 0.98q1
165:
166: Some codes had been disabled in order to simplify and Vn*age was
167: working in the optimization phase, ie, giving correct MLE parameters,
168: but, as usual, outputs were not correct and program core dumped.
169:
1.186 brouard 170: Revision 1.185 2015/03/11 13:26:42 brouard
171: Summary: Inclusion of compile and links command line for Intel Compiler
172:
1.185 brouard 173: Revision 1.184 2015/03/11 11:52:39 brouard
174: Summary: Back from Windows 8. Intel Compiler
175:
1.184 brouard 176: Revision 1.183 2015/03/10 20:34:32 brouard
177: Summary: 0.98q0, trying with directest, mnbrak fixed
178:
179: We use directest instead of original Powell test; probably no
180: incidence on the results, but better justifications;
181: We fixed Numerical Recipes mnbrak routine which was wrong and gave
182: wrong results.
183:
1.183 brouard 184: Revision 1.182 2015/02/12 08:19:57 brouard
185: Summary: Trying to keep directest which seems simpler and more general
186: Author: Nicolas Brouard
187:
1.182 brouard 188: Revision 1.181 2015/02/11 23:22:24 brouard
189: Summary: Comments on Powell added
190:
191: Author:
192:
1.181 brouard 193: Revision 1.180 2015/02/11 17:33:45 brouard
194: Summary: Finishing move from main to function (hpijx and prevalence_limit)
195:
1.180 brouard 196: Revision 1.179 2015/01/04 09:57:06 brouard
197: Summary: back to OS/X
198:
1.179 brouard 199: Revision 1.178 2015/01/04 09:35:48 brouard
200: *** empty log message ***
201:
1.178 brouard 202: Revision 1.177 2015/01/03 18:40:56 brouard
203: Summary: Still testing ilc32 on OSX
204:
1.177 brouard 205: Revision 1.176 2015/01/03 16:45:04 brouard
206: *** empty log message ***
207:
1.176 brouard 208: Revision 1.175 2015/01/03 16:33:42 brouard
209: *** empty log message ***
210:
1.175 brouard 211: Revision 1.174 2015/01/03 16:15:49 brouard
212: Summary: Still in cross-compilation
213:
1.174 brouard 214: Revision 1.173 2015/01/03 12:06:26 brouard
215: Summary: trying to detect cross-compilation
216:
1.173 brouard 217: Revision 1.172 2014/12/27 12:07:47 brouard
218: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
219:
1.172 brouard 220: Revision 1.171 2014/12/23 13:26:59 brouard
221: Summary: Back from Visual C
222:
223: Still problem with utsname.h on Windows
224:
1.171 brouard 225: Revision 1.170 2014/12/23 11:17:12 brouard
226: Summary: Cleaning some \%% back to %%
227:
228: The escape was mandatory for a specific compiler (which one?), but too many warnings.
229:
1.170 brouard 230: Revision 1.169 2014/12/22 23:08:31 brouard
231: Summary: 0.98p
232:
233: Outputs some informations on compiler used, OS etc. Testing on different platforms.
234:
1.169 brouard 235: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 236: Summary: update
1.169 brouard 237:
1.168 brouard 238: Revision 1.167 2014/12/22 13:50:56 brouard
239: Summary: Testing uname and compiler version and if compiled 32 or 64
240:
241: Testing on Linux 64
242:
1.167 brouard 243: Revision 1.166 2014/12/22 11:40:47 brouard
244: *** empty log message ***
245:
1.166 brouard 246: Revision 1.165 2014/12/16 11:20:36 brouard
247: Summary: After compiling on Visual C
248:
249: * imach.c (Module): Merging 1.61 to 1.162
250:
1.165 brouard 251: Revision 1.164 2014/12/16 10:52:11 brouard
252: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
253:
254: * imach.c (Module): Merging 1.61 to 1.162
255:
1.164 brouard 256: Revision 1.163 2014/12/16 10:30:11 brouard
257: * imach.c (Module): Merging 1.61 to 1.162
258:
1.163 brouard 259: Revision 1.162 2014/09/25 11:43:39 brouard
260: Summary: temporary backup 0.99!
261:
1.162 brouard 262: Revision 1.1 2014/09/16 11:06:58 brouard
263: Summary: With some code (wrong) for nlopt
264:
265: Author:
266:
267: Revision 1.161 2014/09/15 20:41:41 brouard
268: Summary: Problem with macro SQR on Intel compiler
269:
1.161 brouard 270: Revision 1.160 2014/09/02 09:24:05 brouard
271: *** empty log message ***
272:
1.160 brouard 273: Revision 1.159 2014/09/01 10:34:10 brouard
274: Summary: WIN32
275: Author: Brouard
276:
1.159 brouard 277: Revision 1.158 2014/08/27 17:11:51 brouard
278: *** empty log message ***
279:
1.158 brouard 280: Revision 1.157 2014/08/27 16:26:55 brouard
281: Summary: Preparing windows Visual studio version
282: Author: Brouard
283:
284: In order to compile on Visual studio, time.h is now correct and time_t
285: and tm struct should be used. difftime should be used but sometimes I
286: just make the differences in raw time format (time(&now).
287: Trying to suppress #ifdef LINUX
288: Add xdg-open for __linux in order to open default browser.
289:
1.157 brouard 290: Revision 1.156 2014/08/25 20:10:10 brouard
291: *** empty log message ***
292:
1.156 brouard 293: Revision 1.155 2014/08/25 18:32:34 brouard
294: Summary: New compile, minor changes
295: Author: Brouard
296:
1.155 brouard 297: Revision 1.154 2014/06/20 17:32:08 brouard
298: Summary: Outputs now all graphs of convergence to period prevalence
299:
1.154 brouard 300: Revision 1.153 2014/06/20 16:45:46 brouard
301: Summary: If 3 live state, convergence to period prevalence on same graph
302: Author: Brouard
303:
1.153 brouard 304: Revision 1.152 2014/06/18 17:54:09 brouard
305: Summary: open browser, use gnuplot on same dir than imach if not found in the path
306:
1.152 brouard 307: Revision 1.151 2014/06/18 16:43:30 brouard
308: *** empty log message ***
309:
1.151 brouard 310: Revision 1.150 2014/06/18 16:42:35 brouard
311: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
312: Author: brouard
313:
1.150 brouard 314: Revision 1.149 2014/06/18 15:51:14 brouard
315: Summary: Some fixes in parameter files errors
316: Author: Nicolas Brouard
317:
1.149 brouard 318: Revision 1.148 2014/06/17 17:38:48 brouard
319: Summary: Nothing new
320: Author: Brouard
321:
322: Just a new packaging for OS/X version 0.98nS
323:
1.148 brouard 324: Revision 1.147 2014/06/16 10:33:11 brouard
325: *** empty log message ***
326:
1.147 brouard 327: Revision 1.146 2014/06/16 10:20:28 brouard
328: Summary: Merge
329: Author: Brouard
330:
331: Merge, before building revised version.
332:
1.146 brouard 333: Revision 1.145 2014/06/10 21:23:15 brouard
334: Summary: Debugging with valgrind
335: Author: Nicolas Brouard
336:
337: Lot of changes in order to output the results with some covariates
338: After the Edimburgh REVES conference 2014, it seems mandatory to
339: improve the code.
340: No more memory valgrind error but a lot has to be done in order to
341: continue the work of splitting the code into subroutines.
342: Also, decodemodel has been improved. Tricode is still not
343: optimal. nbcode should be improved. Documentation has been added in
344: the source code.
345:
1.144 brouard 346: Revision 1.143 2014/01/26 09:45:38 brouard
347: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
348:
349: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
350: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
351:
1.143 brouard 352: Revision 1.142 2014/01/26 03:57:36 brouard
353: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
354:
355: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
356:
1.142 brouard 357: Revision 1.141 2014/01/26 02:42:01 brouard
358: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
359:
1.141 brouard 360: Revision 1.140 2011/09/02 10:37:54 brouard
361: Summary: times.h is ok with mingw32 now.
362:
1.140 brouard 363: Revision 1.139 2010/06/14 07:50:17 brouard
364: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
365: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
366:
1.139 brouard 367: Revision 1.138 2010/04/30 18:19:40 brouard
368: *** empty log message ***
369:
1.138 brouard 370: Revision 1.137 2010/04/29 18:11:38 brouard
371: (Module): Checking covariates for more complex models
372: than V1+V2. A lot of change to be done. Unstable.
373:
1.137 brouard 374: Revision 1.136 2010/04/26 20:30:53 brouard
375: (Module): merging some libgsl code. Fixing computation
376: of likelione (using inter/intrapolation if mle = 0) in order to
377: get same likelihood as if mle=1.
378: Some cleaning of code and comments added.
379:
1.136 brouard 380: Revision 1.135 2009/10/29 15:33:14 brouard
381: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
382:
1.135 brouard 383: Revision 1.134 2009/10/29 13:18:53 brouard
384: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
385:
1.134 brouard 386: Revision 1.133 2009/07/06 10:21:25 brouard
387: just nforces
388:
1.133 brouard 389: Revision 1.132 2009/07/06 08:22:05 brouard
390: Many tings
391:
1.132 brouard 392: Revision 1.131 2009/06/20 16:22:47 brouard
393: Some dimensions resccaled
394:
1.131 brouard 395: Revision 1.130 2009/05/26 06:44:34 brouard
396: (Module): Max Covariate is now set to 20 instead of 8. A
397: lot of cleaning with variables initialized to 0. Trying to make
398: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
399:
1.130 brouard 400: Revision 1.129 2007/08/31 13:49:27 lievre
401: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
402:
1.129 lievre 403: Revision 1.128 2006/06/30 13:02:05 brouard
404: (Module): Clarifications on computing e.j
405:
1.128 brouard 406: Revision 1.127 2006/04/28 18:11:50 brouard
407: (Module): Yes the sum of survivors was wrong since
408: imach-114 because nhstepm was no more computed in the age
409: loop. Now we define nhstepma in the age loop.
410: (Module): In order to speed up (in case of numerous covariates) we
411: compute health expectancies (without variances) in a first step
412: and then all the health expectancies with variances or standard
413: deviation (needs data from the Hessian matrices) which slows the
414: computation.
415: In the future we should be able to stop the program is only health
416: expectancies and graph are needed without standard deviations.
417:
1.127 brouard 418: Revision 1.126 2006/04/28 17:23:28 brouard
419: (Module): Yes the sum of survivors was wrong since
420: imach-114 because nhstepm was no more computed in the age
421: loop. Now we define nhstepma in the age loop.
422: Version 0.98h
423:
1.126 brouard 424: Revision 1.125 2006/04/04 15:20:31 lievre
425: Errors in calculation of health expectancies. Age was not initialized.
426: Forecasting file added.
427:
428: Revision 1.124 2006/03/22 17:13:53 lievre
429: Parameters are printed with %lf instead of %f (more numbers after the comma).
430: The log-likelihood is printed in the log file
431:
432: Revision 1.123 2006/03/20 10:52:43 brouard
433: * imach.c (Module): <title> changed, corresponds to .htm file
434: name. <head> headers where missing.
435:
436: * imach.c (Module): Weights can have a decimal point as for
437: English (a comma might work with a correct LC_NUMERIC environment,
438: otherwise the weight is truncated).
439: Modification of warning when the covariates values are not 0 or
440: 1.
441: Version 0.98g
442:
443: Revision 1.122 2006/03/20 09:45:41 brouard
444: (Module): Weights can have a decimal point as for
445: English (a comma might work with a correct LC_NUMERIC environment,
446: otherwise the weight is truncated).
447: Modification of warning when the covariates values are not 0 or
448: 1.
449: Version 0.98g
450:
451: Revision 1.121 2006/03/16 17:45:01 lievre
452: * imach.c (Module): Comments concerning covariates added
453:
454: * imach.c (Module): refinements in the computation of lli if
455: status=-2 in order to have more reliable computation if stepm is
456: not 1 month. Version 0.98f
457:
458: Revision 1.120 2006/03/16 15:10:38 lievre
459: (Module): refinements in the computation of lli if
460: status=-2 in order to have more reliable computation if stepm is
461: not 1 month. Version 0.98f
462:
463: Revision 1.119 2006/03/15 17:42:26 brouard
464: (Module): Bug if status = -2, the loglikelihood was
465: computed as likelihood omitting the logarithm. Version O.98e
466:
467: Revision 1.118 2006/03/14 18:20:07 brouard
468: (Module): varevsij Comments added explaining the second
469: table of variances if popbased=1 .
470: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
471: (Module): Function pstamp added
472: (Module): Version 0.98d
473:
474: Revision 1.117 2006/03/14 17:16:22 brouard
475: (Module): varevsij Comments added explaining the second
476: table of variances if popbased=1 .
477: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
478: (Module): Function pstamp added
479: (Module): Version 0.98d
480:
481: Revision 1.116 2006/03/06 10:29:27 brouard
482: (Module): Variance-covariance wrong links and
483: varian-covariance of ej. is needed (Saito).
484:
485: Revision 1.115 2006/02/27 12:17:45 brouard
486: (Module): One freematrix added in mlikeli! 0.98c
487:
488: Revision 1.114 2006/02/26 12:57:58 brouard
489: (Module): Some improvements in processing parameter
490: filename with strsep.
491:
492: Revision 1.113 2006/02/24 14:20:24 brouard
493: (Module): Memory leaks checks with valgrind and:
494: datafile was not closed, some imatrix were not freed and on matrix
495: allocation too.
496:
497: Revision 1.112 2006/01/30 09:55:26 brouard
498: (Module): Back to gnuplot.exe instead of wgnuplot.exe
499:
500: Revision 1.111 2006/01/25 20:38:18 brouard
501: (Module): Lots of cleaning and bugs added (Gompertz)
502: (Module): Comments can be added in data file. Missing date values
503: can be a simple dot '.'.
504:
505: Revision 1.110 2006/01/25 00:51:50 brouard
506: (Module): Lots of cleaning and bugs added (Gompertz)
507:
508: Revision 1.109 2006/01/24 19:37:15 brouard
509: (Module): Comments (lines starting with a #) are allowed in data.
510:
511: Revision 1.108 2006/01/19 18:05:42 lievre
512: Gnuplot problem appeared...
513: To be fixed
514:
515: Revision 1.107 2006/01/19 16:20:37 brouard
516: Test existence of gnuplot in imach path
517:
518: Revision 1.106 2006/01/19 13:24:36 brouard
519: Some cleaning and links added in html output
520:
521: Revision 1.105 2006/01/05 20:23:19 lievre
522: *** empty log message ***
523:
524: Revision 1.104 2005/09/30 16:11:43 lievre
525: (Module): sump fixed, loop imx fixed, and simplifications.
526: (Module): If the status is missing at the last wave but we know
527: that the person is alive, then we can code his/her status as -2
528: (instead of missing=-1 in earlier versions) and his/her
529: contributions to the likelihood is 1 - Prob of dying from last
530: health status (= 1-p13= p11+p12 in the easiest case of somebody in
531: the healthy state at last known wave). Version is 0.98
532:
533: Revision 1.103 2005/09/30 15:54:49 lievre
534: (Module): sump fixed, loop imx fixed, and simplifications.
535:
536: Revision 1.102 2004/09/15 17:31:30 brouard
537: Add the possibility to read data file including tab characters.
538:
539: Revision 1.101 2004/09/15 10:38:38 brouard
540: Fix on curr_time
541:
542: Revision 1.100 2004/07/12 18:29:06 brouard
543: Add version for Mac OS X. Just define UNIX in Makefile
544:
545: Revision 1.99 2004/06/05 08:57:40 brouard
546: *** empty log message ***
547:
548: Revision 1.98 2004/05/16 15:05:56 brouard
549: New version 0.97 . First attempt to estimate force of mortality
550: directly from the data i.e. without the need of knowing the health
551: state at each age, but using a Gompertz model: log u =a + b*age .
552: This is the basic analysis of mortality and should be done before any
553: other analysis, in order to test if the mortality estimated from the
554: cross-longitudinal survey is different from the mortality estimated
555: from other sources like vital statistic data.
556:
557: The same imach parameter file can be used but the option for mle should be -3.
558:
1.133 brouard 559: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 560: former routines in order to include the new code within the former code.
561:
562: The output is very simple: only an estimate of the intercept and of
563: the slope with 95% confident intervals.
564:
565: Current limitations:
566: A) Even if you enter covariates, i.e. with the
567: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
568: B) There is no computation of Life Expectancy nor Life Table.
569:
570: Revision 1.97 2004/02/20 13:25:42 lievre
571: Version 0.96d. Population forecasting command line is (temporarily)
572: suppressed.
573:
574: Revision 1.96 2003/07/15 15:38:55 brouard
575: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
576: rewritten within the same printf. Workaround: many printfs.
577:
578: Revision 1.95 2003/07/08 07:54:34 brouard
579: * imach.c (Repository):
580: (Repository): Using imachwizard code to output a more meaningful covariance
581: matrix (cov(a12,c31) instead of numbers.
582:
583: Revision 1.94 2003/06/27 13:00:02 brouard
584: Just cleaning
585:
586: Revision 1.93 2003/06/25 16:33:55 brouard
587: (Module): On windows (cygwin) function asctime_r doesn't
588: exist so I changed back to asctime which exists.
589: (Module): Version 0.96b
590:
591: Revision 1.92 2003/06/25 16:30:45 brouard
592: (Module): On windows (cygwin) function asctime_r doesn't
593: exist so I changed back to asctime which exists.
594:
595: Revision 1.91 2003/06/25 15:30:29 brouard
596: * imach.c (Repository): Duplicated warning errors corrected.
597: (Repository): Elapsed time after each iteration is now output. It
598: helps to forecast when convergence will be reached. Elapsed time
599: is stamped in powell. We created a new html file for the graphs
600: concerning matrix of covariance. It has extension -cov.htm.
601:
602: Revision 1.90 2003/06/24 12:34:15 brouard
603: (Module): Some bugs corrected for windows. Also, when
604: mle=-1 a template is output in file "or"mypar.txt with the design
605: of the covariance matrix to be input.
606:
607: Revision 1.89 2003/06/24 12:30:52 brouard
608: (Module): Some bugs corrected for windows. Also, when
609: mle=-1 a template is output in file "or"mypar.txt with the design
610: of the covariance matrix to be input.
611:
612: Revision 1.88 2003/06/23 17:54:56 brouard
613: * 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.
614:
615: Revision 1.87 2003/06/18 12:26:01 brouard
616: Version 0.96
617:
618: Revision 1.86 2003/06/17 20:04:08 brouard
619: (Module): Change position of html and gnuplot routines and added
620: routine fileappend.
621:
622: Revision 1.85 2003/06/17 13:12:43 brouard
623: * imach.c (Repository): Check when date of death was earlier that
624: current date of interview. It may happen when the death was just
625: prior to the death. In this case, dh was negative and likelihood
626: was wrong (infinity). We still send an "Error" but patch by
627: assuming that the date of death was just one stepm after the
628: interview.
629: (Repository): Because some people have very long ID (first column)
630: we changed int to long in num[] and we added a new lvector for
631: memory allocation. But we also truncated to 8 characters (left
632: truncation)
633: (Repository): No more line truncation errors.
634:
635: Revision 1.84 2003/06/13 21:44:43 brouard
636: * imach.c (Repository): Replace "freqsummary" at a correct
637: place. It differs from routine "prevalence" which may be called
638: many times. Probs is memory consuming and must be used with
639: parcimony.
640: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
641:
642: Revision 1.83 2003/06/10 13:39:11 lievre
643: *** empty log message ***
644:
645: Revision 1.82 2003/06/05 15:57:20 brouard
646: Add log in imach.c and fullversion number is now printed.
647:
648: */
649: /*
650: Interpolated Markov Chain
651:
652: Short summary of the programme:
653:
1.227 brouard 654: This program computes Healthy Life Expectancies or State-specific
655: (if states aren't health statuses) Expectancies from
656: cross-longitudinal data. Cross-longitudinal data consist in:
657:
658: -1- a first survey ("cross") where individuals from different ages
659: are interviewed on their health status or degree of disability (in
660: the case of a health survey which is our main interest)
661:
662: -2- at least a second wave of interviews ("longitudinal") which
663: measure each change (if any) in individual health status. Health
664: expectancies are computed from the time spent in each health state
665: according to a model. More health states you consider, more time is
666: necessary to reach the Maximum Likelihood of the parameters involved
667: in the model. The simplest model is the multinomial logistic model
668: where pij is the probability to be observed in state j at the second
669: wave conditional to be observed in state i at the first
670: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
671: etc , where 'age' is age and 'sex' is a covariate. If you want to
672: have a more complex model than "constant and age", you should modify
673: the program where the markup *Covariates have to be included here
674: again* invites you to do it. More covariates you add, slower the
1.126 brouard 675: convergence.
676:
677: The advantage of this computer programme, compared to a simple
678: multinomial logistic model, is clear when the delay between waves is not
679: identical for each individual. Also, if a individual missed an
680: intermediate interview, the information is lost, but taken into
681: account using an interpolation or extrapolation.
682:
683: hPijx is the probability to be observed in state i at age x+h
684: conditional to the observed state i at age x. The delay 'h' can be
685: split into an exact number (nh*stepm) of unobserved intermediate
686: states. This elementary transition (by month, quarter,
687: semester or year) is modelled as a multinomial logistic. The hPx
688: matrix is simply the matrix product of nh*stepm elementary matrices
689: and the contribution of each individual to the likelihood is simply
690: hPijx.
691:
692: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 693: of the life expectancies. It also computes the period (stable) prevalence.
694:
695: Back prevalence and projections:
1.227 brouard 696:
697: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
698: double agemaxpar, double ftolpl, int *ncvyearp, double
699: dateprev1,double dateprev2, int firstpass, int lastpass, int
700: mobilavproj)
701:
702: Computes the back prevalence limit for any combination of
703: covariate values k at any age between ageminpar and agemaxpar and
704: returns it in **bprlim. In the loops,
705:
706: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
707: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
708:
709: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 710: Computes for any combination of covariates k and any age between bage and fage
711: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
712: oldm=oldms;savm=savms;
1.227 brouard 713:
714: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 715: Computes the transition matrix starting at age 'age' over
716: 'nhstepm*hstepm*stepm' months (i.e. until
717: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 718: nhstepm*hstepm matrices.
719:
720: Returns p3mat[i][j][h] after calling
721: p3mat[i][j][h]=matprod2(newm,
722: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
723: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
724: oldm);
1.226 brouard 725:
726: Important routines
727:
728: - func (or funcone), computes logit (pij) distinguishing
729: o fixed variables (single or product dummies or quantitative);
730: o varying variables by:
731: (1) wave (single, product dummies, quantitative),
732: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
733: % fixed dummy (treated) or quantitative (not done because time-consuming);
734: % varying dummy (not done) or quantitative (not done);
735: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
736: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
737: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
738: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
739: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 740:
1.226 brouard 741:
742:
1.133 brouard 743: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
744: Institut national d'études démographiques, Paris.
1.126 brouard 745: This software have been partly granted by Euro-REVES, a concerted action
746: from the European Union.
747: It is copyrighted identically to a GNU software product, ie programme and
748: software can be distributed freely for non commercial use. Latest version
749: can be accessed at http://euroreves.ined.fr/imach .
750:
751: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
752: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
753:
754: **********************************************************************/
755: /*
756: main
757: read parameterfile
758: read datafile
759: concatwav
760: freqsummary
761: if (mle >= 1)
762: mlikeli
763: print results files
764: if mle==1
765: computes hessian
766: read end of parameter file: agemin, agemax, bage, fage, estepm
767: begin-prev-date,...
768: open gnuplot file
769: open html file
1.145 brouard 770: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
771: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
772: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
773: freexexit2 possible for memory heap.
774:
775: h Pij x | pij_nom ficrestpij
776: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
777: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
778: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
779:
780: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
781: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
782: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
783: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
784: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
785:
1.126 brouard 786: forecasting if prevfcast==1 prevforecast call prevalence()
787: health expectancies
788: Variance-covariance of DFLE
789: prevalence()
790: movingaverage()
791: varevsij()
792: if popbased==1 varevsij(,popbased)
793: total life expectancies
794: Variance of period (stable) prevalence
795: end
796: */
797:
1.187 brouard 798: /* #define DEBUG */
799: /* #define DEBUGBRENT */
1.203 brouard 800: /* #define DEBUGLINMIN */
801: /* #define DEBUGHESS */
802: #define DEBUGHESSIJ
1.224 brouard 803: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 804: #define POWELL /* Instead of NLOPT */
1.224 brouard 805: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 806: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
807: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 808:
809: #include <math.h>
810: #include <stdio.h>
811: #include <stdlib.h>
812: #include <string.h>
1.226 brouard 813: #include <ctype.h>
1.159 brouard 814:
815: #ifdef _WIN32
816: #include <io.h>
1.172 brouard 817: #include <windows.h>
818: #include <tchar.h>
1.159 brouard 819: #else
1.126 brouard 820: #include <unistd.h>
1.159 brouard 821: #endif
1.126 brouard 822:
823: #include <limits.h>
824: #include <sys/types.h>
1.171 brouard 825:
826: #if defined(__GNUC__)
827: #include <sys/utsname.h> /* Doesn't work on Windows */
828: #endif
829:
1.126 brouard 830: #include <sys/stat.h>
831: #include <errno.h>
1.159 brouard 832: /* extern int errno; */
1.126 brouard 833:
1.157 brouard 834: /* #ifdef LINUX */
835: /* #include <time.h> */
836: /* #include "timeval.h" */
837: /* #else */
838: /* #include <sys/time.h> */
839: /* #endif */
840:
1.126 brouard 841: #include <time.h>
842:
1.136 brouard 843: #ifdef GSL
844: #include <gsl/gsl_errno.h>
845: #include <gsl/gsl_multimin.h>
846: #endif
847:
1.167 brouard 848:
1.162 brouard 849: #ifdef NLOPT
850: #include <nlopt.h>
851: typedef struct {
852: double (* function)(double [] );
853: } myfunc_data ;
854: #endif
855:
1.126 brouard 856: /* #include <libintl.h> */
857: /* #define _(String) gettext (String) */
858:
1.141 brouard 859: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 860:
861: #define GNUPLOTPROGRAM "gnuplot"
862: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
863: #define FILENAMELENGTH 132
864:
865: #define GLOCK_ERROR_NOPATH -1 /* empty path */
866: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
867:
1.144 brouard 868: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
869: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 870:
871: #define NINTERVMAX 8
1.144 brouard 872: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
873: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
874: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 875: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 876: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
877: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 878: #define MAXN 20000
1.144 brouard 879: #define YEARM 12. /**< Number of months per year */
1.218 brouard 880: /* #define AGESUP 130 */
881: #define AGESUP 150
882: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 883: #define AGEBASE 40
1.194 brouard 884: #define AGEOVERFLOW 1.e20
1.164 brouard 885: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 886: #ifdef _WIN32
887: #define DIRSEPARATOR '\\'
888: #define CHARSEPARATOR "\\"
889: #define ODIRSEPARATOR '/'
890: #else
1.126 brouard 891: #define DIRSEPARATOR '/'
892: #define CHARSEPARATOR "/"
893: #define ODIRSEPARATOR '\\'
894: #endif
895:
1.232 ! brouard 896: /* $Id: imach.c,v 1.231 2016/08/22 07:17:15 brouard Exp $ */
1.126 brouard 897: /* $State: Exp $ */
1.196 brouard 898: #include "version.h"
899: char version[]=__IMACH_VERSION__;
1.224 brouard 900: 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";
1.232 ! brouard 901: char fullversion[]="$Revision: 1.231 $ $Date: 2016/08/22 07:17:15 $";
1.126 brouard 902: char strstart[80];
903: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 904: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 905: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 906: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
907: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
908: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 909: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
910: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 911: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
912: int cptcovprodnoage=0; /**< Number of covariate products without age */
913: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.232 ! brouard 914: int ncovf=0; /* Total number of effective fixed covariates (dummy of quantitative) in the model */
! 915: int ncovv=0; /* Total number of effective (wave) varying covariates (dummy of quantitative) in the model */
! 916: int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
! 917:
! 918: int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
1.225 brouard 919: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 920: int ntveff=0; /**< ntveff number of effective time varying variables */
921: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 922: int cptcov=0; /* Working variable */
1.218 brouard 923: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 924: int npar=NPARMAX;
925: int nlstate=2; /* Number of live states */
926: int ndeath=1; /* Number of dead states */
1.130 brouard 927: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 928: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 929: int popbased=0;
930:
931: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 932: int maxwav=0; /* Maxim number of waves */
933: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
934: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
935: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 936: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 937: int mle=1, weightopt=0;
1.126 brouard 938: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
939: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
940: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
941: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 942: int countcallfunc=0; /* Count the number of calls to func */
1.230 brouard 943: int selected(int kvar); /* Is covariate kvar selected for printing results */
944:
1.130 brouard 945: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 946: double **matprod2(); /* test */
1.126 brouard 947: double **oldm, **newm, **savm; /* Working pointers to matrices */
948: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 949: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
950:
1.136 brouard 951: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 952: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 953: FILE *ficlog, *ficrespow;
1.130 brouard 954: int globpr=0; /* Global variable for printing or not */
1.126 brouard 955: double fretone; /* Only one call to likelihood */
1.130 brouard 956: long ipmx=0; /* Number of contributions */
1.126 brouard 957: double sw; /* Sum of weights */
958: char filerespow[FILENAMELENGTH];
959: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
960: FILE *ficresilk;
961: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
962: FILE *ficresprobmorprev;
963: FILE *fichtm, *fichtmcov; /* Html File */
964: FILE *ficreseij;
965: char filerese[FILENAMELENGTH];
966: FILE *ficresstdeij;
967: char fileresstde[FILENAMELENGTH];
968: FILE *ficrescveij;
969: char filerescve[FILENAMELENGTH];
970: FILE *ficresvij;
971: char fileresv[FILENAMELENGTH];
972: FILE *ficresvpl;
973: char fileresvpl[FILENAMELENGTH];
974: char title[MAXLINE];
1.217 brouard 975: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 976: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
977: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
978: char command[FILENAMELENGTH];
979: int outcmd=0;
980:
1.217 brouard 981: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 982: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 983: char filelog[FILENAMELENGTH]; /* Log file */
984: char filerest[FILENAMELENGTH];
985: char fileregp[FILENAMELENGTH];
986: char popfile[FILENAMELENGTH];
987:
988: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
989:
1.157 brouard 990: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
991: /* struct timezone tzp; */
992: /* extern int gettimeofday(); */
993: struct tm tml, *gmtime(), *localtime();
994:
995: extern time_t time();
996:
997: struct tm start_time, end_time, curr_time, last_time, forecast_time;
998: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
999: struct tm tm;
1000:
1.126 brouard 1001: char strcurr[80], strfor[80];
1002:
1003: char *endptr;
1004: long lval;
1005: double dval;
1006:
1007: #define NR_END 1
1008: #define FREE_ARG char*
1009: #define FTOL 1.0e-10
1010:
1011: #define NRANSI
1012: #define ITMAX 200
1013:
1014: #define TOL 2.0e-4
1015:
1016: #define CGOLD 0.3819660
1017: #define ZEPS 1.0e-10
1018: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1019:
1020: #define GOLD 1.618034
1021: #define GLIMIT 100.0
1022: #define TINY 1.0e-20
1023:
1024: static double maxarg1,maxarg2;
1025: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1026: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1027:
1028: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1029: #define rint(a) floor(a+0.5)
1.166 brouard 1030: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1031: #define mytinydouble 1.0e-16
1.166 brouard 1032: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1033: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1034: /* static double dsqrarg; */
1035: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1036: static double sqrarg;
1037: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1038: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1039: int agegomp= AGEGOMP;
1040:
1041: int imx;
1042: int stepm=1;
1043: /* Stepm, step in month: minimum step interpolation*/
1044:
1045: int estepm;
1046: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1047:
1048: int m,nb;
1049: long *num;
1.197 brouard 1050: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1051: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1052: covariate for which somebody answered excluding
1053: undefined. Usually 2: 0 and 1. */
1054: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1055: covariate for which somebody answered including
1056: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1057: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1058: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1059: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1060: double *ageexmed,*agecens;
1061: double dateintmean=0;
1062:
1063: double *weight;
1064: int **s; /* Status */
1.141 brouard 1065: double *agedc;
1.145 brouard 1066: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1067: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1068: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1069: double **coqvar; /* Fixed quantitative covariate iqv */
1070: double ***cotvar; /* Time varying covariate itv */
1071: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1072: double idx;
1073: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.232 ! brouard 1074: 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 */
! 1075: 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 */
! 1076: 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 */
! 1077: int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
! 1078: 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 */
! 1079: 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 1080: int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1081: int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1082: int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1083: int *TvarFQind; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1084: int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1085: int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
1086: 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 */
1087: 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 */
1088:
1.230 brouard 1089: int *Tvarsel; /**< Selected covariates for output */
1090: double *Tvalsel; /**< Selected modality value of covariate for output */
1.226 brouard 1091: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1092: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1093: 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 */
1.197 brouard 1094: int *Tage;
1.227 brouard 1095: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 brouard 1096: 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 1097: 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*/
1098: 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 1099: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1100: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1101: int **Tvard;
1102: int *Tprod;/**< Gives the k position of the k1 product */
1103: int *Tposprod; /**< Gives the k1 product from the k position */
1104: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
1105: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1106: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1107: */
1108: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1109: double *lsurv, *lpop, *tpop;
1110:
1.231 brouard 1111: #define FD 1; /* Fixed dummy covariate */
1112: #define FQ 2; /* Fixed quantitative covariate */
1113: #define FP 3; /* Fixed product covariate */
1114: #define FPDD 7; /* Fixed product dummy*dummy covariate */
1115: #define FPDQ 8; /* Fixed product dummy*quantitative covariate */
1116: #define FPQQ 9; /* Fixed product quantitative*quantitative covariate */
1117: #define VD 10; /* Varying dummy covariate */
1118: #define VQ 11; /* Varying quantitative covariate */
1119: #define VP 12; /* Varying product covariate */
1120: #define VPDD 13; /* Varying product dummy*dummy covariate */
1121: #define VPDQ 14; /* Varying product dummy*quantitative covariate */
1122: #define VPQQ 15; /* Varying product quantitative*quantitative covariate */
1123: #define APFD 16; /* Age product * fixed dummy covariate */
1124: #define APFQ 17; /* Age product * fixed quantitative covariate */
1125: #define APVD 18; /* Age product * varying dummy covariate */
1126: #define APVQ 19; /* Age product * varying quantitative covariate */
1127:
1128: #define FTYPE 1; /* Fixed covariate */
1129: #define VTYPE 2; /* Varying covariate (loop in wave) */
1130: #define ATYPE 2; /* Age product covariate (loop in dh within wave)*/
1131:
1132: struct kmodel{
1133: int maintype; /* main type */
1134: int subtype; /* subtype */
1135: };
1136: struct kmodel modell[NCOVMAX];
1137:
1.143 brouard 1138: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1139: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1140:
1141: /**************** split *************************/
1142: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1143: {
1144: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1145: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1146: */
1147: char *ss; /* pointer */
1.186 brouard 1148: int l1=0, l2=0; /* length counters */
1.126 brouard 1149:
1150: l1 = strlen(path ); /* length of path */
1151: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1152: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1153: if ( ss == NULL ) { /* no directory, so determine current directory */
1154: strcpy( name, path ); /* we got the fullname name because no directory */
1155: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1156: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1157: /* get current working directory */
1158: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1159: #ifdef WIN32
1160: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1161: #else
1162: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1163: #endif
1.126 brouard 1164: return( GLOCK_ERROR_GETCWD );
1165: }
1166: /* got dirc from getcwd*/
1167: printf(" DIRC = %s \n",dirc);
1.205 brouard 1168: } else { /* strip directory from path */
1.126 brouard 1169: ss++; /* after this, the filename */
1170: l2 = strlen( ss ); /* length of filename */
1171: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1172: strcpy( name, ss ); /* save file name */
1173: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1174: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1175: printf(" DIRC2 = %s \n",dirc);
1176: }
1177: /* We add a separator at the end of dirc if not exists */
1178: l1 = strlen( dirc ); /* length of directory */
1179: if( dirc[l1-1] != DIRSEPARATOR ){
1180: dirc[l1] = DIRSEPARATOR;
1181: dirc[l1+1] = 0;
1182: printf(" DIRC3 = %s \n",dirc);
1183: }
1184: ss = strrchr( name, '.' ); /* find last / */
1185: if (ss >0){
1186: ss++;
1187: strcpy(ext,ss); /* save extension */
1188: l1= strlen( name);
1189: l2= strlen(ss)+1;
1190: strncpy( finame, name, l1-l2);
1191: finame[l1-l2]= 0;
1192: }
1193:
1194: return( 0 ); /* we're done */
1195: }
1196:
1197:
1198: /******************************************/
1199:
1200: void replace_back_to_slash(char *s, char*t)
1201: {
1202: int i;
1203: int lg=0;
1204: i=0;
1205: lg=strlen(t);
1206: for(i=0; i<= lg; i++) {
1207: (s[i] = t[i]);
1208: if (t[i]== '\\') s[i]='/';
1209: }
1210: }
1211:
1.132 brouard 1212: char *trimbb(char *out, char *in)
1.137 brouard 1213: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1214: char *s;
1215: s=out;
1216: while (*in != '\0'){
1.137 brouard 1217: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1218: in++;
1219: }
1220: *out++ = *in++;
1221: }
1222: *out='\0';
1223: return s;
1224: }
1225:
1.187 brouard 1226: /* char *substrchaine(char *out, char *in, char *chain) */
1227: /* { */
1228: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1229: /* char *s, *t; */
1230: /* t=in;s=out; */
1231: /* while ((*in != *chain) && (*in != '\0')){ */
1232: /* *out++ = *in++; */
1233: /* } */
1234:
1235: /* /\* *in matches *chain *\/ */
1236: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1237: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1238: /* } */
1239: /* in--; chain--; */
1240: /* while ( (*in != '\0')){ */
1241: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1242: /* *out++ = *in++; */
1243: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1244: /* } */
1245: /* *out='\0'; */
1246: /* out=s; */
1247: /* return out; */
1248: /* } */
1249: char *substrchaine(char *out, char *in, char *chain)
1250: {
1251: /* Substract chain 'chain' from 'in', return and output 'out' */
1252: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1253:
1254: char *strloc;
1255:
1256: strcpy (out, in);
1257: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1258: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1259: if(strloc != NULL){
1260: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1261: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1262: /* strcpy (strloc, strloc +strlen(chain));*/
1263: }
1264: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1265: return out;
1266: }
1267:
1268:
1.145 brouard 1269: char *cutl(char *blocc, char *alocc, char *in, char occ)
1270: {
1.187 brouard 1271: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1272: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1273: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1274: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1275: */
1.160 brouard 1276: char *s, *t;
1.145 brouard 1277: t=in;s=in;
1278: while ((*in != occ) && (*in != '\0')){
1279: *alocc++ = *in++;
1280: }
1281: if( *in == occ){
1282: *(alocc)='\0';
1283: s=++in;
1284: }
1285:
1286: if (s == t) {/* occ not found */
1287: *(alocc-(in-s))='\0';
1288: in=s;
1289: }
1290: while ( *in != '\0'){
1291: *blocc++ = *in++;
1292: }
1293:
1294: *blocc='\0';
1295: return t;
1296: }
1.137 brouard 1297: char *cutv(char *blocc, char *alocc, char *in, char occ)
1298: {
1.187 brouard 1299: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1300: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1301: gives blocc="abcdef2ghi" and alocc="j".
1302: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1303: */
1304: char *s, *t;
1305: t=in;s=in;
1306: while (*in != '\0'){
1307: while( *in == occ){
1308: *blocc++ = *in++;
1309: s=in;
1310: }
1311: *blocc++ = *in++;
1312: }
1313: if (s == t) /* occ not found */
1314: *(blocc-(in-s))='\0';
1315: else
1316: *(blocc-(in-s)-1)='\0';
1317: in=s;
1318: while ( *in != '\0'){
1319: *alocc++ = *in++;
1320: }
1321:
1322: *alocc='\0';
1323: return s;
1324: }
1325:
1.126 brouard 1326: int nbocc(char *s, char occ)
1327: {
1328: int i,j=0;
1329: int lg=20;
1330: i=0;
1331: lg=strlen(s);
1332: for(i=0; i<= lg; i++) {
1333: if (s[i] == occ ) j++;
1334: }
1335: return j;
1336: }
1337:
1.137 brouard 1338: /* void cutv(char *u,char *v, char*t, char occ) */
1339: /* { */
1340: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1341: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1342: /* gives u="abcdef2ghi" and v="j" *\/ */
1343: /* int i,lg,j,p=0; */
1344: /* i=0; */
1345: /* lg=strlen(t); */
1346: /* for(j=0; j<=lg-1; j++) { */
1347: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1348: /* } */
1.126 brouard 1349:
1.137 brouard 1350: /* for(j=0; j<p; j++) { */
1351: /* (u[j] = t[j]); */
1352: /* } */
1353: /* u[p]='\0'; */
1.126 brouard 1354:
1.137 brouard 1355: /* for(j=0; j<= lg; j++) { */
1356: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1357: /* } */
1358: /* } */
1.126 brouard 1359:
1.160 brouard 1360: #ifdef _WIN32
1361: char * strsep(char **pp, const char *delim)
1362: {
1363: char *p, *q;
1364:
1365: if ((p = *pp) == NULL)
1366: return 0;
1367: if ((q = strpbrk (p, delim)) != NULL)
1368: {
1369: *pp = q + 1;
1370: *q = '\0';
1371: }
1372: else
1373: *pp = 0;
1374: return p;
1375: }
1376: #endif
1377:
1.126 brouard 1378: /********************** nrerror ********************/
1379:
1380: void nrerror(char error_text[])
1381: {
1382: fprintf(stderr,"ERREUR ...\n");
1383: fprintf(stderr,"%s\n",error_text);
1384: exit(EXIT_FAILURE);
1385: }
1386: /*********************** vector *******************/
1387: double *vector(int nl, int nh)
1388: {
1389: double *v;
1390: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1391: if (!v) nrerror("allocation failure in vector");
1392: return v-nl+NR_END;
1393: }
1394:
1395: /************************ free vector ******************/
1396: void free_vector(double*v, int nl, int nh)
1397: {
1398: free((FREE_ARG)(v+nl-NR_END));
1399: }
1400:
1401: /************************ivector *******************************/
1402: int *ivector(long nl,long nh)
1403: {
1404: int *v;
1405: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1406: if (!v) nrerror("allocation failure in ivector");
1407: return v-nl+NR_END;
1408: }
1409:
1410: /******************free ivector **************************/
1411: void free_ivector(int *v, long nl, long nh)
1412: {
1413: free((FREE_ARG)(v+nl-NR_END));
1414: }
1415:
1416: /************************lvector *******************************/
1417: long *lvector(long nl,long nh)
1418: {
1419: long *v;
1420: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1421: if (!v) nrerror("allocation failure in ivector");
1422: return v-nl+NR_END;
1423: }
1424:
1425: /******************free lvector **************************/
1426: void free_lvector(long *v, long nl, long nh)
1427: {
1428: free((FREE_ARG)(v+nl-NR_END));
1429: }
1430:
1431: /******************* imatrix *******************************/
1432: int **imatrix(long nrl, long nrh, long ncl, long nch)
1433: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1434: {
1435: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1436: int **m;
1437:
1438: /* allocate pointers to rows */
1439: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1440: if (!m) nrerror("allocation failure 1 in matrix()");
1441: m += NR_END;
1442: m -= nrl;
1443:
1444:
1445: /* allocate rows and set pointers to them */
1446: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1447: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1448: m[nrl] += NR_END;
1449: m[nrl] -= ncl;
1450:
1451: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1452:
1453: /* return pointer to array of pointers to rows */
1454: return m;
1455: }
1456:
1457: /****************** free_imatrix *************************/
1458: void free_imatrix(m,nrl,nrh,ncl,nch)
1459: int **m;
1460: long nch,ncl,nrh,nrl;
1461: /* free an int matrix allocated by imatrix() */
1462: {
1463: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1464: free((FREE_ARG) (m+nrl-NR_END));
1465: }
1466:
1467: /******************* matrix *******************************/
1468: double **matrix(long nrl, long nrh, long ncl, long nch)
1469: {
1470: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1471: double **m;
1472:
1473: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1474: if (!m) nrerror("allocation failure 1 in matrix()");
1475: m += NR_END;
1476: m -= nrl;
1477:
1478: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1479: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1480: m[nrl] += NR_END;
1481: m[nrl] -= ncl;
1482:
1483: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1484: return m;
1.145 brouard 1485: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1486: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1487: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1488: */
1489: }
1490:
1491: /*************************free matrix ************************/
1492: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1493: {
1494: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1495: free((FREE_ARG)(m+nrl-NR_END));
1496: }
1497:
1498: /******************* ma3x *******************************/
1499: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1500: {
1501: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1502: double ***m;
1503:
1504: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1505: if (!m) nrerror("allocation failure 1 in matrix()");
1506: m += NR_END;
1507: m -= nrl;
1508:
1509: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1510: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1511: m[nrl] += NR_END;
1512: m[nrl] -= ncl;
1513:
1514: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1515:
1516: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1517: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1518: m[nrl][ncl] += NR_END;
1519: m[nrl][ncl] -= nll;
1520: for (j=ncl+1; j<=nch; j++)
1521: m[nrl][j]=m[nrl][j-1]+nlay;
1522:
1523: for (i=nrl+1; i<=nrh; i++) {
1524: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1525: for (j=ncl+1; j<=nch; j++)
1526: m[i][j]=m[i][j-1]+nlay;
1527: }
1528: return m;
1529: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1530: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1531: */
1532: }
1533:
1534: /*************************free ma3x ************************/
1535: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1536: {
1537: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1538: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1539: free((FREE_ARG)(m+nrl-NR_END));
1540: }
1541:
1542: /*************** function subdirf ***********/
1543: char *subdirf(char fileres[])
1544: {
1545: /* Caution optionfilefiname is hidden */
1546: strcpy(tmpout,optionfilefiname);
1547: strcat(tmpout,"/"); /* Add to the right */
1548: strcat(tmpout,fileres);
1549: return tmpout;
1550: }
1551:
1552: /*************** function subdirf2 ***********/
1553: char *subdirf2(char fileres[], char *preop)
1554: {
1555:
1556: /* Caution optionfilefiname is hidden */
1557: strcpy(tmpout,optionfilefiname);
1558: strcat(tmpout,"/");
1559: strcat(tmpout,preop);
1560: strcat(tmpout,fileres);
1561: return tmpout;
1562: }
1563:
1564: /*************** function subdirf3 ***********/
1565: char *subdirf3(char fileres[], char *preop, char *preop2)
1566: {
1567:
1568: /* Caution optionfilefiname is hidden */
1569: strcpy(tmpout,optionfilefiname);
1570: strcat(tmpout,"/");
1571: strcat(tmpout,preop);
1572: strcat(tmpout,preop2);
1573: strcat(tmpout,fileres);
1574: return tmpout;
1575: }
1.213 brouard 1576:
1577: /*************** function subdirfext ***********/
1578: char *subdirfext(char fileres[], char *preop, char *postop)
1579: {
1580:
1581: strcpy(tmpout,preop);
1582: strcat(tmpout,fileres);
1583: strcat(tmpout,postop);
1584: return tmpout;
1585: }
1.126 brouard 1586:
1.213 brouard 1587: /*************** function subdirfext3 ***********/
1588: char *subdirfext3(char fileres[], char *preop, char *postop)
1589: {
1590:
1591: /* Caution optionfilefiname is hidden */
1592: strcpy(tmpout,optionfilefiname);
1593: strcat(tmpout,"/");
1594: strcat(tmpout,preop);
1595: strcat(tmpout,fileres);
1596: strcat(tmpout,postop);
1597: return tmpout;
1598: }
1599:
1.162 brouard 1600: char *asc_diff_time(long time_sec, char ascdiff[])
1601: {
1602: long sec_left, days, hours, minutes;
1603: days = (time_sec) / (60*60*24);
1604: sec_left = (time_sec) % (60*60*24);
1605: hours = (sec_left) / (60*60) ;
1606: sec_left = (sec_left) %(60*60);
1607: minutes = (sec_left) /60;
1608: sec_left = (sec_left) % (60);
1609: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1610: return ascdiff;
1611: }
1612:
1.126 brouard 1613: /***************** f1dim *************************/
1614: extern int ncom;
1615: extern double *pcom,*xicom;
1616: extern double (*nrfunc)(double []);
1617:
1618: double f1dim(double x)
1619: {
1620: int j;
1621: double f;
1622: double *xt;
1623:
1624: xt=vector(1,ncom);
1625: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1626: f=(*nrfunc)(xt);
1627: free_vector(xt,1,ncom);
1628: return f;
1629: }
1630:
1631: /*****************brent *************************/
1632: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1633: {
1634: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1635: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1636: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1637: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1638: * returned function value.
1639: */
1.126 brouard 1640: int iter;
1641: double a,b,d,etemp;
1.159 brouard 1642: double fu=0,fv,fw,fx;
1.164 brouard 1643: double ftemp=0.;
1.126 brouard 1644: double p,q,r,tol1,tol2,u,v,w,x,xm;
1645: double e=0.0;
1646:
1647: a=(ax < cx ? ax : cx);
1648: b=(ax > cx ? ax : cx);
1649: x=w=v=bx;
1650: fw=fv=fx=(*f)(x);
1651: for (iter=1;iter<=ITMAX;iter++) {
1652: xm=0.5*(a+b);
1653: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1654: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1655: printf(".");fflush(stdout);
1656: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1657: #ifdef DEBUGBRENT
1.126 brouard 1658: 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);
1659: 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);
1660: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1661: #endif
1662: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1663: *xmin=x;
1664: return fx;
1665: }
1666: ftemp=fu;
1667: if (fabs(e) > tol1) {
1668: r=(x-w)*(fx-fv);
1669: q=(x-v)*(fx-fw);
1670: p=(x-v)*q-(x-w)*r;
1671: q=2.0*(q-r);
1672: if (q > 0.0) p = -p;
1673: q=fabs(q);
1674: etemp=e;
1675: e=d;
1676: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1677: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1678: else {
1.224 brouard 1679: d=p/q;
1680: u=x+d;
1681: if (u-a < tol2 || b-u < tol2)
1682: d=SIGN(tol1,xm-x);
1.126 brouard 1683: }
1684: } else {
1685: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1686: }
1687: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1688: fu=(*f)(u);
1689: if (fu <= fx) {
1690: if (u >= x) a=x; else b=x;
1691: SHFT(v,w,x,u)
1.183 brouard 1692: SHFT(fv,fw,fx,fu)
1693: } else {
1694: if (u < x) a=u; else b=u;
1695: if (fu <= fw || w == x) {
1.224 brouard 1696: v=w;
1697: w=u;
1698: fv=fw;
1699: fw=fu;
1.183 brouard 1700: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1701: v=u;
1702: fv=fu;
1.183 brouard 1703: }
1704: }
1.126 brouard 1705: }
1706: nrerror("Too many iterations in brent");
1707: *xmin=x;
1708: return fx;
1709: }
1710:
1711: /****************** mnbrak ***********************/
1712:
1713: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1714: double (*func)(double))
1.183 brouard 1715: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1716: the downhill direction (defined by the function as evaluated at the initial points) and returns
1717: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1718: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1719: */
1.126 brouard 1720: double ulim,u,r,q, dum;
1721: double fu;
1.187 brouard 1722:
1723: double scale=10.;
1724: int iterscale=0;
1725:
1726: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1727: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1728:
1729:
1730: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1731: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1732: /* *bx = *ax - (*ax - *bx)/scale; */
1733: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1734: /* } */
1735:
1.126 brouard 1736: if (*fb > *fa) {
1737: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1738: SHFT(dum,*fb,*fa,dum)
1739: }
1.126 brouard 1740: *cx=(*bx)+GOLD*(*bx-*ax);
1741: *fc=(*func)(*cx);
1.183 brouard 1742: #ifdef DEBUG
1.224 brouard 1743: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1744: 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 1745: #endif
1.224 brouard 1746: 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 1747: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1748: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1749: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1750: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1751: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1752: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1753: fu=(*func)(u);
1.163 brouard 1754: #ifdef DEBUG
1755: /* f(x)=A(x-u)**2+f(u) */
1756: double A, fparabu;
1757: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1758: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1759: 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);
1760: 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 1761: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1762: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1763: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1764: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1765: #endif
1.184 brouard 1766: #ifdef MNBRAKORIGINAL
1.183 brouard 1767: #else
1.191 brouard 1768: /* if (fu > *fc) { */
1769: /* #ifdef DEBUG */
1770: /* printf("mnbrak4 fu > fc \n"); */
1771: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1772: /* #endif */
1773: /* /\* 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 *\\/ *\/ */
1774: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1775: /* dum=u; /\* Shifting c and u *\/ */
1776: /* u = *cx; */
1777: /* *cx = dum; */
1778: /* dum = fu; */
1779: /* fu = *fc; */
1780: /* *fc =dum; */
1781: /* } else { /\* end *\/ */
1782: /* #ifdef DEBUG */
1783: /* printf("mnbrak3 fu < fc \n"); */
1784: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1785: /* #endif */
1786: /* dum=u; /\* Shifting c and u *\/ */
1787: /* u = *cx; */
1788: /* *cx = dum; */
1789: /* dum = fu; */
1790: /* fu = *fc; */
1791: /* *fc =dum; */
1792: /* } */
1.224 brouard 1793: #ifdef DEBUGMNBRAK
1794: double A, fparabu;
1795: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1796: fparabu= *fa - A*(*ax-u)*(*ax-u);
1797: 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);
1798: 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 1799: #endif
1.191 brouard 1800: dum=u; /* Shifting c and u */
1801: u = *cx;
1802: *cx = dum;
1803: dum = fu;
1804: fu = *fc;
1805: *fc =dum;
1.183 brouard 1806: #endif
1.162 brouard 1807: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1808: #ifdef DEBUG
1.224 brouard 1809: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1810: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1811: #endif
1.126 brouard 1812: fu=(*func)(u);
1813: if (fu < *fc) {
1.183 brouard 1814: #ifdef DEBUG
1.224 brouard 1815: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1816: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1817: #endif
1818: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1819: SHFT(*fb,*fc,fu,(*func)(u))
1820: #ifdef DEBUG
1821: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1822: #endif
1823: }
1.162 brouard 1824: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1825: #ifdef DEBUG
1.224 brouard 1826: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1827: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1828: #endif
1.126 brouard 1829: u=ulim;
1830: fu=(*func)(u);
1.183 brouard 1831: } else { /* u could be left to b (if r > q parabola has a maximum) */
1832: #ifdef DEBUG
1.224 brouard 1833: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1834: 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 1835: #endif
1.126 brouard 1836: u=(*cx)+GOLD*(*cx-*bx);
1837: fu=(*func)(u);
1.224 brouard 1838: #ifdef DEBUG
1839: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1840: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1841: #endif
1.183 brouard 1842: } /* end tests */
1.126 brouard 1843: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1844: SHFT(*fa,*fb,*fc,fu)
1845: #ifdef DEBUG
1.224 brouard 1846: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1847: 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 1848: #endif
1849: } /* 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 1850: }
1851:
1852: /*************** linmin ************************/
1.162 brouard 1853: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1854: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1855: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1856: the value of func at the returned location p . This is actually all accomplished by calling the
1857: routines mnbrak and brent .*/
1.126 brouard 1858: int ncom;
1859: double *pcom,*xicom;
1860: double (*nrfunc)(double []);
1861:
1.224 brouard 1862: #ifdef LINMINORIGINAL
1.126 brouard 1863: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1864: #else
1865: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1866: #endif
1.126 brouard 1867: {
1868: double brent(double ax, double bx, double cx,
1869: double (*f)(double), double tol, double *xmin);
1870: double f1dim(double x);
1871: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1872: double *fc, double (*func)(double));
1873: int j;
1874: double xx,xmin,bx,ax;
1875: double fx,fb,fa;
1.187 brouard 1876:
1.203 brouard 1877: #ifdef LINMINORIGINAL
1878: #else
1879: double scale=10., axs, xxs; /* Scale added for infinity */
1880: #endif
1881:
1.126 brouard 1882: ncom=n;
1883: pcom=vector(1,n);
1884: xicom=vector(1,n);
1885: nrfunc=func;
1886: for (j=1;j<=n;j++) {
1887: pcom[j]=p[j];
1.202 brouard 1888: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1889: }
1.187 brouard 1890:
1.203 brouard 1891: #ifdef LINMINORIGINAL
1892: xx=1.;
1893: #else
1894: axs=0.0;
1895: xxs=1.;
1896: do{
1897: xx= xxs;
1898: #endif
1.187 brouard 1899: ax=0.;
1900: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1901: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1902: /* 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)) */
1903: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1904: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1905: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1906: /* 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 1907: #ifdef LINMINORIGINAL
1908: #else
1909: if (fx != fx){
1.224 brouard 1910: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1911: printf("|");
1912: fprintf(ficlog,"|");
1.203 brouard 1913: #ifdef DEBUGLINMIN
1.224 brouard 1914: 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 1915: #endif
1916: }
1.224 brouard 1917: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1918: #endif
1919:
1.191 brouard 1920: #ifdef DEBUGLINMIN
1921: 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 1922: 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 1923: #endif
1.224 brouard 1924: #ifdef LINMINORIGINAL
1925: #else
1926: if(fb == fx){ /* Flat function in the direction */
1927: xmin=xx;
1928: *flat=1;
1929: }else{
1930: *flat=0;
1931: #endif
1932: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1933: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1934: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1935: /* fmin = f(p[j] + xmin * xi[j]) */
1936: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1937: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1938: #ifdef DEBUG
1.224 brouard 1939: 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);
1940: 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);
1941: #endif
1942: #ifdef LINMINORIGINAL
1943: #else
1944: }
1.126 brouard 1945: #endif
1.191 brouard 1946: #ifdef DEBUGLINMIN
1947: printf("linmin end ");
1.202 brouard 1948: fprintf(ficlog,"linmin end ");
1.191 brouard 1949: #endif
1.126 brouard 1950: for (j=1;j<=n;j++) {
1.203 brouard 1951: #ifdef LINMINORIGINAL
1952: xi[j] *= xmin;
1953: #else
1954: #ifdef DEBUGLINMIN
1955: if(xxs <1.0)
1956: printf(" before xi[%d]=%12.8f", j,xi[j]);
1957: #endif
1958: 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) */
1959: #ifdef DEBUGLINMIN
1960: if(xxs <1.0)
1961: 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 );
1962: #endif
1963: #endif
1.187 brouard 1964: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1965: }
1.191 brouard 1966: #ifdef DEBUGLINMIN
1.203 brouard 1967: printf("\n");
1.191 brouard 1968: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1969: 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 1970: for (j=1;j<=n;j++) {
1.202 brouard 1971: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1972: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1973: if(j % ncovmodel == 0){
1.191 brouard 1974: printf("\n");
1.202 brouard 1975: fprintf(ficlog,"\n");
1976: }
1.191 brouard 1977: }
1.203 brouard 1978: #else
1.191 brouard 1979: #endif
1.126 brouard 1980: free_vector(xicom,1,n);
1981: free_vector(pcom,1,n);
1982: }
1983:
1984:
1985: /*************** powell ************************/
1.162 brouard 1986: /*
1987: Minimization of a function func of n variables. Input consists of an initial starting point
1988: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1989: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1990: such that failure to decrease by more than this amount on one iteration signals doneness. On
1991: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1992: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1993: */
1.224 brouard 1994: #ifdef LINMINORIGINAL
1995: #else
1996: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 1997: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 1998: #endif
1.126 brouard 1999: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
2000: double (*func)(double []))
2001: {
1.224 brouard 2002: #ifdef LINMINORIGINAL
2003: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 2004: double (*func)(double []));
1.224 brouard 2005: #else
2006: void linmin(double p[], double xi[], int n, double *fret,
2007: double (*func)(double []),int *flat);
2008: #endif
1.126 brouard 2009: int i,ibig,j;
2010: double del,t,*pt,*ptt,*xit;
1.181 brouard 2011: double directest;
1.126 brouard 2012: double fp,fptt;
2013: double *xits;
2014: int niterf, itmp;
1.224 brouard 2015: #ifdef LINMINORIGINAL
2016: #else
2017:
2018: flatdir=ivector(1,n);
2019: for (j=1;j<=n;j++) flatdir[j]=0;
2020: #endif
1.126 brouard 2021:
2022: pt=vector(1,n);
2023: ptt=vector(1,n);
2024: xit=vector(1,n);
2025: xits=vector(1,n);
2026: *fret=(*func)(p);
2027: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 2028: rcurr_time = time(NULL);
1.126 brouard 2029: for (*iter=1;;++(*iter)) {
1.187 brouard 2030: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 2031: ibig=0;
2032: del=0.0;
1.157 brouard 2033: rlast_time=rcurr_time;
2034: /* (void) gettimeofday(&curr_time,&tzp); */
2035: rcurr_time = time(NULL);
2036: curr_time = *localtime(&rcurr_time);
2037: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
2038: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
2039: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 2040: for (i=1;i<=n;i++) {
1.126 brouard 2041: printf(" %d %.12f",i, p[i]);
2042: fprintf(ficlog," %d %.12lf",i, p[i]);
2043: fprintf(ficrespow," %.12lf", p[i]);
2044: }
2045: printf("\n");
2046: fprintf(ficlog,"\n");
2047: fprintf(ficrespow,"\n");fflush(ficrespow);
2048: if(*iter <=3){
1.157 brouard 2049: tml = *localtime(&rcurr_time);
2050: strcpy(strcurr,asctime(&tml));
2051: rforecast_time=rcurr_time;
1.126 brouard 2052: itmp = strlen(strcurr);
2053: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 2054: strcurr[itmp-1]='\0';
1.162 brouard 2055: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 2056: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 2057: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 2058: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
2059: forecast_time = *localtime(&rforecast_time);
2060: strcpy(strfor,asctime(&forecast_time));
2061: itmp = strlen(strfor);
2062: if(strfor[itmp-1]=='\n')
2063: strfor[itmp-1]='\0';
2064: 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);
2065: 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 2066: }
2067: }
1.187 brouard 2068: for (i=1;i<=n;i++) { /* For each direction i */
2069: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2070: fptt=(*fret);
2071: #ifdef DEBUG
1.203 brouard 2072: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2073: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2074: #endif
1.203 brouard 2075: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2076: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2077: #ifdef LINMINORIGINAL
1.188 brouard 2078: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2079: #else
2080: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2081: flatdir[i]=flat; /* Function is vanishing in that direction i */
2082: #endif
2083: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2084: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2085: /* because that direction will be replaced unless the gain del is small */
2086: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2087: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2088: /* with the new direction. */
2089: del=fabs(fptt-(*fret));
2090: ibig=i;
1.126 brouard 2091: }
2092: #ifdef DEBUG
2093: printf("%d %.12e",i,(*fret));
2094: fprintf(ficlog,"%d %.12e",i,(*fret));
2095: for (j=1;j<=n;j++) {
1.224 brouard 2096: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2097: printf(" x(%d)=%.12e",j,xit[j]);
2098: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2099: }
2100: for(j=1;j<=n;j++) {
1.225 brouard 2101: printf(" p(%d)=%.12e",j,p[j]);
2102: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2103: }
2104: printf("\n");
2105: fprintf(ficlog,"\n");
2106: #endif
1.187 brouard 2107: } /* end loop on each direction i */
2108: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2109: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2110: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2111: for(j=1;j<=n;j++) {
1.225 brouard 2112: if(flatdir[j] >0){
2113: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2114: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2115: }
2116: /* printf("\n"); */
2117: /* fprintf(ficlog,"\n"); */
2118: }
1.182 brouard 2119: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2120: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2121: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2122: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2123: /* decreased of more than 3.84 */
2124: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2125: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2126: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2127:
1.188 brouard 2128: /* Starting the program with initial values given by a former maximization will simply change */
2129: /* the scales of the directions and the directions, because the are reset to canonical directions */
2130: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2131: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2132: #ifdef DEBUG
2133: int k[2],l;
2134: k[0]=1;
2135: k[1]=-1;
2136: printf("Max: %.12e",(*func)(p));
2137: fprintf(ficlog,"Max: %.12e",(*func)(p));
2138: for (j=1;j<=n;j++) {
2139: printf(" %.12e",p[j]);
2140: fprintf(ficlog," %.12e",p[j]);
2141: }
2142: printf("\n");
2143: fprintf(ficlog,"\n");
2144: for(l=0;l<=1;l++) {
2145: for (j=1;j<=n;j++) {
2146: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2147: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2148: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2149: }
2150: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2151: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2152: }
2153: #endif
2154:
1.224 brouard 2155: #ifdef LINMINORIGINAL
2156: #else
2157: free_ivector(flatdir,1,n);
2158: #endif
1.126 brouard 2159: free_vector(xit,1,n);
2160: free_vector(xits,1,n);
2161: free_vector(ptt,1,n);
2162: free_vector(pt,1,n);
2163: return;
1.192 brouard 2164: } /* enough precision */
1.126 brouard 2165: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2166: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2167: ptt[j]=2.0*p[j]-pt[j];
2168: xit[j]=p[j]-pt[j];
2169: pt[j]=p[j];
2170: }
1.181 brouard 2171: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2172: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2173: if (*iter <=4) {
1.225 brouard 2174: #else
2175: #endif
1.224 brouard 2176: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2177: #else
1.161 brouard 2178: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2179: #endif
1.162 brouard 2180: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2181: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2182: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2183: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2184: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2185: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2186: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2187: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2188: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2189: /* Even if f3 <f1, directest can be negative and t >0 */
2190: /* mu² and del² are equal when f3=f1 */
2191: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2192: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2193: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2194: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2195: #ifdef NRCORIGINAL
2196: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2197: #else
2198: 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 2199: t= t- del*SQR(fp-fptt);
1.183 brouard 2200: #endif
1.202 brouard 2201: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2202: #ifdef DEBUG
1.181 brouard 2203: 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);
2204: 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 2205: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2206: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2207: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2208: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2209: 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);
2210: 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);
2211: #endif
1.183 brouard 2212: #ifdef POWELLORIGINAL
2213: if (t < 0.0) { /* Then we use it for new direction */
2214: #else
1.182 brouard 2215: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2216: 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 2217: 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 2218: 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 2219: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2220: }
1.181 brouard 2221: if (directest < 0.0) { /* Then we use it for new direction */
2222: #endif
1.191 brouard 2223: #ifdef DEBUGLINMIN
1.224 brouard 2224: printf("Before linmin in direction P%d-P0\n",n);
2225: for (j=1;j<=n;j++) {
2226: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2227: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2228: if(j % ncovmodel == 0){
2229: printf("\n");
2230: fprintf(ficlog,"\n");
2231: }
2232: }
2233: #endif
2234: #ifdef LINMINORIGINAL
2235: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2236: #else
2237: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2238: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2239: #endif
1.224 brouard 2240:
1.191 brouard 2241: #ifdef DEBUGLINMIN
1.224 brouard 2242: for (j=1;j<=n;j++) {
2243: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2244: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2245: if(j % ncovmodel == 0){
2246: printf("\n");
2247: fprintf(ficlog,"\n");
2248: }
2249: }
2250: #endif
2251: for (j=1;j<=n;j++) {
2252: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2253: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2254: }
2255: #ifdef LINMINORIGINAL
2256: #else
1.225 brouard 2257: for (j=1, flatd=0;j<=n;j++) {
2258: if(flatdir[j]>0)
2259: flatd++;
2260: }
2261: if(flatd >0){
2262: printf("%d flat directions\n",flatd);
2263: fprintf(ficlog,"%d flat directions\n",flatd);
2264: for (j=1;j<=n;j++) {
2265: if(flatdir[j]>0){
2266: printf("%d ",j);
2267: fprintf(ficlog,"%d ",j);
2268: }
2269: }
2270: printf("\n");
2271: fprintf(ficlog,"\n");
2272: }
1.191 brouard 2273: #endif
1.224 brouard 2274: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2275: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2276:
1.126 brouard 2277: #ifdef DEBUG
1.224 brouard 2278: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2279: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2280: for(j=1;j<=n;j++){
2281: printf(" %lf",xit[j]);
2282: fprintf(ficlog," %lf",xit[j]);
2283: }
2284: printf("\n");
2285: fprintf(ficlog,"\n");
1.126 brouard 2286: #endif
1.192 brouard 2287: } /* end of t or directest negative */
1.224 brouard 2288: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2289: #else
1.162 brouard 2290: } /* end if (fptt < fp) */
1.192 brouard 2291: #endif
1.225 brouard 2292: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.224 brouard 2293: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2294: #else
1.224 brouard 2295: #endif
1.192 brouard 2296: } /* loop iteration */
1.126 brouard 2297: }
2298:
2299: /**** Prevalence limit (stable or period prevalence) ****************/
2300:
1.203 brouard 2301: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2302: {
1.218 brouard 2303: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2304: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2305: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2306: /* Wx is row vector: population in state 1, population in state 2, population dead */
2307: /* or prevalence in state 1, prevalence in state 2, 0 */
2308: /* newm is the matrix after multiplications, its rows are identical at a factor */
2309: /* Initial matrix pimij */
2310: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2311: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2312: /* 0, 0 , 1} */
2313: /*
2314: * and after some iteration: */
2315: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2316: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2317: /* 0, 0 , 1} */
2318: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2319: /* {0.51571254859325999, 0.4842874514067399, */
2320: /* 0.51326036147820708, 0.48673963852179264} */
2321: /* If we start from prlim again, prlim tends to a constant matrix */
2322:
1.126 brouard 2323: int i, ii,j,k;
1.209 brouard 2324: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2325: /* double **matprod2(); */ /* test */
1.218 brouard 2326: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2327: double **newm;
1.209 brouard 2328: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2329: int ncvloop=0;
1.169 brouard 2330:
1.209 brouard 2331: min=vector(1,nlstate);
2332: max=vector(1,nlstate);
2333: meandiff=vector(1,nlstate);
2334:
1.218 brouard 2335: /* Starting with matrix unity */
1.126 brouard 2336: for (ii=1;ii<=nlstate+ndeath;ii++)
2337: for (j=1;j<=nlstate+ndeath;j++){
2338: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2339: }
1.169 brouard 2340:
2341: cov[1]=1.;
2342:
2343: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2344: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2345: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2346: ncvloop++;
1.126 brouard 2347: newm=savm;
2348: /* Covariates have to be included here again */
1.138 brouard 2349: cov[2]=agefin;
1.187 brouard 2350: if(nagesqr==1)
2351: cov[3]= agefin*agefin;;
1.138 brouard 2352: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2353: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2354: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2355: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2356: /* 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])]); */
1.138 brouard 2357: }
1.186 brouard 2358: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2359: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2360: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2361: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2362: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2363: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2364:
2365: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2366: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2367: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2368: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2369: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2370: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2371: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2372:
1.126 brouard 2373: savm=oldm;
2374: oldm=newm;
1.209 brouard 2375:
2376: for(j=1; j<=nlstate; j++){
2377: max[j]=0.;
2378: min[j]=1.;
2379: }
2380: for(i=1;i<=nlstate;i++){
2381: sumnew=0;
2382: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2383: for(j=1; j<=nlstate; j++){
2384: prlim[i][j]= newm[i][j]/(1-sumnew);
2385: max[j]=FMAX(max[j],prlim[i][j]);
2386: min[j]=FMIN(min[j],prlim[i][j]);
2387: }
2388: }
2389:
1.126 brouard 2390: maxmax=0.;
1.209 brouard 2391: for(j=1; j<=nlstate; j++){
2392: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2393: maxmax=FMAX(maxmax,meandiff[j]);
2394: /* 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 2395: } /* j loop */
1.203 brouard 2396: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2397: /* 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 2398: if(maxmax < ftolpl){
1.209 brouard 2399: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2400: free_vector(min,1,nlstate);
2401: free_vector(max,1,nlstate);
2402: free_vector(meandiff,1,nlstate);
1.126 brouard 2403: return prlim;
2404: }
1.169 brouard 2405: } /* age loop */
1.208 brouard 2406: /* After some age loop it doesn't converge */
1.209 brouard 2407: 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 2408: 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 2409: /* 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); */
2410: free_vector(min,1,nlstate);
2411: free_vector(max,1,nlstate);
2412: free_vector(meandiff,1,nlstate);
1.208 brouard 2413:
1.169 brouard 2414: return prlim; /* should not reach here */
1.126 brouard 2415: }
2416:
1.217 brouard 2417:
2418: /**** Back Prevalence limit (stable or period prevalence) ****************/
2419:
1.218 brouard 2420: /* 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) */
2421: /* 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) */
2422: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2423: {
1.218 brouard 2424: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2425: matrix by transitions matrix until convergence is reached with precision ftolpl */
2426: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2427: /* Wx is row vector: population in state 1, population in state 2, population dead */
2428: /* or prevalence in state 1, prevalence in state 2, 0 */
2429: /* newm is the matrix after multiplications, its rows are identical at a factor */
2430: /* Initial matrix pimij */
2431: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2432: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2433: /* 0, 0 , 1} */
2434: /*
2435: * and after some iteration: */
2436: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2437: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2438: /* 0, 0 , 1} */
2439: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2440: /* {0.51571254859325999, 0.4842874514067399, */
2441: /* 0.51326036147820708, 0.48673963852179264} */
2442: /* If we start from prlim again, prlim tends to a constant matrix */
2443:
2444: int i, ii,j,k;
2445: double *min, *max, *meandiff, maxmax,sumnew=0.;
2446: /* double **matprod2(); */ /* test */
2447: double **out, cov[NCOVMAX+1], **bmij();
2448: double **newm;
1.218 brouard 2449: double **dnewm, **doldm, **dsavm; /* for use */
2450: double **oldm, **savm; /* for use */
2451:
1.217 brouard 2452: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2453: int ncvloop=0;
2454:
2455: min=vector(1,nlstate);
2456: max=vector(1,nlstate);
2457: meandiff=vector(1,nlstate);
2458:
1.218 brouard 2459: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2460: oldm=oldms; savm=savms;
2461:
2462: /* Starting with matrix unity */
2463: for (ii=1;ii<=nlstate+ndeath;ii++)
2464: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2465: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2466: }
2467:
2468: cov[1]=1.;
2469:
2470: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2471: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2472: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2473: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2474: ncvloop++;
1.218 brouard 2475: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2476: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2477: /* Covariates have to be included here again */
2478: cov[2]=agefin;
2479: if(nagesqr==1)
2480: cov[3]= agefin*agefin;;
2481: for (k=1; k<=cptcovn;k++) {
2482: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2483: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2484: /* 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])]); */
2485: }
2486: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2487: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2488: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2489: for (k=1; k<=cptcovprod;k++) /* Useless */
2490: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2491: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2492:
2493: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2494: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2495: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2496: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2497: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2498: /* ij should be linked to the correct index of cov */
2499: /* age and covariate values ij are in 'cov', but we need to pass
2500: * ij for the observed prevalence at age and status and covariate
2501: * number: prevacurrent[(int)agefin][ii][ij]
2502: */
2503: /* 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 *\/ */
2504: /* 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 *\/ */
2505: 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 2506: savm=oldm;
2507: oldm=newm;
2508: for(j=1; j<=nlstate; j++){
2509: max[j]=0.;
2510: min[j]=1.;
2511: }
2512: for(j=1; j<=nlstate; j++){
2513: for(i=1;i<=nlstate;i++){
1.218 brouard 2514: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2515: bprlim[i][j]= newm[i][j];
2516: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2517: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2518: }
2519: }
1.218 brouard 2520:
1.217 brouard 2521: maxmax=0.;
2522: for(i=1; i<=nlstate; i++){
2523: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2524: maxmax=FMAX(maxmax,meandiff[i]);
2525: /* 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); */
2526: } /* j loop */
2527: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2528: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2529: if(maxmax < ftolpl){
1.220 brouard 2530: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2531: free_vector(min,1,nlstate);
2532: free_vector(max,1,nlstate);
2533: free_vector(meandiff,1,nlstate);
2534: return bprlim;
2535: }
2536: } /* age loop */
2537: /* After some age loop it doesn't converge */
2538: 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\
2539: 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);
2540: /* 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); */
2541: free_vector(min,1,nlstate);
2542: free_vector(max,1,nlstate);
2543: free_vector(meandiff,1,nlstate);
2544:
2545: return bprlim; /* should not reach here */
2546: }
2547:
1.126 brouard 2548: /*************** transition probabilities ***************/
2549:
2550: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2551: {
1.138 brouard 2552: /* According to parameters values stored in x and the covariate's values stored in cov,
2553: computes the probability to be observed in state j being in state i by appying the
2554: model to the ncovmodel covariates (including constant and age).
2555: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2556: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2557: ncth covariate in the global vector x is given by the formula:
2558: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2559: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2560: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2561: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2562: Outputs ps[i][j] the probability to be observed in j being in j according to
2563: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2564: */
2565: double s1, lnpijopii;
1.126 brouard 2566: /*double t34;*/
1.164 brouard 2567: int i,j, nc, ii, jj;
1.126 brouard 2568:
1.223 brouard 2569: for(i=1; i<= nlstate; i++){
2570: for(j=1; j<i;j++){
2571: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2572: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2573: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2574: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2575: }
2576: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2577: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2578: }
2579: for(j=i+1; j<=nlstate+ndeath;j++){
2580: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2581: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2582: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2583: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2584: }
2585: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2586: }
2587: }
1.218 brouard 2588:
1.223 brouard 2589: for(i=1; i<= nlstate; i++){
2590: s1=0;
2591: for(j=1; j<i; j++){
2592: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2593: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2594: }
2595: for(j=i+1; j<=nlstate+ndeath; j++){
2596: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2597: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2598: }
2599: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2600: ps[i][i]=1./(s1+1.);
2601: /* Computing other pijs */
2602: for(j=1; j<i; j++)
2603: ps[i][j]= exp(ps[i][j])*ps[i][i];
2604: for(j=i+1; j<=nlstate+ndeath; j++)
2605: ps[i][j]= exp(ps[i][j])*ps[i][i];
2606: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2607: } /* end i */
1.218 brouard 2608:
1.223 brouard 2609: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2610: for(jj=1; jj<= nlstate+ndeath; jj++){
2611: ps[ii][jj]=0;
2612: ps[ii][ii]=1;
2613: }
2614: }
1.218 brouard 2615:
2616:
1.223 brouard 2617: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2618: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2619: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2620: /* } */
2621: /* printf("\n "); */
2622: /* } */
2623: /* printf("\n ");printf("%lf ",cov[2]);*/
2624: /*
2625: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2626: goto end;*/
1.223 brouard 2627: return ps;
1.126 brouard 2628: }
2629:
1.218 brouard 2630: /*************** backward transition probabilities ***************/
2631:
2632: /* 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 ) */
2633: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2634: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2635: {
1.222 brouard 2636: /* Computes the backward probability at age agefin and covariate ij
2637: * and returns in **ps as well as **bmij.
2638: */
1.218 brouard 2639: int i, ii, j,k;
1.222 brouard 2640:
2641: double **out, **pmij();
2642: double sumnew=0.;
1.218 brouard 2643: double agefin;
1.222 brouard 2644:
2645: double **dnewm, **dsavm, **doldm;
2646: double **bbmij;
2647:
1.218 brouard 2648: doldm=ddoldms; /* global pointers */
1.222 brouard 2649: dnewm=ddnewms;
2650: dsavm=ddsavms;
2651:
2652: agefin=cov[2];
2653: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2654: the observed prevalence (with this covariate ij) */
2655: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2656: /* We do have the matrix Px in savm and we need pij */
2657: for (j=1;j<=nlstate+ndeath;j++){
2658: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2659: for (ii=1;ii<=nlstate;ii++){
2660: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2661: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2662: for (ii=1;ii<=nlstate+ndeath;ii++){
2663: if(sumnew >= 1.e-10){
2664: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2665: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2666: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2667: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2668: /* }else */
2669: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2670: }else{
2671: 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);
2672: }
2673: } /*End ii */
2674: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2675: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2676: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2677: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2678: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2679: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2680: /* left Product of this matrix by diag matrix of prevalences (savm) */
2681: for (j=1;j<=nlstate+ndeath;j++){
2682: for (ii=1;ii<=nlstate+ndeath;ii++){
2683: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2684: }
2685: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2686: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2687: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2688: /* end bmij */
2689: return ps;
1.218 brouard 2690: }
1.217 brouard 2691: /*************** transition probabilities ***************/
2692:
1.218 brouard 2693: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2694: {
2695: /* According to parameters values stored in x and the covariate's values stored in cov,
2696: computes the probability to be observed in state j being in state i by appying the
2697: model to the ncovmodel covariates (including constant and age).
2698: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2699: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2700: ncth covariate in the global vector x is given by the formula:
2701: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2702: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2703: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2704: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2705: Outputs ps[i][j] the probability to be observed in j being in j according to
2706: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2707: */
2708: double s1, lnpijopii;
2709: /*double t34;*/
2710: int i,j, nc, ii, jj;
2711:
1.218 brouard 2712: for(i=1; i<= nlstate; i++){
2713: for(j=1; j<i;j++){
2714: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2715: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2716: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2717: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2718: }
2719: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2720: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2721: }
2722: for(j=i+1; j<=nlstate+ndeath;j++){
2723: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2724: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2725: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2726: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2727: }
2728: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2729: }
2730: }
2731:
2732: for(i=1; i<= nlstate; i++){
2733: s1=0;
2734: for(j=1; j<i; j++){
2735: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2736: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2737: }
2738: for(j=i+1; j<=nlstate+ndeath; j++){
2739: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2740: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2741: }
2742: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2743: ps[i][i]=1./(s1+1.);
2744: /* Computing other pijs */
2745: for(j=1; j<i; j++)
2746: ps[i][j]= exp(ps[i][j])*ps[i][i];
2747: for(j=i+1; j<=nlstate+ndeath; j++)
2748: ps[i][j]= exp(ps[i][j])*ps[i][i];
2749: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2750: } /* end i */
2751:
2752: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2753: for(jj=1; jj<= nlstate+ndeath; jj++){
2754: ps[ii][jj]=0;
2755: ps[ii][ii]=1;
2756: }
2757: }
2758: /* Added for backcast */ /* Transposed matrix too */
2759: for(jj=1; jj<= nlstate+ndeath; jj++){
2760: s1=0.;
2761: for(ii=1; ii<= nlstate+ndeath; ii++){
2762: s1+=ps[ii][jj];
2763: }
2764: for(ii=1; ii<= nlstate; ii++){
2765: ps[ii][jj]=ps[ii][jj]/s1;
2766: }
2767: }
2768: /* Transposition */
2769: for(jj=1; jj<= nlstate+ndeath; jj++){
2770: for(ii=jj; ii<= nlstate+ndeath; ii++){
2771: s1=ps[ii][jj];
2772: ps[ii][jj]=ps[jj][ii];
2773: ps[jj][ii]=s1;
2774: }
2775: }
2776: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2777: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2778: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2779: /* } */
2780: /* printf("\n "); */
2781: /* } */
2782: /* printf("\n ");printf("%lf ",cov[2]);*/
2783: /*
2784: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2785: goto end;*/
2786: return ps;
1.217 brouard 2787: }
2788:
2789:
1.126 brouard 2790: /**************** Product of 2 matrices ******************/
2791:
1.145 brouard 2792: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2793: {
2794: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2795: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2796: /* in, b, out are matrice of pointers which should have been initialized
2797: before: only the contents of out is modified. The function returns
2798: a pointer to pointers identical to out */
1.145 brouard 2799: int i, j, k;
1.126 brouard 2800: for(i=nrl; i<= nrh; i++)
1.145 brouard 2801: for(k=ncolol; k<=ncoloh; k++){
2802: out[i][k]=0.;
2803: for(j=ncl; j<=nch; j++)
2804: out[i][k] +=in[i][j]*b[j][k];
2805: }
1.126 brouard 2806: return out;
2807: }
2808:
2809:
2810: /************* Higher Matrix Product ***************/
2811:
2812: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2813: {
1.218 brouard 2814: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2815: 'nhstepm*hstepm*stepm' months (i.e. until
2816: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2817: nhstepm*hstepm matrices.
2818: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2819: (typically every 2 years instead of every month which is too big
2820: for the memory).
2821: Model is determined by parameters x and covariates have to be
2822: included manually here.
2823:
2824: */
2825:
2826: int i, j, d, h, k;
1.131 brouard 2827: double **out, cov[NCOVMAX+1];
1.126 brouard 2828: double **newm;
1.187 brouard 2829: double agexact;
1.214 brouard 2830: double agebegin, ageend;
1.126 brouard 2831:
2832: /* Hstepm could be zero and should return the unit matrix */
2833: for (i=1;i<=nlstate+ndeath;i++)
2834: for (j=1;j<=nlstate+ndeath;j++){
2835: oldm[i][j]=(i==j ? 1.0 : 0.0);
2836: po[i][j][0]=(i==j ? 1.0 : 0.0);
2837: }
2838: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2839: for(h=1; h <=nhstepm; h++){
2840: for(d=1; d <=hstepm; d++){
2841: newm=savm;
2842: /* Covariates have to be included here again */
2843: cov[1]=1.;
1.214 brouard 2844: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2845: cov[2]=agexact;
2846: if(nagesqr==1)
1.227 brouard 2847: cov[3]= agexact*agexact;
1.131 brouard 2848: for (k=1; k<=cptcovn;k++)
1.227 brouard 2849: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2850: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2851: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.227 brouard 2852: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2853: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2854: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2855: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.227 brouard 2856: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2857: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2858:
2859:
1.126 brouard 2860: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2861: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2862: /* right multiplication of oldm by the current matrix */
1.126 brouard 2863: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2864: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2865: /* if((int)age == 70){ */
2866: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2867: /* for(i=1; i<=nlstate+ndeath; i++) { */
2868: /* printf("%d pmmij ",i); */
2869: /* for(j=1;j<=nlstate+ndeath;j++) { */
2870: /* printf("%f ",pmmij[i][j]); */
2871: /* } */
2872: /* printf(" oldm "); */
2873: /* for(j=1;j<=nlstate+ndeath;j++) { */
2874: /* printf("%f ",oldm[i][j]); */
2875: /* } */
2876: /* printf("\n"); */
2877: /* } */
2878: /* } */
1.126 brouard 2879: savm=oldm;
2880: oldm=newm;
2881: }
2882: for(i=1; i<=nlstate+ndeath; i++)
2883: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2884: po[i][j][h]=newm[i][j];
2885: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2886: }
1.128 brouard 2887: /*printf("h=%d ",h);*/
1.126 brouard 2888: } /* end h */
1.218 brouard 2889: /* printf("\n H=%d \n",h); */
1.126 brouard 2890: return po;
2891: }
2892:
1.217 brouard 2893: /************* Higher Back Matrix Product ***************/
1.218 brouard 2894: /* 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 2895: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2896: {
1.218 brouard 2897: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2898: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2899: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2900: nhstepm*hstepm matrices.
2901: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2902: (typically every 2 years instead of every month which is too big
1.217 brouard 2903: for the memory).
1.218 brouard 2904: Model is determined by parameters x and covariates have to be
2905: included manually here.
1.217 brouard 2906:
1.222 brouard 2907: */
1.217 brouard 2908:
2909: int i, j, d, h, k;
2910: double **out, cov[NCOVMAX+1];
2911: double **newm;
2912: double agexact;
2913: double agebegin, ageend;
1.222 brouard 2914: double **oldm, **savm;
1.217 brouard 2915:
1.222 brouard 2916: oldm=oldms;savm=savms;
1.217 brouard 2917: /* Hstepm could be zero and should return the unit matrix */
2918: for (i=1;i<=nlstate+ndeath;i++)
2919: for (j=1;j<=nlstate+ndeath;j++){
2920: oldm[i][j]=(i==j ? 1.0 : 0.0);
2921: po[i][j][0]=(i==j ? 1.0 : 0.0);
2922: }
2923: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2924: for(h=1; h <=nhstepm; h++){
2925: for(d=1; d <=hstepm; d++){
2926: newm=savm;
2927: /* Covariates have to be included here again */
2928: cov[1]=1.;
2929: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2930: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2931: cov[2]=agexact;
2932: if(nagesqr==1)
1.222 brouard 2933: cov[3]= agexact*agexact;
1.218 brouard 2934: for (k=1; k<=cptcovn;k++)
1.222 brouard 2935: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2936: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2937: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2938: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2939: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2940: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2941: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2942: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2943: /* 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 2944:
2945:
1.217 brouard 2946: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2947: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2948: /* Careful transposed matrix */
1.222 brouard 2949: /* age is in cov[2] */
1.218 brouard 2950: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2951: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2952: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2953: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2954: /* if((int)age == 70){ */
2955: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2956: /* for(i=1; i<=nlstate+ndeath; i++) { */
2957: /* printf("%d pmmij ",i); */
2958: /* for(j=1;j<=nlstate+ndeath;j++) { */
2959: /* printf("%f ",pmmij[i][j]); */
2960: /* } */
2961: /* printf(" oldm "); */
2962: /* for(j=1;j<=nlstate+ndeath;j++) { */
2963: /* printf("%f ",oldm[i][j]); */
2964: /* } */
2965: /* printf("\n"); */
2966: /* } */
2967: /* } */
2968: savm=oldm;
2969: oldm=newm;
2970: }
2971: for(i=1; i<=nlstate+ndeath; i++)
2972: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2973: po[i][j][h]=newm[i][j];
2974: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2975: }
2976: /*printf("h=%d ",h);*/
2977: } /* end h */
1.222 brouard 2978: /* printf("\n H=%d \n",h); */
1.217 brouard 2979: return po;
2980: }
2981:
2982:
1.162 brouard 2983: #ifdef NLOPT
2984: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2985: double fret;
2986: double *xt;
2987: int j;
2988: myfunc_data *d2 = (myfunc_data *) pd;
2989: /* xt = (p1-1); */
2990: xt=vector(1,n);
2991: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2992:
2993: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2994: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2995: printf("Function = %.12lf ",fret);
2996: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2997: printf("\n");
2998: free_vector(xt,1,n);
2999: return fret;
3000: }
3001: #endif
1.126 brouard 3002:
3003: /*************** log-likelihood *************/
3004: double func( double *x)
3005: {
1.226 brouard 3006: int i, ii, j, k, mi, d, kk;
3007: int ioffset=0;
3008: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
3009: double **out;
3010: double lli; /* Individual log likelihood */
3011: int s1, s2;
1.228 brouard 3012: 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 3013: double bbh, survp;
3014: long ipmx;
3015: double agexact;
3016: /*extern weight */
3017: /* We are differentiating ll according to initial status */
3018: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3019: /*for(i=1;i<imx;i++)
3020: printf(" %d\n",s[4][i]);
3021: */
1.162 brouard 3022:
1.226 brouard 3023: ++countcallfunc;
1.162 brouard 3024:
1.226 brouard 3025: cov[1]=1.;
1.126 brouard 3026:
1.226 brouard 3027: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3028: ioffset=0;
1.226 brouard 3029: if(mle==1){
3030: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3031: /* Computes the values of the ncovmodel covariates of the model
3032: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
3033: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
3034: to be observed in j being in i according to the model.
3035: */
3036: ioffset=2+nagesqr+cptcovage;
3037: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
3038: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
1.232 ! brouard 3039: cov[++ioffset]=covar[Tvar[k]][i];
1.226 brouard 3040: }
3041: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
1.232 ! brouard 3042: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.226 brouard 3043: }
3044:
3045: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
3046: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
3047: has been calculated etc */
3048: /* For an individual i, wav[i] gives the number of effective waves */
3049: /* We compute the contribution to Likelihood of each effective transition
3050: mw[mi][i] is real wave of the mi th effectve wave */
3051: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
3052: s2=s[mw[mi+1][i]][i];
3053: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
3054: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
3055: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
3056: */
3057: for(mi=1; mi<= wav[i]-1; mi++){
1.231 brouard 3058: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
3059: /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
3060: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
3061: }
3062: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
3063: if(cotqvar[mw[mi][i]][iqtv][i] == -1){
3064: printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
3065: }
3066: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
3067: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
3068: }
3069: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
3070: for (ii=1;ii<=nlstate+ndeath;ii++)
3071: for (j=1;j<=nlstate+ndeath;j++){
3072: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3073: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3074: }
3075: for(d=0; d<dh[mi][i]; d++){
3076: newm=savm;
3077: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3078: cov[2]=agexact;
3079: if(nagesqr==1)
3080: cov[3]= agexact*agexact; /* Should be changed here */
3081: for (kk=1; kk<=cptcovage;kk++) {
3082: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3083: }
3084: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3085: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3086: savm=oldm;
3087: oldm=newm;
3088: } /* end mult */
1.224 brouard 3089:
1.231 brouard 3090: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3091: /* But now since version 0.9 we anticipate for bias at large stepm.
3092: * If stepm is larger than one month (smallest stepm) and if the exact delay
3093: * (in months) between two waves is not a multiple of stepm, we rounded to
3094: * the nearest (and in case of equal distance, to the lowest) interval but now
3095: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3096: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3097: * probability in order to take into account the bias as a fraction of the way
3098: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3099: * -stepm/2 to stepm/2 .
3100: * For stepm=1 the results are the same as for previous versions of Imach.
3101: * For stepm > 1 the results are less biased than in previous versions.
3102: */
3103: s1=s[mw[mi][i]][i];
3104: s2=s[mw[mi+1][i]][i];
3105: bbh=(double)bh[mi][i]/(double)stepm;
3106: /* bias bh is positive if real duration
3107: * is higher than the multiple of stepm and negative otherwise.
3108: */
3109: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3110: if( s2 > nlstate){
3111: /* i.e. if s2 is a death state and if the date of death is known
3112: then the contribution to the likelihood is the probability to
3113: die between last step unit time and current step unit time,
3114: which is also equal to probability to die before dh
3115: minus probability to die before dh-stepm .
3116: In version up to 0.92 likelihood was computed
3117: as if date of death was unknown. Death was treated as any other
3118: health state: the date of the interview describes the actual state
3119: and not the date of a change in health state. The former idea was
3120: to consider that at each interview the state was recorded
3121: (healthy, disable or death) and IMaCh was corrected; but when we
3122: introduced the exact date of death then we should have modified
3123: the contribution of an exact death to the likelihood. This new
3124: contribution is smaller and very dependent of the step unit
3125: stepm. It is no more the probability to die between last interview
3126: and month of death but the probability to survive from last
3127: interview up to one month before death multiplied by the
3128: probability to die within a month. Thanks to Chris
3129: Jackson for correcting this bug. Former versions increased
3130: mortality artificially. The bad side is that we add another loop
3131: which slows down the processing. The difference can be up to 10%
3132: lower mortality.
3133: */
3134: /* If, at the beginning of the maximization mostly, the
3135: cumulative probability or probability to be dead is
3136: constant (ie = 1) over time d, the difference is equal to
3137: 0. out[s1][3] = savm[s1][3]: probability, being at state
3138: s1 at precedent wave, to be dead a month before current
3139: wave is equal to probability, being at state s1 at
3140: precedent wave, to be dead at mont of the current
3141: wave. Then the observed probability (that this person died)
3142: is null according to current estimated parameter. In fact,
3143: it should be very low but not zero otherwise the log go to
3144: infinity.
3145: */
1.183 brouard 3146: /* #ifdef INFINITYORIGINAL */
3147: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3148: /* #else */
3149: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3150: /* lli=log(mytinydouble); */
3151: /* else */
3152: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3153: /* #endif */
1.226 brouard 3154: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3155:
1.226 brouard 3156: } else if ( s2==-1 ) { /* alive */
3157: for (j=1,survp=0. ; j<=nlstate; j++)
3158: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3159: /*survp += out[s1][j]; */
3160: lli= log(survp);
3161: }
3162: else if (s2==-4) {
3163: for (j=3,survp=0. ; j<=nlstate; j++)
3164: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3165: lli= log(survp);
3166: }
3167: else if (s2==-5) {
3168: for (j=1,survp=0. ; j<=2; j++)
3169: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3170: lli= log(survp);
3171: }
3172: else{
3173: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3174: /* 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 */
3175: }
3176: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3177: /*if(lli ==000.0)*/
3178: /*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); */
3179: ipmx +=1;
3180: sw += weight[i];
3181: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3182: /* if (lli < log(mytinydouble)){ */
3183: /* 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); */
3184: /* 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]); */
3185: /* } */
3186: } /* end of wave */
3187: } /* end of individual */
3188: } else if(mle==2){
3189: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3190: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3191: for(mi=1; mi<= wav[i]-1; mi++){
3192: for (ii=1;ii<=nlstate+ndeath;ii++)
3193: for (j=1;j<=nlstate+ndeath;j++){
3194: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3195: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3196: }
3197: for(d=0; d<=dh[mi][i]; d++){
3198: newm=savm;
3199: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3200: cov[2]=agexact;
3201: if(nagesqr==1)
3202: cov[3]= agexact*agexact;
3203: for (kk=1; kk<=cptcovage;kk++) {
3204: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3205: }
3206: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3207: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3208: savm=oldm;
3209: oldm=newm;
3210: } /* end mult */
3211:
3212: s1=s[mw[mi][i]][i];
3213: s2=s[mw[mi+1][i]][i];
3214: bbh=(double)bh[mi][i]/(double)stepm;
3215: 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 */
3216: ipmx +=1;
3217: sw += weight[i];
3218: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3219: } /* end of wave */
3220: } /* end of individual */
3221: } else if(mle==3){ /* exponential inter-extrapolation */
3222: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3223: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3224: for(mi=1; mi<= wav[i]-1; mi++){
3225: for (ii=1;ii<=nlstate+ndeath;ii++)
3226: for (j=1;j<=nlstate+ndeath;j++){
3227: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3228: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3229: }
3230: for(d=0; d<dh[mi][i]; d++){
3231: newm=savm;
3232: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3233: cov[2]=agexact;
3234: if(nagesqr==1)
3235: cov[3]= agexact*agexact;
3236: for (kk=1; kk<=cptcovage;kk++) {
3237: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3238: }
3239: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3240: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3241: savm=oldm;
3242: oldm=newm;
3243: } /* end mult */
3244:
3245: s1=s[mw[mi][i]][i];
3246: s2=s[mw[mi+1][i]][i];
3247: bbh=(double)bh[mi][i]/(double)stepm;
3248: 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 */
3249: ipmx +=1;
3250: sw += weight[i];
3251: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3252: } /* end of wave */
3253: } /* end of individual */
3254: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3255: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3256: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3257: for(mi=1; mi<= wav[i]-1; mi++){
3258: for (ii=1;ii<=nlstate+ndeath;ii++)
3259: for (j=1;j<=nlstate+ndeath;j++){
3260: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3261: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3262: }
3263: for(d=0; d<dh[mi][i]; d++){
3264: newm=savm;
3265: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3266: cov[2]=agexact;
3267: if(nagesqr==1)
3268: cov[3]= agexact*agexact;
3269: for (kk=1; kk<=cptcovage;kk++) {
3270: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3271: }
1.126 brouard 3272:
1.226 brouard 3273: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3274: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3275: savm=oldm;
3276: oldm=newm;
3277: } /* end mult */
3278:
3279: s1=s[mw[mi][i]][i];
3280: s2=s[mw[mi+1][i]][i];
3281: if( s2 > nlstate){
3282: lli=log(out[s1][s2] - savm[s1][s2]);
3283: } else if ( s2==-1 ) { /* alive */
3284: for (j=1,survp=0. ; j<=nlstate; j++)
3285: survp += out[s1][j];
3286: lli= log(survp);
3287: }else{
3288: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3289: }
3290: ipmx +=1;
3291: sw += weight[i];
3292: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3293: /* 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 3294: } /* end of wave */
3295: } /* end of individual */
3296: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3297: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3298: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3299: for(mi=1; mi<= wav[i]-1; mi++){
3300: for (ii=1;ii<=nlstate+ndeath;ii++)
3301: for (j=1;j<=nlstate+ndeath;j++){
3302: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3303: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3304: }
3305: for(d=0; d<dh[mi][i]; d++){
3306: newm=savm;
3307: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3308: cov[2]=agexact;
3309: if(nagesqr==1)
3310: cov[3]= agexact*agexact;
3311: for (kk=1; kk<=cptcovage;kk++) {
3312: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3313: }
1.126 brouard 3314:
1.226 brouard 3315: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3316: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3317: savm=oldm;
3318: oldm=newm;
3319: } /* end mult */
3320:
3321: s1=s[mw[mi][i]][i];
3322: s2=s[mw[mi+1][i]][i];
3323: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3324: ipmx +=1;
3325: sw += weight[i];
3326: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3327: /*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]);*/
3328: } /* end of wave */
3329: } /* end of individual */
3330: } /* End of if */
3331: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3332: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3333: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3334: return -l;
1.126 brouard 3335: }
3336:
3337: /*************** log-likelihood *************/
3338: double funcone( double *x)
3339: {
1.228 brouard 3340: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3341: int i, ii, j, k, mi, d, kk;
1.228 brouard 3342: int ioffset=0;
1.131 brouard 3343: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3344: double **out;
3345: double lli; /* Individual log likelihood */
3346: double llt;
3347: int s1, s2;
1.228 brouard 3348: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
3349:
1.126 brouard 3350: double bbh, survp;
1.187 brouard 3351: double agexact;
1.214 brouard 3352: double agebegin, ageend;
1.126 brouard 3353: /*extern weight */
3354: /* We are differentiating ll according to initial status */
3355: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3356: /*for(i=1;i<imx;i++)
3357: printf(" %d\n",s[4][i]);
3358: */
3359: cov[1]=1.;
3360:
3361: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3362: ioffset=0;
3363: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3364: ioffset=2+nagesqr+cptcovage;
1.232 ! brouard 3365: /* Fixed */
1.224 brouard 3366: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.232 ! brouard 3367: /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
! 3368: for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
! 3369: 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)*/
! 3370: /* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
! 3371: /* cov[2+6]=covar[Tvar[6]][i]; */
! 3372: /* cov[2+6]=covar[2][i]; V2 */
! 3373: /* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
! 3374: /* cov[2+7]=covar[Tvar[7]][i]; */
! 3375: /* cov[2+7]=covar[7][i]; V7=V1*V2 */
! 3376: /* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
! 3377: /* cov[2+9]=covar[Tvar[9]][i]; */
! 3378: /* cov[2+9]=covar[1][i]; V1 */
1.225 brouard 3379: }
1.232 ! brouard 3380: /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
! 3381: /* 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?)*\/ */
! 3382: /* } */
1.231 brouard 3383: /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
3384: /* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
3385: /* } */
1.225 brouard 3386:
1.232 ! brouard 3387: /* Wave varying (but not age varying) */
1.226 brouard 3388: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.232 ! brouard 3389: for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
! 3390: cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarFind[k]]][i];
! 3391: }
! 3392: /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
1.231 brouard 3393: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
3394: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
1.232 ! brouard 3395: /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
! 3396: /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
1.231 brouard 3397: /* 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 3398: /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
! 3399: /* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
! 3400: /* /\* 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]); *\/ */
! 3401: /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
! 3402: /* } */
1.126 brouard 3403: for (ii=1;ii<=nlstate+ndeath;ii++)
1.231 brouard 3404: for (j=1;j<=nlstate+ndeath;j++){
3405: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3406: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3407: }
1.214 brouard 3408:
3409: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3410: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3411: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.231 brouard 3412: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3413: and mw[mi+1][i]. dh depends on stepm.*/
3414: newm=savm;
3415: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3416: cov[2]=agexact;
3417: if(nagesqr==1)
3418: cov[3]= agexact*agexact;
3419: for (kk=1; kk<=cptcovage;kk++) {
3420: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3421: }
3422: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3423: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3424: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3425: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3426: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3427: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3428: savm=oldm;
3429: oldm=newm;
1.126 brouard 3430: } /* end mult */
3431:
3432: s1=s[mw[mi][i]][i];
3433: s2=s[mw[mi+1][i]][i];
1.217 brouard 3434: /* if(s2==-1){ */
3435: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3436: /* /\* exit(1); *\/ */
3437: /* } */
1.126 brouard 3438: bbh=(double)bh[mi][i]/(double)stepm;
3439: /* bias is positive if real duration
3440: * is higher than the multiple of stepm and negative otherwise.
3441: */
3442: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.232 ! brouard 3443: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3444: } else if ( s2==-1 ) { /* alive */
1.232 ! brouard 3445: for (j=1,survp=0. ; j<=nlstate; j++)
! 3446: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
! 3447: lli= log(survp);
1.126 brouard 3448: }else if (mle==1){
1.232 ! brouard 3449: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3450: } else if(mle==2){
1.232 ! brouard 3451: 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 3452: } else if(mle==3){ /* exponential inter-extrapolation */
1.232 ! brouard 3453: 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 3454: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.232 ! brouard 3455: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3456: } else{ /* mle=0 back to 1 */
1.232 ! brouard 3457: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 3458: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3459: } /* End of if */
3460: ipmx +=1;
3461: sw += weight[i];
3462: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3463: /*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 3464: if(globpr){
1.232 ! brouard 3465: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3466: %11.6f %11.6f %11.6f ", \
1.232 ! brouard 3467: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
! 3468: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
! 3469: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
! 3470: llt +=ll[k]*gipmx/gsw;
! 3471: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
! 3472: }
! 3473: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3474: }
1.232 ! brouard 3475: } /* end of wave */
! 3476: } /* end of individual */
! 3477: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
! 3478: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
! 3479: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
! 3480: if(globpr==0){ /* First time we count the contributions and weights */
! 3481: gipmx=ipmx;
! 3482: gsw=sw;
! 3483: }
! 3484: return -l;
1.126 brouard 3485: }
3486:
3487:
3488: /*************** function likelione ***********/
3489: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3490: {
3491: /* This routine should help understanding what is done with
3492: the selection of individuals/waves and
3493: to check the exact contribution to the likelihood.
3494: Plotting could be done.
3495: */
3496: int k;
3497:
3498: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3499: strcpy(fileresilk,"ILK_");
1.202 brouard 3500: strcat(fileresilk,fileresu);
1.126 brouard 3501: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3502: printf("Problem with resultfile: %s\n", fileresilk);
3503: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3504: }
1.214 brouard 3505: 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");
3506: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3507: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3508: for(k=1; k<=nlstate; k++)
3509: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3510: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3511: }
3512:
3513: *fretone=(*funcone)(p);
3514: if(*globpri !=0){
3515: fclose(ficresilk);
1.205 brouard 3516: if (mle ==0)
3517: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3518: else if(mle >=1)
3519: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3520: 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 3521:
1.208 brouard 3522:
3523: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3524: 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 3525: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3526: }
1.207 brouard 3527: 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 3528: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3529: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3530: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3531: fflush(fichtm);
1.205 brouard 3532: }
1.126 brouard 3533: return;
3534: }
3535:
3536:
3537: /*********** Maximum Likelihood Estimation ***************/
3538:
3539: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3540: {
1.165 brouard 3541: int i,j, iter=0;
1.126 brouard 3542: double **xi;
3543: double fret;
3544: double fretone; /* Only one call to likelihood */
3545: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3546:
3547: #ifdef NLOPT
3548: int creturn;
3549: nlopt_opt opt;
3550: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3551: double *lb;
3552: double minf; /* the minimum objective value, upon return */
3553: double * p1; /* Shifted parameters from 0 instead of 1 */
3554: myfunc_data dinst, *d = &dinst;
3555: #endif
3556:
3557:
1.126 brouard 3558: xi=matrix(1,npar,1,npar);
3559: for (i=1;i<=npar;i++)
3560: for (j=1;j<=npar;j++)
3561: xi[i][j]=(i==j ? 1.0 : 0.0);
3562: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3563: strcpy(filerespow,"POW_");
1.126 brouard 3564: strcat(filerespow,fileres);
3565: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3566: printf("Problem with resultfile: %s\n", filerespow);
3567: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3568: }
3569: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3570: for (i=1;i<=nlstate;i++)
3571: for(j=1;j<=nlstate+ndeath;j++)
3572: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3573: fprintf(ficrespow,"\n");
1.162 brouard 3574: #ifdef POWELL
1.126 brouard 3575: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3576: #endif
1.126 brouard 3577:
1.162 brouard 3578: #ifdef NLOPT
3579: #ifdef NEWUOA
3580: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3581: #else
3582: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3583: #endif
3584: lb=vector(0,npar-1);
3585: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3586: nlopt_set_lower_bounds(opt, lb);
3587: nlopt_set_initial_step1(opt, 0.1);
3588:
3589: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3590: d->function = func;
3591: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3592: nlopt_set_min_objective(opt, myfunc, d);
3593: nlopt_set_xtol_rel(opt, ftol);
3594: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3595: printf("nlopt failed! %d\n",creturn);
3596: }
3597: else {
3598: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3599: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3600: iter=1; /* not equal */
3601: }
3602: nlopt_destroy(opt);
3603: #endif
1.126 brouard 3604: free_matrix(xi,1,npar,1,npar);
3605: fclose(ficrespow);
1.203 brouard 3606: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3607: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3608: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3609:
3610: }
3611:
3612: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3613: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3614: {
3615: double **a,**y,*x,pd;
1.203 brouard 3616: /* double **hess; */
1.164 brouard 3617: int i, j;
1.126 brouard 3618: int *indx;
3619:
3620: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3621: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3622: void lubksb(double **a, int npar, int *indx, double b[]) ;
3623: void ludcmp(double **a, int npar, int *indx, double *d) ;
3624: double gompertz(double p[]);
1.203 brouard 3625: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3626:
3627: printf("\nCalculation of the hessian matrix. Wait...\n");
3628: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3629: for (i=1;i<=npar;i++){
1.203 brouard 3630: printf("%d-",i);fflush(stdout);
3631: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3632:
3633: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3634:
3635: /* printf(" %f ",p[i]);
3636: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3637: }
3638:
3639: for (i=1;i<=npar;i++) {
3640: for (j=1;j<=npar;j++) {
3641: if (j>i) {
1.203 brouard 3642: printf(".%d-%d",i,j);fflush(stdout);
3643: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3644: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3645:
3646: hess[j][i]=hess[i][j];
3647: /*printf(" %lf ",hess[i][j]);*/
3648: }
3649: }
3650: }
3651: printf("\n");
3652: fprintf(ficlog,"\n");
3653:
3654: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3655: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3656:
3657: a=matrix(1,npar,1,npar);
3658: y=matrix(1,npar,1,npar);
3659: x=vector(1,npar);
3660: indx=ivector(1,npar);
3661: for (i=1;i<=npar;i++)
3662: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3663: ludcmp(a,npar,indx,&pd);
3664:
3665: for (j=1;j<=npar;j++) {
3666: for (i=1;i<=npar;i++) x[i]=0;
3667: x[j]=1;
3668: lubksb(a,npar,indx,x);
3669: for (i=1;i<=npar;i++){
3670: matcov[i][j]=x[i];
3671: }
3672: }
3673:
3674: printf("\n#Hessian matrix#\n");
3675: fprintf(ficlog,"\n#Hessian matrix#\n");
3676: for (i=1;i<=npar;i++) {
3677: for (j=1;j<=npar;j++) {
1.203 brouard 3678: printf("%.6e ",hess[i][j]);
3679: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3680: }
3681: printf("\n");
3682: fprintf(ficlog,"\n");
3683: }
3684:
1.203 brouard 3685: /* printf("\n#Covariance matrix#\n"); */
3686: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3687: /* for (i=1;i<=npar;i++) { */
3688: /* for (j=1;j<=npar;j++) { */
3689: /* printf("%.6e ",matcov[i][j]); */
3690: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3691: /* } */
3692: /* printf("\n"); */
3693: /* fprintf(ficlog,"\n"); */
3694: /* } */
3695:
1.126 brouard 3696: /* Recompute Inverse */
1.203 brouard 3697: /* for (i=1;i<=npar;i++) */
3698: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3699: /* ludcmp(a,npar,indx,&pd); */
3700:
3701: /* printf("\n#Hessian matrix recomputed#\n"); */
3702:
3703: /* for (j=1;j<=npar;j++) { */
3704: /* for (i=1;i<=npar;i++) x[i]=0; */
3705: /* x[j]=1; */
3706: /* lubksb(a,npar,indx,x); */
3707: /* for (i=1;i<=npar;i++){ */
3708: /* y[i][j]=x[i]; */
3709: /* printf("%.3e ",y[i][j]); */
3710: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3711: /* } */
3712: /* printf("\n"); */
3713: /* fprintf(ficlog,"\n"); */
3714: /* } */
3715:
3716: /* Verifying the inverse matrix */
3717: #ifdef DEBUGHESS
3718: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3719:
1.203 brouard 3720: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3721: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3722:
3723: for (j=1;j<=npar;j++) {
3724: for (i=1;i<=npar;i++){
1.203 brouard 3725: printf("%.2f ",y[i][j]);
3726: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3727: }
3728: printf("\n");
3729: fprintf(ficlog,"\n");
3730: }
1.203 brouard 3731: #endif
1.126 brouard 3732:
3733: free_matrix(a,1,npar,1,npar);
3734: free_matrix(y,1,npar,1,npar);
3735: free_vector(x,1,npar);
3736: free_ivector(indx,1,npar);
1.203 brouard 3737: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3738:
3739:
3740: }
3741:
3742: /*************** hessian matrix ****************/
3743: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3744: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3745: int i;
3746: int l=1, lmax=20;
1.203 brouard 3747: double k1,k2, res, fx;
1.132 brouard 3748: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3749: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3750: int k=0,kmax=10;
3751: double l1;
3752:
3753: fx=func(x);
3754: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3755: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3756: l1=pow(10,l);
3757: delts=delt;
3758: for(k=1 ; k <kmax; k=k+1){
3759: delt = delta*(l1*k);
3760: p2[theta]=x[theta] +delt;
1.145 brouard 3761: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3762: p2[theta]=x[theta]-delt;
3763: k2=func(p2)-fx;
3764: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3765: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3766:
1.203 brouard 3767: #ifdef DEBUGHESSII
1.126 brouard 3768: 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);
3769: 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);
3770: #endif
3771: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3772: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3773: k=kmax;
3774: }
3775: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3776: k=kmax; l=lmax*10;
1.126 brouard 3777: }
3778: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3779: delts=delt;
3780: }
1.203 brouard 3781: } /* End loop k */
1.126 brouard 3782: }
3783: delti[theta]=delts;
3784: return res;
3785:
3786: }
3787:
1.203 brouard 3788: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3789: {
3790: int i;
1.164 brouard 3791: int l=1, lmax=20;
1.126 brouard 3792: double k1,k2,k3,k4,res,fx;
1.132 brouard 3793: double p2[MAXPARM+1];
1.203 brouard 3794: int k, kmax=1;
3795: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3796:
3797: int firstime=0;
1.203 brouard 3798:
1.126 brouard 3799: fx=func(x);
1.203 brouard 3800: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3801: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3802: p2[thetai]=x[thetai]+delti[thetai]*k;
3803: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3804: k1=func(p2)-fx;
3805:
1.203 brouard 3806: p2[thetai]=x[thetai]+delti[thetai]*k;
3807: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3808: k2=func(p2)-fx;
3809:
1.203 brouard 3810: p2[thetai]=x[thetai]-delti[thetai]*k;
3811: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3812: k3=func(p2)-fx;
3813:
1.203 brouard 3814: p2[thetai]=x[thetai]-delti[thetai]*k;
3815: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3816: k4=func(p2)-fx;
1.203 brouard 3817: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3818: if(k1*k2*k3*k4 <0.){
1.208 brouard 3819: firstime=1;
1.203 brouard 3820: kmax=kmax+10;
1.208 brouard 3821: }
3822: if(kmax >=10 || firstime ==1){
1.218 brouard 3823: 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);
3824: 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 3825: 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);
3826: 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);
3827: }
3828: #ifdef DEBUGHESSIJ
3829: v1=hess[thetai][thetai];
3830: v2=hess[thetaj][thetaj];
3831: cv12=res;
3832: /* Computing eigen value of Hessian matrix */
3833: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3834: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3835: if ((lc2 <0) || (lc1 <0) ){
3836: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3837: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3838: 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);
3839: 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);
3840: }
1.126 brouard 3841: #endif
3842: }
3843: return res;
3844: }
3845:
1.203 brouard 3846: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3847: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3848: /* { */
3849: /* int i; */
3850: /* int l=1, lmax=20; */
3851: /* double k1,k2,k3,k4,res,fx; */
3852: /* double p2[MAXPARM+1]; */
3853: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3854: /* int k=0,kmax=10; */
3855: /* double l1; */
3856:
3857: /* fx=func(x); */
3858: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3859: /* l1=pow(10,l); */
3860: /* delts=delt; */
3861: /* for(k=1 ; k <kmax; k=k+1){ */
3862: /* delt = delti*(l1*k); */
3863: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3864: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3865: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3866: /* k1=func(p2)-fx; */
3867:
3868: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3869: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3870: /* k2=func(p2)-fx; */
3871:
3872: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3873: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3874: /* k3=func(p2)-fx; */
3875:
3876: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3877: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3878: /* k4=func(p2)-fx; */
3879: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3880: /* #ifdef DEBUGHESSIJ */
3881: /* 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); */
3882: /* 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); */
3883: /* #endif */
3884: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3885: /* k=kmax; */
3886: /* } */
3887: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3888: /* k=kmax; l=lmax*10; */
3889: /* } */
3890: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3891: /* delts=delt; */
3892: /* } */
3893: /* } /\* End loop k *\/ */
3894: /* } */
3895: /* delti[theta]=delts; */
3896: /* return res; */
3897: /* } */
3898:
3899:
1.126 brouard 3900: /************** Inverse of matrix **************/
3901: void ludcmp(double **a, int n, int *indx, double *d)
3902: {
3903: int i,imax,j,k;
3904: double big,dum,sum,temp;
3905: double *vv;
3906:
3907: vv=vector(1,n);
3908: *d=1.0;
3909: for (i=1;i<=n;i++) {
3910: big=0.0;
3911: for (j=1;j<=n;j++)
3912: if ((temp=fabs(a[i][j])) > big) big=temp;
3913: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3914: vv[i]=1.0/big;
3915: }
3916: for (j=1;j<=n;j++) {
3917: for (i=1;i<j;i++) {
3918: sum=a[i][j];
3919: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3920: a[i][j]=sum;
3921: }
3922: big=0.0;
3923: for (i=j;i<=n;i++) {
3924: sum=a[i][j];
3925: for (k=1;k<j;k++)
3926: sum -= a[i][k]*a[k][j];
3927: a[i][j]=sum;
3928: if ( (dum=vv[i]*fabs(sum)) >= big) {
3929: big=dum;
3930: imax=i;
3931: }
3932: }
3933: if (j != imax) {
3934: for (k=1;k<=n;k++) {
3935: dum=a[imax][k];
3936: a[imax][k]=a[j][k];
3937: a[j][k]=dum;
3938: }
3939: *d = -(*d);
3940: vv[imax]=vv[j];
3941: }
3942: indx[j]=imax;
3943: if (a[j][j] == 0.0) a[j][j]=TINY;
3944: if (j != n) {
3945: dum=1.0/(a[j][j]);
3946: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3947: }
3948: }
3949: free_vector(vv,1,n); /* Doesn't work */
3950: ;
3951: }
3952:
3953: void lubksb(double **a, int n, int *indx, double b[])
3954: {
3955: int i,ii=0,ip,j;
3956: double sum;
3957:
3958: for (i=1;i<=n;i++) {
3959: ip=indx[i];
3960: sum=b[ip];
3961: b[ip]=b[i];
3962: if (ii)
3963: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3964: else if (sum) ii=i;
3965: b[i]=sum;
3966: }
3967: for (i=n;i>=1;i--) {
3968: sum=b[i];
3969: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3970: b[i]=sum/a[i][i];
3971: }
3972: }
3973:
3974: void pstamp(FILE *fichier)
3975: {
1.196 brouard 3976: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3977: }
3978:
3979: /************ Frequencies ********************/
1.226 brouard 3980: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3981: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3982: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3983: { /* Some frequencies */
3984:
1.227 brouard 3985: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 3986: int iind=0, iage=0;
3987: int mi; /* Effective wave */
3988: int first;
3989: double ***freq; /* Frequencies */
3990: double *meanq;
3991: double **meanqt;
3992: double *pp, **prop, *posprop, *pospropt;
3993: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3994: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3995: double agebegin, ageend;
3996:
3997: pp=vector(1,nlstate);
3998: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3999: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
4000: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
4001: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
4002: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
4003: meanqt=matrix(1,lastpass,1,nqtveff);
4004: strcpy(fileresp,"P_");
4005: strcat(fileresp,fileresu);
4006: /*strcat(fileresphtm,fileresu);*/
4007: if((ficresp=fopen(fileresp,"w"))==NULL) {
4008: printf("Problem with prevalence resultfile: %s\n", fileresp);
4009: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
4010: exit(0);
4011: }
1.214 brouard 4012:
1.226 brouard 4013: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
4014: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
4015: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4016: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
4017: fflush(ficlog);
4018: exit(70);
4019: }
4020: else{
4021: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 4022: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4023: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4024: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4025: }
4026: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
1.214 brouard 4027:
1.226 brouard 4028: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
4029: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
4030: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4031: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
4032: fflush(ficlog);
4033: exit(70);
4034: }
4035: else{
4036: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 4037: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4038: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 4039: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4040: }
4041: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
1.214 brouard 4042:
1.226 brouard 4043: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4044: j1=0;
1.126 brouard 4045:
1.227 brouard 4046: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
4047: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 4048: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 4049:
1.226 brouard 4050: first=1;
1.220 brouard 4051:
1.226 brouard 4052: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
4053: reference=low_education V1=0,V2=0
4054: med_educ V1=1 V2=0,
4055: high_educ V1=0 V2=1
4056: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
4057: */
1.126 brouard 4058:
1.227 brouard 4059: 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 4060: posproptt=0.;
4061: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
4062: scanf("%d", i);*/
4063: for (i=-5; i<=nlstate+ndeath; i++)
4064: for (jk=-5; jk<=nlstate+ndeath; jk++)
1.231 brouard 4065: for(m=iagemin; m <= iagemax+3; m++)
4066: freq[i][jk][m]=0;
4067:
1.226 brouard 4068: for (i=1; i<=nlstate; i++) {
4069: for(m=iagemin; m <= iagemax+3; m++)
1.231 brouard 4070: prop[i][m]=0;
1.226 brouard 4071: posprop[i]=0;
4072: pospropt[i]=0;
4073: }
1.227 brouard 4074: /* for (z1=1; z1<= nqfveff; z1++) { */
4075: /* meanq[z1]+=0.; */
4076: /* for(m=1;m<=lastpass;m++){ */
4077: /* meanqt[m][z1]=0.; */
4078: /* } */
4079: /* } */
1.231 brouard 4080:
1.226 brouard 4081: dateintsum=0;
4082: k2cpt=0;
1.227 brouard 4083: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4084: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4085: bool=1;
1.227 brouard 4086: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
1.231 brouard 4087: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.227 brouard 4088: /* for (z1=1; z1<= nqfveff; z1++) { */
4089: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4090: /* } */
1.231 brouard 4091: for (z1=1; z1<=cptcoveff; z1++) {
4092: /* if(Tvaraff[z1] ==-20){ */
4093: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4094: /* }else if(Tvaraff[z1] ==-10){ */
4095: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4096: /* }else */
4097: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4098: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4099: bool=0;
4100: /* 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",
4101: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4102: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4103: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4104: } /* Onlyf fixed */
4105: } /* end z1 */
4106: } /* cptcovn > 0 */
1.227 brouard 4107: } /* end any */
4108: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.231 brouard 4109: /* for(m=firstpass; m<=lastpass; m++){ */
4110: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
4111: m=mw[mi][iind];
4112: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4113: for (z1=1; z1<=cptcoveff; z1++) {
4114: if( Fixed[Tmodelind[z1]]==1){
4115: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4116: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4117: bool=0;
4118: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4119: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4120: bool=0;
4121: }
4122: }
4123: }
4124: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4125: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4126: if(bool==1){
4127: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4128: and mw[mi+1][iind]. dh depends on stepm. */
4129: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4130: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4131: if(m >=firstpass && m <=lastpass){
4132: k2=anint[m][iind]+(mint[m][iind]/12.);
4133: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4134: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4135: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4136: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4137: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4138: if (m<lastpass) {
4139: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4140: /* 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]); */
4141: if(s[m][iind]==-1)
4142: 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.));
4143: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4144: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4145: 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 */
4146: }
4147: } /* end if between passes */
4148: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4149: dateintsum=dateintsum+k2;
4150: k2cpt++;
4151: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
4152: }
4153: } /* end bool 2 */
4154: } /* end m */
1.226 brouard 4155: } /* end bool */
4156: } /* end iind = 1 to imx */
4157: /* prop[s][age] is feeded for any initial and valid live state as well as
4158: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
1.231 brouard 4159:
4160:
1.226 brouard 4161: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4162: pstamp(ficresp);
1.227 brouard 4163: /* if (ncoveff>0) { */
4164: if (cptcoveff>0) {
1.226 brouard 4165: fprintf(ficresp, "\n#********** Variable ");
4166: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4167: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 brouard 4168: for (z1=1; z1<=cptcoveff; z1++){
1.231 brouard 4169: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4170: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4171: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4172: }
4173: fprintf(ficresp, "**********\n#");
4174: fprintf(ficresphtm, "**********</h3>\n");
4175: fprintf(ficresphtmfr, "**********</h3>\n");
4176: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4177: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4178: fprintf(ficlog, "**********\n");
4179: }
4180: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4181: for(i=1; i<=nlstate;i++) {
4182: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4183: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4184: }
4185: fprintf(ficresp, "\n");
4186: fprintf(ficresphtm, "\n");
1.231 brouard 4187:
1.226 brouard 4188: /* Header of frequency table by age */
4189: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4190: fprintf(ficresphtmfr,"<th>Age</th> ");
4191: for(jk=-1; jk <=nlstate+ndeath; jk++){
4192: for(m=-1; m <=nlstate+ndeath; m++){
1.231 brouard 4193: if(jk!=0 && m!=0)
4194: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
1.226 brouard 4195: }
4196: }
4197: fprintf(ficresphtmfr, "\n");
1.231 brouard 4198:
1.226 brouard 4199: /* For each age */
4200: for(iage=iagemin; iage <= iagemax+3; iage++){
4201: fprintf(ficresphtm,"<tr>");
4202: if(iage==iagemax+1){
1.231 brouard 4203: fprintf(ficlog,"1");
4204: fprintf(ficresphtmfr,"<tr><th>0</th> ");
1.226 brouard 4205: }else if(iage==iagemax+2){
1.231 brouard 4206: fprintf(ficlog,"0");
4207: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
1.226 brouard 4208: }else if(iage==iagemax+3){
1.231 brouard 4209: fprintf(ficlog,"Total");
4210: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.226 brouard 4211: }else{
1.231 brouard 4212: if(first==1){
4213: first=0;
4214: printf("See log file for details...\n");
4215: }
4216: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4217: fprintf(ficlog,"Age %d", iage);
1.226 brouard 4218: }
4219: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4220: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4221: pp[jk] += freq[jk][m][iage];
1.226 brouard 4222: }
4223: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4224: for(m=-1, pos=0; m <=0 ; m++)
4225: pos += freq[jk][m][iage];
4226: if(pp[jk]>=1.e-10){
4227: if(first==1){
4228: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4229: }
4230: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4231: }else{
4232: if(first==1)
4233: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4234: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4235: }
1.226 brouard 4236: }
1.231 brouard 4237:
1.226 brouard 4238: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4239: /* posprop[jk]=0; */
4240: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4241: pp[jk] += freq[jk][m][iage];
1.226 brouard 4242: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
1.231 brouard 4243:
1.226 brouard 4244: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
1.231 brouard 4245: pos += pp[jk]; /* pos is the total number of transitions until this age */
4246: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4247: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4248: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4249: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
1.226 brouard 4250: }
4251: for(jk=1; jk <=nlstate ; jk++){
1.231 brouard 4252: if(pos>=1.e-5){
4253: if(first==1)
4254: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4255: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4256: }else{
4257: if(first==1)
4258: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4259: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4260: }
4261: if( iage <= iagemax){
4262: if(pos>=1.e-5){
4263: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4264: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4265: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4266: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4267: }
4268: else{
4269: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4270: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4271: }
4272: }
4273: pospropt[jk] +=posprop[jk];
1.226 brouard 4274: } /* end loop jk */
4275: /* pospropt=0.; */
4276: for(jk=-1; jk <=nlstate+ndeath; jk++){
1.231 brouard 4277: for(m=-1; m <=nlstate+ndeath; m++){
4278: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4279: if(first==1){
4280: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4281: }
4282: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4283: }
4284: if(jk!=0 && m!=0)
4285: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4286: }
1.226 brouard 4287: } /* end loop jk */
4288: posproptt=0.;
4289: for(jk=1; jk <=nlstate; jk++){
1.231 brouard 4290: posproptt += pospropt[jk];
1.226 brouard 4291: }
4292: fprintf(ficresphtmfr,"</tr>\n ");
4293: if(iage <= iagemax){
1.231 brouard 4294: fprintf(ficresp,"\n");
4295: fprintf(ficresphtm,"</tr>\n");
1.226 brouard 4296: }
4297: if(first==1)
1.231 brouard 4298: printf("Others in log...\n");
1.226 brouard 4299: fprintf(ficlog,"\n");
4300: } /* end loop age iage */
4301: fprintf(ficresphtm,"<tr><th>Tot</th>");
4302: for(jk=1; jk <=nlstate ; jk++){
4303: if(posproptt < 1.e-5){
1.231 brouard 4304: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
1.226 brouard 4305: }else{
1.231 brouard 4306: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
1.226 brouard 4307: }
4308: }
4309: fprintf(ficresphtm,"</tr>\n");
4310: fprintf(ficresphtm,"</table>\n");
4311: fprintf(ficresphtmfr,"</table>\n");
4312: if(posproptt < 1.e-5){
4313: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4314: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4315: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4316: invalidvarcomb[j1]=1;
4317: }else{
4318: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4319: invalidvarcomb[j1]=0;
4320: }
4321: fprintf(ficresphtmfr,"</table>\n");
4322: } /* end selected combination of covariate j1 */
4323: dateintmean=dateintsum/k2cpt;
1.231 brouard 4324:
1.226 brouard 4325: fclose(ficresp);
4326: fclose(ficresphtm);
4327: fclose(ficresphtmfr);
4328: free_vector(meanq,1,nqfveff);
4329: free_matrix(meanqt,1,lastpass,1,nqtveff);
4330: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4331: free_vector(pospropt,1,nlstate);
4332: free_vector(posprop,1,nlstate);
4333: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4334: free_vector(pp,1,nlstate);
4335: /* End of freqsummary */
4336: }
1.126 brouard 4337:
4338: /************ Prevalence ********************/
1.227 brouard 4339: 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)
4340: {
4341: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4342: in each health status at the date of interview (if between dateprev1 and dateprev2).
4343: We still use firstpass and lastpass as another selection.
4344: */
1.126 brouard 4345:
1.227 brouard 4346: int i, m, jk, j1, bool, z1,j, iv;
4347: int mi; /* Effective wave */
4348: int iage;
4349: double agebegin, ageend;
4350:
4351: double **prop;
4352: double posprop;
4353: double y2; /* in fractional years */
4354: int iagemin, iagemax;
4355: int first; /** to stop verbosity which is redirected to log file */
4356:
4357: iagemin= (int) agemin;
4358: iagemax= (int) agemax;
4359: /*pp=vector(1,nlstate);*/
4360: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4361: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4362: j1=0;
1.222 brouard 4363:
1.227 brouard 4364: /*j=cptcoveff;*/
4365: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4366:
1.227 brouard 4367: first=1;
4368: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4369: for (i=1; i<=nlstate; i++)
4370: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4371: prop[i][iage]=0.0;
4372: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4373: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4374: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4375:
4376: for (i=1; i<=imx; i++) { /* Each individual */
4377: bool=1;
4378: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4379: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4380: m=mw[mi][i];
4381: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4382: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4383: for (z1=1; z1<=cptcoveff; z1++){
4384: if( Fixed[Tmodelind[z1]]==1){
4385: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4386: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4387: bool=0;
4388: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4389: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4390: bool=0;
4391: }
4392: }
4393: if(bool==1){ /* Otherwise we skip that wave/person */
4394: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4395: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4396: if(m >=firstpass && m <=lastpass){
4397: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4398: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4399: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4400: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4401: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4402: 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);
4403: exit(1);
4404: }
4405: if (s[m][i]>0 && s[m][i]<=nlstate) {
4406: /*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]]);*/
4407: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4408: prop[s[m][i]][iagemax+3] += weight[i];
4409: } /* end valid statuses */
4410: } /* end selection of dates */
4411: } /* end selection of waves */
4412: } /* end bool */
4413: } /* end wave */
4414: } /* end individual */
4415: for(i=iagemin; i <= iagemax+3; i++){
4416: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4417: posprop += prop[jk][i];
4418: }
4419:
4420: for(jk=1; jk <=nlstate ; jk++){
4421: if( i <= iagemax){
4422: if(posprop>=1.e-5){
4423: probs[i][jk][j1]= prop[jk][i]/posprop;
4424: } else{
4425: if(first==1){
4426: first=0;
4427: 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]);
4428: }
4429: }
4430: }
4431: }/* end jk */
4432: }/* end i */
1.222 brouard 4433: /*} *//* end i1 */
1.227 brouard 4434: } /* end j1 */
1.222 brouard 4435:
1.227 brouard 4436: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4437: /*free_vector(pp,1,nlstate);*/
4438: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4439: } /* End of prevalence */
1.126 brouard 4440:
4441: /************* Waves Concatenation ***************/
4442:
4443: 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)
4444: {
4445: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4446: Death is a valid wave (if date is known).
4447: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4448: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4449: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4450: */
1.126 brouard 4451:
1.224 brouard 4452: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4453: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4454: double sum=0., jmean=0.;*/
1.224 brouard 4455: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4456: int j, k=0,jk, ju, jl;
4457: double sum=0.;
4458: first=0;
1.214 brouard 4459: firstwo=0;
1.217 brouard 4460: firsthree=0;
1.218 brouard 4461: firstfour=0;
1.164 brouard 4462: jmin=100000;
1.126 brouard 4463: jmax=-1;
4464: jmean=0.;
1.224 brouard 4465:
4466: /* Treating live states */
1.214 brouard 4467: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4468: mi=0; /* First valid wave */
1.227 brouard 4469: mli=0; /* Last valid wave */
1.126 brouard 4470: m=firstpass;
1.214 brouard 4471: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4472: 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 */
4473: mli=m-1;/* mw[++mi][i]=m-1; */
4474: }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 */
4475: mw[++mi][i]=m;
4476: mli=m;
1.224 brouard 4477: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4478: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4479: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4480: }
1.227 brouard 4481: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4482: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4483: break;
1.224 brouard 4484: #else
1.227 brouard 4485: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4486: if(firsthree == 0){
4487: 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);
4488: firsthree=1;
4489: }
4490: 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);
4491: mw[++mi][i]=m;
4492: mli=m;
4493: }
4494: if(s[m][i]==-2){ /* Vital status is really unknown */
4495: nbwarn++;
4496: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4497: 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);
4498: 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);
4499: }
4500: break;
4501: }
4502: break;
1.224 brouard 4503: #endif
1.227 brouard 4504: }/* End m >= lastpass */
1.126 brouard 4505: }/* end while */
1.224 brouard 4506:
1.227 brouard 4507: /* 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 4508: /* After last pass */
1.224 brouard 4509: /* Treating death states */
1.214 brouard 4510: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4511: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4512: /* } */
1.126 brouard 4513: mi++; /* Death is another wave */
4514: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4515: /* Only death is a correct wave */
1.126 brouard 4516: mw[mi][i]=m;
1.224 brouard 4517: }
4518: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4519: 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 4520: /* m++; */
4521: /* mi++; */
4522: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4523: /* mw[mi][i]=m; */
1.218 brouard 4524: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4525: 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 */
4526: nbwarn++;
4527: if(firstfiv==0){
4528: 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 );
4529: firstfiv=1;
4530: }else{
4531: 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 );
4532: }
4533: }else{ /* Death occured afer last wave potential bias */
4534: nberr++;
4535: if(firstwo==0){
4536: 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 );
4537: firstwo=1;
4538: }
4539: 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 );
4540: }
1.218 brouard 4541: }else{ /* end date of interview is known */
1.227 brouard 4542: /* death is known but not confirmed by death status at any wave */
4543: if(firstfour==0){
4544: 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 );
4545: firstfour=1;
4546: }
4547: 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 4548: }
1.224 brouard 4549: } /* end if date of death is known */
4550: #endif
4551: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4552: /* wav[i]=mw[mi][i]; */
1.126 brouard 4553: if(mi==0){
4554: nbwarn++;
4555: if(first==0){
1.227 brouard 4556: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4557: first=1;
1.126 brouard 4558: }
4559: if(first==1){
1.227 brouard 4560: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4561: }
4562: } /* end mi==0 */
4563: } /* End individuals */
1.214 brouard 4564: /* wav and mw are no more changed */
1.223 brouard 4565:
1.214 brouard 4566:
1.126 brouard 4567: for(i=1; i<=imx; i++){
4568: for(mi=1; mi<wav[i];mi++){
4569: if (stepm <=0)
1.227 brouard 4570: dh[mi][i]=1;
1.126 brouard 4571: else{
1.227 brouard 4572: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4573: if (agedc[i] < 2*AGESUP) {
4574: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4575: if(j==0) j=1; /* Survives at least one month after exam */
4576: else if(j<0){
4577: nberr++;
4578: 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]);
4579: j=1; /* Temporary Dangerous patch */
4580: 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);
4581: 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]);
4582: 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);
4583: }
4584: k=k+1;
4585: if (j >= jmax){
4586: jmax=j;
4587: ijmax=i;
4588: }
4589: if (j <= jmin){
4590: jmin=j;
4591: ijmin=i;
4592: }
4593: sum=sum+j;
4594: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4595: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4596: }
4597: }
4598: else{
4599: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4600: /* 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 4601:
1.227 brouard 4602: k=k+1;
4603: if (j >= jmax) {
4604: jmax=j;
4605: ijmax=i;
4606: }
4607: else if (j <= jmin){
4608: jmin=j;
4609: ijmin=i;
4610: }
4611: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4612: /*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]);*/
4613: if(j<0){
4614: nberr++;
4615: 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]);
4616: 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]);
4617: }
4618: sum=sum+j;
4619: }
4620: jk= j/stepm;
4621: jl= j -jk*stepm;
4622: ju= j -(jk+1)*stepm;
4623: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4624: if(jl==0){
4625: dh[mi][i]=jk;
4626: bh[mi][i]=0;
4627: }else{ /* We want a negative bias in order to only have interpolation ie
4628: * to avoid the price of an extra matrix product in likelihood */
4629: dh[mi][i]=jk+1;
4630: bh[mi][i]=ju;
4631: }
4632: }else{
4633: if(jl <= -ju){
4634: dh[mi][i]=jk;
4635: bh[mi][i]=jl; /* bias is positive if real duration
4636: * is higher than the multiple of stepm and negative otherwise.
4637: */
4638: }
4639: else{
4640: dh[mi][i]=jk+1;
4641: bh[mi][i]=ju;
4642: }
4643: if(dh[mi][i]==0){
4644: dh[mi][i]=1; /* At least one step */
4645: bh[mi][i]=ju; /* At least one step */
4646: /* 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);*/
4647: }
4648: } /* end if mle */
1.126 brouard 4649: }
4650: } /* end wave */
4651: }
4652: jmean=sum/k;
4653: 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 4654: 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 4655: }
1.126 brouard 4656:
4657: /*********** Tricode ****************************/
1.220 brouard 4658: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4659: {
1.144 brouard 4660: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4661: /* 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 4662: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4663: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4664: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4665: */
1.130 brouard 4666:
1.145 brouard 4667: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4668: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4669: int cptcode=0; /* Modality max of covariates j */
4670: int modmincovj=0; /* Modality min of covariates j */
4671:
4672:
1.220 brouard 4673: /* cptcoveff=0; */
1.224 brouard 4674: /* *cptcov=0; */
1.126 brouard 4675:
1.144 brouard 4676: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4677:
1.224 brouard 4678: /* Loop on covariates without age and products and no quantitative variable */
4679: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4680: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4681: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4682: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4683: switch(Fixed[k]) {
4684: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
1.231 brouard 4685: 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*/
4686: ij=(int)(covar[Tvar[k]][i]);
4687: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4688: * If product of Vn*Vm, still boolean *:
4689: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4690: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4691: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4692: modality of the nth covariate of individual i. */
4693: if (ij > modmaxcovj)
4694: modmaxcovj=ij;
4695: else if (ij < modmincovj)
4696: modmincovj=ij;
4697: if ((ij < -1) && (ij > NCOVMAX)){
4698: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4699: exit(1);
4700: }else
4701: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4702: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4703: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4704: /* getting the maximum value of the modality of the covariate
4705: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4706: female ies 1, then modmaxcovj=1.
4707: */
4708: } /* end for loop on individuals i */
4709: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4710: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4711: cptcode=modmaxcovj;
4712: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4713: /*for (i=0; i<=cptcode; i++) {*/
4714: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4715: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4716: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4717: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4718: if( j != -1){
4719: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4720: covariate for which somebody answered excluding
4721: undefined. Usually 2: 0 and 1. */
4722: }
4723: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4724: covariate for which somebody answered including
4725: undefined. Usually 3: -1, 0 and 1. */
4726: } /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4727: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4728: } /* Ndum[-1] number of undefined modalities */
4729:
4730: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4731: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
4732: /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
4733: /* modmincovj=3; modmaxcovj = 7; */
4734: /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
4735: /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
4736: /* defining two dummy variables: variables V1_1 and V1_2.*/
4737: /* nbcode[Tvar[j]][ij]=k; */
4738: /* nbcode[Tvar[j]][1]=0; */
4739: /* nbcode[Tvar[j]][2]=1; */
4740: /* nbcode[Tvar[j]][3]=2; */
4741: /* To be continued (not working yet). */
4742: ij=0; /* ij is similar to i but can jump over null modalities */
4743: 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*/
4744: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4745: break;
4746: }
4747: ij++;
4748: 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*/
4749: cptcode = ij; /* New max modality for covar j */
4750: } /* end of loop on modality i=-1 to 1 or more */
4751: break;
1.227 brouard 4752: case 1: /* Testing on varying covariate, could be simple and
4753: * should look at waves or product of fixed *
4754: * varying. No time to test -1, assuming 0 and 1 only */
1.231 brouard 4755: ij=0;
4756: for(i=0; i<=1;i++){
4757: nbcode[Tvar[k]][++ij]=i;
4758: }
4759: break;
1.227 brouard 4760: default:
1.231 brouard 4761: break;
1.227 brouard 4762: } /* end switch */
4763: } /* end dummy test */
1.225 brouard 4764:
1.192 brouard 4765: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4766: /* /\*recode from 0 *\/ */
4767: /* k is a modality. If we have model=V1+V1*sex */
4768: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4769: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4770: /* } */
4771: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4772: /* if (ij > ncodemax[j]) { */
4773: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4774: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4775: /* break; */
4776: /* } */
4777: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4778: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4779:
1.225 brouard 4780: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4781: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4782: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4783: /* 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 4784: 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 */
4785: 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 */
4786: /* 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 4787: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4788:
4789: ij=0;
1.227 brouard 4790: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4791: 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 4792: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4793: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4794: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4795: /* If product not in single variable we don't print results */
1.225 brouard 4796: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.230 brouard 4797: ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
4798: 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*/
4799: 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 4800: 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 4801: if(Fixed[k]!=0)
4802: anyvaryingduminmodel=1;
1.231 brouard 4803: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
4804: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
4805: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
4806: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
4807: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
4808: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
1.227 brouard 4809: }
1.225 brouard 4810: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4811: /* ij--; */
4812: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4813: *cptcov=ij; /*Number of total real effective covariates: effective
1.231 brouard 4814: * because they can be excluded from the model and real
4815: * if in the model but excluded because missing values, but how to get k from ij?*/
1.227 brouard 4816: for(j=ij+1; j<= cptcovt; j++){
4817: Tvaraff[j]=0;
4818: Tmodelind[j]=0;
4819: }
1.228 brouard 4820: for(j=ntveff+1; j<= cptcovt; j++){
4821: TmodelInvind[j]=0;
4822: }
1.227 brouard 4823: /* To be sorted */
4824: ;
1.126 brouard 4825: }
4826:
1.145 brouard 4827:
1.126 brouard 4828: /*********** Health Expectancies ****************/
4829:
1.127 brouard 4830: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 4831:
4832: {
4833: /* Health expectancies, no variances */
1.164 brouard 4834: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4835: int nhstepma, nstepma; /* Decreasing with age */
4836: double age, agelim, hf;
4837: double ***p3mat;
4838: double eip;
4839:
4840: pstamp(ficreseij);
4841: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4842: fprintf(ficreseij,"# Age");
4843: for(i=1; i<=nlstate;i++){
4844: for(j=1; j<=nlstate;j++){
4845: fprintf(ficreseij," e%1d%1d ",i,j);
4846: }
4847: fprintf(ficreseij," e%1d. ",i);
4848: }
4849: fprintf(ficreseij,"\n");
4850:
4851:
4852: if(estepm < stepm){
4853: printf ("Problem %d lower than %d\n",estepm, stepm);
4854: }
4855: else hstepm=estepm;
4856: /* We compute the life expectancy from trapezoids spaced every estepm months
4857: * This is mainly to measure the difference between two models: for example
4858: * if stepm=24 months pijx are given only every 2 years and by summing them
4859: * we are calculating an estimate of the Life Expectancy assuming a linear
4860: * progression in between and thus overestimating or underestimating according
4861: * to the curvature of the survival function. If, for the same date, we
4862: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4863: * to compare the new estimate of Life expectancy with the same linear
4864: * hypothesis. A more precise result, taking into account a more precise
4865: * curvature will be obtained if estepm is as small as stepm. */
4866:
4867: /* For example we decided to compute the life expectancy with the smallest unit */
4868: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4869: nhstepm is the number of hstepm from age to agelim
4870: nstepm is the number of stepm from age to agelin.
4871: Look at hpijx to understand the reason of that which relies in memory size
4872: and note for a fixed period like estepm months */
4873: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4874: survival function given by stepm (the optimization length). Unfortunately it
4875: means that if the survival funtion is printed only each two years of age and if
4876: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4877: results. So we changed our mind and took the option of the best precision.
4878: */
4879: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4880:
4881: agelim=AGESUP;
4882: /* If stepm=6 months */
4883: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4884: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4885:
4886: /* nhstepm age range expressed in number of stepm */
4887: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4888: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4889: /* if (stepm >= YEARM) hstepm=1;*/
4890: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4891: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4892:
4893: for (age=bage; age<=fage; age ++){
4894: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4895: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4896: /* if (stepm >= YEARM) hstepm=1;*/
4897: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4898:
4899: /* If stepm=6 months */
4900: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4901: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4902:
4903: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4904:
4905: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4906:
4907: printf("%d|",(int)age);fflush(stdout);
4908: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4909:
4910: /* Computing expectancies */
4911: for(i=1; i<=nlstate;i++)
4912: for(j=1; j<=nlstate;j++)
4913: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4914: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4915:
4916: /* 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]);*/
4917:
4918: }
4919:
4920: fprintf(ficreseij,"%3.0f",age );
4921: for(i=1; i<=nlstate;i++){
4922: eip=0;
4923: for(j=1; j<=nlstate;j++){
4924: eip +=eij[i][j][(int)age];
4925: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4926: }
4927: fprintf(ficreseij,"%9.4f", eip );
4928: }
4929: fprintf(ficreseij,"\n");
4930:
4931: }
4932: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4933: printf("\n");
4934: fprintf(ficlog,"\n");
4935:
4936: }
4937:
1.127 brouard 4938: 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[] )
1.126 brouard 4939:
4940: {
4941: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4942: to initial status i, ei. .
1.126 brouard 4943: */
4944: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4945: int nhstepma, nstepma; /* Decreasing with age */
4946: double age, agelim, hf;
4947: double ***p3matp, ***p3matm, ***varhe;
4948: double **dnewm,**doldm;
4949: double *xp, *xm;
4950: double **gp, **gm;
4951: double ***gradg, ***trgradg;
4952: int theta;
4953:
4954: double eip, vip;
4955:
4956: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4957: xp=vector(1,npar);
4958: xm=vector(1,npar);
4959: dnewm=matrix(1,nlstate*nlstate,1,npar);
4960: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4961:
4962: pstamp(ficresstdeij);
4963: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4964: fprintf(ficresstdeij,"# Age");
4965: for(i=1; i<=nlstate;i++){
4966: for(j=1; j<=nlstate;j++)
4967: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4968: fprintf(ficresstdeij," e%1d. ",i);
4969: }
4970: fprintf(ficresstdeij,"\n");
4971:
4972: pstamp(ficrescveij);
4973: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4974: fprintf(ficrescveij,"# Age");
4975: for(i=1; i<=nlstate;i++)
4976: for(j=1; j<=nlstate;j++){
4977: cptj= (j-1)*nlstate+i;
4978: for(i2=1; i2<=nlstate;i2++)
4979: for(j2=1; j2<=nlstate;j2++){
4980: cptj2= (j2-1)*nlstate+i2;
4981: if(cptj2 <= cptj)
4982: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4983: }
4984: }
4985: fprintf(ficrescveij,"\n");
4986:
4987: if(estepm < stepm){
4988: printf ("Problem %d lower than %d\n",estepm, stepm);
4989: }
4990: else hstepm=estepm;
4991: /* We compute the life expectancy from trapezoids spaced every estepm months
4992: * This is mainly to measure the difference between two models: for example
4993: * if stepm=24 months pijx are given only every 2 years and by summing them
4994: * we are calculating an estimate of the Life Expectancy assuming a linear
4995: * progression in between and thus overestimating or underestimating according
4996: * to the curvature of the survival function. If, for the same date, we
4997: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4998: * to compare the new estimate of Life expectancy with the same linear
4999: * hypothesis. A more precise result, taking into account a more precise
5000: * curvature will be obtained if estepm is as small as stepm. */
5001:
5002: /* For example we decided to compute the life expectancy with the smallest unit */
5003: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5004: nhstepm is the number of hstepm from age to agelim
5005: nstepm is the number of stepm from age to agelin.
5006: Look at hpijx to understand the reason of that which relies in memory size
5007: and note for a fixed period like estepm months */
5008: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
5009: survival function given by stepm (the optimization length). Unfortunately it
5010: means that if the survival funtion is printed only each two years of age and if
5011: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5012: results. So we changed our mind and took the option of the best precision.
5013: */
5014: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5015:
5016: /* If stepm=6 months */
5017: /* nhstepm age range expressed in number of stepm */
5018: agelim=AGESUP;
5019: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
5020: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5021: /* if (stepm >= YEARM) hstepm=1;*/
5022: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5023:
5024: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5025: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5026: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
5027: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
5028: gp=matrix(0,nhstepm,1,nlstate*nlstate);
5029: gm=matrix(0,nhstepm,1,nlstate*nlstate);
5030:
5031: for (age=bage; age<=fage; age ++){
5032: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
5033: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
5034: /* if (stepm >= YEARM) hstepm=1;*/
5035: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 5036:
1.126 brouard 5037: /* If stepm=6 months */
5038: /* Computed by stepm unit matrices, product of hstepma matrices, stored
5039: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
5040:
5041: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 5042:
1.126 brouard 5043: /* Computing Variances of health expectancies */
5044: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
5045: decrease memory allocation */
5046: for(theta=1; theta <=npar; theta++){
5047: for(i=1; i<=npar; i++){
1.222 brouard 5048: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5049: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 5050: }
5051: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
5052: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 5053:
1.126 brouard 5054: for(j=1; j<= nlstate; j++){
1.222 brouard 5055: for(i=1; i<=nlstate; i++){
5056: for(h=0; h<=nhstepm-1; h++){
5057: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
5058: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
5059: }
5060: }
1.126 brouard 5061: }
1.218 brouard 5062:
1.126 brouard 5063: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 5064: for(h=0; h<=nhstepm-1; h++){
5065: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
5066: }
1.126 brouard 5067: }/* End theta */
5068:
5069:
5070: for(h=0; h<=nhstepm-1; h++)
5071: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 5072: for(theta=1; theta <=npar; theta++)
5073: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 5074:
1.218 brouard 5075:
1.222 brouard 5076: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 5077: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 5078: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5079:
1.222 brouard 5080: printf("%d|",(int)age);fflush(stdout);
5081: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5082: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5083: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5084: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5085: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5086: for(ij=1;ij<=nlstate*nlstate;ij++)
5087: for(ji=1;ji<=nlstate*nlstate;ji++)
5088: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5089: }
5090: }
1.218 brouard 5091:
1.126 brouard 5092: /* Computing expectancies */
5093: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
5094: for(i=1; i<=nlstate;i++)
5095: for(j=1; j<=nlstate;j++)
1.222 brouard 5096: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5097: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5098:
1.222 brouard 5099: /* 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 5100:
1.222 brouard 5101: }
1.218 brouard 5102:
1.126 brouard 5103: fprintf(ficresstdeij,"%3.0f",age );
5104: for(i=1; i<=nlstate;i++){
5105: eip=0.;
5106: vip=0.;
5107: for(j=1; j<=nlstate;j++){
1.222 brouard 5108: eip += eij[i][j][(int)age];
5109: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5110: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5111: 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 5112: }
5113: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5114: }
5115: fprintf(ficresstdeij,"\n");
1.218 brouard 5116:
1.126 brouard 5117: fprintf(ficrescveij,"%3.0f",age );
5118: for(i=1; i<=nlstate;i++)
5119: for(j=1; j<=nlstate;j++){
1.222 brouard 5120: cptj= (j-1)*nlstate+i;
5121: for(i2=1; i2<=nlstate;i2++)
5122: for(j2=1; j2<=nlstate;j2++){
5123: cptj2= (j2-1)*nlstate+i2;
5124: if(cptj2 <= cptj)
5125: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5126: }
1.126 brouard 5127: }
5128: fprintf(ficrescveij,"\n");
1.218 brouard 5129:
1.126 brouard 5130: }
5131: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5132: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5133: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5134: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5135: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5136: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5137: printf("\n");
5138: fprintf(ficlog,"\n");
1.218 brouard 5139:
1.126 brouard 5140: free_vector(xm,1,npar);
5141: free_vector(xp,1,npar);
5142: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5143: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5144: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5145: }
1.218 brouard 5146:
1.126 brouard 5147: /************ Variance ******************/
1.209 brouard 5148: 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[])
1.218 brouard 5149: {
5150: /* Variance of health expectancies */
5151: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5152: /* double **newm;*/
5153: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5154:
5155: /* int movingaverage(); */
5156: double **dnewm,**doldm;
5157: double **dnewmp,**doldmp;
5158: int i, j, nhstepm, hstepm, h, nstepm ;
5159: int k;
5160: double *xp;
5161: double **gp, **gm; /* for var eij */
5162: double ***gradg, ***trgradg; /*for var eij */
5163: double **gradgp, **trgradgp; /* for var p point j */
5164: double *gpp, *gmp; /* for var p point j */
5165: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5166: double ***p3mat;
5167: double age,agelim, hf;
5168: /* double ***mobaverage; */
5169: int theta;
5170: char digit[4];
5171: char digitp[25];
5172:
5173: char fileresprobmorprev[FILENAMELENGTH];
5174:
5175: if(popbased==1){
5176: if(mobilav!=0)
5177: strcpy(digitp,"-POPULBASED-MOBILAV_");
5178: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5179: }
5180: else
5181: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5182:
1.218 brouard 5183: /* if (mobilav!=0) { */
5184: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5185: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5186: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5187: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5188: /* } */
5189: /* } */
5190:
5191: strcpy(fileresprobmorprev,"PRMORPREV-");
5192: sprintf(digit,"%-d",ij);
5193: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5194: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5195: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5196: strcat(fileresprobmorprev,fileresu);
5197: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5198: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5199: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5200: }
5201: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5202: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5203: pstamp(ficresprobmorprev);
5204: 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);
5205: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5206: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5207: fprintf(ficresprobmorprev," p.%-d SE",j);
5208: for(i=1; i<=nlstate;i++)
5209: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5210: }
5211: fprintf(ficresprobmorprev,"\n");
5212:
5213: fprintf(ficgp,"\n# Routine varevsij");
5214: fprintf(ficgp,"\nunset title \n");
5215: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5216: 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");
5217: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5218: /* } */
5219: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5220: pstamp(ficresvij);
5221: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5222: if(popbased==1)
5223: 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);
5224: else
5225: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5226: fprintf(ficresvij,"# Age");
5227: for(i=1; i<=nlstate;i++)
5228: for(j=1; j<=nlstate;j++)
5229: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5230: fprintf(ficresvij,"\n");
5231:
5232: xp=vector(1,npar);
5233: dnewm=matrix(1,nlstate,1,npar);
5234: doldm=matrix(1,nlstate,1,nlstate);
5235: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5236: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5237:
5238: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5239: gpp=vector(nlstate+1,nlstate+ndeath);
5240: gmp=vector(nlstate+1,nlstate+ndeath);
5241: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5242:
1.218 brouard 5243: if(estepm < stepm){
5244: printf ("Problem %d lower than %d\n",estepm, stepm);
5245: }
5246: else hstepm=estepm;
5247: /* For example we decided to compute the life expectancy with the smallest unit */
5248: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5249: nhstepm is the number of hstepm from age to agelim
5250: nstepm is the number of stepm from age to agelim.
5251: Look at function hpijx to understand why because of memory size limitations,
5252: we decided (b) to get a life expectancy respecting the most precise curvature of the
5253: survival function given by stepm (the optimization length). Unfortunately it
5254: means that if the survival funtion is printed every two years of age and if
5255: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5256: results. So we changed our mind and took the option of the best precision.
5257: */
5258: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5259: agelim = AGESUP;
5260: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5261: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5262: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5263: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5264: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5265: gp=matrix(0,nhstepm,1,nlstate);
5266: gm=matrix(0,nhstepm,1,nlstate);
5267:
5268:
5269: for(theta=1; theta <=npar; theta++){
5270: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5271: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5272: }
5273:
5274: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5275:
5276: if (popbased==1) {
5277: if(mobilav ==0){
5278: for(i=1; i<=nlstate;i++)
5279: prlim[i][i]=probs[(int)age][i][ij];
5280: }else{ /* mobilav */
5281: for(i=1; i<=nlstate;i++)
5282: prlim[i][i]=mobaverage[(int)age][i][ij];
5283: }
5284: }
5285:
5286: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5287: for(j=1; j<= nlstate; j++){
5288: for(h=0; h<=nhstepm; h++){
5289: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5290: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5291: }
5292: }
5293: /* Next for computing probability of death (h=1 means
5294: computed over hstepm matrices product = hstepm*stepm months)
5295: as a weighted average of prlim.
5296: */
5297: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5298: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5299: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5300: }
5301: /* end probability of death */
5302:
5303: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5304: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5305:
5306: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5307:
5308: if (popbased==1) {
5309: if(mobilav ==0){
5310: for(i=1; i<=nlstate;i++)
5311: prlim[i][i]=probs[(int)age][i][ij];
5312: }else{ /* mobilav */
5313: for(i=1; i<=nlstate;i++)
5314: prlim[i][i]=mobaverage[(int)age][i][ij];
5315: }
5316: }
5317:
5318: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5319:
5320: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5321: for(h=0; h<=nhstepm; h++){
5322: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5323: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5324: }
5325: }
5326: /* This for computing probability of death (h=1 means
5327: computed over hstepm matrices product = hstepm*stepm months)
5328: as a weighted average of prlim.
5329: */
5330: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5331: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5332: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5333: }
5334: /* end probability of death */
5335:
5336: for(j=1; j<= nlstate; j++) /* vareij */
5337: for(h=0; h<=nhstepm; h++){
5338: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5339: }
5340:
5341: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5342: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5343: }
5344:
5345: } /* End theta */
5346:
5347: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5348:
5349: for(h=0; h<=nhstepm; h++) /* veij */
5350: for(j=1; j<=nlstate;j++)
5351: for(theta=1; theta <=npar; theta++)
5352: trgradg[h][j][theta]=gradg[h][theta][j];
5353:
5354: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5355: for(theta=1; theta <=npar; theta++)
5356: trgradgp[j][theta]=gradgp[theta][j];
5357:
5358:
5359: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5360: for(i=1;i<=nlstate;i++)
5361: for(j=1;j<=nlstate;j++)
5362: vareij[i][j][(int)age] =0.;
5363:
5364: for(h=0;h<=nhstepm;h++){
5365: for(k=0;k<=nhstepm;k++){
5366: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5367: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5368: for(i=1;i<=nlstate;i++)
5369: for(j=1;j<=nlstate;j++)
5370: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5371: }
5372: }
5373:
5374: /* pptj */
5375: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5376: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5377: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5378: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5379: varppt[j][i]=doldmp[j][i];
5380: /* end ppptj */
5381: /* x centered again */
5382:
5383: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5384:
5385: if (popbased==1) {
5386: if(mobilav ==0){
5387: for(i=1; i<=nlstate;i++)
5388: prlim[i][i]=probs[(int)age][i][ij];
5389: }else{ /* mobilav */
5390: for(i=1; i<=nlstate;i++)
5391: prlim[i][i]=mobaverage[(int)age][i][ij];
5392: }
5393: }
5394:
5395: /* This for computing probability of death (h=1 means
5396: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5397: as a weighted average of prlim.
5398: */
5399: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5400: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5401: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5402: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5403: }
5404: /* end probability of death */
5405:
5406: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5407: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5408: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5409: for(i=1; i<=nlstate;i++){
5410: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5411: }
5412: }
5413: fprintf(ficresprobmorprev,"\n");
5414:
5415: fprintf(ficresvij,"%.0f ",age );
5416: for(i=1; i<=nlstate;i++)
5417: for(j=1; j<=nlstate;j++){
5418: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5419: }
5420: fprintf(ficresvij,"\n");
5421: free_matrix(gp,0,nhstepm,1,nlstate);
5422: free_matrix(gm,0,nhstepm,1,nlstate);
5423: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5424: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5425: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5426: } /* End age */
5427: free_vector(gpp,nlstate+1,nlstate+ndeath);
5428: free_vector(gmp,nlstate+1,nlstate+ndeath);
5429: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5430: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5431: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5432: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5433: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5434: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5435: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5436: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5437: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5438: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5439: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5440: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5441: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5442: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5443: 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);
5444: /* 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 5445: */
1.218 brouard 5446: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5447: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5448:
1.218 brouard 5449: free_vector(xp,1,npar);
5450: free_matrix(doldm,1,nlstate,1,nlstate);
5451: free_matrix(dnewm,1,nlstate,1,npar);
5452: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5453: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5454: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5455: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5456: fclose(ficresprobmorprev);
5457: fflush(ficgp);
5458: fflush(fichtm);
5459: } /* end varevsij */
1.126 brouard 5460:
5461: /************ Variance of prevlim ******************/
1.209 brouard 5462: 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[])
1.126 brouard 5463: {
1.205 brouard 5464: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5465: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5466:
1.126 brouard 5467: double **dnewm,**doldm;
5468: int i, j, nhstepm, hstepm;
5469: double *xp;
5470: double *gp, *gm;
5471: double **gradg, **trgradg;
1.208 brouard 5472: double **mgm, **mgp;
1.126 brouard 5473: double age,agelim;
5474: int theta;
5475:
5476: pstamp(ficresvpl);
5477: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5478: fprintf(ficresvpl,"# Age");
5479: for(i=1; i<=nlstate;i++)
5480: fprintf(ficresvpl," %1d-%1d",i,i);
5481: fprintf(ficresvpl,"\n");
5482:
5483: xp=vector(1,npar);
5484: dnewm=matrix(1,nlstate,1,npar);
5485: doldm=matrix(1,nlstate,1,nlstate);
5486:
5487: hstepm=1*YEARM; /* Every year of age */
5488: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5489: agelim = AGESUP;
5490: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5491: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5492: if (stepm >= YEARM) hstepm=1;
5493: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5494: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5495: mgp=matrix(1,npar,1,nlstate);
5496: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5497: gp=vector(1,nlstate);
5498: gm=vector(1,nlstate);
5499:
5500: for(theta=1; theta <=npar; theta++){
5501: for(i=1; i<=npar; i++){ /* Computes gradient */
5502: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5503: }
1.209 brouard 5504: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5505: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5506: else
5507: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5508: for(i=1;i<=nlstate;i++){
1.126 brouard 5509: gp[i] = prlim[i][i];
1.208 brouard 5510: mgp[theta][i] = prlim[i][i];
5511: }
1.126 brouard 5512: for(i=1; i<=npar; i++) /* Computes gradient */
5513: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5514: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5515: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5516: else
5517: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5518: for(i=1;i<=nlstate;i++){
1.126 brouard 5519: gm[i] = prlim[i][i];
1.208 brouard 5520: mgm[theta][i] = prlim[i][i];
5521: }
1.126 brouard 5522: for(i=1;i<=nlstate;i++)
5523: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5524: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5525: } /* End theta */
5526:
5527: trgradg =matrix(1,nlstate,1,npar);
5528:
5529: for(j=1; j<=nlstate;j++)
5530: for(theta=1; theta <=npar; theta++)
5531: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5532: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5533: /* printf("\nmgm mgp %d ",(int)age); */
5534: /* for(j=1; j<=nlstate;j++){ */
5535: /* printf(" %d ",j); */
5536: /* for(theta=1; theta <=npar; theta++) */
5537: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5538: /* printf("\n "); */
5539: /* } */
5540: /* } */
5541: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5542: /* printf("\n gradg %d ",(int)age); */
5543: /* for(j=1; j<=nlstate;j++){ */
5544: /* printf("%d ",j); */
5545: /* for(theta=1; theta <=npar; theta++) */
5546: /* printf("%d %lf ",theta,gradg[theta][j]); */
5547: /* printf("\n "); */
5548: /* } */
5549: /* } */
1.126 brouard 5550:
5551: for(i=1;i<=nlstate;i++)
5552: varpl[i][(int)age] =0.;
1.209 brouard 5553: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5554: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5555: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5556: }else{
1.126 brouard 5557: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5558: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5559: }
1.126 brouard 5560: for(i=1;i<=nlstate;i++)
5561: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5562:
5563: fprintf(ficresvpl,"%.0f ",age );
5564: for(i=1; i<=nlstate;i++)
5565: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5566: fprintf(ficresvpl,"\n");
5567: free_vector(gp,1,nlstate);
5568: free_vector(gm,1,nlstate);
1.208 brouard 5569: free_matrix(mgm,1,npar,1,nlstate);
5570: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5571: free_matrix(gradg,1,npar,1,nlstate);
5572: free_matrix(trgradg,1,nlstate,1,npar);
5573: } /* End age */
5574:
5575: free_vector(xp,1,npar);
5576: free_matrix(doldm,1,nlstate,1,npar);
5577: free_matrix(dnewm,1,nlstate,1,nlstate);
5578:
5579: }
5580:
5581: /************ Variance of one-step probabilities ******************/
5582: 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 5583: {
5584: int i, j=0, k1, l1, tj;
5585: int k2, l2, j1, z1;
5586: int k=0, l;
5587: int first=1, first1, first2;
5588: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5589: double **dnewm,**doldm;
5590: double *xp;
5591: double *gp, *gm;
5592: double **gradg, **trgradg;
5593: double **mu;
5594: double age, cov[NCOVMAX+1];
5595: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5596: int theta;
5597: char fileresprob[FILENAMELENGTH];
5598: char fileresprobcov[FILENAMELENGTH];
5599: char fileresprobcor[FILENAMELENGTH];
5600: double ***varpij;
5601:
5602: strcpy(fileresprob,"PROB_");
5603: strcat(fileresprob,fileres);
5604: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5605: printf("Problem with resultfile: %s\n", fileresprob);
5606: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5607: }
5608: strcpy(fileresprobcov,"PROBCOV_");
5609: strcat(fileresprobcov,fileresu);
5610: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5611: printf("Problem with resultfile: %s\n", fileresprobcov);
5612: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5613: }
5614: strcpy(fileresprobcor,"PROBCOR_");
5615: strcat(fileresprobcor,fileresu);
5616: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5617: printf("Problem with resultfile: %s\n", fileresprobcor);
5618: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5619: }
5620: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5621: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5622: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5623: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5624: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5625: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5626: pstamp(ficresprob);
5627: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5628: fprintf(ficresprob,"# Age");
5629: pstamp(ficresprobcov);
5630: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5631: fprintf(ficresprobcov,"# Age");
5632: pstamp(ficresprobcor);
5633: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5634: fprintf(ficresprobcor,"# Age");
1.126 brouard 5635:
5636:
1.222 brouard 5637: for(i=1; i<=nlstate;i++)
5638: for(j=1; j<=(nlstate+ndeath);j++){
5639: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5640: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5641: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5642: }
5643: /* fprintf(ficresprob,"\n");
5644: fprintf(ficresprobcov,"\n");
5645: fprintf(ficresprobcor,"\n");
5646: */
5647: xp=vector(1,npar);
5648: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5649: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5650: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5651: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5652: first=1;
5653: fprintf(ficgp,"\n# Routine varprob");
5654: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5655: fprintf(fichtm,"\n");
5656:
5657: 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);
5658: 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);
5659: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5660: and drawn. It helps understanding how is the covariance between two incidences.\
5661: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5662: 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 5663: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5664: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5665: standard deviations wide on each axis. <br>\
5666: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5667: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5668: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5669:
1.222 brouard 5670: cov[1]=1;
5671: /* tj=cptcoveff; */
1.225 brouard 5672: tj = (int) pow(2,cptcoveff);
1.222 brouard 5673: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5674: j1=0;
1.224 brouard 5675: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5676: if (cptcovn>0) {
5677: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5678: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5679: fprintf(ficresprob, "**********\n#\n");
5680: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5681: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5682: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5683:
1.222 brouard 5684: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5685: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5686: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5687:
5688:
1.222 brouard 5689: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5690: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5691: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5692:
1.222 brouard 5693: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5694: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5695: fprintf(ficresprobcor, "**********\n#");
5696: if(invalidvarcomb[j1]){
5697: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5698: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5699: continue;
5700: }
5701: }
5702: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5703: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5704: gp=vector(1,(nlstate)*(nlstate+ndeath));
5705: gm=vector(1,(nlstate)*(nlstate+ndeath));
5706: for (age=bage; age<=fage; age ++){
5707: cov[2]=age;
5708: if(nagesqr==1)
5709: cov[3]= age*age;
5710: for (k=1; k<=cptcovn;k++) {
5711: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5712: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5713: * 1 1 1 1 1
5714: * 2 2 1 1 1
5715: * 3 1 2 1 1
5716: */
5717: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5718: }
5719: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5720: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5721: for (k=1; k<=cptcovprod;k++)
5722: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5723:
5724:
1.222 brouard 5725: for(theta=1; theta <=npar; theta++){
5726: for(i=1; i<=npar; i++)
5727: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5728:
1.222 brouard 5729: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5730:
1.222 brouard 5731: k=0;
5732: for(i=1; i<= (nlstate); i++){
5733: for(j=1; j<=(nlstate+ndeath);j++){
5734: k=k+1;
5735: gp[k]=pmmij[i][j];
5736: }
5737: }
1.220 brouard 5738:
1.222 brouard 5739: for(i=1; i<=npar; i++)
5740: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5741:
1.222 brouard 5742: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5743: k=0;
5744: for(i=1; i<=(nlstate); i++){
5745: for(j=1; j<=(nlstate+ndeath);j++){
5746: k=k+1;
5747: gm[k]=pmmij[i][j];
5748: }
5749: }
1.220 brouard 5750:
1.222 brouard 5751: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5752: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5753: }
1.126 brouard 5754:
1.222 brouard 5755: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5756: for(theta=1; theta <=npar; theta++)
5757: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5758:
1.222 brouard 5759: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5760: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5761:
1.222 brouard 5762: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5763:
1.222 brouard 5764: k=0;
5765: for(i=1; i<=(nlstate); i++){
5766: for(j=1; j<=(nlstate+ndeath);j++){
5767: k=k+1;
5768: mu[k][(int) age]=pmmij[i][j];
5769: }
5770: }
5771: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5772: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5773: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5774:
1.222 brouard 5775: /*printf("\n%d ",(int)age);
5776: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5777: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5778: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5779: }*/
1.220 brouard 5780:
1.222 brouard 5781: fprintf(ficresprob,"\n%d ",(int)age);
5782: fprintf(ficresprobcov,"\n%d ",(int)age);
5783: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5784:
1.222 brouard 5785: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5786: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5787: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5788: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5789: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5790: }
5791: i=0;
5792: for (k=1; k<=(nlstate);k++){
5793: for (l=1; l<=(nlstate+ndeath);l++){
5794: i++;
5795: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5796: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5797: for (j=1; j<=i;j++){
5798: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5799: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5800: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5801: }
5802: }
5803: }/* end of loop for state */
5804: } /* end of loop for age */
5805: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5806: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5807: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5808: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5809:
5810: /* Confidence intervalle of pij */
5811: /*
5812: fprintf(ficgp,"\nunset parametric;unset label");
5813: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5814: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5815: 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);
5816: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5817: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5818: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5819: */
5820:
5821: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5822: first1=1;first2=2;
5823: for (k2=1; k2<=(nlstate);k2++){
5824: for (l2=1; l2<=(nlstate+ndeath);l2++){
5825: if(l2==k2) continue;
5826: j=(k2-1)*(nlstate+ndeath)+l2;
5827: for (k1=1; k1<=(nlstate);k1++){
5828: for (l1=1; l1<=(nlstate+ndeath);l1++){
5829: if(l1==k1) continue;
5830: i=(k1-1)*(nlstate+ndeath)+l1;
5831: if(i<=j) continue;
5832: for (age=bage; age<=fage; age ++){
5833: if ((int)age %5==0){
5834: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5835: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5836: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5837: mu1=mu[i][(int) age]/stepm*YEARM ;
5838: mu2=mu[j][(int) age]/stepm*YEARM;
5839: c12=cv12/sqrt(v1*v2);
5840: /* Computing eigen value of matrix of covariance */
5841: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5842: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5843: if ((lc2 <0) || (lc1 <0) ){
5844: if(first2==1){
5845: first1=0;
5846: 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);
5847: }
5848: 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);
5849: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5850: /* lc2=fabs(lc2); */
5851: }
1.220 brouard 5852:
1.222 brouard 5853: /* Eigen vectors */
5854: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5855: /*v21=sqrt(1.-v11*v11); *//* error */
5856: v21=(lc1-v1)/cv12*v11;
5857: v12=-v21;
5858: v22=v11;
5859: tnalp=v21/v11;
5860: if(first1==1){
5861: first1=0;
5862: 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);
5863: }
5864: 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);
5865: /*printf(fignu*/
5866: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5867: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5868: if(first==1){
5869: first=0;
5870: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5871: fprintf(ficgp,"\nset parametric;unset label");
5872: 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);
5873: fprintf(ficgp,"\nset ter svg size 640, 480");
5874: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5875: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5876: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5877: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5878: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5879: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5880: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5881: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5882: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5883: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5884: 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", \
5885: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5886: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5887: }else{
5888: first=0;
5889: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5890: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5891: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5892: 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", \
5893: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5894: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5895: }/* if first */
5896: } /* age mod 5 */
5897: } /* end loop age */
5898: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5899: first=1;
5900: } /*l12 */
5901: } /* k12 */
5902: } /*l1 */
5903: }/* k1 */
5904: } /* loop on combination of covariates j1 */
5905: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5906: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5907: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5908: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5909: free_vector(xp,1,npar);
5910: fclose(ficresprob);
5911: fclose(ficresprobcov);
5912: fclose(ficresprobcor);
5913: fflush(ficgp);
5914: fflush(fichtmcov);
5915: }
1.126 brouard 5916:
5917:
5918: /******************* Printing html file ***********/
1.201 brouard 5919: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5920: int lastpass, int stepm, int weightopt, char model[],\
5921: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5922: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5923: double jprev1, double mprev1,double anprev1, double dateprev1, \
5924: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5925: int jj1, k1, i1, cpt;
5926:
5927: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5928: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5929: </ul>");
1.214 brouard 5930: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5931: 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",
5932: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5933: 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 5934: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5935: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5936: fprintf(fichtm,"\
5937: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5938: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5939: fprintf(fichtm,"\
1.217 brouard 5940: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5941: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5942: fprintf(fichtm,"\
1.126 brouard 5943: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5944: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5945: fprintf(fichtm,"\
1.217 brouard 5946: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5947: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5948: fprintf(fichtm,"\
1.211 brouard 5949: - (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 5950: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5951: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5952: if(prevfcast==1){
5953: fprintf(fichtm,"\
5954: - Prevalence projections by age and states: \
1.201 brouard 5955: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5956: }
1.126 brouard 5957:
1.222 brouard 5958: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5959:
1.225 brouard 5960: m=pow(2,cptcoveff);
1.222 brouard 5961: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5962:
1.222 brouard 5963: jj1=0;
5964: for(k1=1; k1<=m;k1++){
1.220 brouard 5965:
1.222 brouard 5966: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5967: jj1++;
5968: if (cptcovn > 0) {
5969: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5970: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 5971: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5972: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5973: }
1.230 brouard 5974: /* if(nqfveff+nqtveff 0) */ /* Test to be done */
1.222 brouard 5975: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5976: if(invalidvarcomb[k1]){
5977: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5978: printf("\nCombination (%d) ignored because no cases \n",k1);
5979: continue;
5980: }
5981: }
5982: /* aij, bij */
5983: 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 5984: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5985: /* Pij */
5986: 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 5987: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5988: /* Quasi-incidences */
5989: 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 5990: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5991: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5992: 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 5993: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5994: /* Survival functions (period) in state j */
5995: for(cpt=1; cpt<=nlstate;cpt++){
5996: 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 5997: <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 5998: }
5999: /* State specific survival functions (period) */
6000: for(cpt=1; cpt<=nlstate;cpt++){
6001: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 6002: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 6003: <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 6004: }
6005: /* Period (stable) prevalence in each health state */
6006: for(cpt=1; cpt<=nlstate;cpt++){
6007: 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 6008: <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 6009: }
6010: if(backcast==1){
6011: /* Period (stable) back prevalence in each health state */
6012: for(cpt=1; cpt<=nlstate;cpt++){
6013: 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 6014: <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 6015: }
1.217 brouard 6016: }
1.222 brouard 6017: if(prevfcast==1){
6018: /* Projection of prevalence up to period (stable) prevalence in each health state */
6019: for(cpt=1; cpt<=nlstate;cpt++){
6020: 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 6021: <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 6022: }
6023: }
1.220 brouard 6024:
1.222 brouard 6025: for(cpt=1; cpt<=nlstate;cpt++) {
6026: 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 6027: <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 6028: }
6029: /* } /\* end i1 *\/ */
6030: }/* End k1 */
6031: fprintf(fichtm,"</ul>");
1.126 brouard 6032:
1.222 brouard 6033: fprintf(fichtm,"\
1.126 brouard 6034: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 6035: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 6036: - 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 6037: But because parameters are usually highly correlated (a higher incidence of disability \
6038: and a higher incidence of recovery can give very close observed transition) it might \
6039: be very useful to look not only at linear confidence intervals estimated from the \
6040: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
6041: (parameters) of the logistic regression, it might be more meaningful to visualize the \
6042: covariance matrix of the one-step probabilities. \
6043: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 6044:
1.222 brouard 6045: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
6046: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
6047: fprintf(fichtm,"\
1.126 brouard 6048: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6049: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 6050:
1.222 brouard 6051: fprintf(fichtm,"\
1.126 brouard 6052: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 6053: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
6054: fprintf(fichtm,"\
1.126 brouard 6055: - 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): \
6056: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6057: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 6058: fprintf(fichtm,"\
1.126 brouard 6059: - (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): \
6060: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 6061: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 6062: fprintf(fichtm,"\
1.128 brouard 6063: - 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 6064: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
6065: fprintf(fichtm,"\
1.128 brouard 6066: - 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 6067: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
6068: fprintf(fichtm,"\
1.126 brouard 6069: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 6070: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 6071:
6072: /* if(popforecast==1) fprintf(fichtm,"\n */
6073: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
6074: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
6075: /* <br>",fileres,fileres,fileres,fileres); */
6076: /* else */
6077: /* 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 6078: fflush(fichtm);
6079: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6080:
1.225 brouard 6081: m=pow(2,cptcoveff);
1.222 brouard 6082: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6083:
1.222 brouard 6084: jj1=0;
6085: for(k1=1; k1<=m;k1++){
6086: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6087: jj1++;
1.126 brouard 6088: if (cptcovn > 0) {
6089: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6090: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 6091: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6092: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6093:
1.222 brouard 6094: if(invalidvarcomb[k1]){
6095: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6096: continue;
6097: }
1.126 brouard 6098: }
6099: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6100: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6101: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6102: <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 6103: }
6104: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6105: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6106: true period expectancies (those weighted with period prevalences are also\
6107: drawn in addition to the population based expectancies computed using\
1.218 brouard 6108: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6109: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6110: /* } /\* end i1 *\/ */
6111: }/* End k1 */
6112: fprintf(fichtm,"</ul>");
6113: fflush(fichtm);
1.126 brouard 6114: }
6115:
6116: /******************* Gnuplot file **************/
1.223 brouard 6117: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6118:
6119: char dirfileres[132],optfileres[132];
1.223 brouard 6120: char gplotcondition[132];
1.164 brouard 6121: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 6122: int lv=0, vlv=0, kl=0;
1.130 brouard 6123: int ng=0;
1.201 brouard 6124: int vpopbased;
1.223 brouard 6125: int ioffset; /* variable offset for columns */
1.219 brouard 6126:
1.126 brouard 6127: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6128: /* printf("Problem with file %s",optionfilegnuplot); */
6129: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6130: /* } */
6131:
6132: /*#ifdef windows */
6133: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6134: /*#endif */
1.225 brouard 6135: m=pow(2,cptcoveff);
1.126 brouard 6136:
1.202 brouard 6137: /* Contribution to likelihood */
6138: /* Plot the probability implied in the likelihood */
1.223 brouard 6139: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6140: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6141: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6142: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6143: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6144: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6145: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6146: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6147: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6148: 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));
6149: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6150: 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));
6151: for (i=1; i<= nlstate ; i ++) {
6152: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6153: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6154: 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);
6155: for (j=2; j<= nlstate+ndeath ; j ++) {
6156: 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);
6157: }
6158: fprintf(ficgp,";\nset out; unset ylabel;\n");
6159: }
6160: /* 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 */
6161: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6162: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6163: fprintf(ficgp,"\nset out;unset log\n");
6164: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6165:
1.126 brouard 6166: strcpy(dirfileres,optionfilefiname);
6167: strcpy(optfileres,"vpl");
1.223 brouard 6168: /* 1eme*/
1.211 brouard 6169: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.230 brouard 6170: for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 6171: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6172: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.225 brouard 6173: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6174: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6175: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6176: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6177: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6178: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6179: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6180: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6181: }
6182: fprintf(ficgp,"\n#\n");
1.223 brouard 6183: if(invalidvarcomb[k1]){
6184: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6185: continue;
6186: }
1.211 brouard 6187:
1.223 brouard 6188: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6189: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6190: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 6191: set ylabel \"Probability\" \n \
6192: set ter svg size 640, 480\n \
1.201 brouard 6193: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 6194:
1.223 brouard 6195: for (i=1; i<= nlstate ; i ++) {
6196: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6197: else fprintf(ficgp," %%*lf (%%*lf)");
6198: }
6199: 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);
6200: for (i=1; i<= nlstate ; i ++) {
6201: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6202: else fprintf(ficgp," %%*lf (%%*lf)");
6203: }
6204: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6205: for (i=1; i<= nlstate ; i ++) {
6206: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6207: else fprintf(ficgp," %%*lf (%%*lf)");
6208: }
6209: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6210: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6211: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6212: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6213: if(cptcoveff ==0){
1.223 brouard 6214: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6215: }else{
6216: kl=0;
1.225 brouard 6217: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6218: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6219: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6220: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6221: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6222: vlv= nbcode[Tvaraff[k]][lv];
6223: kl++;
6224: /* 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 *\/ */
6225: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6226: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6227: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6228: if(k==cptcoveff){
1.227 brouard 6229: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6230: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6231: }else{
6232: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6233: kl++;
6234: }
6235: } /* end covariate */
6236: } /* end if no covariate */
6237: } /* end if backcast */
6238: fprintf(ficgp,"\nset out \n");
1.201 brouard 6239: } /* k1 */
6240: } /* cpt */
1.126 brouard 6241: /*2 eme*/
6242: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6243:
1.223 brouard 6244: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.225 brouard 6245: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6246: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6247: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6248: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6249: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6250: vlv= nbcode[Tvaraff[k]][lv];
6251: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6252: }
6253: fprintf(ficgp,"\n#\n");
6254: if(invalidvarcomb[k1]){
6255: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6256: continue;
6257: }
1.219 brouard 6258:
1.223 brouard 6259: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6260: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6261: if(vpopbased==0)
6262: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6263: else
6264: fprintf(ficgp,"\nreplot ");
6265: for (i=1; i<= nlstate+1 ; i ++) {
6266: k=2*i;
6267: 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);
6268: for (j=1; j<= nlstate+1 ; j ++) {
6269: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6270: else fprintf(ficgp," %%*lf (%%*lf)");
6271: }
6272: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6273: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6274: 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);
6275: for (j=1; j<= nlstate+1 ; j ++) {
6276: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6277: else fprintf(ficgp," %%*lf (%%*lf)");
6278: }
6279: fprintf(ficgp,"\" t\"\" w l lt 0,");
6280: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6281: for (j=1; j<= nlstate+1 ; j ++) {
6282: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6283: else fprintf(ficgp," %%*lf (%%*lf)");
6284: }
6285: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6286: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6287: } /* state */
6288: } /* vpopbased */
6289: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6290: } /* k1 */
1.219 brouard 6291:
6292:
1.126 brouard 6293: /*3eme*/
6294: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6295:
1.126 brouard 6296: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6297: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.225 brouard 6298: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6299: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6300: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6301: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6302: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6303: vlv= nbcode[Tvaraff[k]][lv];
6304: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6305: }
6306: fprintf(ficgp,"\n#\n");
1.223 brouard 6307: if(invalidvarcomb[k1]){
6308: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6309: continue;
6310: }
1.219 brouard 6311:
1.126 brouard 6312: /* k=2+nlstate*(2*cpt-2); */
6313: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6314: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6315: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6316: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6317: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6318: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6319: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6320: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6321: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6322: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6323:
1.126 brouard 6324: */
6325: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6326: 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);
6327: /* 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 6328:
1.126 brouard 6329: }
1.201 brouard 6330: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
1.126 brouard 6331: }
6332: }
6333:
1.223 brouard 6334: /* 4eme */
1.201 brouard 6335: /* Survival functions (period) from state i in state j by initial state i */
6336: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6337:
1.201 brouard 6338: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6339: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6340: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6341: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6342: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6343: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6344: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6345: vlv= nbcode[Tvaraff[k]][lv];
6346: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6347: }
6348: fprintf(ficgp,"\n#\n");
1.223 brouard 6349: if(invalidvarcomb[k1]){
6350: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6351: continue;
6352: }
1.220 brouard 6353:
1.201 brouard 6354: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6355: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6356: set ter svg size 640, 480\n \
6357: unset log y\n \
1.201 brouard 6358: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6359: k=3;
1.201 brouard 6360: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6361: if(i==1){
6362: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6363: }else{
6364: fprintf(ficgp,", '' ");
6365: }
6366: l=(nlstate+ndeath)*(i-1)+1;
6367: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6368: for (j=2; j<= nlstate+ndeath ; j ++)
6369: fprintf(ficgp,"+$%d",k+l+j-1);
6370: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6371: } /* nlstate */
6372: fprintf(ficgp,"\nset out\n");
6373: } /* end cpt state*/
6374: } /* end covariate */
1.220 brouard 6375:
6376: /* 5eme */
1.201 brouard 6377: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6378: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6379: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6380:
1.201 brouard 6381: 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);
1.225 brouard 6382: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6383: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6384: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6385: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6386: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6387: vlv= nbcode[Tvaraff[k]][lv];
6388: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6389: }
6390: fprintf(ficgp,"\n#\n");
1.223 brouard 6391: if(invalidvarcomb[k1]){
1.227 brouard 6392: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6393: continue;
1.223 brouard 6394: }
1.227 brouard 6395:
1.201 brouard 6396: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6397: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 brouard 6398: set ter svg size 640, 480\n \
6399: unset log y\n \
1.201 brouard 6400: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6401: k=3;
1.201 brouard 6402: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6403: if(j==1)
6404: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6405: else
6406: fprintf(ficgp,", '' ");
6407: l=(nlstate+ndeath)*(cpt-1) +j;
6408: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6409: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6410: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6411: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6412: } /* nlstate */
6413: fprintf(ficgp,", '' ");
6414: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6415: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6416: l=(nlstate+ndeath)*(cpt-1) +j;
6417: if(j < nlstate)
6418: fprintf(ficgp,"$%d +",k+l);
6419: else
6420: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6421: }
6422: fprintf(ficgp,"\nset out\n");
6423: } /* end cpt state*/
6424: } /* end covariate */
1.227 brouard 6425:
1.220 brouard 6426: /* 6eme */
1.202 brouard 6427: /* CV preval stable (period) for each covariate */
1.211 brouard 6428: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6429: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6430:
1.211 brouard 6431: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6432: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6433: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6434: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6435: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6436: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6437: vlv= nbcode[Tvaraff[k]][lv];
6438: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6439: }
6440: fprintf(ficgp,"\n#\n");
1.223 brouard 6441: if(invalidvarcomb[k1]){
1.227 brouard 6442: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6443: continue;
1.223 brouard 6444: }
1.227 brouard 6445:
1.201 brouard 6446: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6447: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 brouard 6448: set ter svg size 640, 480\n \
6449: unset log y\n \
1.153 brouard 6450: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6451: k=3; /* Offset */
1.153 brouard 6452: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6453: if(i==1)
6454: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6455: else
6456: fprintf(ficgp,", '' ");
6457: l=(nlstate+ndeath)*(i-1)+1;
6458: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6459: for (j=2; j<= nlstate ; j ++)
6460: fprintf(ficgp,"+$%d",k+l+j-1);
6461: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6462: } /* nlstate */
1.201 brouard 6463: fprintf(ficgp,"\nset out\n");
1.153 brouard 6464: } /* end cpt state*/
6465: } /* end covariate */
1.227 brouard 6466:
6467:
1.220 brouard 6468: /* 7eme */
1.218 brouard 6469: if(backcast == 1){
1.217 brouard 6470: /* CV back preval stable (period) for each covariate */
1.218 brouard 6471: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6472: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6473: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6474: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6475: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6476: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6477: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6478: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6479: vlv= nbcode[Tvaraff[k]][lv];
6480: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6481: }
6482: fprintf(ficgp,"\n#\n");
6483: if(invalidvarcomb[k1]){
6484: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6485: continue;
6486: }
6487:
6488: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6489: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6490: set ter svg size 640, 480\n \
6491: unset log y\n \
1.218 brouard 6492: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6493: k=3; /* Offset */
6494: for (i=1; i<= nlstate ; i ++){
6495: if(i==1)
6496: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6497: else
6498: fprintf(ficgp,", '' ");
6499: /* l=(nlstate+ndeath)*(i-1)+1; */
6500: l=(nlstate+ndeath)*(cpt-1)+1;
6501: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6502: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6503: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6504: /* for (j=2; j<= nlstate ; j ++) */
6505: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6506: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6507: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6508: } /* nlstate */
6509: fprintf(ficgp,"\nset out\n");
1.218 brouard 6510: } /* end cpt state*/
6511: } /* end covariate */
6512: } /* End if backcast */
6513:
1.223 brouard 6514: /* 8eme */
1.218 brouard 6515: if(prevfcast==1){
6516: /* Projection from cross-sectional to stable (period) for each covariate */
6517:
6518: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6519: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6520: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6521: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6522: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6523: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6524: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6525: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6526: vlv= nbcode[Tvaraff[k]][lv];
6527: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6528: }
6529: fprintf(ficgp,"\n#\n");
6530: if(invalidvarcomb[k1]){
6531: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6532: continue;
6533: }
6534:
6535: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6536: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6537: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6538: set ter svg size 640, 480\n \
6539: unset log y\n \
1.219 brouard 6540: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6541: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6542: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6543: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6544: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6545: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6546: if(i==1){
6547: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6548: }else{
6549: fprintf(ficgp,",\\\n '' ");
6550: }
6551: if(cptcoveff ==0){ /* No covariate */
6552: ioffset=2; /* Age is in 2 */
6553: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6554: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6555: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6556: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6557: fprintf(ficgp," u %d:(", ioffset);
6558: if(i==nlstate+1)
6559: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6560: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6561: else
6562: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6563: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6564: }else{ /* more than 2 covariates */
6565: if(cptcoveff ==1){
6566: ioffset=4; /* Age is in 4 */
6567: }else{
6568: ioffset=6; /* Age is in 6 */
6569: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6570: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6571: }
6572: fprintf(ficgp," u %d:(",ioffset);
6573: kl=0;
6574: strcpy(gplotcondition,"(");
6575: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6576: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6577: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6578: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6579: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6580: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6581: kl++;
6582: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6583: kl++;
6584: if(k <cptcoveff && cptcoveff>1)
6585: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6586: }
6587: strcpy(gplotcondition+strlen(gplotcondition),")");
6588: /* 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 *\/ */
6589: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6590: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6591: /* '' 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*/
6592: if(i==nlstate+1){
6593: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6594: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6595: }else{
6596: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6597: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6598: }
6599: } /* end if covariate */
6600: } /* nlstate */
6601: fprintf(ficgp,"\nset out\n");
1.223 brouard 6602: } /* end cpt state*/
6603: } /* end covariate */
6604: } /* End if prevfcast */
1.227 brouard 6605:
6606:
1.223 brouard 6607: /* proba elementaires */
6608: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6609: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6610: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6611: for(k=1; k <=(nlstate+ndeath); k++){
6612: if (k != i) {
1.227 brouard 6613: fprintf(ficgp,"# current state %d\n",k);
6614: for(j=1; j <=ncovmodel; j++){
6615: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6616: jk++;
6617: }
6618: fprintf(ficgp,"\n");
1.126 brouard 6619: }
6620: }
1.223 brouard 6621: }
1.187 brouard 6622: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6623:
1.145 brouard 6624: /*goto avoid;*/
1.200 brouard 6625: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6626: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6627: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6628: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6629: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6630: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6631: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6632: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6633: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6634: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6635: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6636: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6637: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6638: fprintf(ficgp,"#\n");
1.223 brouard 6639: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6640: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6641: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6642: for(jk=1; jk <=m; jk++) {
6643: fprintf(ficgp,"# jk=%d\n",jk);
6644: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6645: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6646: if (ng==1){
6647: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6648: fprintf(ficgp,"\nunset log y");
6649: }else if (ng==2){
6650: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6651: fprintf(ficgp,"\nset log y");
6652: }else if (ng==3){
6653: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6654: fprintf(ficgp,"\nset log y");
6655: }else
6656: fprintf(ficgp,"\nunset title ");
6657: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6658: i=1;
6659: for(k2=1; k2<=nlstate; k2++) {
6660: k3=i;
6661: for(k=1; k<=(nlstate+ndeath); k++) {
6662: if (k != k2){
6663: switch( ng) {
6664: case 1:
6665: if(nagesqr==0)
6666: fprintf(ficgp," p%d+p%d*x",i,i+1);
6667: else /* nagesqr =1 */
6668: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6669: break;
6670: case 2: /* ng=2 */
6671: if(nagesqr==0)
6672: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6673: else /* nagesqr =1 */
6674: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6675: break;
6676: case 3:
6677: if(nagesqr==0)
6678: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6679: else /* nagesqr =1 */
6680: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6681: break;
6682: }
6683: ij=1;/* To be checked else nbcode[0][0] wrong */
6684: for(j=3; j <=ncovmodel-nagesqr; j++) {
6685: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6686: if(ij <=cptcovage) { /* Bug valgrind */
6687: if((j-2)==Tage[ij]) { /* Bug valgrind */
6688: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6689: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6690: ij++;
6691: }
6692: }
6693: else
1.227 brouard 6694: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6695: }
6696: }else{
6697: i=i-ncovmodel;
6698: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6699: fprintf(ficgp," (1.");
6700: }
1.227 brouard 6701:
1.223 brouard 6702: if(ng != 1){
6703: fprintf(ficgp,")/(1");
1.227 brouard 6704:
1.223 brouard 6705: for(k1=1; k1 <=nlstate; k1++){
6706: if(nagesqr==0)
6707: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6708: else /* nagesqr =1 */
6709: 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 6710:
1.223 brouard 6711: ij=1;
6712: for(j=3; j <=ncovmodel-nagesqr; j++){
6713: if(ij <=cptcovage) { /* Bug valgrind */
6714: if((j-2)==Tage[ij]) { /* Bug valgrind */
6715: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6716: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6717: ij++;
6718: }
6719: }
6720: else
1.225 brouard 6721: 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 6722: }
6723: fprintf(ficgp,")");
6724: }
6725: fprintf(ficgp,")");
6726: if(ng ==2)
6727: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6728: else /* ng= 3 */
6729: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6730: }else{ /* end ng <> 1 */
6731: if( k !=k2) /* logit p11 is hard to draw */
6732: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6733: }
6734: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6735: fprintf(ficgp,",");
6736: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6737: fprintf(ficgp,",");
6738: i=i+ncovmodel;
6739: } /* end k */
6740: } /* end k2 */
6741: fprintf(ficgp,"\n set out\n");
6742: } /* end jk */
6743: } /* end ng */
6744: /* avoid: */
6745: fflush(ficgp);
1.126 brouard 6746: } /* end gnuplot */
6747:
6748:
6749: /*************** Moving average **************/
1.219 brouard 6750: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6751: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6752:
1.222 brouard 6753: int i, cpt, cptcod;
6754: int modcovmax =1;
6755: int mobilavrange, mob;
6756: int iage=0;
6757:
6758: double sum=0.;
6759: double age;
6760: double *sumnewp, *sumnewm;
6761: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6762:
6763:
1.225 brouard 6764: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6765: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6766:
6767: sumnewp = vector(1,ncovcombmax);
6768: sumnewm = vector(1,ncovcombmax);
6769: agemingood = vector(1,ncovcombmax);
6770: agemaxgood = vector(1,ncovcombmax);
6771:
6772: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6773: sumnewm[cptcod]=0.;
6774: sumnewp[cptcod]=0.;
6775: agemingood[cptcod]=0;
6776: agemaxgood[cptcod]=0;
6777: }
6778: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6779:
6780: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6781: if(mobilav==1) mobilavrange=5; /* default */
6782: else mobilavrange=mobilav;
6783: for (age=bage; age<=fage; age++)
6784: for (i=1; i<=nlstate;i++)
6785: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6786: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6787: /* We keep the original values on the extreme ages bage, fage and for
6788: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6789: we use a 5 terms etc. until the borders are no more concerned.
6790: */
6791: for (mob=3;mob <=mobilavrange;mob=mob+2){
6792: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6793: for (i=1; i<=nlstate;i++){
6794: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6795: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6796: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6797: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6798: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6799: }
6800: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6801: }
6802: }
6803: }/* end age */
6804: }/* end mob */
6805: }else
6806: return -1;
6807: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6808: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6809: if(invalidvarcomb[cptcod]){
6810: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6811: continue;
6812: }
1.219 brouard 6813:
1.222 brouard 6814: agemingood[cptcod]=fage-(mob-1)/2;
6815: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6816: sumnewm[cptcod]=0.;
6817: for (i=1; i<=nlstate;i++){
6818: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6819: }
6820: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6821: agemingood[cptcod]=age;
6822: }else{ /* bad */
6823: for (i=1; i<=nlstate;i++){
6824: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6825: } /* i */
6826: } /* end bad */
6827: }/* age */
6828: sum=0.;
6829: for (i=1; i<=nlstate;i++){
6830: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6831: }
6832: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6833: 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);
6834: /* for (i=1; i<=nlstate;i++){ */
6835: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6836: /* } /\* i *\/ */
6837: } /* end bad */
6838: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6839: /* From youngest, finding the oldest wrong */
6840: agemaxgood[cptcod]=bage+(mob-1)/2;
6841: for (age=bage+(mob-1)/2; age<=fage; age++){
6842: sumnewm[cptcod]=0.;
6843: for (i=1; i<=nlstate;i++){
6844: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6845: }
6846: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6847: agemaxgood[cptcod]=age;
6848: }else{ /* bad */
6849: for (i=1; i<=nlstate;i++){
6850: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6851: } /* i */
6852: } /* end bad */
6853: }/* age */
6854: sum=0.;
6855: for (i=1; i<=nlstate;i++){
6856: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6857: }
6858: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6859: 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);
6860: /* for (i=1; i<=nlstate;i++){ */
6861: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6862: /* } /\* i *\/ */
6863: } /* end bad */
6864:
6865: for (age=bage; age<=fage; age++){
6866: printf("%d %d ", cptcod, (int)age);
6867: sumnewp[cptcod]=0.;
6868: sumnewm[cptcod]=0.;
6869: for (i=1; i<=nlstate;i++){
6870: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6871: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6872: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6873: }
6874: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6875: }
6876: /* printf("\n"); */
6877: /* } */
6878: /* brutal averaging */
6879: for (i=1; i<=nlstate;i++){
6880: for (age=1; age<=bage; age++){
6881: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6882: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6883: }
6884: for (age=fage; age<=AGESUP; age++){
6885: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6886: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6887: }
6888: } /* end i status */
6889: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6890: for (age=1; age<=AGESUP; age++){
6891: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6892: mobaverage[(int)age][i][cptcod]=0.;
6893: }
6894: }
6895: }/* end cptcod */
6896: free_vector(sumnewm,1, ncovcombmax);
6897: free_vector(sumnewp,1, ncovcombmax);
6898: free_vector(agemaxgood,1, ncovcombmax);
6899: free_vector(agemingood,1, ncovcombmax);
6900: return 0;
6901: }/* End movingaverage */
1.218 brouard 6902:
1.126 brouard 6903:
6904: /************** Forecasting ******************/
1.225 brouard 6905: 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 6906: /* proj1, year, month, day of starting projection
6907: agemin, agemax range of age
6908: dateprev1 dateprev2 range of dates during which prevalence is computed
6909: anproj2 year of en of projection (same day and month as proj1).
6910: */
1.164 brouard 6911: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6912: double agec; /* generic age */
6913: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6914: double *popeffectif,*popcount;
6915: double ***p3mat;
1.218 brouard 6916: /* double ***mobaverage; */
1.126 brouard 6917: char fileresf[FILENAMELENGTH];
6918:
6919: agelim=AGESUP;
1.211 brouard 6920: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6921: in each health status at the date of interview (if between dateprev1 and dateprev2).
6922: We still use firstpass and lastpass as another selection.
6923: */
1.214 brouard 6924: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6925: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6926:
1.201 brouard 6927: strcpy(fileresf,"F_");
6928: strcat(fileresf,fileresu);
1.126 brouard 6929: if((ficresf=fopen(fileresf,"w"))==NULL) {
6930: printf("Problem with forecast resultfile: %s\n", fileresf);
6931: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6932: }
1.215 brouard 6933: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6934: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6935:
1.225 brouard 6936: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 6937:
6938:
6939: stepsize=(int) (stepm+YEARM-1)/YEARM;
6940: if (stepm<=12) stepsize=1;
6941: if(estepm < stepm){
6942: printf ("Problem %d lower than %d\n",estepm, stepm);
6943: }
6944: else hstepm=estepm;
6945:
6946: hstepm=hstepm/stepm;
6947: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6948: fractional in yp1 */
6949: anprojmean=yp;
6950: yp2=modf((yp1*12),&yp);
6951: mprojmean=yp;
6952: yp1=modf((yp2*30.5),&yp);
6953: jprojmean=yp;
6954: if(jprojmean==0) jprojmean=1;
6955: if(mprojmean==0) jprojmean=1;
6956:
1.227 brouard 6957: i1=pow(2,cptcoveff);
1.126 brouard 6958: if (cptcovn < 1){i1=1;}
6959:
6960: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6961:
6962: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 6963:
1.126 brouard 6964: /* if (h==(int)(YEARM*yearp)){ */
1.227 brouard 6965: for(k=1;k<=i1;k++){
6966: if(invalidvarcomb[k]){
6967: printf("\nCombination (%d) projection ignored because no cases \n",k);
6968: continue;
6969: }
6970: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
6971: for(j=1;j<=cptcoveff;j++) {
6972: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6973: }
6974: fprintf(ficresf," yearproj age");
6975: for(j=1; j<=nlstate+ndeath;j++){
6976: for(i=1; i<=nlstate;i++)
6977: fprintf(ficresf," p%d%d",i,j);
6978: fprintf(ficresf," wp.%d",j);
6979: }
6980: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
6981: fprintf(ficresf,"\n");
6982: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6983: for (agec=fage; agec>=(ageminpar-1); agec--){
6984: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6985: nhstepm = nhstepm/hstepm;
6986: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6987: oldm=oldms;savm=savms;
6988: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6989:
6990: for (h=0; h<=nhstepm; h++){
6991: if (h*hstepm/YEARM*stepm ==yearp) {
6992: fprintf(ficresf,"\n");
6993: for(j=1;j<=cptcoveff;j++)
6994: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6995: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6996: }
6997: for(j=1; j<=nlstate+ndeath;j++) {
6998: ppij=0.;
6999: for(i=1; i<=nlstate;i++) {
7000: if (mobilav==1)
7001: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
7002: else {
7003: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
7004: }
7005: if (h*hstepm/YEARM*stepm== yearp) {
7006: fprintf(ficresf," %.3f", p3mat[i][j][h]);
7007: }
7008: } /* end i */
7009: if (h*hstepm/YEARM*stepm==yearp) {
7010: fprintf(ficresf," %.3f", ppij);
7011: }
7012: }/* end j */
7013: } /* end h */
7014: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7015: } /* end agec */
7016: } /* end yearp */
7017: } /* end k */
1.219 brouard 7018:
1.126 brouard 7019: fclose(ficresf);
1.215 brouard 7020: printf("End of Computing forecasting \n");
7021: fprintf(ficlog,"End of Computing forecasting\n");
7022:
1.126 brouard 7023: }
7024:
1.218 brouard 7025: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 7026: /* 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 7027: /* /\* back1, year, month, day of starting backection */
7028: /* agemin, agemax range of age */
7029: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
7030: /* anback2 year of en of backection (same day and month as back1). */
7031: /* *\/ */
7032: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
7033: /* double agec; /\* generic age *\/ */
7034: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
7035: /* double *popeffectif,*popcount; */
7036: /* double ***p3mat; */
7037: /* /\* double ***mobaverage; *\/ */
7038: /* char fileresfb[FILENAMELENGTH]; */
7039:
7040: /* agelim=AGESUP; */
7041: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
7042: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
7043: /* We still use firstpass and lastpass as another selection. */
7044: /* *\/ */
7045: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
7046: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
7047: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
7048:
7049: /* strcpy(fileresfb,"FB_"); */
7050: /* strcat(fileresfb,fileresu); */
7051: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
7052: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
7053: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
7054: /* } */
7055: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7056: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
7057:
1.225 brouard 7058: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 7059:
7060: /* /\* if (mobilav!=0) { *\/ */
7061: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7062: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7063: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7064: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7065: /* /\* } *\/ */
7066: /* /\* } *\/ */
7067:
7068: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7069: /* if (stepm<=12) stepsize=1; */
7070: /* if(estepm < stepm){ */
7071: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
7072: /* } */
7073: /* else hstepm=estepm; */
7074:
7075: /* hstepm=hstepm/stepm; */
7076: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
7077: /* fractional in yp1 *\/ */
7078: /* anprojmean=yp; */
7079: /* yp2=modf((yp1*12),&yp); */
7080: /* mprojmean=yp; */
7081: /* yp1=modf((yp2*30.5),&yp); */
7082: /* jprojmean=yp; */
7083: /* if(jprojmean==0) jprojmean=1; */
7084: /* if(mprojmean==0) jprojmean=1; */
7085:
1.225 brouard 7086: /* i1=cptcoveff; */
1.218 brouard 7087: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7088:
1.218 brouard 7089: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7090:
1.218 brouard 7091: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7092:
7093: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7094: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7095: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7096: /* k=k+1; */
7097: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7098: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7099: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7100: /* } */
7101: /* fprintf(ficresfb," yearbproj age"); */
7102: /* for(j=1; j<=nlstate+ndeath;j++){ */
7103: /* for(i=1; i<=nlstate;i++) */
7104: /* fprintf(ficresfb," p%d%d",i,j); */
7105: /* fprintf(ficresfb," p.%d",j); */
7106: /* } */
7107: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7108: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7109: /* fprintf(ficresfb,"\n"); */
7110: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7111: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7112: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7113: /* nhstepm = nhstepm/hstepm; */
7114: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7115: /* oldm=oldms;savm=savms; */
7116: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7117: /* for (h=0; h<=nhstepm; h++){ */
7118: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7119: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7120: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7121: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7122: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7123: /* } */
7124: /* for(j=1; j<=nlstate+ndeath;j++) { */
7125: /* ppij=0.; */
7126: /* for(i=1; i<=nlstate;i++) { */
7127: /* if (mobilav==1) */
7128: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7129: /* else { */
7130: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7131: /* } */
7132: /* if (h*hstepm/YEARM*stepm== yearp) { */
7133: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7134: /* } */
7135: /* } /\* end i *\/ */
7136: /* if (h*hstepm/YEARM*stepm==yearp) { */
7137: /* fprintf(ficresfb," %.3f", ppij); */
7138: /* } */
7139: /* }/\* end j *\/ */
7140: /* } /\* end h *\/ */
7141: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7142: /* } /\* end agec *\/ */
7143: /* } /\* end yearp *\/ */
7144: /* } /\* end cptcod *\/ */
7145: /* } /\* end cptcov *\/ */
7146:
7147: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7148:
7149: /* fclose(ficresfb); */
7150: /* printf("End of Computing Back forecasting \n"); */
7151: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7152:
1.218 brouard 7153: /* } */
1.217 brouard 7154:
1.126 brouard 7155: /************** Forecasting *****not tested NB*************/
1.227 brouard 7156: /* 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 7157:
1.227 brouard 7158: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7159: /* int *popage; */
7160: /* double calagedatem, agelim, kk1, kk2; */
7161: /* double *popeffectif,*popcount; */
7162: /* double ***p3mat,***tabpop,***tabpopprev; */
7163: /* /\* double ***mobaverage; *\/ */
7164: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7165:
1.227 brouard 7166: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7167: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7168: /* agelim=AGESUP; */
7169: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7170:
1.227 brouard 7171: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7172:
7173:
1.227 brouard 7174: /* strcpy(filerespop,"POP_"); */
7175: /* strcat(filerespop,fileresu); */
7176: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7177: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7178: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7179: /* } */
7180: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7181: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7182:
1.227 brouard 7183: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7184:
1.227 brouard 7185: /* /\* if (mobilav!=0) { *\/ */
7186: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7187: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7188: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7189: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7190: /* /\* } *\/ */
7191: /* /\* } *\/ */
1.126 brouard 7192:
1.227 brouard 7193: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7194: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7195:
1.227 brouard 7196: /* agelim=AGESUP; */
1.126 brouard 7197:
1.227 brouard 7198: /* hstepm=1; */
7199: /* hstepm=hstepm/stepm; */
1.218 brouard 7200:
1.227 brouard 7201: /* if (popforecast==1) { */
7202: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7203: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7204: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7205: /* } */
7206: /* popage=ivector(0,AGESUP); */
7207: /* popeffectif=vector(0,AGESUP); */
7208: /* popcount=vector(0,AGESUP); */
1.126 brouard 7209:
1.227 brouard 7210: /* i=1; */
7211: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7212:
1.227 brouard 7213: /* imx=i; */
7214: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7215: /* } */
1.218 brouard 7216:
1.227 brouard 7217: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7218: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7219: /* k=k+1; */
7220: /* fprintf(ficrespop,"\n#******"); */
7221: /* for(j=1;j<=cptcoveff;j++) { */
7222: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7223: /* } */
7224: /* fprintf(ficrespop,"******\n"); */
7225: /* fprintf(ficrespop,"# Age"); */
7226: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7227: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7228:
1.227 brouard 7229: /* for (cpt=0; cpt<=0;cpt++) { */
7230: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7231:
1.227 brouard 7232: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7233: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7234: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7235:
1.227 brouard 7236: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7237: /* oldm=oldms;savm=savms; */
7238: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7239:
1.227 brouard 7240: /* for (h=0; h<=nhstepm; h++){ */
7241: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7242: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7243: /* } */
7244: /* for(j=1; j<=nlstate+ndeath;j++) { */
7245: /* kk1=0.;kk2=0; */
7246: /* for(i=1; i<=nlstate;i++) { */
7247: /* if (mobilav==1) */
7248: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7249: /* else { */
7250: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7251: /* } */
7252: /* } */
7253: /* if (h==(int)(calagedatem+12*cpt)){ */
7254: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7255: /* /\*fprintf(ficrespop," %.3f", kk1); */
7256: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7257: /* } */
7258: /* } */
7259: /* for(i=1; i<=nlstate;i++){ */
7260: /* kk1=0.; */
7261: /* for(j=1; j<=nlstate;j++){ */
7262: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7263: /* } */
7264: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7265: /* } */
1.218 brouard 7266:
1.227 brouard 7267: /* if (h==(int)(calagedatem+12*cpt)) */
7268: /* for(j=1; j<=nlstate;j++) */
7269: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7270: /* } */
7271: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7272: /* } */
7273: /* } */
1.218 brouard 7274:
1.227 brouard 7275: /* /\******\/ */
1.218 brouard 7276:
1.227 brouard 7277: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7278: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7279: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7280: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7281: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7282:
1.227 brouard 7283: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7284: /* oldm=oldms;savm=savms; */
7285: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7286: /* for (h=0; h<=nhstepm; h++){ */
7287: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7288: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7289: /* } */
7290: /* for(j=1; j<=nlstate+ndeath;j++) { */
7291: /* kk1=0.;kk2=0; */
7292: /* for(i=1; i<=nlstate;i++) { */
7293: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7294: /* } */
7295: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7296: /* } */
7297: /* } */
7298: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7299: /* } */
7300: /* } */
7301: /* } */
7302: /* } */
1.218 brouard 7303:
1.227 brouard 7304: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7305:
1.227 brouard 7306: /* if (popforecast==1) { */
7307: /* free_ivector(popage,0,AGESUP); */
7308: /* free_vector(popeffectif,0,AGESUP); */
7309: /* free_vector(popcount,0,AGESUP); */
7310: /* } */
7311: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7312: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7313: /* fclose(ficrespop); */
7314: /* } /\* End of popforecast *\/ */
1.218 brouard 7315:
1.126 brouard 7316: int fileappend(FILE *fichier, char *optionfich)
7317: {
7318: if((fichier=fopen(optionfich,"a"))==NULL) {
7319: printf("Problem with file: %s\n", optionfich);
7320: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7321: return (0);
7322: }
7323: fflush(fichier);
7324: return (1);
7325: }
7326:
7327:
7328: /**************** function prwizard **********************/
7329: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7330: {
7331:
7332: /* Wizard to print covariance matrix template */
7333:
1.164 brouard 7334: char ca[32], cb[32];
7335: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7336: int numlinepar;
7337:
7338: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7339: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7340: for(i=1; i <=nlstate; i++){
7341: jj=0;
7342: for(j=1; j <=nlstate+ndeath; j++){
7343: if(j==i) continue;
7344: jj++;
7345: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7346: printf("%1d%1d",i,j);
7347: fprintf(ficparo,"%1d%1d",i,j);
7348: for(k=1; k<=ncovmodel;k++){
7349: /* printf(" %lf",param[i][j][k]); */
7350: /* fprintf(ficparo," %lf",param[i][j][k]); */
7351: printf(" 0.");
7352: fprintf(ficparo," 0.");
7353: }
7354: printf("\n");
7355: fprintf(ficparo,"\n");
7356: }
7357: }
7358: printf("# Scales (for hessian or gradient estimation)\n");
7359: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7360: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7361: for(i=1; i <=nlstate; i++){
7362: jj=0;
7363: for(j=1; j <=nlstate+ndeath; j++){
7364: if(j==i) continue;
7365: jj++;
7366: fprintf(ficparo,"%1d%1d",i,j);
7367: printf("%1d%1d",i,j);
7368: fflush(stdout);
7369: for(k=1; k<=ncovmodel;k++){
7370: /* printf(" %le",delti3[i][j][k]); */
7371: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7372: printf(" 0.");
7373: fprintf(ficparo," 0.");
7374: }
7375: numlinepar++;
7376: printf("\n");
7377: fprintf(ficparo,"\n");
7378: }
7379: }
7380: printf("# Covariance matrix\n");
7381: /* # 121 Var(a12)\n\ */
7382: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7383: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7384: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7385: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7386: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7387: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7388: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7389: fflush(stdout);
7390: fprintf(ficparo,"# Covariance matrix\n");
7391: /* # 121 Var(a12)\n\ */
7392: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7393: /* # ...\n\ */
7394: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7395:
7396: for(itimes=1;itimes<=2;itimes++){
7397: jj=0;
7398: for(i=1; i <=nlstate; i++){
7399: for(j=1; j <=nlstate+ndeath; j++){
7400: if(j==i) continue;
7401: for(k=1; k<=ncovmodel;k++){
7402: jj++;
7403: ca[0]= k+'a'-1;ca[1]='\0';
7404: if(itimes==1){
7405: printf("#%1d%1d%d",i,j,k);
7406: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7407: }else{
7408: printf("%1d%1d%d",i,j,k);
7409: fprintf(ficparo,"%1d%1d%d",i,j,k);
7410: /* printf(" %.5le",matcov[i][j]); */
7411: }
7412: ll=0;
7413: for(li=1;li <=nlstate; li++){
7414: for(lj=1;lj <=nlstate+ndeath; lj++){
7415: if(lj==li) continue;
7416: for(lk=1;lk<=ncovmodel;lk++){
7417: ll++;
7418: if(ll<=jj){
7419: cb[0]= lk +'a'-1;cb[1]='\0';
7420: if(ll<jj){
7421: if(itimes==1){
7422: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7423: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7424: }else{
7425: printf(" 0.");
7426: fprintf(ficparo," 0.");
7427: }
7428: }else{
7429: if(itimes==1){
7430: printf(" Var(%s%1d%1d)",ca,i,j);
7431: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7432: }else{
7433: printf(" 0.");
7434: fprintf(ficparo," 0.");
7435: }
7436: }
7437: }
7438: } /* end lk */
7439: } /* end lj */
7440: } /* end li */
7441: printf("\n");
7442: fprintf(ficparo,"\n");
7443: numlinepar++;
7444: } /* end k*/
7445: } /*end j */
7446: } /* end i */
7447: } /* end itimes */
7448:
7449: } /* end of prwizard */
7450: /******************* Gompertz Likelihood ******************************/
7451: double gompertz(double x[])
7452: {
7453: double A,B,L=0.0,sump=0.,num=0.;
7454: int i,n=0; /* n is the size of the sample */
7455:
1.220 brouard 7456: for (i=1;i<=imx ; i++) {
1.126 brouard 7457: sump=sump+weight[i];
7458: /* sump=sump+1;*/
7459: num=num+1;
7460: }
7461:
7462:
7463: /* for (i=0; i<=imx; i++)
7464: 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]);*/
7465:
7466: for (i=1;i<=imx ; i++)
7467: {
7468: if (cens[i] == 1 && wav[i]>1)
7469: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7470:
7471: if (cens[i] == 0 && wav[i]>1)
7472: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7473: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7474:
7475: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7476: if (wav[i] > 1 ) { /* ??? */
7477: L=L+A*weight[i];
7478: /* 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]);*/
7479: }
7480: }
7481:
7482: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7483:
7484: return -2*L*num/sump;
7485: }
7486:
1.136 brouard 7487: #ifdef GSL
7488: /******************* Gompertz_f Likelihood ******************************/
7489: double gompertz_f(const gsl_vector *v, void *params)
7490: {
7491: double A,B,LL=0.0,sump=0.,num=0.;
7492: double *x= (double *) v->data;
7493: int i,n=0; /* n is the size of the sample */
7494:
7495: for (i=0;i<=imx-1 ; i++) {
7496: sump=sump+weight[i];
7497: /* sump=sump+1;*/
7498: num=num+1;
7499: }
7500:
7501:
7502: /* for (i=0; i<=imx; i++)
7503: 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]);*/
7504: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7505: for (i=1;i<=imx ; i++)
7506: {
7507: if (cens[i] == 1 && wav[i]>1)
7508: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7509:
7510: if (cens[i] == 0 && wav[i]>1)
7511: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7512: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7513:
7514: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7515: if (wav[i] > 1 ) { /* ??? */
7516: LL=LL+A*weight[i];
7517: /* 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]);*/
7518: }
7519: }
7520:
7521: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7522: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7523:
7524: return -2*LL*num/sump;
7525: }
7526: #endif
7527:
1.126 brouard 7528: /******************* Printing html file ***********/
1.201 brouard 7529: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7530: int lastpass, int stepm, int weightopt, char model[],\
7531: int imx, double p[],double **matcov,double agemortsup){
7532: int i,k;
7533:
7534: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7535: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7536: for (i=1;i<=2;i++)
7537: 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 7538: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7539: fprintf(fichtm,"</ul>");
7540:
7541: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7542:
7543: 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>");
7544:
7545: for (k=agegomp;k<(agemortsup-2);k++)
7546: 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]);
7547:
7548:
7549: fflush(fichtm);
7550: }
7551:
7552: /******************* Gnuplot file **************/
1.201 brouard 7553: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7554:
7555: char dirfileres[132],optfileres[132];
1.164 brouard 7556:
1.126 brouard 7557: int ng;
7558:
7559:
7560: /*#ifdef windows */
7561: fprintf(ficgp,"cd \"%s\" \n",pathc);
7562: /*#endif */
7563:
7564:
7565: strcpy(dirfileres,optionfilefiname);
7566: strcpy(optfileres,"vpl");
1.199 brouard 7567: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7568: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7569: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7570: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7571: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7572:
7573: }
7574:
1.136 brouard 7575: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7576: {
1.126 brouard 7577:
1.136 brouard 7578: /*-------- data file ----------*/
7579: FILE *fic;
7580: char dummy[]=" ";
1.223 brouard 7581: int i=0, j=0, n=0, iv=0;
7582: int lstra;
1.136 brouard 7583: int linei, month, year,iout;
7584: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7585: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7586: char *stratrunc;
1.223 brouard 7587:
1.126 brouard 7588:
7589:
1.136 brouard 7590: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7591: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7592: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7593: }
1.126 brouard 7594:
1.136 brouard 7595: i=1;
7596: linei=0;
7597: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7598: linei=linei+1;
7599: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7600: if(line[j] == '\t')
7601: line[j] = ' ';
7602: }
7603: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7604: ;
7605: };
7606: line[j+1]=0; /* Trims blanks at end of line */
7607: if(line[0]=='#'){
7608: fprintf(ficlog,"Comment line\n%s\n",line);
7609: printf("Comment line\n%s\n",line);
7610: continue;
7611: }
7612: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7613: strcpy(line, linetmp);
1.223 brouard 7614:
7615: /* Loops on waves */
7616: for (j=maxwav;j>=1;j--){
7617: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.232 ! brouard 7618: cutv(stra, strb, line, ' ');
! 7619: if(strb[0]=='.') { /* Missing value */
! 7620: lval=-1;
! 7621: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
! 7622: cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
! 7623: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
! 7624: 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);
! 7625: 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);
! 7626: return 1;
! 7627: }
! 7628: }else{
! 7629: errno=0;
! 7630: /* what_kind_of_number(strb); */
! 7631: dval=strtod(strb,&endptr);
! 7632: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
! 7633: /* if(strb != endptr && *endptr == '\0') */
! 7634: /* dval=dlval; */
! 7635: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
! 7636: if( strb[0]=='\0' || (*endptr != '\0')){
! 7637: 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);
! 7638: 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);
! 7639: return 1;
! 7640: }
! 7641: cotqvar[j][iv][i]=dval;
! 7642: cotvar[j][ntv+iv][i]=dval;
! 7643: }
! 7644: strcpy(line,stra);
1.223 brouard 7645: }/* end loop ntqv */
1.225 brouard 7646:
1.223 brouard 7647: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.232 ! brouard 7648: cutv(stra, strb, line, ' ');
! 7649: if(strb[0]=='.') { /* Missing value */
! 7650: lval=-1;
! 7651: }else{
! 7652: errno=0;
! 7653: lval=strtol(strb,&endptr,10);
! 7654: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 7655: if( strb[0]=='\0' || (*endptr != '\0')){
! 7656: 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);
! 7657: 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);
! 7658: return 1;
! 7659: }
! 7660: }
! 7661: if(lval <-1 || lval >1){
! 7662: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7663: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7664: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.232 ! brouard 7665: For example, for multinomial values like 1, 2 and 3,\n \
! 7666: build V1=0 V2=0 for the reference value (1),\n \
! 7667: V1=1 V2=0 for (2) \n \
1.223 brouard 7668: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.232 ! brouard 7669: output of IMaCh is often meaningless.\n \
1.223 brouard 7670: Exiting.\n",lval,linei, i,line,j);
1.232 ! brouard 7671: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7672: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7673: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.232 ! brouard 7674: For example, for multinomial values like 1, 2 and 3,\n \
! 7675: build V1=0 V2=0 for the reference value (1),\n \
! 7676: V1=1 V2=0 for (2) \n \
1.223 brouard 7677: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.232 ! brouard 7678: output of IMaCh is often meaningless.\n \
1.223 brouard 7679: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.232 ! brouard 7680: return 1;
! 7681: }
! 7682: cotvar[j][iv][i]=(double)(lval);
! 7683: strcpy(line,stra);
1.223 brouard 7684: }/* end loop ntv */
1.225 brouard 7685:
1.223 brouard 7686: /* Statuses at wave */
1.137 brouard 7687: cutv(stra, strb, line, ' ');
1.223 brouard 7688: if(strb[0]=='.') { /* Missing value */
1.232 ! brouard 7689: lval=-1;
1.136 brouard 7690: }else{
1.232 ! brouard 7691: errno=0;
! 7692: lval=strtol(strb,&endptr,10);
! 7693: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 7694: if( strb[0]=='\0' || (*endptr != '\0')){
! 7695: 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);
! 7696: 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);
! 7697: return 1;
! 7698: }
1.136 brouard 7699: }
1.225 brouard 7700:
1.136 brouard 7701: s[j][i]=lval;
1.225 brouard 7702:
1.223 brouard 7703: /* Date of Interview */
1.136 brouard 7704: strcpy(line,stra);
7705: cutv(stra, strb,line,' ');
1.169 brouard 7706: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7707: }
1.169 brouard 7708: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7709: month=99;
7710: year=9999;
1.136 brouard 7711: }else{
1.225 brouard 7712: 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);
7713: 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);
7714: return 1;
1.136 brouard 7715: }
7716: anint[j][i]= (double) year;
7717: mint[j][i]= (double)month;
7718: strcpy(line,stra);
1.223 brouard 7719: } /* End loop on waves */
1.225 brouard 7720:
1.223 brouard 7721: /* Date of death */
1.136 brouard 7722: cutv(stra, strb,line,' ');
1.169 brouard 7723: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7724: }
1.169 brouard 7725: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7726: month=99;
7727: year=9999;
7728: }else{
1.141 brouard 7729: 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 7730: 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);
7731: return 1;
1.136 brouard 7732: }
7733: andc[i]=(double) year;
7734: moisdc[i]=(double) month;
7735: strcpy(line,stra);
7736:
1.223 brouard 7737: /* Date of birth */
1.136 brouard 7738: cutv(stra, strb,line,' ');
1.169 brouard 7739: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7740: }
1.169 brouard 7741: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7742: month=99;
7743: year=9999;
7744: }else{
1.141 brouard 7745: 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);
7746: 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 7747: return 1;
1.136 brouard 7748: }
7749: if (year==9999) {
1.141 brouard 7750: 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);
7751: 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 7752: return 1;
7753:
1.136 brouard 7754: }
7755: annais[i]=(double)(year);
7756: moisnais[i]=(double)(month);
7757: strcpy(line,stra);
1.225 brouard 7758:
1.223 brouard 7759: /* Sample weight */
1.136 brouard 7760: cutv(stra, strb,line,' ');
7761: errno=0;
7762: dval=strtod(strb,&endptr);
7763: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7764: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7765: 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 7766: fflush(ficlog);
7767: return 1;
7768: }
7769: weight[i]=dval;
7770: strcpy(line,stra);
1.225 brouard 7771:
1.223 brouard 7772: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7773: cutv(stra, strb, line, ' ');
7774: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7775: lval=-1;
1.223 brouard 7776: }else{
1.225 brouard 7777: errno=0;
7778: /* what_kind_of_number(strb); */
7779: dval=strtod(strb,&endptr);
7780: /* if(strb != endptr && *endptr == '\0') */
7781: /* dval=dlval; */
7782: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7783: if( strb[0]=='\0' || (*endptr != '\0')){
7784: 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);
7785: 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);
7786: return 1;
7787: }
7788: coqvar[iv][i]=dval;
1.226 brouard 7789: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7790: }
7791: strcpy(line,stra);
7792: }/* end loop nqv */
1.136 brouard 7793:
1.223 brouard 7794: /* Covariate values */
1.136 brouard 7795: for (j=ncovcol;j>=1;j--){
7796: cutv(stra, strb,line,' ');
1.223 brouard 7797: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7798: lval=-1;
1.136 brouard 7799: }else{
1.225 brouard 7800: errno=0;
7801: lval=strtol(strb,&endptr,10);
7802: if( strb[0]=='\0' || (*endptr != '\0')){
7803: 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);
7804: 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);
7805: return 1;
7806: }
1.136 brouard 7807: }
7808: if(lval <-1 || lval >1){
1.225 brouard 7809: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7810: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7811: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7812: For example, for multinomial values like 1, 2 and 3,\n \
7813: build V1=0 V2=0 for the reference value (1),\n \
7814: V1=1 V2=0 for (2) \n \
1.136 brouard 7815: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7816: output of IMaCh is often meaningless.\n \
1.136 brouard 7817: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7818: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7819: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7820: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7821: For example, for multinomial values like 1, 2 and 3,\n \
7822: build V1=0 V2=0 for the reference value (1),\n \
7823: V1=1 V2=0 for (2) \n \
1.136 brouard 7824: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7825: output of IMaCh is often meaningless.\n \
1.136 brouard 7826: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7827: return 1;
1.136 brouard 7828: }
7829: covar[j][i]=(double)(lval);
7830: strcpy(line,stra);
7831: }
7832: lstra=strlen(stra);
1.225 brouard 7833:
1.136 brouard 7834: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7835: stratrunc = &(stra[lstra-9]);
7836: num[i]=atol(stratrunc);
7837: }
7838: else
7839: num[i]=atol(stra);
7840: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7841: 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;}*/
7842:
7843: i=i+1;
7844: } /* End loop reading data */
1.225 brouard 7845:
1.136 brouard 7846: *imax=i-1; /* Number of individuals */
7847: fclose(fic);
1.225 brouard 7848:
1.136 brouard 7849: return (0);
1.164 brouard 7850: /* endread: */
1.225 brouard 7851: printf("Exiting readdata: ");
7852: fclose(fic);
7853: return (1);
1.223 brouard 7854: }
1.126 brouard 7855:
1.230 brouard 7856: void removespace(char **stri){/*, char stro[]) {*/
7857: char *p1 = *stri, *p2 = *stri;
1.145 brouard 7858: do
7859: while (*p2 == ' ')
7860: p2++;
1.169 brouard 7861: while (*p1++ == *p2++);
1.230 brouard 7862: *stri=p1;
1.145 brouard 7863: }
7864:
1.230 brouard 7865: int decoderesult ( char resultline[])
7866: /**< This routine decode one result line and returns the combination # of dummy covariates only **/
7867: {
7868: int j=0, k=0;
7869: char resultsav[MAXLINE];
7870: char stra[80], strb[80], strc[80], strd[80],stre[80];
7871:
7872: removespace(&resultline);
7873: printf("decoderesult=%s\n",resultline);
7874:
7875: if (strstr(resultline,"v") !=0){
7876: printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
7877: fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
7878: return 1;
7879: }
7880: trimbb(resultsav, resultline);
7881: if (strlen(resultsav) >1){
7882: j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
7883: }
7884:
7885: for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
7886: cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
7887: resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
7888: cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
7889: Tvalsel[k]=atof(strc); /* 1 */
7890:
7891: cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
7892: Tvarsel[k]=atoi(strc);
7893: /* Typevarsel[k]=1; /\* 1 for age product *\/ */
7894: /* cptcovsel++; */
7895: if (nbocc(stra,'=') >0)
7896: strcpy(resultsav,stra); /* and analyzes it */
7897: }
7898: return (0);
7899: }
7900: int selected( int kvar){ /* Selected combination of covariates */
7901: if(Tvarsel[kvar])
7902: return (0);
7903: else
7904: return(1);
7905: }
7906: int decodemodel( char model[], int lastobs)
7907: /**< This routine decodes the model and returns:
1.224 brouard 7908: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7909: * - nagesqr = 1 if age*age in the model, otherwise 0.
7910: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7911: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
7912: * - cptcovage number of covariates with age*products =2
7913: * - cptcovs number of simple covariates
7914: * - 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
7915: * which is a new column after the 9 (ncovcol) variables.
7916: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7917: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7918: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7919: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7920: */
1.136 brouard 7921: {
1.145 brouard 7922: int i, j, k, ks;
1.227 brouard 7923: int j1, k1, k2, k3, k4;
1.136 brouard 7924: char modelsav[80];
1.145 brouard 7925: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7926: char *strpt;
1.136 brouard 7927:
1.145 brouard 7928: /*removespace(model);*/
1.136 brouard 7929: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7930: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7931: if (strstr(model,"AGE") !=0){
1.192 brouard 7932: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7933: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7934: return 1;
7935: }
1.141 brouard 7936: if (strstr(model,"v") !=0){
7937: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7938: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7939: return 1;
7940: }
1.187 brouard 7941: strcpy(modelsav,model);
7942: if ((strpt=strstr(model,"age*age")) !=0){
7943: printf(" strpt=%s, model=%s\n",strpt, model);
7944: if(strpt != model){
1.231 brouard 7945: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7946: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7947: corresponding column of parameters.\n",model);
1.231 brouard 7948: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7949: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7950: corresponding column of parameters.\n",model); fflush(ficlog);
1.231 brouard 7951: return 1;
1.225 brouard 7952: }
1.187 brouard 7953: nagesqr=1;
7954: if (strstr(model,"+age*age") !=0)
1.231 brouard 7955: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7956: else if (strstr(model,"age*age+") !=0)
1.231 brouard 7957: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7958: else
1.231 brouard 7959: substrchaine(modelsav, model, "age*age");
1.187 brouard 7960: }else
7961: nagesqr=0;
7962: if (strlen(modelsav) >1){
7963: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7964: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 7965: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7966: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 7967: * cst, age and age*age
7968: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
7969: /* including age products which are counted in cptcovage.
7970: * but the covariates which are products must be treated
7971: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7972: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7973: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 7974:
7975:
1.187 brouard 7976: /* Design
7977: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7978: * < ncovcol=8 >
7979: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7980: * k= 1 2 3 4 5 6 7 8
7981: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7982: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 7983: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
7984: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7985: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7986: * Tage[++cptcovage]=k
7987: * if products, new covar are created after ncovcol with k1
7988: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7989: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7990: * 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
7991: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7992: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7993: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7994: * < ncovcol=8 >
7995: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7996: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7997: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7998: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7999: * p Tprod[1]@2={ 6, 5}
8000: *p Tvard[1][1]@4= {7, 8, 5, 6}
8001: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
8002: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
8003: *How to reorganize?
8004: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
8005: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
8006: * {2, 1, 4, 8, 5, 6, 3, 7}
8007: * Struct []
8008: */
1.225 brouard 8009:
1.187 brouard 8010: /* This loop fills the array Tvar from the string 'model'.*/
8011: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
8012: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
8013: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
8014: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
8015: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
8016: /* k=1 Tvar[1]=2 (from V2) */
8017: /* k=5 Tvar[5] */
8018: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 8019: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 8020: /* } */
1.198 brouard 8021: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 8022: /*
8023: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 8024: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
8025: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
8026: }
1.187 brouard 8027: cptcovage=0;
8028: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.232 ! brouard 8029: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
1.225 brouard 8030: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.232 ! brouard 8031: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
! 8032: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 8033: /*scanf("%d",i);*/
! 8034: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
! 8035: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 8036: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
! 8037: /* covar is not filled and then is empty */
! 8038: cptcovprod--;
! 8039: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
! 8040: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
! 8041: Typevar[k]=1; /* 1 for age product */
! 8042: cptcovage++; /* Sums the number of covariates which include age as a product */
! 8043: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
! 8044: /*printf("stre=%s ", stre);*/
! 8045: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 8046: cptcovprod--;
! 8047: cutl(stre,strb,strc,'V');
! 8048: Tvar[k]=atoi(stre);
! 8049: Typevar[k]=1; /* 1 for age product */
! 8050: cptcovage++;
! 8051: Tage[cptcovage]=k;
! 8052: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
! 8053: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
! 8054: cptcovn++;
! 8055: cptcovprodnoage++;k1++;
! 8056: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 8057: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
! 8058: because this model-covariate is a construction we invent a new column
! 8059: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
! 8060: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
! 8061: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
! 8062: Typevar[k]=2; /* 2 for double fixed dummy covariates */
! 8063: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
! 8064: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
! 8065: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
! 8066: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
! 8067: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
! 8068: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
! 8069: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
! 8070: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
1.225 brouard 8071: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
1.232 ! brouard 8072: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
! 8073: for (i=1; i<=lastobs;i++){
! 8074: /* Computes the new covariate which is a product of
! 8075: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
! 8076: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
! 8077: }
! 8078: } /* End age is not in the model */
! 8079: } /* End if model includes a product */
! 8080: else { /* no more sum */
! 8081: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 8082: /* scanf("%d",i);*/
! 8083: cutl(strd,strc,strb,'V');
! 8084: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
! 8085: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
! 8086: Tvar[k]=atoi(strd);
! 8087: Typevar[k]=0; /* 0 for simple covariates */
! 8088: }
! 8089: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 8090: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 8091: scanf("%d",i);*/
1.187 brouard 8092: } /* end of loop + on total covariates */
8093: } /* end if strlen(modelsave == 0) age*age might exist */
8094: } /* end if strlen(model == 0) */
1.136 brouard 8095:
8096: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
8097: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 8098:
1.136 brouard 8099: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 8100: printf("cptcovprod=%d ", cptcovprod);
8101: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
8102: scanf("%d ",i);*/
8103:
8104:
1.230 brouard 8105: /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
8106: of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
1.226 brouard 8107: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
8108: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
8109: k = 1 2 3 4 5 6 7 8 9
8110: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
8111: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 8112: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
8113: Dummy[k] 1 0 0 0 3 1 1 2 3
8114: Tmodelind[combination of covar]=k;
1.225 brouard 8115: */
8116: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 8117: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 8118: /* 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 8119: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 8120: printf("Model=%s\n\
8121: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8122: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8123: 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);
8124: fprintf(ficlog,"Model=%s\n\
8125: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8126: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8127: 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);
8128:
1.232 ! brouard 8129: for(k=1, ncovf=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
1.231 brouard 8130: if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy (<=ncovcol) covariates */
1.227 brouard 8131: Fixed[k]= 0;
8132: Dummy[k]= 0;
1.225 brouard 8133: ncoveff++;
1.232 ! brouard 8134: ncovf++;
1.231 brouard 8135: modell[k].maintype= FTYPE;
1.232 ! brouard 8136: TvarF[ncovf]=Tvar[k];
! 8137: TvarFind[ncovf]=k;
1.230 brouard 8138: TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
1.231 brouard 8139: TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
8140: }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 8141: Fixed[k]= 0;
8142: Dummy[k]= 1;
1.230 brouard 8143: nqfveff++;
1.231 brouard 8144: modell[k].maintype= FTYPE;
8145: modell[k].subtype= FQ;
1.232 ! brouard 8146: ncovf++;
! 8147: TvarF[ncovf]=Tvar[k];
! 8148: TvarFind[ncovf]=k;
1.231 brouard 8149: 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 8150: 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 */
1.225 brouard 8151: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
1.227 brouard 8152: Fixed[k]= 1;
8153: Dummy[k]= 0;
1.225 brouard 8154: ntveff++; /* Only simple time varying dummy variable */
1.231 brouard 8155: modell[k].maintype= VTYPE;
8156: modell[k].subtype= VD;
1.232 ! brouard 8157: ncovv++; /* Only simple time varying variables */
! 8158: TvarV[ncovv]=Tvar[k];
! 8159: TvarVind[ncovv]=k;
1.231 brouard 8160: 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 */
8161: 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 8162: 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);
8163: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.231 brouard 8164: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
8165: Fixed[k]= 1;
8166: Dummy[k]= 1;
8167: nqtveff++;
8168: modell[k].maintype= VTYPE;
8169: modell[k].subtype= VQ;
1.232 ! brouard 8170: ncovv++; /* Only simple time varying variables */
! 8171: TvarV[ncovv]=Tvar[k];
! 8172: TvarVind[ncovv]=k;
1.231 brouard 8173: 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 */
8174: 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 */
8175: TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
8176: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
8177: 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 8178: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8179: }else if (Typevar[k] == 1) { /* product with age */
1.232 ! brouard 8180: ncova++;
! 8181: TvarA[ncova]=Tvar[k];
! 8182: TvarAind[ncova]=k;
1.231 brouard 8183: if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
8184: Fixed[k]= 2;
8185: Dummy[k]= 2;
8186: modell[k].maintype= ATYPE;
8187: modell[k].subtype= APFD;
8188: /* ncoveff++; */
1.227 brouard 8189: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
1.231 brouard 8190: Fixed[k]= 2;
8191: Dummy[k]= 3;
8192: modell[k].maintype= ATYPE;
8193: modell[k].subtype= APFQ; /* Product age * fixed quantitative */
8194: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
1.227 brouard 8195: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
1.231 brouard 8196: Fixed[k]= 3;
8197: Dummy[k]= 2;
8198: modell[k].maintype= ATYPE;
8199: modell[k].subtype= APVD; /* Product age * varying dummy */
8200: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
1.227 brouard 8201: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
1.231 brouard 8202: Fixed[k]= 3;
8203: Dummy[k]= 3;
8204: modell[k].maintype= ATYPE;
8205: modell[k].subtype= APVQ; /* Product age * varying quantitative */
8206: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
1.227 brouard 8207: }
8208: }else if (Typevar[k] == 2) { /* product without age */
8209: k1=Tposprod[k];
1.232 ! brouard 8210: ncovv++; /* Only time varying variables */
! 8211: TvarV[ncovv]=Tvar[k];
! 8212: TvarVind[ncovv]=k;
1.227 brouard 8213: if(Tvard[k1][1] <=ncovcol){
1.231 brouard 8214: if(Tvard[k1][2] <=ncovcol){
8215: Fixed[k]= 1;
8216: Dummy[k]= 0;
8217: modell[k].maintype= FTYPE;
8218: modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
8219: }else if(Tvard[k1][2] <=ncovcol+nqv){
8220: Fixed[k]= 0; /* or 2 ?*/
8221: Dummy[k]= 1;
8222: modell[k].maintype= FTYPE;
8223: modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
8224: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8225: Fixed[k]= 1;
8226: Dummy[k]= 0;
8227: modell[k].maintype= VTYPE;
8228: modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
8229: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8230: Fixed[k]= 1;
8231: Dummy[k]= 1;
8232: modell[k].maintype= VTYPE;
8233: modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
8234: }
1.227 brouard 8235: }else if(Tvard[k1][1] <=ncovcol+nqv){
1.231 brouard 8236: if(Tvard[k1][2] <=ncovcol){
8237: Fixed[k]= 0; /* or 2 ?*/
8238: Dummy[k]= 1;
8239: modell[k].maintype= FTYPE;
8240: modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
8241: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8242: Fixed[k]= 1;
8243: Dummy[k]= 1;
8244: modell[k].maintype= VTYPE;
8245: modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
8246: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8247: Fixed[k]= 1;
8248: Dummy[k]= 1;
8249: modell[k].maintype= VTYPE;
8250: modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
8251: }
1.227 brouard 8252: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
1.231 brouard 8253: if(Tvard[k1][2] <=ncovcol){
8254: Fixed[k]= 1;
8255: Dummy[k]= 1;
8256: modell[k].maintype= VTYPE;
8257: modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
8258: }else if(Tvard[k1][2] <=ncovcol+nqv){
8259: Fixed[k]= 1;
8260: Dummy[k]= 1;
8261: modell[k].maintype= VTYPE;
8262: modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
8263: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8264: Fixed[k]= 1;
8265: Dummy[k]= 0;
8266: modell[k].maintype= VTYPE;
8267: modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
8268: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8269: Fixed[k]= 1;
8270: Dummy[k]= 1;
8271: modell[k].maintype= VTYPE;
8272: modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
8273: }
1.227 brouard 8274: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
1.231 brouard 8275: if(Tvard[k1][2] <=ncovcol){
8276: Fixed[k]= 1;
8277: Dummy[k]= 1;
8278: modell[k].maintype= VTYPE;
8279: modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
8280: }else if(Tvard[k1][2] <=ncovcol+nqv){
8281: Fixed[k]= 1;
8282: Dummy[k]= 1;
8283: modell[k].maintype= VTYPE;
8284: modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
8285: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8286: Fixed[k]= 1;
8287: Dummy[k]= 1;
8288: modell[k].maintype= VTYPE;
8289: modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
8290: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8291: Fixed[k]= 1;
8292: Dummy[k]= 1;
8293: modell[k].maintype= VTYPE;
8294: modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
8295: }
1.227 brouard 8296: }else{
1.231 brouard 8297: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
8298: fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
1.226 brouard 8299: } /* end k1 */
1.225 brouard 8300: }else{
1.226 brouard 8301: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8302: 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 8303: }
1.227 brouard 8304: 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 8305: printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);
1.227 brouard 8306: 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]);
8307: }
8308: /* Searching for doublons in the model */
8309: for(k1=1; k1<= cptcovt;k1++){
8310: for(k2=1; k2 <k1;k2++){
8311: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
1.231 brouard 8312: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8313: if(Tvar[k1]==Tvar[k2]){
8314: 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]]);
8315: 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);
8316: return(1);
8317: }
8318: }else if (Typevar[k1] ==2){
8319: k3=Tposprod[k1];
8320: k4=Tposprod[k2];
8321: 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])) ){
8322: 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]]);
8323: 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);
8324: return(1);
8325: }
8326: }
1.227 brouard 8327: }
8328: }
1.225 brouard 8329: }
8330: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8331: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.232 ! brouard 8332: printf("ncovf=%d, ncovv=%d, ncova=%d\n",ncovf,ncovv,ncova);
! 8333: fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d\n",ncovf,ncovv,ncova);
1.137 brouard 8334: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8335: /*endread:*/
1.225 brouard 8336: printf("Exiting decodemodel: ");
8337: return (1);
1.136 brouard 8338: }
8339:
1.169 brouard 8340: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8341: {
8342: int i, m;
1.218 brouard 8343: int firstone=0;
8344:
1.136 brouard 8345: for (i=1; i<=imx; i++) {
8346: for(m=2; (m<= maxwav); m++) {
8347: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8348: anint[m][i]=9999;
1.216 brouard 8349: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8350: s[m][i]=-1;
1.136 brouard 8351: }
8352: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8353: *nberr = *nberr + 1;
1.218 brouard 8354: if(firstone == 0){
8355: firstone=1;
8356: 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);
8357: }
8358: 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 8359: s[m][i]=-1;
8360: }
8361: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8362: (*nberr)++;
1.136 brouard 8363: 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]);
8364: 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]);
8365: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8366: }
8367: }
8368: }
8369:
8370: for (i=1; i<=imx; i++) {
8371: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8372: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8373: 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 8374: if (s[m][i] >= nlstate+1) {
1.169 brouard 8375: if(agedc[i]>0){
8376: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8377: agev[m][i]=agedc[i];
1.214 brouard 8378: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8379: }else {
1.136 brouard 8380: if ((int)andc[i]!=9999){
8381: nbwarn++;
8382: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8383: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8384: agev[m][i]=-1;
8385: }
8386: }
1.169 brouard 8387: } /* agedc > 0 */
1.214 brouard 8388: } /* end if */
1.136 brouard 8389: else if(s[m][i] !=9){ /* Standard case, age in fractional
8390: years but with the precision of a month */
8391: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8392: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8393: agev[m][i]=1;
8394: else if(agev[m][i] < *agemin){
8395: *agemin=agev[m][i];
8396: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8397: }
8398: else if(agev[m][i] >*agemax){
8399: *agemax=agev[m][i];
1.156 brouard 8400: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8401: }
8402: /*agev[m][i]=anint[m][i]-annais[i];*/
8403: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8404: } /* en if 9*/
1.136 brouard 8405: else { /* =9 */
1.214 brouard 8406: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8407: agev[m][i]=1;
8408: s[m][i]=-1;
8409: }
8410: }
1.214 brouard 8411: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8412: agev[m][i]=1;
1.214 brouard 8413: else{
8414: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8415: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8416: agev[m][i]=0;
8417: }
8418: } /* End for lastpass */
8419: }
1.136 brouard 8420:
8421: for (i=1; i<=imx; i++) {
8422: for(m=firstpass; (m<=lastpass); m++){
8423: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8424: (*nberr)++;
1.136 brouard 8425: 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);
8426: 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);
8427: return 1;
8428: }
8429: }
8430: }
8431:
8432: /*for (i=1; i<=imx; i++){
8433: for (m=firstpass; (m<lastpass); m++){
8434: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8435: }
8436:
8437: }*/
8438:
8439:
1.139 brouard 8440: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8441: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8442:
8443: return (0);
1.164 brouard 8444: /* endread:*/
1.136 brouard 8445: printf("Exiting calandcheckages: ");
8446: return (1);
8447: }
8448:
1.172 brouard 8449: #if defined(_MSC_VER)
8450: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8451: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8452: //#include "stdafx.h"
8453: //#include <stdio.h>
8454: //#include <tchar.h>
8455: //#include <windows.h>
8456: //#include <iostream>
8457: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8458:
8459: LPFN_ISWOW64PROCESS fnIsWow64Process;
8460:
8461: BOOL IsWow64()
8462: {
8463: BOOL bIsWow64 = FALSE;
8464:
8465: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8466: // (HANDLE, PBOOL);
8467:
8468: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8469:
8470: HMODULE module = GetModuleHandle(_T("kernel32"));
8471: const char funcName[] = "IsWow64Process";
8472: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8473: GetProcAddress(module, funcName);
8474:
8475: if (NULL != fnIsWow64Process)
8476: {
8477: if (!fnIsWow64Process(GetCurrentProcess(),
8478: &bIsWow64))
8479: //throw std::exception("Unknown error");
8480: printf("Unknown error\n");
8481: }
8482: return bIsWow64 != FALSE;
8483: }
8484: #endif
1.177 brouard 8485:
1.191 brouard 8486: void syscompilerinfo(int logged)
1.167 brouard 8487: {
8488: /* #include "syscompilerinfo.h"*/
1.185 brouard 8489: /* command line Intel compiler 32bit windows, XP compatible:*/
8490: /* /GS /W3 /Gy
8491: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8492: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8493: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8494: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8495: */
8496: /* 64 bits */
1.185 brouard 8497: /*
8498: /GS /W3 /Gy
8499: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8500: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8501: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8502: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8503: /* Optimization are useless and O3 is slower than O2 */
8504: /*
8505: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8506: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8507: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8508: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8509: */
1.186 brouard 8510: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8511: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8512: /PDB:"visual studio
8513: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8514: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8515: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8516: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8517: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8518: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8519: uiAccess='false'"
8520: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8521: /NOLOGO /TLBID:1
8522: */
1.177 brouard 8523: #if defined __INTEL_COMPILER
1.178 brouard 8524: #if defined(__GNUC__)
8525: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8526: #endif
1.177 brouard 8527: #elif defined(__GNUC__)
1.179 brouard 8528: #ifndef __APPLE__
1.174 brouard 8529: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8530: #endif
1.177 brouard 8531: struct utsname sysInfo;
1.178 brouard 8532: int cross = CROSS;
8533: if (cross){
8534: printf("Cross-");
1.191 brouard 8535: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8536: }
1.174 brouard 8537: #endif
8538:
1.171 brouard 8539: #include <stdint.h>
1.178 brouard 8540:
1.191 brouard 8541: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8542: #if defined(__clang__)
1.191 brouard 8543: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8544: #endif
8545: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8546: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8547: #endif
8548: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8549: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8550: #endif
8551: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8552: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8553: #endif
8554: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8555: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8556: #endif
8557: #if defined(_MSC_VER)
1.191 brouard 8558: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8559: #endif
8560: #if defined(__PGI)
1.191 brouard 8561: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8562: #endif
8563: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8564: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8565: #endif
1.191 brouard 8566: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8567:
1.167 brouard 8568: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8569: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8570: // Windows (x64 and x86)
1.191 brouard 8571: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8572: #elif __unix__ // all unices, not all compilers
8573: // Unix
1.191 brouard 8574: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8575: #elif __linux__
8576: // linux
1.191 brouard 8577: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8578: #elif __APPLE__
1.174 brouard 8579: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8580: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8581: #endif
8582:
8583: /* __MINGW32__ */
8584: /* __CYGWIN__ */
8585: /* __MINGW64__ */
8586: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8587: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8588: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8589: /* _WIN64 // Defined for applications for Win64. */
8590: /* _M_X64 // Defined for compilations that target x64 processors. */
8591: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8592:
1.167 brouard 8593: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8594: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8595: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8596: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8597: #else
1.191 brouard 8598: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8599: #endif
8600:
1.169 brouard 8601: #if defined(__GNUC__)
8602: # if defined(__GNUC_PATCHLEVEL__)
8603: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8604: + __GNUC_MINOR__ * 100 \
8605: + __GNUC_PATCHLEVEL__)
8606: # else
8607: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8608: + __GNUC_MINOR__ * 100)
8609: # endif
1.174 brouard 8610: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8611: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8612:
8613: if (uname(&sysInfo) != -1) {
8614: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8615: 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 8616: }
8617: else
8618: perror("uname() error");
1.179 brouard 8619: //#ifndef __INTEL_COMPILER
8620: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8621: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8622: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8623: #endif
1.169 brouard 8624: #endif
1.172 brouard 8625:
8626: // void main()
8627: // {
1.169 brouard 8628: #if defined(_MSC_VER)
1.174 brouard 8629: if (IsWow64()){
1.191 brouard 8630: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8631: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8632: }
8633: else{
1.191 brouard 8634: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8635: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8636: }
1.172 brouard 8637: // printf("\nPress Enter to continue...");
8638: // getchar();
8639: // }
8640:
1.169 brouard 8641: #endif
8642:
1.167 brouard 8643:
1.219 brouard 8644: }
1.136 brouard 8645:
1.219 brouard 8646: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8647: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8648: int i, j, k, i1 ;
1.202 brouard 8649: /* double ftolpl = 1.e-10; */
1.180 brouard 8650: double age, agebase, agelim;
1.203 brouard 8651: double tot;
1.180 brouard 8652:
1.202 brouard 8653: strcpy(filerespl,"PL_");
8654: strcat(filerespl,fileresu);
8655: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8656: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8657: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8658: }
1.227 brouard 8659: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
8660: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8661: pstamp(ficrespl);
1.203 brouard 8662: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8663: fprintf(ficrespl,"#Age ");
8664: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8665: fprintf(ficrespl,"\n");
1.180 brouard 8666:
1.219 brouard 8667: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8668:
1.219 brouard 8669: agebase=ageminpar;
8670: agelim=agemaxpar;
1.180 brouard 8671:
1.227 brouard 8672: /* i1=pow(2,ncoveff); */
8673: i1=pow(2,cptcoveff); /* Number of dummy covariates */
1.219 brouard 8674: if (cptcovn < 1){i1=1;}
1.180 brouard 8675:
1.220 brouard 8676: for(k=1; k<=i1;k++){
8677: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8678: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8679: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8680: /* k=k+1; */
1.219 brouard 8681: /* to clean */
8682: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8683: fprintf(ficrespl,"#******");
8684: printf("#******");
8685: fprintf(ficlog,"#******");
1.227 brouard 8686: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
8687: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8688: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8689: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8690: }
8691: fprintf(ficrespl,"******\n");
8692: printf("******\n");
8693: fprintf(ficlog,"******\n");
1.227 brouard 8694: if(invalidvarcomb[k]){
8695: printf("\nCombination (%d) ignored because no case \n",k);
8696: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
8697: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8698: continue;
1.227 brouard 8699: }
1.219 brouard 8700:
8701: fprintf(ficrespl,"#Age ");
1.227 brouard 8702: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8703: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8704: }
8705: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8706: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 8707:
1.219 brouard 8708: for (age=agebase; age<=agelim; age++){
8709: /* for (age=agebase; age<=agebase; age++){ */
8710: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8711: fprintf(ficrespl,"%.0f ",age );
1.227 brouard 8712: for(j=1;j<=cptcoveff;j++)
8713: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8714: tot=0.;
8715: for(i=1; i<=nlstate;i++){
1.227 brouard 8716: tot += prlim[i][i];
8717: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8718: }
8719: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8720: } /* Age */
8721: /* was end of cptcod */
8722: } /* cptcov */
8723: return 0;
1.180 brouard 8724: }
8725:
1.218 brouard 8726: 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){
8727: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8728:
8729: /* Computes the back prevalence limit for any combination of covariate values
8730: * at any age between ageminpar and agemaxpar
8731: */
1.217 brouard 8732: int i, j, k, i1 ;
8733: /* double ftolpl = 1.e-10; */
8734: double age, agebase, agelim;
8735: double tot;
1.218 brouard 8736: /* double ***mobaverage; */
8737: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8738:
8739: strcpy(fileresplb,"PLB_");
8740: strcat(fileresplb,fileresu);
8741: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8742: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8743: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8744: }
8745: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8746: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8747: pstamp(ficresplb);
8748: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8749: fprintf(ficresplb,"#Age ");
8750: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8751: fprintf(ficresplb,"\n");
8752:
1.218 brouard 8753:
8754: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8755:
8756: agebase=ageminpar;
8757: agelim=agemaxpar;
8758:
8759:
1.227 brouard 8760: i1=pow(2,cptcoveff);
1.218 brouard 8761: if (cptcovn < 1){i1=1;}
1.227 brouard 8762:
8763: for(k=1; k<=i1;k++){
1.218 brouard 8764: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8765: fprintf(ficresplb,"#******");
8766: printf("#******");
8767: fprintf(ficlog,"#******");
1.227 brouard 8768: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 8769: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8770: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8771: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8772: }
8773: fprintf(ficresplb,"******\n");
8774: printf("******\n");
8775: fprintf(ficlog,"******\n");
1.227 brouard 8776: if(invalidvarcomb[k]){
8777: printf("\nCombination (%d) ignored because no cases \n",k);
8778: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8779: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8780: continue;
8781: }
1.218 brouard 8782:
8783: fprintf(ficresplb,"#Age ");
1.227 brouard 8784: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 8785: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8786: }
8787: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8788: fprintf(ficresplb,"Total Years_to_converge\n");
8789:
8790:
8791: for (age=agebase; age<=agelim; age++){
8792: /* for (age=agebase; age<=agebase; age++){ */
8793: if(mobilavproj > 0){
8794: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8795: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 brouard 8796: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8797: }else if (mobilavproj == 0){
1.227 brouard 8798: 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);
8799: 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);
8800: exit(1);
1.218 brouard 8801: }else{
1.227 brouard 8802: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8803: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8804: }
8805: fprintf(ficresplb,"%.0f ",age );
1.227 brouard 8806: for(j=1;j<=cptcoveff;j++)
8807: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8808: tot=0.;
8809: for(i=1; i<=nlstate;i++){
1.227 brouard 8810: tot += bprlim[i][i];
8811: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8812: }
8813: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8814: } /* Age */
8815: /* was end of cptcod */
8816: } /* cptcov */
8817:
8818: /* hBijx(p, bage, fage); */
8819: /* fclose(ficrespijb); */
8820:
8821: return 0;
1.217 brouard 8822: }
1.218 brouard 8823:
1.180 brouard 8824: int hPijx(double *p, int bage, int fage){
8825: /*------------- h Pij x at various ages ------------*/
8826:
8827: int stepsize;
8828: int agelim;
8829: int hstepm;
8830: int nhstepm;
8831: int h, i, i1, j, k;
8832:
8833: double agedeb;
8834: double ***p3mat;
8835:
1.201 brouard 8836: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8837: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8838: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8839: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8840: }
8841: printf("Computing pij: result on file '%s' \n", filerespij);
8842: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8843:
8844: stepsize=(int) (stepm+YEARM-1)/YEARM;
8845: /*if (stepm<=24) stepsize=2;*/
8846:
8847: agelim=AGESUP;
8848: hstepm=stepsize*YEARM; /* Every year of age */
8849: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8850:
1.180 brouard 8851: /* hstepm=1; aff par mois*/
8852: pstamp(ficrespij);
8853: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 8854: i1= pow(2,cptcoveff);
1.218 brouard 8855: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8856: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8857: /* k=k+1; */
1.227 brouard 8858: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.183 brouard 8859: fprintf(ficrespij,"\n#****** ");
1.227 brouard 8860: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8861: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8862: fprintf(ficrespij,"******\n");
8863:
8864: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8865: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8866: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8867:
8868: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8869:
1.183 brouard 8870: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8871: oldm=oldms;savm=savms;
8872: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8873: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8874: for(i=1; i<=nlstate;i++)
8875: for(j=1; j<=nlstate+ndeath;j++)
8876: fprintf(ficrespij," %1d-%1d",i,j);
8877: fprintf(ficrespij,"\n");
8878: for (h=0; h<=nhstepm; h++){
8879: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8880: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8881: for(i=1; i<=nlstate;i++)
8882: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8883: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8884: fprintf(ficrespij,"\n");
8885: }
1.183 brouard 8886: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8887: fprintf(ficrespij,"\n");
8888: }
1.180 brouard 8889: /*}*/
8890: }
1.218 brouard 8891: return 0;
1.180 brouard 8892: }
1.218 brouard 8893:
8894: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8895: /*------------- h Bij x at various ages ------------*/
8896:
8897: int stepsize;
1.218 brouard 8898: /* int agelim; */
8899: int ageminl;
1.217 brouard 8900: int hstepm;
8901: int nhstepm;
8902: int h, i, i1, j, k;
1.218 brouard 8903:
1.217 brouard 8904: double agedeb;
8905: double ***p3mat;
1.218 brouard 8906:
8907: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8908: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8909: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8910: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8911: }
8912: printf("Computing pij back: result on file '%s' \n", filerespijb);
8913: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8914:
8915: stepsize=(int) (stepm+YEARM-1)/YEARM;
8916: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8917:
1.218 brouard 8918: /* agelim=AGESUP; */
8919: ageminl=30;
8920: hstepm=stepsize*YEARM; /* Every year of age */
8921: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8922:
8923: /* hstepm=1; aff par mois*/
8924: pstamp(ficrespijb);
8925: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 8926: i1= pow(2,cptcoveff);
1.218 brouard 8927: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8928: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8929: /* k=k+1; */
1.227 brouard 8930: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 8931: fprintf(ficrespijb,"\n#****** ");
1.227 brouard 8932: for(j=1;j<=cptcoveff;j++)
1.218 brouard 8933: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8934: fprintf(ficrespijb,"******\n");
1.222 brouard 8935: if(invalidvarcomb[k]){
8936: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8937: continue;
8938: }
1.218 brouard 8939:
8940: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8941: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8942: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8943: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8944: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8945:
8946: /* nhstepm=nhstepm*YEARM; aff par mois*/
8947:
8948: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8949: /* oldm=oldms;savm=savms; */
8950: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8951: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8952: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8953: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8954: for(i=1; i<=nlstate;i++)
8955: for(j=1; j<=nlstate+ndeath;j++)
8956: fprintf(ficrespijb," %1d-%1d",i,j);
8957: fprintf(ficrespijb,"\n");
8958: for (h=0; h<=nhstepm; h++){
8959: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8960: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8961: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8962: for(i=1; i<=nlstate;i++)
8963: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8964: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8965: fprintf(ficrespijb,"\n");
8966: }
1.218 brouard 8967: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8968: fprintf(ficrespijb,"\n");
1.217 brouard 8969: }
1.218 brouard 8970: /*}*/
8971: }
8972: return 0;
8973: } /* hBijx */
1.217 brouard 8974:
1.180 brouard 8975:
1.136 brouard 8976: /***********************************************/
8977: /**************** Main Program *****************/
8978: /***********************************************/
8979:
8980: int main(int argc, char *argv[])
8981: {
8982: #ifdef GSL
8983: const gsl_multimin_fminimizer_type *T;
8984: size_t iteri = 0, it;
8985: int rval = GSL_CONTINUE;
8986: int status = GSL_SUCCESS;
8987: double ssval;
8988: #endif
8989: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8990: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8991: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8992: int jj, ll, li, lj, lk;
1.136 brouard 8993: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8994: int num_filled;
1.136 brouard 8995: int itimes;
8996: int NDIM=2;
8997: int vpopbased=0;
8998:
1.164 brouard 8999: char ca[32], cb[32];
1.136 brouard 9000: /* FILE *fichtm; *//* Html File */
9001: /* FILE *ficgp;*/ /*Gnuplot File */
9002: struct stat info;
1.191 brouard 9003: double agedeb=0.;
1.194 brouard 9004:
9005: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 9006: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 9007:
1.165 brouard 9008: double fret;
1.191 brouard 9009: double dum=0.; /* Dummy variable */
1.136 brouard 9010: double ***p3mat;
1.218 brouard 9011: /* double ***mobaverage; */
1.164 brouard 9012:
9013: char line[MAXLINE];
1.197 brouard 9014: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
9015:
9016: char model[MAXLINE], modeltemp[MAXLINE];
1.230 brouard 9017: char resultline[MAXLINE];
9018:
1.136 brouard 9019: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 9020: char *tok, *val; /* pathtot */
1.136 brouard 9021: int firstobs=1, lastobs=10;
1.195 brouard 9022: int c, h , cpt, c2;
1.191 brouard 9023: int jl=0;
9024: int i1, j1, jk, stepsize=0;
1.194 brouard 9025: int count=0;
9026:
1.164 brouard 9027: int *tab;
1.136 brouard 9028: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 9029: int backcast=0;
1.136 brouard 9030: int mobilav=0,popforecast=0;
1.191 brouard 9031: int hstepm=0, nhstepm=0;
1.136 brouard 9032: int agemortsup;
9033: float sumlpop=0.;
9034: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
9035: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
9036:
1.191 brouard 9037: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 9038: double ftolpl=FTOL;
9039: double **prlim;
1.217 brouard 9040: double **bprlim;
1.136 brouard 9041: double ***param; /* Matrix of parameters */
9042: double *p;
9043: double **matcov; /* Matrix of covariance */
1.203 brouard 9044: double **hess; /* Hessian matrix */
1.136 brouard 9045: double ***delti3; /* Scale */
9046: double *delti; /* Scale */
9047: double ***eij, ***vareij;
9048: double **varpl; /* Variances of prevalence limits by age */
9049: double *epj, vepp;
1.164 brouard 9050:
1.136 brouard 9051: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 9052: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
9053:
1.136 brouard 9054: double **ximort;
1.145 brouard 9055: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 9056: int *dcwave;
9057:
1.164 brouard 9058: char z[1]="c";
1.136 brouard 9059:
9060: /*char *strt;*/
9061: char strtend[80];
1.126 brouard 9062:
1.164 brouard 9063:
1.126 brouard 9064: /* setlocale (LC_ALL, ""); */
9065: /* bindtextdomain (PACKAGE, LOCALEDIR); */
9066: /* textdomain (PACKAGE); */
9067: /* setlocale (LC_CTYPE, ""); */
9068: /* setlocale (LC_MESSAGES, ""); */
9069:
9070: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 9071: rstart_time = time(NULL);
9072: /* (void) gettimeofday(&start_time,&tzp);*/
9073: start_time = *localtime(&rstart_time);
1.126 brouard 9074: curr_time=start_time;
1.157 brouard 9075: /*tml = *localtime(&start_time.tm_sec);*/
9076: /* strcpy(strstart,asctime(&tml)); */
9077: strcpy(strstart,asctime(&start_time));
1.126 brouard 9078:
9079: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 9080: /* tp.tm_sec = tp.tm_sec +86400; */
9081: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 9082: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
9083: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
9084: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 9085: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 9086: /* strt=asctime(&tmg); */
9087: /* printf("Time(after) =%s",strstart); */
9088: /* (void) time (&time_value);
9089: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
9090: * tm = *localtime(&time_value);
9091: * strstart=asctime(&tm);
9092: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
9093: */
9094:
9095: nberr=0; /* Number of errors and warnings */
9096: nbwarn=0;
1.184 brouard 9097: #ifdef WIN32
9098: _getcwd(pathcd, size);
9099: #else
1.126 brouard 9100: getcwd(pathcd, size);
1.184 brouard 9101: #endif
1.191 brouard 9102: syscompilerinfo(0);
1.196 brouard 9103: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 9104: if(argc <=1){
9105: printf("\nEnter the parameter file name: ");
1.205 brouard 9106: if(!fgets(pathr,FILENAMELENGTH,stdin)){
9107: printf("ERROR Empty parameter file name\n");
9108: goto end;
9109: }
1.126 brouard 9110: i=strlen(pathr);
9111: if(pathr[i-1]=='\n')
9112: pathr[i-1]='\0';
1.156 brouard 9113: i=strlen(pathr);
1.205 brouard 9114: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 9115: pathr[i-1]='\0';
1.205 brouard 9116: }
9117: i=strlen(pathr);
9118: if( i==0 ){
9119: printf("ERROR Empty parameter file name\n");
9120: goto end;
9121: }
9122: for (tok = pathr; tok != NULL; ){
1.126 brouard 9123: printf("Pathr |%s|\n",pathr);
9124: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
9125: printf("val= |%s| pathr=%s\n",val,pathr);
9126: strcpy (pathtot, val);
9127: if(pathr[0] == '\0') break; /* Dirty */
9128: }
9129: }
9130: else{
9131: strcpy(pathtot,argv[1]);
9132: }
9133: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
9134: /*cygwin_split_path(pathtot,path,optionfile);
9135: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
9136: /* cutv(path,optionfile,pathtot,'\\');*/
9137:
9138: /* Split argv[0], imach program to get pathimach */
9139: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
9140: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9141: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
9142: /* strcpy(pathimach,argv[0]); */
9143: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
9144: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
9145: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 9146: #ifdef WIN32
9147: _chdir(path); /* Can be a relative path */
9148: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
9149: #else
1.126 brouard 9150: chdir(path); /* Can be a relative path */
1.184 brouard 9151: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
9152: #endif
9153: printf("Current directory %s!\n",pathcd);
1.126 brouard 9154: strcpy(command,"mkdir ");
9155: strcat(command,optionfilefiname);
9156: if((outcmd=system(command)) != 0){
1.169 brouard 9157: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 9158: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
9159: /* fclose(ficlog); */
9160: /* exit(1); */
9161: }
9162: /* if((imk=mkdir(optionfilefiname))<0){ */
9163: /* perror("mkdir"); */
9164: /* } */
9165:
9166: /*-------- arguments in the command line --------*/
9167:
1.186 brouard 9168: /* Main Log file */
1.126 brouard 9169: strcat(filelog, optionfilefiname);
9170: strcat(filelog,".log"); /* */
9171: if((ficlog=fopen(filelog,"w"))==NULL) {
9172: printf("Problem with logfile %s\n",filelog);
9173: goto end;
9174: }
9175: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 9176: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 9177: fprintf(ficlog,"\nEnter the parameter file name: \n");
9178: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
9179: path=%s \n\
9180: optionfile=%s\n\
9181: optionfilext=%s\n\
1.156 brouard 9182: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 9183:
1.197 brouard 9184: syscompilerinfo(1);
1.167 brouard 9185:
1.126 brouard 9186: printf("Local time (at start):%s",strstart);
9187: fprintf(ficlog,"Local time (at start): %s",strstart);
9188: fflush(ficlog);
9189: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 9190: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 9191:
9192: /* */
9193: strcpy(fileres,"r");
9194: strcat(fileres, optionfilefiname);
1.201 brouard 9195: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 9196: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 9197: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9198:
1.186 brouard 9199: /* Main ---------arguments file --------*/
1.126 brouard 9200:
9201: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9202: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9203: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9204: fflush(ficlog);
1.149 brouard 9205: /* goto end; */
9206: exit(70);
1.126 brouard 9207: }
9208:
9209:
9210:
9211: strcpy(filereso,"o");
1.201 brouard 9212: strcat(filereso,fileresu);
1.126 brouard 9213: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9214: printf("Problem with Output resultfile: %s\n", filereso);
9215: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9216: fflush(ficlog);
9217: goto end;
9218: }
9219:
9220: /* Reads comments: lines beginning with '#' */
9221: numlinepar=0;
1.197 brouard 9222:
9223: /* First parameter line */
9224: while(fgets(line, MAXLINE, ficpar)) {
9225: /* If line starts with a # it is a comment */
9226: if (line[0] == '#') {
9227: numlinepar++;
9228: fputs(line,stdout);
9229: fputs(line,ficparo);
9230: fputs(line,ficlog);
9231: continue;
9232: }else
9233: break;
9234: }
9235: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9236: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9237: if (num_filled != 5) {
9238: printf("Should be 5 parameters\n");
9239: }
1.126 brouard 9240: numlinepar++;
1.197 brouard 9241: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9242: }
9243: /* Second parameter line */
9244: while(fgets(line, MAXLINE, ficpar)) {
9245: /* If line starts with a # it is a comment */
9246: if (line[0] == '#') {
9247: numlinepar++;
9248: fputs(line,stdout);
9249: fputs(line,ficparo);
9250: fputs(line,ficlog);
9251: continue;
9252: }else
9253: break;
9254: }
1.223 brouard 9255: 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", \
9256: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9257: if (num_filled != 11) {
9258: 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 9259: printf("but line=%s\n",line);
1.197 brouard 9260: }
1.223 brouard 9261: 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 9262: }
1.203 brouard 9263: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9264: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9265: /* Third parameter line */
9266: while(fgets(line, MAXLINE, ficpar)) {
9267: /* If line starts with a # it is a comment */
9268: if (line[0] == '#') {
9269: numlinepar++;
9270: fputs(line,stdout);
9271: fputs(line,ficparo);
9272: fputs(line,ficlog);
9273: continue;
9274: }else
9275: break;
9276: }
1.201 brouard 9277: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9278: if (num_filled == 0)
9279: model[0]='\0';
9280: else if (num_filled != 1){
1.197 brouard 9281: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9282: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9283: model[0]='\0';
9284: goto end;
9285: }
9286: else{
9287: if (model[0]=='+'){
9288: for(i=1; i<=strlen(model);i++)
9289: modeltemp[i-1]=model[i];
1.201 brouard 9290: strcpy(model,modeltemp);
1.197 brouard 9291: }
9292: }
1.199 brouard 9293: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9294: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9295: }
9296: /* 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); */
9297: /* numlinepar=numlinepar+3; /\* In general *\/ */
9298: /* 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 9299: 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);
9300: 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 9301: fflush(ficlog);
1.190 brouard 9302: /* if(model[0]=='#'|| model[0]== '\0'){ */
9303: if(model[0]=='#'){
1.187 brouard 9304: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9305: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9306: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9307: if(mle != -1){
9308: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9309: exit(1);
9310: }
9311: }
1.126 brouard 9312: while((c=getc(ficpar))=='#' && c!= EOF){
9313: ungetc(c,ficpar);
9314: fgets(line, MAXLINE, ficpar);
9315: numlinepar++;
1.195 brouard 9316: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9317: z[0]=line[1];
9318: }
9319: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9320: fputs(line, stdout);
9321: //puts(line);
1.126 brouard 9322: fputs(line,ficparo);
9323: fputs(line,ficlog);
9324: }
9325: ungetc(c,ficpar);
9326:
9327:
1.145 brouard 9328: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9329: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
9330: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */
9331: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9332: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9333: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9334: v1+v2*age+v2*v3 makes cptcovn = 3
9335: */
9336: if (strlen(model)>1)
1.187 brouard 9337: 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 9338: else
1.187 brouard 9339: ncovmodel=2; /* Constant and age */
1.133 brouard 9340: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9341: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9342: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9343: 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);
9344: 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);
9345: fflush(stdout);
9346: fclose (ficlog);
9347: goto end;
9348: }
1.126 brouard 9349: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9350: delti=delti3[1][1];
9351: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9352: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9353: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9354: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9355: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9356: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9357: fclose (ficparo);
9358: fclose (ficlog);
9359: goto end;
9360: exit(0);
1.220 brouard 9361: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9362: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9363: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9364: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9365: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9366: matcov=matrix(1,npar,1,npar);
1.203 brouard 9367: hess=matrix(1,npar,1,npar);
1.220 brouard 9368: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9369: /* Read guessed parameters */
1.126 brouard 9370: /* Reads comments: lines beginning with '#' */
9371: while((c=getc(ficpar))=='#' && c!= EOF){
9372: ungetc(c,ficpar);
9373: fgets(line, MAXLINE, ficpar);
9374: numlinepar++;
1.141 brouard 9375: fputs(line,stdout);
1.126 brouard 9376: fputs(line,ficparo);
9377: fputs(line,ficlog);
9378: }
9379: ungetc(c,ficpar);
9380:
9381: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9382: for(i=1; i <=nlstate; i++){
1.220 brouard 9383: j=0;
1.126 brouard 9384: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 9385: if(jj==i) continue;
9386: j++;
9387: fscanf(ficpar,"%1d%1d",&i1,&j1);
9388: if ((i1 != i) || (j1 != jj)){
9389: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9390: It might be a problem of design; if ncovcol and the model are correct\n \
9391: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 9392: exit(1);
9393: }
9394: fprintf(ficparo,"%1d%1d",i1,j1);
9395: if(mle==1)
9396: printf("%1d%1d",i,jj);
9397: fprintf(ficlog,"%1d%1d",i,jj);
9398: for(k=1; k<=ncovmodel;k++){
9399: fscanf(ficpar," %lf",¶m[i][j][k]);
9400: if(mle==1){
9401: printf(" %lf",param[i][j][k]);
9402: fprintf(ficlog," %lf",param[i][j][k]);
9403: }
9404: else
9405: fprintf(ficlog," %lf",param[i][j][k]);
9406: fprintf(ficparo," %lf",param[i][j][k]);
9407: }
9408: fscanf(ficpar,"\n");
9409: numlinepar++;
9410: if(mle==1)
9411: printf("\n");
9412: fprintf(ficlog,"\n");
9413: fprintf(ficparo,"\n");
1.126 brouard 9414: }
9415: }
9416: fflush(ficlog);
9417:
1.145 brouard 9418: /* Reads scales values */
1.126 brouard 9419: p=param[1][1];
9420:
9421: /* Reads comments: lines beginning with '#' */
9422: while((c=getc(ficpar))=='#' && c!= EOF){
9423: ungetc(c,ficpar);
9424: fgets(line, MAXLINE, ficpar);
9425: numlinepar++;
1.141 brouard 9426: fputs(line,stdout);
1.126 brouard 9427: fputs(line,ficparo);
9428: fputs(line,ficlog);
9429: }
9430: ungetc(c,ficpar);
9431:
9432: for(i=1; i <=nlstate; i++){
9433: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 9434: fscanf(ficpar,"%1d%1d",&i1,&j1);
9435: if ( (i1-i) * (j1-j) != 0){
9436: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9437: exit(1);
9438: }
9439: printf("%1d%1d",i,j);
9440: fprintf(ficparo,"%1d%1d",i1,j1);
9441: fprintf(ficlog,"%1d%1d",i1,j1);
9442: for(k=1; k<=ncovmodel;k++){
9443: fscanf(ficpar,"%le",&delti3[i][j][k]);
9444: printf(" %le",delti3[i][j][k]);
9445: fprintf(ficparo," %le",delti3[i][j][k]);
9446: fprintf(ficlog," %le",delti3[i][j][k]);
9447: }
9448: fscanf(ficpar,"\n");
9449: numlinepar++;
9450: printf("\n");
9451: fprintf(ficparo,"\n");
9452: fprintf(ficlog,"\n");
1.126 brouard 9453: }
9454: }
9455: fflush(ficlog);
1.220 brouard 9456:
1.145 brouard 9457: /* Reads covariance matrix */
1.126 brouard 9458: delti=delti3[1][1];
1.220 brouard 9459:
9460:
1.126 brouard 9461: /* 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 9462:
1.126 brouard 9463: /* Reads comments: lines beginning with '#' */
9464: while((c=getc(ficpar))=='#' && c!= EOF){
9465: ungetc(c,ficpar);
9466: fgets(line, MAXLINE, ficpar);
9467: numlinepar++;
1.141 brouard 9468: fputs(line,stdout);
1.126 brouard 9469: fputs(line,ficparo);
9470: fputs(line,ficlog);
9471: }
9472: ungetc(c,ficpar);
1.220 brouard 9473:
1.126 brouard 9474: matcov=matrix(1,npar,1,npar);
1.203 brouard 9475: hess=matrix(1,npar,1,npar);
1.131 brouard 9476: for(i=1; i <=npar; i++)
9477: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9478:
1.194 brouard 9479: /* Scans npar lines */
1.126 brouard 9480: for(i=1; i <=npar; i++){
1.226 brouard 9481: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9482: if(count != 3){
1.226 brouard 9483: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9484: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9485: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9486: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9487: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9488: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9489: exit(1);
1.220 brouard 9490: }else{
1.226 brouard 9491: if(mle==1)
9492: printf("%1d%1d%d",i1,j1,jk);
9493: }
9494: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9495: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9496: for(j=1; j <=i; j++){
1.226 brouard 9497: fscanf(ficpar," %le",&matcov[i][j]);
9498: if(mle==1){
9499: printf(" %.5le",matcov[i][j]);
9500: }
9501: fprintf(ficlog," %.5le",matcov[i][j]);
9502: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9503: }
9504: fscanf(ficpar,"\n");
9505: numlinepar++;
9506: if(mle==1)
1.220 brouard 9507: printf("\n");
1.126 brouard 9508: fprintf(ficlog,"\n");
9509: fprintf(ficparo,"\n");
9510: }
1.194 brouard 9511: /* End of read covariance matrix npar lines */
1.126 brouard 9512: for(i=1; i <=npar; i++)
9513: for(j=i+1;j<=npar;j++)
1.226 brouard 9514: matcov[i][j]=matcov[j][i];
1.126 brouard 9515:
9516: if(mle==1)
9517: printf("\n");
9518: fprintf(ficlog,"\n");
9519:
9520: fflush(ficlog);
9521:
9522: /*-------- Rewriting parameter file ----------*/
9523: strcpy(rfileres,"r"); /* "Rparameterfile */
9524: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9525: strcat(rfileres,"."); /* */
9526: strcat(rfileres,optionfilext); /* Other files have txt extension */
9527: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9528: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9529: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9530: }
9531: fprintf(ficres,"#%s\n",version);
9532: } /* End of mle != -3 */
1.218 brouard 9533:
1.186 brouard 9534: /* Main data
9535: */
1.126 brouard 9536: n= lastobs;
9537: num=lvector(1,n);
9538: moisnais=vector(1,n);
9539: annais=vector(1,n);
9540: moisdc=vector(1,n);
9541: andc=vector(1,n);
1.220 brouard 9542: weight=vector(1,n);
1.126 brouard 9543: agedc=vector(1,n);
9544: cod=ivector(1,n);
1.220 brouard 9545: for(i=1;i<=n;i++){
9546: num[i]=0;
9547: moisnais[i]=0;
9548: annais[i]=0;
9549: moisdc[i]=0;
9550: andc[i]=0;
9551: agedc[i]=0;
9552: cod[i]=0;
9553: weight[i]=1.0; /* Equal weights, 1 by default */
9554: }
1.126 brouard 9555: mint=matrix(1,maxwav,1,n);
9556: anint=matrix(1,maxwav,1,n);
1.131 brouard 9557: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9558: tab=ivector(1,NCOVMAX);
1.144 brouard 9559: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9560: 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 9561:
1.136 brouard 9562: /* Reads data from file datafile */
9563: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9564: goto end;
9565:
9566: /* Calculation of the number of parameters from char model */
1.137 brouard 9567: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9568: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9569: k=3 V4 Tvar[k=3]= 4 (from V4)
9570: k=2 V1 Tvar[k=2]= 1 (from V1)
9571: k=1 Tvar[1]=2 (from V2)
9572: */
1.231 brouard 9573:
9574: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
1.232 ! brouard 9575: TvarF=ivector(1,NCOVMAX); /* */
! 9576: TvarFind=ivector(1,NCOVMAX); /* */
! 9577: TvarV=ivector(1,NCOVMAX); /* */
! 9578: TvarVind=ivector(1,NCOVMAX); /* */
! 9579: TvarA=ivector(1,NCOVMAX); /* */
! 9580: TvarAind=ivector(1,NCOVMAX); /* */
1.231 brouard 9581: TvarFD=ivector(1,NCOVMAX); /* */
9582: TvarFDind=ivector(1,NCOVMAX); /* */
9583: TvarFQ=ivector(1,NCOVMAX); /* */
9584: TvarFQind=ivector(1,NCOVMAX); /* */
9585: TvarVD=ivector(1,NCOVMAX); /* */
9586: TvarVDind=ivector(1,NCOVMAX); /* */
9587: TvarVQ=ivector(1,NCOVMAX); /* */
9588: TvarVQind=ivector(1,NCOVMAX); /* */
9589:
1.230 brouard 9590: Tvalsel=vector(1,NCOVMAX); /* */
1.226 brouard 9591: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9592: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9593: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9594: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9595: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9596: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9597: */
9598: /* For model-covariate k tells which data-covariate to use but
9599: because this model-covariate is a construction we invent a new column
9600: ncovcol + k1
9601: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9602: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 9603: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
9604: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9605: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9606: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 9607: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9608: */
1.145 brouard 9609: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9610: 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 9611: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9612: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9613: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9614: 4 covariates (3 plus signs)
9615: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9616: */
1.230 brouard 9617: Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
1.227 brouard 9618: * individual dummy, fixed or varying:
9619: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
9620: * 3, 1, 0, 0, 0, 0, 0, 0},
1.230 brouard 9621: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 ,
9622: * V1 df, V2 qf, V3 & V4 dv, V5 qv
9623: * Tmodelind[1]@9={9,0,3,2,}*/
9624: TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
9625: TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
1.228 brouard 9626: * individual quantitative, fixed or varying:
9627: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
9628: * 3, 1, 0, 0, 0, 0, 0, 0},
9629: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9630: /* Main decodemodel */
9631:
1.187 brouard 9632:
1.223 brouard 9633: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9634: goto end;
9635:
1.137 brouard 9636: if((double)(lastobs-imx)/(double)imx > 1.10){
9637: nbwarn++;
9638: 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);
9639: 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);
9640: }
1.136 brouard 9641: /* if(mle==1){*/
1.137 brouard 9642: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9643: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9644: }
9645:
9646: /*-calculation of age at interview from date of interview and age at death -*/
9647: agev=matrix(1,maxwav,1,imx);
9648:
9649: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9650: goto end;
9651:
1.126 brouard 9652:
1.136 brouard 9653: agegomp=(int)agemin;
9654: free_vector(moisnais,1,n);
9655: free_vector(annais,1,n);
1.126 brouard 9656: /* free_matrix(mint,1,maxwav,1,n);
9657: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9658: /* free_vector(moisdc,1,n); */
9659: /* free_vector(andc,1,n); */
1.145 brouard 9660: /* */
9661:
1.126 brouard 9662: wav=ivector(1,imx);
1.214 brouard 9663: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9664: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9665: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9666: 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.*/
9667: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9668: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9669:
9670: /* Concatenates waves */
1.214 brouard 9671: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9672: Death is a valid wave (if date is known).
9673: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9674: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9675: and mw[mi+1][i]. dh depends on stepm.
9676: */
9677:
1.126 brouard 9678: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9679: /* */
9680:
1.215 brouard 9681: free_vector(moisdc,1,n);
9682: free_vector(andc,1,n);
9683:
1.126 brouard 9684: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9685: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9686: ncodemax[1]=1;
1.145 brouard 9687: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9688: cptcoveff=0;
1.220 brouard 9689: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9690: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 9691: }
9692:
9693: ncovcombmax=pow(2,cptcoveff);
9694: invalidvarcomb=ivector(1, ncovcombmax);
9695: for(i=1;i<ncovcombmax;i++)
9696: invalidvarcomb[i]=0;
9697:
1.211 brouard 9698: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9699: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9700: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 9701:
1.200 brouard 9702: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9703: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9704: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9705: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9706: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9707: * (currently 0 or 1) in the data.
9708: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9709: * corresponding modality (h,j).
9710: */
9711:
1.145 brouard 9712: h=0;
9713: /*if (cptcovn > 0) */
1.126 brouard 9714: m=pow(2,cptcoveff);
9715:
1.144 brouard 9716: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9717: * For k=4 covariates, h goes from 1 to m=2**k
9718: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9719: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9720: * h\k 1 2 3 4
1.143 brouard 9721: *______________________________
9722: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9723: * 2 2 1 1 1
9724: * 3 i=2 1 2 1 1
9725: * 4 2 2 1 1
9726: * 5 i=3 1 i=2 1 2 1
9727: * 6 2 1 2 1
9728: * 7 i=4 1 2 2 1
9729: * 8 2 2 2 1
1.197 brouard 9730: * 9 i=5 1 i=3 1 i=2 1 2
9731: * 10 2 1 1 2
9732: * 11 i=6 1 2 1 2
9733: * 12 2 2 1 2
9734: * 13 i=7 1 i=4 1 2 2
9735: * 14 2 1 2 2
9736: * 15 i=8 1 2 2 2
9737: * 16 2 2 2 2
1.143 brouard 9738: */
1.212 brouard 9739: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9740: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9741: * and the value of each covariate?
9742: * V1=1, V2=1, V3=2, V4=1 ?
9743: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9744: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9745: * In order to get the real value in the data, we use nbcode
9746: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9747: * We are keeping this crazy system in order to be able (in the future?)
9748: * to have more than 2 values (0 or 1) for a covariate.
9749: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9750: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9751: * bbbbbbbb
9752: * 76543210
9753: * h-1 00000101 (6-1=5)
1.219 brouard 9754: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9755: * &
9756: * 1 00000001 (1)
1.219 brouard 9757: * 00000000 = 1 & ((h-1) >> (k-1))
9758: * +1= 00000001 =1
1.211 brouard 9759: *
9760: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9761: * h' 1101 =2^3+2^2+0x2^1+2^0
9762: * >>k' 11
9763: * & 00000001
9764: * = 00000001
9765: * +1 = 00000010=2 = codtabm(14,3)
9766: * Reverse h=6 and m=16?
9767: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9768: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9769: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9770: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9771: * V3=decodtabm(14,3,2**4)=2
9772: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9773: *(h-1) >> (j-1) 0011 =13 >> 2
9774: * &1 000000001
9775: * = 000000001
9776: * +1= 000000010 =2
9777: * 2211
9778: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9779: * V3=2
1.220 brouard 9780: * codtabm and decodtabm are identical
1.211 brouard 9781: */
9782:
1.145 brouard 9783:
9784: free_ivector(Ndum,-1,NCOVMAX);
9785:
9786:
1.126 brouard 9787:
1.186 brouard 9788: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9789: strcpy(optionfilegnuplot,optionfilefiname);
9790: if(mle==-3)
1.201 brouard 9791: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9792: strcat(optionfilegnuplot,".gp");
9793:
9794: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9795: printf("Problem with file %s",optionfilegnuplot);
9796: }
9797: else{
1.204 brouard 9798: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9799: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9800: //fprintf(ficgp,"set missing 'NaNq'\n");
9801: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9802: }
9803: /* fclose(ficgp);*/
1.186 brouard 9804:
9805:
9806: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9807:
9808: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9809: if(mle==-3)
1.201 brouard 9810: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9811: strcat(optionfilehtm,".htm");
9812: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9813: printf("Problem with %s \n",optionfilehtm);
9814: exit(0);
1.126 brouard 9815: }
9816:
9817: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9818: strcat(optionfilehtmcov,"-cov.htm");
9819: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9820: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9821: }
9822: else{
9823: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9824: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9825: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9826: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9827: }
9828:
1.213 brouard 9829: 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 9830: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9831: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9832: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9833: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9834: \n\
9835: <hr size=\"2\" color=\"#EC5E5E\">\
9836: <ul><li><h4>Parameter files</h4>\n\
9837: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9838: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9839: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9840: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9841: - Date and time at start: %s</ul>\n",\
9842: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9843: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9844: fileres,fileres,\
9845: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9846: fflush(fichtm);
9847:
9848: strcpy(pathr,path);
9849: strcat(pathr,optionfilefiname);
1.184 brouard 9850: #ifdef WIN32
9851: _chdir(optionfilefiname); /* Move to directory named optionfile */
9852: #else
1.126 brouard 9853: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9854: #endif
9855:
1.126 brouard 9856:
1.220 brouard 9857: /* Calculates basic frequencies. Computes observed prevalence at single age
9858: and for any valid combination of covariates
1.126 brouard 9859: and prints on file fileres'p'. */
1.227 brouard 9860: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
9861: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9862:
9863: fprintf(fichtm,"\n");
9864: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9865: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9866: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9867: imx,agemin,agemax,jmin,jmax,jmean);
9868: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9869: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9870: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9871: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9872: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9873:
1.126 brouard 9874: /* For Powell, parameters are in a vector p[] starting at p[1]
9875: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9876: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9877:
9878: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9879: /* For mortality only */
1.126 brouard 9880: if (mle==-3){
1.136 brouard 9881: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9882: for(i=1;i<=NDIM;i++)
9883: for(j=1;j<=NDIM;j++)
9884: ximort[i][j]=0.;
1.186 brouard 9885: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9886: cens=ivector(1,n);
9887: ageexmed=vector(1,n);
9888: agecens=vector(1,n);
9889: dcwave=ivector(1,n);
1.223 brouard 9890:
1.126 brouard 9891: for (i=1; i<=imx; i++){
9892: dcwave[i]=-1;
9893: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 9894: if (s[m][i]>nlstate) {
9895: dcwave[i]=m;
9896: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9897: break;
9898: }
1.126 brouard 9899: }
1.226 brouard 9900:
1.126 brouard 9901: for (i=1; i<=imx; i++) {
9902: if (wav[i]>0){
1.226 brouard 9903: ageexmed[i]=agev[mw[1][i]][i];
9904: j=wav[i];
9905: agecens[i]=1.;
9906:
9907: if (ageexmed[i]> 1 && wav[i] > 0){
9908: agecens[i]=agev[mw[j][i]][i];
9909: cens[i]= 1;
9910: }else if (ageexmed[i]< 1)
9911: cens[i]= -1;
9912: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9913: cens[i]=0 ;
1.126 brouard 9914: }
9915: else cens[i]=-1;
9916: }
9917:
9918: for (i=1;i<=NDIM;i++) {
9919: for (j=1;j<=NDIM;j++)
1.226 brouard 9920: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9921: }
9922:
1.145 brouard 9923: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9924: /*printf("%lf %lf", p[1], p[2]);*/
9925:
9926:
1.136 brouard 9927: #ifdef GSL
9928: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9929: #else
1.126 brouard 9930: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9931: #endif
1.201 brouard 9932: strcpy(filerespow,"POW-MORT_");
9933: strcat(filerespow,fileresu);
1.126 brouard 9934: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9935: printf("Problem with resultfile: %s\n", filerespow);
9936: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9937: }
1.136 brouard 9938: #ifdef GSL
9939: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9940: #else
1.126 brouard 9941: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9942: #endif
1.126 brouard 9943: /* for (i=1;i<=nlstate;i++)
9944: for(j=1;j<=nlstate+ndeath;j++)
9945: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9946: */
9947: fprintf(ficrespow,"\n");
1.136 brouard 9948: #ifdef GSL
9949: /* gsl starts here */
9950: T = gsl_multimin_fminimizer_nmsimplex;
9951: gsl_multimin_fminimizer *sfm = NULL;
9952: gsl_vector *ss, *x;
9953: gsl_multimin_function minex_func;
9954:
9955: /* Initial vertex size vector */
9956: ss = gsl_vector_alloc (NDIM);
9957:
9958: if (ss == NULL){
9959: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9960: }
9961: /* Set all step sizes to 1 */
9962: gsl_vector_set_all (ss, 0.001);
9963:
9964: /* Starting point */
1.126 brouard 9965:
1.136 brouard 9966: x = gsl_vector_alloc (NDIM);
9967:
9968: if (x == NULL){
9969: gsl_vector_free(ss);
9970: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9971: }
9972:
9973: /* Initialize method and iterate */
9974: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9975: /* gsl_vector_set(x, 0, 0.0268); */
9976: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9977: gsl_vector_set(x, 0, p[1]);
9978: gsl_vector_set(x, 1, p[2]);
9979:
9980: minex_func.f = &gompertz_f;
9981: minex_func.n = NDIM;
9982: minex_func.params = (void *)&p; /* ??? */
9983:
9984: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9985: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9986:
9987: printf("Iterations beginning .....\n\n");
9988: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9989:
9990: iteri=0;
9991: while (rval == GSL_CONTINUE){
9992: iteri++;
9993: status = gsl_multimin_fminimizer_iterate(sfm);
9994:
9995: if (status) printf("error: %s\n", gsl_strerror (status));
9996: fflush(0);
9997:
9998: if (status)
9999: break;
10000:
10001: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
10002: ssval = gsl_multimin_fminimizer_size (sfm);
10003:
10004: if (rval == GSL_SUCCESS)
10005: printf ("converged to a local maximum at\n");
10006:
10007: printf("%5d ", iteri);
10008: for (it = 0; it < NDIM; it++){
10009: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
10010: }
10011: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
10012: }
10013:
10014: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
10015:
10016: gsl_vector_free(x); /* initial values */
10017: gsl_vector_free(ss); /* inital step size */
10018: for (it=0; it<NDIM; it++){
10019: p[it+1]=gsl_vector_get(sfm->x,it);
10020: fprintf(ficrespow," %.12lf", p[it]);
10021: }
10022: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
10023: #endif
10024: #ifdef POWELL
10025: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
10026: #endif
1.126 brouard 10027: fclose(ficrespow);
10028:
1.203 brouard 10029: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 10030:
10031: for(i=1; i <=NDIM; i++)
10032: for(j=i+1;j<=NDIM;j++)
1.220 brouard 10033: matcov[i][j]=matcov[j][i];
1.126 brouard 10034:
10035: printf("\nCovariance matrix\n ");
1.203 brouard 10036: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 10037: for(i=1; i <=NDIM; i++) {
10038: for(j=1;j<=NDIM;j++){
1.220 brouard 10039: printf("%f ",matcov[i][j]);
10040: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 10041: }
1.203 brouard 10042: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 10043: }
10044:
10045: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 10046: for (i=1;i<=NDIM;i++) {
1.126 brouard 10047: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 10048: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
10049: }
1.126 brouard 10050: lsurv=vector(1,AGESUP);
10051: lpop=vector(1,AGESUP);
10052: tpop=vector(1,AGESUP);
10053: lsurv[agegomp]=100000;
10054:
10055: for (k=agegomp;k<=AGESUP;k++) {
10056: agemortsup=k;
10057: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
10058: }
10059:
10060: for (k=agegomp;k<agemortsup;k++)
10061: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
10062:
10063: for (k=agegomp;k<agemortsup;k++){
10064: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
10065: sumlpop=sumlpop+lpop[k];
10066: }
10067:
10068: tpop[agegomp]=sumlpop;
10069: for (k=agegomp;k<(agemortsup-3);k++){
10070: /* tpop[k+1]=2;*/
10071: tpop[k+1]=tpop[k]-lpop[k];
10072: }
10073:
10074:
10075: printf("\nAge lx qx dx Lx Tx e(x)\n");
10076: for (k=agegomp;k<(agemortsup-2);k++)
10077: 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]);
10078:
10079:
10080: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 10081: ageminpar=50;
10082: agemaxpar=100;
1.194 brouard 10083: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
10084: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10085: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10086: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
10087: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
10088: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10089: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10090: }else{
10091: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
10092: 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 10093: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 10094: }
1.201 brouard 10095: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 10096: stepm, weightopt,\
10097: model,imx,p,matcov,agemortsup);
10098:
10099: free_vector(lsurv,1,AGESUP);
10100: free_vector(lpop,1,AGESUP);
10101: free_vector(tpop,1,AGESUP);
1.220 brouard 10102: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 10103: free_ivector(cens,1,n);
10104: free_vector(agecens,1,n);
10105: free_ivector(dcwave,1,n);
1.220 brouard 10106: #ifdef GSL
1.136 brouard 10107: #endif
1.186 brouard 10108: } /* Endof if mle==-3 mortality only */
1.205 brouard 10109: /* Standard */
10110: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
10111: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10112: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 10113: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 10114: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10115: for (k=1; k<=npar;k++)
10116: printf(" %d %8.5f",k,p[k]);
10117: printf("\n");
1.205 brouard 10118: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
10119: /* mlikeli uses func not funcone */
10120: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
10121: }
10122: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
10123: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
10124: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
10125: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10126: }
10127: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 10128: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
10129: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
10130: for (k=1; k<=npar;k++)
10131: printf(" %d %8.5f",k,p[k]);
10132: printf("\n");
10133:
10134: /*--------- results files --------------*/
1.224 brouard 10135: 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 10136:
10137:
10138: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10139: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10140: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
10141: for(i=1,jk=1; i <=nlstate; i++){
10142: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 10143: if (k != i) {
10144: printf("%d%d ",i,k);
10145: fprintf(ficlog,"%d%d ",i,k);
10146: fprintf(ficres,"%1d%1d ",i,k);
10147: for(j=1; j <=ncovmodel; j++){
10148: printf("%12.7f ",p[jk]);
10149: fprintf(ficlog,"%12.7f ",p[jk]);
10150: fprintf(ficres,"%12.7f ",p[jk]);
10151: jk++;
10152: }
10153: printf("\n");
10154: fprintf(ficlog,"\n");
10155: fprintf(ficres,"\n");
10156: }
1.126 brouard 10157: }
10158: }
1.203 brouard 10159: if(mle != 0){
10160: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 10161: ftolhess=ftol; /* Usually correct */
1.203 brouard 10162: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
10163: 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");
10164: 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");
10165: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 10166: for(k=1; k <=(nlstate+ndeath); k++){
10167: if (k != i) {
10168: printf("%d%d ",i,k);
10169: fprintf(ficlog,"%d%d ",i,k);
10170: for(j=1; j <=ncovmodel; j++){
10171: 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]));
10172: 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]));
10173: jk++;
10174: }
10175: printf("\n");
10176: fprintf(ficlog,"\n");
10177: }
10178: }
1.193 brouard 10179: }
1.203 brouard 10180: } /* end of hesscov and Wald tests */
1.225 brouard 10181:
1.203 brouard 10182: /* */
1.126 brouard 10183: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
10184: printf("# Scales (for hessian or gradient estimation)\n");
10185: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
10186: for(i=1,jk=1; i <=nlstate; i++){
10187: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 10188: if (j!=i) {
10189: fprintf(ficres,"%1d%1d",i,j);
10190: printf("%1d%1d",i,j);
10191: fprintf(ficlog,"%1d%1d",i,j);
10192: for(k=1; k<=ncovmodel;k++){
10193: printf(" %.5e",delti[jk]);
10194: fprintf(ficlog," %.5e",delti[jk]);
10195: fprintf(ficres," %.5e",delti[jk]);
10196: jk++;
10197: }
10198: printf("\n");
10199: fprintf(ficlog,"\n");
10200: fprintf(ficres,"\n");
10201: }
1.126 brouard 10202: }
10203: }
10204:
10205: 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 10206: if(mle >= 1) /* To big for the screen */
1.126 brouard 10207: 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");
10208: 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");
10209: /* # 121 Var(a12)\n\ */
10210: /* # 122 Cov(b12,a12) Var(b12)\n\ */
10211: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
10212: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
10213: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
10214: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
10215: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
10216: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10217:
10218:
10219: /* Just to have a covariance matrix which will be more understandable
10220: even is we still don't want to manage dictionary of variables
10221: */
10222: for(itimes=1;itimes<=2;itimes++){
10223: jj=0;
10224: for(i=1; i <=nlstate; i++){
1.225 brouard 10225: for(j=1; j <=nlstate+ndeath; j++){
10226: if(j==i) continue;
10227: for(k=1; k<=ncovmodel;k++){
10228: jj++;
10229: ca[0]= k+'a'-1;ca[1]='\0';
10230: if(itimes==1){
10231: if(mle>=1)
10232: printf("#%1d%1d%d",i,j,k);
10233: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10234: fprintf(ficres,"#%1d%1d%d",i,j,k);
10235: }else{
10236: if(mle>=1)
10237: printf("%1d%1d%d",i,j,k);
10238: fprintf(ficlog,"%1d%1d%d",i,j,k);
10239: fprintf(ficres,"%1d%1d%d",i,j,k);
10240: }
10241: ll=0;
10242: for(li=1;li <=nlstate; li++){
10243: for(lj=1;lj <=nlstate+ndeath; lj++){
10244: if(lj==li) continue;
10245: for(lk=1;lk<=ncovmodel;lk++){
10246: ll++;
10247: if(ll<=jj){
10248: cb[0]= lk +'a'-1;cb[1]='\0';
10249: if(ll<jj){
10250: if(itimes==1){
10251: if(mle>=1)
10252: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10253: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10254: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10255: }else{
10256: if(mle>=1)
10257: printf(" %.5e",matcov[jj][ll]);
10258: fprintf(ficlog," %.5e",matcov[jj][ll]);
10259: fprintf(ficres," %.5e",matcov[jj][ll]);
10260: }
10261: }else{
10262: if(itimes==1){
10263: if(mle>=1)
10264: printf(" Var(%s%1d%1d)",ca,i,j);
10265: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10266: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10267: }else{
10268: if(mle>=1)
10269: printf(" %.7e",matcov[jj][ll]);
10270: fprintf(ficlog," %.7e",matcov[jj][ll]);
10271: fprintf(ficres," %.7e",matcov[jj][ll]);
10272: }
10273: }
10274: }
10275: } /* end lk */
10276: } /* end lj */
10277: } /* end li */
10278: if(mle>=1)
10279: printf("\n");
10280: fprintf(ficlog,"\n");
10281: fprintf(ficres,"\n");
10282: numlinepar++;
10283: } /* end k*/
10284: } /*end j */
1.126 brouard 10285: } /* end i */
10286: } /* end itimes */
10287:
10288: fflush(ficlog);
10289: fflush(ficres);
1.225 brouard 10290: while(fgets(line, MAXLINE, ficpar)) {
10291: /* If line starts with a # it is a comment */
10292: if (line[0] == '#') {
10293: numlinepar++;
10294: fputs(line,stdout);
10295: fputs(line,ficparo);
10296: fputs(line,ficlog);
10297: continue;
10298: }else
10299: break;
10300: }
10301:
1.209 brouard 10302: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10303: /* ungetc(c,ficpar); */
10304: /* fgets(line, MAXLINE, ficpar); */
10305: /* fputs(line,stdout); */
10306: /* fputs(line,ficparo); */
10307: /* } */
10308: /* ungetc(c,ficpar); */
1.126 brouard 10309:
10310: estepm=0;
1.209 brouard 10311: 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 10312:
10313: if (num_filled != 6) {
10314: 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);
10315: 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);
10316: goto end;
10317: }
10318: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10319: }
10320: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10321: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10322:
1.209 brouard 10323: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10324: if (estepm==0 || estepm < stepm) estepm=stepm;
10325: if (fage <= 2) {
10326: bage = ageminpar;
10327: fage = agemaxpar;
10328: }
10329:
10330: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10331: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10332: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10333:
1.186 brouard 10334: /* Other stuffs, more or less useful */
1.126 brouard 10335: while((c=getc(ficpar))=='#' && c!= EOF){
10336: ungetc(c,ficpar);
10337: fgets(line, MAXLINE, ficpar);
1.141 brouard 10338: fputs(line,stdout);
1.126 brouard 10339: fputs(line,ficparo);
10340: }
10341: ungetc(c,ficpar);
10342:
10343: 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);
10344: 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);
10345: 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);
10346: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10347: 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);
10348:
10349: while((c=getc(ficpar))=='#' && c!= EOF){
10350: ungetc(c,ficpar);
10351: fgets(line, MAXLINE, ficpar);
1.141 brouard 10352: fputs(line,stdout);
1.126 brouard 10353: fputs(line,ficparo);
10354: }
10355: ungetc(c,ficpar);
10356:
10357:
10358: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10359: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10360:
10361: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10362: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10363: fprintf(ficparo,"pop_based=%d\n",popbased);
10364: fprintf(ficres,"pop_based=%d\n",popbased);
10365:
10366: while((c=getc(ficpar))=='#' && c!= EOF){
10367: ungetc(c,ficpar);
10368: fgets(line, MAXLINE, ficpar);
1.141 brouard 10369: fputs(line,stdout);
1.126 brouard 10370: fputs(line,ficparo);
10371: }
10372: ungetc(c,ficpar);
10373:
10374: 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);
10375: 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);
10376: 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);
10377: 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);
10378: 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);
10379: /* day and month of proj2 are not used but only year anproj2.*/
10380:
1.217 brouard 10381: while((c=getc(ficpar))=='#' && c!= EOF){
10382: ungetc(c,ficpar);
10383: fgets(line, MAXLINE, ficpar);
10384: fputs(line,stdout);
10385: fputs(line,ficparo);
10386: }
10387: ungetc(c,ficpar);
10388:
10389: 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 10390: 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);
10391: 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);
10392: 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 10393: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10394:
1.230 brouard 10395: /* Results */
10396: while(fgets(line, MAXLINE, ficpar)) {
10397: /* If line starts with a # it is a comment */
10398: if (line[0] == '#') {
10399: numlinepar++;
10400: fputs(line,stdout);
10401: fputs(line,ficparo);
10402: fputs(line,ficlog);
10403: continue;
10404: }else
10405: break;
10406: }
10407: while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
10408: if (num_filled == 0)
10409: resultline[0]='\0';
10410: else if (num_filled != 1){
10411: printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
10412: }
10413: printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
10414: decoderesult(resultline);
10415: while(fgets(line, MAXLINE, ficpar)) {
10416: /* If line starts with a # it is a comment */
10417: if (line[0] == '#') {
10418: numlinepar++;
10419: fputs(line,stdout);
10420: fputs(line,ficparo);
10421: fputs(line,ficlog);
10422: continue;
10423: }else
10424: break;
10425: }
10426: if (feof(ficpar))
10427: break;
10428: else{ /* Processess output results for this combination of covariate values */
10429: }
10430: }
10431:
10432:
1.126 brouard 10433:
1.230 brouard 10434: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10435: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10436:
10437: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10438: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.230 brouard 10439: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10440: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10441: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.230 brouard 10442: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10443: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10444: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10445: }else{
1.218 brouard 10446: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10447: }
10448: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10449: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10450: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10451:
1.225 brouard 10452: /*------------ free_vector -------------*/
10453: /* chdir(path); */
1.220 brouard 10454:
1.215 brouard 10455: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10456: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10457: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10458: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10459: free_lvector(num,1,n);
10460: free_vector(agedc,1,n);
10461: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10462: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10463: fclose(ficparo);
10464: fclose(ficres);
1.220 brouard 10465:
10466:
1.186 brouard 10467: /* Other results (useful)*/
1.220 brouard 10468:
10469:
1.126 brouard 10470: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10471: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10472: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10473: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10474: fclose(ficrespl);
10475:
10476: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10477: /*#include "hpijx.h"*/
10478: hPijx(p, bage, fage);
1.145 brouard 10479: fclose(ficrespij);
1.227 brouard 10480:
1.220 brouard 10481: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10482: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10483: k=1;
1.126 brouard 10484: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10485:
1.219 brouard 10486: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10487: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10488: for(i=1;i<=AGESUP;i++)
1.219 brouard 10489: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10490: for(k=1;k<=ncovcombmax;k++)
10491: probs[i][j][k]=0.;
1.219 brouard 10492: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10493: if (mobilav!=0 ||mobilavproj !=0 ) {
10494: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10495: for(i=1;i<=AGESUP;i++)
10496: for(j=1;j<=nlstate;j++)
10497: for(k=1;k<=ncovcombmax;k++)
10498: mobaverages[i][j][k]=0.;
1.219 brouard 10499: mobaverage=mobaverages;
10500: if (mobilav!=0) {
1.227 brouard 10501: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10502: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10503: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10504: }
1.219 brouard 10505: }
10506: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10507: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10508: else if (mobilavproj !=0) {
1.227 brouard 10509: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10510: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10511: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10512: }
1.219 brouard 10513: }
10514: }/* end if moving average */
1.227 brouard 10515:
1.126 brouard 10516: /*---------- Forecasting ------------------*/
10517: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10518: if(prevfcast==1){
10519: /* if(stepm ==1){*/
1.225 brouard 10520: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10521: }
1.217 brouard 10522: if(backcast==1){
1.219 brouard 10523: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10524: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10525: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10526:
10527: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10528:
10529: bprlim=matrix(1,nlstate,1,nlstate);
10530: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10531: fclose(ficresplb);
10532:
1.222 brouard 10533: hBijx(p, bage, fage, mobaverage);
10534: fclose(ficrespijb);
1.219 brouard 10535: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10536:
10537: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10538: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10539: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10540: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10541: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10542: }
1.217 brouard 10543:
1.186 brouard 10544:
10545: /* ------ Other prevalence ratios------------ */
1.126 brouard 10546:
1.215 brouard 10547: free_ivector(wav,1,imx);
10548: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10549: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10550: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10551:
10552:
1.127 brouard 10553: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10554:
1.201 brouard 10555: strcpy(filerese,"E_");
10556: strcat(filerese,fileresu);
1.126 brouard 10557: if((ficreseij=fopen(filerese,"w"))==NULL) {
10558: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10559: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10560: }
1.208 brouard 10561: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10562: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10563:
1.227 brouard 10564: for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
1.219 brouard 10565: fprintf(ficreseij,"\n#****** ");
1.225 brouard 10566: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10567: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10568: }
10569: fprintf(ficreseij,"******\n");
10570:
10571: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10572: oldm=oldms;savm=savms;
10573: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10574:
1.219 brouard 10575: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10576: }
10577: fclose(ficreseij);
1.208 brouard 10578: printf("done evsij\n");fflush(stdout);
10579: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10580:
1.227 brouard 10581: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10582:
10583:
1.201 brouard 10584: strcpy(filerest,"T_");
10585: strcat(filerest,fileresu);
1.127 brouard 10586: if((ficrest=fopen(filerest,"w"))==NULL) {
10587: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10588: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10589: }
1.208 brouard 10590: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10591: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10592:
1.126 brouard 10593:
1.201 brouard 10594: strcpy(fileresstde,"STDE_");
10595: strcat(fileresstde,fileresu);
1.126 brouard 10596: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 10597: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10598: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10599: }
1.227 brouard 10600: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
10601: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10602:
1.201 brouard 10603: strcpy(filerescve,"CVE_");
10604: strcat(filerescve,fileresu);
1.126 brouard 10605: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 10606: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
10607: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10608: }
1.227 brouard 10609: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
10610: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10611:
1.201 brouard 10612: strcpy(fileresv,"V_");
10613: strcat(fileresv,fileresu);
1.126 brouard 10614: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10615: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10616: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10617: }
1.227 brouard 10618: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
10619: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10620:
1.145 brouard 10621: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10622: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10623:
1.225 brouard 10624: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10625: printf("\n#****** ");
1.208 brouard 10626: fprintf(ficrest,"\n#****** ");
1.227 brouard 10627: fprintf(ficlog,"\n#****** ");
10628: for(j=1;j<=cptcoveff;j++){
10629: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10630: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10631: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10632: }
1.208 brouard 10633: fprintf(ficrest,"******\n");
1.227 brouard 10634: fprintf(ficlog,"******\n");
10635: printf("******\n");
1.208 brouard 10636:
10637: fprintf(ficresstdeij,"\n#****** ");
10638: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10639: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10640: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10641: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10642: }
10643: fprintf(ficresstdeij,"******\n");
10644: fprintf(ficrescveij,"******\n");
10645:
10646: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10647: for(j=1;j<=cptcoveff;j++)
1.227 brouard 10648: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10649: fprintf(ficresvij,"******\n");
10650:
10651: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10652: oldm=oldms;savm=savms;
1.227 brouard 10653: printf(" cvevsij combination#=%d, ",k);
10654: fprintf(ficlog, " cvevsij combination#=%d, ",k);
1.208 brouard 10655: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10656: printf(" end cvevsij \n ");
10657: fprintf(ficlog, " end cvevsij \n ");
10658:
10659: /*
10660: */
10661: /* goto endfree; */
10662:
10663: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10664: pstamp(ficrest);
10665:
10666:
10667: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 10668: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10669: cptcod= 0; /* To be deleted */
10670: printf("varevsij vpopbased=%d \n",vpopbased);
10671: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
10672: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
10673: 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 ");
10674: if(vpopbased==1)
10675: 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);
10676: else
10677: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10678: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10679: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10680: fprintf(ficrest,"\n");
10681: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10682: epj=vector(1,nlstate+1);
10683: printf("Computing age specific period (stable) prevalences in each health state \n");
10684: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10685: for(age=bage; age <=fage ;age++){
10686: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
10687: if (vpopbased==1) {
10688: if(mobilav ==0){
10689: for(i=1; i<=nlstate;i++)
10690: prlim[i][i]=probs[(int)age][i][k];
10691: }else{ /* mobilav */
10692: for(i=1; i<=nlstate;i++)
10693: prlim[i][i]=mobaverage[(int)age][i][k];
10694: }
10695: }
1.219 brouard 10696:
1.227 brouard 10697: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
10698: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
10699: /* printf(" age %4.0f ",age); */
10700: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
10701: for(i=1, epj[j]=0.;i <=nlstate;i++) {
10702: epj[j] += prlim[i][i]*eij[i][j][(int)age];
10703: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
10704: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
10705: }
10706: epj[nlstate+1] +=epj[j];
10707: }
10708: /* printf(" age %4.0f \n",age); */
1.219 brouard 10709:
1.227 brouard 10710: for(i=1, vepp=0.;i <=nlstate;i++)
10711: for(j=1;j <=nlstate;j++)
10712: vepp += vareij[i][j][(int)age];
10713: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
10714: for(j=1;j <=nlstate;j++){
10715: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
10716: }
10717: fprintf(ficrest,"\n");
10718: }
1.208 brouard 10719: } /* End vpopbased */
10720: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10721: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10722: free_vector(epj,1,nlstate+1);
10723: printf("done \n");fflush(stdout);
10724: fprintf(ficlog,"done\n");fflush(ficlog);
10725:
1.145 brouard 10726: /*}*/
1.208 brouard 10727: } /* End k */
1.227 brouard 10728:
10729: printf("done State-specific expectancies\n");fflush(stdout);
10730: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
10731:
1.126 brouard 10732: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 10733:
1.201 brouard 10734: strcpy(fileresvpl,"VPL_");
10735: strcat(fileresvpl,fileresu);
1.126 brouard 10736: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10737: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10738: exit(0);
10739: }
1.208 brouard 10740: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10741: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 10742:
1.145 brouard 10743: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10744: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 10745:
1.225 brouard 10746: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10747: fprintf(ficresvpl,"\n#****** ");
10748: printf("\n#****** ");
10749: fprintf(ficlog,"\n#****** ");
10750: for(j=1;j<=cptcoveff;j++) {
10751: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10752: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10753: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10754: }
10755: fprintf(ficresvpl,"******\n");
10756: printf("******\n");
10757: fprintf(ficlog,"******\n");
10758:
10759: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10760: oldm=oldms;savm=savms;
10761: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10762: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10763: /*}*/
1.126 brouard 10764: }
1.227 brouard 10765:
1.126 brouard 10766: fclose(ficresvpl);
1.208 brouard 10767: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10768: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 10769:
10770: free_vector(weight,1,n);
10771: free_imatrix(Tvard,1,NCOVMAX,1,2);
10772: free_imatrix(s,1,maxwav+1,1,n);
10773: free_matrix(anint,1,maxwav,1,n);
10774: free_matrix(mint,1,maxwav,1,n);
10775: free_ivector(cod,1,n);
10776: free_ivector(tab,1,NCOVMAX);
10777: fclose(ficresstdeij);
10778: fclose(ficrescveij);
10779: fclose(ficresvij);
10780: fclose(ficrest);
10781: fclose(ficpar);
10782:
10783:
1.126 brouard 10784: /*---------- End : free ----------------*/
1.219 brouard 10785: if (mobilav!=0 ||mobilavproj !=0)
10786: 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 10787: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10788: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10789: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10790: } /* mle==-3 arrives here for freeing */
1.227 brouard 10791: /* endfree:*/
10792: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10793: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10794: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
10795: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
10796: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
10797: free_matrix(coqvar,1,maxwav,1,n);
10798: free_matrix(covar,0,NCOVMAX,1,n);
10799: free_matrix(matcov,1,npar,1,npar);
10800: free_matrix(hess,1,npar,1,npar);
10801: /*free_vector(delti,1,npar);*/
10802: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10803: free_matrix(agev,1,maxwav,1,imx);
10804: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10805:
10806: free_ivector(ncodemax,1,NCOVMAX);
10807: free_ivector(ncodemaxwundef,1,NCOVMAX);
10808: free_ivector(Dummy,-1,NCOVMAX);
10809: free_ivector(Fixed,-1,NCOVMAX);
10810: free_ivector(Typevar,-1,NCOVMAX);
10811: free_ivector(Tvar,1,NCOVMAX);
1.231 brouard 10812: free_ivector(TvarFD,1,NCOVMAX);
10813: free_ivector(TvarFDind,1,NCOVMAX);
1.232 ! brouard 10814: free_ivector(TvarF,1,NCOVMAX);
! 10815: free_ivector(TvarFind,1,NCOVMAX);
! 10816: free_ivector(TvarV,1,NCOVMAX);
! 10817: free_ivector(TvarVind,1,NCOVMAX);
! 10818: free_ivector(TvarA,1,NCOVMAX);
! 10819: free_ivector(TvarAind,1,NCOVMAX);
1.231 brouard 10820: free_ivector(TvarFQ,1,NCOVMAX);
10821: free_ivector(TvarFQind,1,NCOVMAX);
10822: free_ivector(TvarVD,1,NCOVMAX);
10823: free_ivector(TvarVDind,1,NCOVMAX);
10824: free_ivector(TvarVQ,1,NCOVMAX);
10825: free_ivector(TvarVQind,1,NCOVMAX);
1.230 brouard 10826: free_ivector(Tvarsel,1,NCOVMAX);
10827: free_vector(Tvalsel,1,NCOVMAX);
1.227 brouard 10828: free_ivector(Tposprod,1,NCOVMAX);
10829: free_ivector(Tprod,1,NCOVMAX);
10830: free_ivector(Tvaraff,1,NCOVMAX);
10831: free_ivector(invalidvarcomb,1,ncovcombmax);
10832: free_ivector(Tage,1,NCOVMAX);
10833: free_ivector(Tmodelind,1,NCOVMAX);
1.228 brouard 10834: free_ivector(TmodelInvind,1,NCOVMAX);
10835: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 10836:
10837: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
10838: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10839: fflush(fichtm);
10840: fflush(ficgp);
10841:
1.227 brouard 10842:
1.126 brouard 10843: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10844: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10845: 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 10846: }else{
10847: printf("End of Imach\n");
10848: fprintf(ficlog,"End of Imach\n");
10849: }
10850: printf("See log file on %s\n",filelog);
10851: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10852: /*(void) gettimeofday(&end_time,&tzp);*/
10853: rend_time = time(NULL);
10854: end_time = *localtime(&rend_time);
10855: /* tml = *localtime(&end_time.tm_sec); */
10856: strcpy(strtend,asctime(&end_time));
1.126 brouard 10857: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10858: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10859: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 10860:
1.157 brouard 10861: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10862: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10863: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10864: /* printf("Total time was %d uSec.\n", total_usecs);*/
10865: /* if(fileappend(fichtm,optionfilehtm)){ */
10866: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10867: fclose(fichtm);
10868: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10869: fclose(fichtmcov);
10870: fclose(ficgp);
10871: fclose(ficlog);
10872: /*------ End -----------*/
1.227 brouard 10873:
10874:
10875: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10876: #ifdef WIN32
1.227 brouard 10877: if (_chdir(pathcd) != 0)
10878: printf("Can't move to directory %s!\n",path);
10879: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 10880: #else
1.227 brouard 10881: if(chdir(pathcd) != 0)
10882: printf("Can't move to directory %s!\n", path);
10883: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 10884: #endif
1.126 brouard 10885: printf("Current directory %s!\n",pathcd);
10886: /*strcat(plotcmd,CHARSEPARATOR);*/
10887: sprintf(plotcmd,"gnuplot");
1.157 brouard 10888: #ifdef _WIN32
1.126 brouard 10889: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10890: #endif
10891: if(!stat(plotcmd,&info)){
1.158 brouard 10892: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10893: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10894: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10895: }else
10896: strcpy(pplotcmd,plotcmd);
1.157 brouard 10897: #ifdef __unix
1.126 brouard 10898: strcpy(plotcmd,GNUPLOTPROGRAM);
10899: if(!stat(plotcmd,&info)){
1.158 brouard 10900: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10901: }else
10902: strcpy(pplotcmd,plotcmd);
10903: #endif
10904: }else
10905: strcpy(pplotcmd,plotcmd);
10906:
10907: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10908: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 10909:
1.126 brouard 10910: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10911: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10912: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10913: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10914: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10915: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10916: }
1.158 brouard 10917: printf(" Successful, please wait...");
1.126 brouard 10918: while (z[0] != 'q') {
10919: /* chdir(path); */
1.154 brouard 10920: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10921: scanf("%s",z);
10922: /* if (z[0] == 'c') system("./imach"); */
10923: if (z[0] == 'e') {
1.158 brouard 10924: #ifdef __APPLE__
1.152 brouard 10925: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10926: #elif __linux
10927: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10928: #else
1.152 brouard 10929: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10930: #endif
10931: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10932: system(pplotcmd);
1.126 brouard 10933: }
10934: else if (z[0] == 'g') system(plotcmd);
10935: else if (z[0] == 'q') exit(0);
10936: }
1.227 brouard 10937: end:
1.126 brouard 10938: while (z[0] != 'q') {
1.195 brouard 10939: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10940: scanf("%s",z);
10941: }
10942: }
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