Annotation of imach/src/imach.c, revision 1.228
1.227 brouard 1: /* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.227 brouard 4: Revision 1.226 2016/07/12 18:42:34 brouard
5: Summary: temp
6:
1.226 brouard 7: Revision 1.225 2016/07/12 08:40:03 brouard
8: Summary: saving but not running
9:
1.225 brouard 10: Revision 1.224 2016/07/01 13:16:01 brouard
11: Summary: Fixes
12:
1.224 brouard 13: Revision 1.223 2016/02/19 09:23:35 brouard
14: Summary: temporary
15:
1.223 brouard 16: Revision 1.222 2016/02/17 08:14:50 brouard
17: Summary: Probably last 0.98 stable version 0.98r6
18:
1.222 brouard 19: Revision 1.221 2016/02/15 23:35:36 brouard
20: Summary: minor bug
21:
1.220 brouard 22: Revision 1.219 2016/02/15 00:48:12 brouard
23: *** empty log message ***
24:
1.219 brouard 25: Revision 1.218 2016/02/12 11:29:23 brouard
26: Summary: 0.99 Back projections
27:
1.218 brouard 28: Revision 1.217 2015/12/23 17:18:31 brouard
29: Summary: Experimental backcast
30:
1.217 brouard 31: Revision 1.216 2015/12/18 17:32:11 brouard
32: Summary: 0.98r4 Warning and status=-2
33:
34: Version 0.98r4 is now:
35: - displaying an error when status is -1, date of interview unknown and date of death known;
36: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
37: Older changes concerning s=-2, dating from 2005 have been supersed.
38:
1.216 brouard 39: Revision 1.215 2015/12/16 08:52:24 brouard
40: Summary: 0.98r4 working
41:
1.215 brouard 42: Revision 1.214 2015/12/16 06:57:54 brouard
43: Summary: temporary not working
44:
1.214 brouard 45: Revision 1.213 2015/12/11 18:22:17 brouard
46: Summary: 0.98r4
47:
1.213 brouard 48: Revision 1.212 2015/11/21 12:47:24 brouard
49: Summary: minor typo
50:
1.212 brouard 51: Revision 1.211 2015/11/21 12:41:11 brouard
52: Summary: 0.98r3 with some graph of projected cross-sectional
53:
54: Author: Nicolas Brouard
55:
1.211 brouard 56: Revision 1.210 2015/11/18 17:41:20 brouard
57: Summary: Start working on projected prevalences
58:
1.210 brouard 59: Revision 1.209 2015/11/17 22:12:03 brouard
60: Summary: Adding ftolpl parameter
61: Author: N Brouard
62:
63: We had difficulties to get smoothed confidence intervals. It was due
64: to the period prevalence which wasn't computed accurately. The inner
65: parameter ftolpl is now an outer parameter of the .imach parameter
66: file after estepm. If ftolpl is small 1.e-4 and estepm too,
67: computation are long.
68:
1.209 brouard 69: Revision 1.208 2015/11/17 14:31:57 brouard
70: Summary: temporary
71:
1.208 brouard 72: Revision 1.207 2015/10/27 17:36:57 brouard
73: *** empty log message ***
74:
1.207 brouard 75: Revision 1.206 2015/10/24 07:14:11 brouard
76: *** empty log message ***
77:
1.206 brouard 78: Revision 1.205 2015/10/23 15:50:53 brouard
79: Summary: 0.98r3 some clarification for graphs on likelihood contributions
80:
1.205 brouard 81: Revision 1.204 2015/10/01 16:20:26 brouard
82: Summary: Some new graphs of contribution to likelihood
83:
1.204 brouard 84: Revision 1.203 2015/09/30 17:45:14 brouard
85: Summary: looking at better estimation of the hessian
86:
87: Also a better criteria for convergence to the period prevalence And
88: therefore adding the number of years needed to converge. (The
89: prevalence in any alive state shold sum to one
90:
1.203 brouard 91: Revision 1.202 2015/09/22 19:45:16 brouard
92: Summary: Adding some overall graph on contribution to likelihood. Might change
93:
1.202 brouard 94: Revision 1.201 2015/09/15 17:34:58 brouard
95: Summary: 0.98r0
96:
97: - Some new graphs like suvival functions
98: - Some bugs fixed like model=1+age+V2.
99:
1.201 brouard 100: Revision 1.200 2015/09/09 16:53:55 brouard
101: Summary: Big bug thanks to Flavia
102:
103: Even model=1+age+V2. did not work anymore
104:
1.200 brouard 105: Revision 1.199 2015/09/07 14:09:23 brouard
106: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
107:
1.199 brouard 108: Revision 1.198 2015/09/03 07:14:39 brouard
109: Summary: 0.98q5 Flavia
110:
1.198 brouard 111: Revision 1.197 2015/09/01 18:24:39 brouard
112: *** empty log message ***
113:
1.197 brouard 114: Revision 1.196 2015/08/18 23:17:52 brouard
115: Summary: 0.98q5
116:
1.196 brouard 117: Revision 1.195 2015/08/18 16:28:39 brouard
118: Summary: Adding a hack for testing purpose
119:
120: After reading the title, ftol and model lines, if the comment line has
121: a q, starting with #q, the answer at the end of the run is quit. It
122: permits to run test files in batch with ctest. The former workaround was
123: $ echo q | imach foo.imach
124:
1.195 brouard 125: Revision 1.194 2015/08/18 13:32:00 brouard
126: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
127:
1.194 brouard 128: Revision 1.193 2015/08/04 07:17:42 brouard
129: Summary: 0.98q4
130:
1.193 brouard 131: Revision 1.192 2015/07/16 16:49:02 brouard
132: Summary: Fixing some outputs
133:
1.192 brouard 134: Revision 1.191 2015/07/14 10:00:33 brouard
135: Summary: Some fixes
136:
1.191 brouard 137: Revision 1.190 2015/05/05 08:51:13 brouard
138: Summary: Adding digits in output parameters (7 digits instead of 6)
139:
140: Fix 1+age+.
141:
1.190 brouard 142: Revision 1.189 2015/04/30 14:45:16 brouard
143: Summary: 0.98q2
144:
1.189 brouard 145: Revision 1.188 2015/04/30 08:27:53 brouard
146: *** empty log message ***
147:
1.188 brouard 148: Revision 1.187 2015/04/29 09:11:15 brouard
149: *** empty log message ***
150:
1.187 brouard 151: Revision 1.186 2015/04/23 12:01:52 brouard
152: Summary: V1*age is working now, version 0.98q1
153:
154: Some codes had been disabled in order to simplify and Vn*age was
155: working in the optimization phase, ie, giving correct MLE parameters,
156: but, as usual, outputs were not correct and program core dumped.
157:
1.186 brouard 158: Revision 1.185 2015/03/11 13:26:42 brouard
159: Summary: Inclusion of compile and links command line for Intel Compiler
160:
1.185 brouard 161: Revision 1.184 2015/03/11 11:52:39 brouard
162: Summary: Back from Windows 8. Intel Compiler
163:
1.184 brouard 164: Revision 1.183 2015/03/10 20:34:32 brouard
165: Summary: 0.98q0, trying with directest, mnbrak fixed
166:
167: We use directest instead of original Powell test; probably no
168: incidence on the results, but better justifications;
169: We fixed Numerical Recipes mnbrak routine which was wrong and gave
170: wrong results.
171:
1.183 brouard 172: Revision 1.182 2015/02/12 08:19:57 brouard
173: Summary: Trying to keep directest which seems simpler and more general
174: Author: Nicolas Brouard
175:
1.182 brouard 176: Revision 1.181 2015/02/11 23:22:24 brouard
177: Summary: Comments on Powell added
178:
179: Author:
180:
1.181 brouard 181: Revision 1.180 2015/02/11 17:33:45 brouard
182: Summary: Finishing move from main to function (hpijx and prevalence_limit)
183:
1.180 brouard 184: Revision 1.179 2015/01/04 09:57:06 brouard
185: Summary: back to OS/X
186:
1.179 brouard 187: Revision 1.178 2015/01/04 09:35:48 brouard
188: *** empty log message ***
189:
1.178 brouard 190: Revision 1.177 2015/01/03 18:40:56 brouard
191: Summary: Still testing ilc32 on OSX
192:
1.177 brouard 193: Revision 1.176 2015/01/03 16:45:04 brouard
194: *** empty log message ***
195:
1.176 brouard 196: Revision 1.175 2015/01/03 16:33:42 brouard
197: *** empty log message ***
198:
1.175 brouard 199: Revision 1.174 2015/01/03 16:15:49 brouard
200: Summary: Still in cross-compilation
201:
1.174 brouard 202: Revision 1.173 2015/01/03 12:06:26 brouard
203: Summary: trying to detect cross-compilation
204:
1.173 brouard 205: Revision 1.172 2014/12/27 12:07:47 brouard
206: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
207:
1.172 brouard 208: Revision 1.171 2014/12/23 13:26:59 brouard
209: Summary: Back from Visual C
210:
211: Still problem with utsname.h on Windows
212:
1.171 brouard 213: Revision 1.170 2014/12/23 11:17:12 brouard
214: Summary: Cleaning some \%% back to %%
215:
216: The escape was mandatory for a specific compiler (which one?), but too many warnings.
217:
1.170 brouard 218: Revision 1.169 2014/12/22 23:08:31 brouard
219: Summary: 0.98p
220:
221: Outputs some informations on compiler used, OS etc. Testing on different platforms.
222:
1.169 brouard 223: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 224: Summary: update
1.169 brouard 225:
1.168 brouard 226: Revision 1.167 2014/12/22 13:50:56 brouard
227: Summary: Testing uname and compiler version and if compiled 32 or 64
228:
229: Testing on Linux 64
230:
1.167 brouard 231: Revision 1.166 2014/12/22 11:40:47 brouard
232: *** empty log message ***
233:
1.166 brouard 234: Revision 1.165 2014/12/16 11:20:36 brouard
235: Summary: After compiling on Visual C
236:
237: * imach.c (Module): Merging 1.61 to 1.162
238:
1.165 brouard 239: Revision 1.164 2014/12/16 10:52:11 brouard
240: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
241:
242: * imach.c (Module): Merging 1.61 to 1.162
243:
1.164 brouard 244: Revision 1.163 2014/12/16 10:30:11 brouard
245: * imach.c (Module): Merging 1.61 to 1.162
246:
1.163 brouard 247: Revision 1.162 2014/09/25 11:43:39 brouard
248: Summary: temporary backup 0.99!
249:
1.162 brouard 250: Revision 1.1 2014/09/16 11:06:58 brouard
251: Summary: With some code (wrong) for nlopt
252:
253: Author:
254:
255: Revision 1.161 2014/09/15 20:41:41 brouard
256: Summary: Problem with macro SQR on Intel compiler
257:
1.161 brouard 258: Revision 1.160 2014/09/02 09:24:05 brouard
259: *** empty log message ***
260:
1.160 brouard 261: Revision 1.159 2014/09/01 10:34:10 brouard
262: Summary: WIN32
263: Author: Brouard
264:
1.159 brouard 265: Revision 1.158 2014/08/27 17:11:51 brouard
266: *** empty log message ***
267:
1.158 brouard 268: Revision 1.157 2014/08/27 16:26:55 brouard
269: Summary: Preparing windows Visual studio version
270: Author: Brouard
271:
272: In order to compile on Visual studio, time.h is now correct and time_t
273: and tm struct should be used. difftime should be used but sometimes I
274: just make the differences in raw time format (time(&now).
275: Trying to suppress #ifdef LINUX
276: Add xdg-open for __linux in order to open default browser.
277:
1.157 brouard 278: Revision 1.156 2014/08/25 20:10:10 brouard
279: *** empty log message ***
280:
1.156 brouard 281: Revision 1.155 2014/08/25 18:32:34 brouard
282: Summary: New compile, minor changes
283: Author: Brouard
284:
1.155 brouard 285: Revision 1.154 2014/06/20 17:32:08 brouard
286: Summary: Outputs now all graphs of convergence to period prevalence
287:
1.154 brouard 288: Revision 1.153 2014/06/20 16:45:46 brouard
289: Summary: If 3 live state, convergence to period prevalence on same graph
290: Author: Brouard
291:
1.153 brouard 292: Revision 1.152 2014/06/18 17:54:09 brouard
293: Summary: open browser, use gnuplot on same dir than imach if not found in the path
294:
1.152 brouard 295: Revision 1.151 2014/06/18 16:43:30 brouard
296: *** empty log message ***
297:
1.151 brouard 298: Revision 1.150 2014/06/18 16:42:35 brouard
299: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
300: Author: brouard
301:
1.150 brouard 302: Revision 1.149 2014/06/18 15:51:14 brouard
303: Summary: Some fixes in parameter files errors
304: Author: Nicolas Brouard
305:
1.149 brouard 306: Revision 1.148 2014/06/17 17:38:48 brouard
307: Summary: Nothing new
308: Author: Brouard
309:
310: Just a new packaging for OS/X version 0.98nS
311:
1.148 brouard 312: Revision 1.147 2014/06/16 10:33:11 brouard
313: *** empty log message ***
314:
1.147 brouard 315: Revision 1.146 2014/06/16 10:20:28 brouard
316: Summary: Merge
317: Author: Brouard
318:
319: Merge, before building revised version.
320:
1.146 brouard 321: Revision 1.145 2014/06/10 21:23:15 brouard
322: Summary: Debugging with valgrind
323: Author: Nicolas Brouard
324:
325: Lot of changes in order to output the results with some covariates
326: After the Edimburgh REVES conference 2014, it seems mandatory to
327: improve the code.
328: No more memory valgrind error but a lot has to be done in order to
329: continue the work of splitting the code into subroutines.
330: Also, decodemodel has been improved. Tricode is still not
331: optimal. nbcode should be improved. Documentation has been added in
332: the source code.
333:
1.144 brouard 334: Revision 1.143 2014/01/26 09:45:38 brouard
335: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
336:
337: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
338: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
339:
1.143 brouard 340: Revision 1.142 2014/01/26 03:57:36 brouard
341: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
342:
343: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
344:
1.142 brouard 345: Revision 1.141 2014/01/26 02:42:01 brouard
346: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
347:
1.141 brouard 348: Revision 1.140 2011/09/02 10:37:54 brouard
349: Summary: times.h is ok with mingw32 now.
350:
1.140 brouard 351: Revision 1.139 2010/06/14 07:50:17 brouard
352: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
353: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
354:
1.139 brouard 355: Revision 1.138 2010/04/30 18:19:40 brouard
356: *** empty log message ***
357:
1.138 brouard 358: Revision 1.137 2010/04/29 18:11:38 brouard
359: (Module): Checking covariates for more complex models
360: than V1+V2. A lot of change to be done. Unstable.
361:
1.137 brouard 362: Revision 1.136 2010/04/26 20:30:53 brouard
363: (Module): merging some libgsl code. Fixing computation
364: of likelione (using inter/intrapolation if mle = 0) in order to
365: get same likelihood as if mle=1.
366: Some cleaning of code and comments added.
367:
1.136 brouard 368: Revision 1.135 2009/10/29 15:33:14 brouard
369: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
370:
1.135 brouard 371: Revision 1.134 2009/10/29 13:18:53 brouard
372: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
373:
1.134 brouard 374: Revision 1.133 2009/07/06 10:21:25 brouard
375: just nforces
376:
1.133 brouard 377: Revision 1.132 2009/07/06 08:22:05 brouard
378: Many tings
379:
1.132 brouard 380: Revision 1.131 2009/06/20 16:22:47 brouard
381: Some dimensions resccaled
382:
1.131 brouard 383: Revision 1.130 2009/05/26 06:44:34 brouard
384: (Module): Max Covariate is now set to 20 instead of 8. A
385: lot of cleaning with variables initialized to 0. Trying to make
386: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
387:
1.130 brouard 388: Revision 1.129 2007/08/31 13:49:27 lievre
389: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
390:
1.129 lievre 391: Revision 1.128 2006/06/30 13:02:05 brouard
392: (Module): Clarifications on computing e.j
393:
1.128 brouard 394: Revision 1.127 2006/04/28 18:11:50 brouard
395: (Module): Yes the sum of survivors was wrong since
396: imach-114 because nhstepm was no more computed in the age
397: loop. Now we define nhstepma in the age loop.
398: (Module): In order to speed up (in case of numerous covariates) we
399: compute health expectancies (without variances) in a first step
400: and then all the health expectancies with variances or standard
401: deviation (needs data from the Hessian matrices) which slows the
402: computation.
403: In the future we should be able to stop the program is only health
404: expectancies and graph are needed without standard deviations.
405:
1.127 brouard 406: Revision 1.126 2006/04/28 17:23:28 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: Version 0.98h
411:
1.126 brouard 412: Revision 1.125 2006/04/04 15:20:31 lievre
413: Errors in calculation of health expectancies. Age was not initialized.
414: Forecasting file added.
415:
416: Revision 1.124 2006/03/22 17:13:53 lievre
417: Parameters are printed with %lf instead of %f (more numbers after the comma).
418: The log-likelihood is printed in the log file
419:
420: Revision 1.123 2006/03/20 10:52:43 brouard
421: * imach.c (Module): <title> changed, corresponds to .htm file
422: name. <head> headers where missing.
423:
424: * imach.c (Module): Weights can have a decimal point as for
425: English (a comma might work with a correct LC_NUMERIC environment,
426: otherwise the weight is truncated).
427: Modification of warning when the covariates values are not 0 or
428: 1.
429: Version 0.98g
430:
431: Revision 1.122 2006/03/20 09:45:41 brouard
432: (Module): Weights can have a decimal point as for
433: English (a comma might work with a correct LC_NUMERIC environment,
434: otherwise the weight is truncated).
435: Modification of warning when the covariates values are not 0 or
436: 1.
437: Version 0.98g
438:
439: Revision 1.121 2006/03/16 17:45:01 lievre
440: * imach.c (Module): Comments concerning covariates added
441:
442: * imach.c (Module): refinements in the computation of lli if
443: status=-2 in order to have more reliable computation if stepm is
444: not 1 month. Version 0.98f
445:
446: Revision 1.120 2006/03/16 15:10:38 lievre
447: (Module): refinements in the computation of lli if
448: status=-2 in order to have more reliable computation if stepm is
449: not 1 month. Version 0.98f
450:
451: Revision 1.119 2006/03/15 17:42:26 brouard
452: (Module): Bug if status = -2, the loglikelihood was
453: computed as likelihood omitting the logarithm. Version O.98e
454:
455: Revision 1.118 2006/03/14 18:20:07 brouard
456: (Module): varevsij Comments added explaining the second
457: table of variances if popbased=1 .
458: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
459: (Module): Function pstamp added
460: (Module): Version 0.98d
461:
462: Revision 1.117 2006/03/14 17:16:22 brouard
463: (Module): varevsij Comments added explaining the second
464: table of variances if popbased=1 .
465: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
466: (Module): Function pstamp added
467: (Module): Version 0.98d
468:
469: Revision 1.116 2006/03/06 10:29:27 brouard
470: (Module): Variance-covariance wrong links and
471: varian-covariance of ej. is needed (Saito).
472:
473: Revision 1.115 2006/02/27 12:17:45 brouard
474: (Module): One freematrix added in mlikeli! 0.98c
475:
476: Revision 1.114 2006/02/26 12:57:58 brouard
477: (Module): Some improvements in processing parameter
478: filename with strsep.
479:
480: Revision 1.113 2006/02/24 14:20:24 brouard
481: (Module): Memory leaks checks with valgrind and:
482: datafile was not closed, some imatrix were not freed and on matrix
483: allocation too.
484:
485: Revision 1.112 2006/01/30 09:55:26 brouard
486: (Module): Back to gnuplot.exe instead of wgnuplot.exe
487:
488: Revision 1.111 2006/01/25 20:38:18 brouard
489: (Module): Lots of cleaning and bugs added (Gompertz)
490: (Module): Comments can be added in data file. Missing date values
491: can be a simple dot '.'.
492:
493: Revision 1.110 2006/01/25 00:51:50 brouard
494: (Module): Lots of cleaning and bugs added (Gompertz)
495:
496: Revision 1.109 2006/01/24 19:37:15 brouard
497: (Module): Comments (lines starting with a #) are allowed in data.
498:
499: Revision 1.108 2006/01/19 18:05:42 lievre
500: Gnuplot problem appeared...
501: To be fixed
502:
503: Revision 1.107 2006/01/19 16:20:37 brouard
504: Test existence of gnuplot in imach path
505:
506: Revision 1.106 2006/01/19 13:24:36 brouard
507: Some cleaning and links added in html output
508:
509: Revision 1.105 2006/01/05 20:23:19 lievre
510: *** empty log message ***
511:
512: Revision 1.104 2005/09/30 16:11:43 lievre
513: (Module): sump fixed, loop imx fixed, and simplifications.
514: (Module): If the status is missing at the last wave but we know
515: that the person is alive, then we can code his/her status as -2
516: (instead of missing=-1 in earlier versions) and his/her
517: contributions to the likelihood is 1 - Prob of dying from last
518: health status (= 1-p13= p11+p12 in the easiest case of somebody in
519: the healthy state at last known wave). Version is 0.98
520:
521: Revision 1.103 2005/09/30 15:54:49 lievre
522: (Module): sump fixed, loop imx fixed, and simplifications.
523:
524: Revision 1.102 2004/09/15 17:31:30 brouard
525: Add the possibility to read data file including tab characters.
526:
527: Revision 1.101 2004/09/15 10:38:38 brouard
528: Fix on curr_time
529:
530: Revision 1.100 2004/07/12 18:29:06 brouard
531: Add version for Mac OS X. Just define UNIX in Makefile
532:
533: Revision 1.99 2004/06/05 08:57:40 brouard
534: *** empty log message ***
535:
536: Revision 1.98 2004/05/16 15:05:56 brouard
537: New version 0.97 . First attempt to estimate force of mortality
538: directly from the data i.e. without the need of knowing the health
539: state at each age, but using a Gompertz model: log u =a + b*age .
540: This is the basic analysis of mortality and should be done before any
541: other analysis, in order to test if the mortality estimated from the
542: cross-longitudinal survey is different from the mortality estimated
543: from other sources like vital statistic data.
544:
545: The same imach parameter file can be used but the option for mle should be -3.
546:
1.133 brouard 547: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 548: former routines in order to include the new code within the former code.
549:
550: The output is very simple: only an estimate of the intercept and of
551: the slope with 95% confident intervals.
552:
553: Current limitations:
554: A) Even if you enter covariates, i.e. with the
555: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
556: B) There is no computation of Life Expectancy nor Life Table.
557:
558: Revision 1.97 2004/02/20 13:25:42 lievre
559: Version 0.96d. Population forecasting command line is (temporarily)
560: suppressed.
561:
562: Revision 1.96 2003/07/15 15:38:55 brouard
563: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
564: rewritten within the same printf. Workaround: many printfs.
565:
566: Revision 1.95 2003/07/08 07:54:34 brouard
567: * imach.c (Repository):
568: (Repository): Using imachwizard code to output a more meaningful covariance
569: matrix (cov(a12,c31) instead of numbers.
570:
571: Revision 1.94 2003/06/27 13:00:02 brouard
572: Just cleaning
573:
574: Revision 1.93 2003/06/25 16:33:55 brouard
575: (Module): On windows (cygwin) function asctime_r doesn't
576: exist so I changed back to asctime which exists.
577: (Module): Version 0.96b
578:
579: Revision 1.92 2003/06/25 16:30:45 brouard
580: (Module): On windows (cygwin) function asctime_r doesn't
581: exist so I changed back to asctime which exists.
582:
583: Revision 1.91 2003/06/25 15:30:29 brouard
584: * imach.c (Repository): Duplicated warning errors corrected.
585: (Repository): Elapsed time after each iteration is now output. It
586: helps to forecast when convergence will be reached. Elapsed time
587: is stamped in powell. We created a new html file for the graphs
588: concerning matrix of covariance. It has extension -cov.htm.
589:
590: Revision 1.90 2003/06/24 12:34:15 brouard
591: (Module): Some bugs corrected for windows. Also, when
592: mle=-1 a template is output in file "or"mypar.txt with the design
593: of the covariance matrix to be input.
594:
595: Revision 1.89 2003/06/24 12:30:52 brouard
596: (Module): Some bugs corrected for windows. Also, when
597: mle=-1 a template is output in file "or"mypar.txt with the design
598: of the covariance matrix to be input.
599:
600: Revision 1.88 2003/06/23 17:54:56 brouard
601: * 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.
602:
603: Revision 1.87 2003/06/18 12:26:01 brouard
604: Version 0.96
605:
606: Revision 1.86 2003/06/17 20:04:08 brouard
607: (Module): Change position of html and gnuplot routines and added
608: routine fileappend.
609:
610: Revision 1.85 2003/06/17 13:12:43 brouard
611: * imach.c (Repository): Check when date of death was earlier that
612: current date of interview. It may happen when the death was just
613: prior to the death. In this case, dh was negative and likelihood
614: was wrong (infinity). We still send an "Error" but patch by
615: assuming that the date of death was just one stepm after the
616: interview.
617: (Repository): Because some people have very long ID (first column)
618: we changed int to long in num[] and we added a new lvector for
619: memory allocation. But we also truncated to 8 characters (left
620: truncation)
621: (Repository): No more line truncation errors.
622:
623: Revision 1.84 2003/06/13 21:44:43 brouard
624: * imach.c (Repository): Replace "freqsummary" at a correct
625: place. It differs from routine "prevalence" which may be called
626: many times. Probs is memory consuming and must be used with
627: parcimony.
628: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
629:
630: Revision 1.83 2003/06/10 13:39:11 lievre
631: *** empty log message ***
632:
633: Revision 1.82 2003/06/05 15:57:20 brouard
634: Add log in imach.c and fullversion number is now printed.
635:
636: */
637: /*
638: Interpolated Markov Chain
639:
640: Short summary of the programme:
641:
1.227 brouard 642: This program computes Healthy Life Expectancies or State-specific
643: (if states aren't health statuses) Expectancies from
644: cross-longitudinal data. Cross-longitudinal data consist in:
645:
646: -1- a first survey ("cross") where individuals from different ages
647: are interviewed on their health status or degree of disability (in
648: the case of a health survey which is our main interest)
649:
650: -2- at least a second wave of interviews ("longitudinal") which
651: measure each change (if any) in individual health status. Health
652: expectancies are computed from the time spent in each health state
653: according to a model. More health states you consider, more time is
654: necessary to reach the Maximum Likelihood of the parameters involved
655: in the model. The simplest model is the multinomial logistic model
656: where pij is the probability to be observed in state j at the second
657: wave conditional to be observed in state i at the first
658: wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
659: etc , where 'age' is age and 'sex' is a covariate. If you want to
660: have a more complex model than "constant and age", you should modify
661: the program where the markup *Covariates have to be included here
662: again* invites you to do it. More covariates you add, slower the
1.126 brouard 663: convergence.
664:
665: The advantage of this computer programme, compared to a simple
666: multinomial logistic model, is clear when the delay between waves is not
667: identical for each individual. Also, if a individual missed an
668: intermediate interview, the information is lost, but taken into
669: account using an interpolation or extrapolation.
670:
671: hPijx is the probability to be observed in state i at age x+h
672: conditional to the observed state i at age x. The delay 'h' can be
673: split into an exact number (nh*stepm) of unobserved intermediate
674: states. This elementary transition (by month, quarter,
675: semester or year) is modelled as a multinomial logistic. The hPx
676: matrix is simply the matrix product of nh*stepm elementary matrices
677: and the contribution of each individual to the likelihood is simply
678: hPijx.
679:
680: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 681: of the life expectancies. It also computes the period (stable) prevalence.
682:
683: Back prevalence and projections:
1.227 brouard 684:
685: - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
686: double agemaxpar, double ftolpl, int *ncvyearp, double
687: dateprev1,double dateprev2, int firstpass, int lastpass, int
688: mobilavproj)
689:
690: Computes the back prevalence limit for any combination of
691: covariate values k at any age between ageminpar and agemaxpar and
692: returns it in **bprlim. In the loops,
693:
694: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
695: **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
696:
697: - hBijx Back Probability to be in state i at age x-h being in j at x
1.218 brouard 698: Computes for any combination of covariates k and any age between bage and fage
699: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
700: oldm=oldms;savm=savms;
1.227 brouard 701:
702: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 703: Computes the transition matrix starting at age 'age' over
704: 'nhstepm*hstepm*stepm' months (i.e. until
705: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1.227 brouard 706: nhstepm*hstepm matrices.
707:
708: Returns p3mat[i][j][h] after calling
709: p3mat[i][j][h]=matprod2(newm,
710: bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
711: dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
712: oldm);
1.226 brouard 713:
714: Important routines
715:
716: - func (or funcone), computes logit (pij) distinguishing
717: o fixed variables (single or product dummies or quantitative);
718: o varying variables by:
719: (1) wave (single, product dummies, quantitative),
720: (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
721: % fixed dummy (treated) or quantitative (not done because time-consuming);
722: % varying dummy (not done) or quantitative (not done);
723: - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
724: and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
725: - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
726: o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
727: race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
1.218 brouard 728:
1.226 brouard 729:
730:
1.133 brouard 731: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
732: Institut national d'études démographiques, Paris.
1.126 brouard 733: This software have been partly granted by Euro-REVES, a concerted action
734: from the European Union.
735: It is copyrighted identically to a GNU software product, ie programme and
736: software can be distributed freely for non commercial use. Latest version
737: can be accessed at http://euroreves.ined.fr/imach .
738:
739: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
740: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
741:
742: **********************************************************************/
743: /*
744: main
745: read parameterfile
746: read datafile
747: concatwav
748: freqsummary
749: if (mle >= 1)
750: mlikeli
751: print results files
752: if mle==1
753: computes hessian
754: read end of parameter file: agemin, agemax, bage, fage, estepm
755: begin-prev-date,...
756: open gnuplot file
757: open html file
1.145 brouard 758: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
759: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
760: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
761: freexexit2 possible for memory heap.
762:
763: h Pij x | pij_nom ficrestpij
764: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
765: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
766: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
767:
768: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
769: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
770: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
771: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
772: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
773:
1.126 brouard 774: forecasting if prevfcast==1 prevforecast call prevalence()
775: health expectancies
776: Variance-covariance of DFLE
777: prevalence()
778: movingaverage()
779: varevsij()
780: if popbased==1 varevsij(,popbased)
781: total life expectancies
782: Variance of period (stable) prevalence
783: end
784: */
785:
1.187 brouard 786: /* #define DEBUG */
787: /* #define DEBUGBRENT */
1.203 brouard 788: /* #define DEBUGLINMIN */
789: /* #define DEBUGHESS */
790: #define DEBUGHESSIJ
1.224 brouard 791: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan) *\/ */
1.165 brouard 792: #define POWELL /* Instead of NLOPT */
1.224 brouard 793: #define POWELLNOF3INFF1TEST /* Skip test */
1.186 brouard 794: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
795: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 796:
797: #include <math.h>
798: #include <stdio.h>
799: #include <stdlib.h>
800: #include <string.h>
1.226 brouard 801: #include <ctype.h>
1.159 brouard 802:
803: #ifdef _WIN32
804: #include <io.h>
1.172 brouard 805: #include <windows.h>
806: #include <tchar.h>
1.159 brouard 807: #else
1.126 brouard 808: #include <unistd.h>
1.159 brouard 809: #endif
1.126 brouard 810:
811: #include <limits.h>
812: #include <sys/types.h>
1.171 brouard 813:
814: #if defined(__GNUC__)
815: #include <sys/utsname.h> /* Doesn't work on Windows */
816: #endif
817:
1.126 brouard 818: #include <sys/stat.h>
819: #include <errno.h>
1.159 brouard 820: /* extern int errno; */
1.126 brouard 821:
1.157 brouard 822: /* #ifdef LINUX */
823: /* #include <time.h> */
824: /* #include "timeval.h" */
825: /* #else */
826: /* #include <sys/time.h> */
827: /* #endif */
828:
1.126 brouard 829: #include <time.h>
830:
1.136 brouard 831: #ifdef GSL
832: #include <gsl/gsl_errno.h>
833: #include <gsl/gsl_multimin.h>
834: #endif
835:
1.167 brouard 836:
1.162 brouard 837: #ifdef NLOPT
838: #include <nlopt.h>
839: typedef struct {
840: double (* function)(double [] );
841: } myfunc_data ;
842: #endif
843:
1.126 brouard 844: /* #include <libintl.h> */
845: /* #define _(String) gettext (String) */
846:
1.141 brouard 847: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 848:
849: #define GNUPLOTPROGRAM "gnuplot"
850: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
851: #define FILENAMELENGTH 132
852:
853: #define GLOCK_ERROR_NOPATH -1 /* empty path */
854: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
855:
1.144 brouard 856: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
857: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 858:
859: #define NINTERVMAX 8
1.144 brouard 860: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
861: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
862: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 863: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 864: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
865: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 866: #define MAXN 20000
1.144 brouard 867: #define YEARM 12. /**< Number of months per year */
1.218 brouard 868: /* #define AGESUP 130 */
869: #define AGESUP 150
870: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 871: #define AGEBASE 40
1.194 brouard 872: #define AGEOVERFLOW 1.e20
1.164 brouard 873: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 874: #ifdef _WIN32
875: #define DIRSEPARATOR '\\'
876: #define CHARSEPARATOR "\\"
877: #define ODIRSEPARATOR '/'
878: #else
1.126 brouard 879: #define DIRSEPARATOR '/'
880: #define CHARSEPARATOR "/"
881: #define ODIRSEPARATOR '\\'
882: #endif
883:
1.227 brouard 884: /* $Id: imach.c,v 1.226 2016/07/12 18:42:34 brouard Exp $ */
1.126 brouard 885: /* $State: Exp $ */
1.196 brouard 886: #include "version.h"
887: char version[]=__IMACH_VERSION__;
1.224 brouard 888: 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";
1.227 brouard 889: char fullversion[]="$Revision: 1.226 $ $Date: 2016/07/12 18:42:34 $";
1.126 brouard 890: char strstart[80];
891: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 892: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 893: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 894: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
895: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
896: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
1.225 brouard 897: int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */
898: int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */
1.145 brouard 899: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
900: int cptcovprodnoage=0; /**< Number of covariate products without age */
901: int cptcoveff=0; /* Total number of covariates to vary for printing results */
1.224 brouard 902: int ncoveff=0; /* Total number of effective covariates in the model */
1.225 brouard 903: int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
1.224 brouard 904: int ntveff=0; /**< ntveff number of effective time varying variables */
905: int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
1.145 brouard 906: int cptcov=0; /* Working variable */
1.218 brouard 907: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 908: int npar=NPARMAX;
909: int nlstate=2; /* Number of live states */
910: int ndeath=1; /* Number of dead states */
1.130 brouard 911: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.223 brouard 912: int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */
1.126 brouard 913: int popbased=0;
914:
915: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 916: int maxwav=0; /* Maxim number of waves */
917: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
918: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
919: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 920: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 921: int mle=1, weightopt=0;
1.126 brouard 922: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
923: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
924: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
925: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 926: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 927: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 928: double **matprod2(); /* test */
1.126 brouard 929: double **oldm, **newm, **savm; /* Working pointers to matrices */
930: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 931: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
932:
1.136 brouard 933: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 934: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 935: FILE *ficlog, *ficrespow;
1.130 brouard 936: int globpr=0; /* Global variable for printing or not */
1.126 brouard 937: double fretone; /* Only one call to likelihood */
1.130 brouard 938: long ipmx=0; /* Number of contributions */
1.126 brouard 939: double sw; /* Sum of weights */
940: char filerespow[FILENAMELENGTH];
941: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
942: FILE *ficresilk;
943: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
944: FILE *ficresprobmorprev;
945: FILE *fichtm, *fichtmcov; /* Html File */
946: FILE *ficreseij;
947: char filerese[FILENAMELENGTH];
948: FILE *ficresstdeij;
949: char fileresstde[FILENAMELENGTH];
950: FILE *ficrescveij;
951: char filerescve[FILENAMELENGTH];
952: FILE *ficresvij;
953: char fileresv[FILENAMELENGTH];
954: FILE *ficresvpl;
955: char fileresvpl[FILENAMELENGTH];
956: char title[MAXLINE];
1.217 brouard 957: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 958: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
959: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
960: char command[FILENAMELENGTH];
961: int outcmd=0;
962:
1.217 brouard 963: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 964: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 965: char filelog[FILENAMELENGTH]; /* Log file */
966: char filerest[FILENAMELENGTH];
967: char fileregp[FILENAMELENGTH];
968: char popfile[FILENAMELENGTH];
969:
970: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
971:
1.157 brouard 972: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
973: /* struct timezone tzp; */
974: /* extern int gettimeofday(); */
975: struct tm tml, *gmtime(), *localtime();
976:
977: extern time_t time();
978:
979: struct tm start_time, end_time, curr_time, last_time, forecast_time;
980: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
981: struct tm tm;
982:
1.126 brouard 983: char strcurr[80], strfor[80];
984:
985: char *endptr;
986: long lval;
987: double dval;
988:
989: #define NR_END 1
990: #define FREE_ARG char*
991: #define FTOL 1.0e-10
992:
993: #define NRANSI
994: #define ITMAX 200
995:
996: #define TOL 2.0e-4
997:
998: #define CGOLD 0.3819660
999: #define ZEPS 1.0e-10
1000: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
1001:
1002: #define GOLD 1.618034
1003: #define GLIMIT 100.0
1004: #define TINY 1.0e-20
1005:
1006: static double maxarg1,maxarg2;
1007: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
1008: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
1009:
1010: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
1011: #define rint(a) floor(a+0.5)
1.166 brouard 1012: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 1013: #define mytinydouble 1.0e-16
1.166 brouard 1014: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
1015: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
1016: /* static double dsqrarg; */
1017: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 1018: static double sqrarg;
1019: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
1020: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
1021: int agegomp= AGEGOMP;
1022:
1023: int imx;
1024: int stepm=1;
1025: /* Stepm, step in month: minimum step interpolation*/
1026:
1027: int estepm;
1028: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
1029:
1030: int m,nb;
1031: long *num;
1.197 brouard 1032: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 1033: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
1034: covariate for which somebody answered excluding
1035: undefined. Usually 2: 0 and 1. */
1036: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
1037: covariate for which somebody answered including
1038: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 1039: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 1040: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 1041: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 1042: double *ageexmed,*agecens;
1043: double dateintmean=0;
1044:
1045: double *weight;
1046: int **s; /* Status */
1.141 brouard 1047: double *agedc;
1.145 brouard 1048: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 1049: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 1050: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.225 brouard 1051: double **coqvar; /* Fixed quantitative covariate iqv */
1052: double ***cotvar; /* Time varying covariate itv */
1053: double ***cotqvar; /* Time varying quantitative covariate itqv */
1.141 brouard 1054: double idx;
1055: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.226 brouard 1056: int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
1.227 brouard 1057: int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
1058: 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 1059: int *Tage;
1.227 brouard 1060: int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */
1.228 ! brouard 1061: 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*/
! 1062: 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*/
! 1063: 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 1064: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 1065: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.227 brouard 1066: int **Tvard;
1067: int *Tprod;/**< Gives the k position of the k1 product */
1068: int *Tposprod; /**< Gives the k1 product from the k position */
1069: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
1070: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1071: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1072: */
1073: int cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 1074: double *lsurv, *lpop, *tpop;
1075:
1.143 brouard 1076: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1077: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1078:
1079: /**************** split *************************/
1080: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1081: {
1082: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1083: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1084: */
1085: char *ss; /* pointer */
1.186 brouard 1086: int l1=0, l2=0; /* length counters */
1.126 brouard 1087:
1088: l1 = strlen(path ); /* length of path */
1089: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1090: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1091: if ( ss == NULL ) { /* no directory, so determine current directory */
1092: strcpy( name, path ); /* we got the fullname name because no directory */
1093: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1094: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1095: /* get current working directory */
1096: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1097: #ifdef WIN32
1098: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1099: #else
1100: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1101: #endif
1.126 brouard 1102: return( GLOCK_ERROR_GETCWD );
1103: }
1104: /* got dirc from getcwd*/
1105: printf(" DIRC = %s \n",dirc);
1.205 brouard 1106: } else { /* strip directory from path */
1.126 brouard 1107: ss++; /* after this, the filename */
1108: l2 = strlen( ss ); /* length of filename */
1109: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1110: strcpy( name, ss ); /* save file name */
1111: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1112: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1113: printf(" DIRC2 = %s \n",dirc);
1114: }
1115: /* We add a separator at the end of dirc if not exists */
1116: l1 = strlen( dirc ); /* length of directory */
1117: if( dirc[l1-1] != DIRSEPARATOR ){
1118: dirc[l1] = DIRSEPARATOR;
1119: dirc[l1+1] = 0;
1120: printf(" DIRC3 = %s \n",dirc);
1121: }
1122: ss = strrchr( name, '.' ); /* find last / */
1123: if (ss >0){
1124: ss++;
1125: strcpy(ext,ss); /* save extension */
1126: l1= strlen( name);
1127: l2= strlen(ss)+1;
1128: strncpy( finame, name, l1-l2);
1129: finame[l1-l2]= 0;
1130: }
1131:
1132: return( 0 ); /* we're done */
1133: }
1134:
1135:
1136: /******************************************/
1137:
1138: void replace_back_to_slash(char *s, char*t)
1139: {
1140: int i;
1141: int lg=0;
1142: i=0;
1143: lg=strlen(t);
1144: for(i=0; i<= lg; i++) {
1145: (s[i] = t[i]);
1146: if (t[i]== '\\') s[i]='/';
1147: }
1148: }
1149:
1.132 brouard 1150: char *trimbb(char *out, char *in)
1.137 brouard 1151: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1152: char *s;
1153: s=out;
1154: while (*in != '\0'){
1.137 brouard 1155: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1156: in++;
1157: }
1158: *out++ = *in++;
1159: }
1160: *out='\0';
1161: return s;
1162: }
1163:
1.187 brouard 1164: /* char *substrchaine(char *out, char *in, char *chain) */
1165: /* { */
1166: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1167: /* char *s, *t; */
1168: /* t=in;s=out; */
1169: /* while ((*in != *chain) && (*in != '\0')){ */
1170: /* *out++ = *in++; */
1171: /* } */
1172:
1173: /* /\* *in matches *chain *\/ */
1174: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1175: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1176: /* } */
1177: /* in--; chain--; */
1178: /* while ( (*in != '\0')){ */
1179: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1180: /* *out++ = *in++; */
1181: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1182: /* } */
1183: /* *out='\0'; */
1184: /* out=s; */
1185: /* return out; */
1186: /* } */
1187: char *substrchaine(char *out, char *in, char *chain)
1188: {
1189: /* Substract chain 'chain' from 'in', return and output 'out' */
1190: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1191:
1192: char *strloc;
1193:
1194: strcpy (out, in);
1195: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1196: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1197: if(strloc != NULL){
1198: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1199: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1200: /* strcpy (strloc, strloc +strlen(chain));*/
1201: }
1202: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1203: return out;
1204: }
1205:
1206:
1.145 brouard 1207: char *cutl(char *blocc, char *alocc, char *in, char occ)
1208: {
1.187 brouard 1209: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1210: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1211: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1212: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1213: */
1.160 brouard 1214: char *s, *t;
1.145 brouard 1215: t=in;s=in;
1216: while ((*in != occ) && (*in != '\0')){
1217: *alocc++ = *in++;
1218: }
1219: if( *in == occ){
1220: *(alocc)='\0';
1221: s=++in;
1222: }
1223:
1224: if (s == t) {/* occ not found */
1225: *(alocc-(in-s))='\0';
1226: in=s;
1227: }
1228: while ( *in != '\0'){
1229: *blocc++ = *in++;
1230: }
1231:
1232: *blocc='\0';
1233: return t;
1234: }
1.137 brouard 1235: char *cutv(char *blocc, char *alocc, char *in, char occ)
1236: {
1.187 brouard 1237: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1238: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1239: gives blocc="abcdef2ghi" and alocc="j".
1240: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1241: */
1242: char *s, *t;
1243: t=in;s=in;
1244: while (*in != '\0'){
1245: while( *in == occ){
1246: *blocc++ = *in++;
1247: s=in;
1248: }
1249: *blocc++ = *in++;
1250: }
1251: if (s == t) /* occ not found */
1252: *(blocc-(in-s))='\0';
1253: else
1254: *(blocc-(in-s)-1)='\0';
1255: in=s;
1256: while ( *in != '\0'){
1257: *alocc++ = *in++;
1258: }
1259:
1260: *alocc='\0';
1261: return s;
1262: }
1263:
1.126 brouard 1264: int nbocc(char *s, char occ)
1265: {
1266: int i,j=0;
1267: int lg=20;
1268: i=0;
1269: lg=strlen(s);
1270: for(i=0; i<= lg; i++) {
1271: if (s[i] == occ ) j++;
1272: }
1273: return j;
1274: }
1275:
1.137 brouard 1276: /* void cutv(char *u,char *v, char*t, char occ) */
1277: /* { */
1278: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1279: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1280: /* gives u="abcdef2ghi" and v="j" *\/ */
1281: /* int i,lg,j,p=0; */
1282: /* i=0; */
1283: /* lg=strlen(t); */
1284: /* for(j=0; j<=lg-1; j++) { */
1285: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1286: /* } */
1.126 brouard 1287:
1.137 brouard 1288: /* for(j=0; j<p; j++) { */
1289: /* (u[j] = t[j]); */
1290: /* } */
1291: /* u[p]='\0'; */
1.126 brouard 1292:
1.137 brouard 1293: /* for(j=0; j<= lg; j++) { */
1294: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1295: /* } */
1296: /* } */
1.126 brouard 1297:
1.160 brouard 1298: #ifdef _WIN32
1299: char * strsep(char **pp, const char *delim)
1300: {
1301: char *p, *q;
1302:
1303: if ((p = *pp) == NULL)
1304: return 0;
1305: if ((q = strpbrk (p, delim)) != NULL)
1306: {
1307: *pp = q + 1;
1308: *q = '\0';
1309: }
1310: else
1311: *pp = 0;
1312: return p;
1313: }
1314: #endif
1315:
1.126 brouard 1316: /********************** nrerror ********************/
1317:
1318: void nrerror(char error_text[])
1319: {
1320: fprintf(stderr,"ERREUR ...\n");
1321: fprintf(stderr,"%s\n",error_text);
1322: exit(EXIT_FAILURE);
1323: }
1324: /*********************** vector *******************/
1325: double *vector(int nl, int nh)
1326: {
1327: double *v;
1328: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1329: if (!v) nrerror("allocation failure in vector");
1330: return v-nl+NR_END;
1331: }
1332:
1333: /************************ free vector ******************/
1334: void free_vector(double*v, int nl, int nh)
1335: {
1336: free((FREE_ARG)(v+nl-NR_END));
1337: }
1338:
1339: /************************ivector *******************************/
1340: int *ivector(long nl,long nh)
1341: {
1342: int *v;
1343: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1344: if (!v) nrerror("allocation failure in ivector");
1345: return v-nl+NR_END;
1346: }
1347:
1348: /******************free ivector **************************/
1349: void free_ivector(int *v, long nl, long nh)
1350: {
1351: free((FREE_ARG)(v+nl-NR_END));
1352: }
1353:
1354: /************************lvector *******************************/
1355: long *lvector(long nl,long nh)
1356: {
1357: long *v;
1358: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1359: if (!v) nrerror("allocation failure in ivector");
1360: return v-nl+NR_END;
1361: }
1362:
1363: /******************free lvector **************************/
1364: void free_lvector(long *v, long nl, long nh)
1365: {
1366: free((FREE_ARG)(v+nl-NR_END));
1367: }
1368:
1369: /******************* imatrix *******************************/
1370: int **imatrix(long nrl, long nrh, long ncl, long nch)
1371: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1372: {
1373: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1374: int **m;
1375:
1376: /* allocate pointers to rows */
1377: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1378: if (!m) nrerror("allocation failure 1 in matrix()");
1379: m += NR_END;
1380: m -= nrl;
1381:
1382:
1383: /* allocate rows and set pointers to them */
1384: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1385: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1386: m[nrl] += NR_END;
1387: m[nrl] -= ncl;
1388:
1389: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1390:
1391: /* return pointer to array of pointers to rows */
1392: return m;
1393: }
1394:
1395: /****************** free_imatrix *************************/
1396: void free_imatrix(m,nrl,nrh,ncl,nch)
1397: int **m;
1398: long nch,ncl,nrh,nrl;
1399: /* free an int matrix allocated by imatrix() */
1400: {
1401: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1402: free((FREE_ARG) (m+nrl-NR_END));
1403: }
1404:
1405: /******************* matrix *******************************/
1406: double **matrix(long nrl, long nrh, long ncl, long nch)
1407: {
1408: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1409: double **m;
1410:
1411: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1412: if (!m) nrerror("allocation failure 1 in matrix()");
1413: m += NR_END;
1414: m -= nrl;
1415:
1416: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1417: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1418: m[nrl] += NR_END;
1419: m[nrl] -= ncl;
1420:
1421: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1422: return m;
1.145 brouard 1423: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1424: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1425: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1426: */
1427: }
1428:
1429: /*************************free matrix ************************/
1430: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1431: {
1432: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1433: free((FREE_ARG)(m+nrl-NR_END));
1434: }
1435:
1436: /******************* ma3x *******************************/
1437: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1438: {
1439: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1440: double ***m;
1441:
1442: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1443: if (!m) nrerror("allocation failure 1 in matrix()");
1444: m += NR_END;
1445: m -= nrl;
1446:
1447: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1448: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1449: m[nrl] += NR_END;
1450: m[nrl] -= ncl;
1451:
1452: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1453:
1454: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1455: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1456: m[nrl][ncl] += NR_END;
1457: m[nrl][ncl] -= nll;
1458: for (j=ncl+1; j<=nch; j++)
1459: m[nrl][j]=m[nrl][j-1]+nlay;
1460:
1461: for (i=nrl+1; i<=nrh; i++) {
1462: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1463: for (j=ncl+1; j<=nch; j++)
1464: m[i][j]=m[i][j-1]+nlay;
1465: }
1466: return m;
1467: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1468: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1469: */
1470: }
1471:
1472: /*************************free ma3x ************************/
1473: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1474: {
1475: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1476: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1477: free((FREE_ARG)(m+nrl-NR_END));
1478: }
1479:
1480: /*************** function subdirf ***********/
1481: char *subdirf(char fileres[])
1482: {
1483: /* Caution optionfilefiname is hidden */
1484: strcpy(tmpout,optionfilefiname);
1485: strcat(tmpout,"/"); /* Add to the right */
1486: strcat(tmpout,fileres);
1487: return tmpout;
1488: }
1489:
1490: /*************** function subdirf2 ***********/
1491: char *subdirf2(char fileres[], char *preop)
1492: {
1493:
1494: /* Caution optionfilefiname is hidden */
1495: strcpy(tmpout,optionfilefiname);
1496: strcat(tmpout,"/");
1497: strcat(tmpout,preop);
1498: strcat(tmpout,fileres);
1499: return tmpout;
1500: }
1501:
1502: /*************** function subdirf3 ***********/
1503: char *subdirf3(char fileres[], char *preop, char *preop2)
1504: {
1505:
1506: /* Caution optionfilefiname is hidden */
1507: strcpy(tmpout,optionfilefiname);
1508: strcat(tmpout,"/");
1509: strcat(tmpout,preop);
1510: strcat(tmpout,preop2);
1511: strcat(tmpout,fileres);
1512: return tmpout;
1513: }
1.213 brouard 1514:
1515: /*************** function subdirfext ***********/
1516: char *subdirfext(char fileres[], char *preop, char *postop)
1517: {
1518:
1519: strcpy(tmpout,preop);
1520: strcat(tmpout,fileres);
1521: strcat(tmpout,postop);
1522: return tmpout;
1523: }
1.126 brouard 1524:
1.213 brouard 1525: /*************** function subdirfext3 ***********/
1526: char *subdirfext3(char fileres[], char *preop, char *postop)
1527: {
1528:
1529: /* Caution optionfilefiname is hidden */
1530: strcpy(tmpout,optionfilefiname);
1531: strcat(tmpout,"/");
1532: strcat(tmpout,preop);
1533: strcat(tmpout,fileres);
1534: strcat(tmpout,postop);
1535: return tmpout;
1536: }
1537:
1.162 brouard 1538: char *asc_diff_time(long time_sec, char ascdiff[])
1539: {
1540: long sec_left, days, hours, minutes;
1541: days = (time_sec) / (60*60*24);
1542: sec_left = (time_sec) % (60*60*24);
1543: hours = (sec_left) / (60*60) ;
1544: sec_left = (sec_left) %(60*60);
1545: minutes = (sec_left) /60;
1546: sec_left = (sec_left) % (60);
1547: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1548: return ascdiff;
1549: }
1550:
1.126 brouard 1551: /***************** f1dim *************************/
1552: extern int ncom;
1553: extern double *pcom,*xicom;
1554: extern double (*nrfunc)(double []);
1555:
1556: double f1dim(double x)
1557: {
1558: int j;
1559: double f;
1560: double *xt;
1561:
1562: xt=vector(1,ncom);
1563: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1564: f=(*nrfunc)(xt);
1565: free_vector(xt,1,ncom);
1566: return f;
1567: }
1568:
1569: /*****************brent *************************/
1570: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1571: {
1572: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1573: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1574: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1575: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1576: * returned function value.
1577: */
1.126 brouard 1578: int iter;
1579: double a,b,d,etemp;
1.159 brouard 1580: double fu=0,fv,fw,fx;
1.164 brouard 1581: double ftemp=0.;
1.126 brouard 1582: double p,q,r,tol1,tol2,u,v,w,x,xm;
1583: double e=0.0;
1584:
1585: a=(ax < cx ? ax : cx);
1586: b=(ax > cx ? ax : cx);
1587: x=w=v=bx;
1588: fw=fv=fx=(*f)(x);
1589: for (iter=1;iter<=ITMAX;iter++) {
1590: xm=0.5*(a+b);
1591: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1592: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1593: printf(".");fflush(stdout);
1594: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1595: #ifdef DEBUGBRENT
1.126 brouard 1596: 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);
1597: 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);
1598: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1599: #endif
1600: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1601: *xmin=x;
1602: return fx;
1603: }
1604: ftemp=fu;
1605: if (fabs(e) > tol1) {
1606: r=(x-w)*(fx-fv);
1607: q=(x-v)*(fx-fw);
1608: p=(x-v)*q-(x-w)*r;
1609: q=2.0*(q-r);
1610: if (q > 0.0) p = -p;
1611: q=fabs(q);
1612: etemp=e;
1613: e=d;
1614: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1.224 brouard 1615: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1.126 brouard 1616: else {
1.224 brouard 1617: d=p/q;
1618: u=x+d;
1619: if (u-a < tol2 || b-u < tol2)
1620: d=SIGN(tol1,xm-x);
1.126 brouard 1621: }
1622: } else {
1623: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1624: }
1625: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1626: fu=(*f)(u);
1627: if (fu <= fx) {
1628: if (u >= x) a=x; else b=x;
1629: SHFT(v,w,x,u)
1.183 brouard 1630: SHFT(fv,fw,fx,fu)
1631: } else {
1632: if (u < x) a=u; else b=u;
1633: if (fu <= fw || w == x) {
1.224 brouard 1634: v=w;
1635: w=u;
1636: fv=fw;
1637: fw=fu;
1.183 brouard 1638: } else if (fu <= fv || v == x || v == w) {
1.224 brouard 1639: v=u;
1640: fv=fu;
1.183 brouard 1641: }
1642: }
1.126 brouard 1643: }
1644: nrerror("Too many iterations in brent");
1645: *xmin=x;
1646: return fx;
1647: }
1648:
1649: /****************** mnbrak ***********************/
1650:
1651: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1652: double (*func)(double))
1.183 brouard 1653: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1654: the downhill direction (defined by the function as evaluated at the initial points) and returns
1655: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1656: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1657: */
1.126 brouard 1658: double ulim,u,r,q, dum;
1659: double fu;
1.187 brouard 1660:
1661: double scale=10.;
1662: int iterscale=0;
1663:
1664: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1665: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1666:
1667:
1668: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1669: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1670: /* *bx = *ax - (*ax - *bx)/scale; */
1671: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1672: /* } */
1673:
1.126 brouard 1674: if (*fb > *fa) {
1675: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1676: SHFT(dum,*fb,*fa,dum)
1677: }
1.126 brouard 1678: *cx=(*bx)+GOLD*(*bx-*ax);
1679: *fc=(*func)(*cx);
1.183 brouard 1680: #ifdef DEBUG
1.224 brouard 1681: printf("mnbrak0 a=%lf *fa=%lf, b=%lf *fb=%lf, c=%lf *fc=%lf\n",*ax,*fa,*bx,*fb,*cx, *fc);
1682: 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 1683: #endif
1.224 brouard 1684: 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 1685: r=(*bx-*ax)*(*fb-*fc);
1.224 brouard 1686: q=(*bx-*cx)*(*fb-*fa); /* What if fa=inf */
1.126 brouard 1687: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1688: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1689: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1690: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1691: fu=(*func)(u);
1.163 brouard 1692: #ifdef DEBUG
1693: /* f(x)=A(x-u)**2+f(u) */
1694: double A, fparabu;
1695: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1696: fparabu= *fa - A*(*ax-u)*(*ax-u);
1.224 brouard 1697: 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);
1698: 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 1699: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1700: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1701: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1702: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1703: #endif
1.184 brouard 1704: #ifdef MNBRAKORIGINAL
1.183 brouard 1705: #else
1.191 brouard 1706: /* if (fu > *fc) { */
1707: /* #ifdef DEBUG */
1708: /* printf("mnbrak4 fu > fc \n"); */
1709: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1710: /* #endif */
1711: /* /\* 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 *\\/ *\/ */
1712: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1713: /* dum=u; /\* Shifting c and u *\/ */
1714: /* u = *cx; */
1715: /* *cx = dum; */
1716: /* dum = fu; */
1717: /* fu = *fc; */
1718: /* *fc =dum; */
1719: /* } else { /\* end *\/ */
1720: /* #ifdef DEBUG */
1721: /* printf("mnbrak3 fu < fc \n"); */
1722: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1723: /* #endif */
1724: /* dum=u; /\* Shifting c and u *\/ */
1725: /* u = *cx; */
1726: /* *cx = dum; */
1727: /* dum = fu; */
1728: /* fu = *fc; */
1729: /* *fc =dum; */
1730: /* } */
1.224 brouard 1731: #ifdef DEBUGMNBRAK
1732: double A, fparabu;
1733: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1734: fparabu= *fa - A*(*ax-u)*(*ax-u);
1735: 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);
1736: 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 1737: #endif
1.191 brouard 1738: dum=u; /* Shifting c and u */
1739: u = *cx;
1740: *cx = dum;
1741: dum = fu;
1742: fu = *fc;
1743: *fc =dum;
1.183 brouard 1744: #endif
1.162 brouard 1745: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1746: #ifdef DEBUG
1.224 brouard 1747: printf("\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1748: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim\n",u,*cx);
1.183 brouard 1749: #endif
1.126 brouard 1750: fu=(*func)(u);
1751: if (fu < *fc) {
1.183 brouard 1752: #ifdef DEBUG
1.224 brouard 1753: printf("\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1754: fprintf(ficlog,"\nmnbrak2 u=%lf after c=%lf but before ulim=%lf AND fu=%lf < %lf=fc\n",u,*cx,ulim,fu, *fc);
1755: #endif
1756: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1757: SHFT(*fb,*fc,fu,(*func)(u))
1758: #ifdef DEBUG
1759: printf("\nmnbrak2 shift GOLD c=%lf",*cx+GOLD*(*cx-*bx));
1.183 brouard 1760: #endif
1761: }
1.162 brouard 1762: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1763: #ifdef DEBUG
1.224 brouard 1764: printf("\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1765: fprintf(ficlog,"\nmnbrak2 u=%lf outside ulim=%lf (verifying that ulim is beyond c=%lf)\n",u,ulim,*cx);
1.183 brouard 1766: #endif
1.126 brouard 1767: u=ulim;
1768: fu=(*func)(u);
1.183 brouard 1769: } else { /* u could be left to b (if r > q parabola has a maximum) */
1770: #ifdef DEBUG
1.224 brouard 1771: printf("\nmnbrak2 u=%lf could be left to b=%lf (if r=%lf > q=%lf parabola has a maximum)\n",u,*bx,r,q);
1772: 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 1773: #endif
1.126 brouard 1774: u=(*cx)+GOLD*(*cx-*bx);
1775: fu=(*func)(u);
1.224 brouard 1776: #ifdef DEBUG
1777: printf("\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1778: fprintf(ficlog,"\nmnbrak2 new u=%lf fu=%lf shifted gold left from c=%lf and b=%lf \n",u,fu,*cx,*bx);
1779: #endif
1.183 brouard 1780: } /* end tests */
1.126 brouard 1781: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1782: SHFT(*fa,*fb,*fc,fu)
1783: #ifdef DEBUG
1.224 brouard 1784: printf("\nmnbrak2 shift (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc);
1785: 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 1786: #endif
1787: } /* 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 1788: }
1789:
1790: /*************** linmin ************************/
1.162 brouard 1791: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1792: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1793: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1794: the value of func at the returned location p . This is actually all accomplished by calling the
1795: routines mnbrak and brent .*/
1.126 brouard 1796: int ncom;
1797: double *pcom,*xicom;
1798: double (*nrfunc)(double []);
1799:
1.224 brouard 1800: #ifdef LINMINORIGINAL
1.126 brouard 1801: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1.224 brouard 1802: #else
1803: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []), int *flat)
1804: #endif
1.126 brouard 1805: {
1806: double brent(double ax, double bx, double cx,
1807: double (*f)(double), double tol, double *xmin);
1808: double f1dim(double x);
1809: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1810: double *fc, double (*func)(double));
1811: int j;
1812: double xx,xmin,bx,ax;
1813: double fx,fb,fa;
1.187 brouard 1814:
1.203 brouard 1815: #ifdef LINMINORIGINAL
1816: #else
1817: double scale=10., axs, xxs; /* Scale added for infinity */
1818: #endif
1819:
1.126 brouard 1820: ncom=n;
1821: pcom=vector(1,n);
1822: xicom=vector(1,n);
1823: nrfunc=func;
1824: for (j=1;j<=n;j++) {
1825: pcom[j]=p[j];
1.202 brouard 1826: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1827: }
1.187 brouard 1828:
1.203 brouard 1829: #ifdef LINMINORIGINAL
1830: xx=1.;
1831: #else
1832: axs=0.0;
1833: xxs=1.;
1834: do{
1835: xx= xxs;
1836: #endif
1.187 brouard 1837: ax=0.;
1838: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1839: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1840: /* 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)) */
1841: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1842: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1843: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1844: /* 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 1845: #ifdef LINMINORIGINAL
1846: #else
1847: if (fx != fx){
1.224 brouard 1848: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1849: printf("|");
1850: fprintf(ficlog,"|");
1.203 brouard 1851: #ifdef DEBUGLINMIN
1.224 brouard 1852: 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 1853: #endif
1854: }
1.224 brouard 1855: }while(fx != fx && xxs > 1.e-5);
1.203 brouard 1856: #endif
1857:
1.191 brouard 1858: #ifdef DEBUGLINMIN
1859: 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 1860: 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 1861: #endif
1.224 brouard 1862: #ifdef LINMINORIGINAL
1863: #else
1864: if(fb == fx){ /* Flat function in the direction */
1865: xmin=xx;
1866: *flat=1;
1867: }else{
1868: *flat=0;
1869: #endif
1870: /*Flat mnbrak2 shift (*ax=0.000000000000, *fa=51626.272983130431), (*bx=-1.618034000000, *fb=51590.149499362531), (*cx=-4.236068025156, *fc=51590.149499362531) */
1.187 brouard 1871: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1872: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1873: /* fmin = f(p[j] + xmin * xi[j]) */
1874: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1875: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1876: #ifdef DEBUG
1.224 brouard 1877: 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);
1878: 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);
1879: #endif
1880: #ifdef LINMINORIGINAL
1881: #else
1882: }
1.126 brouard 1883: #endif
1.191 brouard 1884: #ifdef DEBUGLINMIN
1885: printf("linmin end ");
1.202 brouard 1886: fprintf(ficlog,"linmin end ");
1.191 brouard 1887: #endif
1.126 brouard 1888: for (j=1;j<=n;j++) {
1.203 brouard 1889: #ifdef LINMINORIGINAL
1890: xi[j] *= xmin;
1891: #else
1892: #ifdef DEBUGLINMIN
1893: if(xxs <1.0)
1894: printf(" before xi[%d]=%12.8f", j,xi[j]);
1895: #endif
1896: 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) */
1897: #ifdef DEBUGLINMIN
1898: if(xxs <1.0)
1899: 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 );
1900: #endif
1901: #endif
1.187 brouard 1902: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1903: }
1.191 brouard 1904: #ifdef DEBUGLINMIN
1.203 brouard 1905: printf("\n");
1.191 brouard 1906: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1907: 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 1908: for (j=1;j<=n;j++) {
1.202 brouard 1909: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1910: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1911: if(j % ncovmodel == 0){
1.191 brouard 1912: printf("\n");
1.202 brouard 1913: fprintf(ficlog,"\n");
1914: }
1.191 brouard 1915: }
1.203 brouard 1916: #else
1.191 brouard 1917: #endif
1.126 brouard 1918: free_vector(xicom,1,n);
1919: free_vector(pcom,1,n);
1920: }
1921:
1922:
1923: /*************** powell ************************/
1.162 brouard 1924: /*
1925: Minimization of a function func of n variables. Input consists of an initial starting point
1926: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1927: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1928: such that failure to decrease by more than this amount on one iteration signals doneness. On
1929: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1930: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1931: */
1.224 brouard 1932: #ifdef LINMINORIGINAL
1933: #else
1934: int *flatdir; /* Function is vanishing in that direction */
1.225 brouard 1935: int flat=0, flatd=0; /* Function is vanishing in that direction */
1.224 brouard 1936: #endif
1.126 brouard 1937: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1938: double (*func)(double []))
1939: {
1.224 brouard 1940: #ifdef LINMINORIGINAL
1941: void linmin(double p[], double xi[], int n, double *fret,
1.126 brouard 1942: double (*func)(double []));
1.224 brouard 1943: #else
1944: void linmin(double p[], double xi[], int n, double *fret,
1945: double (*func)(double []),int *flat);
1946: #endif
1.126 brouard 1947: int i,ibig,j;
1948: double del,t,*pt,*ptt,*xit;
1.181 brouard 1949: double directest;
1.126 brouard 1950: double fp,fptt;
1951: double *xits;
1952: int niterf, itmp;
1.224 brouard 1953: #ifdef LINMINORIGINAL
1954: #else
1955:
1956: flatdir=ivector(1,n);
1957: for (j=1;j<=n;j++) flatdir[j]=0;
1958: #endif
1.126 brouard 1959:
1960: pt=vector(1,n);
1961: ptt=vector(1,n);
1962: xit=vector(1,n);
1963: xits=vector(1,n);
1964: *fret=(*func)(p);
1965: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1966: rcurr_time = time(NULL);
1.126 brouard 1967: for (*iter=1;;++(*iter)) {
1.187 brouard 1968: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1969: ibig=0;
1970: del=0.0;
1.157 brouard 1971: rlast_time=rcurr_time;
1972: /* (void) gettimeofday(&curr_time,&tzp); */
1973: rcurr_time = time(NULL);
1974: curr_time = *localtime(&rcurr_time);
1975: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1976: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1977: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1978: for (i=1;i<=n;i++) {
1.126 brouard 1979: printf(" %d %.12f",i, p[i]);
1980: fprintf(ficlog," %d %.12lf",i, p[i]);
1981: fprintf(ficrespow," %.12lf", p[i]);
1982: }
1983: printf("\n");
1984: fprintf(ficlog,"\n");
1985: fprintf(ficrespow,"\n");fflush(ficrespow);
1986: if(*iter <=3){
1.157 brouard 1987: tml = *localtime(&rcurr_time);
1988: strcpy(strcurr,asctime(&tml));
1989: rforecast_time=rcurr_time;
1.126 brouard 1990: itmp = strlen(strcurr);
1991: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1.224 brouard 1992: strcurr[itmp-1]='\0';
1.162 brouard 1993: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1994: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1995: for(niterf=10;niterf<=30;niterf+=10){
1.224 brouard 1996: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1997: forecast_time = *localtime(&rforecast_time);
1998: strcpy(strfor,asctime(&forecast_time));
1999: itmp = strlen(strfor);
2000: if(strfor[itmp-1]=='\n')
2001: strfor[itmp-1]='\0';
2002: 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);
2003: 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 2004: }
2005: }
1.187 brouard 2006: for (i=1;i<=n;i++) { /* For each direction i */
2007: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 2008: fptt=(*fret);
2009: #ifdef DEBUG
1.203 brouard 2010: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
2011: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 2012: #endif
1.203 brouard 2013: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 2014: fprintf(ficlog,"%d",i);fflush(ficlog);
1.224 brouard 2015: #ifdef LINMINORIGINAL
1.188 brouard 2016: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1.224 brouard 2017: #else
2018: linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
2019: flatdir[i]=flat; /* Function is vanishing in that direction i */
2020: #endif
2021: /* Outputs are fret(new point p) p is updated and xit rescaled */
1.188 brouard 2022: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1.224 brouard 2023: /* because that direction will be replaced unless the gain del is small */
2024: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
2025: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
2026: /* with the new direction. */
2027: del=fabs(fptt-(*fret));
2028: ibig=i;
1.126 brouard 2029: }
2030: #ifdef DEBUG
2031: printf("%d %.12e",i,(*fret));
2032: fprintf(ficlog,"%d %.12e",i,(*fret));
2033: for (j=1;j<=n;j++) {
1.224 brouard 2034: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
2035: printf(" x(%d)=%.12e",j,xit[j]);
2036: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1.126 brouard 2037: }
2038: for(j=1;j<=n;j++) {
1.225 brouard 2039: printf(" p(%d)=%.12e",j,p[j]);
2040: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 2041: }
2042: printf("\n");
2043: fprintf(ficlog,"\n");
2044: #endif
1.187 brouard 2045: } /* end loop on each direction i */
2046: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 2047: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 2048: /* New value of last point Pn is not computed, P(n-1) */
1.224 brouard 2049: for(j=1;j<=n;j++) {
1.225 brouard 2050: if(flatdir[j] >0){
2051: printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2052: fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
2053: }
2054: /* printf("\n"); */
2055: /* fprintf(ficlog,"\n"); */
2056: }
1.182 brouard 2057: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 2058: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
2059: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
2060: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
2061: /* decreased of more than 3.84 */
2062: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
2063: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
2064: /* By adding 10 parameters more the gain should be 18.31 */
1.224 brouard 2065:
1.188 brouard 2066: /* Starting the program with initial values given by a former maximization will simply change */
2067: /* the scales of the directions and the directions, because the are reset to canonical directions */
2068: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
2069: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 2070: #ifdef DEBUG
2071: int k[2],l;
2072: k[0]=1;
2073: k[1]=-1;
2074: printf("Max: %.12e",(*func)(p));
2075: fprintf(ficlog,"Max: %.12e",(*func)(p));
2076: for (j=1;j<=n;j++) {
2077: printf(" %.12e",p[j]);
2078: fprintf(ficlog," %.12e",p[j]);
2079: }
2080: printf("\n");
2081: fprintf(ficlog,"\n");
2082: for(l=0;l<=1;l++) {
2083: for (j=1;j<=n;j++) {
2084: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
2085: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2086: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
2087: }
2088: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2089: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
2090: }
2091: #endif
2092:
1.224 brouard 2093: #ifdef LINMINORIGINAL
2094: #else
2095: free_ivector(flatdir,1,n);
2096: #endif
1.126 brouard 2097: free_vector(xit,1,n);
2098: free_vector(xits,1,n);
2099: free_vector(ptt,1,n);
2100: free_vector(pt,1,n);
2101: return;
1.192 brouard 2102: } /* enough precision */
1.126 brouard 2103: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 2104: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 2105: ptt[j]=2.0*p[j]-pt[j];
2106: xit[j]=p[j]-pt[j];
2107: pt[j]=p[j];
2108: }
1.181 brouard 2109: fptt=(*func)(ptt); /* f_3 */
1.224 brouard 2110: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
2111: if (*iter <=4) {
1.225 brouard 2112: #else
2113: #endif
1.224 brouard 2114: #ifdef POWELLNOF3INFF1TEST /* skips test F3 <F1 */
1.192 brouard 2115: #else
1.161 brouard 2116: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 2117: #endif
1.162 brouard 2118: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 2119: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 2120: /* Let f"(x2) be the 2nd derivative equal everywhere. */
2121: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
2122: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.224 brouard 2123: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del or directest <0 */
2124: /* also lamda^2=(f1-f2)^2/mu² is a parasite solution of powell */
2125: /* For powell, inclusion of this average direction is only if t(del)<0 or del inbetween mu^2 and lambda^2 */
1.161 brouard 2126: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.224 brouard 2127: /* Even if f3 <f1, directest can be negative and t >0 */
2128: /* mu² and del² are equal when f3=f1 */
2129: /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
2130: /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
2131: /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0 */
2132: /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0 */
1.183 brouard 2133: #ifdef NRCORIGINAL
2134: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
2135: #else
2136: 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 2137: t= t- del*SQR(fp-fptt);
1.183 brouard 2138: #endif
1.202 brouard 2139: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 2140: #ifdef DEBUG
1.181 brouard 2141: 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);
2142: 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 2143: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2144: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2145: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
2146: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2147: 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);
2148: 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);
2149: #endif
1.183 brouard 2150: #ifdef POWELLORIGINAL
2151: if (t < 0.0) { /* Then we use it for new direction */
2152: #else
1.182 brouard 2153: if (directest*t < 0.0) { /* Contradiction between both tests */
1.224 brouard 2154: 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 2155: 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 2156: 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 2157: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2158: }
1.181 brouard 2159: if (directest < 0.0) { /* Then we use it for new direction */
2160: #endif
1.191 brouard 2161: #ifdef DEBUGLINMIN
1.224 brouard 2162: printf("Before linmin in direction P%d-P0\n",n);
2163: for (j=1;j<=n;j++) {
2164: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2165: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2166: if(j % ncovmodel == 0){
2167: printf("\n");
2168: fprintf(ficlog,"\n");
2169: }
2170: }
2171: #endif
2172: #ifdef LINMINORIGINAL
2173: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2174: #else
2175: linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
2176: flatdir[i]=flat; /* Function is vanishing in that direction i */
1.191 brouard 2177: #endif
1.224 brouard 2178:
1.191 brouard 2179: #ifdef DEBUGLINMIN
1.224 brouard 2180: for (j=1;j<=n;j++) {
2181: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2182: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2183: if(j % ncovmodel == 0){
2184: printf("\n");
2185: fprintf(ficlog,"\n");
2186: }
2187: }
2188: #endif
2189: for (j=1;j<=n;j++) {
2190: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2191: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
2192: }
2193: #ifdef LINMINORIGINAL
2194: #else
1.225 brouard 2195: for (j=1, flatd=0;j<=n;j++) {
2196: if(flatdir[j]>0)
2197: flatd++;
2198: }
2199: if(flatd >0){
2200: printf("%d flat directions\n",flatd);
2201: fprintf(ficlog,"%d flat directions\n",flatd);
2202: for (j=1;j<=n;j++) {
2203: if(flatdir[j]>0){
2204: printf("%d ",j);
2205: fprintf(ficlog,"%d ",j);
2206: }
2207: }
2208: printf("\n");
2209: fprintf(ficlog,"\n");
2210: }
1.191 brouard 2211: #endif
1.224 brouard 2212: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2213: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2214:
1.126 brouard 2215: #ifdef DEBUG
1.224 brouard 2216: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2217: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2218: for(j=1;j<=n;j++){
2219: printf(" %lf",xit[j]);
2220: fprintf(ficlog," %lf",xit[j]);
2221: }
2222: printf("\n");
2223: fprintf(ficlog,"\n");
1.126 brouard 2224: #endif
1.192 brouard 2225: } /* end of t or directest negative */
1.224 brouard 2226: #ifdef POWELLNOF3INFF1TEST
1.192 brouard 2227: #else
1.162 brouard 2228: } /* end if (fptt < fp) */
1.192 brouard 2229: #endif
1.225 brouard 2230: #ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
1.224 brouard 2231: } /*NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done */
1.225 brouard 2232: #else
1.224 brouard 2233: #endif
1.192 brouard 2234: } /* loop iteration */
1.126 brouard 2235: }
2236:
2237: /**** Prevalence limit (stable or period prevalence) ****************/
2238:
1.203 brouard 2239: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2240: {
1.218 brouard 2241: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2242: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2243: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2244: /* Wx is row vector: population in state 1, population in state 2, population dead */
2245: /* or prevalence in state 1, prevalence in state 2, 0 */
2246: /* newm is the matrix after multiplications, its rows are identical at a factor */
2247: /* Initial matrix pimij */
2248: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2249: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2250: /* 0, 0 , 1} */
2251: /*
2252: * and after some iteration: */
2253: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2254: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2255: /* 0, 0 , 1} */
2256: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2257: /* {0.51571254859325999, 0.4842874514067399, */
2258: /* 0.51326036147820708, 0.48673963852179264} */
2259: /* If we start from prlim again, prlim tends to a constant matrix */
2260:
1.126 brouard 2261: int i, ii,j,k;
1.209 brouard 2262: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2263: /* double **matprod2(); */ /* test */
1.218 brouard 2264: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2265: double **newm;
1.209 brouard 2266: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2267: int ncvloop=0;
1.169 brouard 2268:
1.209 brouard 2269: min=vector(1,nlstate);
2270: max=vector(1,nlstate);
2271: meandiff=vector(1,nlstate);
2272:
1.218 brouard 2273: /* Starting with matrix unity */
1.126 brouard 2274: for (ii=1;ii<=nlstate+ndeath;ii++)
2275: for (j=1;j<=nlstate+ndeath;j++){
2276: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2277: }
1.169 brouard 2278:
2279: cov[1]=1.;
2280:
2281: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2282: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2283: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2284: ncvloop++;
1.126 brouard 2285: newm=savm;
2286: /* Covariates have to be included here again */
1.138 brouard 2287: cov[2]=agefin;
1.187 brouard 2288: if(nagesqr==1)
2289: cov[3]= agefin*agefin;;
1.138 brouard 2290: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2291: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2292: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2293: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2294: /* 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 2295: }
1.186 brouard 2296: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2297: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2298: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2299: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2300: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2301: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2302:
2303: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2304: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2305: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2306: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2307: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2308: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2309: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2310:
1.126 brouard 2311: savm=oldm;
2312: oldm=newm;
1.209 brouard 2313:
2314: for(j=1; j<=nlstate; j++){
2315: max[j]=0.;
2316: min[j]=1.;
2317: }
2318: for(i=1;i<=nlstate;i++){
2319: sumnew=0;
2320: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2321: for(j=1; j<=nlstate; j++){
2322: prlim[i][j]= newm[i][j]/(1-sumnew);
2323: max[j]=FMAX(max[j],prlim[i][j]);
2324: min[j]=FMIN(min[j],prlim[i][j]);
2325: }
2326: }
2327:
1.126 brouard 2328: maxmax=0.;
1.209 brouard 2329: for(j=1; j<=nlstate; j++){
2330: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2331: maxmax=FMAX(maxmax,meandiff[j]);
2332: /* 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 2333: } /* j loop */
1.203 brouard 2334: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2335: /* 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 2336: if(maxmax < ftolpl){
1.209 brouard 2337: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2338: free_vector(min,1,nlstate);
2339: free_vector(max,1,nlstate);
2340: free_vector(meandiff,1,nlstate);
1.126 brouard 2341: return prlim;
2342: }
1.169 brouard 2343: } /* age loop */
1.208 brouard 2344: /* After some age loop it doesn't converge */
1.209 brouard 2345: 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 2346: 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 2347: /* 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); */
2348: free_vector(min,1,nlstate);
2349: free_vector(max,1,nlstate);
2350: free_vector(meandiff,1,nlstate);
1.208 brouard 2351:
1.169 brouard 2352: return prlim; /* should not reach here */
1.126 brouard 2353: }
2354:
1.217 brouard 2355:
2356: /**** Back Prevalence limit (stable or period prevalence) ****************/
2357:
1.218 brouard 2358: /* 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) */
2359: /* 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) */
2360: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2361: {
1.218 brouard 2362: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2363: matrix by transitions matrix until convergence is reached with precision ftolpl */
2364: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2365: /* Wx is row vector: population in state 1, population in state 2, population dead */
2366: /* or prevalence in state 1, prevalence in state 2, 0 */
2367: /* newm is the matrix after multiplications, its rows are identical at a factor */
2368: /* Initial matrix pimij */
2369: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2370: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2371: /* 0, 0 , 1} */
2372: /*
2373: * and after some iteration: */
2374: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2375: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2376: /* 0, 0 , 1} */
2377: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2378: /* {0.51571254859325999, 0.4842874514067399, */
2379: /* 0.51326036147820708, 0.48673963852179264} */
2380: /* If we start from prlim again, prlim tends to a constant matrix */
2381:
2382: int i, ii,j,k;
2383: double *min, *max, *meandiff, maxmax,sumnew=0.;
2384: /* double **matprod2(); */ /* test */
2385: double **out, cov[NCOVMAX+1], **bmij();
2386: double **newm;
1.218 brouard 2387: double **dnewm, **doldm, **dsavm; /* for use */
2388: double **oldm, **savm; /* for use */
2389:
1.217 brouard 2390: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2391: int ncvloop=0;
2392:
2393: min=vector(1,nlstate);
2394: max=vector(1,nlstate);
2395: meandiff=vector(1,nlstate);
2396:
1.218 brouard 2397: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2398: oldm=oldms; savm=savms;
2399:
2400: /* Starting with matrix unity */
2401: for (ii=1;ii<=nlstate+ndeath;ii++)
2402: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2403: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2404: }
2405:
2406: cov[1]=1.;
2407:
2408: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2409: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2410: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2411: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2412: ncvloop++;
1.218 brouard 2413: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2414: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2415: /* Covariates have to be included here again */
2416: cov[2]=agefin;
2417: if(nagesqr==1)
2418: cov[3]= agefin*agefin;;
2419: for (k=1; k<=cptcovn;k++) {
2420: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2421: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2422: /* 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])]); */
2423: }
2424: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2425: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2426: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2427: for (k=1; k<=cptcovprod;k++) /* Useless */
2428: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2429: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2430:
2431: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2432: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2433: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2434: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2435: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2436: /* ij should be linked to the correct index of cov */
2437: /* age and covariate values ij are in 'cov', but we need to pass
2438: * ij for the observed prevalence at age and status and covariate
2439: * number: prevacurrent[(int)agefin][ii][ij]
2440: */
2441: /* 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 *\/ */
2442: /* 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 *\/ */
2443: 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 2444: savm=oldm;
2445: oldm=newm;
2446: for(j=1; j<=nlstate; j++){
2447: max[j]=0.;
2448: min[j]=1.;
2449: }
2450: for(j=1; j<=nlstate; j++){
2451: for(i=1;i<=nlstate;i++){
1.218 brouard 2452: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2453: bprlim[i][j]= newm[i][j];
2454: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2455: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2456: }
2457: }
1.218 brouard 2458:
1.217 brouard 2459: maxmax=0.;
2460: for(i=1; i<=nlstate; i++){
2461: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2462: maxmax=FMAX(maxmax,meandiff[i]);
2463: /* 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); */
2464: } /* j loop */
2465: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2466: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2467: if(maxmax < ftolpl){
1.220 brouard 2468: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2469: free_vector(min,1,nlstate);
2470: free_vector(max,1,nlstate);
2471: free_vector(meandiff,1,nlstate);
2472: return bprlim;
2473: }
2474: } /* age loop */
2475: /* After some age loop it doesn't converge */
2476: 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\
2477: 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);
2478: /* 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); */
2479: free_vector(min,1,nlstate);
2480: free_vector(max,1,nlstate);
2481: free_vector(meandiff,1,nlstate);
2482:
2483: return bprlim; /* should not reach here */
2484: }
2485:
1.126 brouard 2486: /*************** transition probabilities ***************/
2487:
2488: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2489: {
1.138 brouard 2490: /* According to parameters values stored in x and the covariate's values stored in cov,
2491: computes the probability to be observed in state j being in state i by appying the
2492: model to the ncovmodel covariates (including constant and age).
2493: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2494: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2495: ncth covariate in the global vector x is given by the formula:
2496: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2497: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2498: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2499: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2500: Outputs ps[i][j] the probability to be observed in j being in j according to
2501: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2502: */
2503: double s1, lnpijopii;
1.126 brouard 2504: /*double t34;*/
1.164 brouard 2505: int i,j, nc, ii, jj;
1.126 brouard 2506:
1.223 brouard 2507: for(i=1; i<= nlstate; i++){
2508: for(j=1; j<i;j++){
2509: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2510: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2511: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2512: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2513: }
2514: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2515: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2516: }
2517: for(j=i+1; j<=nlstate+ndeath;j++){
2518: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2519: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2520: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2521: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2522: }
2523: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2524: }
2525: }
1.218 brouard 2526:
1.223 brouard 2527: for(i=1; i<= nlstate; i++){
2528: s1=0;
2529: for(j=1; j<i; j++){
2530: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2531: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2532: }
2533: for(j=i+1; j<=nlstate+ndeath; j++){
2534: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2535: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2536: }
2537: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2538: ps[i][i]=1./(s1+1.);
2539: /* Computing other pijs */
2540: for(j=1; j<i; j++)
2541: ps[i][j]= exp(ps[i][j])*ps[i][i];
2542: for(j=i+1; j<=nlstate+ndeath; j++)
2543: ps[i][j]= exp(ps[i][j])*ps[i][i];
2544: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2545: } /* end i */
1.218 brouard 2546:
1.223 brouard 2547: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2548: for(jj=1; jj<= nlstate+ndeath; jj++){
2549: ps[ii][jj]=0;
2550: ps[ii][ii]=1;
2551: }
2552: }
1.218 brouard 2553:
2554:
1.223 brouard 2555: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2556: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2557: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2558: /* } */
2559: /* printf("\n "); */
2560: /* } */
2561: /* printf("\n ");printf("%lf ",cov[2]);*/
2562: /*
2563: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1.218 brouard 2564: goto end;*/
1.223 brouard 2565: return ps;
1.126 brouard 2566: }
2567:
1.218 brouard 2568: /*************** backward transition probabilities ***************/
2569:
2570: /* 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 ) */
2571: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2572: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2573: {
1.222 brouard 2574: /* Computes the backward probability at age agefin and covariate ij
2575: * and returns in **ps as well as **bmij.
2576: */
1.218 brouard 2577: int i, ii, j,k;
1.222 brouard 2578:
2579: double **out, **pmij();
2580: double sumnew=0.;
1.218 brouard 2581: double agefin;
1.222 brouard 2582:
2583: double **dnewm, **dsavm, **doldm;
2584: double **bbmij;
2585:
1.218 brouard 2586: doldm=ddoldms; /* global pointers */
1.222 brouard 2587: dnewm=ddnewms;
2588: dsavm=ddsavms;
2589:
2590: agefin=cov[2];
2591: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2592: the observed prevalence (with this covariate ij) */
2593: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2594: /* We do have the matrix Px in savm and we need pij */
2595: for (j=1;j<=nlstate+ndeath;j++){
2596: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2597: for (ii=1;ii<=nlstate;ii++){
2598: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2599: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2600: for (ii=1;ii<=nlstate+ndeath;ii++){
2601: if(sumnew >= 1.e-10){
2602: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2603: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2604: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2605: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2606: /* }else */
2607: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2608: }else{
2609: 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);
2610: }
2611: } /*End ii */
2612: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2613: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2614: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2615: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2616: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2617: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2618: /* left Product of this matrix by diag matrix of prevalences (savm) */
2619: for (j=1;j<=nlstate+ndeath;j++){
2620: for (ii=1;ii<=nlstate+ndeath;ii++){
2621: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2622: }
2623: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2624: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2625: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2626: /* end bmij */
2627: return ps;
1.218 brouard 2628: }
1.217 brouard 2629: /*************** transition probabilities ***************/
2630:
1.218 brouard 2631: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2632: {
2633: /* According to parameters values stored in x and the covariate's values stored in cov,
2634: computes the probability to be observed in state j being in state i by appying the
2635: model to the ncovmodel covariates (including constant and age).
2636: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2637: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2638: ncth covariate in the global vector x is given by the formula:
2639: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2640: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2641: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2642: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2643: Outputs ps[i][j] the probability to be observed in j being in j according to
2644: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2645: */
2646: double s1, lnpijopii;
2647: /*double t34;*/
2648: int i,j, nc, ii, jj;
2649:
1.218 brouard 2650: for(i=1; i<= nlstate; i++){
2651: for(j=1; j<i;j++){
2652: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2653: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2654: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2655: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2656: }
2657: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2658: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2659: }
2660: for(j=i+1; j<=nlstate+ndeath;j++){
2661: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2662: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2663: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2664: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2665: }
2666: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2667: }
2668: }
2669:
2670: for(i=1; i<= nlstate; i++){
2671: s1=0;
2672: for(j=1; j<i; j++){
2673: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2674: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2675: }
2676: for(j=i+1; j<=nlstate+ndeath; j++){
2677: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2678: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2679: }
2680: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2681: ps[i][i]=1./(s1+1.);
2682: /* Computing other pijs */
2683: for(j=1; j<i; j++)
2684: ps[i][j]= exp(ps[i][j])*ps[i][i];
2685: for(j=i+1; j<=nlstate+ndeath; j++)
2686: ps[i][j]= exp(ps[i][j])*ps[i][i];
2687: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2688: } /* end i */
2689:
2690: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2691: for(jj=1; jj<= nlstate+ndeath; jj++){
2692: ps[ii][jj]=0;
2693: ps[ii][ii]=1;
2694: }
2695: }
2696: /* Added for backcast */ /* Transposed matrix too */
2697: for(jj=1; jj<= nlstate+ndeath; jj++){
2698: s1=0.;
2699: for(ii=1; ii<= nlstate+ndeath; ii++){
2700: s1+=ps[ii][jj];
2701: }
2702: for(ii=1; ii<= nlstate; ii++){
2703: ps[ii][jj]=ps[ii][jj]/s1;
2704: }
2705: }
2706: /* Transposition */
2707: for(jj=1; jj<= nlstate+ndeath; jj++){
2708: for(ii=jj; ii<= nlstate+ndeath; ii++){
2709: s1=ps[ii][jj];
2710: ps[ii][jj]=ps[jj][ii];
2711: ps[jj][ii]=s1;
2712: }
2713: }
2714: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2715: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2716: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2717: /* } */
2718: /* printf("\n "); */
2719: /* } */
2720: /* printf("\n ");printf("%lf ",cov[2]);*/
2721: /*
2722: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2723: goto end;*/
2724: return ps;
1.217 brouard 2725: }
2726:
2727:
1.126 brouard 2728: /**************** Product of 2 matrices ******************/
2729:
1.145 brouard 2730: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2731: {
2732: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2733: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2734: /* in, b, out are matrice of pointers which should have been initialized
2735: before: only the contents of out is modified. The function returns
2736: a pointer to pointers identical to out */
1.145 brouard 2737: int i, j, k;
1.126 brouard 2738: for(i=nrl; i<= nrh; i++)
1.145 brouard 2739: for(k=ncolol; k<=ncoloh; k++){
2740: out[i][k]=0.;
2741: for(j=ncl; j<=nch; j++)
2742: out[i][k] +=in[i][j]*b[j][k];
2743: }
1.126 brouard 2744: return out;
2745: }
2746:
2747:
2748: /************* Higher Matrix Product ***************/
2749:
2750: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2751: {
1.218 brouard 2752: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2753: 'nhstepm*hstepm*stepm' months (i.e. until
2754: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2755: nhstepm*hstepm matrices.
2756: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2757: (typically every 2 years instead of every month which is too big
2758: for the memory).
2759: Model is determined by parameters x and covariates have to be
2760: included manually here.
2761:
2762: */
2763:
2764: int i, j, d, h, k;
1.131 brouard 2765: double **out, cov[NCOVMAX+1];
1.126 brouard 2766: double **newm;
1.187 brouard 2767: double agexact;
1.214 brouard 2768: double agebegin, ageend;
1.126 brouard 2769:
2770: /* Hstepm could be zero and should return the unit matrix */
2771: for (i=1;i<=nlstate+ndeath;i++)
2772: for (j=1;j<=nlstate+ndeath;j++){
2773: oldm[i][j]=(i==j ? 1.0 : 0.0);
2774: po[i][j][0]=(i==j ? 1.0 : 0.0);
2775: }
2776: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2777: for(h=1; h <=nhstepm; h++){
2778: for(d=1; d <=hstepm; d++){
2779: newm=savm;
2780: /* Covariates have to be included here again */
2781: cov[1]=1.;
1.214 brouard 2782: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2783: cov[2]=agexact;
2784: if(nagesqr==1)
1.227 brouard 2785: cov[3]= agexact*agexact;
1.131 brouard 2786: for (k=1; k<=cptcovn;k++)
1.227 brouard 2787: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2788: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2789: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.227 brouard 2790: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2791: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2792: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2793: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.227 brouard 2794: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2795: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2796:
2797:
1.126 brouard 2798: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2799: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2800: /* right multiplication of oldm by the current matrix */
1.126 brouard 2801: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2802: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2803: /* if((int)age == 70){ */
2804: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2805: /* for(i=1; i<=nlstate+ndeath; i++) { */
2806: /* printf("%d pmmij ",i); */
2807: /* for(j=1;j<=nlstate+ndeath;j++) { */
2808: /* printf("%f ",pmmij[i][j]); */
2809: /* } */
2810: /* printf(" oldm "); */
2811: /* for(j=1;j<=nlstate+ndeath;j++) { */
2812: /* printf("%f ",oldm[i][j]); */
2813: /* } */
2814: /* printf("\n"); */
2815: /* } */
2816: /* } */
1.126 brouard 2817: savm=oldm;
2818: oldm=newm;
2819: }
2820: for(i=1; i<=nlstate+ndeath; i++)
2821: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2822: po[i][j][h]=newm[i][j];
2823: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2824: }
1.128 brouard 2825: /*printf("h=%d ",h);*/
1.126 brouard 2826: } /* end h */
1.218 brouard 2827: /* printf("\n H=%d \n",h); */
1.126 brouard 2828: return po;
2829: }
2830:
1.217 brouard 2831: /************* Higher Back Matrix Product ***************/
1.218 brouard 2832: /* 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 2833: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2834: {
1.218 brouard 2835: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2836: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2837: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2838: nhstepm*hstepm matrices.
2839: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2840: (typically every 2 years instead of every month which is too big
1.217 brouard 2841: for the memory).
1.218 brouard 2842: Model is determined by parameters x and covariates have to be
2843: included manually here.
1.217 brouard 2844:
1.222 brouard 2845: */
1.217 brouard 2846:
2847: int i, j, d, h, k;
2848: double **out, cov[NCOVMAX+1];
2849: double **newm;
2850: double agexact;
2851: double agebegin, ageend;
1.222 brouard 2852: double **oldm, **savm;
1.217 brouard 2853:
1.222 brouard 2854: oldm=oldms;savm=savms;
1.217 brouard 2855: /* Hstepm could be zero and should return the unit matrix */
2856: for (i=1;i<=nlstate+ndeath;i++)
2857: for (j=1;j<=nlstate+ndeath;j++){
2858: oldm[i][j]=(i==j ? 1.0 : 0.0);
2859: po[i][j][0]=(i==j ? 1.0 : 0.0);
2860: }
2861: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2862: for(h=1; h <=nhstepm; h++){
2863: for(d=1; d <=hstepm; d++){
2864: newm=savm;
2865: /* Covariates have to be included here again */
2866: cov[1]=1.;
2867: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2868: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2869: cov[2]=agexact;
2870: if(nagesqr==1)
1.222 brouard 2871: cov[3]= agexact*agexact;
1.218 brouard 2872: for (k=1; k<=cptcovn;k++)
1.222 brouard 2873: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2874: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2875: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.222 brouard 2876: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2877: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2878: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2879: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.222 brouard 2880: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2881: /* 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 2882:
2883:
1.217 brouard 2884: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2885: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2886: /* Careful transposed matrix */
1.222 brouard 2887: /* age is in cov[2] */
1.218 brouard 2888: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
1.222 brouard 2889: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
1.218 brouard 2890: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1.222 brouard 2891: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2892: /* if((int)age == 70){ */
2893: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2894: /* for(i=1; i<=nlstate+ndeath; i++) { */
2895: /* printf("%d pmmij ",i); */
2896: /* for(j=1;j<=nlstate+ndeath;j++) { */
2897: /* printf("%f ",pmmij[i][j]); */
2898: /* } */
2899: /* printf(" oldm "); */
2900: /* for(j=1;j<=nlstate+ndeath;j++) { */
2901: /* printf("%f ",oldm[i][j]); */
2902: /* } */
2903: /* printf("\n"); */
2904: /* } */
2905: /* } */
2906: savm=oldm;
2907: oldm=newm;
2908: }
2909: for(i=1; i<=nlstate+ndeath; i++)
2910: for(j=1;j<=nlstate+ndeath;j++) {
1.222 brouard 2911: po[i][j][h]=newm[i][j];
2912: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2913: }
2914: /*printf("h=%d ",h);*/
2915: } /* end h */
1.222 brouard 2916: /* printf("\n H=%d \n",h); */
1.217 brouard 2917: return po;
2918: }
2919:
2920:
1.162 brouard 2921: #ifdef NLOPT
2922: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2923: double fret;
2924: double *xt;
2925: int j;
2926: myfunc_data *d2 = (myfunc_data *) pd;
2927: /* xt = (p1-1); */
2928: xt=vector(1,n);
2929: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2930:
2931: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2932: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2933: printf("Function = %.12lf ",fret);
2934: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2935: printf("\n");
2936: free_vector(xt,1,n);
2937: return fret;
2938: }
2939: #endif
1.126 brouard 2940:
2941: /*************** log-likelihood *************/
2942: double func( double *x)
2943: {
1.226 brouard 2944: int i, ii, j, k, mi, d, kk;
2945: int ioffset=0;
2946: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2947: double **out;
2948: double lli; /* Individual log likelihood */
2949: int s1, s2;
1.228 ! brouard 2950: 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 2951: double bbh, survp;
2952: long ipmx;
2953: double agexact;
2954: /*extern weight */
2955: /* We are differentiating ll according to initial status */
2956: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2957: /*for(i=1;i<imx;i++)
2958: printf(" %d\n",s[4][i]);
2959: */
1.162 brouard 2960:
1.226 brouard 2961: ++countcallfunc;
1.162 brouard 2962:
1.226 brouard 2963: cov[1]=1.;
1.126 brouard 2964:
1.226 brouard 2965: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 2966: ioffset=0;
1.226 brouard 2967: if(mle==1){
2968: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2969: /* Computes the values of the ncovmodel covariates of the model
2970: depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
2971: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2972: to be observed in j being in i according to the model.
2973: */
2974: ioffset=2+nagesqr+cptcovage;
2975: /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
2976: for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
2977: cov[++ioffset]=covar[Tvar[k]][i];
2978: }
2979: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
1.228 ! brouard 2980: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.226 brouard 2981: }
2982:
2983: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2984: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2985: has been calculated etc */
2986: /* For an individual i, wav[i] gives the number of effective waves */
2987: /* We compute the contribution to Likelihood of each effective transition
2988: mw[mi][i] is real wave of the mi th effectve wave */
2989: /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
2990: s2=s[mw[mi+1][i]][i];
2991: And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
2992: But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
2993: meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
2994: */
2995: for(mi=1; mi<= wav[i]-1; mi++){
2996: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.228 ! brouard 2997: cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /* Not sure, Tvar V4+V3+V5 Tvaraff ? */
1.226 brouard 2998: }
2999: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
3000: if(cotqvar[mw[mi][i]][iqtv][i] == -1){
3001: printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
3002: }
3003: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];
3004: }
3005: /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
3006: for (ii=1;ii<=nlstate+ndeath;ii++)
3007: for (j=1;j<=nlstate+ndeath;j++){
3008: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3009: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3010: }
3011: for(d=0; d<dh[mi][i]; d++){
3012: newm=savm;
3013: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3014: cov[2]=agexact;
3015: if(nagesqr==1)
3016: cov[3]= agexact*agexact; /* Should be changed here */
3017: for (kk=1; kk<=cptcovage;kk++) {
3018: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
3019: }
3020: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3021: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3022: savm=oldm;
3023: oldm=newm;
3024: } /* end mult */
1.224 brouard 3025:
1.226 brouard 3026: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
3027: /* But now since version 0.9 we anticipate for bias at large stepm.
3028: * If stepm is larger than one month (smallest stepm) and if the exact delay
3029: * (in months) between two waves is not a multiple of stepm, we rounded to
3030: * the nearest (and in case of equal distance, to the lowest) interval but now
3031: * we keep into memory the bias bh[mi][i] and also the previous matrix product
3032: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
3033: * probability in order to take into account the bias as a fraction of the way
3034: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
3035: * -stepm/2 to stepm/2 .
3036: * For stepm=1 the results are the same as for previous versions of Imach.
3037: * For stepm > 1 the results are less biased than in previous versions.
3038: */
3039: s1=s[mw[mi][i]][i];
3040: s2=s[mw[mi+1][i]][i];
3041: bbh=(double)bh[mi][i]/(double)stepm;
3042: /* bias bh is positive if real duration
3043: * is higher than the multiple of stepm and negative otherwise.
3044: */
3045: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
3046: if( s2 > nlstate){
3047: /* i.e. if s2 is a death state and if the date of death is known
3048: then the contribution to the likelihood is the probability to
3049: die between last step unit time and current step unit time,
3050: which is also equal to probability to die before dh
3051: minus probability to die before dh-stepm .
3052: In version up to 0.92 likelihood was computed
3053: as if date of death was unknown. Death was treated as any other
3054: health state: the date of the interview describes the actual state
3055: and not the date of a change in health state. The former idea was
3056: to consider that at each interview the state was recorded
3057: (healthy, disable or death) and IMaCh was corrected; but when we
3058: introduced the exact date of death then we should have modified
3059: the contribution of an exact death to the likelihood. This new
3060: contribution is smaller and very dependent of the step unit
3061: stepm. It is no more the probability to die between last interview
3062: and month of death but the probability to survive from last
3063: interview up to one month before death multiplied by the
3064: probability to die within a month. Thanks to Chris
3065: Jackson for correcting this bug. Former versions increased
3066: mortality artificially. The bad side is that we add another loop
3067: which slows down the processing. The difference can be up to 10%
3068: lower mortality.
3069: */
3070: /* If, at the beginning of the maximization mostly, the
3071: cumulative probability or probability to be dead is
3072: constant (ie = 1) over time d, the difference is equal to
3073: 0. out[s1][3] = savm[s1][3]: probability, being at state
3074: s1 at precedent wave, to be dead a month before current
3075: wave is equal to probability, being at state s1 at
3076: precedent wave, to be dead at mont of the current
3077: wave. Then the observed probability (that this person died)
3078: is null according to current estimated parameter. In fact,
3079: it should be very low but not zero otherwise the log go to
3080: infinity.
3081: */
1.183 brouard 3082: /* #ifdef INFINITYORIGINAL */
3083: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3084: /* #else */
3085: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
3086: /* lli=log(mytinydouble); */
3087: /* else */
3088: /* lli=log(out[s1][s2] - savm[s1][s2]); */
3089: /* #endif */
1.226 brouard 3090: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3091:
1.226 brouard 3092: } else if ( s2==-1 ) { /* alive */
3093: for (j=1,survp=0. ; j<=nlstate; j++)
3094: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3095: /*survp += out[s1][j]; */
3096: lli= log(survp);
3097: }
3098: else if (s2==-4) {
3099: for (j=3,survp=0. ; j<=nlstate; j++)
3100: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3101: lli= log(survp);
3102: }
3103: else if (s2==-5) {
3104: for (j=1,survp=0. ; j<=2; j++)
3105: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3106: lli= log(survp);
3107: }
3108: else{
3109: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3110: /* 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 */
3111: }
3112: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
3113: /*if(lli ==000.0)*/
3114: /*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); */
3115: ipmx +=1;
3116: sw += weight[i];
3117: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3118: /* if (lli < log(mytinydouble)){ */
3119: /* 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); */
3120: /* 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]); */
3121: /* } */
3122: } /* end of wave */
3123: } /* end of individual */
3124: } else if(mle==2){
3125: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3126: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3127: for(mi=1; mi<= wav[i]-1; mi++){
3128: for (ii=1;ii<=nlstate+ndeath;ii++)
3129: for (j=1;j<=nlstate+ndeath;j++){
3130: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3131: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3132: }
3133: for(d=0; d<=dh[mi][i]; d++){
3134: newm=savm;
3135: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3136: cov[2]=agexact;
3137: if(nagesqr==1)
3138: cov[3]= agexact*agexact;
3139: for (kk=1; kk<=cptcovage;kk++) {
3140: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3141: }
3142: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3143: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3144: savm=oldm;
3145: oldm=newm;
3146: } /* end mult */
3147:
3148: s1=s[mw[mi][i]][i];
3149: s2=s[mw[mi+1][i]][i];
3150: bbh=(double)bh[mi][i]/(double)stepm;
3151: 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 */
3152: ipmx +=1;
3153: sw += weight[i];
3154: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3155: } /* end of wave */
3156: } /* end of individual */
3157: } else if(mle==3){ /* exponential inter-extrapolation */
3158: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3159: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3160: for(mi=1; mi<= wav[i]-1; mi++){
3161: for (ii=1;ii<=nlstate+ndeath;ii++)
3162: for (j=1;j<=nlstate+ndeath;j++){
3163: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3164: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3165: }
3166: for(d=0; d<dh[mi][i]; d++){
3167: newm=savm;
3168: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3169: cov[2]=agexact;
3170: if(nagesqr==1)
3171: cov[3]= agexact*agexact;
3172: for (kk=1; kk<=cptcovage;kk++) {
3173: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3174: }
3175: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3176: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3177: savm=oldm;
3178: oldm=newm;
3179: } /* end mult */
3180:
3181: s1=s[mw[mi][i]][i];
3182: s2=s[mw[mi+1][i]][i];
3183: bbh=(double)bh[mi][i]/(double)stepm;
3184: 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 */
3185: ipmx +=1;
3186: sw += weight[i];
3187: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3188: } /* end of wave */
3189: } /* end of individual */
3190: }else if (mle==4){ /* ml=4 no inter-extrapolation */
3191: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3192: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3193: for(mi=1; mi<= wav[i]-1; mi++){
3194: for (ii=1;ii<=nlstate+ndeath;ii++)
3195: for (j=1;j<=nlstate+ndeath;j++){
3196: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3197: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3198: }
3199: for(d=0; d<dh[mi][i]; d++){
3200: newm=savm;
3201: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3202: cov[2]=agexact;
3203: if(nagesqr==1)
3204: cov[3]= agexact*agexact;
3205: for (kk=1; kk<=cptcovage;kk++) {
3206: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3207: }
1.126 brouard 3208:
1.226 brouard 3209: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3210: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3211: savm=oldm;
3212: oldm=newm;
3213: } /* end mult */
3214:
3215: s1=s[mw[mi][i]][i];
3216: s2=s[mw[mi+1][i]][i];
3217: if( s2 > nlstate){
3218: lli=log(out[s1][s2] - savm[s1][s2]);
3219: } else if ( s2==-1 ) { /* alive */
3220: for (j=1,survp=0. ; j<=nlstate; j++)
3221: survp += out[s1][j];
3222: lli= log(survp);
3223: }else{
3224: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3225: }
3226: ipmx +=1;
3227: sw += weight[i];
3228: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.126 brouard 3229: /* 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 3230: } /* end of wave */
3231: } /* end of individual */
3232: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3233: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
3234: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
3235: for(mi=1; mi<= wav[i]-1; mi++){
3236: for (ii=1;ii<=nlstate+ndeath;ii++)
3237: for (j=1;j<=nlstate+ndeath;j++){
3238: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3239: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3240: }
3241: for(d=0; d<dh[mi][i]; d++){
3242: newm=savm;
3243: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3244: cov[2]=agexact;
3245: if(nagesqr==1)
3246: cov[3]= agexact*agexact;
3247: for (kk=1; kk<=cptcovage;kk++) {
3248: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3249: }
1.126 brouard 3250:
1.226 brouard 3251: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3252: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3253: savm=oldm;
3254: oldm=newm;
3255: } /* end mult */
3256:
3257: s1=s[mw[mi][i]][i];
3258: s2=s[mw[mi+1][i]][i];
3259: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3260: ipmx +=1;
3261: sw += weight[i];
3262: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3263: /*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]);*/
3264: } /* end of wave */
3265: } /* end of individual */
3266: } /* End of if */
3267: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3268: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3269: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3270: return -l;
1.126 brouard 3271: }
3272:
3273: /*************** log-likelihood *************/
3274: double funcone( double *x)
3275: {
1.228 ! brouard 3276: /* Same as func but slower because of a lot of printf and if */
1.126 brouard 3277: int i, ii, j, k, mi, d, kk;
1.228 ! brouard 3278: int ioffset=0;
1.131 brouard 3279: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3280: double **out;
3281: double lli; /* Individual log likelihood */
3282: double llt;
3283: int s1, s2;
1.228 ! brouard 3284: int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
! 3285:
1.126 brouard 3286: double bbh, survp;
1.187 brouard 3287: double agexact;
1.214 brouard 3288: double agebegin, ageend;
1.126 brouard 3289: /*extern weight */
3290: /* We are differentiating ll according to initial status */
3291: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3292: /*for(i=1;i<imx;i++)
3293: printf(" %d\n",s[4][i]);
3294: */
3295: cov[1]=1.;
3296:
3297: for(k=1; k<=nlstate; k++) ll[k]=0.;
1.224 brouard 3298: ioffset=0;
3299: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.225 brouard 3300: ioffset=2+nagesqr+cptcovage;
1.224 brouard 3301: /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
1.226 brouard 3302: for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed covariates without age* products */
1.225 brouard 3303: cov[++ioffset]=covar[Tvar[k]][i];
3304: }
1.226 brouard 3305: for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
3306: cov[++ioffset]=coqvar[Tvar[iqv]][i];
1.225 brouard 3307: }
3308:
1.226 brouard 3309: for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
1.225 brouard 3310: for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
1.228 ! brouard 3311: /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
! 3312: /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
! 3313: k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
! 3314: cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
! 3315: 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]);
1.225 brouard 3316: }
3317: for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
1.228 ! brouard 3318: iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */
! 3319: 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]);
! 3320: cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
1.225 brouard 3321: }
1.126 brouard 3322: for (ii=1;ii<=nlstate+ndeath;ii++)
1.225 brouard 3323: for (j=1;j<=nlstate+ndeath;j++){
3324: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3325: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3326: }
1.214 brouard 3327:
3328: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3329: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3330: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
1.225 brouard 3331: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3332: and mw[mi+1][i]. dh depends on stepm.*/
3333: newm=savm;
3334: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3335: cov[2]=agexact;
3336: if(nagesqr==1)
3337: cov[3]= agexact*agexact;
3338: for (kk=1; kk<=cptcovage;kk++) {
3339: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
3340: }
3341: /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
3342: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
3343: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3344: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3345: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3346: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
3347: savm=oldm;
3348: oldm=newm;
1.126 brouard 3349: } /* end mult */
3350:
3351: s1=s[mw[mi][i]][i];
3352: s2=s[mw[mi+1][i]][i];
1.217 brouard 3353: /* if(s2==-1){ */
3354: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3355: /* /\* exit(1); *\/ */
3356: /* } */
1.126 brouard 3357: bbh=(double)bh[mi][i]/(double)stepm;
3358: /* bias is positive if real duration
3359: * is higher than the multiple of stepm and negative otherwise.
3360: */
3361: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1.225 brouard 3362: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3363: } else if ( s2==-1 ) { /* alive */
1.225 brouard 3364: for (j=1,survp=0. ; j<=nlstate; j++)
3365: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3366: lli= log(survp);
1.126 brouard 3367: }else if (mle==1){
1.225 brouard 3368: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1.126 brouard 3369: } else if(mle==2){
1.225 brouard 3370: 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 3371: } else if(mle==3){ /* exponential inter-extrapolation */
1.225 brouard 3372: 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 3373: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1.225 brouard 3374: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3375: } else{ /* mle=0 back to 1 */
1.225 brouard 3376: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3377: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3378: } /* End of if */
3379: ipmx +=1;
3380: sw += weight[i];
3381: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3382: /*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 3383: if(globpr){
1.225 brouard 3384: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
1.126 brouard 3385: %11.6f %11.6f %11.6f ", \
1.225 brouard 3386: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
3387: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3388: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3389: llt +=ll[k]*gipmx/gsw;
3390: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3391: }
3392: fprintf(ficresilk," %10.6f\n", -llt);
1.126 brouard 3393: }
3394: } /* end of wave */
3395: } /* end of individual */
3396: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3397: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3398: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3399: if(globpr==0){ /* First time we count the contributions and weights */
3400: gipmx=ipmx;
3401: gsw=sw;
3402: }
3403: return -l;
3404: }
3405:
3406:
3407: /*************** function likelione ***********/
3408: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3409: {
3410: /* This routine should help understanding what is done with
3411: the selection of individuals/waves and
3412: to check the exact contribution to the likelihood.
3413: Plotting could be done.
3414: */
3415: int k;
3416:
3417: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3418: strcpy(fileresilk,"ILK_");
1.202 brouard 3419: strcat(fileresilk,fileresu);
1.126 brouard 3420: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3421: printf("Problem with resultfile: %s\n", fileresilk);
3422: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3423: }
1.214 brouard 3424: 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");
3425: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3426: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3427: for(k=1; k<=nlstate; k++)
3428: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3429: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3430: }
3431:
3432: *fretone=(*funcone)(p);
3433: if(*globpri !=0){
3434: fclose(ficresilk);
1.205 brouard 3435: if (mle ==0)
3436: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3437: else if(mle >=1)
3438: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3439: 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 3440:
1.208 brouard 3441:
3442: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3443: 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 3444: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3445: }
1.207 brouard 3446: 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 3447: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3448: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3449: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3450: fflush(fichtm);
1.205 brouard 3451: }
1.126 brouard 3452: return;
3453: }
3454:
3455:
3456: /*********** Maximum Likelihood Estimation ***************/
3457:
3458: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3459: {
1.165 brouard 3460: int i,j, iter=0;
1.126 brouard 3461: double **xi;
3462: double fret;
3463: double fretone; /* Only one call to likelihood */
3464: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3465:
3466: #ifdef NLOPT
3467: int creturn;
3468: nlopt_opt opt;
3469: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3470: double *lb;
3471: double minf; /* the minimum objective value, upon return */
3472: double * p1; /* Shifted parameters from 0 instead of 1 */
3473: myfunc_data dinst, *d = &dinst;
3474: #endif
3475:
3476:
1.126 brouard 3477: xi=matrix(1,npar,1,npar);
3478: for (i=1;i<=npar;i++)
3479: for (j=1;j<=npar;j++)
3480: xi[i][j]=(i==j ? 1.0 : 0.0);
3481: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3482: strcpy(filerespow,"POW_");
1.126 brouard 3483: strcat(filerespow,fileres);
3484: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3485: printf("Problem with resultfile: %s\n", filerespow);
3486: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3487: }
3488: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3489: for (i=1;i<=nlstate;i++)
3490: for(j=1;j<=nlstate+ndeath;j++)
3491: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3492: fprintf(ficrespow,"\n");
1.162 brouard 3493: #ifdef POWELL
1.126 brouard 3494: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3495: #endif
1.126 brouard 3496:
1.162 brouard 3497: #ifdef NLOPT
3498: #ifdef NEWUOA
3499: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3500: #else
3501: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3502: #endif
3503: lb=vector(0,npar-1);
3504: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3505: nlopt_set_lower_bounds(opt, lb);
3506: nlopt_set_initial_step1(opt, 0.1);
3507:
3508: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3509: d->function = func;
3510: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3511: nlopt_set_min_objective(opt, myfunc, d);
3512: nlopt_set_xtol_rel(opt, ftol);
3513: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3514: printf("nlopt failed! %d\n",creturn);
3515: }
3516: else {
3517: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3518: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3519: iter=1; /* not equal */
3520: }
3521: nlopt_destroy(opt);
3522: #endif
1.126 brouard 3523: free_matrix(xi,1,npar,1,npar);
3524: fclose(ficrespow);
1.203 brouard 3525: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3526: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3527: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3528:
3529: }
3530:
3531: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3532: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3533: {
3534: double **a,**y,*x,pd;
1.203 brouard 3535: /* double **hess; */
1.164 brouard 3536: int i, j;
1.126 brouard 3537: int *indx;
3538:
3539: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3540: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3541: void lubksb(double **a, int npar, int *indx, double b[]) ;
3542: void ludcmp(double **a, int npar, int *indx, double *d) ;
3543: double gompertz(double p[]);
1.203 brouard 3544: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3545:
3546: printf("\nCalculation of the hessian matrix. Wait...\n");
3547: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3548: for (i=1;i<=npar;i++){
1.203 brouard 3549: printf("%d-",i);fflush(stdout);
3550: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3551:
3552: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3553:
3554: /* printf(" %f ",p[i]);
3555: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3556: }
3557:
3558: for (i=1;i<=npar;i++) {
3559: for (j=1;j<=npar;j++) {
3560: if (j>i) {
1.203 brouard 3561: printf(".%d-%d",i,j);fflush(stdout);
3562: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3563: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3564:
3565: hess[j][i]=hess[i][j];
3566: /*printf(" %lf ",hess[i][j]);*/
3567: }
3568: }
3569: }
3570: printf("\n");
3571: fprintf(ficlog,"\n");
3572:
3573: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3574: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3575:
3576: a=matrix(1,npar,1,npar);
3577: y=matrix(1,npar,1,npar);
3578: x=vector(1,npar);
3579: indx=ivector(1,npar);
3580: for (i=1;i<=npar;i++)
3581: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3582: ludcmp(a,npar,indx,&pd);
3583:
3584: for (j=1;j<=npar;j++) {
3585: for (i=1;i<=npar;i++) x[i]=0;
3586: x[j]=1;
3587: lubksb(a,npar,indx,x);
3588: for (i=1;i<=npar;i++){
3589: matcov[i][j]=x[i];
3590: }
3591: }
3592:
3593: printf("\n#Hessian matrix#\n");
3594: fprintf(ficlog,"\n#Hessian matrix#\n");
3595: for (i=1;i<=npar;i++) {
3596: for (j=1;j<=npar;j++) {
1.203 brouard 3597: printf("%.6e ",hess[i][j]);
3598: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3599: }
3600: printf("\n");
3601: fprintf(ficlog,"\n");
3602: }
3603:
1.203 brouard 3604: /* printf("\n#Covariance matrix#\n"); */
3605: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3606: /* for (i=1;i<=npar;i++) { */
3607: /* for (j=1;j<=npar;j++) { */
3608: /* printf("%.6e ",matcov[i][j]); */
3609: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3610: /* } */
3611: /* printf("\n"); */
3612: /* fprintf(ficlog,"\n"); */
3613: /* } */
3614:
1.126 brouard 3615: /* Recompute Inverse */
1.203 brouard 3616: /* for (i=1;i<=npar;i++) */
3617: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3618: /* ludcmp(a,npar,indx,&pd); */
3619:
3620: /* printf("\n#Hessian matrix recomputed#\n"); */
3621:
3622: /* for (j=1;j<=npar;j++) { */
3623: /* for (i=1;i<=npar;i++) x[i]=0; */
3624: /* x[j]=1; */
3625: /* lubksb(a,npar,indx,x); */
3626: /* for (i=1;i<=npar;i++){ */
3627: /* y[i][j]=x[i]; */
3628: /* printf("%.3e ",y[i][j]); */
3629: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3630: /* } */
3631: /* printf("\n"); */
3632: /* fprintf(ficlog,"\n"); */
3633: /* } */
3634:
3635: /* Verifying the inverse matrix */
3636: #ifdef DEBUGHESS
3637: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3638:
1.203 brouard 3639: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3640: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3641:
3642: for (j=1;j<=npar;j++) {
3643: for (i=1;i<=npar;i++){
1.203 brouard 3644: printf("%.2f ",y[i][j]);
3645: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3646: }
3647: printf("\n");
3648: fprintf(ficlog,"\n");
3649: }
1.203 brouard 3650: #endif
1.126 brouard 3651:
3652: free_matrix(a,1,npar,1,npar);
3653: free_matrix(y,1,npar,1,npar);
3654: free_vector(x,1,npar);
3655: free_ivector(indx,1,npar);
1.203 brouard 3656: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3657:
3658:
3659: }
3660:
3661: /*************** hessian matrix ****************/
3662: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3663: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3664: int i;
3665: int l=1, lmax=20;
1.203 brouard 3666: double k1,k2, res, fx;
1.132 brouard 3667: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3668: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3669: int k=0,kmax=10;
3670: double l1;
3671:
3672: fx=func(x);
3673: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3674: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3675: l1=pow(10,l);
3676: delts=delt;
3677: for(k=1 ; k <kmax; k=k+1){
3678: delt = delta*(l1*k);
3679: p2[theta]=x[theta] +delt;
1.145 brouard 3680: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3681: p2[theta]=x[theta]-delt;
3682: k2=func(p2)-fx;
3683: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3684: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3685:
1.203 brouard 3686: #ifdef DEBUGHESSII
1.126 brouard 3687: 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);
3688: 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);
3689: #endif
3690: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3691: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3692: k=kmax;
3693: }
3694: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3695: k=kmax; l=lmax*10;
1.126 brouard 3696: }
3697: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3698: delts=delt;
3699: }
1.203 brouard 3700: } /* End loop k */
1.126 brouard 3701: }
3702: delti[theta]=delts;
3703: return res;
3704:
3705: }
3706:
1.203 brouard 3707: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3708: {
3709: int i;
1.164 brouard 3710: int l=1, lmax=20;
1.126 brouard 3711: double k1,k2,k3,k4,res,fx;
1.132 brouard 3712: double p2[MAXPARM+1];
1.203 brouard 3713: int k, kmax=1;
3714: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3715:
3716: int firstime=0;
1.203 brouard 3717:
1.126 brouard 3718: fx=func(x);
1.203 brouard 3719: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3720: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3721: p2[thetai]=x[thetai]+delti[thetai]*k;
3722: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3723: k1=func(p2)-fx;
3724:
1.203 brouard 3725: p2[thetai]=x[thetai]+delti[thetai]*k;
3726: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3727: k2=func(p2)-fx;
3728:
1.203 brouard 3729: p2[thetai]=x[thetai]-delti[thetai]*k;
3730: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3731: k3=func(p2)-fx;
3732:
1.203 brouard 3733: p2[thetai]=x[thetai]-delti[thetai]*k;
3734: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3735: k4=func(p2)-fx;
1.203 brouard 3736: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3737: if(k1*k2*k3*k4 <0.){
1.208 brouard 3738: firstime=1;
1.203 brouard 3739: kmax=kmax+10;
1.208 brouard 3740: }
3741: if(kmax >=10 || firstime ==1){
1.218 brouard 3742: 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);
3743: 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 3744: 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);
3745: 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);
3746: }
3747: #ifdef DEBUGHESSIJ
3748: v1=hess[thetai][thetai];
3749: v2=hess[thetaj][thetaj];
3750: cv12=res;
3751: /* Computing eigen value of Hessian matrix */
3752: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3753: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3754: if ((lc2 <0) || (lc1 <0) ){
3755: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3756: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3757: 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);
3758: 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);
3759: }
1.126 brouard 3760: #endif
3761: }
3762: return res;
3763: }
3764:
1.203 brouard 3765: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3766: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3767: /* { */
3768: /* int i; */
3769: /* int l=1, lmax=20; */
3770: /* double k1,k2,k3,k4,res,fx; */
3771: /* double p2[MAXPARM+1]; */
3772: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3773: /* int k=0,kmax=10; */
3774: /* double l1; */
3775:
3776: /* fx=func(x); */
3777: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3778: /* l1=pow(10,l); */
3779: /* delts=delt; */
3780: /* for(k=1 ; k <kmax; k=k+1){ */
3781: /* delt = delti*(l1*k); */
3782: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3783: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3784: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3785: /* k1=func(p2)-fx; */
3786:
3787: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3788: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3789: /* k2=func(p2)-fx; */
3790:
3791: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3792: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3793: /* k3=func(p2)-fx; */
3794:
3795: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3796: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3797: /* k4=func(p2)-fx; */
3798: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3799: /* #ifdef DEBUGHESSIJ */
3800: /* 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); */
3801: /* 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); */
3802: /* #endif */
3803: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3804: /* k=kmax; */
3805: /* } */
3806: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3807: /* k=kmax; l=lmax*10; */
3808: /* } */
3809: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3810: /* delts=delt; */
3811: /* } */
3812: /* } /\* End loop k *\/ */
3813: /* } */
3814: /* delti[theta]=delts; */
3815: /* return res; */
3816: /* } */
3817:
3818:
1.126 brouard 3819: /************** Inverse of matrix **************/
3820: void ludcmp(double **a, int n, int *indx, double *d)
3821: {
3822: int i,imax,j,k;
3823: double big,dum,sum,temp;
3824: double *vv;
3825:
3826: vv=vector(1,n);
3827: *d=1.0;
3828: for (i=1;i<=n;i++) {
3829: big=0.0;
3830: for (j=1;j<=n;j++)
3831: if ((temp=fabs(a[i][j])) > big) big=temp;
3832: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3833: vv[i]=1.0/big;
3834: }
3835: for (j=1;j<=n;j++) {
3836: for (i=1;i<j;i++) {
3837: sum=a[i][j];
3838: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3839: a[i][j]=sum;
3840: }
3841: big=0.0;
3842: for (i=j;i<=n;i++) {
3843: sum=a[i][j];
3844: for (k=1;k<j;k++)
3845: sum -= a[i][k]*a[k][j];
3846: a[i][j]=sum;
3847: if ( (dum=vv[i]*fabs(sum)) >= big) {
3848: big=dum;
3849: imax=i;
3850: }
3851: }
3852: if (j != imax) {
3853: for (k=1;k<=n;k++) {
3854: dum=a[imax][k];
3855: a[imax][k]=a[j][k];
3856: a[j][k]=dum;
3857: }
3858: *d = -(*d);
3859: vv[imax]=vv[j];
3860: }
3861: indx[j]=imax;
3862: if (a[j][j] == 0.0) a[j][j]=TINY;
3863: if (j != n) {
3864: dum=1.0/(a[j][j]);
3865: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3866: }
3867: }
3868: free_vector(vv,1,n); /* Doesn't work */
3869: ;
3870: }
3871:
3872: void lubksb(double **a, int n, int *indx, double b[])
3873: {
3874: int i,ii=0,ip,j;
3875: double sum;
3876:
3877: for (i=1;i<=n;i++) {
3878: ip=indx[i];
3879: sum=b[ip];
3880: b[ip]=b[i];
3881: if (ii)
3882: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3883: else if (sum) ii=i;
3884: b[i]=sum;
3885: }
3886: for (i=n;i>=1;i--) {
3887: sum=b[i];
3888: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3889: b[i]=sum/a[i][i];
3890: }
3891: }
3892:
3893: void pstamp(FILE *fichier)
3894: {
1.196 brouard 3895: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3896: }
3897:
3898: /************ Frequencies ********************/
1.226 brouard 3899: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3900: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3901: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3902: { /* Some frequencies */
3903:
1.227 brouard 3904: int i, m, jk, j1, bool, z1,j, k, iv;
1.226 brouard 3905: int iind=0, iage=0;
3906: int mi; /* Effective wave */
3907: int first;
3908: double ***freq; /* Frequencies */
3909: double *meanq;
3910: double **meanqt;
3911: double *pp, **prop, *posprop, *pospropt;
3912: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3913: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3914: double agebegin, ageend;
3915:
3916: pp=vector(1,nlstate);
3917: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3918: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3919: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3920: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3921: meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
3922: meanqt=matrix(1,lastpass,1,nqtveff);
3923: strcpy(fileresp,"P_");
3924: strcat(fileresp,fileresu);
3925: /*strcat(fileresphtm,fileresu);*/
3926: if((ficresp=fopen(fileresp,"w"))==NULL) {
3927: printf("Problem with prevalence resultfile: %s\n", fileresp);
3928: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3929: exit(0);
3930: }
1.214 brouard 3931:
1.226 brouard 3932: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3933: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3934: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3935: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3936: fflush(ficlog);
3937: exit(70);
3938: }
3939: else{
3940: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3941: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3942: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3943: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3944: }
3945: 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 3946:
1.226 brouard 3947: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3948: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3949: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3950: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3951: fflush(ficlog);
3952: exit(70);
3953: }
3954: else{
3955: 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 3956: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3957: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.226 brouard 3958: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3959: }
3960: 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 3961:
1.226 brouard 3962: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3963: j1=0;
1.126 brouard 3964:
1.227 brouard 3965: /* j=ncoveff; /\* Only fixed dummy covariates *\/ */
3966: j=cptcoveff; /* Only dummy covariates of the model */
1.226 brouard 3967: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.220 brouard 3968:
1.226 brouard 3969: first=1;
1.220 brouard 3970:
1.226 brouard 3971: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3972: reference=low_education V1=0,V2=0
3973: med_educ V1=1 V2=0,
3974: high_educ V1=0 V2=1
3975: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3976: */
1.126 brouard 3977:
1.227 brouard 3978: 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 3979: posproptt=0.;
3980: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3981: scanf("%d", i);*/
3982: for (i=-5; i<=nlstate+ndeath; i++)
3983: for (jk=-5; jk<=nlstate+ndeath; jk++)
3984: for(m=iagemin; m <= iagemax+3; m++)
3985: freq[i][jk][m]=0;
3986:
3987: for (i=1; i<=nlstate; i++) {
3988: for(m=iagemin; m <= iagemax+3; m++)
3989: prop[i][m]=0;
3990: posprop[i]=0;
3991: pospropt[i]=0;
3992: }
1.227 brouard 3993: /* for (z1=1; z1<= nqfveff; z1++) { */
3994: /* meanq[z1]+=0.; */
3995: /* for(m=1;m<=lastpass;m++){ */
3996: /* meanqt[m][z1]=0.; */
3997: /* } */
3998: /* } */
1.220 brouard 3999:
1.226 brouard 4000: dateintsum=0;
4001: k2cpt=0;
1.227 brouard 4002: /* For that combination of covariate j1, we count and print the frequencies in one pass */
1.226 brouard 4003: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
4004: bool=1;
1.227 brouard 4005: if(anyvaryingduminmodel==0){ /* If All fixed covariates */
4006: if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
4007: /* for (z1=1; z1<= nqfveff; z1++) { */
4008: /* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter *\/ */
4009: /* } */
4010: for (z1=1; z1<=cptcoveff; z1++) {
4011: /* if(Tvaraff[z1] ==-20){ */
4012: /* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
4013: /* }else if(Tvaraff[z1] ==-10){ */
4014: /* /\* sumnew+=coqvar[z1][iind]; *\/ */
4015: /* }else */
4016: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
4017: /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
4018: bool=0;
4019: /* 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",
4020: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
4021: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
4022: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
4023: } /* Onlyf fixed */
4024: } /* end z1 */
4025: } /* cptcovn > 0 */
4026: } /* end any */
4027: if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
1.226 brouard 4028: /* for(m=firstpass; m<=lastpass; m++){ */
1.227 brouard 4029: for(mi=1; mi<wav[iind];mi++){ /* For that wave */
1.226 brouard 4030: m=mw[mi][iind];
1.227 brouard 4031: if(anyvaryingduminmodel==1){ /* Some are varying covariates */
4032: for (z1=1; z1<=cptcoveff; z1++) {
4033: if( Fixed[Tmodelind[z1]]==1){
4034: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4035: if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4036: bool=0;
4037: }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
4038: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4039: bool=0;
4040: }
4041: }
4042: }
4043: }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
4044: /* bool =0 we keep that guy which corresponds to the combination of dummy values */
4045: if(bool==1){
4046: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
4047: and mw[mi+1][iind]. dh depends on stepm. */
4048: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
4049: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
4050: if(m >=firstpass && m <=lastpass){
4051: k2=anint[m][iind]+(mint[m][iind]/12.);
4052: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
4053: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
4054: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
4055: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
4056: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4057: if (m<lastpass) {
4058: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
4059: /* 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]); */
4060: if(s[m][iind]==-1)
4061: 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.));
4062: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
4063: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
4064: 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 */
4065: }
4066: } /* end if between passes */
4067: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
4068: dateintsum=dateintsum+k2;
4069: k2cpt++;
4070: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
1.226 brouard 4071: }
1.227 brouard 4072: } /* end bool 2 */
1.226 brouard 4073: } /* end m */
4074: } /* end bool */
4075: } /* end iind = 1 to imx */
4076: /* prop[s][age] is feeded for any initial and valid live state as well as
4077: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
4078:
4079:
4080: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
4081: pstamp(ficresp);
1.227 brouard 4082: /* if (ncoveff>0) { */
4083: if (cptcoveff>0) {
1.226 brouard 4084: fprintf(ficresp, "\n#********** Variable ");
4085: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
4086: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.227 brouard 4087: for (z1=1; z1<=cptcoveff; z1++){
1.226 brouard 4088: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4089: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4090: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
4091: }
4092: fprintf(ficresp, "**********\n#");
4093: fprintf(ficresphtm, "**********</h3>\n");
4094: fprintf(ficresphtmfr, "**********</h3>\n");
4095: fprintf(ficlog, "\n#********** Variable ");
1.227 brouard 4096: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.226 brouard 4097: fprintf(ficlog, "**********\n");
4098: }
4099: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
4100: for(i=1; i<=nlstate;i++) {
4101: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
4102: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
4103: }
4104: fprintf(ficresp, "\n");
4105: fprintf(ficresphtm, "\n");
4106:
4107: /* Header of frequency table by age */
4108: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
4109: fprintf(ficresphtmfr,"<th>Age</th> ");
4110: for(jk=-1; jk <=nlstate+ndeath; jk++){
4111: for(m=-1; m <=nlstate+ndeath; m++){
4112: if(jk!=0 && m!=0)
4113: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
4114: }
4115: }
4116: fprintf(ficresphtmfr, "\n");
4117:
4118: /* For each age */
4119: for(iage=iagemin; iage <= iagemax+3; iage++){
4120: fprintf(ficresphtm,"<tr>");
4121: if(iage==iagemax+1){
4122: fprintf(ficlog,"1");
4123: fprintf(ficresphtmfr,"<tr><th>0</th> ");
4124: }else if(iage==iagemax+2){
4125: fprintf(ficlog,"0");
4126: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
4127: }else if(iage==iagemax+3){
4128: fprintf(ficlog,"Total");
4129: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
4130: }else{
4131: if(first==1){
4132: first=0;
4133: printf("See log file for details...\n");
4134: }
4135: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
4136: fprintf(ficlog,"Age %d", iage);
4137: }
4138: for(jk=1; jk <=nlstate ; jk++){
4139: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
4140: pp[jk] += freq[jk][m][iage];
4141: }
4142: for(jk=1; jk <=nlstate ; jk++){
4143: for(m=-1, pos=0; m <=0 ; m++)
4144: pos += freq[jk][m][iage];
4145: if(pp[jk]>=1.e-10){
4146: if(first==1){
4147: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4148: }
4149: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
4150: }else{
4151: if(first==1)
4152: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4153: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
4154: }
4155: }
4156:
4157: for(jk=1; jk <=nlstate ; jk++){
4158: /* posprop[jk]=0; */
4159: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
4160: pp[jk] += freq[jk][m][iage];
4161: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
4162:
4163: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
4164: pos += pp[jk]; /* pos is the total number of transitions until this age */
4165: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
4166: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4167: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
4168: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
4169: }
4170: for(jk=1; jk <=nlstate ; jk++){
4171: if(pos>=1.e-5){
4172: if(first==1)
4173: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4174: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
4175: }else{
4176: if(first==1)
4177: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4178: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
4179: }
4180: if( iage <= iagemax){
4181: if(pos>=1.e-5){
4182: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4183: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
4184: /*probs[iage][jk][j1]= pp[jk]/pos;*/
4185: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
4186: }
4187: else{
4188: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
4189: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
4190: }
4191: }
4192: pospropt[jk] +=posprop[jk];
4193: } /* end loop jk */
4194: /* pospropt=0.; */
4195: for(jk=-1; jk <=nlstate+ndeath; jk++){
4196: for(m=-1; m <=nlstate+ndeath; m++){
4197: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
4198: if(first==1){
4199: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
4200: }
4201: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
4202: }
4203: if(jk!=0 && m!=0)
4204: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
4205: }
4206: } /* end loop jk */
4207: posproptt=0.;
4208: for(jk=1; jk <=nlstate; jk++){
4209: posproptt += pospropt[jk];
4210: }
4211: fprintf(ficresphtmfr,"</tr>\n ");
4212: if(iage <= iagemax){
4213: fprintf(ficresp,"\n");
4214: fprintf(ficresphtm,"</tr>\n");
4215: }
4216: if(first==1)
4217: printf("Others in log...\n");
4218: fprintf(ficlog,"\n");
4219: } /* end loop age iage */
4220: fprintf(ficresphtm,"<tr><th>Tot</th>");
4221: for(jk=1; jk <=nlstate ; jk++){
4222: if(posproptt < 1.e-5){
4223: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
4224: }else{
4225: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
4226: }
4227: }
4228: fprintf(ficresphtm,"</tr>\n");
4229: fprintf(ficresphtm,"</table>\n");
4230: fprintf(ficresphtmfr,"</table>\n");
4231: if(posproptt < 1.e-5){
4232: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4233: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
4234: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
4235: invalidvarcomb[j1]=1;
4236: }else{
4237: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
4238: invalidvarcomb[j1]=0;
4239: }
4240: fprintf(ficresphtmfr,"</table>\n");
4241: } /* end selected combination of covariate j1 */
4242: dateintmean=dateintsum/k2cpt;
1.220 brouard 4243:
1.226 brouard 4244: fclose(ficresp);
4245: fclose(ficresphtm);
4246: fclose(ficresphtmfr);
4247: free_vector(meanq,1,nqfveff);
4248: free_matrix(meanqt,1,lastpass,1,nqtveff);
4249: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4250: free_vector(pospropt,1,nlstate);
4251: free_vector(posprop,1,nlstate);
4252: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
4253: free_vector(pp,1,nlstate);
4254: /* End of freqsummary */
4255: }
1.126 brouard 4256:
4257: /************ Prevalence ********************/
1.227 brouard 4258: 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)
4259: {
4260: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
4261: in each health status at the date of interview (if between dateprev1 and dateprev2).
4262: We still use firstpass and lastpass as another selection.
4263: */
1.126 brouard 4264:
1.227 brouard 4265: int i, m, jk, j1, bool, z1,j, iv;
4266: int mi; /* Effective wave */
4267: int iage;
4268: double agebegin, ageend;
4269:
4270: double **prop;
4271: double posprop;
4272: double y2; /* in fractional years */
4273: int iagemin, iagemax;
4274: int first; /** to stop verbosity which is redirected to log file */
4275:
4276: iagemin= (int) agemin;
4277: iagemax= (int) agemax;
4278: /*pp=vector(1,nlstate);*/
4279: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4280: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4281: j1=0;
1.222 brouard 4282:
1.227 brouard 4283: /*j=cptcoveff;*/
4284: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1.222 brouard 4285:
1.227 brouard 4286: first=1;
4287: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
4288: for (i=1; i<=nlstate; i++)
4289: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4290: prop[i][iage]=0.0;
4291: printf("Prevalence combination of varying and fixed dummies %d\n",j1);
4292: /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
4293: fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
4294:
4295: for (i=1; i<=imx; i++) { /* Each individual */
4296: bool=1;
4297: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4298: for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
4299: m=mw[mi][i];
4300: /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
4301: /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
4302: for (z1=1; z1<=cptcoveff; z1++){
4303: if( Fixed[Tmodelind[z1]]==1){
4304: iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
4305: if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
4306: bool=0;
4307: }else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
4308: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
4309: bool=0;
4310: }
4311: }
4312: if(bool==1){ /* Otherwise we skip that wave/person */
4313: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4314: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4315: if(m >=firstpass && m <=lastpass){
4316: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4317: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4318: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4319: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4320: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4321: 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);
4322: exit(1);
4323: }
4324: if (s[m][i]>0 && s[m][i]<=nlstate) {
4325: /*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]]);*/
4326: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4327: prop[s[m][i]][iagemax+3] += weight[i];
4328: } /* end valid statuses */
4329: } /* end selection of dates */
4330: } /* end selection of waves */
4331: } /* end bool */
4332: } /* end wave */
4333: } /* end individual */
4334: for(i=iagemin; i <= iagemax+3; i++){
4335: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
4336: posprop += prop[jk][i];
4337: }
4338:
4339: for(jk=1; jk <=nlstate ; jk++){
4340: if( i <= iagemax){
4341: if(posprop>=1.e-5){
4342: probs[i][jk][j1]= prop[jk][i]/posprop;
4343: } else{
4344: if(first==1){
4345: first=0;
4346: 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]);
4347: }
4348: }
4349: }
4350: }/* end jk */
4351: }/* end i */
1.222 brouard 4352: /*} *//* end i1 */
1.227 brouard 4353: } /* end j1 */
1.222 brouard 4354:
1.227 brouard 4355: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4356: /*free_vector(pp,1,nlstate);*/
4357: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
4358: } /* End of prevalence */
1.126 brouard 4359:
4360: /************* Waves Concatenation ***************/
4361:
4362: 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)
4363: {
4364: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4365: Death is a valid wave (if date is known).
4366: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4367: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4368: and mw[mi+1][i]. dh depends on stepm.
1.227 brouard 4369: */
1.126 brouard 4370:
1.224 brouard 4371: int i=0, mi=0, m=0, mli=0;
1.126 brouard 4372: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4373: double sum=0., jmean=0.;*/
1.224 brouard 4374: int first=0, firstwo=0, firsthree=0, firstfour=0, firstfiv=0;
1.126 brouard 4375: int j, k=0,jk, ju, jl;
4376: double sum=0.;
4377: first=0;
1.214 brouard 4378: firstwo=0;
1.217 brouard 4379: firsthree=0;
1.218 brouard 4380: firstfour=0;
1.164 brouard 4381: jmin=100000;
1.126 brouard 4382: jmax=-1;
4383: jmean=0.;
1.224 brouard 4384:
4385: /* Treating live states */
1.214 brouard 4386: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.224 brouard 4387: mi=0; /* First valid wave */
1.227 brouard 4388: mli=0; /* Last valid wave */
1.126 brouard 4389: m=firstpass;
1.214 brouard 4390: while(s[m][i] <= nlstate){ /* a live state */
1.227 brouard 4391: 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 */
4392: mli=m-1;/* mw[++mi][i]=m-1; */
4393: }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 */
4394: mw[++mi][i]=m;
4395: mli=m;
1.224 brouard 4396: } /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
4397: if(m < lastpass){ /* m < lastpass, standard case */
1.227 brouard 4398: m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
1.216 brouard 4399: }
1.227 brouard 4400: else{ /* m >= lastpass, eventual special issue with warning */
1.224 brouard 4401: #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
1.227 brouard 4402: break;
1.224 brouard 4403: #else
1.227 brouard 4404: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
4405: if(firsthree == 0){
4406: 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);
4407: firsthree=1;
4408: }
4409: 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);
4410: mw[++mi][i]=m;
4411: mli=m;
4412: }
4413: if(s[m][i]==-2){ /* Vital status is really unknown */
4414: nbwarn++;
4415: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4416: 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);
4417: 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);
4418: }
4419: break;
4420: }
4421: break;
1.224 brouard 4422: #endif
1.227 brouard 4423: }/* End m >= lastpass */
1.126 brouard 4424: }/* end while */
1.224 brouard 4425:
1.227 brouard 4426: /* 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 4427: /* After last pass */
1.224 brouard 4428: /* Treating death states */
1.214 brouard 4429: if (s[m][i] > nlstate){ /* In a death state */
1.227 brouard 4430: /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
4431: /* } */
1.126 brouard 4432: mi++; /* Death is another wave */
4433: /* if(mi==0) never been interviewed correctly before death */
1.227 brouard 4434: /* Only death is a correct wave */
1.126 brouard 4435: mw[mi][i]=m;
1.224 brouard 4436: }
4437: #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
1.227 brouard 4438: 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 4439: /* m++; */
4440: /* mi++; */
4441: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4442: /* mw[mi][i]=m; */
1.218 brouard 4443: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
1.227 brouard 4444: 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 */
4445: nbwarn++;
4446: if(firstfiv==0){
4447: 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 );
4448: firstfiv=1;
4449: }else{
4450: 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 );
4451: }
4452: }else{ /* Death occured afer last wave potential bias */
4453: nberr++;
4454: if(firstwo==0){
4455: 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 );
4456: firstwo=1;
4457: }
4458: 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 );
4459: }
1.218 brouard 4460: }else{ /* end date of interview is known */
1.227 brouard 4461: /* death is known but not confirmed by death status at any wave */
4462: if(firstfour==0){
4463: 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 );
4464: firstfour=1;
4465: }
4466: 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 4467: }
1.224 brouard 4468: } /* end if date of death is known */
4469: #endif
4470: wav[i]=mi; /* mi should be the last effective wave (or mli) */
4471: /* wav[i]=mw[mi][i]; */
1.126 brouard 4472: if(mi==0){
4473: nbwarn++;
4474: if(first==0){
1.227 brouard 4475: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4476: first=1;
1.126 brouard 4477: }
4478: if(first==1){
1.227 brouard 4479: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
1.126 brouard 4480: }
4481: } /* end mi==0 */
4482: } /* End individuals */
1.214 brouard 4483: /* wav and mw are no more changed */
1.223 brouard 4484:
1.214 brouard 4485:
1.126 brouard 4486: for(i=1; i<=imx; i++){
4487: for(mi=1; mi<wav[i];mi++){
4488: if (stepm <=0)
1.227 brouard 4489: dh[mi][i]=1;
1.126 brouard 4490: else{
1.227 brouard 4491: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4492: if (agedc[i] < 2*AGESUP) {
4493: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4494: if(j==0) j=1; /* Survives at least one month after exam */
4495: else if(j<0){
4496: nberr++;
4497: 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]);
4498: j=1; /* Temporary Dangerous patch */
4499: 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);
4500: 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]);
4501: 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);
4502: }
4503: k=k+1;
4504: if (j >= jmax){
4505: jmax=j;
4506: ijmax=i;
4507: }
4508: if (j <= jmin){
4509: jmin=j;
4510: ijmin=i;
4511: }
4512: sum=sum+j;
4513: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4514: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4515: }
4516: }
4517: else{
4518: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1.126 brouard 4519: /* 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 4520:
1.227 brouard 4521: k=k+1;
4522: if (j >= jmax) {
4523: jmax=j;
4524: ijmax=i;
4525: }
4526: else if (j <= jmin){
4527: jmin=j;
4528: ijmin=i;
4529: }
4530: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4531: /*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]);*/
4532: if(j<0){
4533: nberr++;
4534: 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]);
4535: 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]);
4536: }
4537: sum=sum+j;
4538: }
4539: jk= j/stepm;
4540: jl= j -jk*stepm;
4541: ju= j -(jk+1)*stepm;
4542: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4543: if(jl==0){
4544: dh[mi][i]=jk;
4545: bh[mi][i]=0;
4546: }else{ /* We want a negative bias in order to only have interpolation ie
4547: * to avoid the price of an extra matrix product in likelihood */
4548: dh[mi][i]=jk+1;
4549: bh[mi][i]=ju;
4550: }
4551: }else{
4552: if(jl <= -ju){
4553: dh[mi][i]=jk;
4554: bh[mi][i]=jl; /* bias is positive if real duration
4555: * is higher than the multiple of stepm and negative otherwise.
4556: */
4557: }
4558: else{
4559: dh[mi][i]=jk+1;
4560: bh[mi][i]=ju;
4561: }
4562: if(dh[mi][i]==0){
4563: dh[mi][i]=1; /* At least one step */
4564: bh[mi][i]=ju; /* At least one step */
4565: /* 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);*/
4566: }
4567: } /* end if mle */
1.126 brouard 4568: }
4569: } /* end wave */
4570: }
4571: jmean=sum/k;
4572: 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 4573: 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 4574: }
1.126 brouard 4575:
4576: /*********** Tricode ****************************/
1.220 brouard 4577: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4578: {
1.144 brouard 4579: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4580: /* 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 4581: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.224 brouard 4582: * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
4583: * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
1.144 brouard 4584: */
1.130 brouard 4585:
1.145 brouard 4586: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4587: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4588: int cptcode=0; /* Modality max of covariates j */
4589: int modmincovj=0; /* Modality min of covariates j */
4590:
4591:
1.220 brouard 4592: /* cptcoveff=0; */
1.224 brouard 4593: /* *cptcov=0; */
1.126 brouard 4594:
1.144 brouard 4595: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4596:
1.224 brouard 4597: /* Loop on covariates without age and products and no quantitative variable */
4598: /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
1.227 brouard 4599: for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
4600: for (j=-1; (j < maxncov); j++) Ndum[j]=0;
4601: if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
4602: switch(Fixed[k]) {
4603: case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
4604: 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*/
4605: ij=(int)(covar[Tvar[k]][i]);
4606: /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
4607: * If product of Vn*Vm, still boolean *:
4608: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4609: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
4610: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
4611: modality of the nth covariate of individual i. */
4612: if (ij > modmaxcovj)
4613: modmaxcovj=ij;
4614: else if (ij < modmincovj)
4615: modmincovj=ij;
4616: if ((ij < -1) && (ij > NCOVMAX)){
4617: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4618: exit(1);
4619: }else
4620: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
4621: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
4622: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
4623: /* getting the maximum value of the modality of the covariate
4624: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4625: female ies 1, then modmaxcovj=1.
4626: */
4627: } /* end for loop on individuals i */
4628: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4629: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
4630: cptcode=modmaxcovj;
4631: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
4632: /*for (i=0; i<=cptcode; i++) {*/
4633: for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
4634: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4635: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
4636: if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
4637: if( j != -1){
4638: ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
4639: covariate for which somebody answered excluding
4640: undefined. Usually 2: 0 and 1. */
4641: }
4642: ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
4643: covariate for which somebody answered including
4644: undefined. Usually 3: -1, 0 and 1. */
4645: }
4646: /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
4647: * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
4648: } /* Ndum[-1] number of undefined modalities */
4649:
4650: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
4651: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4652: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
4653: modmincovj=3; modmaxcovj = 7;
4654: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4655: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4656: defining two dummy variables: variables V1_1 and V1_2.
4657: nbcode[Tvar[j]][ij]=k;
4658: nbcode[Tvar[j]][1]=0;
4659: nbcode[Tvar[j]][2]=1;
4660: nbcode[Tvar[j]][3]=2;
4661: To be continued (not working yet).
4662: */
4663: ij=0; /* ij is similar to i but can jump over null modalities */
4664: 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*/
4665: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
4666: break;
4667: }
4668: ij++;
4669: 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*/
4670: cptcode = ij; /* New max modality for covar j */
4671: } /* end of loop on modality i=-1 to 1 or more */
4672: break;
4673: case 1: /* Testing on varying covariate, could be simple and
4674: * should look at waves or product of fixed *
4675: * varying. No time to test -1, assuming 0 and 1 only */
4676: ij=0;
4677: for(i=0; i<=1;i++){
4678: nbcode[Tvar[k]][++ij]=i;
4679: }
1.225 brouard 4680: break;
1.227 brouard 4681: default:
1.225 brouard 4682: break;
1.227 brouard 4683: } /* end switch */
4684: } /* end dummy test */
1.225 brouard 4685:
1.192 brouard 4686: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4687: /* /\*recode from 0 *\/ */
4688: /* k is a modality. If we have model=V1+V1*sex */
4689: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4690: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4691: /* } */
4692: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4693: /* if (ij > ncodemax[j]) { */
4694: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4695: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4696: /* break; */
4697: /* } */
4698: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4699: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4700:
1.225 brouard 4701: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.227 brouard 4702: /* Look at fixed dummy (single or product) covariates to check empty modalities */
1.187 brouard 4703: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.225 brouard 4704: /* 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 4705: 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 */
4706: 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 */
4707: /* 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 4708: } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
4709:
4710: ij=0;
1.227 brouard 4711: /* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
4712: 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 4713: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4714: /* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? *\/ */
4715: if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
4716: /* If product not in single variable we don't print results */
1.225 brouard 4717: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
1.227 brouard 4718: ++ij;
4719: Tvaraff[ij]=Tvar[k]; /*For printing */
4720: Tmodelind[ij]=k;
1.228 ! brouard 4721: TmodelInvind[k]=Tvar[k]- ncovcol-nqv;
1.227 brouard 4722: if(Fixed[k]!=0)
4723: anyvaryingduminmodel=1;
4724: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
4725: /* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
4726: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
4727: /* Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
4728: /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
4729: /* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
4730: }
1.225 brouard 4731: } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
4732: /* ij--; */
4733: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4734: *cptcov=ij; /*Number of total real effective covariates: effective
4735: * because they can be excluded from the model and real
1.227 brouard 4736: * if in the model but excluded because missing values, but how to get k from ij?*/
4737: for(j=ij+1; j<= cptcovt; j++){
4738: Tvaraff[j]=0;
4739: Tmodelind[j]=0;
4740: }
1.228 ! brouard 4741: for(j=ntveff+1; j<= cptcovt; j++){
! 4742: TmodelInvind[j]=0;
! 4743: }
1.227 brouard 4744: /* To be sorted */
4745: ;
1.126 brouard 4746: }
4747:
1.145 brouard 4748:
1.126 brouard 4749: /*********** Health Expectancies ****************/
4750:
1.127 brouard 4751: 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 4752:
4753: {
4754: /* Health expectancies, no variances */
1.164 brouard 4755: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4756: int nhstepma, nstepma; /* Decreasing with age */
4757: double age, agelim, hf;
4758: double ***p3mat;
4759: double eip;
4760:
4761: pstamp(ficreseij);
4762: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4763: fprintf(ficreseij,"# Age");
4764: for(i=1; i<=nlstate;i++){
4765: for(j=1; j<=nlstate;j++){
4766: fprintf(ficreseij," e%1d%1d ",i,j);
4767: }
4768: fprintf(ficreseij," e%1d. ",i);
4769: }
4770: fprintf(ficreseij,"\n");
4771:
4772:
4773: if(estepm < stepm){
4774: printf ("Problem %d lower than %d\n",estepm, stepm);
4775: }
4776: else hstepm=estepm;
4777: /* We compute the life expectancy from trapezoids spaced every estepm months
4778: * This is mainly to measure the difference between two models: for example
4779: * if stepm=24 months pijx are given only every 2 years and by summing them
4780: * we are calculating an estimate of the Life Expectancy assuming a linear
4781: * progression in between and thus overestimating or underestimating according
4782: * to the curvature of the survival function. If, for the same date, we
4783: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4784: * to compare the new estimate of Life expectancy with the same linear
4785: * hypothesis. A more precise result, taking into account a more precise
4786: * curvature will be obtained if estepm is as small as stepm. */
4787:
4788: /* For example we decided to compute the life expectancy with the smallest unit */
4789: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4790: nhstepm is the number of hstepm from age to agelim
4791: nstepm is the number of stepm from age to agelin.
4792: Look at hpijx to understand the reason of that which relies in memory size
4793: and note for a fixed period like estepm months */
4794: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4795: survival function given by stepm (the optimization length). Unfortunately it
4796: means that if the survival funtion is printed only each two years of age and if
4797: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4798: results. So we changed our mind and took the option of the best precision.
4799: */
4800: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4801:
4802: agelim=AGESUP;
4803: /* If stepm=6 months */
4804: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4805: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4806:
4807: /* nhstepm age range expressed in number of stepm */
4808: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4809: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4810: /* if (stepm >= YEARM) hstepm=1;*/
4811: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4812: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4813:
4814: for (age=bage; age<=fage; age ++){
4815: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4816: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4817: /* if (stepm >= YEARM) hstepm=1;*/
4818: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4819:
4820: /* If stepm=6 months */
4821: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4822: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4823:
4824: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4825:
4826: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4827:
4828: printf("%d|",(int)age);fflush(stdout);
4829: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4830:
4831: /* Computing expectancies */
4832: for(i=1; i<=nlstate;i++)
4833: for(j=1; j<=nlstate;j++)
4834: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4835: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4836:
4837: /* 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]);*/
4838:
4839: }
4840:
4841: fprintf(ficreseij,"%3.0f",age );
4842: for(i=1; i<=nlstate;i++){
4843: eip=0;
4844: for(j=1; j<=nlstate;j++){
4845: eip +=eij[i][j][(int)age];
4846: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4847: }
4848: fprintf(ficreseij,"%9.4f", eip );
4849: }
4850: fprintf(ficreseij,"\n");
4851:
4852: }
4853: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4854: printf("\n");
4855: fprintf(ficlog,"\n");
4856:
4857: }
4858:
1.127 brouard 4859: 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 4860:
4861: {
4862: /* Covariances of health expectancies eij and of total life expectancies according
1.222 brouard 4863: to initial status i, ei. .
1.126 brouard 4864: */
4865: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4866: int nhstepma, nstepma; /* Decreasing with age */
4867: double age, agelim, hf;
4868: double ***p3matp, ***p3matm, ***varhe;
4869: double **dnewm,**doldm;
4870: double *xp, *xm;
4871: double **gp, **gm;
4872: double ***gradg, ***trgradg;
4873: int theta;
4874:
4875: double eip, vip;
4876:
4877: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4878: xp=vector(1,npar);
4879: xm=vector(1,npar);
4880: dnewm=matrix(1,nlstate*nlstate,1,npar);
4881: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4882:
4883: pstamp(ficresstdeij);
4884: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4885: fprintf(ficresstdeij,"# Age");
4886: for(i=1; i<=nlstate;i++){
4887: for(j=1; j<=nlstate;j++)
4888: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4889: fprintf(ficresstdeij," e%1d. ",i);
4890: }
4891: fprintf(ficresstdeij,"\n");
4892:
4893: pstamp(ficrescveij);
4894: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4895: fprintf(ficrescveij,"# Age");
4896: for(i=1; i<=nlstate;i++)
4897: for(j=1; j<=nlstate;j++){
4898: cptj= (j-1)*nlstate+i;
4899: for(i2=1; i2<=nlstate;i2++)
4900: for(j2=1; j2<=nlstate;j2++){
4901: cptj2= (j2-1)*nlstate+i2;
4902: if(cptj2 <= cptj)
4903: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4904: }
4905: }
4906: fprintf(ficrescveij,"\n");
4907:
4908: if(estepm < stepm){
4909: printf ("Problem %d lower than %d\n",estepm, stepm);
4910: }
4911: else hstepm=estepm;
4912: /* We compute the life expectancy from trapezoids spaced every estepm months
4913: * This is mainly to measure the difference between two models: for example
4914: * if stepm=24 months pijx are given only every 2 years and by summing them
4915: * we are calculating an estimate of the Life Expectancy assuming a linear
4916: * progression in between and thus overestimating or underestimating according
4917: * to the curvature of the survival function. If, for the same date, we
4918: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4919: * to compare the new estimate of Life expectancy with the same linear
4920: * hypothesis. A more precise result, taking into account a more precise
4921: * curvature will be obtained if estepm is as small as stepm. */
4922:
4923: /* For example we decided to compute the life expectancy with the smallest unit */
4924: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4925: nhstepm is the number of hstepm from age to agelim
4926: nstepm is the number of stepm from age to agelin.
4927: Look at hpijx to understand the reason of that which relies in memory size
4928: and note for a fixed period like estepm months */
4929: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4930: survival function given by stepm (the optimization length). Unfortunately it
4931: means that if the survival funtion is printed only each two years of age and if
4932: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4933: results. So we changed our mind and took the option of the best precision.
4934: */
4935: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4936:
4937: /* If stepm=6 months */
4938: /* nhstepm age range expressed in number of stepm */
4939: agelim=AGESUP;
4940: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4941: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4942: /* if (stepm >= YEARM) hstepm=1;*/
4943: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4944:
4945: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4946: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4947: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4948: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4949: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4950: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4951:
4952: for (age=bage; age<=fage; age ++){
4953: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4954: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4955: /* if (stepm >= YEARM) hstepm=1;*/
4956: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4957:
1.126 brouard 4958: /* If stepm=6 months */
4959: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4960: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4961:
4962: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4963:
1.126 brouard 4964: /* Computing Variances of health expectancies */
4965: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4966: decrease memory allocation */
4967: for(theta=1; theta <=npar; theta++){
4968: for(i=1; i<=npar; i++){
1.222 brouard 4969: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4970: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4971: }
4972: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4973: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4974:
1.126 brouard 4975: for(j=1; j<= nlstate; j++){
1.222 brouard 4976: for(i=1; i<=nlstate; i++){
4977: for(h=0; h<=nhstepm-1; h++){
4978: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4979: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4980: }
4981: }
1.126 brouard 4982: }
1.218 brouard 4983:
1.126 brouard 4984: for(ij=1; ij<= nlstate*nlstate; ij++)
1.222 brouard 4985: for(h=0; h<=nhstepm-1; h++){
4986: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4987: }
1.126 brouard 4988: }/* End theta */
4989:
4990:
4991: for(h=0; h<=nhstepm-1; h++)
4992: for(j=1; j<=nlstate*nlstate;j++)
1.222 brouard 4993: for(theta=1; theta <=npar; theta++)
4994: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4995:
1.218 brouard 4996:
1.222 brouard 4997: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4998: for(ji=1;ji<=nlstate*nlstate;ji++)
1.222 brouard 4999: varhe[ij][ji][(int)age] =0.;
1.218 brouard 5000:
1.222 brouard 5001: printf("%d|",(int)age);fflush(stdout);
5002: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
5003: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 5004: for(k=0;k<=nhstepm-1;k++){
1.222 brouard 5005: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
5006: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
5007: for(ij=1;ij<=nlstate*nlstate;ij++)
5008: for(ji=1;ji<=nlstate*nlstate;ji++)
5009: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 5010: }
5011: }
1.218 brouard 5012:
1.126 brouard 5013: /* Computing expectancies */
5014: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
5015: for(i=1; i<=nlstate;i++)
5016: for(j=1; j<=nlstate;j++)
1.222 brouard 5017: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
5018: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
1.218 brouard 5019:
1.222 brouard 5020: /* 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 5021:
1.222 brouard 5022: }
1.218 brouard 5023:
1.126 brouard 5024: fprintf(ficresstdeij,"%3.0f",age );
5025: for(i=1; i<=nlstate;i++){
5026: eip=0.;
5027: vip=0.;
5028: for(j=1; j<=nlstate;j++){
1.222 brouard 5029: eip += eij[i][j][(int)age];
5030: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
5031: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
5032: 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 5033: }
5034: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
5035: }
5036: fprintf(ficresstdeij,"\n");
1.218 brouard 5037:
1.126 brouard 5038: fprintf(ficrescveij,"%3.0f",age );
5039: for(i=1; i<=nlstate;i++)
5040: for(j=1; j<=nlstate;j++){
1.222 brouard 5041: cptj= (j-1)*nlstate+i;
5042: for(i2=1; i2<=nlstate;i2++)
5043: for(j2=1; j2<=nlstate;j2++){
5044: cptj2= (j2-1)*nlstate+i2;
5045: if(cptj2 <= cptj)
5046: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
5047: }
1.126 brouard 5048: }
5049: fprintf(ficrescveij,"\n");
1.218 brouard 5050:
1.126 brouard 5051: }
5052: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
5053: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
5054: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
5055: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
5056: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5057: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5058: printf("\n");
5059: fprintf(ficlog,"\n");
1.218 brouard 5060:
1.126 brouard 5061: free_vector(xm,1,npar);
5062: free_vector(xp,1,npar);
5063: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
5064: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
5065: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
5066: }
1.218 brouard 5067:
1.126 brouard 5068: /************ Variance ******************/
1.209 brouard 5069: 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 5070: {
5071: /* Variance of health expectancies */
5072: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
5073: /* double **newm;*/
5074: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
5075:
5076: /* int movingaverage(); */
5077: double **dnewm,**doldm;
5078: double **dnewmp,**doldmp;
5079: int i, j, nhstepm, hstepm, h, nstepm ;
5080: int k;
5081: double *xp;
5082: double **gp, **gm; /* for var eij */
5083: double ***gradg, ***trgradg; /*for var eij */
5084: double **gradgp, **trgradgp; /* for var p point j */
5085: double *gpp, *gmp; /* for var p point j */
5086: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
5087: double ***p3mat;
5088: double age,agelim, hf;
5089: /* double ***mobaverage; */
5090: int theta;
5091: char digit[4];
5092: char digitp[25];
5093:
5094: char fileresprobmorprev[FILENAMELENGTH];
5095:
5096: if(popbased==1){
5097: if(mobilav!=0)
5098: strcpy(digitp,"-POPULBASED-MOBILAV_");
5099: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
5100: }
5101: else
5102: strcpy(digitp,"-STABLBASED_");
1.126 brouard 5103:
1.218 brouard 5104: /* if (mobilav!=0) { */
5105: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5106: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
5107: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
5108: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
5109: /* } */
5110: /* } */
5111:
5112: strcpy(fileresprobmorprev,"PRMORPREV-");
5113: sprintf(digit,"%-d",ij);
5114: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
5115: strcat(fileresprobmorprev,digit); /* Tvar to be done */
5116: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
5117: strcat(fileresprobmorprev,fileresu);
5118: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
5119: printf("Problem with resultfile: %s\n", fileresprobmorprev);
5120: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
5121: }
5122: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5123: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
5124: pstamp(ficresprobmorprev);
5125: 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);
5126: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
5127: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5128: fprintf(ficresprobmorprev," p.%-d SE",j);
5129: for(i=1; i<=nlstate;i++)
5130: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
5131: }
5132: fprintf(ficresprobmorprev,"\n");
5133:
5134: fprintf(ficgp,"\n# Routine varevsij");
5135: fprintf(ficgp,"\nunset title \n");
5136: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
5137: 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");
5138: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
5139: /* } */
5140: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5141: pstamp(ficresvij);
5142: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
5143: if(popbased==1)
5144: 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);
5145: else
5146: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
5147: fprintf(ficresvij,"# Age");
5148: for(i=1; i<=nlstate;i++)
5149: for(j=1; j<=nlstate;j++)
5150: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
5151: fprintf(ficresvij,"\n");
5152:
5153: xp=vector(1,npar);
5154: dnewm=matrix(1,nlstate,1,npar);
5155: doldm=matrix(1,nlstate,1,nlstate);
5156: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
5157: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5158:
5159: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
5160: gpp=vector(nlstate+1,nlstate+ndeath);
5161: gmp=vector(nlstate+1,nlstate+ndeath);
5162: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 5163:
1.218 brouard 5164: if(estepm < stepm){
5165: printf ("Problem %d lower than %d\n",estepm, stepm);
5166: }
5167: else hstepm=estepm;
5168: /* For example we decided to compute the life expectancy with the smallest unit */
5169: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
5170: nhstepm is the number of hstepm from age to agelim
5171: nstepm is the number of stepm from age to agelim.
5172: Look at function hpijx to understand why because of memory size limitations,
5173: we decided (b) to get a life expectancy respecting the most precise curvature of the
5174: survival function given by stepm (the optimization length). Unfortunately it
5175: means that if the survival funtion is printed every two years of age and if
5176: you sum them up and add 1 year (area under the trapezoids) you won't get the same
5177: results. So we changed our mind and took the option of the best precision.
5178: */
5179: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
5180: agelim = AGESUP;
5181: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5182: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5183: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
5184: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5185: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
5186: gp=matrix(0,nhstepm,1,nlstate);
5187: gm=matrix(0,nhstepm,1,nlstate);
5188:
5189:
5190: for(theta=1; theta <=npar; theta++){
5191: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
5192: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5193: }
5194:
5195: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5196:
5197: if (popbased==1) {
5198: if(mobilav ==0){
5199: for(i=1; i<=nlstate;i++)
5200: prlim[i][i]=probs[(int)age][i][ij];
5201: }else{ /* mobilav */
5202: for(i=1; i<=nlstate;i++)
5203: prlim[i][i]=mobaverage[(int)age][i][ij];
5204: }
5205: }
5206:
5207: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
5208: for(j=1; j<= nlstate; j++){
5209: for(h=0; h<=nhstepm; h++){
5210: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
5211: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
5212: }
5213: }
5214: /* Next for computing probability of death (h=1 means
5215: computed over hstepm matrices product = hstepm*stepm months)
5216: as a weighted average of prlim.
5217: */
5218: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5219: for(i=1,gpp[j]=0.; i<= nlstate; i++)
5220: gpp[j] += prlim[i][i]*p3mat[i][j][1];
5221: }
5222: /* end probability of death */
5223:
5224: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
5225: xp[i] = x[i] - (i==theta ?delti[theta]:0);
5226:
5227: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
5228:
5229: if (popbased==1) {
5230: if(mobilav ==0){
5231: for(i=1; i<=nlstate;i++)
5232: prlim[i][i]=probs[(int)age][i][ij];
5233: }else{ /* mobilav */
5234: for(i=1; i<=nlstate;i++)
5235: prlim[i][i]=mobaverage[(int)age][i][ij];
5236: }
5237: }
5238:
5239: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
5240:
5241: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
5242: for(h=0; h<=nhstepm; h++){
5243: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
5244: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
5245: }
5246: }
5247: /* This for computing probability of death (h=1 means
5248: computed over hstepm matrices product = hstepm*stepm months)
5249: as a weighted average of prlim.
5250: */
5251: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5252: for(i=1,gmp[j]=0.; i<= nlstate; i++)
5253: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5254: }
5255: /* end probability of death */
5256:
5257: for(j=1; j<= nlstate; j++) /* vareij */
5258: for(h=0; h<=nhstepm; h++){
5259: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
5260: }
5261:
5262: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
5263: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
5264: }
5265:
5266: } /* End theta */
5267:
5268: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
5269:
5270: for(h=0; h<=nhstepm; h++) /* veij */
5271: for(j=1; j<=nlstate;j++)
5272: for(theta=1; theta <=npar; theta++)
5273: trgradg[h][j][theta]=gradg[h][theta][j];
5274:
5275: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
5276: for(theta=1; theta <=npar; theta++)
5277: trgradgp[j][theta]=gradgp[theta][j];
5278:
5279:
5280: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
5281: for(i=1;i<=nlstate;i++)
5282: for(j=1;j<=nlstate;j++)
5283: vareij[i][j][(int)age] =0.;
5284:
5285: for(h=0;h<=nhstepm;h++){
5286: for(k=0;k<=nhstepm;k++){
5287: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
5288: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
5289: for(i=1;i<=nlstate;i++)
5290: for(j=1;j<=nlstate;j++)
5291: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
5292: }
5293: }
5294:
5295: /* pptj */
5296: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
5297: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
5298: for(j=nlstate+1;j<=nlstate+ndeath;j++)
5299: for(i=nlstate+1;i<=nlstate+ndeath;i++)
5300: varppt[j][i]=doldmp[j][i];
5301: /* end ppptj */
5302: /* x centered again */
5303:
5304: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
5305:
5306: if (popbased==1) {
5307: if(mobilav ==0){
5308: for(i=1; i<=nlstate;i++)
5309: prlim[i][i]=probs[(int)age][i][ij];
5310: }else{ /* mobilav */
5311: for(i=1; i<=nlstate;i++)
5312: prlim[i][i]=mobaverage[(int)age][i][ij];
5313: }
5314: }
5315:
5316: /* This for computing probability of death (h=1 means
5317: computed over hstepm (estepm) matrices product = hstepm*stepm months)
5318: as a weighted average of prlim.
5319: */
5320: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
5321: for(j=nlstate+1;j<=nlstate+ndeath;j++){
5322: for(i=1,gmp[j]=0.;i<= nlstate; i++)
5323: gmp[j] += prlim[i][i]*p3mat[i][j][1];
5324: }
5325: /* end probability of death */
5326:
5327: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
5328: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
5329: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
5330: for(i=1; i<=nlstate;i++){
5331: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
5332: }
5333: }
5334: fprintf(ficresprobmorprev,"\n");
5335:
5336: fprintf(ficresvij,"%.0f ",age );
5337: for(i=1; i<=nlstate;i++)
5338: for(j=1; j<=nlstate;j++){
5339: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
5340: }
5341: fprintf(ficresvij,"\n");
5342: free_matrix(gp,0,nhstepm,1,nlstate);
5343: free_matrix(gm,0,nhstepm,1,nlstate);
5344: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5345: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5346: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5347: } /* End age */
5348: free_vector(gpp,nlstate+1,nlstate+ndeath);
5349: free_vector(gmp,nlstate+1,nlstate+ndeath);
5350: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5351: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5352: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5353: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5354: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5355: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5356: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5357: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5358: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5359: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5360: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5361: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5362: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5363: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5364: 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);
5365: /* 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 5366: */
1.218 brouard 5367: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5368: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5369:
1.218 brouard 5370: free_vector(xp,1,npar);
5371: free_matrix(doldm,1,nlstate,1,nlstate);
5372: free_matrix(dnewm,1,nlstate,1,npar);
5373: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5374: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5375: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5376: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5377: fclose(ficresprobmorprev);
5378: fflush(ficgp);
5379: fflush(fichtm);
5380: } /* end varevsij */
1.126 brouard 5381:
5382: /************ Variance of prevlim ******************/
1.209 brouard 5383: 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 5384: {
1.205 brouard 5385: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5386: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5387:
1.126 brouard 5388: double **dnewm,**doldm;
5389: int i, j, nhstepm, hstepm;
5390: double *xp;
5391: double *gp, *gm;
5392: double **gradg, **trgradg;
1.208 brouard 5393: double **mgm, **mgp;
1.126 brouard 5394: double age,agelim;
5395: int theta;
5396:
5397: pstamp(ficresvpl);
5398: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5399: fprintf(ficresvpl,"# Age");
5400: for(i=1; i<=nlstate;i++)
5401: fprintf(ficresvpl," %1d-%1d",i,i);
5402: fprintf(ficresvpl,"\n");
5403:
5404: xp=vector(1,npar);
5405: dnewm=matrix(1,nlstate,1,npar);
5406: doldm=matrix(1,nlstate,1,nlstate);
5407:
5408: hstepm=1*YEARM; /* Every year of age */
5409: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5410: agelim = AGESUP;
5411: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5412: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5413: if (stepm >= YEARM) hstepm=1;
5414: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5415: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5416: mgp=matrix(1,npar,1,nlstate);
5417: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5418: gp=vector(1,nlstate);
5419: gm=vector(1,nlstate);
5420:
5421: for(theta=1; theta <=npar; theta++){
5422: for(i=1; i<=npar; i++){ /* Computes gradient */
5423: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5424: }
1.209 brouard 5425: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5426: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5427: else
5428: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5429: for(i=1;i<=nlstate;i++){
1.126 brouard 5430: gp[i] = prlim[i][i];
1.208 brouard 5431: mgp[theta][i] = prlim[i][i];
5432: }
1.126 brouard 5433: for(i=1; i<=npar; i++) /* Computes gradient */
5434: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5435: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5436: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5437: else
5438: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5439: for(i=1;i<=nlstate;i++){
1.126 brouard 5440: gm[i] = prlim[i][i];
1.208 brouard 5441: mgm[theta][i] = prlim[i][i];
5442: }
1.126 brouard 5443: for(i=1;i<=nlstate;i++)
5444: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5445: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5446: } /* End theta */
5447:
5448: trgradg =matrix(1,nlstate,1,npar);
5449:
5450: for(j=1; j<=nlstate;j++)
5451: for(theta=1; theta <=npar; theta++)
5452: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5453: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5454: /* printf("\nmgm mgp %d ",(int)age); */
5455: /* for(j=1; j<=nlstate;j++){ */
5456: /* printf(" %d ",j); */
5457: /* for(theta=1; theta <=npar; theta++) */
5458: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5459: /* printf("\n "); */
5460: /* } */
5461: /* } */
5462: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5463: /* printf("\n gradg %d ",(int)age); */
5464: /* for(j=1; j<=nlstate;j++){ */
5465: /* printf("%d ",j); */
5466: /* for(theta=1; theta <=npar; theta++) */
5467: /* printf("%d %lf ",theta,gradg[theta][j]); */
5468: /* printf("\n "); */
5469: /* } */
5470: /* } */
1.126 brouard 5471:
5472: for(i=1;i<=nlstate;i++)
5473: varpl[i][(int)age] =0.;
1.209 brouard 5474: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5475: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5476: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5477: }else{
1.126 brouard 5478: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5479: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5480: }
1.126 brouard 5481: for(i=1;i<=nlstate;i++)
5482: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5483:
5484: fprintf(ficresvpl,"%.0f ",age );
5485: for(i=1; i<=nlstate;i++)
5486: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5487: fprintf(ficresvpl,"\n");
5488: free_vector(gp,1,nlstate);
5489: free_vector(gm,1,nlstate);
1.208 brouard 5490: free_matrix(mgm,1,npar,1,nlstate);
5491: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5492: free_matrix(gradg,1,npar,1,nlstate);
5493: free_matrix(trgradg,1,nlstate,1,npar);
5494: } /* End age */
5495:
5496: free_vector(xp,1,npar);
5497: free_matrix(doldm,1,nlstate,1,npar);
5498: free_matrix(dnewm,1,nlstate,1,nlstate);
5499:
5500: }
5501:
5502: /************ Variance of one-step probabilities ******************/
5503: 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 5504: {
5505: int i, j=0, k1, l1, tj;
5506: int k2, l2, j1, z1;
5507: int k=0, l;
5508: int first=1, first1, first2;
5509: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5510: double **dnewm,**doldm;
5511: double *xp;
5512: double *gp, *gm;
5513: double **gradg, **trgradg;
5514: double **mu;
5515: double age, cov[NCOVMAX+1];
5516: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5517: int theta;
5518: char fileresprob[FILENAMELENGTH];
5519: char fileresprobcov[FILENAMELENGTH];
5520: char fileresprobcor[FILENAMELENGTH];
5521: double ***varpij;
5522:
5523: strcpy(fileresprob,"PROB_");
5524: strcat(fileresprob,fileres);
5525: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5526: printf("Problem with resultfile: %s\n", fileresprob);
5527: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5528: }
5529: strcpy(fileresprobcov,"PROBCOV_");
5530: strcat(fileresprobcov,fileresu);
5531: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5532: printf("Problem with resultfile: %s\n", fileresprobcov);
5533: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5534: }
5535: strcpy(fileresprobcor,"PROBCOR_");
5536: strcat(fileresprobcor,fileresu);
5537: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5538: printf("Problem with resultfile: %s\n", fileresprobcor);
5539: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5540: }
5541: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5542: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5543: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5544: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5545: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5546: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5547: pstamp(ficresprob);
5548: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5549: fprintf(ficresprob,"# Age");
5550: pstamp(ficresprobcov);
5551: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5552: fprintf(ficresprobcov,"# Age");
5553: pstamp(ficresprobcor);
5554: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5555: fprintf(ficresprobcor,"# Age");
1.126 brouard 5556:
5557:
1.222 brouard 5558: for(i=1; i<=nlstate;i++)
5559: for(j=1; j<=(nlstate+ndeath);j++){
5560: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5561: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5562: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5563: }
5564: /* fprintf(ficresprob,"\n");
5565: fprintf(ficresprobcov,"\n");
5566: fprintf(ficresprobcor,"\n");
5567: */
5568: xp=vector(1,npar);
5569: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5570: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5571: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5572: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5573: first=1;
5574: fprintf(ficgp,"\n# Routine varprob");
5575: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5576: fprintf(fichtm,"\n");
5577:
5578: 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);
5579: 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);
5580: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5581: and drawn. It helps understanding how is the covariance between two incidences.\
5582: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
1.222 brouard 5583: 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 5584: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5585: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5586: standard deviations wide on each axis. <br>\
5587: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5588: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5589: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5590:
1.222 brouard 5591: cov[1]=1;
5592: /* tj=cptcoveff; */
1.225 brouard 5593: tj = (int) pow(2,cptcoveff);
1.222 brouard 5594: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5595: j1=0;
1.224 brouard 5596: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
1.222 brouard 5597: if (cptcovn>0) {
5598: fprintf(ficresprob, "\n#********** Variable ");
1.225 brouard 5599: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5600: fprintf(ficresprob, "**********\n#\n");
5601: fprintf(ficresprobcov, "\n#********** Variable ");
1.225 brouard 5602: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5603: fprintf(ficresprobcov, "**********\n#\n");
1.220 brouard 5604:
1.222 brouard 5605: fprintf(ficgp, "\n#********** Variable ");
1.225 brouard 5606: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5607: fprintf(ficgp, "**********\n#\n");
1.220 brouard 5608:
5609:
1.222 brouard 5610: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.225 brouard 5611: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5612: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5613:
1.222 brouard 5614: fprintf(ficresprobcor, "\n#********** Variable ");
1.225 brouard 5615: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.222 brouard 5616: fprintf(ficresprobcor, "**********\n#");
5617: if(invalidvarcomb[j1]){
5618: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5619: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5620: continue;
5621: }
5622: }
5623: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5624: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5625: gp=vector(1,(nlstate)*(nlstate+ndeath));
5626: gm=vector(1,(nlstate)*(nlstate+ndeath));
5627: for (age=bage; age<=fage; age ++){
5628: cov[2]=age;
5629: if(nagesqr==1)
5630: cov[3]= age*age;
5631: for (k=1; k<=cptcovn;k++) {
5632: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5633: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5634: * 1 1 1 1 1
5635: * 2 2 1 1 1
5636: * 3 1 2 1 1
5637: */
5638: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5639: }
5640: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5641: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5642: for (k=1; k<=cptcovprod;k++)
5643: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.220 brouard 5644:
5645:
1.222 brouard 5646: for(theta=1; theta <=npar; theta++){
5647: for(i=1; i<=npar; i++)
5648: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
1.220 brouard 5649:
1.222 brouard 5650: pmij(pmmij,cov,ncovmodel,xp,nlstate);
1.220 brouard 5651:
1.222 brouard 5652: k=0;
5653: for(i=1; i<= (nlstate); i++){
5654: for(j=1; j<=(nlstate+ndeath);j++){
5655: k=k+1;
5656: gp[k]=pmmij[i][j];
5657: }
5658: }
1.220 brouard 5659:
1.222 brouard 5660: for(i=1; i<=npar; i++)
5661: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
1.220 brouard 5662:
1.222 brouard 5663: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5664: k=0;
5665: for(i=1; i<=(nlstate); i++){
5666: for(j=1; j<=(nlstate+ndeath);j++){
5667: k=k+1;
5668: gm[k]=pmmij[i][j];
5669: }
5670: }
1.220 brouard 5671:
1.222 brouard 5672: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5673: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5674: }
1.126 brouard 5675:
1.222 brouard 5676: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5677: for(theta=1; theta <=npar; theta++)
5678: trgradg[j][theta]=gradg[theta][j];
1.220 brouard 5679:
1.222 brouard 5680: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5681: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
1.220 brouard 5682:
1.222 brouard 5683: pmij(pmmij,cov,ncovmodel,x,nlstate);
1.220 brouard 5684:
1.222 brouard 5685: k=0;
5686: for(i=1; i<=(nlstate); i++){
5687: for(j=1; j<=(nlstate+ndeath);j++){
5688: k=k+1;
5689: mu[k][(int) age]=pmmij[i][j];
5690: }
5691: }
5692: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
5693: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5694: varpij[i][j][(int)age] = doldm[i][j];
1.220 brouard 5695:
1.222 brouard 5696: /*printf("\n%d ",(int)age);
5697: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5698: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5699: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5700: }*/
1.220 brouard 5701:
1.222 brouard 5702: fprintf(ficresprob,"\n%d ",(int)age);
5703: fprintf(ficresprobcov,"\n%d ",(int)age);
5704: fprintf(ficresprobcor,"\n%d ",(int)age);
1.220 brouard 5705:
1.222 brouard 5706: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5707: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5708: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5709: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5710: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5711: }
5712: i=0;
5713: for (k=1; k<=(nlstate);k++){
5714: for (l=1; l<=(nlstate+ndeath);l++){
5715: i++;
5716: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5717: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5718: for (j=1; j<=i;j++){
5719: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5720: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5721: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5722: }
5723: }
5724: }/* end of loop for state */
5725: } /* end of loop for age */
5726: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5727: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5728: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5729: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5730:
5731: /* Confidence intervalle of pij */
5732: /*
5733: fprintf(ficgp,"\nunset parametric;unset label");
5734: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5735: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5736: 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);
5737: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5738: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5739: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5740: */
5741:
5742: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5743: first1=1;first2=2;
5744: for (k2=1; k2<=(nlstate);k2++){
5745: for (l2=1; l2<=(nlstate+ndeath);l2++){
5746: if(l2==k2) continue;
5747: j=(k2-1)*(nlstate+ndeath)+l2;
5748: for (k1=1; k1<=(nlstate);k1++){
5749: for (l1=1; l1<=(nlstate+ndeath);l1++){
5750: if(l1==k1) continue;
5751: i=(k1-1)*(nlstate+ndeath)+l1;
5752: if(i<=j) continue;
5753: for (age=bage; age<=fage; age ++){
5754: if ((int)age %5==0){
5755: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5756: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5757: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5758: mu1=mu[i][(int) age]/stepm*YEARM ;
5759: mu2=mu[j][(int) age]/stepm*YEARM;
5760: c12=cv12/sqrt(v1*v2);
5761: /* Computing eigen value of matrix of covariance */
5762: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5763: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5764: if ((lc2 <0) || (lc1 <0) ){
5765: if(first2==1){
5766: first1=0;
5767: 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);
5768: }
5769: 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);
5770: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5771: /* lc2=fabs(lc2); */
5772: }
1.220 brouard 5773:
1.222 brouard 5774: /* Eigen vectors */
5775: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5776: /*v21=sqrt(1.-v11*v11); *//* error */
5777: v21=(lc1-v1)/cv12*v11;
5778: v12=-v21;
5779: v22=v11;
5780: tnalp=v21/v11;
5781: if(first1==1){
5782: first1=0;
5783: 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);
5784: }
5785: 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);
5786: /*printf(fignu*/
5787: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5788: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5789: if(first==1){
5790: first=0;
5791: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5792: fprintf(ficgp,"\nset parametric;unset label");
5793: 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);
5794: fprintf(ficgp,"\nset ter svg size 640, 480");
5795: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.220 brouard 5796: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5797: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.222 brouard 5798: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5799: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5800: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5801: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5802: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5803: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5804: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5805: 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", \
5806: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5807: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5808: }else{
5809: first=0;
5810: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5811: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5812: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5813: 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", \
5814: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5815: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5816: }/* if first */
5817: } /* age mod 5 */
5818: } /* end loop age */
5819: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5820: first=1;
5821: } /*l12 */
5822: } /* k12 */
5823: } /*l1 */
5824: }/* k1 */
5825: } /* loop on combination of covariates j1 */
5826: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5827: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5828: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5829: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5830: free_vector(xp,1,npar);
5831: fclose(ficresprob);
5832: fclose(ficresprobcov);
5833: fclose(ficresprobcor);
5834: fflush(ficgp);
5835: fflush(fichtmcov);
5836: }
1.126 brouard 5837:
5838:
5839: /******************* Printing html file ***********/
1.201 brouard 5840: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5841: int lastpass, int stepm, int weightopt, char model[],\
5842: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5843: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5844: double jprev1, double mprev1,double anprev1, double dateprev1, \
5845: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5846: int jj1, k1, i1, cpt;
5847:
5848: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5849: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5850: </ul>");
1.214 brouard 5851: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5852: 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",
5853: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5854: 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 5855: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5856: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5857: fprintf(fichtm,"\
5858: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5859: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5860: fprintf(fichtm,"\
1.217 brouard 5861: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5862: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5863: fprintf(fichtm,"\
1.126 brouard 5864: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5865: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5866: fprintf(fichtm,"\
1.217 brouard 5867: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5868: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5869: fprintf(fichtm,"\
1.211 brouard 5870: - (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 5871: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5872: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5873: if(prevfcast==1){
5874: fprintf(fichtm,"\
5875: - Prevalence projections by age and states: \
1.201 brouard 5876: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5877: }
1.126 brouard 5878:
1.222 brouard 5879: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
1.126 brouard 5880:
1.225 brouard 5881: m=pow(2,cptcoveff);
1.222 brouard 5882: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 5883:
1.222 brouard 5884: jj1=0;
5885: for(k1=1; k1<=m;k1++){
1.220 brouard 5886:
1.222 brouard 5887: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5888: jj1++;
5889: if (cptcovn > 0) {
5890: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 5891: for (cpt=1; cpt<=cptcoveff;cpt++){
1.222 brouard 5892: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5893: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5894: }
5895: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5896: if(invalidvarcomb[k1]){
5897: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5898: printf("\nCombination (%d) ignored because no cases \n",k1);
5899: continue;
5900: }
5901: }
5902: /* aij, bij */
5903: 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 5904: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5905: /* Pij */
5906: 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 5907: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5908: /* Quasi-incidences */
5909: 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 5910: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5911: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5912: 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 5913: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.222 brouard 5914: /* Survival functions (period) in state j */
5915: for(cpt=1; cpt<=nlstate;cpt++){
5916: 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 5917: <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 5918: }
5919: /* State specific survival functions (period) */
5920: for(cpt=1; cpt<=nlstate;cpt++){
5921: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.220 brouard 5922: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5923: <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 5924: }
5925: /* Period (stable) prevalence in each health state */
5926: for(cpt=1; cpt<=nlstate;cpt++){
5927: 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 5928: <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 5929: }
5930: if(backcast==1){
5931: /* Period (stable) back prevalence in each health state */
5932: for(cpt=1; cpt<=nlstate;cpt++){
5933: 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 5934: <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 5935: }
1.217 brouard 5936: }
1.222 brouard 5937: if(prevfcast==1){
5938: /* Projection of prevalence up to period (stable) prevalence in each health state */
5939: for(cpt=1; cpt<=nlstate;cpt++){
5940: 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 5941: <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 5942: }
5943: }
1.220 brouard 5944:
1.222 brouard 5945: for(cpt=1; cpt<=nlstate;cpt++) {
5946: 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 5947: <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 5948: }
5949: /* } /\* end i1 *\/ */
5950: }/* End k1 */
5951: fprintf(fichtm,"</ul>");
1.126 brouard 5952:
1.222 brouard 5953: fprintf(fichtm,"\
1.126 brouard 5954: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5955: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5956: - 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 5957: But because parameters are usually highly correlated (a higher incidence of disability \
5958: and a higher incidence of recovery can give very close observed transition) it might \
5959: be very useful to look not only at linear confidence intervals estimated from the \
5960: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5961: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5962: covariance matrix of the one-step probabilities. \
5963: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5964:
1.222 brouard 5965: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
5966: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
5967: fprintf(fichtm,"\
1.126 brouard 5968: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5969: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5970:
1.222 brouard 5971: fprintf(fichtm,"\
1.126 brouard 5972: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.222 brouard 5973: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
5974: fprintf(fichtm,"\
1.126 brouard 5975: - 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): \
5976: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5977: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.222 brouard 5978: fprintf(fichtm,"\
1.126 brouard 5979: - (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): \
5980: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5981: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.222 brouard 5982: fprintf(fichtm,"\
1.128 brouard 5983: - 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 5984: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
5985: fprintf(fichtm,"\
1.128 brouard 5986: - 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 5987: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
5988: fprintf(fichtm,"\
1.126 brouard 5989: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.222 brouard 5990: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5991:
5992: /* if(popforecast==1) fprintf(fichtm,"\n */
5993: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5994: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5995: /* <br>",fileres,fileres,fileres,fileres); */
5996: /* else */
5997: /* 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 5998: fflush(fichtm);
5999: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
1.126 brouard 6000:
1.225 brouard 6001: m=pow(2,cptcoveff);
1.222 brouard 6002: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
1.126 brouard 6003:
1.222 brouard 6004: jj1=0;
6005: for(k1=1; k1<=m;k1++){
6006: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
6007: jj1++;
1.126 brouard 6008: if (cptcovn > 0) {
6009: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.225 brouard 6010: for (cpt=1; cpt<=cptcoveff;cpt++) /**< cptcoveff number of variables */
1.222 brouard 6011: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 6012: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 6013:
1.222 brouard 6014: if(invalidvarcomb[k1]){
6015: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
6016: continue;
6017: }
1.126 brouard 6018: }
6019: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 6020: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
6021: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 6022: <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 6023: }
6024: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 6025: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
6026: true period expectancies (those weighted with period prevalences are also\
6027: drawn in addition to the population based expectancies computed using\
1.218 brouard 6028: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 6029: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.222 brouard 6030: /* } /\* end i1 *\/ */
6031: }/* End k1 */
6032: fprintf(fichtm,"</ul>");
6033: fflush(fichtm);
1.126 brouard 6034: }
6035:
6036: /******************* Gnuplot file **************/
1.223 brouard 6037: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 6038:
6039: char dirfileres[132],optfileres[132];
1.223 brouard 6040: char gplotcondition[132];
1.164 brouard 6041: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 6042: int lv=0, vlv=0, kl=0;
1.130 brouard 6043: int ng=0;
1.201 brouard 6044: int vpopbased;
1.223 brouard 6045: int ioffset; /* variable offset for columns */
1.219 brouard 6046:
1.126 brouard 6047: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
6048: /* printf("Problem with file %s",optionfilegnuplot); */
6049: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
6050: /* } */
6051:
6052: /*#ifdef windows */
6053: fprintf(ficgp,"cd \"%s\" \n",pathc);
1.223 brouard 6054: /*#endif */
1.225 brouard 6055: m=pow(2,cptcoveff);
1.126 brouard 6056:
1.202 brouard 6057: /* Contribution to likelihood */
6058: /* Plot the probability implied in the likelihood */
1.223 brouard 6059: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
6060: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
6061: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
6062: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 6063: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 6064: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
6065: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
1.223 brouard 6066: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
6067: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
6068: 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));
6069: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
6070: 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));
6071: for (i=1; i<= nlstate ; i ++) {
6072: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
6073: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
6074: 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);
6075: for (j=2; j<= nlstate+ndeath ; j ++) {
6076: 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);
6077: }
6078: fprintf(ficgp,";\nset out; unset ylabel;\n");
6079: }
6080: /* 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 */
6081: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
6082: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
6083: fprintf(ficgp,"\nset out;unset log\n");
6084: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
1.202 brouard 6085:
1.126 brouard 6086: strcpy(dirfileres,optionfilefiname);
6087: strcpy(optfileres,"vpl");
1.223 brouard 6088: /* 1eme*/
1.211 brouard 6089: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 6090: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 6091: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
6092: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.225 brouard 6093: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
6094: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
1.223 brouard 6095: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6096: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6097: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6098: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
6099: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
6100: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6101: }
6102: fprintf(ficgp,"\n#\n");
1.223 brouard 6103: if(invalidvarcomb[k1]){
6104: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6105: continue;
6106: }
1.211 brouard 6107:
1.223 brouard 6108: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
6109: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
6110: fprintf(ficgp,"set xlabel \"Age\" \n\
1.219 brouard 6111: set ylabel \"Probability\" \n \
6112: set ter svg size 640, 480\n \
1.201 brouard 6113: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 6114:
1.223 brouard 6115: for (i=1; i<= nlstate ; i ++) {
6116: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6117: else fprintf(ficgp," %%*lf (%%*lf)");
6118: }
6119: 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);
6120: for (i=1; i<= nlstate ; i ++) {
6121: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6122: else fprintf(ficgp," %%*lf (%%*lf)");
6123: }
6124: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
6125: for (i=1; i<= nlstate ; i ++) {
6126: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
6127: else fprintf(ficgp," %%*lf (%%*lf)");
6128: }
6129: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
6130: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
6131: /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
6132: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
1.225 brouard 6133: if(cptcoveff ==0){
1.223 brouard 6134: fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );
6135: }else{
6136: kl=0;
1.225 brouard 6137: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
6138: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
1.223 brouard 6139: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6140: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6141: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6142: vlv= nbcode[Tvaraff[k]][lv];
6143: kl++;
6144: /* 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 *\/ */
6145: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6146: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6147: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
1.225 brouard 6148: if(k==cptcoveff){
1.227 brouard 6149: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
6150: 4+(cpt-1), cpt ); /* 4 or 6 ?*/
1.223 brouard 6151: }else{
6152: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
6153: kl++;
6154: }
6155: } /* end covariate */
6156: } /* end if no covariate */
6157: } /* end if backcast */
6158: fprintf(ficgp,"\nset out \n");
1.201 brouard 6159: } /* k1 */
6160: } /* cpt */
1.126 brouard 6161: /*2 eme*/
6162: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6163:
1.223 brouard 6164: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
1.225 brouard 6165: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6166: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6167: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6168: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6169: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6170: vlv= nbcode[Tvaraff[k]][lv];
6171: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6172: }
6173: fprintf(ficgp,"\n#\n");
6174: if(invalidvarcomb[k1]){
6175: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6176: continue;
6177: }
1.219 brouard 6178:
1.223 brouard 6179: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
6180: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6181: if(vpopbased==0)
6182: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
6183: else
6184: fprintf(ficgp,"\nreplot ");
6185: for (i=1; i<= nlstate+1 ; i ++) {
6186: k=2*i;
6187: 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);
6188: for (j=1; j<= nlstate+1 ; j ++) {
6189: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6190: else fprintf(ficgp," %%*lf (%%*lf)");
6191: }
6192: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
6193: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
6194: 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);
6195: for (j=1; j<= nlstate+1 ; j ++) {
6196: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6197: else fprintf(ficgp," %%*lf (%%*lf)");
6198: }
6199: fprintf(ficgp,"\" t\"\" w l lt 0,");
6200: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
6201: for (j=1; j<= nlstate+1 ; j ++) {
6202: if (j==i) fprintf(ficgp," %%lf (%%lf)");
6203: else fprintf(ficgp," %%*lf (%%*lf)");
6204: }
6205: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
6206: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
6207: } /* state */
6208: } /* vpopbased */
6209: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 6210: } /* k1 */
1.219 brouard 6211:
6212:
1.126 brouard 6213: /*3eme*/
6214: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 6215:
1.126 brouard 6216: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 6217: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
1.225 brouard 6218: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6219: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6220: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6221: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6222: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6223: vlv= nbcode[Tvaraff[k]][lv];
6224: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6225: }
6226: fprintf(ficgp,"\n#\n");
1.223 brouard 6227: if(invalidvarcomb[k1]){
6228: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6229: continue;
6230: }
1.219 brouard 6231:
1.126 brouard 6232: /* k=2+nlstate*(2*cpt-2); */
6233: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 6234: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 6235: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 6236: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 6237: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.223 brouard 6238: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6239: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
6240: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
6241: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
6242: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
1.219 brouard 6243:
1.126 brouard 6244: */
6245: for (i=1; i< nlstate ; i ++) {
1.223 brouard 6246: 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);
6247: /* 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 6248:
1.126 brouard 6249: }
1.201 brouard 6250: 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 6251: }
6252: }
6253:
1.223 brouard 6254: /* 4eme */
1.201 brouard 6255: /* Survival functions (period) from state i in state j by initial state i */
6256: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 6257:
1.201 brouard 6258: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 6259: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
1.225 brouard 6260: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6261: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
1.223 brouard 6262: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6263: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6264: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6265: vlv= nbcode[Tvaraff[k]][lv];
6266: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6267: }
6268: fprintf(ficgp,"\n#\n");
1.223 brouard 6269: if(invalidvarcomb[k1]){
6270: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6271: continue;
6272: }
1.220 brouard 6273:
1.201 brouard 6274: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
6275: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 6276: set ter svg size 640, 480\n \
6277: unset log y\n \
1.201 brouard 6278: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6279: k=3;
1.201 brouard 6280: for (i=1; i<= nlstate ; i ++){
1.223 brouard 6281: if(i==1){
6282: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6283: }else{
6284: fprintf(ficgp,", '' ");
6285: }
6286: l=(nlstate+ndeath)*(i-1)+1;
6287: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6288: for (j=2; j<= nlstate+ndeath ; j ++)
6289: fprintf(ficgp,"+$%d",k+l+j-1);
6290: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 6291: } /* nlstate */
6292: fprintf(ficgp,"\nset out\n");
6293: } /* end cpt state*/
6294: } /* end covariate */
1.220 brouard 6295:
6296: /* 5eme */
1.201 brouard 6297: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 6298: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 6299: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.223 brouard 6300:
1.201 brouard 6301: 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 6302: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6303: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6304: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6305: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6306: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6307: vlv= nbcode[Tvaraff[k]][lv];
6308: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6309: }
6310: fprintf(ficgp,"\n#\n");
1.223 brouard 6311: if(invalidvarcomb[k1]){
1.227 brouard 6312: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6313: continue;
1.223 brouard 6314: }
1.227 brouard 6315:
1.201 brouard 6316: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
6317: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.227 brouard 6318: set ter svg size 640, 480\n \
6319: unset log y\n \
1.201 brouard 6320: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6321: k=3;
1.201 brouard 6322: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6323: if(j==1)
6324: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6325: else
6326: fprintf(ficgp,", '' ");
6327: l=(nlstate+ndeath)*(cpt-1) +j;
6328: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
6329: /* for (i=2; i<= nlstate+ndeath ; i ++) */
6330: /* fprintf(ficgp,"+$%d",k+l+i-1); */
6331: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 6332: } /* nlstate */
6333: fprintf(ficgp,", '' ");
6334: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
6335: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.227 brouard 6336: l=(nlstate+ndeath)*(cpt-1) +j;
6337: if(j < nlstate)
6338: fprintf(ficgp,"$%d +",k+l);
6339: else
6340: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 6341: }
6342: fprintf(ficgp,"\nset out\n");
6343: } /* end cpt state*/
6344: } /* end covariate */
1.227 brouard 6345:
1.220 brouard 6346: /* 6eme */
1.202 brouard 6347: /* CV preval stable (period) for each covariate */
1.211 brouard 6348: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6349: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6350:
1.211 brouard 6351: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
1.225 brouard 6352: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.227 brouard 6353: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6354: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6355: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6356: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6357: vlv= nbcode[Tvaraff[k]][lv];
6358: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6359: }
6360: fprintf(ficgp,"\n#\n");
1.223 brouard 6361: if(invalidvarcomb[k1]){
1.227 brouard 6362: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6363: continue;
1.223 brouard 6364: }
1.227 brouard 6365:
1.201 brouard 6366: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6367: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.227 brouard 6368: set ter svg size 640, 480\n \
6369: unset log y\n \
1.153 brouard 6370: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6371: k=3; /* Offset */
1.153 brouard 6372: for (i=1; i<= nlstate ; i ++){
1.227 brouard 6373: if(i==1)
6374: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6375: else
6376: fprintf(ficgp,", '' ");
6377: l=(nlstate+ndeath)*(i-1)+1;
6378: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6379: for (j=2; j<= nlstate ; j ++)
6380: fprintf(ficgp,"+$%d",k+l+j-1);
6381: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6382: } /* nlstate */
1.201 brouard 6383: fprintf(ficgp,"\nset out\n");
1.153 brouard 6384: } /* end cpt state*/
6385: } /* end covariate */
1.227 brouard 6386:
6387:
1.220 brouard 6388: /* 7eme */
1.218 brouard 6389: if(backcast == 1){
1.217 brouard 6390: /* CV back preval stable (period) for each covariate */
1.218 brouard 6391: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6392: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6393: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6394: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6395: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6396: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6397: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
1.223 brouard 6398: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.227 brouard 6399: vlv= nbcode[Tvaraff[k]][lv];
6400: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6401: }
6402: fprintf(ficgp,"\n#\n");
6403: if(invalidvarcomb[k1]){
6404: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6405: continue;
6406: }
6407:
6408: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6409: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6410: set ter svg size 640, 480\n \
6411: unset log y\n \
1.218 brouard 6412: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6413: k=3; /* Offset */
6414: for (i=1; i<= nlstate ; i ++){
6415: if(i==1)
6416: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6417: else
6418: fprintf(ficgp,", '' ");
6419: /* l=(nlstate+ndeath)*(i-1)+1; */
6420: l=(nlstate+ndeath)*(cpt-1)+1;
6421: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6422: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6423: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6424: /* for (j=2; j<= nlstate ; j ++) */
6425: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6426: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6427: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6428: } /* nlstate */
6429: fprintf(ficgp,"\nset out\n");
1.218 brouard 6430: } /* end cpt state*/
6431: } /* end covariate */
6432: } /* End if backcast */
6433:
1.223 brouard 6434: /* 8eme */
1.218 brouard 6435: if(prevfcast==1){
6436: /* Projection from cross-sectional to stable (period) for each covariate */
6437:
6438: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6439: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.227 brouard 6440: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6441: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6442: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6443: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6444: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6445: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6446: vlv= nbcode[Tvaraff[k]][lv];
6447: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6448: }
6449: fprintf(ficgp,"\n#\n");
6450: if(invalidvarcomb[k1]){
6451: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6452: continue;
6453: }
6454:
6455: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6456: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6457: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6458: set ter svg size 640, 480\n \
6459: unset log y\n \
1.219 brouard 6460: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.227 brouard 6461: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6462: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6463: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6464: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6465: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6466: if(i==1){
6467: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6468: }else{
6469: fprintf(ficgp,",\\\n '' ");
6470: }
6471: if(cptcoveff ==0){ /* No covariate */
6472: ioffset=2; /* Age is in 2 */
6473: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6474: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6475: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6476: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6477: fprintf(ficgp," u %d:(", ioffset);
6478: if(i==nlstate+1)
6479: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6480: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6481: else
6482: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6483: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6484: }else{ /* more than 2 covariates */
6485: if(cptcoveff ==1){
6486: ioffset=4; /* Age is in 4 */
6487: }else{
6488: ioffset=6; /* Age is in 6 */
6489: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6490: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6491: }
6492: fprintf(ficgp," u %d:(",ioffset);
6493: kl=0;
6494: strcpy(gplotcondition,"(");
6495: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
6496: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6497: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6498: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6499: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6500: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6501: kl++;
6502: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
6503: kl++;
6504: if(k <cptcoveff && cptcoveff>1)
6505: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6506: }
6507: strcpy(gplotcondition+strlen(gplotcondition),")");
6508: /* 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 *\/ */
6509: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6510: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6511: /* '' 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*/
6512: if(i==nlstate+1){
6513: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6514: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6515: }else{
6516: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6517: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6518: }
6519: } /* end if covariate */
6520: } /* nlstate */
6521: fprintf(ficgp,"\nset out\n");
1.223 brouard 6522: } /* end cpt state*/
6523: } /* end covariate */
6524: } /* End if prevfcast */
1.227 brouard 6525:
6526:
1.223 brouard 6527: /* proba elementaires */
6528: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6529: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6530: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6531: for(k=1; k <=(nlstate+ndeath); k++){
6532: if (k != i) {
1.227 brouard 6533: fprintf(ficgp,"# current state %d\n",k);
6534: for(j=1; j <=ncovmodel; j++){
6535: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
6536: jk++;
6537: }
6538: fprintf(ficgp,"\n");
1.126 brouard 6539: }
6540: }
1.223 brouard 6541: }
1.187 brouard 6542: fprintf(ficgp,"##############\n#\n");
1.227 brouard 6543:
1.145 brouard 6544: /*goto avoid;*/
1.200 brouard 6545: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6546: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6547: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6548: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6549: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6550: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6551: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6552: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6553: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6554: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6555: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6556: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6557: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6558: fprintf(ficgp,"#\n");
1.223 brouard 6559: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
6560: fprintf(ficgp,"# ng=%d\n",ng);
1.225 brouard 6561: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.223 brouard 6562: for(jk=1; jk <=m; jk++) {
6563: fprintf(ficgp,"# jk=%d\n",jk);
6564: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6565: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6566: if (ng==1){
6567: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6568: fprintf(ficgp,"\nunset log y");
6569: }else if (ng==2){
6570: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6571: fprintf(ficgp,"\nset log y");
6572: }else if (ng==3){
6573: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
6574: fprintf(ficgp,"\nset log y");
6575: }else
6576: fprintf(ficgp,"\nunset title ");
6577: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
6578: i=1;
6579: for(k2=1; k2<=nlstate; k2++) {
6580: k3=i;
6581: for(k=1; k<=(nlstate+ndeath); k++) {
6582: if (k != k2){
6583: switch( ng) {
6584: case 1:
6585: if(nagesqr==0)
6586: fprintf(ficgp," p%d+p%d*x",i,i+1);
6587: else /* nagesqr =1 */
6588: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6589: break;
6590: case 2: /* ng=2 */
6591: if(nagesqr==0)
6592: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6593: else /* nagesqr =1 */
6594: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6595: break;
6596: case 3:
6597: if(nagesqr==0)
6598: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6599: else /* nagesqr =1 */
6600: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6601: break;
6602: }
6603: ij=1;/* To be checked else nbcode[0][0] wrong */
6604: for(j=3; j <=ncovmodel-nagesqr; j++) {
6605: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6606: if(ij <=cptcovage) { /* Bug valgrind */
6607: if((j-2)==Tage[ij]) { /* Bug valgrind */
6608: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6609: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6610: ij++;
6611: }
6612: }
6613: else
1.227 brouard 6614: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */
1.223 brouard 6615: }
6616: }else{
6617: i=i-ncovmodel;
6618: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6619: fprintf(ficgp," (1.");
6620: }
1.227 brouard 6621:
1.223 brouard 6622: if(ng != 1){
6623: fprintf(ficgp,")/(1");
1.227 brouard 6624:
1.223 brouard 6625: for(k1=1; k1 <=nlstate; k1++){
6626: if(nagesqr==0)
6627: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6628: else /* nagesqr =1 */
6629: 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 6630:
1.223 brouard 6631: ij=1;
6632: for(j=3; j <=ncovmodel-nagesqr; j++){
6633: if(ij <=cptcovage) { /* Bug valgrind */
6634: if((j-2)==Tage[ij]) { /* Bug valgrind */
6635: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6636: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6637: ij++;
6638: }
6639: }
6640: else
1.225 brouard 6641: 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 6642: }
6643: fprintf(ficgp,")");
6644: }
6645: fprintf(ficgp,")");
6646: if(ng ==2)
6647: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6648: else /* ng= 3 */
6649: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6650: }else{ /* end ng <> 1 */
6651: if( k !=k2) /* logit p11 is hard to draw */
6652: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
6653: }
6654: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6655: fprintf(ficgp,",");
6656: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6657: fprintf(ficgp,",");
6658: i=i+ncovmodel;
6659: } /* end k */
6660: } /* end k2 */
6661: fprintf(ficgp,"\n set out\n");
6662: } /* end jk */
6663: } /* end ng */
6664: /* avoid: */
6665: fflush(ficgp);
1.126 brouard 6666: } /* end gnuplot */
6667:
6668:
6669: /*************** Moving average **************/
1.219 brouard 6670: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.222 brouard 6671: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
1.218 brouard 6672:
1.222 brouard 6673: int i, cpt, cptcod;
6674: int modcovmax =1;
6675: int mobilavrange, mob;
6676: int iage=0;
6677:
6678: double sum=0.;
6679: double age;
6680: double *sumnewp, *sumnewm;
6681: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6682:
6683:
1.225 brouard 6684: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
1.222 brouard 6685: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
6686:
6687: sumnewp = vector(1,ncovcombmax);
6688: sumnewm = vector(1,ncovcombmax);
6689: agemingood = vector(1,ncovcombmax);
6690: agemaxgood = vector(1,ncovcombmax);
6691:
6692: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6693: sumnewm[cptcod]=0.;
6694: sumnewp[cptcod]=0.;
6695: agemingood[cptcod]=0;
6696: agemaxgood[cptcod]=0;
6697: }
6698: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
6699:
6700: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6701: if(mobilav==1) mobilavrange=5; /* default */
6702: else mobilavrange=mobilav;
6703: for (age=bage; age<=fage; age++)
6704: for (i=1; i<=nlstate;i++)
6705: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
6706: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
6707: /* We keep the original values on the extreme ages bage, fage and for
6708: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6709: we use a 5 terms etc. until the borders are no more concerned.
6710: */
6711: for (mob=3;mob <=mobilavrange;mob=mob+2){
6712: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
6713: for (i=1; i<=nlstate;i++){
6714: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6715: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6716: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6717: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6718: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6719: }
6720: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6721: }
6722: }
6723: }/* end age */
6724: }/* end mob */
6725: }else
6726: return -1;
6727: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
6728: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
6729: if(invalidvarcomb[cptcod]){
6730: printf("\nCombination (%d) ignored because no cases \n",cptcod);
6731: continue;
6732: }
1.219 brouard 6733:
1.222 brouard 6734: agemingood[cptcod]=fage-(mob-1)/2;
6735: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6736: sumnewm[cptcod]=0.;
6737: for (i=1; i<=nlstate;i++){
6738: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6739: }
6740: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6741: agemingood[cptcod]=age;
6742: }else{ /* bad */
6743: for (i=1; i<=nlstate;i++){
6744: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6745: } /* i */
6746: } /* end bad */
6747: }/* age */
6748: sum=0.;
6749: for (i=1; i<=nlstate;i++){
6750: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6751: }
6752: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6753: 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);
6754: /* for (i=1; i<=nlstate;i++){ */
6755: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6756: /* } /\* i *\/ */
6757: } /* end bad */
6758: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6759: /* From youngest, finding the oldest wrong */
6760: agemaxgood[cptcod]=bage+(mob-1)/2;
6761: for (age=bage+(mob-1)/2; age<=fage; age++){
6762: sumnewm[cptcod]=0.;
6763: for (i=1; i<=nlstate;i++){
6764: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6765: }
6766: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6767: agemaxgood[cptcod]=age;
6768: }else{ /* bad */
6769: for (i=1; i<=nlstate;i++){
6770: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6771: } /* i */
6772: } /* end bad */
6773: }/* age */
6774: sum=0.;
6775: for (i=1; i<=nlstate;i++){
6776: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6777: }
6778: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6779: 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);
6780: /* for (i=1; i<=nlstate;i++){ */
6781: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6782: /* } /\* i *\/ */
6783: } /* end bad */
6784:
6785: for (age=bage; age<=fage; age++){
6786: printf("%d %d ", cptcod, (int)age);
6787: sumnewp[cptcod]=0.;
6788: sumnewm[cptcod]=0.;
6789: for (i=1; i<=nlstate;i++){
6790: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6791: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6792: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6793: }
6794: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6795: }
6796: /* printf("\n"); */
6797: /* } */
6798: /* brutal averaging */
6799: for (i=1; i<=nlstate;i++){
6800: for (age=1; age<=bage; age++){
6801: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6802: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6803: }
6804: for (age=fage; age<=AGESUP; age++){
6805: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6806: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
6807: }
6808: } /* end i status */
6809: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6810: for (age=1; age<=AGESUP; age++){
6811: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6812: mobaverage[(int)age][i][cptcod]=0.;
6813: }
6814: }
6815: }/* end cptcod */
6816: free_vector(sumnewm,1, ncovcombmax);
6817: free_vector(sumnewp,1, ncovcombmax);
6818: free_vector(agemaxgood,1, ncovcombmax);
6819: free_vector(agemingood,1, ncovcombmax);
6820: return 0;
6821: }/* End movingaverage */
1.218 brouard 6822:
1.126 brouard 6823:
6824: /************** Forecasting ******************/
1.225 brouard 6825: 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 6826: /* proj1, year, month, day of starting projection
6827: agemin, agemax range of age
6828: dateprev1 dateprev2 range of dates during which prevalence is computed
6829: anproj2 year of en of projection (same day and month as proj1).
6830: */
1.164 brouard 6831: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6832: double agec; /* generic age */
6833: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6834: double *popeffectif,*popcount;
6835: double ***p3mat;
1.218 brouard 6836: /* double ***mobaverage; */
1.126 brouard 6837: char fileresf[FILENAMELENGTH];
6838:
6839: agelim=AGESUP;
1.211 brouard 6840: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6841: in each health status at the date of interview (if between dateprev1 and dateprev2).
6842: We still use firstpass and lastpass as another selection.
6843: */
1.214 brouard 6844: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6845: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6846:
1.201 brouard 6847: strcpy(fileresf,"F_");
6848: strcat(fileresf,fileresu);
1.126 brouard 6849: if((ficresf=fopen(fileresf,"w"))==NULL) {
6850: printf("Problem with forecast resultfile: %s\n", fileresf);
6851: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6852: }
1.215 brouard 6853: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6854: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6855:
1.225 brouard 6856: if (cptcoveff==0) ncodemax[cptcoveff]=1;
1.126 brouard 6857:
6858:
6859: stepsize=(int) (stepm+YEARM-1)/YEARM;
6860: if (stepm<=12) stepsize=1;
6861: if(estepm < stepm){
6862: printf ("Problem %d lower than %d\n",estepm, stepm);
6863: }
6864: else hstepm=estepm;
6865:
6866: hstepm=hstepm/stepm;
6867: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6868: fractional in yp1 */
6869: anprojmean=yp;
6870: yp2=modf((yp1*12),&yp);
6871: mprojmean=yp;
6872: yp1=modf((yp2*30.5),&yp);
6873: jprojmean=yp;
6874: if(jprojmean==0) jprojmean=1;
6875: if(mprojmean==0) jprojmean=1;
6876:
1.227 brouard 6877: i1=pow(2,cptcoveff);
1.126 brouard 6878: if (cptcovn < 1){i1=1;}
6879:
6880: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6881:
6882: fprintf(ficresf,"#****** Routine prevforecast **\n");
1.227 brouard 6883:
1.126 brouard 6884: /* if (h==(int)(YEARM*yearp)){ */
1.227 brouard 6885: for(k=1;k<=i1;k++){
6886: if(invalidvarcomb[k]){
6887: printf("\nCombination (%d) projection ignored because no cases \n",k);
6888: continue;
6889: }
6890: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
6891: for(j=1;j<=cptcoveff;j++) {
6892: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6893: }
6894: fprintf(ficresf," yearproj age");
6895: for(j=1; j<=nlstate+ndeath;j++){
6896: for(i=1; i<=nlstate;i++)
6897: fprintf(ficresf," p%d%d",i,j);
6898: fprintf(ficresf," wp.%d",j);
6899: }
6900: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
6901: fprintf(ficresf,"\n");
6902: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6903: for (agec=fage; agec>=(ageminpar-1); agec--){
6904: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6905: nhstepm = nhstepm/hstepm;
6906: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6907: oldm=oldms;savm=savms;
6908: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6909:
6910: for (h=0; h<=nhstepm; h++){
6911: if (h*hstepm/YEARM*stepm ==yearp) {
6912: fprintf(ficresf,"\n");
6913: for(j=1;j<=cptcoveff;j++)
6914: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6915: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6916: }
6917: for(j=1; j<=nlstate+ndeath;j++) {
6918: ppij=0.;
6919: for(i=1; i<=nlstate;i++) {
6920: if (mobilav==1)
6921: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
6922: else {
6923: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
6924: }
6925: if (h*hstepm/YEARM*stepm== yearp) {
6926: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6927: }
6928: } /* end i */
6929: if (h*hstepm/YEARM*stepm==yearp) {
6930: fprintf(ficresf," %.3f", ppij);
6931: }
6932: }/* end j */
6933: } /* end h */
6934: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6935: } /* end agec */
6936: } /* end yearp */
6937: } /* end k */
1.219 brouard 6938:
1.126 brouard 6939: fclose(ficresf);
1.215 brouard 6940: printf("End of Computing forecasting \n");
6941: fprintf(ficlog,"End of Computing forecasting\n");
6942:
1.126 brouard 6943: }
6944:
1.218 brouard 6945: /* /\************** Back Forecasting ******************\/ */
1.225 brouard 6946: /* 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 6947: /* /\* back1, year, month, day of starting backection */
6948: /* agemin, agemax range of age */
6949: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6950: /* anback2 year of en of backection (same day and month as back1). */
6951: /* *\/ */
6952: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6953: /* double agec; /\* generic age *\/ */
6954: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6955: /* double *popeffectif,*popcount; */
6956: /* double ***p3mat; */
6957: /* /\* double ***mobaverage; *\/ */
6958: /* char fileresfb[FILENAMELENGTH]; */
6959:
6960: /* agelim=AGESUP; */
6961: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6962: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6963: /* We still use firstpass and lastpass as another selection. */
6964: /* *\/ */
6965: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6966: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6967: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6968:
6969: /* strcpy(fileresfb,"FB_"); */
6970: /* strcat(fileresfb,fileresu); */
6971: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6972: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6973: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6974: /* } */
6975: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6976: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6977:
1.225 brouard 6978: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.218 brouard 6979:
6980: /* /\* if (mobilav!=0) { *\/ */
6981: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6982: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6983: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6984: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6985: /* /\* } *\/ */
6986: /* /\* } *\/ */
6987:
6988: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6989: /* if (stepm<=12) stepsize=1; */
6990: /* if(estepm < stepm){ */
6991: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6992: /* } */
6993: /* else hstepm=estepm; */
6994:
6995: /* hstepm=hstepm/stepm; */
6996: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6997: /* fractional in yp1 *\/ */
6998: /* anprojmean=yp; */
6999: /* yp2=modf((yp1*12),&yp); */
7000: /* mprojmean=yp; */
7001: /* yp1=modf((yp2*30.5),&yp); */
7002: /* jprojmean=yp; */
7003: /* if(jprojmean==0) jprojmean=1; */
7004: /* if(mprojmean==0) jprojmean=1; */
7005:
1.225 brouard 7006: /* i1=cptcoveff; */
1.218 brouard 7007: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 7008:
1.218 brouard 7009: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 7010:
1.218 brouard 7011: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
7012:
7013: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
7014: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
1.225 brouard 7015: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
1.218 brouard 7016: /* k=k+1; */
7017: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
1.225 brouard 7018: /* for(j=1;j<=cptcoveff;j++) { */
1.218 brouard 7019: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7020: /* } */
7021: /* fprintf(ficresfb," yearbproj age"); */
7022: /* for(j=1; j<=nlstate+ndeath;j++){ */
7023: /* for(i=1; i<=nlstate;i++) */
7024: /* fprintf(ficresfb," p%d%d",i,j); */
7025: /* fprintf(ficresfb," p.%d",j); */
7026: /* } */
7027: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
7028: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
7029: /* fprintf(ficresfb,"\n"); */
7030: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
7031: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
7032: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
7033: /* nhstepm = nhstepm/hstepm; */
7034: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7035: /* oldm=oldms;savm=savms; */
7036: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
7037: /* for (h=0; h<=nhstepm; h++){ */
7038: /* if (h*hstepm/YEARM*stepm ==yearp) { */
7039: /* fprintf(ficresfb,"\n"); */
1.225 brouard 7040: /* for(j=1;j<=cptcoveff;j++) */
1.218 brouard 7041: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7042: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
7043: /* } */
7044: /* for(j=1; j<=nlstate+ndeath;j++) { */
7045: /* ppij=0.; */
7046: /* for(i=1; i<=nlstate;i++) { */
7047: /* if (mobilav==1) */
7048: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
7049: /* else { */
7050: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
7051: /* } */
7052: /* if (h*hstepm/YEARM*stepm== yearp) { */
7053: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
7054: /* } */
7055: /* } /\* end i *\/ */
7056: /* if (h*hstepm/YEARM*stepm==yearp) { */
7057: /* fprintf(ficresfb," %.3f", ppij); */
7058: /* } */
7059: /* }/\* end j *\/ */
7060: /* } /\* end h *\/ */
7061: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7062: /* } /\* end agec *\/ */
7063: /* } /\* end yearp *\/ */
7064: /* } /\* end cptcod *\/ */
7065: /* } /\* end cptcov *\/ */
7066:
7067: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7068:
7069: /* fclose(ficresfb); */
7070: /* printf("End of Computing Back forecasting \n"); */
7071: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 7072:
1.218 brouard 7073: /* } */
1.217 brouard 7074:
1.126 brouard 7075: /************** Forecasting *****not tested NB*************/
1.227 brouard 7076: /* 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 7077:
1.227 brouard 7078: /* int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
7079: /* int *popage; */
7080: /* double calagedatem, agelim, kk1, kk2; */
7081: /* double *popeffectif,*popcount; */
7082: /* double ***p3mat,***tabpop,***tabpopprev; */
7083: /* /\* double ***mobaverage; *\/ */
7084: /* char filerespop[FILENAMELENGTH]; */
1.126 brouard 7085:
1.227 brouard 7086: /* tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7087: /* tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7088: /* agelim=AGESUP; */
7089: /* calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
1.126 brouard 7090:
1.227 brouard 7091: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
1.126 brouard 7092:
7093:
1.227 brouard 7094: /* strcpy(filerespop,"POP_"); */
7095: /* strcat(filerespop,fileresu); */
7096: /* if((ficrespop=fopen(filerespop,"w"))==NULL) { */
7097: /* printf("Problem with forecast resultfile: %s\n", filerespop); */
7098: /* fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
7099: /* } */
7100: /* printf("Computing forecasting: result on file '%s' \n", filerespop); */
7101: /* fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
1.126 brouard 7102:
1.227 brouard 7103: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
1.126 brouard 7104:
1.227 brouard 7105: /* /\* if (mobilav!=0) { *\/ */
7106: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
7107: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
7108: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7109: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
7110: /* /\* } *\/ */
7111: /* /\* } *\/ */
1.126 brouard 7112:
1.227 brouard 7113: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
7114: /* if (stepm<=12) stepsize=1; */
1.126 brouard 7115:
1.227 brouard 7116: /* agelim=AGESUP; */
1.126 brouard 7117:
1.227 brouard 7118: /* hstepm=1; */
7119: /* hstepm=hstepm/stepm; */
1.218 brouard 7120:
1.227 brouard 7121: /* if (popforecast==1) { */
7122: /* if((ficpop=fopen(popfile,"r"))==NULL) { */
7123: /* printf("Problem with population file : %s\n",popfile);exit(0); */
7124: /* fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
7125: /* } */
7126: /* popage=ivector(0,AGESUP); */
7127: /* popeffectif=vector(0,AGESUP); */
7128: /* popcount=vector(0,AGESUP); */
1.126 brouard 7129:
1.227 brouard 7130: /* i=1; */
7131: /* while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
1.218 brouard 7132:
1.227 brouard 7133: /* imx=i; */
7134: /* for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
7135: /* } */
1.218 brouard 7136:
1.227 brouard 7137: /* for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
7138: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
7139: /* k=k+1; */
7140: /* fprintf(ficrespop,"\n#******"); */
7141: /* for(j=1;j<=cptcoveff;j++) { */
7142: /* fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
7143: /* } */
7144: /* fprintf(ficrespop,"******\n"); */
7145: /* fprintf(ficrespop,"# Age"); */
7146: /* for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
7147: /* if (popforecast==1) fprintf(ficrespop," [Population]"); */
1.126 brouard 7148:
1.227 brouard 7149: /* for (cpt=0; cpt<=0;cpt++) { */
7150: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
1.126 brouard 7151:
1.227 brouard 7152: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7153: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7154: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7155:
1.227 brouard 7156: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7157: /* oldm=oldms;savm=savms; */
7158: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
1.218 brouard 7159:
1.227 brouard 7160: /* for (h=0; h<=nhstepm; h++){ */
7161: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7162: /* fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7163: /* } */
7164: /* for(j=1; j<=nlstate+ndeath;j++) { */
7165: /* kk1=0.;kk2=0; */
7166: /* for(i=1; i<=nlstate;i++) { */
7167: /* if (mobilav==1) */
7168: /* kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
7169: /* else { */
7170: /* kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
7171: /* } */
7172: /* } */
7173: /* if (h==(int)(calagedatem+12*cpt)){ */
7174: /* tabpop[(int)(agedeb)][j][cptcod]=kk1; */
7175: /* /\*fprintf(ficrespop," %.3f", kk1); */
7176: /* if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
7177: /* } */
7178: /* } */
7179: /* for(i=1; i<=nlstate;i++){ */
7180: /* kk1=0.; */
7181: /* for(j=1; j<=nlstate;j++){ */
7182: /* kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; */
7183: /* } */
7184: /* tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
7185: /* } */
1.218 brouard 7186:
1.227 brouard 7187: /* if (h==(int)(calagedatem+12*cpt)) */
7188: /* for(j=1; j<=nlstate;j++) */
7189: /* fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
7190: /* } */
7191: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7192: /* } */
7193: /* } */
1.218 brouard 7194:
1.227 brouard 7195: /* /\******\/ */
1.218 brouard 7196:
1.227 brouard 7197: /* for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { */
7198: /* fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); */
7199: /* for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ */
7200: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); */
7201: /* nhstepm = nhstepm/hstepm; */
1.126 brouard 7202:
1.227 brouard 7203: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7204: /* oldm=oldms;savm=savms; */
7205: /* hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
7206: /* for (h=0; h<=nhstepm; h++){ */
7207: /* if (h==(int) (calagedatem+YEARM*cpt)) { */
7208: /* fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
7209: /* } */
7210: /* for(j=1; j<=nlstate+ndeath;j++) { */
7211: /* kk1=0.;kk2=0; */
7212: /* for(i=1; i<=nlstate;i++) { */
7213: /* kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; */
7214: /* } */
7215: /* if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); */
7216: /* } */
7217: /* } */
7218: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
7219: /* } */
7220: /* } */
7221: /* } */
7222: /* } */
1.218 brouard 7223:
1.227 brouard 7224: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
1.218 brouard 7225:
1.227 brouard 7226: /* if (popforecast==1) { */
7227: /* free_ivector(popage,0,AGESUP); */
7228: /* free_vector(popeffectif,0,AGESUP); */
7229: /* free_vector(popcount,0,AGESUP); */
7230: /* } */
7231: /* free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7232: /* free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
7233: /* fclose(ficrespop); */
7234: /* } /\* End of popforecast *\/ */
1.218 brouard 7235:
1.126 brouard 7236: int fileappend(FILE *fichier, char *optionfich)
7237: {
7238: if((fichier=fopen(optionfich,"a"))==NULL) {
7239: printf("Problem with file: %s\n", optionfich);
7240: fprintf(ficlog,"Problem with file: %s\n", optionfich);
7241: return (0);
7242: }
7243: fflush(fichier);
7244: return (1);
7245: }
7246:
7247:
7248: /**************** function prwizard **********************/
7249: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
7250: {
7251:
7252: /* Wizard to print covariance matrix template */
7253:
1.164 brouard 7254: char ca[32], cb[32];
7255: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 7256: int numlinepar;
7257:
7258: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7259: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7260: for(i=1; i <=nlstate; i++){
7261: jj=0;
7262: for(j=1; j <=nlstate+ndeath; j++){
7263: if(j==i) continue;
7264: jj++;
7265: /*ca[0]= k+'a'-1;ca[1]='\0';*/
7266: printf("%1d%1d",i,j);
7267: fprintf(ficparo,"%1d%1d",i,j);
7268: for(k=1; k<=ncovmodel;k++){
7269: /* printf(" %lf",param[i][j][k]); */
7270: /* fprintf(ficparo," %lf",param[i][j][k]); */
7271: printf(" 0.");
7272: fprintf(ficparo," 0.");
7273: }
7274: printf("\n");
7275: fprintf(ficparo,"\n");
7276: }
7277: }
7278: printf("# Scales (for hessian or gradient estimation)\n");
7279: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
7280: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
7281: for(i=1; i <=nlstate; i++){
7282: jj=0;
7283: for(j=1; j <=nlstate+ndeath; j++){
7284: if(j==i) continue;
7285: jj++;
7286: fprintf(ficparo,"%1d%1d",i,j);
7287: printf("%1d%1d",i,j);
7288: fflush(stdout);
7289: for(k=1; k<=ncovmodel;k++){
7290: /* printf(" %le",delti3[i][j][k]); */
7291: /* fprintf(ficparo," %le",delti3[i][j][k]); */
7292: printf(" 0.");
7293: fprintf(ficparo," 0.");
7294: }
7295: numlinepar++;
7296: printf("\n");
7297: fprintf(ficparo,"\n");
7298: }
7299: }
7300: printf("# Covariance matrix\n");
7301: /* # 121 Var(a12)\n\ */
7302: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7303: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7304: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7305: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7306: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7307: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7308: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7309: fflush(stdout);
7310: fprintf(ficparo,"# Covariance matrix\n");
7311: /* # 121 Var(a12)\n\ */
7312: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7313: /* # ...\n\ */
7314: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7315:
7316: for(itimes=1;itimes<=2;itimes++){
7317: jj=0;
7318: for(i=1; i <=nlstate; i++){
7319: for(j=1; j <=nlstate+ndeath; j++){
7320: if(j==i) continue;
7321: for(k=1; k<=ncovmodel;k++){
7322: jj++;
7323: ca[0]= k+'a'-1;ca[1]='\0';
7324: if(itimes==1){
7325: printf("#%1d%1d%d",i,j,k);
7326: fprintf(ficparo,"#%1d%1d%d",i,j,k);
7327: }else{
7328: printf("%1d%1d%d",i,j,k);
7329: fprintf(ficparo,"%1d%1d%d",i,j,k);
7330: /* printf(" %.5le",matcov[i][j]); */
7331: }
7332: ll=0;
7333: for(li=1;li <=nlstate; li++){
7334: for(lj=1;lj <=nlstate+ndeath; lj++){
7335: if(lj==li) continue;
7336: for(lk=1;lk<=ncovmodel;lk++){
7337: ll++;
7338: if(ll<=jj){
7339: cb[0]= lk +'a'-1;cb[1]='\0';
7340: if(ll<jj){
7341: if(itimes==1){
7342: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7343: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7344: }else{
7345: printf(" 0.");
7346: fprintf(ficparo," 0.");
7347: }
7348: }else{
7349: if(itimes==1){
7350: printf(" Var(%s%1d%1d)",ca,i,j);
7351: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
7352: }else{
7353: printf(" 0.");
7354: fprintf(ficparo," 0.");
7355: }
7356: }
7357: }
7358: } /* end lk */
7359: } /* end lj */
7360: } /* end li */
7361: printf("\n");
7362: fprintf(ficparo,"\n");
7363: numlinepar++;
7364: } /* end k*/
7365: } /*end j */
7366: } /* end i */
7367: } /* end itimes */
7368:
7369: } /* end of prwizard */
7370: /******************* Gompertz Likelihood ******************************/
7371: double gompertz(double x[])
7372: {
7373: double A,B,L=0.0,sump=0.,num=0.;
7374: int i,n=0; /* n is the size of the sample */
7375:
1.220 brouard 7376: for (i=1;i<=imx ; i++) {
1.126 brouard 7377: sump=sump+weight[i];
7378: /* sump=sump+1;*/
7379: num=num+1;
7380: }
7381:
7382:
7383: /* for (i=0; i<=imx; i++)
7384: 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]);*/
7385:
7386: for (i=1;i<=imx ; i++)
7387: {
7388: if (cens[i] == 1 && wav[i]>1)
7389: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7390:
7391: if (cens[i] == 0 && wav[i]>1)
7392: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7393: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7394:
7395: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7396: if (wav[i] > 1 ) { /* ??? */
7397: L=L+A*weight[i];
7398: /* 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]);*/
7399: }
7400: }
7401:
7402: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7403:
7404: return -2*L*num/sump;
7405: }
7406:
1.136 brouard 7407: #ifdef GSL
7408: /******************* Gompertz_f Likelihood ******************************/
7409: double gompertz_f(const gsl_vector *v, void *params)
7410: {
7411: double A,B,LL=0.0,sump=0.,num=0.;
7412: double *x= (double *) v->data;
7413: int i,n=0; /* n is the size of the sample */
7414:
7415: for (i=0;i<=imx-1 ; i++) {
7416: sump=sump+weight[i];
7417: /* sump=sump+1;*/
7418: num=num+1;
7419: }
7420:
7421:
7422: /* for (i=0; i<=imx; i++)
7423: 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]);*/
7424: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7425: for (i=1;i<=imx ; i++)
7426: {
7427: if (cens[i] == 1 && wav[i]>1)
7428: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7429:
7430: if (cens[i] == 0 && wav[i]>1)
7431: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7432: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7433:
7434: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7435: if (wav[i] > 1 ) { /* ??? */
7436: LL=LL+A*weight[i];
7437: /* 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]);*/
7438: }
7439: }
7440:
7441: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7442: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7443:
7444: return -2*LL*num/sump;
7445: }
7446: #endif
7447:
1.126 brouard 7448: /******************* Printing html file ***********/
1.201 brouard 7449: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7450: int lastpass, int stepm, int weightopt, char model[],\
7451: int imx, double p[],double **matcov,double agemortsup){
7452: int i,k;
7453:
7454: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7455: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7456: for (i=1;i<=2;i++)
7457: 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 7458: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7459: fprintf(fichtm,"</ul>");
7460:
7461: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7462:
7463: 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>");
7464:
7465: for (k=agegomp;k<(agemortsup-2);k++)
7466: 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]);
7467:
7468:
7469: fflush(fichtm);
7470: }
7471:
7472: /******************* Gnuplot file **************/
1.201 brouard 7473: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7474:
7475: char dirfileres[132],optfileres[132];
1.164 brouard 7476:
1.126 brouard 7477: int ng;
7478:
7479:
7480: /*#ifdef windows */
7481: fprintf(ficgp,"cd \"%s\" \n",pathc);
7482: /*#endif */
7483:
7484:
7485: strcpy(dirfileres,optionfilefiname);
7486: strcpy(optfileres,"vpl");
1.199 brouard 7487: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7488: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7489: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7490: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7491: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7492:
7493: }
7494:
1.136 brouard 7495: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7496: {
1.126 brouard 7497:
1.136 brouard 7498: /*-------- data file ----------*/
7499: FILE *fic;
7500: char dummy[]=" ";
1.223 brouard 7501: int i=0, j=0, n=0, iv=0;
7502: int lstra;
1.136 brouard 7503: int linei, month, year,iout;
7504: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7505: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7506: char *stratrunc;
1.223 brouard 7507:
1.126 brouard 7508:
7509:
1.136 brouard 7510: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7511: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7512: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7513: }
1.126 brouard 7514:
1.136 brouard 7515: i=1;
7516: linei=0;
7517: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7518: linei=linei+1;
7519: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7520: if(line[j] == '\t')
7521: line[j] = ' ';
7522: }
7523: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7524: ;
7525: };
7526: line[j+1]=0; /* Trims blanks at end of line */
7527: if(line[0]=='#'){
7528: fprintf(ficlog,"Comment line\n%s\n",line);
7529: printf("Comment line\n%s\n",line);
7530: continue;
7531: }
7532: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7533: strcpy(line, linetmp);
1.223 brouard 7534:
7535: /* Loops on waves */
7536: for (j=maxwav;j>=1;j--){
7537: for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
1.225 brouard 7538: cutv(stra, strb, line, ' ');
7539: if(strb[0]=='.') { /* Missing value */
7540: lval=-1;
7541: cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
7542: if(isalpha(strb[1])) { /* .m or .d Really Missing value */
7543: 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);
7544: 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);
7545: return 1;
7546: }
7547: }else{
7548: errno=0;
7549: /* what_kind_of_number(strb); */
7550: dval=strtod(strb,&endptr);
7551: /* if( strb[0]=='\0' || (*endptr != '\0')){ */
7552: /* if(strb != endptr && *endptr == '\0') */
7553: /* dval=dlval; */
7554: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7555: if( strb[0]=='\0' || (*endptr != '\0')){
7556: 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);
7557: 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);
7558: return 1;
7559: }
7560: cotqvar[j][iv][i]=dval;
7561: }
7562: strcpy(line,stra);
1.223 brouard 7563: }/* end loop ntqv */
1.225 brouard 7564:
1.223 brouard 7565: for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
1.225 brouard 7566: cutv(stra, strb, line, ' ');
7567: if(strb[0]=='.') { /* Missing value */
7568: lval=-1;
7569: }else{
7570: errno=0;
7571: lval=strtol(strb,&endptr,10);
7572: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7573: if( strb[0]=='\0' || (*endptr != '\0')){
7574: 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);
7575: 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);
7576: return 1;
7577: }
7578: }
7579: if(lval <-1 || lval >1){
7580: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7581: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7582: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7583: For example, for multinomial values like 1, 2 and 3,\n \
7584: build V1=0 V2=0 for the reference value (1),\n \
7585: V1=1 V2=0 for (2) \n \
1.223 brouard 7586: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7587: output of IMaCh is often meaningless.\n \
1.223 brouard 7588: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7589: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.223 brouard 7590: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7591: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7592: For example, for multinomial values like 1, 2 and 3,\n \
7593: build V1=0 V2=0 for the reference value (1),\n \
7594: V1=1 V2=0 for (2) \n \
1.223 brouard 7595: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7596: output of IMaCh is often meaningless.\n \
7597: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7598: return 1;
7599: }
7600: cotvar[j][iv][i]=(double)(lval);
7601: strcpy(line,stra);
1.223 brouard 7602: }/* end loop ntv */
1.225 brouard 7603:
1.223 brouard 7604: /* Statuses at wave */
1.137 brouard 7605: cutv(stra, strb, line, ' ');
1.223 brouard 7606: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7607: lval=-1;
1.136 brouard 7608: }else{
1.225 brouard 7609: errno=0;
7610: lval=strtol(strb,&endptr,10);
7611: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7612: if( strb[0]=='\0' || (*endptr != '\0')){
7613: 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);
7614: 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);
7615: return 1;
7616: }
1.136 brouard 7617: }
1.225 brouard 7618:
1.136 brouard 7619: s[j][i]=lval;
1.225 brouard 7620:
1.223 brouard 7621: /* Date of Interview */
1.136 brouard 7622: strcpy(line,stra);
7623: cutv(stra, strb,line,' ');
1.169 brouard 7624: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7625: }
1.169 brouard 7626: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.225 brouard 7627: month=99;
7628: year=9999;
1.136 brouard 7629: }else{
1.225 brouard 7630: 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);
7631: 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);
7632: return 1;
1.136 brouard 7633: }
7634: anint[j][i]= (double) year;
7635: mint[j][i]= (double)month;
7636: strcpy(line,stra);
1.223 brouard 7637: } /* End loop on waves */
1.225 brouard 7638:
1.223 brouard 7639: /* Date of death */
1.136 brouard 7640: cutv(stra, strb,line,' ');
1.169 brouard 7641: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7642: }
1.169 brouard 7643: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7644: month=99;
7645: year=9999;
7646: }else{
1.141 brouard 7647: 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 7648: 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);
7649: return 1;
1.136 brouard 7650: }
7651: andc[i]=(double) year;
7652: moisdc[i]=(double) month;
7653: strcpy(line,stra);
7654:
1.223 brouard 7655: /* Date of birth */
1.136 brouard 7656: cutv(stra, strb,line,' ');
1.169 brouard 7657: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7658: }
1.169 brouard 7659: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7660: month=99;
7661: year=9999;
7662: }else{
1.141 brouard 7663: 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);
7664: 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 7665: return 1;
1.136 brouard 7666: }
7667: if (year==9999) {
1.141 brouard 7668: 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);
7669: 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 7670: return 1;
7671:
1.136 brouard 7672: }
7673: annais[i]=(double)(year);
7674: moisnais[i]=(double)(month);
7675: strcpy(line,stra);
1.225 brouard 7676:
1.223 brouard 7677: /* Sample weight */
1.136 brouard 7678: cutv(stra, strb,line,' ');
7679: errno=0;
7680: dval=strtod(strb,&endptr);
7681: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7682: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7683: 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 7684: fflush(ficlog);
7685: return 1;
7686: }
7687: weight[i]=dval;
7688: strcpy(line,stra);
1.225 brouard 7689:
1.223 brouard 7690: for (iv=nqv;iv>=1;iv--){ /* Loop on fixed quantitative variables */
7691: cutv(stra, strb, line, ' ');
7692: if(strb[0]=='.') { /* Missing value */
1.225 brouard 7693: lval=-1;
1.223 brouard 7694: }else{
1.225 brouard 7695: errno=0;
7696: /* what_kind_of_number(strb); */
7697: dval=strtod(strb,&endptr);
7698: /* if(strb != endptr && *endptr == '\0') */
7699: /* dval=dlval; */
7700: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN)) */
7701: if( strb[0]=='\0' || (*endptr != '\0')){
7702: 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);
7703: 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);
7704: return 1;
7705: }
7706: coqvar[iv][i]=dval;
1.226 brouard 7707: covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */
1.223 brouard 7708: }
7709: strcpy(line,stra);
7710: }/* end loop nqv */
1.136 brouard 7711:
1.223 brouard 7712: /* Covariate values */
1.136 brouard 7713: for (j=ncovcol;j>=1;j--){
7714: cutv(stra, strb,line,' ');
1.223 brouard 7715: if(strb[0]=='.') { /* Missing covariate value */
1.225 brouard 7716: lval=-1;
1.136 brouard 7717: }else{
1.225 brouard 7718: errno=0;
7719: lval=strtol(strb,&endptr,10);
7720: if( strb[0]=='\0' || (*endptr != '\0')){
7721: 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);
7722: 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);
7723: return 1;
7724: }
1.136 brouard 7725: }
7726: if(lval <-1 || lval >1){
1.225 brouard 7727: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7728: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7729: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7730: For example, for multinomial values like 1, 2 and 3,\n \
7731: build V1=0 V2=0 for the reference value (1),\n \
7732: V1=1 V2=0 for (2) \n \
1.136 brouard 7733: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7734: output of IMaCh is often meaningless.\n \
1.136 brouard 7735: Exiting.\n",lval,linei, i,line,j);
1.225 brouard 7736: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7737: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7738: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
1.225 brouard 7739: For example, for multinomial values like 1, 2 and 3,\n \
7740: build V1=0 V2=0 for the reference value (1),\n \
7741: V1=1 V2=0 for (2) \n \
1.136 brouard 7742: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
1.225 brouard 7743: output of IMaCh is often meaningless.\n \
1.136 brouard 7744: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
1.225 brouard 7745: return 1;
1.136 brouard 7746: }
7747: covar[j][i]=(double)(lval);
7748: strcpy(line,stra);
7749: }
7750: lstra=strlen(stra);
1.225 brouard 7751:
1.136 brouard 7752: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7753: stratrunc = &(stra[lstra-9]);
7754: num[i]=atol(stratrunc);
7755: }
7756: else
7757: num[i]=atol(stra);
7758: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7759: 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;}*/
7760:
7761: i=i+1;
7762: } /* End loop reading data */
1.225 brouard 7763:
1.136 brouard 7764: *imax=i-1; /* Number of individuals */
7765: fclose(fic);
1.225 brouard 7766:
1.136 brouard 7767: return (0);
1.164 brouard 7768: /* endread: */
1.225 brouard 7769: printf("Exiting readdata: ");
7770: fclose(fic);
7771: return (1);
1.223 brouard 7772: }
1.126 brouard 7773:
1.145 brouard 7774: void removespace(char *str) {
7775: char *p1 = str, *p2 = str;
7776: do
7777: while (*p2 == ' ')
7778: p2++;
1.169 brouard 7779: while (*p1++ == *p2++);
1.145 brouard 7780: }
7781:
1.224 brouard 7782: int decodemodel ( char model[], int lastobs)
7783: /**< This routine decode the model and returns:
7784: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7785: * - nagesqr = 1 if age*age in the model, otherwise 0.
7786: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7787: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
7788: * - cptcovage number of covariates with age*products =2
7789: * - cptcovs number of simple covariates
7790: * - 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
7791: * which is a new column after the 9 (ncovcol) variables.
7792: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7793: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7794: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7795: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7796: */
1.136 brouard 7797: {
1.145 brouard 7798: int i, j, k, ks;
1.227 brouard 7799: int j1, k1, k2, k3, k4;
1.136 brouard 7800: char modelsav[80];
1.145 brouard 7801: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7802: char *strpt;
1.136 brouard 7803:
1.145 brouard 7804: /*removespace(model);*/
1.136 brouard 7805: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7806: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7807: if (strstr(model,"AGE") !=0){
1.192 brouard 7808: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7809: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7810: return 1;
7811: }
1.141 brouard 7812: if (strstr(model,"v") !=0){
7813: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7814: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7815: return 1;
7816: }
1.187 brouard 7817: strcpy(modelsav,model);
7818: if ((strpt=strstr(model,"age*age")) !=0){
7819: printf(" strpt=%s, model=%s\n",strpt, model);
7820: if(strpt != model){
1.225 brouard 7821: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7822: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7823: corresponding column of parameters.\n",model);
1.225 brouard 7824: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7825: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7826: corresponding column of parameters.\n",model); fflush(ficlog);
1.225 brouard 7827: return 1;
7828: }
1.187 brouard 7829: nagesqr=1;
7830: if (strstr(model,"+age*age") !=0)
1.225 brouard 7831: substrchaine(modelsav, model, "+age*age");
1.187 brouard 7832: else if (strstr(model,"age*age+") !=0)
1.225 brouard 7833: substrchaine(modelsav, model, "age*age+");
1.187 brouard 7834: else
1.225 brouard 7835: substrchaine(modelsav, model, "age*age");
1.187 brouard 7836: }else
7837: nagesqr=0;
7838: if (strlen(modelsav) >1){
7839: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7840: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
1.224 brouard 7841: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2 */
1.187 brouard 7842: cptcovt= j+1; /* Number of total covariates in the model, not including
1.225 brouard 7843: * cst, age and age*age
7844: * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
7845: /* including age products which are counted in cptcovage.
7846: * but the covariates which are products must be treated
7847: * separately: ncovn=4- 2=2 (V1+V3). */
1.187 brouard 7848: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7849: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.225 brouard 7850:
7851:
1.187 brouard 7852: /* Design
7853: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7854: * < ncovcol=8 >
7855: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7856: * k= 1 2 3 4 5 6 7 8
7857: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7858: * covar[k,i], value of kth covariate if not including age for individual i:
1.224 brouard 7859: * covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
7860: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
1.187 brouard 7861: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7862: * Tage[++cptcovage]=k
7863: * if products, new covar are created after ncovcol with k1
7864: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7865: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7866: * 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
7867: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7868: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7869: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7870: * < ncovcol=8 >
7871: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7872: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7873: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7874: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7875: * p Tprod[1]@2={ 6, 5}
7876: *p Tvard[1][1]@4= {7, 8, 5, 6}
7877: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7878: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7879: *How to reorganize?
7880: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7881: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7882: * {2, 1, 4, 8, 5, 6, 3, 7}
7883: * Struct []
7884: */
1.225 brouard 7885:
1.187 brouard 7886: /* This loop fills the array Tvar from the string 'model'.*/
7887: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7888: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7889: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7890: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7891: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7892: /* k=1 Tvar[1]=2 (from V2) */
7893: /* k=5 Tvar[5] */
7894: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7895: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7896: /* } */
1.198 brouard 7897: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7898: /*
7899: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
1.227 brouard 7900: for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
7901: Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
7902: }
1.187 brouard 7903: cptcovage=0;
7904: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
1.225 brouard 7905: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7906: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7907: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7908: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7909: /*scanf("%d",i);*/
7910: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7911: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7912: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7913: /* covar is not filled and then is empty */
7914: cptcovprod--;
7915: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7916: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
1.226 brouard 7917: Typevar[k]=1; /* 1 for age product */
1.225 brouard 7918: cptcovage++; /* Sums the number of covariates which include age as a product */
7919: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7920: /*printf("stre=%s ", stre);*/
7921: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7922: cptcovprod--;
7923: cutl(stre,strb,strc,'V');
7924: Tvar[k]=atoi(stre);
7925: Typevar[k]=1; /* 1 for age product */
7926: cptcovage++;
7927: Tage[cptcovage]=k;
7928: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7929: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7930: cptcovn++;
7931: cptcovprodnoage++;k1++;
7932: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7933: Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
7934: because this model-covariate is a construction we invent a new column
7935: which is after existing variables ncovcol+nqv+ntv+nqtv + k1
7936: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7937: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7938: Typevar[k]=2; /* 2 for double fixed dummy covariates */
7939: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7940: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.227 brouard 7941: Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
1.225 brouard 7942: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7943: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7944: k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
7945: /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
7946: /* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
7947: /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
7948: /* 1 2 3 4 5 | Tvar[5+1)=1, Tvar[7]=2 */
7949: for (i=1; i<=lastobs;i++){
7950: /* Computes the new covariate which is a product of
7951: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7952: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7953: }
7954: } /* End age is not in the model */
7955: } /* End if model includes a product */
7956: else { /* no more sum */
7957: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7958: /* scanf("%d",i);*/
7959: cutl(strd,strc,strb,'V');
1.227 brouard 7960: ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
1.225 brouard 7961: cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
7962: Tvar[k]=atoi(strd);
7963: Typevar[k]=0; /* 0 for simple covariates */
7964: }
7965: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.223 brouard 7966: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
1.225 brouard 7967: scanf("%d",i);*/
1.187 brouard 7968: } /* end of loop + on total covariates */
7969: } /* end if strlen(modelsave == 0) age*age might exist */
7970: } /* end if strlen(model == 0) */
1.136 brouard 7971:
7972: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7973: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
1.225 brouard 7974:
1.136 brouard 7975: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
1.225 brouard 7976: printf("cptcovprod=%d ", cptcovprod);
7977: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7978: scanf("%d ",i);*/
7979:
7980:
7981: /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
7982: of variable (dummy vs quantitative, fixed vs time varying) is behind */
1.226 brouard 7983: /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1 = 5 possible variables data: 2 fixed 3, varying
7984: model= V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
7985: k = 1 2 3 4 5 6 7 8 9
7986: Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
7987: Typevar[k]= 0 0 0 2 1 0 2 1 1
1.227 brouard 7988: Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
7989: Dummy[k] 1 0 0 0 3 1 1 2 3
7990: Tmodelind[combination of covar]=k;
1.225 brouard 7991: */
7992: /* Dispatching between quantitative and time varying covariates */
1.226 brouard 7993: /* If Tvar[k] >ncovcol it is a product */
1.225 brouard 7994: /* 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 7995: /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
1.227 brouard 7996: printf("Model=%s\n\
7997: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
7998: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
7999: 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);
8000: fprintf(ficlog,"Model=%s\n\
8001: Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
8002: Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
8003: 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);
8004:
1.225 brouard 8005: for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
1.226 brouard 8006: if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
1.227 brouard 8007: Fixed[k]= 0;
8008: Dummy[k]= 0;
1.225 brouard 8009: ncoveff++;
8010: }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
1.227 brouard 8011: Fixed[k]= 0;
8012: Dummy[k]= 1;
1.225 brouard 8013: nqfveff++; /* Only simple fixed quantitative variable */
8014: }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){
1.227 brouard 8015: Fixed[k]= 1;
8016: Dummy[k]= 0;
1.225 brouard 8017: ntveff++; /* Only simple time varying dummy variable */
1.228 ! brouard 8018: 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);
! 8019: printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
1.227 brouard 8020: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){
8021: Fixed[k]= 1;
8022: Dummy[k]= 1;
1.228 ! brouard 8023: TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
! 8024: /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
! 8025: 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);
! 8026: printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
1.227 brouard 8027: }else if (Typevar[k] == 1) { /* product with age */
8028: if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
8029: Fixed[k]= 2;
8030: Dummy[k]= 2;
8031: /* ncoveff++; */
8032: }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
8033: Fixed[k]= 2;
8034: Dummy[k]= 3;
8035: /* nqfveff++; /\* Only simple fixed quantitative variable *\/ */
8036: }else if( Tvar[k] <=ncovcol+nqv+ntv ){
8037: Fixed[k]= 3;
8038: Dummy[k]= 2;
8039: /* ntveff++; /\* Only simple time varying dummy variable *\/ */
8040: }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
8041: Fixed[k]= 3;
8042: Dummy[k]= 3;
8043: /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
8044: }
8045: }else if (Typevar[k] == 2) { /* product without age */
8046: k1=Tposprod[k];
8047: if(Tvard[k1][1] <=ncovcol){
8048: if(Tvard[k1][2] <=ncovcol){
8049: Fixed[k]= 1;
8050: Dummy[k]= 0;
8051: }else if(Tvard[k1][2] <=ncovcol+nqv){
8052: Fixed[k]= 0; /* or 2 ?*/
8053: Dummy[k]= 1;
8054: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8055: Fixed[k]= 1;
8056: Dummy[k]= 0;
8057: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8058: Fixed[k]= 1;
8059: Dummy[k]= 1;
8060: }
8061: }else if(Tvard[k1][1] <=ncovcol+nqv){
8062: if(Tvard[k1][2] <=ncovcol){
8063: Fixed[k]= 0; /* or 2 ?*/
8064: Dummy[k]= 1;
8065: }else if(Tvard[k1][2] <=ncovcol+nqv){
8066: Fixed[k]= 0; /* or 2 ?*/
8067: Dummy[k]= 1;
8068: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8069: Fixed[k]= 1;
8070: Dummy[k]= 1;
8071: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8072: Fixed[k]= 1;
8073: Dummy[k]= 1;
8074: }
8075: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
8076: if(Tvard[k1][2] <=ncovcol){
8077: Fixed[k]= 1;
8078: Dummy[k]= 1;
8079: }else if(Tvard[k1][2] <=ncovcol+nqv){
8080: Fixed[k]= 1;
8081: Dummy[k]= 1;
8082: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8083: Fixed[k]= 1;
8084: Dummy[k]= 0;
8085: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8086: Fixed[k]= 1;
8087: Dummy[k]= 1;
8088: }
8089: }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
8090: if(Tvard[k1][2] <=ncovcol){
8091: Fixed[k]= 1;
8092: Dummy[k]= 1;
8093: }else if(Tvard[k1][2] <=ncovcol+nqv){
8094: Fixed[k]= 1;
8095: Dummy[k]= 1;
8096: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
8097: Fixed[k]= 1;
8098: Dummy[k]= 1;
8099: }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
8100: Fixed[k]= 1;
8101: Dummy[k]= 1;
8102: }
8103: }else{
8104: printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
8105: 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 8106: } /* end k1 */
1.225 brouard 8107: }else{
1.226 brouard 8108: printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
8109: 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 8110: }
1.227 brouard 8111: 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]);
8112: 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]);
8113: }
8114: /* Searching for doublons in the model */
8115: for(k1=1; k1<= cptcovt;k1++){
8116: for(k2=1; k2 <k1;k2++){
8117: if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
8118: if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
8119: if(Tvar[k1]==Tvar[k2]){
8120: 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]]);
8121: 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);
8122: return(1);
8123: }
8124: }else if (Typevar[k1] ==2){
8125: k3=Tposprod[k1];
8126: k4=Tposprod[k2];
8127: 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])) ){
8128: 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]]);
8129: 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);
8130: return(1);
8131: }
8132: }
8133: }
8134: }
1.225 brouard 8135: }
8136: printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
8137: fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
1.137 brouard 8138: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 8139: /*endread:*/
1.225 brouard 8140: printf("Exiting decodemodel: ");
8141: return (1);
1.136 brouard 8142: }
8143:
1.169 brouard 8144: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 8145: {
8146: int i, m;
1.218 brouard 8147: int firstone=0;
8148:
1.136 brouard 8149: for (i=1; i<=imx; i++) {
8150: for(m=2; (m<= maxwav); m++) {
8151: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
8152: anint[m][i]=9999;
1.216 brouard 8153: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
8154: s[m][i]=-1;
1.136 brouard 8155: }
8156: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 8157: *nberr = *nberr + 1;
1.218 brouard 8158: if(firstone == 0){
8159: firstone=1;
8160: 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);
8161: }
8162: 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 8163: s[m][i]=-1;
8164: }
8165: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 8166: (*nberr)++;
1.136 brouard 8167: 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]);
8168: 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]);
8169: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
8170: }
8171: }
8172: }
8173:
8174: for (i=1; i<=imx; i++) {
8175: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
8176: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 8177: 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 8178: if (s[m][i] >= nlstate+1) {
1.169 brouard 8179: if(agedc[i]>0){
8180: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 8181: agev[m][i]=agedc[i];
1.214 brouard 8182: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 8183: }else {
1.136 brouard 8184: if ((int)andc[i]!=9999){
8185: nbwarn++;
8186: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
8187: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
8188: agev[m][i]=-1;
8189: }
8190: }
1.169 brouard 8191: } /* agedc > 0 */
1.214 brouard 8192: } /* end if */
1.136 brouard 8193: else if(s[m][i] !=9){ /* Standard case, age in fractional
8194: years but with the precision of a month */
8195: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
8196: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
8197: agev[m][i]=1;
8198: else if(agev[m][i] < *agemin){
8199: *agemin=agev[m][i];
8200: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
8201: }
8202: else if(agev[m][i] >*agemax){
8203: *agemax=agev[m][i];
1.156 brouard 8204: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 8205: }
8206: /*agev[m][i]=anint[m][i]-annais[i];*/
8207: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 8208: } /* en if 9*/
1.136 brouard 8209: else { /* =9 */
1.214 brouard 8210: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 8211: agev[m][i]=1;
8212: s[m][i]=-1;
8213: }
8214: }
1.214 brouard 8215: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 8216: agev[m][i]=1;
1.214 brouard 8217: else{
8218: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8219: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
8220: agev[m][i]=0;
8221: }
8222: } /* End for lastpass */
8223: }
1.136 brouard 8224:
8225: for (i=1; i<=imx; i++) {
8226: for(m=firstpass; (m<=lastpass); m++){
8227: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 8228: (*nberr)++;
1.136 brouard 8229: 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);
8230: 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);
8231: return 1;
8232: }
8233: }
8234: }
8235:
8236: /*for (i=1; i<=imx; i++){
8237: for (m=firstpass; (m<lastpass); m++){
8238: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
8239: }
8240:
8241: }*/
8242:
8243:
1.139 brouard 8244: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
8245: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 8246:
8247: return (0);
1.164 brouard 8248: /* endread:*/
1.136 brouard 8249: printf("Exiting calandcheckages: ");
8250: return (1);
8251: }
8252:
1.172 brouard 8253: #if defined(_MSC_VER)
8254: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8255: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
8256: //#include "stdafx.h"
8257: //#include <stdio.h>
8258: //#include <tchar.h>
8259: //#include <windows.h>
8260: //#include <iostream>
8261: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
8262:
8263: LPFN_ISWOW64PROCESS fnIsWow64Process;
8264:
8265: BOOL IsWow64()
8266: {
8267: BOOL bIsWow64 = FALSE;
8268:
8269: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
8270: // (HANDLE, PBOOL);
8271:
8272: //LPFN_ISWOW64PROCESS fnIsWow64Process;
8273:
8274: HMODULE module = GetModuleHandle(_T("kernel32"));
8275: const char funcName[] = "IsWow64Process";
8276: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
8277: GetProcAddress(module, funcName);
8278:
8279: if (NULL != fnIsWow64Process)
8280: {
8281: if (!fnIsWow64Process(GetCurrentProcess(),
8282: &bIsWow64))
8283: //throw std::exception("Unknown error");
8284: printf("Unknown error\n");
8285: }
8286: return bIsWow64 != FALSE;
8287: }
8288: #endif
1.177 brouard 8289:
1.191 brouard 8290: void syscompilerinfo(int logged)
1.167 brouard 8291: {
8292: /* #include "syscompilerinfo.h"*/
1.185 brouard 8293: /* command line Intel compiler 32bit windows, XP compatible:*/
8294: /* /GS /W3 /Gy
8295: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
8296: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
8297: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 8298: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
8299: */
8300: /* 64 bits */
1.185 brouard 8301: /*
8302: /GS /W3 /Gy
8303: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
8304: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
8305: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
8306: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
8307: /* Optimization are useless and O3 is slower than O2 */
8308: /*
8309: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
8310: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
8311: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
8312: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
8313: */
1.186 brouard 8314: /* Link is */ /* /OUT:"visual studio
1.185 brouard 8315: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
8316: /PDB:"visual studio
8317: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
8318: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
8319: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
8320: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
8321: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
8322: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
8323: uiAccess='false'"
8324: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
8325: /NOLOGO /TLBID:1
8326: */
1.177 brouard 8327: #if defined __INTEL_COMPILER
1.178 brouard 8328: #if defined(__GNUC__)
8329: struct utsname sysInfo; /* For Intel on Linux and OS/X */
8330: #endif
1.177 brouard 8331: #elif defined(__GNUC__)
1.179 brouard 8332: #ifndef __APPLE__
1.174 brouard 8333: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 8334: #endif
1.177 brouard 8335: struct utsname sysInfo;
1.178 brouard 8336: int cross = CROSS;
8337: if (cross){
8338: printf("Cross-");
1.191 brouard 8339: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 8340: }
1.174 brouard 8341: #endif
8342:
1.171 brouard 8343: #include <stdint.h>
1.178 brouard 8344:
1.191 brouard 8345: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 8346: #if defined(__clang__)
1.191 brouard 8347: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 8348: #endif
8349: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 8350: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 8351: #endif
8352: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 8353: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 8354: #endif
8355: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 8356: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 8357: #endif
8358: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 8359: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 8360: #endif
8361: #if defined(_MSC_VER)
1.191 brouard 8362: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 8363: #endif
8364: #if defined(__PGI)
1.191 brouard 8365: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 8366: #endif
8367: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 8368: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 8369: #endif
1.191 brouard 8370: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 8371:
1.167 brouard 8372: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
8373: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
8374: // Windows (x64 and x86)
1.191 brouard 8375: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 8376: #elif __unix__ // all unices, not all compilers
8377: // Unix
1.191 brouard 8378: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 8379: #elif __linux__
8380: // linux
1.191 brouard 8381: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 8382: #elif __APPLE__
1.174 brouard 8383: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 8384: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 8385: #endif
8386:
8387: /* __MINGW32__ */
8388: /* __CYGWIN__ */
8389: /* __MINGW64__ */
8390: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
8391: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
8392: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
8393: /* _WIN64 // Defined for applications for Win64. */
8394: /* _M_X64 // Defined for compilations that target x64 processors. */
8395: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 8396:
1.167 brouard 8397: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 8398: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 8399: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 8400: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 8401: #else
1.191 brouard 8402: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 8403: #endif
8404:
1.169 brouard 8405: #if defined(__GNUC__)
8406: # if defined(__GNUC_PATCHLEVEL__)
8407: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8408: + __GNUC_MINOR__ * 100 \
8409: + __GNUC_PATCHLEVEL__)
8410: # else
8411: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
8412: + __GNUC_MINOR__ * 100)
8413: # endif
1.174 brouard 8414: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 8415: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 8416:
8417: if (uname(&sysInfo) != -1) {
8418: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 8419: 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 8420: }
8421: else
8422: perror("uname() error");
1.179 brouard 8423: //#ifndef __INTEL_COMPILER
8424: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 8425: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 8426: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 8427: #endif
1.169 brouard 8428: #endif
1.172 brouard 8429:
8430: // void main()
8431: // {
1.169 brouard 8432: #if defined(_MSC_VER)
1.174 brouard 8433: if (IsWow64()){
1.191 brouard 8434: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
8435: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 8436: }
8437: else{
1.191 brouard 8438: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
8439: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 8440: }
1.172 brouard 8441: // printf("\nPress Enter to continue...");
8442: // getchar();
8443: // }
8444:
1.169 brouard 8445: #endif
8446:
1.167 brouard 8447:
1.219 brouard 8448: }
1.136 brouard 8449:
1.219 brouard 8450: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 8451: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
8452: int i, j, k, i1 ;
1.202 brouard 8453: /* double ftolpl = 1.e-10; */
1.180 brouard 8454: double age, agebase, agelim;
1.203 brouard 8455: double tot;
1.180 brouard 8456:
1.202 brouard 8457: strcpy(filerespl,"PL_");
8458: strcat(filerespl,fileresu);
8459: if((ficrespl=fopen(filerespl,"w"))==NULL) {
8460: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8461: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
8462: }
1.227 brouard 8463: printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
8464: fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
1.202 brouard 8465: pstamp(ficrespl);
1.203 brouard 8466: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 8467: fprintf(ficrespl,"#Age ");
8468: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
8469: fprintf(ficrespl,"\n");
1.180 brouard 8470:
1.219 brouard 8471: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 8472:
1.219 brouard 8473: agebase=ageminpar;
8474: agelim=agemaxpar;
1.180 brouard 8475:
1.227 brouard 8476: /* i1=pow(2,ncoveff); */
8477: i1=pow(2,cptcoveff); /* Number of dummy covariates */
1.219 brouard 8478: if (cptcovn < 1){i1=1;}
1.180 brouard 8479:
1.220 brouard 8480: for(k=1; k<=i1;k++){
8481: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 8482: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 8483: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 8484: /* k=k+1; */
1.219 brouard 8485: /* to clean */
8486: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8487: fprintf(ficrespl,"#******");
8488: printf("#******");
8489: fprintf(ficlog,"#******");
1.227 brouard 8490: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
8491: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
1.219 brouard 8492: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8493: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8494: }
8495: fprintf(ficrespl,"******\n");
8496: printf("******\n");
8497: fprintf(ficlog,"******\n");
1.227 brouard 8498: if(invalidvarcomb[k]){
8499: printf("\nCombination (%d) ignored because no case \n",k);
8500: fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
8501: fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
1.220 brouard 8502: continue;
1.227 brouard 8503: }
1.219 brouard 8504:
8505: fprintf(ficrespl,"#Age ");
1.227 brouard 8506: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 8507: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8508: }
8509: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
8510: fprintf(ficrespl,"Total Years_to_converge\n");
1.227 brouard 8511:
1.219 brouard 8512: for (age=agebase; age<=agelim; age++){
8513: /* for (age=agebase; age<=agebase; age++){ */
8514: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
8515: fprintf(ficrespl,"%.0f ",age );
1.227 brouard 8516: for(j=1;j<=cptcoveff;j++)
8517: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 8518: tot=0.;
8519: for(i=1; i<=nlstate;i++){
1.227 brouard 8520: tot += prlim[i][i];
8521: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 8522: }
8523: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
8524: } /* Age */
8525: /* was end of cptcod */
8526: } /* cptcov */
8527: return 0;
1.180 brouard 8528: }
8529:
1.218 brouard 8530: 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){
8531: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
8532:
8533: /* Computes the back prevalence limit for any combination of covariate values
8534: * at any age between ageminpar and agemaxpar
8535: */
1.217 brouard 8536: int i, j, k, i1 ;
8537: /* double ftolpl = 1.e-10; */
8538: double age, agebase, agelim;
8539: double tot;
1.218 brouard 8540: /* double ***mobaverage; */
8541: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 8542:
8543: strcpy(fileresplb,"PLB_");
8544: strcat(fileresplb,fileresu);
8545: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
8546: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8547: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
8548: }
8549: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8550: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
8551: pstamp(ficresplb);
8552: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
8553: fprintf(ficresplb,"#Age ");
8554: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
8555: fprintf(ficresplb,"\n");
8556:
1.218 brouard 8557:
8558: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
8559:
8560: agebase=ageminpar;
8561: agelim=agemaxpar;
8562:
8563:
1.227 brouard 8564: i1=pow(2,cptcoveff);
1.218 brouard 8565: if (cptcovn < 1){i1=1;}
1.227 brouard 8566:
8567: for(k=1; k<=i1;k++){
1.218 brouard 8568: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
8569: fprintf(ficresplb,"#******");
8570: printf("#******");
8571: fprintf(ficlog,"#******");
1.227 brouard 8572: for(j=1;j<=cptcoveff ;j++) {/* all covariates */
1.218 brouard 8573: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8574: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8575: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8576: }
8577: fprintf(ficresplb,"******\n");
8578: printf("******\n");
8579: fprintf(ficlog,"******\n");
1.227 brouard 8580: if(invalidvarcomb[k]){
8581: printf("\nCombination (%d) ignored because no cases \n",k);
8582: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
8583: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
8584: continue;
8585: }
1.218 brouard 8586:
8587: fprintf(ficresplb,"#Age ");
1.227 brouard 8588: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 8589: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8590: }
8591: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
8592: fprintf(ficresplb,"Total Years_to_converge\n");
8593:
8594:
8595: for (age=agebase; age<=agelim; age++){
8596: /* for (age=agebase; age<=agebase; age++){ */
8597: if(mobilavproj > 0){
8598: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
8599: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.227 brouard 8600: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8601: }else if (mobilavproj == 0){
1.227 brouard 8602: 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);
8603: 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);
8604: exit(1);
1.218 brouard 8605: }else{
1.227 brouard 8606: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
8607: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8608: }
8609: fprintf(ficresplb,"%.0f ",age );
1.227 brouard 8610: for(j=1;j<=cptcoveff;j++)
8611: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8612: tot=0.;
8613: for(i=1; i<=nlstate;i++){
1.227 brouard 8614: tot += bprlim[i][i];
8615: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8616: }
8617: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8618: } /* Age */
8619: /* was end of cptcod */
8620: } /* cptcov */
8621:
8622: /* hBijx(p, bage, fage); */
8623: /* fclose(ficrespijb); */
8624:
8625: return 0;
1.217 brouard 8626: }
1.218 brouard 8627:
1.180 brouard 8628: int hPijx(double *p, int bage, int fage){
8629: /*------------- h Pij x at various ages ------------*/
8630:
8631: int stepsize;
8632: int agelim;
8633: int hstepm;
8634: int nhstepm;
8635: int h, i, i1, j, k;
8636:
8637: double agedeb;
8638: double ***p3mat;
8639:
1.201 brouard 8640: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8641: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8642: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8643: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8644: }
8645: printf("Computing pij: result on file '%s' \n", filerespij);
8646: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8647:
8648: stepsize=(int) (stepm+YEARM-1)/YEARM;
8649: /*if (stepm<=24) stepsize=2;*/
8650:
8651: agelim=AGESUP;
8652: hstepm=stepsize*YEARM; /* Every year of age */
8653: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8654:
1.180 brouard 8655: /* hstepm=1; aff par mois*/
8656: pstamp(ficrespij);
8657: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
1.227 brouard 8658: i1= pow(2,cptcoveff);
1.218 brouard 8659: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8660: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8661: /* k=k+1; */
1.227 brouard 8662: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.183 brouard 8663: fprintf(ficrespij,"\n#****** ");
1.227 brouard 8664: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8665: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8666: fprintf(ficrespij,"******\n");
8667:
8668: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8669: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8670: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8671:
8672: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8673:
1.183 brouard 8674: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8675: oldm=oldms;savm=savms;
8676: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8677: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8678: for(i=1; i<=nlstate;i++)
8679: for(j=1; j<=nlstate+ndeath;j++)
8680: fprintf(ficrespij," %1d-%1d",i,j);
8681: fprintf(ficrespij,"\n");
8682: for (h=0; h<=nhstepm; h++){
8683: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8684: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8685: for(i=1; i<=nlstate;i++)
8686: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8687: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8688: fprintf(ficrespij,"\n");
8689: }
1.183 brouard 8690: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8691: fprintf(ficrespij,"\n");
8692: }
1.180 brouard 8693: /*}*/
8694: }
1.218 brouard 8695: return 0;
1.180 brouard 8696: }
1.218 brouard 8697:
8698: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8699: /*------------- h Bij x at various ages ------------*/
8700:
8701: int stepsize;
1.218 brouard 8702: /* int agelim; */
8703: int ageminl;
1.217 brouard 8704: int hstepm;
8705: int nhstepm;
8706: int h, i, i1, j, k;
1.218 brouard 8707:
1.217 brouard 8708: double agedeb;
8709: double ***p3mat;
1.218 brouard 8710:
8711: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8712: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8713: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8714: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8715: }
8716: printf("Computing pij back: result on file '%s' \n", filerespijb);
8717: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8718:
8719: stepsize=(int) (stepm+YEARM-1)/YEARM;
8720: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8721:
1.218 brouard 8722: /* agelim=AGESUP; */
8723: ageminl=30;
8724: hstepm=stepsize*YEARM; /* Every year of age */
8725: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8726:
8727: /* hstepm=1; aff par mois*/
8728: pstamp(ficrespijb);
8729: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
1.227 brouard 8730: i1= pow(2,cptcoveff);
1.218 brouard 8731: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8732: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8733: /* k=k+1; */
1.227 brouard 8734: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.218 brouard 8735: fprintf(ficrespijb,"\n#****** ");
1.227 brouard 8736: for(j=1;j<=cptcoveff;j++)
1.218 brouard 8737: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8738: fprintf(ficrespijb,"******\n");
1.222 brouard 8739: if(invalidvarcomb[k]){
8740: fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
8741: continue;
8742: }
1.218 brouard 8743:
8744: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8745: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8746: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8747: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8748: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8749:
8750: /* nhstepm=nhstepm*YEARM; aff par mois*/
8751:
8752: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8753: /* oldm=oldms;savm=savms; */
8754: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8755: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8756: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8757: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8758: for(i=1; i<=nlstate;i++)
8759: for(j=1; j<=nlstate+ndeath;j++)
8760: fprintf(ficrespijb," %1d-%1d",i,j);
8761: fprintf(ficrespijb,"\n");
8762: for (h=0; h<=nhstepm; h++){
8763: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8764: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8765: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8766: for(i=1; i<=nlstate;i++)
8767: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8768: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8769: fprintf(ficrespijb,"\n");
8770: }
1.218 brouard 8771: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8772: fprintf(ficrespijb,"\n");
1.217 brouard 8773: }
1.218 brouard 8774: /*}*/
8775: }
8776: return 0;
8777: } /* hBijx */
1.217 brouard 8778:
1.180 brouard 8779:
1.136 brouard 8780: /***********************************************/
8781: /**************** Main Program *****************/
8782: /***********************************************/
8783:
8784: int main(int argc, char *argv[])
8785: {
8786: #ifdef GSL
8787: const gsl_multimin_fminimizer_type *T;
8788: size_t iteri = 0, it;
8789: int rval = GSL_CONTINUE;
8790: int status = GSL_SUCCESS;
8791: double ssval;
8792: #endif
8793: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8794: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8795: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8796: int jj, ll, li, lj, lk;
1.136 brouard 8797: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8798: int num_filled;
1.136 brouard 8799: int itimes;
8800: int NDIM=2;
8801: int vpopbased=0;
8802:
1.164 brouard 8803: char ca[32], cb[32];
1.136 brouard 8804: /* FILE *fichtm; *//* Html File */
8805: /* FILE *ficgp;*/ /*Gnuplot File */
8806: struct stat info;
1.191 brouard 8807: double agedeb=0.;
1.194 brouard 8808:
8809: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8810: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8811:
1.165 brouard 8812: double fret;
1.191 brouard 8813: double dum=0.; /* Dummy variable */
1.136 brouard 8814: double ***p3mat;
1.218 brouard 8815: /* double ***mobaverage; */
1.164 brouard 8816:
8817: char line[MAXLINE];
1.197 brouard 8818: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8819:
8820: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8821: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8822: char *tok, *val; /* pathtot */
1.136 brouard 8823: int firstobs=1, lastobs=10;
1.195 brouard 8824: int c, h , cpt, c2;
1.191 brouard 8825: int jl=0;
8826: int i1, j1, jk, stepsize=0;
1.194 brouard 8827: int count=0;
8828:
1.164 brouard 8829: int *tab;
1.136 brouard 8830: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8831: int backcast=0;
1.136 brouard 8832: int mobilav=0,popforecast=0;
1.191 brouard 8833: int hstepm=0, nhstepm=0;
1.136 brouard 8834: int agemortsup;
8835: float sumlpop=0.;
8836: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8837: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8838:
1.191 brouard 8839: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8840: double ftolpl=FTOL;
8841: double **prlim;
1.217 brouard 8842: double **bprlim;
1.136 brouard 8843: double ***param; /* Matrix of parameters */
8844: double *p;
8845: double **matcov; /* Matrix of covariance */
1.203 brouard 8846: double **hess; /* Hessian matrix */
1.136 brouard 8847: double ***delti3; /* Scale */
8848: double *delti; /* Scale */
8849: double ***eij, ***vareij;
8850: double **varpl; /* Variances of prevalence limits by age */
8851: double *epj, vepp;
1.164 brouard 8852:
1.136 brouard 8853: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8854: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8855:
1.136 brouard 8856: double **ximort;
1.145 brouard 8857: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8858: int *dcwave;
8859:
1.164 brouard 8860: char z[1]="c";
1.136 brouard 8861:
8862: /*char *strt;*/
8863: char strtend[80];
1.126 brouard 8864:
1.164 brouard 8865:
1.126 brouard 8866: /* setlocale (LC_ALL, ""); */
8867: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8868: /* textdomain (PACKAGE); */
8869: /* setlocale (LC_CTYPE, ""); */
8870: /* setlocale (LC_MESSAGES, ""); */
8871:
8872: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8873: rstart_time = time(NULL);
8874: /* (void) gettimeofday(&start_time,&tzp);*/
8875: start_time = *localtime(&rstart_time);
1.126 brouard 8876: curr_time=start_time;
1.157 brouard 8877: /*tml = *localtime(&start_time.tm_sec);*/
8878: /* strcpy(strstart,asctime(&tml)); */
8879: strcpy(strstart,asctime(&start_time));
1.126 brouard 8880:
8881: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8882: /* tp.tm_sec = tp.tm_sec +86400; */
8883: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8884: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8885: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8886: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8887: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8888: /* strt=asctime(&tmg); */
8889: /* printf("Time(after) =%s",strstart); */
8890: /* (void) time (&time_value);
8891: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8892: * tm = *localtime(&time_value);
8893: * strstart=asctime(&tm);
8894: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8895: */
8896:
8897: nberr=0; /* Number of errors and warnings */
8898: nbwarn=0;
1.184 brouard 8899: #ifdef WIN32
8900: _getcwd(pathcd, size);
8901: #else
1.126 brouard 8902: getcwd(pathcd, size);
1.184 brouard 8903: #endif
1.191 brouard 8904: syscompilerinfo(0);
1.196 brouard 8905: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8906: if(argc <=1){
8907: printf("\nEnter the parameter file name: ");
1.205 brouard 8908: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8909: printf("ERROR Empty parameter file name\n");
8910: goto end;
8911: }
1.126 brouard 8912: i=strlen(pathr);
8913: if(pathr[i-1]=='\n')
8914: pathr[i-1]='\0';
1.156 brouard 8915: i=strlen(pathr);
1.205 brouard 8916: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8917: pathr[i-1]='\0';
1.205 brouard 8918: }
8919: i=strlen(pathr);
8920: if( i==0 ){
8921: printf("ERROR Empty parameter file name\n");
8922: goto end;
8923: }
8924: for (tok = pathr; tok != NULL; ){
1.126 brouard 8925: printf("Pathr |%s|\n",pathr);
8926: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8927: printf("val= |%s| pathr=%s\n",val,pathr);
8928: strcpy (pathtot, val);
8929: if(pathr[0] == '\0') break; /* Dirty */
8930: }
8931: }
8932: else{
8933: strcpy(pathtot,argv[1]);
8934: }
8935: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8936: /*cygwin_split_path(pathtot,path,optionfile);
8937: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8938: /* cutv(path,optionfile,pathtot,'\\');*/
8939:
8940: /* Split argv[0], imach program to get pathimach */
8941: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8942: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8943: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8944: /* strcpy(pathimach,argv[0]); */
8945: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8946: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8947: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8948: #ifdef WIN32
8949: _chdir(path); /* Can be a relative path */
8950: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8951: #else
1.126 brouard 8952: chdir(path); /* Can be a relative path */
1.184 brouard 8953: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8954: #endif
8955: printf("Current directory %s!\n",pathcd);
1.126 brouard 8956: strcpy(command,"mkdir ");
8957: strcat(command,optionfilefiname);
8958: if((outcmd=system(command)) != 0){
1.169 brouard 8959: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8960: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8961: /* fclose(ficlog); */
8962: /* exit(1); */
8963: }
8964: /* if((imk=mkdir(optionfilefiname))<0){ */
8965: /* perror("mkdir"); */
8966: /* } */
8967:
8968: /*-------- arguments in the command line --------*/
8969:
1.186 brouard 8970: /* Main Log file */
1.126 brouard 8971: strcat(filelog, optionfilefiname);
8972: strcat(filelog,".log"); /* */
8973: if((ficlog=fopen(filelog,"w"))==NULL) {
8974: printf("Problem with logfile %s\n",filelog);
8975: goto end;
8976: }
8977: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8978: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8979: fprintf(ficlog,"\nEnter the parameter file name: \n");
8980: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8981: path=%s \n\
8982: optionfile=%s\n\
8983: optionfilext=%s\n\
1.156 brouard 8984: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8985:
1.197 brouard 8986: syscompilerinfo(1);
1.167 brouard 8987:
1.126 brouard 8988: printf("Local time (at start):%s",strstart);
8989: fprintf(ficlog,"Local time (at start): %s",strstart);
8990: fflush(ficlog);
8991: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8992: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8993:
8994: /* */
8995: strcpy(fileres,"r");
8996: strcat(fileres, optionfilefiname);
1.201 brouard 8997: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8998: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8999: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 9000:
1.186 brouard 9001: /* Main ---------arguments file --------*/
1.126 brouard 9002:
9003: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 9004: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
9005: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 9006: fflush(ficlog);
1.149 brouard 9007: /* goto end; */
9008: exit(70);
1.126 brouard 9009: }
9010:
9011:
9012:
9013: strcpy(filereso,"o");
1.201 brouard 9014: strcat(filereso,fileresu);
1.126 brouard 9015: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
9016: printf("Problem with Output resultfile: %s\n", filereso);
9017: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
9018: fflush(ficlog);
9019: goto end;
9020: }
9021:
9022: /* Reads comments: lines beginning with '#' */
9023: numlinepar=0;
1.197 brouard 9024:
9025: /* First parameter line */
9026: while(fgets(line, MAXLINE, ficpar)) {
9027: /* If line starts with a # it is a comment */
9028: if (line[0] == '#') {
9029: numlinepar++;
9030: fputs(line,stdout);
9031: fputs(line,ficparo);
9032: fputs(line,ficlog);
9033: continue;
9034: }else
9035: break;
9036: }
9037: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
9038: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
9039: if (num_filled != 5) {
9040: printf("Should be 5 parameters\n");
9041: }
1.126 brouard 9042: numlinepar++;
1.197 brouard 9043: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
9044: }
9045: /* Second parameter line */
9046: while(fgets(line, MAXLINE, ficpar)) {
9047: /* If line starts with a # it is a comment */
9048: if (line[0] == '#') {
9049: numlinepar++;
9050: fputs(line,stdout);
9051: fputs(line,ficparo);
9052: fputs(line,ficlog);
9053: continue;
9054: }else
9055: break;
9056: }
1.223 brouard 9057: 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", \
9058: &ftol, &stepm, &ncovcol, &nqv, &ntv, &nqtv, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
9059: if (num_filled != 11) {
9060: 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 9061: printf("but line=%s\n",line);
1.197 brouard 9062: }
1.223 brouard 9063: 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 9064: }
1.203 brouard 9065: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 9066: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 9067: /* Third parameter line */
9068: while(fgets(line, MAXLINE, ficpar)) {
9069: /* If line starts with a # it is a comment */
9070: if (line[0] == '#') {
9071: numlinepar++;
9072: fputs(line,stdout);
9073: fputs(line,ficparo);
9074: fputs(line,ficlog);
9075: continue;
9076: }else
9077: break;
9078: }
1.201 brouard 9079: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
9080: if (num_filled == 0)
9081: model[0]='\0';
9082: else if (num_filled != 1){
1.197 brouard 9083: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9084: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
9085: model[0]='\0';
9086: goto end;
9087: }
9088: else{
9089: if (model[0]=='+'){
9090: for(i=1; i<=strlen(model);i++)
9091: modeltemp[i-1]=model[i];
1.201 brouard 9092: strcpy(model,modeltemp);
1.197 brouard 9093: }
9094: }
1.199 brouard 9095: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 9096: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 9097: }
9098: /* 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); */
9099: /* numlinepar=numlinepar+3; /\* In general *\/ */
9100: /* 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 9101: 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);
9102: 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 9103: fflush(ficlog);
1.190 brouard 9104: /* if(model[0]=='#'|| model[0]== '\0'){ */
9105: if(model[0]=='#'){
1.187 brouard 9106: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
9107: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
9108: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
9109: if(mle != -1){
9110: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
9111: exit(1);
9112: }
9113: }
1.126 brouard 9114: while((c=getc(ficpar))=='#' && c!= EOF){
9115: ungetc(c,ficpar);
9116: fgets(line, MAXLINE, ficpar);
9117: numlinepar++;
1.195 brouard 9118: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
9119: z[0]=line[1];
9120: }
9121: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 9122: fputs(line, stdout);
9123: //puts(line);
1.126 brouard 9124: fputs(line,ficparo);
9125: fputs(line,ficlog);
9126: }
9127: ungetc(c,ficpar);
9128:
9129:
1.145 brouard 9130: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.225 brouard 9131: coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
9132: cotvar=ma3x(1,maxwav,1,ntv,1,n); /**< Time varying covariate */
9133: cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
1.136 brouard 9134: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
9135: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
9136: v1+v2*age+v2*v3 makes cptcovn = 3
9137: */
9138: if (strlen(model)>1)
1.187 brouard 9139: 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 9140: else
1.187 brouard 9141: ncovmodel=2; /* Constant and age */
1.133 brouard 9142: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
9143: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 9144: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
9145: 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);
9146: 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);
9147: fflush(stdout);
9148: fclose (ficlog);
9149: goto end;
9150: }
1.126 brouard 9151: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9152: delti=delti3[1][1];
9153: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
9154: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
9155: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 9156: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
9157: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9158: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9159: fclose (ficparo);
9160: fclose (ficlog);
9161: goto end;
9162: exit(0);
1.220 brouard 9163: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 9164: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 9165: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
9166: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 9167: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9168: matcov=matrix(1,npar,1,npar);
1.203 brouard 9169: hess=matrix(1,npar,1,npar);
1.220 brouard 9170: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 9171: /* Read guessed parameters */
1.126 brouard 9172: /* Reads comments: lines beginning with '#' */
9173: while((c=getc(ficpar))=='#' && c!= EOF){
9174: ungetc(c,ficpar);
9175: fgets(line, MAXLINE, ficpar);
9176: numlinepar++;
1.141 brouard 9177: fputs(line,stdout);
1.126 brouard 9178: fputs(line,ficparo);
9179: fputs(line,ficlog);
9180: }
9181: ungetc(c,ficpar);
9182:
9183: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
9184: for(i=1; i <=nlstate; i++){
1.220 brouard 9185: j=0;
1.126 brouard 9186: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 9187: if(jj==i) continue;
9188: j++;
9189: fscanf(ficpar,"%1d%1d",&i1,&j1);
9190: if ((i1 != i) || (j1 != jj)){
9191: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 9192: It might be a problem of design; if ncovcol and the model are correct\n \
9193: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 9194: exit(1);
9195: }
9196: fprintf(ficparo,"%1d%1d",i1,j1);
9197: if(mle==1)
9198: printf("%1d%1d",i,jj);
9199: fprintf(ficlog,"%1d%1d",i,jj);
9200: for(k=1; k<=ncovmodel;k++){
9201: fscanf(ficpar," %lf",¶m[i][j][k]);
9202: if(mle==1){
9203: printf(" %lf",param[i][j][k]);
9204: fprintf(ficlog," %lf",param[i][j][k]);
9205: }
9206: else
9207: fprintf(ficlog," %lf",param[i][j][k]);
9208: fprintf(ficparo," %lf",param[i][j][k]);
9209: }
9210: fscanf(ficpar,"\n");
9211: numlinepar++;
9212: if(mle==1)
9213: printf("\n");
9214: fprintf(ficlog,"\n");
9215: fprintf(ficparo,"\n");
1.126 brouard 9216: }
9217: }
9218: fflush(ficlog);
9219:
1.145 brouard 9220: /* Reads scales values */
1.126 brouard 9221: p=param[1][1];
9222:
9223: /* Reads comments: lines beginning with '#' */
9224: while((c=getc(ficpar))=='#' && c!= EOF){
9225: ungetc(c,ficpar);
9226: fgets(line, MAXLINE, ficpar);
9227: numlinepar++;
1.141 brouard 9228: fputs(line,stdout);
1.126 brouard 9229: fputs(line,ficparo);
9230: fputs(line,ficlog);
9231: }
9232: ungetc(c,ficpar);
9233:
9234: for(i=1; i <=nlstate; i++){
9235: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 9236: fscanf(ficpar,"%1d%1d",&i1,&j1);
9237: if ( (i1-i) * (j1-j) != 0){
9238: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
9239: exit(1);
9240: }
9241: printf("%1d%1d",i,j);
9242: fprintf(ficparo,"%1d%1d",i1,j1);
9243: fprintf(ficlog,"%1d%1d",i1,j1);
9244: for(k=1; k<=ncovmodel;k++){
9245: fscanf(ficpar,"%le",&delti3[i][j][k]);
9246: printf(" %le",delti3[i][j][k]);
9247: fprintf(ficparo," %le",delti3[i][j][k]);
9248: fprintf(ficlog," %le",delti3[i][j][k]);
9249: }
9250: fscanf(ficpar,"\n");
9251: numlinepar++;
9252: printf("\n");
9253: fprintf(ficparo,"\n");
9254: fprintf(ficlog,"\n");
1.126 brouard 9255: }
9256: }
9257: fflush(ficlog);
1.220 brouard 9258:
1.145 brouard 9259: /* Reads covariance matrix */
1.126 brouard 9260: delti=delti3[1][1];
1.220 brouard 9261:
9262:
1.126 brouard 9263: /* 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 9264:
1.126 brouard 9265: /* Reads comments: lines beginning with '#' */
9266: while((c=getc(ficpar))=='#' && c!= EOF){
9267: ungetc(c,ficpar);
9268: fgets(line, MAXLINE, ficpar);
9269: numlinepar++;
1.141 brouard 9270: fputs(line,stdout);
1.126 brouard 9271: fputs(line,ficparo);
9272: fputs(line,ficlog);
9273: }
9274: ungetc(c,ficpar);
1.220 brouard 9275:
1.126 brouard 9276: matcov=matrix(1,npar,1,npar);
1.203 brouard 9277: hess=matrix(1,npar,1,npar);
1.131 brouard 9278: for(i=1; i <=npar; i++)
9279: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 9280:
1.194 brouard 9281: /* Scans npar lines */
1.126 brouard 9282: for(i=1; i <=npar; i++){
1.226 brouard 9283: count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
1.194 brouard 9284: if(count != 3){
1.226 brouard 9285: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9286: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9287: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9288: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 9289: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
9290: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.226 brouard 9291: exit(1);
1.220 brouard 9292: }else{
1.226 brouard 9293: if(mle==1)
9294: printf("%1d%1d%d",i1,j1,jk);
9295: }
9296: fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
9297: fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
1.126 brouard 9298: for(j=1; j <=i; j++){
1.226 brouard 9299: fscanf(ficpar," %le",&matcov[i][j]);
9300: if(mle==1){
9301: printf(" %.5le",matcov[i][j]);
9302: }
9303: fprintf(ficlog," %.5le",matcov[i][j]);
9304: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 9305: }
9306: fscanf(ficpar,"\n");
9307: numlinepar++;
9308: if(mle==1)
1.220 brouard 9309: printf("\n");
1.126 brouard 9310: fprintf(ficlog,"\n");
9311: fprintf(ficparo,"\n");
9312: }
1.194 brouard 9313: /* End of read covariance matrix npar lines */
1.126 brouard 9314: for(i=1; i <=npar; i++)
9315: for(j=i+1;j<=npar;j++)
1.226 brouard 9316: matcov[i][j]=matcov[j][i];
1.126 brouard 9317:
9318: if(mle==1)
9319: printf("\n");
9320: fprintf(ficlog,"\n");
9321:
9322: fflush(ficlog);
9323:
9324: /*-------- Rewriting parameter file ----------*/
9325: strcpy(rfileres,"r"); /* "Rparameterfile */
9326: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
9327: strcat(rfileres,"."); /* */
9328: strcat(rfileres,optionfilext); /* Other files have txt extension */
9329: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 9330: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
9331: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 9332: }
9333: fprintf(ficres,"#%s\n",version);
9334: } /* End of mle != -3 */
1.218 brouard 9335:
1.186 brouard 9336: /* Main data
9337: */
1.126 brouard 9338: n= lastobs;
9339: num=lvector(1,n);
9340: moisnais=vector(1,n);
9341: annais=vector(1,n);
9342: moisdc=vector(1,n);
9343: andc=vector(1,n);
1.220 brouard 9344: weight=vector(1,n);
1.126 brouard 9345: agedc=vector(1,n);
9346: cod=ivector(1,n);
1.220 brouard 9347: for(i=1;i<=n;i++){
9348: num[i]=0;
9349: moisnais[i]=0;
9350: annais[i]=0;
9351: moisdc[i]=0;
9352: andc[i]=0;
9353: agedc[i]=0;
9354: cod[i]=0;
9355: weight[i]=1.0; /* Equal weights, 1 by default */
9356: }
1.126 brouard 9357: mint=matrix(1,maxwav,1,n);
9358: anint=matrix(1,maxwav,1,n);
1.131 brouard 9359: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 9360: tab=ivector(1,NCOVMAX);
1.144 brouard 9361: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 9362: 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 9363:
1.136 brouard 9364: /* Reads data from file datafile */
9365: if (readdata(datafile, firstobs, lastobs, &imx)==1)
9366: goto end;
9367:
9368: /* Calculation of the number of parameters from char model */
1.137 brouard 9369: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
9370: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
9371: k=3 V4 Tvar[k=3]= 4 (from V4)
9372: k=2 V1 Tvar[k=2]= 1 (from V1)
9373: k=1 Tvar[1]=2 (from V2)
9374: */
9375: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
1.226 brouard 9376: Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
9377: Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
9378: Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
1.137 brouard 9379: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
9380: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
9381: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
9382: */
9383: /* For model-covariate k tells which data-covariate to use but
9384: because this model-covariate is a construction we invent a new column
9385: ncovcol + k1
9386: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
9387: Tvar[3=V1*V4]=4+1 etc */
1.227 brouard 9388: Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
9389: Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
1.137 brouard 9390: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
9391: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
1.227 brouard 9392: Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
1.137 brouard 9393: */
1.145 brouard 9394: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
9395: 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 9396: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
9397: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 9398: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 9399: 4 covariates (3 plus signs)
9400: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
9401: */
1.227 brouard 9402: Tmodelind=ivector(1,NCOVMAX);/** five the k model position of an
9403: * individual dummy, fixed or varying:
9404: * Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
9405: * 3, 1, 0, 0, 0, 0, 0, 0},
9406: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.228 ! brouard 9407: TmodelInvind=ivector(1,NCOVMAX);
! 9408: TmodelInvQind=ivector(1,NCOVMAX);/** five the k model position of an
! 9409: * individual quantitative, fixed or varying:
! 9410: * Tmodelqind[1]=1,Tvaraff[1]@9={4,
! 9411: * 3, 1, 0, 0, 0, 0, 0, 0},
! 9412: * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
1.186 brouard 9413: /* Main decodemodel */
9414:
1.187 brouard 9415:
1.223 brouard 9416: if(decodemodel(model, lastobs) == 1) /* In order to get Tvar[k] V4+V3+V5 p Tvar[1]@3 = {4, 3, 5}*/
1.136 brouard 9417: goto end;
9418:
1.137 brouard 9419: if((double)(lastobs-imx)/(double)imx > 1.10){
9420: nbwarn++;
9421: 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);
9422: 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);
9423: }
1.136 brouard 9424: /* if(mle==1){*/
1.137 brouard 9425: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
9426: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 9427: }
9428:
9429: /*-calculation of age at interview from date of interview and age at death -*/
9430: agev=matrix(1,maxwav,1,imx);
9431:
9432: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
9433: goto end;
9434:
1.126 brouard 9435:
1.136 brouard 9436: agegomp=(int)agemin;
9437: free_vector(moisnais,1,n);
9438: free_vector(annais,1,n);
1.126 brouard 9439: /* free_matrix(mint,1,maxwav,1,n);
9440: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 9441: /* free_vector(moisdc,1,n); */
9442: /* free_vector(andc,1,n); */
1.145 brouard 9443: /* */
9444:
1.126 brouard 9445: wav=ivector(1,imx);
1.214 brouard 9446: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
9447: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
9448: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
9449: 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.*/
9450: bh=imatrix(1,lastpass-firstpass+2,1,imx);
9451: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 9452:
9453: /* Concatenates waves */
1.214 brouard 9454: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
9455: Death is a valid wave (if date is known).
9456: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
9457: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
9458: and mw[mi+1][i]. dh depends on stepm.
9459: */
9460:
1.126 brouard 9461: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 9462: /* */
9463:
1.215 brouard 9464: free_vector(moisdc,1,n);
9465: free_vector(andc,1,n);
9466:
1.126 brouard 9467: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
9468: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
9469: ncodemax[1]=1;
1.145 brouard 9470: Ndum =ivector(-1,NCOVMAX);
1.225 brouard 9471: cptcoveff=0;
1.220 brouard 9472: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
9473: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.227 brouard 9474: }
9475:
9476: ncovcombmax=pow(2,cptcoveff);
9477: invalidvarcomb=ivector(1, ncovcombmax);
9478: for(i=1;i<ncovcombmax;i++)
9479: invalidvarcomb[i]=0;
9480:
1.211 brouard 9481: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 9482: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 9483: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.227 brouard 9484:
1.200 brouard 9485: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 9486: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 9487: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 9488: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
9489: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
9490: * (currently 0 or 1) in the data.
9491: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
9492: * corresponding modality (h,j).
9493: */
9494:
1.145 brouard 9495: h=0;
9496: /*if (cptcovn > 0) */
1.126 brouard 9497: m=pow(2,cptcoveff);
9498:
1.144 brouard 9499: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 9500: * For k=4 covariates, h goes from 1 to m=2**k
9501: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
9502: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 9503: * h\k 1 2 3 4
1.143 brouard 9504: *______________________________
9505: * 1 i=1 1 i=1 1 i=1 1 i=1 1
9506: * 2 2 1 1 1
9507: * 3 i=2 1 2 1 1
9508: * 4 2 2 1 1
9509: * 5 i=3 1 i=2 1 2 1
9510: * 6 2 1 2 1
9511: * 7 i=4 1 2 2 1
9512: * 8 2 2 2 1
1.197 brouard 9513: * 9 i=5 1 i=3 1 i=2 1 2
9514: * 10 2 1 1 2
9515: * 11 i=6 1 2 1 2
9516: * 12 2 2 1 2
9517: * 13 i=7 1 i=4 1 2 2
9518: * 14 2 1 2 2
9519: * 15 i=8 1 2 2 2
9520: * 16 2 2 2 2
1.143 brouard 9521: */
1.212 brouard 9522: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 9523: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
9524: * and the value of each covariate?
9525: * V1=1, V2=1, V3=2, V4=1 ?
9526: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
9527: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
9528: * In order to get the real value in the data, we use nbcode
9529: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
9530: * We are keeping this crazy system in order to be able (in the future?)
9531: * to have more than 2 values (0 or 1) for a covariate.
9532: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
9533: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
9534: * bbbbbbbb
9535: * 76543210
9536: * h-1 00000101 (6-1=5)
1.219 brouard 9537: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 9538: * &
9539: * 1 00000001 (1)
1.219 brouard 9540: * 00000000 = 1 & ((h-1) >> (k-1))
9541: * +1= 00000001 =1
1.211 brouard 9542: *
9543: * h=14, k=3 => h'=h-1=13, k'=k-1=2
9544: * h' 1101 =2^3+2^2+0x2^1+2^0
9545: * >>k' 11
9546: * & 00000001
9547: * = 00000001
9548: * +1 = 00000010=2 = codtabm(14,3)
9549: * Reverse h=6 and m=16?
9550: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
9551: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
9552: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
9553: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
9554: * V3=decodtabm(14,3,2**4)=2
9555: * h'=13 1101 =2^3+2^2+0x2^1+2^0
9556: *(h-1) >> (j-1) 0011 =13 >> 2
9557: * &1 000000001
9558: * = 000000001
9559: * +1= 000000010 =2
9560: * 2211
9561: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
9562: * V3=2
1.220 brouard 9563: * codtabm and decodtabm are identical
1.211 brouard 9564: */
9565:
1.145 brouard 9566:
9567: free_ivector(Ndum,-1,NCOVMAX);
9568:
9569:
1.126 brouard 9570:
1.186 brouard 9571: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 9572: strcpy(optionfilegnuplot,optionfilefiname);
9573: if(mle==-3)
1.201 brouard 9574: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 9575: strcat(optionfilegnuplot,".gp");
9576:
9577: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
9578: printf("Problem with file %s",optionfilegnuplot);
9579: }
9580: else{
1.204 brouard 9581: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 9582: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 9583: //fprintf(ficgp,"set missing 'NaNq'\n");
9584: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 9585: }
9586: /* fclose(ficgp);*/
1.186 brouard 9587:
9588:
9589: /* Initialisation of --------- index.htm --------*/
1.126 brouard 9590:
9591: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
9592: if(mle==-3)
1.201 brouard 9593: strcat(optionfilehtm,"-MORT_");
1.126 brouard 9594: strcat(optionfilehtm,".htm");
9595: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 9596: printf("Problem with %s \n",optionfilehtm);
9597: exit(0);
1.126 brouard 9598: }
9599:
9600: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
9601: strcat(optionfilehtmcov,"-cov.htm");
9602: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
9603: printf("Problem with %s \n",optionfilehtmcov), exit(0);
9604: }
9605: else{
9606: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
9607: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9608: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 9609: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
9610: }
9611:
1.213 brouard 9612: 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 9613: <hr size=\"2\" color=\"#EC5E5E\"> \n\
9614: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 9615: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 9616: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 9617: \n\
9618: <hr size=\"2\" color=\"#EC5E5E\">\
9619: <ul><li><h4>Parameter files</h4>\n\
9620: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
9621: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
9622: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
9623: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
9624: - Date and time at start: %s</ul>\n",\
9625: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
9626: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
9627: fileres,fileres,\
9628: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
9629: fflush(fichtm);
9630:
9631: strcpy(pathr,path);
9632: strcat(pathr,optionfilefiname);
1.184 brouard 9633: #ifdef WIN32
9634: _chdir(optionfilefiname); /* Move to directory named optionfile */
9635: #else
1.126 brouard 9636: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9637: #endif
9638:
1.126 brouard 9639:
1.220 brouard 9640: /* Calculates basic frequencies. Computes observed prevalence at single age
9641: and for any valid combination of covariates
1.126 brouard 9642: and prints on file fileres'p'. */
1.227 brouard 9643: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
9644: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9645:
9646: fprintf(fichtm,"\n");
9647: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9648: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9649: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9650: imx,agemin,agemax,jmin,jmax,jmean);
9651: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9652: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9653: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9654: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9655: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9656:
1.126 brouard 9657: /* For Powell, parameters are in a vector p[] starting at p[1]
9658: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9659: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9660:
9661: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9662: /* For mortality only */
1.126 brouard 9663: if (mle==-3){
1.136 brouard 9664: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9665: for(i=1;i<=NDIM;i++)
9666: for(j=1;j<=NDIM;j++)
9667: ximort[i][j]=0.;
1.186 brouard 9668: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9669: cens=ivector(1,n);
9670: ageexmed=vector(1,n);
9671: agecens=vector(1,n);
9672: dcwave=ivector(1,n);
1.223 brouard 9673:
1.126 brouard 9674: for (i=1; i<=imx; i++){
9675: dcwave[i]=-1;
9676: for (m=firstpass; m<=lastpass; m++)
1.226 brouard 9677: if (s[m][i]>nlstate) {
9678: dcwave[i]=m;
9679: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9680: break;
9681: }
1.126 brouard 9682: }
1.226 brouard 9683:
1.126 brouard 9684: for (i=1; i<=imx; i++) {
9685: if (wav[i]>0){
1.226 brouard 9686: ageexmed[i]=agev[mw[1][i]][i];
9687: j=wav[i];
9688: agecens[i]=1.;
9689:
9690: if (ageexmed[i]> 1 && wav[i] > 0){
9691: agecens[i]=agev[mw[j][i]][i];
9692: cens[i]= 1;
9693: }else if (ageexmed[i]< 1)
9694: cens[i]= -1;
9695: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9696: cens[i]=0 ;
1.126 brouard 9697: }
9698: else cens[i]=-1;
9699: }
9700:
9701: for (i=1;i<=NDIM;i++) {
9702: for (j=1;j<=NDIM;j++)
1.226 brouard 9703: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9704: }
9705:
1.145 brouard 9706: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9707: /*printf("%lf %lf", p[1], p[2]);*/
9708:
9709:
1.136 brouard 9710: #ifdef GSL
9711: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9712: #else
1.126 brouard 9713: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9714: #endif
1.201 brouard 9715: strcpy(filerespow,"POW-MORT_");
9716: strcat(filerespow,fileresu);
1.126 brouard 9717: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9718: printf("Problem with resultfile: %s\n", filerespow);
9719: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9720: }
1.136 brouard 9721: #ifdef GSL
9722: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9723: #else
1.126 brouard 9724: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9725: #endif
1.126 brouard 9726: /* for (i=1;i<=nlstate;i++)
9727: for(j=1;j<=nlstate+ndeath;j++)
9728: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9729: */
9730: fprintf(ficrespow,"\n");
1.136 brouard 9731: #ifdef GSL
9732: /* gsl starts here */
9733: T = gsl_multimin_fminimizer_nmsimplex;
9734: gsl_multimin_fminimizer *sfm = NULL;
9735: gsl_vector *ss, *x;
9736: gsl_multimin_function minex_func;
9737:
9738: /* Initial vertex size vector */
9739: ss = gsl_vector_alloc (NDIM);
9740:
9741: if (ss == NULL){
9742: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9743: }
9744: /* Set all step sizes to 1 */
9745: gsl_vector_set_all (ss, 0.001);
9746:
9747: /* Starting point */
1.126 brouard 9748:
1.136 brouard 9749: x = gsl_vector_alloc (NDIM);
9750:
9751: if (x == NULL){
9752: gsl_vector_free(ss);
9753: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9754: }
9755:
9756: /* Initialize method and iterate */
9757: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9758: /* gsl_vector_set(x, 0, 0.0268); */
9759: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9760: gsl_vector_set(x, 0, p[1]);
9761: gsl_vector_set(x, 1, p[2]);
9762:
9763: minex_func.f = &gompertz_f;
9764: minex_func.n = NDIM;
9765: minex_func.params = (void *)&p; /* ??? */
9766:
9767: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9768: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9769:
9770: printf("Iterations beginning .....\n\n");
9771: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9772:
9773: iteri=0;
9774: while (rval == GSL_CONTINUE){
9775: iteri++;
9776: status = gsl_multimin_fminimizer_iterate(sfm);
9777:
9778: if (status) printf("error: %s\n", gsl_strerror (status));
9779: fflush(0);
9780:
9781: if (status)
9782: break;
9783:
9784: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9785: ssval = gsl_multimin_fminimizer_size (sfm);
9786:
9787: if (rval == GSL_SUCCESS)
9788: printf ("converged to a local maximum at\n");
9789:
9790: printf("%5d ", iteri);
9791: for (it = 0; it < NDIM; it++){
9792: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9793: }
9794: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9795: }
9796:
9797: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9798:
9799: gsl_vector_free(x); /* initial values */
9800: gsl_vector_free(ss); /* inital step size */
9801: for (it=0; it<NDIM; it++){
9802: p[it+1]=gsl_vector_get(sfm->x,it);
9803: fprintf(ficrespow," %.12lf", p[it]);
9804: }
9805: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9806: #endif
9807: #ifdef POWELL
9808: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9809: #endif
1.126 brouard 9810: fclose(ficrespow);
9811:
1.203 brouard 9812: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9813:
9814: for(i=1; i <=NDIM; i++)
9815: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9816: matcov[i][j]=matcov[j][i];
1.126 brouard 9817:
9818: printf("\nCovariance matrix\n ");
1.203 brouard 9819: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9820: for(i=1; i <=NDIM; i++) {
9821: for(j=1;j<=NDIM;j++){
1.220 brouard 9822: printf("%f ",matcov[i][j]);
9823: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9824: }
1.203 brouard 9825: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9826: }
9827:
9828: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9829: for (i=1;i<=NDIM;i++) {
1.126 brouard 9830: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9831: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9832: }
1.126 brouard 9833: lsurv=vector(1,AGESUP);
9834: lpop=vector(1,AGESUP);
9835: tpop=vector(1,AGESUP);
9836: lsurv[agegomp]=100000;
9837:
9838: for (k=agegomp;k<=AGESUP;k++) {
9839: agemortsup=k;
9840: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9841: }
9842:
9843: for (k=agegomp;k<agemortsup;k++)
9844: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9845:
9846: for (k=agegomp;k<agemortsup;k++){
9847: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9848: sumlpop=sumlpop+lpop[k];
9849: }
9850:
9851: tpop[agegomp]=sumlpop;
9852: for (k=agegomp;k<(agemortsup-3);k++){
9853: /* tpop[k+1]=2;*/
9854: tpop[k+1]=tpop[k]-lpop[k];
9855: }
9856:
9857:
9858: printf("\nAge lx qx dx Lx Tx e(x)\n");
9859: for (k=agegomp;k<(agemortsup-2);k++)
9860: 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]);
9861:
9862:
9863: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9864: ageminpar=50;
9865: agemaxpar=100;
1.194 brouard 9866: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9867: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9868: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9869: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9870: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9871: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9872: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9873: }else{
9874: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9875: 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 9876: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9877: }
1.201 brouard 9878: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9879: stepm, weightopt,\
9880: model,imx,p,matcov,agemortsup);
9881:
9882: free_vector(lsurv,1,AGESUP);
9883: free_vector(lpop,1,AGESUP);
9884: free_vector(tpop,1,AGESUP);
1.220 brouard 9885: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9886: free_ivector(cens,1,n);
9887: free_vector(agecens,1,n);
9888: free_ivector(dcwave,1,n);
1.220 brouard 9889: #ifdef GSL
1.136 brouard 9890: #endif
1.186 brouard 9891: } /* Endof if mle==-3 mortality only */
1.205 brouard 9892: /* Standard */
9893: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9894: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9895: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9896: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9897: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9898: for (k=1; k<=npar;k++)
9899: printf(" %d %8.5f",k,p[k]);
9900: printf("\n");
1.205 brouard 9901: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9902: /* mlikeli uses func not funcone */
9903: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9904: }
9905: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9906: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9907: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9908: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9909: }
9910: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9911: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9912: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9913: for (k=1; k<=npar;k++)
9914: printf(" %d %8.5f",k,p[k]);
9915: printf("\n");
9916:
9917: /*--------- results files --------------*/
1.224 brouard 9918: 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 9919:
9920:
9921: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9922: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9923: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9924: for(i=1,jk=1; i <=nlstate; i++){
9925: for(k=1; k <=(nlstate+ndeath); k++){
1.225 brouard 9926: if (k != i) {
9927: printf("%d%d ",i,k);
9928: fprintf(ficlog,"%d%d ",i,k);
9929: fprintf(ficres,"%1d%1d ",i,k);
9930: for(j=1; j <=ncovmodel; j++){
9931: printf("%12.7f ",p[jk]);
9932: fprintf(ficlog,"%12.7f ",p[jk]);
9933: fprintf(ficres,"%12.7f ",p[jk]);
9934: jk++;
9935: }
9936: printf("\n");
9937: fprintf(ficlog,"\n");
9938: fprintf(ficres,"\n");
9939: }
1.126 brouard 9940: }
9941: }
1.203 brouard 9942: if(mle != 0){
9943: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9944: ftolhess=ftol; /* Usually correct */
1.203 brouard 9945: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9946: 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");
9947: 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");
9948: for(i=1,jk=1; i <=nlstate; i++){
1.225 brouard 9949: for(k=1; k <=(nlstate+ndeath); k++){
9950: if (k != i) {
9951: printf("%d%d ",i,k);
9952: fprintf(ficlog,"%d%d ",i,k);
9953: for(j=1; j <=ncovmodel; j++){
9954: 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]));
9955: 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]));
9956: jk++;
9957: }
9958: printf("\n");
9959: fprintf(ficlog,"\n");
9960: }
9961: }
1.193 brouard 9962: }
1.203 brouard 9963: } /* end of hesscov and Wald tests */
1.225 brouard 9964:
1.203 brouard 9965: /* */
1.126 brouard 9966: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9967: printf("# Scales (for hessian or gradient estimation)\n");
9968: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9969: for(i=1,jk=1; i <=nlstate; i++){
9970: for(j=1; j <=nlstate+ndeath; j++){
1.225 brouard 9971: if (j!=i) {
9972: fprintf(ficres,"%1d%1d",i,j);
9973: printf("%1d%1d",i,j);
9974: fprintf(ficlog,"%1d%1d",i,j);
9975: for(k=1; k<=ncovmodel;k++){
9976: printf(" %.5e",delti[jk]);
9977: fprintf(ficlog," %.5e",delti[jk]);
9978: fprintf(ficres," %.5e",delti[jk]);
9979: jk++;
9980: }
9981: printf("\n");
9982: fprintf(ficlog,"\n");
9983: fprintf(ficres,"\n");
9984: }
1.126 brouard 9985: }
9986: }
9987:
9988: 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 9989: if(mle >= 1) /* To big for the screen */
1.126 brouard 9990: 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");
9991: 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");
9992: /* # 121 Var(a12)\n\ */
9993: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9994: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9995: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9996: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9997: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9998: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9999: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
10000:
10001:
10002: /* Just to have a covariance matrix which will be more understandable
10003: even is we still don't want to manage dictionary of variables
10004: */
10005: for(itimes=1;itimes<=2;itimes++){
10006: jj=0;
10007: for(i=1; i <=nlstate; i++){
1.225 brouard 10008: for(j=1; j <=nlstate+ndeath; j++){
10009: if(j==i) continue;
10010: for(k=1; k<=ncovmodel;k++){
10011: jj++;
10012: ca[0]= k+'a'-1;ca[1]='\0';
10013: if(itimes==1){
10014: if(mle>=1)
10015: printf("#%1d%1d%d",i,j,k);
10016: fprintf(ficlog,"#%1d%1d%d",i,j,k);
10017: fprintf(ficres,"#%1d%1d%d",i,j,k);
10018: }else{
10019: if(mle>=1)
10020: printf("%1d%1d%d",i,j,k);
10021: fprintf(ficlog,"%1d%1d%d",i,j,k);
10022: fprintf(ficres,"%1d%1d%d",i,j,k);
10023: }
10024: ll=0;
10025: for(li=1;li <=nlstate; li++){
10026: for(lj=1;lj <=nlstate+ndeath; lj++){
10027: if(lj==li) continue;
10028: for(lk=1;lk<=ncovmodel;lk++){
10029: ll++;
10030: if(ll<=jj){
10031: cb[0]= lk +'a'-1;cb[1]='\0';
10032: if(ll<jj){
10033: if(itimes==1){
10034: if(mle>=1)
10035: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10036: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10037: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
10038: }else{
10039: if(mle>=1)
10040: printf(" %.5e",matcov[jj][ll]);
10041: fprintf(ficlog," %.5e",matcov[jj][ll]);
10042: fprintf(ficres," %.5e",matcov[jj][ll]);
10043: }
10044: }else{
10045: if(itimes==1){
10046: if(mle>=1)
10047: printf(" Var(%s%1d%1d)",ca,i,j);
10048: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
10049: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
10050: }else{
10051: if(mle>=1)
10052: printf(" %.7e",matcov[jj][ll]);
10053: fprintf(ficlog," %.7e",matcov[jj][ll]);
10054: fprintf(ficres," %.7e",matcov[jj][ll]);
10055: }
10056: }
10057: }
10058: } /* end lk */
10059: } /* end lj */
10060: } /* end li */
10061: if(mle>=1)
10062: printf("\n");
10063: fprintf(ficlog,"\n");
10064: fprintf(ficres,"\n");
10065: numlinepar++;
10066: } /* end k*/
10067: } /*end j */
1.126 brouard 10068: } /* end i */
10069: } /* end itimes */
10070:
10071: fflush(ficlog);
10072: fflush(ficres);
1.225 brouard 10073: while(fgets(line, MAXLINE, ficpar)) {
10074: /* If line starts with a # it is a comment */
10075: if (line[0] == '#') {
10076: numlinepar++;
10077: fputs(line,stdout);
10078: fputs(line,ficparo);
10079: fputs(line,ficlog);
10080: continue;
10081: }else
10082: break;
10083: }
10084:
1.209 brouard 10085: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
10086: /* ungetc(c,ficpar); */
10087: /* fgets(line, MAXLINE, ficpar); */
10088: /* fputs(line,stdout); */
10089: /* fputs(line,ficparo); */
10090: /* } */
10091: /* ungetc(c,ficpar); */
1.126 brouard 10092:
10093: estepm=0;
1.209 brouard 10094: 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 10095:
10096: if (num_filled != 6) {
10097: 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);
10098: 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);
10099: goto end;
10100: }
10101: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
10102: }
10103: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
10104: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
10105:
1.209 brouard 10106: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 10107: if (estepm==0 || estepm < stepm) estepm=stepm;
10108: if (fage <= 2) {
10109: bage = ageminpar;
10110: fage = agemaxpar;
10111: }
10112:
10113: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 10114: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
10115: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 10116:
1.186 brouard 10117: /* Other stuffs, more or less useful */
1.126 brouard 10118: while((c=getc(ficpar))=='#' && c!= EOF){
10119: ungetc(c,ficpar);
10120: fgets(line, MAXLINE, ficpar);
1.141 brouard 10121: fputs(line,stdout);
1.126 brouard 10122: fputs(line,ficparo);
10123: }
10124: ungetc(c,ficpar);
10125:
10126: 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);
10127: 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);
10128: 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);
10129: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
10130: 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);
10131:
10132: while((c=getc(ficpar))=='#' && c!= EOF){
10133: ungetc(c,ficpar);
10134: fgets(line, MAXLINE, ficpar);
1.141 brouard 10135: fputs(line,stdout);
1.126 brouard 10136: fputs(line,ficparo);
10137: }
10138: ungetc(c,ficpar);
10139:
10140:
10141: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
10142: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
10143:
10144: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 10145: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 10146: fprintf(ficparo,"pop_based=%d\n",popbased);
10147: fprintf(ficres,"pop_based=%d\n",popbased);
10148:
10149: while((c=getc(ficpar))=='#' && c!= EOF){
10150: ungetc(c,ficpar);
10151: fgets(line, MAXLINE, ficpar);
1.141 brouard 10152: fputs(line,stdout);
1.126 brouard 10153: fputs(line,ficparo);
10154: }
10155: ungetc(c,ficpar);
10156:
10157: 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);
10158: 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);
10159: 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);
10160: 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);
10161: 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);
10162: /* day and month of proj2 are not used but only year anproj2.*/
10163:
1.217 brouard 10164: while((c=getc(ficpar))=='#' && c!= EOF){
10165: ungetc(c,ficpar);
10166: fgets(line, MAXLINE, ficpar);
10167: fputs(line,stdout);
10168: fputs(line,ficparo);
10169: }
10170: ungetc(c,ficpar);
10171:
10172: 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 10173: 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);
10174: 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);
10175: 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 10176: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 10177:
10178:
1.220 brouard 10179: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 10180: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 10181:
10182: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 10183: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 10184: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10185: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10186: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10187: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 10188: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
10189: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 10190: }else{
1.218 brouard 10191: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 10192: }
10193: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
1.225 brouard 10194: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
10195: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.220 brouard 10196:
1.225 brouard 10197: /*------------ free_vector -------------*/
10198: /* chdir(path); */
1.220 brouard 10199:
1.215 brouard 10200: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
10201: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
10202: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
10203: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 10204: free_lvector(num,1,n);
10205: free_vector(agedc,1,n);
10206: /*free_matrix(covar,0,NCOVMAX,1,n);*/
10207: /*free_matrix(covar,1,NCOVMAX,1,n);*/
10208: fclose(ficparo);
10209: fclose(ficres);
1.220 brouard 10210:
10211:
1.186 brouard 10212: /* Other results (useful)*/
1.220 brouard 10213:
10214:
1.126 brouard 10215: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 10216: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
10217: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 10218: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 10219: fclose(ficrespl);
10220:
10221: /*------------- h Pij x at various ages ------------*/
1.180 brouard 10222: /*#include "hpijx.h"*/
10223: hPijx(p, bage, fage);
1.145 brouard 10224: fclose(ficrespij);
1.227 brouard 10225:
1.220 brouard 10226: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 10227: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 10228: k=1;
1.126 brouard 10229: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
1.227 brouard 10230:
1.219 brouard 10231: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 10232: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 10233: for(i=1;i<=AGESUP;i++)
1.219 brouard 10234: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.225 brouard 10235: for(k=1;k<=ncovcombmax;k++)
10236: probs[i][j][k]=0.;
1.219 brouard 10237: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
10238: if (mobilav!=0 ||mobilavproj !=0 ) {
10239: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.227 brouard 10240: for(i=1;i<=AGESUP;i++)
10241: for(j=1;j<=nlstate;j++)
10242: for(k=1;k<=ncovcombmax;k++)
10243: mobaverages[i][j][k]=0.;
1.219 brouard 10244: mobaverage=mobaverages;
10245: if (mobilav!=0) {
1.227 brouard 10246: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
10247: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
10248: printf(" Error in movingaverage mobilav=%d\n",mobilav);
10249: }
1.219 brouard 10250: }
10251: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
10252: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
10253: else if (mobilavproj !=0) {
1.227 brouard 10254: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
10255: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
10256: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
10257: }
1.219 brouard 10258: }
10259: }/* end if moving average */
1.227 brouard 10260:
1.126 brouard 10261: /*---------- Forecasting ------------------*/
10262: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
10263: if(prevfcast==1){
10264: /* if(stepm ==1){*/
1.225 brouard 10265: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 10266: }
1.217 brouard 10267: if(backcast==1){
1.219 brouard 10268: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10269: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10270: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
10271:
10272: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
10273:
10274: bprlim=matrix(1,nlstate,1,nlstate);
10275: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
10276: fclose(ficresplb);
10277:
1.222 brouard 10278: hBijx(p, bage, fage, mobaverage);
10279: fclose(ficrespijb);
1.219 brouard 10280: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
10281:
10282: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
1.225 brouard 10283: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
1.219 brouard 10284: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10285: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10286: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
10287: }
1.217 brouard 10288:
1.186 brouard 10289:
10290: /* ------ Other prevalence ratios------------ */
1.126 brouard 10291:
1.215 brouard 10292: free_ivector(wav,1,imx);
10293: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
10294: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
10295: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 10296:
10297:
1.127 brouard 10298: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 10299:
1.201 brouard 10300: strcpy(filerese,"E_");
10301: strcat(filerese,fileresu);
1.126 brouard 10302: if((ficreseij=fopen(filerese,"w"))==NULL) {
10303: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10304: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
10305: }
1.208 brouard 10306: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
10307: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 10308:
1.227 brouard 10309: for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
1.219 brouard 10310: fprintf(ficreseij,"\n#****** ");
1.225 brouard 10311: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10312: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 10313: }
10314: fprintf(ficreseij,"******\n");
10315:
10316: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10317: oldm=oldms;savm=savms;
10318: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 10319:
1.219 brouard 10320: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 10321: }
10322: fclose(ficreseij);
1.208 brouard 10323: printf("done evsij\n");fflush(stdout);
10324: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 10325:
1.227 brouard 10326: /*---------- State-specific expectancies and variances ------------*/
1.218 brouard 10327:
10328:
1.201 brouard 10329: strcpy(filerest,"T_");
10330: strcat(filerest,fileresu);
1.127 brouard 10331: if((ficrest=fopen(filerest,"w"))==NULL) {
10332: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
10333: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
10334: }
1.208 brouard 10335: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
10336: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 10337:
1.126 brouard 10338:
1.201 brouard 10339: strcpy(fileresstde,"STDE_");
10340: strcat(fileresstde,fileresu);
1.126 brouard 10341: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
1.227 brouard 10342: printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
10343: fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
1.126 brouard 10344: }
1.227 brouard 10345: printf(" Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
10346: fprintf(ficlog," Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 10347:
1.201 brouard 10348: strcpy(filerescve,"CVE_");
10349: strcat(filerescve,fileresu);
1.126 brouard 10350: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
1.227 brouard 10351: printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
10352: fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
1.126 brouard 10353: }
1.227 brouard 10354: printf(" Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
10355: fprintf(ficlog," Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 10356:
1.201 brouard 10357: strcpy(fileresv,"V_");
10358: strcat(fileresv,fileresu);
1.126 brouard 10359: if((ficresvij=fopen(fileresv,"w"))==NULL) {
10360: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
10361: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
10362: }
1.227 brouard 10363: printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
10364: fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 10365:
1.145 brouard 10366: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10367: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
10368:
1.225 brouard 10369: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10370: printf("\n#****** ");
1.208 brouard 10371: fprintf(ficrest,"\n#****** ");
1.227 brouard 10372: fprintf(ficlog,"\n#****** ");
10373: for(j=1;j<=cptcoveff;j++){
10374: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10375: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10376: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10377: }
1.208 brouard 10378: fprintf(ficrest,"******\n");
1.227 brouard 10379: fprintf(ficlog,"******\n");
10380: printf("******\n");
1.208 brouard 10381:
10382: fprintf(ficresstdeij,"\n#****** ");
10383: fprintf(ficrescveij,"\n#****** ");
1.225 brouard 10384: for(j=1;j<=cptcoveff;j++) {
1.227 brouard 10385: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10386: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10387: }
10388: fprintf(ficresstdeij,"******\n");
10389: fprintf(ficrescveij,"******\n");
10390:
10391: fprintf(ficresvij,"\n#****** ");
1.225 brouard 10392: for(j=1;j<=cptcoveff;j++)
1.227 brouard 10393: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 10394: fprintf(ficresvij,"******\n");
10395:
10396: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10397: oldm=oldms;savm=savms;
1.227 brouard 10398: printf(" cvevsij combination#=%d, ",k);
10399: fprintf(ficlog, " cvevsij combination#=%d, ",k);
1.208 brouard 10400: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
10401: printf(" end cvevsij \n ");
10402: fprintf(ficlog, " end cvevsij \n ");
10403:
10404: /*
10405: */
10406: /* goto endfree; */
10407:
10408: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
10409: pstamp(ficrest);
10410:
10411:
10412: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.227 brouard 10413: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
10414: cptcod= 0; /* To be deleted */
10415: printf("varevsij vpopbased=%d \n",vpopbased);
10416: fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
10417: 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 */
10418: 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 ");
10419: if(vpopbased==1)
10420: 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);
10421: else
10422: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
10423: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
10424: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
10425: fprintf(ficrest,"\n");
10426: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
10427: epj=vector(1,nlstate+1);
10428: printf("Computing age specific period (stable) prevalences in each health state \n");
10429: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
10430: for(age=bage; age <=fage ;age++){
10431: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
10432: if (vpopbased==1) {
10433: if(mobilav ==0){
10434: for(i=1; i<=nlstate;i++)
10435: prlim[i][i]=probs[(int)age][i][k];
10436: }else{ /* mobilav */
10437: for(i=1; i<=nlstate;i++)
10438: prlim[i][i]=mobaverage[(int)age][i][k];
10439: }
10440: }
1.219 brouard 10441:
1.227 brouard 10442: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
10443: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
10444: /* printf(" age %4.0f ",age); */
10445: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
10446: for(i=1, epj[j]=0.;i <=nlstate;i++) {
10447: epj[j] += prlim[i][i]*eij[i][j][(int)age];
10448: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
10449: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
10450: }
10451: epj[nlstate+1] +=epj[j];
10452: }
10453: /* printf(" age %4.0f \n",age); */
1.219 brouard 10454:
1.227 brouard 10455: for(i=1, vepp=0.;i <=nlstate;i++)
10456: for(j=1;j <=nlstate;j++)
10457: vepp += vareij[i][j][(int)age];
10458: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
10459: for(j=1;j <=nlstate;j++){
10460: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
10461: }
10462: fprintf(ficrest,"\n");
10463: }
1.208 brouard 10464: } /* End vpopbased */
10465: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10466: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
10467: free_vector(epj,1,nlstate+1);
10468: printf("done \n");fflush(stdout);
10469: fprintf(ficlog,"done\n");fflush(ficlog);
10470:
1.145 brouard 10471: /*}*/
1.208 brouard 10472: } /* End k */
1.227 brouard 10473:
10474: printf("done State-specific expectancies\n");fflush(stdout);
10475: fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
10476:
1.126 brouard 10477: /*------- Variance of period (stable) prevalence------*/
1.227 brouard 10478:
1.201 brouard 10479: strcpy(fileresvpl,"VPL_");
10480: strcat(fileresvpl,fileresu);
1.126 brouard 10481: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
10482: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
10483: exit(0);
10484: }
1.208 brouard 10485: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
10486: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.227 brouard 10487:
1.145 brouard 10488: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
10489: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
1.227 brouard 10490:
1.225 brouard 10491: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.227 brouard 10492: fprintf(ficresvpl,"\n#****** ");
10493: printf("\n#****** ");
10494: fprintf(ficlog,"\n#****** ");
10495: for(j=1;j<=cptcoveff;j++) {
10496: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10497: fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10498: printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
10499: }
10500: fprintf(ficresvpl,"******\n");
10501: printf("******\n");
10502: fprintf(ficlog,"******\n");
10503:
10504: varpl=matrix(1,nlstate,(int) bage, (int) fage);
10505: oldm=oldms;savm=savms;
10506: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
10507: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 10508: /*}*/
1.126 brouard 10509: }
1.227 brouard 10510:
1.126 brouard 10511: fclose(ficresvpl);
1.208 brouard 10512: printf("done variance-covariance of period prevalence\n");fflush(stdout);
10513: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.227 brouard 10514:
10515: free_vector(weight,1,n);
10516: free_imatrix(Tvard,1,NCOVMAX,1,2);
10517: free_imatrix(s,1,maxwav+1,1,n);
10518: free_matrix(anint,1,maxwav,1,n);
10519: free_matrix(mint,1,maxwav,1,n);
10520: free_ivector(cod,1,n);
10521: free_ivector(tab,1,NCOVMAX);
10522: fclose(ficresstdeij);
10523: fclose(ficrescveij);
10524: fclose(ficresvij);
10525: fclose(ficrest);
10526: fclose(ficpar);
10527:
10528:
1.126 brouard 10529: /*---------- End : free ----------------*/
1.219 brouard 10530: if (mobilav!=0 ||mobilavproj !=0)
10531: 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 10532: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 10533: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
10534: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 10535: } /* mle==-3 arrives here for freeing */
1.227 brouard 10536: /* endfree:*/
10537: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
10538: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
10539: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
10540: free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
10541: free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
10542: free_matrix(coqvar,1,maxwav,1,n);
10543: free_matrix(covar,0,NCOVMAX,1,n);
10544: free_matrix(matcov,1,npar,1,npar);
10545: free_matrix(hess,1,npar,1,npar);
10546: /*free_vector(delti,1,npar);*/
10547: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10548: free_matrix(agev,1,maxwav,1,imx);
10549: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
10550:
10551: free_ivector(ncodemax,1,NCOVMAX);
10552: free_ivector(ncodemaxwundef,1,NCOVMAX);
10553: free_ivector(Dummy,-1,NCOVMAX);
10554: free_ivector(Fixed,-1,NCOVMAX);
10555: free_ivector(Typevar,-1,NCOVMAX);
10556: free_ivector(Tvar,1,NCOVMAX);
10557: free_ivector(Tposprod,1,NCOVMAX);
10558: free_ivector(Tprod,1,NCOVMAX);
10559: free_ivector(Tvaraff,1,NCOVMAX);
10560: free_ivector(invalidvarcomb,1,ncovcombmax);
10561: free_ivector(Tage,1,NCOVMAX);
10562: free_ivector(Tmodelind,1,NCOVMAX);
1.228 ! brouard 10563: free_ivector(TmodelInvind,1,NCOVMAX);
! 10564: free_ivector(TmodelInvQind,1,NCOVMAX);
1.227 brouard 10565:
10566: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
10567: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 10568: fflush(fichtm);
10569: fflush(ficgp);
10570:
1.227 brouard 10571:
1.126 brouard 10572: if((nberr >0) || (nbwarn>0)){
1.216 brouard 10573: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
10574: 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 10575: }else{
10576: printf("End of Imach\n");
10577: fprintf(ficlog,"End of Imach\n");
10578: }
10579: printf("See log file on %s\n",filelog);
10580: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 10581: /*(void) gettimeofday(&end_time,&tzp);*/
10582: rend_time = time(NULL);
10583: end_time = *localtime(&rend_time);
10584: /* tml = *localtime(&end_time.tm_sec); */
10585: strcpy(strtend,asctime(&end_time));
1.126 brouard 10586: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
10587: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 10588: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.227 brouard 10589:
1.157 brouard 10590: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
10591: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
10592: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 10593: /* printf("Total time was %d uSec.\n", total_usecs);*/
10594: /* if(fileappend(fichtm,optionfilehtm)){ */
10595: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10596: fclose(fichtm);
10597: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
10598: fclose(fichtmcov);
10599: fclose(ficgp);
10600: fclose(ficlog);
10601: /*------ End -----------*/
1.227 brouard 10602:
10603:
10604: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 10605: #ifdef WIN32
1.227 brouard 10606: if (_chdir(pathcd) != 0)
10607: printf("Can't move to directory %s!\n",path);
10608: if(_getcwd(pathcd,MAXLINE) > 0)
1.184 brouard 10609: #else
1.227 brouard 10610: if(chdir(pathcd) != 0)
10611: printf("Can't move to directory %s!\n", path);
10612: if (getcwd(pathcd, MAXLINE) > 0)
1.184 brouard 10613: #endif
1.126 brouard 10614: printf("Current directory %s!\n",pathcd);
10615: /*strcat(plotcmd,CHARSEPARATOR);*/
10616: sprintf(plotcmd,"gnuplot");
1.157 brouard 10617: #ifdef _WIN32
1.126 brouard 10618: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
10619: #endif
10620: if(!stat(plotcmd,&info)){
1.158 brouard 10621: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10622: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 10623: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 10624: }else
10625: strcpy(pplotcmd,plotcmd);
1.157 brouard 10626: #ifdef __unix
1.126 brouard 10627: strcpy(plotcmd,GNUPLOTPROGRAM);
10628: if(!stat(plotcmd,&info)){
1.158 brouard 10629: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 10630: }else
10631: strcpy(pplotcmd,plotcmd);
10632: #endif
10633: }else
10634: strcpy(pplotcmd,plotcmd);
10635:
10636: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 10637: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.227 brouard 10638:
1.126 brouard 10639: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 10640: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 10641: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 10642: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 10643: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 10644: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 10645: }
1.158 brouard 10646: printf(" Successful, please wait...");
1.126 brouard 10647: while (z[0] != 'q') {
10648: /* chdir(path); */
1.154 brouard 10649: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 10650: scanf("%s",z);
10651: /* if (z[0] == 'c') system("./imach"); */
10652: if (z[0] == 'e') {
1.158 brouard 10653: #ifdef __APPLE__
1.152 brouard 10654: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 10655: #elif __linux
10656: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10657: #else
1.152 brouard 10658: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10659: #endif
10660: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10661: system(pplotcmd);
1.126 brouard 10662: }
10663: else if (z[0] == 'g') system(plotcmd);
10664: else if (z[0] == 'q') exit(0);
10665: }
1.227 brouard 10666: end:
1.126 brouard 10667: while (z[0] != 'q') {
1.195 brouard 10668: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10669: scanf("%s",z);
10670: }
10671: }
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