Annotation of imach/src/imach.c, revision 1.221
1.220 brouard 1: /* $Id: imach.c,v 1.219 2016/02/15 00:48:12 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.220 brouard 4: Revision 1.219 2016/02/15 00:48:12 brouard
5: *** empty log message ***
6:
1.219 brouard 7: Revision 1.218 2016/02/12 11:29:23 brouard
8: Summary: 0.99 Back projections
9:
1.218 brouard 10: Revision 1.217 2015/12/23 17:18:31 brouard
11: Summary: Experimental backcast
12:
1.217 brouard 13: Revision 1.216 2015/12/18 17:32:11 brouard
14: Summary: 0.98r4 Warning and status=-2
15:
16: Version 0.98r4 is now:
17: - displaying an error when status is -1, date of interview unknown and date of death known;
18: - permitting a status -2 when the vital status is unknown at a known date of right truncation.
19: Older changes concerning s=-2, dating from 2005 have been supersed.
20:
1.216 brouard 21: Revision 1.215 2015/12/16 08:52:24 brouard
22: Summary: 0.98r4 working
23:
1.215 brouard 24: Revision 1.214 2015/12/16 06:57:54 brouard
25: Summary: temporary not working
26:
1.214 brouard 27: Revision 1.213 2015/12/11 18:22:17 brouard
28: Summary: 0.98r4
29:
1.213 brouard 30: Revision 1.212 2015/11/21 12:47:24 brouard
31: Summary: minor typo
32:
1.212 brouard 33: Revision 1.211 2015/11/21 12:41:11 brouard
34: Summary: 0.98r3 with some graph of projected cross-sectional
35:
36: Author: Nicolas Brouard
37:
1.211 brouard 38: Revision 1.210 2015/11/18 17:41:20 brouard
39: Summary: Start working on projected prevalences
40:
1.210 brouard 41: Revision 1.209 2015/11/17 22:12:03 brouard
42: Summary: Adding ftolpl parameter
43: Author: N Brouard
44:
45: We had difficulties to get smoothed confidence intervals. It was due
46: to the period prevalence which wasn't computed accurately. The inner
47: parameter ftolpl is now an outer parameter of the .imach parameter
48: file after estepm. If ftolpl is small 1.e-4 and estepm too,
49: computation are long.
50:
1.209 brouard 51: Revision 1.208 2015/11/17 14:31:57 brouard
52: Summary: temporary
53:
1.208 brouard 54: Revision 1.207 2015/10/27 17:36:57 brouard
55: *** empty log message ***
56:
1.207 brouard 57: Revision 1.206 2015/10/24 07:14:11 brouard
58: *** empty log message ***
59:
1.206 brouard 60: Revision 1.205 2015/10/23 15:50:53 brouard
61: Summary: 0.98r3 some clarification for graphs on likelihood contributions
62:
1.205 brouard 63: Revision 1.204 2015/10/01 16:20:26 brouard
64: Summary: Some new graphs of contribution to likelihood
65:
1.204 brouard 66: Revision 1.203 2015/09/30 17:45:14 brouard
67: Summary: looking at better estimation of the hessian
68:
69: Also a better criteria for convergence to the period prevalence And
70: therefore adding the number of years needed to converge. (The
71: prevalence in any alive state shold sum to one
72:
1.203 brouard 73: Revision 1.202 2015/09/22 19:45:16 brouard
74: Summary: Adding some overall graph on contribution to likelihood. Might change
75:
1.202 brouard 76: Revision 1.201 2015/09/15 17:34:58 brouard
77: Summary: 0.98r0
78:
79: - Some new graphs like suvival functions
80: - Some bugs fixed like model=1+age+V2.
81:
1.201 brouard 82: Revision 1.200 2015/09/09 16:53:55 brouard
83: Summary: Big bug thanks to Flavia
84:
85: Even model=1+age+V2. did not work anymore
86:
1.200 brouard 87: Revision 1.199 2015/09/07 14:09:23 brouard
88: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
89:
1.199 brouard 90: Revision 1.198 2015/09/03 07:14:39 brouard
91: Summary: 0.98q5 Flavia
92:
1.198 brouard 93: Revision 1.197 2015/09/01 18:24:39 brouard
94: *** empty log message ***
95:
1.197 brouard 96: Revision 1.196 2015/08/18 23:17:52 brouard
97: Summary: 0.98q5
98:
1.196 brouard 99: Revision 1.195 2015/08/18 16:28:39 brouard
100: Summary: Adding a hack for testing purpose
101:
102: After reading the title, ftol and model lines, if the comment line has
103: a q, starting with #q, the answer at the end of the run is quit. It
104: permits to run test files in batch with ctest. The former workaround was
105: $ echo q | imach foo.imach
106:
1.195 brouard 107: Revision 1.194 2015/08/18 13:32:00 brouard
108: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
109:
1.194 brouard 110: Revision 1.193 2015/08/04 07:17:42 brouard
111: Summary: 0.98q4
112:
1.193 brouard 113: Revision 1.192 2015/07/16 16:49:02 brouard
114: Summary: Fixing some outputs
115:
1.192 brouard 116: Revision 1.191 2015/07/14 10:00:33 brouard
117: Summary: Some fixes
118:
1.191 brouard 119: Revision 1.190 2015/05/05 08:51:13 brouard
120: Summary: Adding digits in output parameters (7 digits instead of 6)
121:
122: Fix 1+age+.
123:
1.190 brouard 124: Revision 1.189 2015/04/30 14:45:16 brouard
125: Summary: 0.98q2
126:
1.189 brouard 127: Revision 1.188 2015/04/30 08:27:53 brouard
128: *** empty log message ***
129:
1.188 brouard 130: Revision 1.187 2015/04/29 09:11:15 brouard
131: *** empty log message ***
132:
1.187 brouard 133: Revision 1.186 2015/04/23 12:01:52 brouard
134: Summary: V1*age is working now, version 0.98q1
135:
136: Some codes had been disabled in order to simplify and Vn*age was
137: working in the optimization phase, ie, giving correct MLE parameters,
138: but, as usual, outputs were not correct and program core dumped.
139:
1.186 brouard 140: Revision 1.185 2015/03/11 13:26:42 brouard
141: Summary: Inclusion of compile and links command line for Intel Compiler
142:
1.185 brouard 143: Revision 1.184 2015/03/11 11:52:39 brouard
144: Summary: Back from Windows 8. Intel Compiler
145:
1.184 brouard 146: Revision 1.183 2015/03/10 20:34:32 brouard
147: Summary: 0.98q0, trying with directest, mnbrak fixed
148:
149: We use directest instead of original Powell test; probably no
150: incidence on the results, but better justifications;
151: We fixed Numerical Recipes mnbrak routine which was wrong and gave
152: wrong results.
153:
1.183 brouard 154: Revision 1.182 2015/02/12 08:19:57 brouard
155: Summary: Trying to keep directest which seems simpler and more general
156: Author: Nicolas Brouard
157:
1.182 brouard 158: Revision 1.181 2015/02/11 23:22:24 brouard
159: Summary: Comments on Powell added
160:
161: Author:
162:
1.181 brouard 163: Revision 1.180 2015/02/11 17:33:45 brouard
164: Summary: Finishing move from main to function (hpijx and prevalence_limit)
165:
1.180 brouard 166: Revision 1.179 2015/01/04 09:57:06 brouard
167: Summary: back to OS/X
168:
1.179 brouard 169: Revision 1.178 2015/01/04 09:35:48 brouard
170: *** empty log message ***
171:
1.178 brouard 172: Revision 1.177 2015/01/03 18:40:56 brouard
173: Summary: Still testing ilc32 on OSX
174:
1.177 brouard 175: Revision 1.176 2015/01/03 16:45:04 brouard
176: *** empty log message ***
177:
1.176 brouard 178: Revision 1.175 2015/01/03 16:33:42 brouard
179: *** empty log message ***
180:
1.175 brouard 181: Revision 1.174 2015/01/03 16:15:49 brouard
182: Summary: Still in cross-compilation
183:
1.174 brouard 184: Revision 1.173 2015/01/03 12:06:26 brouard
185: Summary: trying to detect cross-compilation
186:
1.173 brouard 187: Revision 1.172 2014/12/27 12:07:47 brouard
188: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
189:
1.172 brouard 190: Revision 1.171 2014/12/23 13:26:59 brouard
191: Summary: Back from Visual C
192:
193: Still problem with utsname.h on Windows
194:
1.171 brouard 195: Revision 1.170 2014/12/23 11:17:12 brouard
196: Summary: Cleaning some \%% back to %%
197:
198: The escape was mandatory for a specific compiler (which one?), but too many warnings.
199:
1.170 brouard 200: Revision 1.169 2014/12/22 23:08:31 brouard
201: Summary: 0.98p
202:
203: Outputs some informations on compiler used, OS etc. Testing on different platforms.
204:
1.169 brouard 205: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 206: Summary: update
1.169 brouard 207:
1.168 brouard 208: Revision 1.167 2014/12/22 13:50:56 brouard
209: Summary: Testing uname and compiler version and if compiled 32 or 64
210:
211: Testing on Linux 64
212:
1.167 brouard 213: Revision 1.166 2014/12/22 11:40:47 brouard
214: *** empty log message ***
215:
1.166 brouard 216: Revision 1.165 2014/12/16 11:20:36 brouard
217: Summary: After compiling on Visual C
218:
219: * imach.c (Module): Merging 1.61 to 1.162
220:
1.165 brouard 221: Revision 1.164 2014/12/16 10:52:11 brouard
222: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
223:
224: * imach.c (Module): Merging 1.61 to 1.162
225:
1.164 brouard 226: Revision 1.163 2014/12/16 10:30:11 brouard
227: * imach.c (Module): Merging 1.61 to 1.162
228:
1.163 brouard 229: Revision 1.162 2014/09/25 11:43:39 brouard
230: Summary: temporary backup 0.99!
231:
1.162 brouard 232: Revision 1.1 2014/09/16 11:06:58 brouard
233: Summary: With some code (wrong) for nlopt
234:
235: Author:
236:
237: Revision 1.161 2014/09/15 20:41:41 brouard
238: Summary: Problem with macro SQR on Intel compiler
239:
1.161 brouard 240: Revision 1.160 2014/09/02 09:24:05 brouard
241: *** empty log message ***
242:
1.160 brouard 243: Revision 1.159 2014/09/01 10:34:10 brouard
244: Summary: WIN32
245: Author: Brouard
246:
1.159 brouard 247: Revision 1.158 2014/08/27 17:11:51 brouard
248: *** empty log message ***
249:
1.158 brouard 250: Revision 1.157 2014/08/27 16:26:55 brouard
251: Summary: Preparing windows Visual studio version
252: Author: Brouard
253:
254: In order to compile on Visual studio, time.h is now correct and time_t
255: and tm struct should be used. difftime should be used but sometimes I
256: just make the differences in raw time format (time(&now).
257: Trying to suppress #ifdef LINUX
258: Add xdg-open for __linux in order to open default browser.
259:
1.157 brouard 260: Revision 1.156 2014/08/25 20:10:10 brouard
261: *** empty log message ***
262:
1.156 brouard 263: Revision 1.155 2014/08/25 18:32:34 brouard
264: Summary: New compile, minor changes
265: Author: Brouard
266:
1.155 brouard 267: Revision 1.154 2014/06/20 17:32:08 brouard
268: Summary: Outputs now all graphs of convergence to period prevalence
269:
1.154 brouard 270: Revision 1.153 2014/06/20 16:45:46 brouard
271: Summary: If 3 live state, convergence to period prevalence on same graph
272: Author: Brouard
273:
1.153 brouard 274: Revision 1.152 2014/06/18 17:54:09 brouard
275: Summary: open browser, use gnuplot on same dir than imach if not found in the path
276:
1.152 brouard 277: Revision 1.151 2014/06/18 16:43:30 brouard
278: *** empty log message ***
279:
1.151 brouard 280: Revision 1.150 2014/06/18 16:42:35 brouard
281: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
282: Author: brouard
283:
1.150 brouard 284: Revision 1.149 2014/06/18 15:51:14 brouard
285: Summary: Some fixes in parameter files errors
286: Author: Nicolas Brouard
287:
1.149 brouard 288: Revision 1.148 2014/06/17 17:38:48 brouard
289: Summary: Nothing new
290: Author: Brouard
291:
292: Just a new packaging for OS/X version 0.98nS
293:
1.148 brouard 294: Revision 1.147 2014/06/16 10:33:11 brouard
295: *** empty log message ***
296:
1.147 brouard 297: Revision 1.146 2014/06/16 10:20:28 brouard
298: Summary: Merge
299: Author: Brouard
300:
301: Merge, before building revised version.
302:
1.146 brouard 303: Revision 1.145 2014/06/10 21:23:15 brouard
304: Summary: Debugging with valgrind
305: Author: Nicolas Brouard
306:
307: Lot of changes in order to output the results with some covariates
308: After the Edimburgh REVES conference 2014, it seems mandatory to
309: improve the code.
310: No more memory valgrind error but a lot has to be done in order to
311: continue the work of splitting the code into subroutines.
312: Also, decodemodel has been improved. Tricode is still not
313: optimal. nbcode should be improved. Documentation has been added in
314: the source code.
315:
1.144 brouard 316: Revision 1.143 2014/01/26 09:45:38 brouard
317: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
318:
319: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
320: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
321:
1.143 brouard 322: Revision 1.142 2014/01/26 03:57:36 brouard
323: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
324:
325: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
326:
1.142 brouard 327: Revision 1.141 2014/01/26 02:42:01 brouard
328: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
329:
1.141 brouard 330: Revision 1.140 2011/09/02 10:37:54 brouard
331: Summary: times.h is ok with mingw32 now.
332:
1.140 brouard 333: Revision 1.139 2010/06/14 07:50:17 brouard
334: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
335: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
336:
1.139 brouard 337: Revision 1.138 2010/04/30 18:19:40 brouard
338: *** empty log message ***
339:
1.138 brouard 340: Revision 1.137 2010/04/29 18:11:38 brouard
341: (Module): Checking covariates for more complex models
342: than V1+V2. A lot of change to be done. Unstable.
343:
1.137 brouard 344: Revision 1.136 2010/04/26 20:30:53 brouard
345: (Module): merging some libgsl code. Fixing computation
346: of likelione (using inter/intrapolation if mle = 0) in order to
347: get same likelihood as if mle=1.
348: Some cleaning of code and comments added.
349:
1.136 brouard 350: Revision 1.135 2009/10/29 15:33:14 brouard
351: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
352:
1.135 brouard 353: Revision 1.134 2009/10/29 13:18:53 brouard
354: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
355:
1.134 brouard 356: Revision 1.133 2009/07/06 10:21:25 brouard
357: just nforces
358:
1.133 brouard 359: Revision 1.132 2009/07/06 08:22:05 brouard
360: Many tings
361:
1.132 brouard 362: Revision 1.131 2009/06/20 16:22:47 brouard
363: Some dimensions resccaled
364:
1.131 brouard 365: Revision 1.130 2009/05/26 06:44:34 brouard
366: (Module): Max Covariate is now set to 20 instead of 8. A
367: lot of cleaning with variables initialized to 0. Trying to make
368: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
369:
1.130 brouard 370: Revision 1.129 2007/08/31 13:49:27 lievre
371: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
372:
1.129 lievre 373: Revision 1.128 2006/06/30 13:02:05 brouard
374: (Module): Clarifications on computing e.j
375:
1.128 brouard 376: Revision 1.127 2006/04/28 18:11:50 brouard
377: (Module): Yes the sum of survivors was wrong since
378: imach-114 because nhstepm was no more computed in the age
379: loop. Now we define nhstepma in the age loop.
380: (Module): In order to speed up (in case of numerous covariates) we
381: compute health expectancies (without variances) in a first step
382: and then all the health expectancies with variances or standard
383: deviation (needs data from the Hessian matrices) which slows the
384: computation.
385: In the future we should be able to stop the program is only health
386: expectancies and graph are needed without standard deviations.
387:
1.127 brouard 388: Revision 1.126 2006/04/28 17:23:28 brouard
389: (Module): Yes the sum of survivors was wrong since
390: imach-114 because nhstepm was no more computed in the age
391: loop. Now we define nhstepma in the age loop.
392: Version 0.98h
393:
1.126 brouard 394: Revision 1.125 2006/04/04 15:20:31 lievre
395: Errors in calculation of health expectancies. Age was not initialized.
396: Forecasting file added.
397:
398: Revision 1.124 2006/03/22 17:13:53 lievre
399: Parameters are printed with %lf instead of %f (more numbers after the comma).
400: The log-likelihood is printed in the log file
401:
402: Revision 1.123 2006/03/20 10:52:43 brouard
403: * imach.c (Module): <title> changed, corresponds to .htm file
404: name. <head> headers where missing.
405:
406: * imach.c (Module): Weights can have a decimal point as for
407: English (a comma might work with a correct LC_NUMERIC environment,
408: otherwise the weight is truncated).
409: Modification of warning when the covariates values are not 0 or
410: 1.
411: Version 0.98g
412:
413: Revision 1.122 2006/03/20 09:45:41 brouard
414: (Module): Weights can have a decimal point as for
415: English (a comma might work with a correct LC_NUMERIC environment,
416: otherwise the weight is truncated).
417: Modification of warning when the covariates values are not 0 or
418: 1.
419: Version 0.98g
420:
421: Revision 1.121 2006/03/16 17:45:01 lievre
422: * imach.c (Module): Comments concerning covariates added
423:
424: * imach.c (Module): refinements in the computation of lli if
425: status=-2 in order to have more reliable computation if stepm is
426: not 1 month. Version 0.98f
427:
428: Revision 1.120 2006/03/16 15:10:38 lievre
429: (Module): refinements in the computation of lli if
430: status=-2 in order to have more reliable computation if stepm is
431: not 1 month. Version 0.98f
432:
433: Revision 1.119 2006/03/15 17:42:26 brouard
434: (Module): Bug if status = -2, the loglikelihood was
435: computed as likelihood omitting the logarithm. Version O.98e
436:
437: Revision 1.118 2006/03/14 18:20:07 brouard
438: (Module): varevsij Comments added explaining the second
439: table of variances if popbased=1 .
440: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
441: (Module): Function pstamp added
442: (Module): Version 0.98d
443:
444: Revision 1.117 2006/03/14 17:16:22 brouard
445: (Module): varevsij Comments added explaining the second
446: table of variances if popbased=1 .
447: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
448: (Module): Function pstamp added
449: (Module): Version 0.98d
450:
451: Revision 1.116 2006/03/06 10:29:27 brouard
452: (Module): Variance-covariance wrong links and
453: varian-covariance of ej. is needed (Saito).
454:
455: Revision 1.115 2006/02/27 12:17:45 brouard
456: (Module): One freematrix added in mlikeli! 0.98c
457:
458: Revision 1.114 2006/02/26 12:57:58 brouard
459: (Module): Some improvements in processing parameter
460: filename with strsep.
461:
462: Revision 1.113 2006/02/24 14:20:24 brouard
463: (Module): Memory leaks checks with valgrind and:
464: datafile was not closed, some imatrix were not freed and on matrix
465: allocation too.
466:
467: Revision 1.112 2006/01/30 09:55:26 brouard
468: (Module): Back to gnuplot.exe instead of wgnuplot.exe
469:
470: Revision 1.111 2006/01/25 20:38:18 brouard
471: (Module): Lots of cleaning and bugs added (Gompertz)
472: (Module): Comments can be added in data file. Missing date values
473: can be a simple dot '.'.
474:
475: Revision 1.110 2006/01/25 00:51:50 brouard
476: (Module): Lots of cleaning and bugs added (Gompertz)
477:
478: Revision 1.109 2006/01/24 19:37:15 brouard
479: (Module): Comments (lines starting with a #) are allowed in data.
480:
481: Revision 1.108 2006/01/19 18:05:42 lievre
482: Gnuplot problem appeared...
483: To be fixed
484:
485: Revision 1.107 2006/01/19 16:20:37 brouard
486: Test existence of gnuplot in imach path
487:
488: Revision 1.106 2006/01/19 13:24:36 brouard
489: Some cleaning and links added in html output
490:
491: Revision 1.105 2006/01/05 20:23:19 lievre
492: *** empty log message ***
493:
494: Revision 1.104 2005/09/30 16:11:43 lievre
495: (Module): sump fixed, loop imx fixed, and simplifications.
496: (Module): If the status is missing at the last wave but we know
497: that the person is alive, then we can code his/her status as -2
498: (instead of missing=-1 in earlier versions) and his/her
499: contributions to the likelihood is 1 - Prob of dying from last
500: health status (= 1-p13= p11+p12 in the easiest case of somebody in
501: the healthy state at last known wave). Version is 0.98
502:
503: Revision 1.103 2005/09/30 15:54:49 lievre
504: (Module): sump fixed, loop imx fixed, and simplifications.
505:
506: Revision 1.102 2004/09/15 17:31:30 brouard
507: Add the possibility to read data file including tab characters.
508:
509: Revision 1.101 2004/09/15 10:38:38 brouard
510: Fix on curr_time
511:
512: Revision 1.100 2004/07/12 18:29:06 brouard
513: Add version for Mac OS X. Just define UNIX in Makefile
514:
515: Revision 1.99 2004/06/05 08:57:40 brouard
516: *** empty log message ***
517:
518: Revision 1.98 2004/05/16 15:05:56 brouard
519: New version 0.97 . First attempt to estimate force of mortality
520: directly from the data i.e. without the need of knowing the health
521: state at each age, but using a Gompertz model: log u =a + b*age .
522: This is the basic analysis of mortality and should be done before any
523: other analysis, in order to test if the mortality estimated from the
524: cross-longitudinal survey is different from the mortality estimated
525: from other sources like vital statistic data.
526:
527: The same imach parameter file can be used but the option for mle should be -3.
528:
1.133 brouard 529: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 530: former routines in order to include the new code within the former code.
531:
532: The output is very simple: only an estimate of the intercept and of
533: the slope with 95% confident intervals.
534:
535: Current limitations:
536: A) Even if you enter covariates, i.e. with the
537: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
538: B) There is no computation of Life Expectancy nor Life Table.
539:
540: Revision 1.97 2004/02/20 13:25:42 lievre
541: Version 0.96d. Population forecasting command line is (temporarily)
542: suppressed.
543:
544: Revision 1.96 2003/07/15 15:38:55 brouard
545: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
546: rewritten within the same printf. Workaround: many printfs.
547:
548: Revision 1.95 2003/07/08 07:54:34 brouard
549: * imach.c (Repository):
550: (Repository): Using imachwizard code to output a more meaningful covariance
551: matrix (cov(a12,c31) instead of numbers.
552:
553: Revision 1.94 2003/06/27 13:00:02 brouard
554: Just cleaning
555:
556: Revision 1.93 2003/06/25 16:33:55 brouard
557: (Module): On windows (cygwin) function asctime_r doesn't
558: exist so I changed back to asctime which exists.
559: (Module): Version 0.96b
560:
561: Revision 1.92 2003/06/25 16:30:45 brouard
562: (Module): On windows (cygwin) function asctime_r doesn't
563: exist so I changed back to asctime which exists.
564:
565: Revision 1.91 2003/06/25 15:30:29 brouard
566: * imach.c (Repository): Duplicated warning errors corrected.
567: (Repository): Elapsed time after each iteration is now output. It
568: helps to forecast when convergence will be reached. Elapsed time
569: is stamped in powell. We created a new html file for the graphs
570: concerning matrix of covariance. It has extension -cov.htm.
571:
572: Revision 1.90 2003/06/24 12:34:15 brouard
573: (Module): Some bugs corrected for windows. Also, when
574: mle=-1 a template is output in file "or"mypar.txt with the design
575: of the covariance matrix to be input.
576:
577: Revision 1.89 2003/06/24 12:30:52 brouard
578: (Module): Some bugs corrected for windows. Also, when
579: mle=-1 a template is output in file "or"mypar.txt with the design
580: of the covariance matrix to be input.
581:
582: Revision 1.88 2003/06/23 17:54:56 brouard
583: * 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.
584:
585: Revision 1.87 2003/06/18 12:26:01 brouard
586: Version 0.96
587:
588: Revision 1.86 2003/06/17 20:04:08 brouard
589: (Module): Change position of html and gnuplot routines and added
590: routine fileappend.
591:
592: Revision 1.85 2003/06/17 13:12:43 brouard
593: * imach.c (Repository): Check when date of death was earlier that
594: current date of interview. It may happen when the death was just
595: prior to the death. In this case, dh was negative and likelihood
596: was wrong (infinity). We still send an "Error" but patch by
597: assuming that the date of death was just one stepm after the
598: interview.
599: (Repository): Because some people have very long ID (first column)
600: we changed int to long in num[] and we added a new lvector for
601: memory allocation. But we also truncated to 8 characters (left
602: truncation)
603: (Repository): No more line truncation errors.
604:
605: Revision 1.84 2003/06/13 21:44:43 brouard
606: * imach.c (Repository): Replace "freqsummary" at a correct
607: place. It differs from routine "prevalence" which may be called
608: many times. Probs is memory consuming and must be used with
609: parcimony.
610: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
611:
612: Revision 1.83 2003/06/10 13:39:11 lievre
613: *** empty log message ***
614:
615: Revision 1.82 2003/06/05 15:57:20 brouard
616: Add log in imach.c and fullversion number is now printed.
617:
618: */
619: /*
620: Interpolated Markov Chain
621:
622: Short summary of the programme:
623:
624: This program computes Healthy Life Expectancies from
625: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
626: first survey ("cross") where individuals from different ages are
627: interviewed on their health status or degree of disability (in the
628: case of a health survey which is our main interest) -2- at least a
629: second wave of interviews ("longitudinal") which measure each change
630: (if any) in individual health status. Health expectancies are
631: computed from the time spent in each health state according to a
632: model. More health states you consider, more time is necessary to reach the
633: Maximum Likelihood of the parameters involved in the model. The
634: simplest model is the multinomial logistic model where pij is the
635: probability to be observed in state j at the second wave
636: conditional to be observed in state i at the first wave. Therefore
637: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
638: 'age' is age and 'sex' is a covariate. If you want to have a more
639: complex model than "constant and age", you should modify the program
640: where the markup *Covariates have to be included here again* invites
641: you to do it. More covariates you add, slower the
642: convergence.
643:
644: The advantage of this computer programme, compared to a simple
645: multinomial logistic model, is clear when the delay between waves is not
646: identical for each individual. Also, if a individual missed an
647: intermediate interview, the information is lost, but taken into
648: account using an interpolation or extrapolation.
649:
650: hPijx is the probability to be observed in state i at age x+h
651: conditional to the observed state i at age x. The delay 'h' can be
652: split into an exact number (nh*stepm) of unobserved intermediate
653: states. This elementary transition (by month, quarter,
654: semester or year) is modelled as a multinomial logistic. The hPx
655: matrix is simply the matrix product of nh*stepm elementary matrices
656: and the contribution of each individual to the likelihood is simply
657: hPijx.
658:
659: Also this programme outputs the covariance matrix of the parameters but also
1.218 brouard 660: of the life expectancies. It also computes the period (stable) prevalence.
661:
662: Back prevalence and projections:
663: - 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)
664: Computes the back prevalence limit for any combination of covariate values k
665: at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,
666: - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
667: - hBijx Back Probability to be in state i at age x-h being in j at x
668: Computes for any combination of covariates k and any age between bage and fage
669: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
670: oldm=oldms;savm=savms;
671: - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
672: Computes the transition matrix starting at age 'age' over
673: 'nhstepm*hstepm*stepm' months (i.e. until
674: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
675: nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling
676: p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\
677: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
678:
1.133 brouard 679: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
680: Institut national d'études démographiques, Paris.
1.126 brouard 681: This software have been partly granted by Euro-REVES, a concerted action
682: from the European Union.
683: It is copyrighted identically to a GNU software product, ie programme and
684: software can be distributed freely for non commercial use. Latest version
685: can be accessed at http://euroreves.ined.fr/imach .
686:
687: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
688: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
689:
690: **********************************************************************/
691: /*
692: main
693: read parameterfile
694: read datafile
695: concatwav
696: freqsummary
697: if (mle >= 1)
698: mlikeli
699: print results files
700: if mle==1
701: computes hessian
702: read end of parameter file: agemin, agemax, bage, fage, estepm
703: begin-prev-date,...
704: open gnuplot file
705: open html file
1.145 brouard 706: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
707: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
708: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
709: freexexit2 possible for memory heap.
710:
711: h Pij x | pij_nom ficrestpij
712: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
713: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
714: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
715:
716: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
717: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
718: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
719: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
720: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
721:
1.126 brouard 722: forecasting if prevfcast==1 prevforecast call prevalence()
723: health expectancies
724: Variance-covariance of DFLE
725: prevalence()
726: movingaverage()
727: varevsij()
728: if popbased==1 varevsij(,popbased)
729: total life expectancies
730: Variance of period (stable) prevalence
731: end
732: */
733:
1.187 brouard 734: /* #define DEBUG */
735: /* #define DEBUGBRENT */
1.203 brouard 736: /* #define DEBUGLINMIN */
737: /* #define DEBUGHESS */
738: #define DEBUGHESSIJ
1.220 brouard 739: #define LINMINORIGINAL /* Don't use loop on scale in linmin (accepting nan)*/
1.165 brouard 740: #define POWELL /* Instead of NLOPT */
1.192 brouard 741: #define POWELLF1F3 /* Skip test */
1.186 brouard 742: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
743: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 744:
745: #include <math.h>
746: #include <stdio.h>
747: #include <stdlib.h>
748: #include <string.h>
1.159 brouard 749:
750: #ifdef _WIN32
751: #include <io.h>
1.172 brouard 752: #include <windows.h>
753: #include <tchar.h>
1.159 brouard 754: #else
1.126 brouard 755: #include <unistd.h>
1.159 brouard 756: #endif
1.126 brouard 757:
758: #include <limits.h>
759: #include <sys/types.h>
1.171 brouard 760:
761: #if defined(__GNUC__)
762: #include <sys/utsname.h> /* Doesn't work on Windows */
763: #endif
764:
1.126 brouard 765: #include <sys/stat.h>
766: #include <errno.h>
1.159 brouard 767: /* extern int errno; */
1.126 brouard 768:
1.157 brouard 769: /* #ifdef LINUX */
770: /* #include <time.h> */
771: /* #include "timeval.h" */
772: /* #else */
773: /* #include <sys/time.h> */
774: /* #endif */
775:
1.126 brouard 776: #include <time.h>
777:
1.136 brouard 778: #ifdef GSL
779: #include <gsl/gsl_errno.h>
780: #include <gsl/gsl_multimin.h>
781: #endif
782:
1.167 brouard 783:
1.162 brouard 784: #ifdef NLOPT
785: #include <nlopt.h>
786: typedef struct {
787: double (* function)(double [] );
788: } myfunc_data ;
789: #endif
790:
1.126 brouard 791: /* #include <libintl.h> */
792: /* #define _(String) gettext (String) */
793:
1.141 brouard 794: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 795:
796: #define GNUPLOTPROGRAM "gnuplot"
797: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
798: #define FILENAMELENGTH 132
799:
800: #define GLOCK_ERROR_NOPATH -1 /* empty path */
801: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
802:
1.144 brouard 803: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
804: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 805:
806: #define NINTERVMAX 8
1.144 brouard 807: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
808: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
809: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 810: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 811: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
812: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 813: #define MAXN 20000
1.144 brouard 814: #define YEARM 12. /**< Number of months per year */
1.218 brouard 815: /* #define AGESUP 130 */
816: #define AGESUP 150
817: #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
1.126 brouard 818: #define AGEBASE 40
1.194 brouard 819: #define AGEOVERFLOW 1.e20
1.164 brouard 820: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 821: #ifdef _WIN32
822: #define DIRSEPARATOR '\\'
823: #define CHARSEPARATOR "\\"
824: #define ODIRSEPARATOR '/'
825: #else
1.126 brouard 826: #define DIRSEPARATOR '/'
827: #define CHARSEPARATOR "/"
828: #define ODIRSEPARATOR '\\'
829: #endif
830:
1.220 brouard 831: /* $Id: imach.c,v 1.219 2016/02/15 00:48:12 brouard Exp $ */
1.126 brouard 832: /* $State: Exp $ */
1.196 brouard 833: #include "version.h"
834: char version[]=__IMACH_VERSION__;
1.204 brouard 835: char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.220 brouard 836: char fullversion[]="$Revision: 1.219 $ $Date: 2016/02/15 00:48:12 $";
1.126 brouard 837: char strstart[80];
838: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 839: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 840: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 841: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
842: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
843: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
844: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
845: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
846: int cptcovprodnoage=0; /**< Number of covariate products without age */
847: int cptcoveff=0; /* Total number of covariates to vary for printing results */
848: int cptcov=0; /* Working variable */
1.218 brouard 849: int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
1.126 brouard 850: int npar=NPARMAX;
851: int nlstate=2; /* Number of live states */
852: int ndeath=1; /* Number of dead states */
1.130 brouard 853: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 854: int popbased=0;
855:
856: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 857: int maxwav=0; /* Maxim number of waves */
858: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
859: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
860: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 861: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 862: int mle=1, weightopt=0;
1.126 brouard 863: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
864: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
865: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
866: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 867: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 868: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 869: double **matprod2(); /* test */
1.126 brouard 870: double **oldm, **newm, **savm; /* Working pointers to matrices */
871: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.218 brouard 872: double **ddnewms, **ddoldms, **ddsavms; /* for freeing later */
873:
1.136 brouard 874: /*FILE *fic ; */ /* Used in readdata only */
1.217 brouard 875: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficresplb,*ficrespij, *ficrespijb, *ficrest,*ficresf, *ficresfb,*ficrespop;
1.126 brouard 876: FILE *ficlog, *ficrespow;
1.130 brouard 877: int globpr=0; /* Global variable for printing or not */
1.126 brouard 878: double fretone; /* Only one call to likelihood */
1.130 brouard 879: long ipmx=0; /* Number of contributions */
1.126 brouard 880: double sw; /* Sum of weights */
881: char filerespow[FILENAMELENGTH];
882: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
883: FILE *ficresilk;
884: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
885: FILE *ficresprobmorprev;
886: FILE *fichtm, *fichtmcov; /* Html File */
887: FILE *ficreseij;
888: char filerese[FILENAMELENGTH];
889: FILE *ficresstdeij;
890: char fileresstde[FILENAMELENGTH];
891: FILE *ficrescveij;
892: char filerescve[FILENAMELENGTH];
893: FILE *ficresvij;
894: char fileresv[FILENAMELENGTH];
895: FILE *ficresvpl;
896: char fileresvpl[FILENAMELENGTH];
897: char title[MAXLINE];
1.217 brouard 898: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
1.126 brouard 899: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
900: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
901: char command[FILENAMELENGTH];
902: int outcmd=0;
903:
1.217 brouard 904: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filerespijb[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 905: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 906: char filelog[FILENAMELENGTH]; /* Log file */
907: char filerest[FILENAMELENGTH];
908: char fileregp[FILENAMELENGTH];
909: char popfile[FILENAMELENGTH];
910:
911: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
912:
1.157 brouard 913: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
914: /* struct timezone tzp; */
915: /* extern int gettimeofday(); */
916: struct tm tml, *gmtime(), *localtime();
917:
918: extern time_t time();
919:
920: struct tm start_time, end_time, curr_time, last_time, forecast_time;
921: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
922: struct tm tm;
923:
1.126 brouard 924: char strcurr[80], strfor[80];
925:
926: char *endptr;
927: long lval;
928: double dval;
929:
930: #define NR_END 1
931: #define FREE_ARG char*
932: #define FTOL 1.0e-10
933:
934: #define NRANSI
935: #define ITMAX 200
936:
937: #define TOL 2.0e-4
938:
939: #define CGOLD 0.3819660
940: #define ZEPS 1.0e-10
941: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
942:
943: #define GOLD 1.618034
944: #define GLIMIT 100.0
945: #define TINY 1.0e-20
946:
947: static double maxarg1,maxarg2;
948: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
949: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
950:
951: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
952: #define rint(a) floor(a+0.5)
1.166 brouard 953: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 954: #define mytinydouble 1.0e-16
1.166 brouard 955: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
956: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
957: /* static double dsqrarg; */
958: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 959: static double sqrarg;
960: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
961: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
962: int agegomp= AGEGOMP;
963:
964: int imx;
965: int stepm=1;
966: /* Stepm, step in month: minimum step interpolation*/
967:
968: int estepm;
969: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
970:
971: int m,nb;
972: long *num;
1.197 brouard 973: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 974: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
975: covariate for which somebody answered excluding
976: undefined. Usually 2: 0 and 1. */
977: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
978: covariate for which somebody answered including
979: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 980: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
1.218 brouard 981: double **pmmij, ***probs; /* Global pointer */
1.219 brouard 982: double ***mobaverage, ***mobaverages; /* New global variable */
1.126 brouard 983: double *ageexmed,*agecens;
984: double dateintmean=0;
985:
986: double *weight;
987: int **s; /* Status */
1.141 brouard 988: double *agedc;
1.145 brouard 989: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 990: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 991: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 992: double idx;
993: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 994: int *Tage;
1.145 brouard 995: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 996: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.220 brouard 997: int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;
1.126 brouard 998: double *lsurv, *lpop, *tpop;
999:
1.143 brouard 1000: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
1001: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 1002:
1003: /**************** split *************************/
1004: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
1005: {
1006: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
1007: the name of the file (name), its extension only (ext) and its first part of the name (finame)
1008: */
1009: char *ss; /* pointer */
1.186 brouard 1010: int l1=0, l2=0; /* length counters */
1.126 brouard 1011:
1012: l1 = strlen(path ); /* length of path */
1013: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
1014: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
1015: if ( ss == NULL ) { /* no directory, so determine current directory */
1016: strcpy( name, path ); /* we got the fullname name because no directory */
1017: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
1018: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
1019: /* get current working directory */
1020: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 1021: #ifdef WIN32
1022: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
1023: #else
1024: if (getcwd(dirc, FILENAME_MAX) == NULL) {
1025: #endif
1.126 brouard 1026: return( GLOCK_ERROR_GETCWD );
1027: }
1028: /* got dirc from getcwd*/
1029: printf(" DIRC = %s \n",dirc);
1.205 brouard 1030: } else { /* strip directory from path */
1.126 brouard 1031: ss++; /* after this, the filename */
1032: l2 = strlen( ss ); /* length of filename */
1033: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
1034: strcpy( name, ss ); /* save file name */
1035: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 1036: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 1037: printf(" DIRC2 = %s \n",dirc);
1038: }
1039: /* We add a separator at the end of dirc if not exists */
1040: l1 = strlen( dirc ); /* length of directory */
1041: if( dirc[l1-1] != DIRSEPARATOR ){
1042: dirc[l1] = DIRSEPARATOR;
1043: dirc[l1+1] = 0;
1044: printf(" DIRC3 = %s \n",dirc);
1045: }
1046: ss = strrchr( name, '.' ); /* find last / */
1047: if (ss >0){
1048: ss++;
1049: strcpy(ext,ss); /* save extension */
1050: l1= strlen( name);
1051: l2= strlen(ss)+1;
1052: strncpy( finame, name, l1-l2);
1053: finame[l1-l2]= 0;
1054: }
1055:
1056: return( 0 ); /* we're done */
1057: }
1058:
1059:
1060: /******************************************/
1061:
1062: void replace_back_to_slash(char *s, char*t)
1063: {
1064: int i;
1065: int lg=0;
1066: i=0;
1067: lg=strlen(t);
1068: for(i=0; i<= lg; i++) {
1069: (s[i] = t[i]);
1070: if (t[i]== '\\') s[i]='/';
1071: }
1072: }
1073:
1.132 brouard 1074: char *trimbb(char *out, char *in)
1.137 brouard 1075: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1076: char *s;
1077: s=out;
1078: while (*in != '\0'){
1.137 brouard 1079: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1080: in++;
1081: }
1082: *out++ = *in++;
1083: }
1084: *out='\0';
1085: return s;
1086: }
1087:
1.187 brouard 1088: /* char *substrchaine(char *out, char *in, char *chain) */
1089: /* { */
1090: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1091: /* char *s, *t; */
1092: /* t=in;s=out; */
1093: /* while ((*in != *chain) && (*in != '\0')){ */
1094: /* *out++ = *in++; */
1095: /* } */
1096:
1097: /* /\* *in matches *chain *\/ */
1098: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1099: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1100: /* } */
1101: /* in--; chain--; */
1102: /* while ( (*in != '\0')){ */
1103: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1104: /* *out++ = *in++; */
1105: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1106: /* } */
1107: /* *out='\0'; */
1108: /* out=s; */
1109: /* return out; */
1110: /* } */
1111: char *substrchaine(char *out, char *in, char *chain)
1112: {
1113: /* Substract chain 'chain' from 'in', return and output 'out' */
1114: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1115:
1116: char *strloc;
1117:
1118: strcpy (out, in);
1119: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1120: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1121: if(strloc != NULL){
1122: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1123: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1124: /* strcpy (strloc, strloc +strlen(chain));*/
1125: }
1126: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1127: return out;
1128: }
1129:
1130:
1.145 brouard 1131: char *cutl(char *blocc, char *alocc, char *in, char occ)
1132: {
1.187 brouard 1133: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1134: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1135: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1136: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1137: */
1.160 brouard 1138: char *s, *t;
1.145 brouard 1139: t=in;s=in;
1140: while ((*in != occ) && (*in != '\0')){
1141: *alocc++ = *in++;
1142: }
1143: if( *in == occ){
1144: *(alocc)='\0';
1145: s=++in;
1146: }
1147:
1148: if (s == t) {/* occ not found */
1149: *(alocc-(in-s))='\0';
1150: in=s;
1151: }
1152: while ( *in != '\0'){
1153: *blocc++ = *in++;
1154: }
1155:
1156: *blocc='\0';
1157: return t;
1158: }
1.137 brouard 1159: char *cutv(char *blocc, char *alocc, char *in, char occ)
1160: {
1.187 brouard 1161: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1162: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1163: gives blocc="abcdef2ghi" and alocc="j".
1164: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1165: */
1166: char *s, *t;
1167: t=in;s=in;
1168: while (*in != '\0'){
1169: while( *in == occ){
1170: *blocc++ = *in++;
1171: s=in;
1172: }
1173: *blocc++ = *in++;
1174: }
1175: if (s == t) /* occ not found */
1176: *(blocc-(in-s))='\0';
1177: else
1178: *(blocc-(in-s)-1)='\0';
1179: in=s;
1180: while ( *in != '\0'){
1181: *alocc++ = *in++;
1182: }
1183:
1184: *alocc='\0';
1185: return s;
1186: }
1187:
1.126 brouard 1188: int nbocc(char *s, char occ)
1189: {
1190: int i,j=0;
1191: int lg=20;
1192: i=0;
1193: lg=strlen(s);
1194: for(i=0; i<= lg; i++) {
1195: if (s[i] == occ ) j++;
1196: }
1197: return j;
1198: }
1199:
1.137 brouard 1200: /* void cutv(char *u,char *v, char*t, char occ) */
1201: /* { */
1202: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1203: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1204: /* gives u="abcdef2ghi" and v="j" *\/ */
1205: /* int i,lg,j,p=0; */
1206: /* i=0; */
1207: /* lg=strlen(t); */
1208: /* for(j=0; j<=lg-1; j++) { */
1209: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1210: /* } */
1.126 brouard 1211:
1.137 brouard 1212: /* for(j=0; j<p; j++) { */
1213: /* (u[j] = t[j]); */
1214: /* } */
1215: /* u[p]='\0'; */
1.126 brouard 1216:
1.137 brouard 1217: /* for(j=0; j<= lg; j++) { */
1218: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1219: /* } */
1220: /* } */
1.126 brouard 1221:
1.160 brouard 1222: #ifdef _WIN32
1223: char * strsep(char **pp, const char *delim)
1224: {
1225: char *p, *q;
1226:
1227: if ((p = *pp) == NULL)
1228: return 0;
1229: if ((q = strpbrk (p, delim)) != NULL)
1230: {
1231: *pp = q + 1;
1232: *q = '\0';
1233: }
1234: else
1235: *pp = 0;
1236: return p;
1237: }
1238: #endif
1239:
1.126 brouard 1240: /********************** nrerror ********************/
1241:
1242: void nrerror(char error_text[])
1243: {
1244: fprintf(stderr,"ERREUR ...\n");
1245: fprintf(stderr,"%s\n",error_text);
1246: exit(EXIT_FAILURE);
1247: }
1248: /*********************** vector *******************/
1249: double *vector(int nl, int nh)
1250: {
1251: double *v;
1252: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1253: if (!v) nrerror("allocation failure in vector");
1254: return v-nl+NR_END;
1255: }
1256:
1257: /************************ free vector ******************/
1258: void free_vector(double*v, int nl, int nh)
1259: {
1260: free((FREE_ARG)(v+nl-NR_END));
1261: }
1262:
1263: /************************ivector *******************************/
1264: int *ivector(long nl,long nh)
1265: {
1266: int *v;
1267: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1268: if (!v) nrerror("allocation failure in ivector");
1269: return v-nl+NR_END;
1270: }
1271:
1272: /******************free ivector **************************/
1273: void free_ivector(int *v, long nl, long nh)
1274: {
1275: free((FREE_ARG)(v+nl-NR_END));
1276: }
1277:
1278: /************************lvector *******************************/
1279: long *lvector(long nl,long nh)
1280: {
1281: long *v;
1282: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1283: if (!v) nrerror("allocation failure in ivector");
1284: return v-nl+NR_END;
1285: }
1286:
1287: /******************free lvector **************************/
1288: void free_lvector(long *v, long nl, long nh)
1289: {
1290: free((FREE_ARG)(v+nl-NR_END));
1291: }
1292:
1293: /******************* imatrix *******************************/
1294: int **imatrix(long nrl, long nrh, long ncl, long nch)
1295: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1296: {
1297: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1298: int **m;
1299:
1300: /* allocate pointers to rows */
1301: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1302: if (!m) nrerror("allocation failure 1 in matrix()");
1303: m += NR_END;
1304: m -= nrl;
1305:
1306:
1307: /* allocate rows and set pointers to them */
1308: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1309: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1310: m[nrl] += NR_END;
1311: m[nrl] -= ncl;
1312:
1313: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1314:
1315: /* return pointer to array of pointers to rows */
1316: return m;
1317: }
1318:
1319: /****************** free_imatrix *************************/
1320: void free_imatrix(m,nrl,nrh,ncl,nch)
1321: int **m;
1322: long nch,ncl,nrh,nrl;
1323: /* free an int matrix allocated by imatrix() */
1324: {
1325: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1326: free((FREE_ARG) (m+nrl-NR_END));
1327: }
1328:
1329: /******************* matrix *******************************/
1330: double **matrix(long nrl, long nrh, long ncl, long nch)
1331: {
1332: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1333: double **m;
1334:
1335: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1336: if (!m) nrerror("allocation failure 1 in matrix()");
1337: m += NR_END;
1338: m -= nrl;
1339:
1340: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1341: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1342: m[nrl] += NR_END;
1343: m[nrl] -= ncl;
1344:
1345: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1346: return m;
1.145 brouard 1347: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1348: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1349: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1350: */
1351: }
1352:
1353: /*************************free matrix ************************/
1354: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1355: {
1356: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1357: free((FREE_ARG)(m+nrl-NR_END));
1358: }
1359:
1360: /******************* ma3x *******************************/
1361: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1362: {
1363: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1364: double ***m;
1365:
1366: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1367: if (!m) nrerror("allocation failure 1 in matrix()");
1368: m += NR_END;
1369: m -= nrl;
1370:
1371: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1372: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1373: m[nrl] += NR_END;
1374: m[nrl] -= ncl;
1375:
1376: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1377:
1378: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1379: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1380: m[nrl][ncl] += NR_END;
1381: m[nrl][ncl] -= nll;
1382: for (j=ncl+1; j<=nch; j++)
1383: m[nrl][j]=m[nrl][j-1]+nlay;
1384:
1385: for (i=nrl+1; i<=nrh; i++) {
1386: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1387: for (j=ncl+1; j<=nch; j++)
1388: m[i][j]=m[i][j-1]+nlay;
1389: }
1390: return m;
1391: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1392: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1393: */
1394: }
1395:
1396: /*************************free ma3x ************************/
1397: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1398: {
1399: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1400: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1401: free((FREE_ARG)(m+nrl-NR_END));
1402: }
1403:
1404: /*************** function subdirf ***********/
1405: char *subdirf(char fileres[])
1406: {
1407: /* Caution optionfilefiname is hidden */
1408: strcpy(tmpout,optionfilefiname);
1409: strcat(tmpout,"/"); /* Add to the right */
1410: strcat(tmpout,fileres);
1411: return tmpout;
1412: }
1413:
1414: /*************** function subdirf2 ***********/
1415: char *subdirf2(char fileres[], char *preop)
1416: {
1417:
1418: /* Caution optionfilefiname is hidden */
1419: strcpy(tmpout,optionfilefiname);
1420: strcat(tmpout,"/");
1421: strcat(tmpout,preop);
1422: strcat(tmpout,fileres);
1423: return tmpout;
1424: }
1425:
1426: /*************** function subdirf3 ***********/
1427: char *subdirf3(char fileres[], char *preop, char *preop2)
1428: {
1429:
1430: /* Caution optionfilefiname is hidden */
1431: strcpy(tmpout,optionfilefiname);
1432: strcat(tmpout,"/");
1433: strcat(tmpout,preop);
1434: strcat(tmpout,preop2);
1435: strcat(tmpout,fileres);
1436: return tmpout;
1437: }
1.213 brouard 1438:
1439: /*************** function subdirfext ***********/
1440: char *subdirfext(char fileres[], char *preop, char *postop)
1441: {
1442:
1443: strcpy(tmpout,preop);
1444: strcat(tmpout,fileres);
1445: strcat(tmpout,postop);
1446: return tmpout;
1447: }
1.126 brouard 1448:
1.213 brouard 1449: /*************** function subdirfext3 ***********/
1450: char *subdirfext3(char fileres[], char *preop, char *postop)
1451: {
1452:
1453: /* Caution optionfilefiname is hidden */
1454: strcpy(tmpout,optionfilefiname);
1455: strcat(tmpout,"/");
1456: strcat(tmpout,preop);
1457: strcat(tmpout,fileres);
1458: strcat(tmpout,postop);
1459: return tmpout;
1460: }
1461:
1.162 brouard 1462: char *asc_diff_time(long time_sec, char ascdiff[])
1463: {
1464: long sec_left, days, hours, minutes;
1465: days = (time_sec) / (60*60*24);
1466: sec_left = (time_sec) % (60*60*24);
1467: hours = (sec_left) / (60*60) ;
1468: sec_left = (sec_left) %(60*60);
1469: minutes = (sec_left) /60;
1470: sec_left = (sec_left) % (60);
1471: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1472: return ascdiff;
1473: }
1474:
1.126 brouard 1475: /***************** f1dim *************************/
1476: extern int ncom;
1477: extern double *pcom,*xicom;
1478: extern double (*nrfunc)(double []);
1479:
1480: double f1dim(double x)
1481: {
1482: int j;
1483: double f;
1484: double *xt;
1485:
1486: xt=vector(1,ncom);
1487: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1488: f=(*nrfunc)(xt);
1489: free_vector(xt,1,ncom);
1490: return f;
1491: }
1492:
1493: /*****************brent *************************/
1494: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1495: {
1496: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1497: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1498: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1499: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1500: * returned function value.
1501: */
1.126 brouard 1502: int iter;
1503: double a,b,d,etemp;
1.159 brouard 1504: double fu=0,fv,fw,fx;
1.164 brouard 1505: double ftemp=0.;
1.126 brouard 1506: double p,q,r,tol1,tol2,u,v,w,x,xm;
1507: double e=0.0;
1508:
1509: a=(ax < cx ? ax : cx);
1510: b=(ax > cx ? ax : cx);
1511: x=w=v=bx;
1512: fw=fv=fx=(*f)(x);
1513: for (iter=1;iter<=ITMAX;iter++) {
1514: xm=0.5*(a+b);
1515: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1516: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1517: printf(".");fflush(stdout);
1518: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1519: #ifdef DEBUGBRENT
1.126 brouard 1520: 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);
1521: 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);
1522: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1523: #endif
1524: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1525: *xmin=x;
1526: return fx;
1527: }
1528: ftemp=fu;
1529: if (fabs(e) > tol1) {
1530: r=(x-w)*(fx-fv);
1531: q=(x-v)*(fx-fw);
1532: p=(x-v)*q-(x-w)*r;
1533: q=2.0*(q-r);
1534: if (q > 0.0) p = -p;
1535: q=fabs(q);
1536: etemp=e;
1537: e=d;
1538: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1539: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1540: else {
1541: d=p/q;
1542: u=x+d;
1543: if (u-a < tol2 || b-u < tol2)
1544: d=SIGN(tol1,xm-x);
1545: }
1546: } else {
1547: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1548: }
1549: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1550: fu=(*f)(u);
1551: if (fu <= fx) {
1552: if (u >= x) a=x; else b=x;
1553: SHFT(v,w,x,u)
1.183 brouard 1554: SHFT(fv,fw,fx,fu)
1555: } else {
1556: if (u < x) a=u; else b=u;
1557: if (fu <= fw || w == x) {
1558: v=w;
1559: w=u;
1560: fv=fw;
1561: fw=fu;
1562: } else if (fu <= fv || v == x || v == w) {
1563: v=u;
1564: fv=fu;
1565: }
1566: }
1.126 brouard 1567: }
1568: nrerror("Too many iterations in brent");
1569: *xmin=x;
1570: return fx;
1571: }
1572:
1573: /****************** mnbrak ***********************/
1574:
1575: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1576: double (*func)(double))
1.183 brouard 1577: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1578: the downhill direction (defined by the function as evaluated at the initial points) and returns
1579: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1580: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1581: */
1.126 brouard 1582: double ulim,u,r,q, dum;
1583: double fu;
1.187 brouard 1584:
1585: double scale=10.;
1586: int iterscale=0;
1587:
1588: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1589: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1590:
1591:
1592: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1593: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1594: /* *bx = *ax - (*ax - *bx)/scale; */
1595: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1596: /* } */
1597:
1.126 brouard 1598: if (*fb > *fa) {
1599: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1600: SHFT(dum,*fb,*fa,dum)
1601: }
1.126 brouard 1602: *cx=(*bx)+GOLD*(*bx-*ax);
1603: *fc=(*func)(*cx);
1.183 brouard 1604: #ifdef DEBUG
1605: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1606: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1607: #endif
1608: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1609: r=(*bx-*ax)*(*fb-*fc);
1610: q=(*bx-*cx)*(*fb-*fa);
1611: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1612: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1613: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1614: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1615: fu=(*func)(u);
1.163 brouard 1616: #ifdef DEBUG
1617: /* f(x)=A(x-u)**2+f(u) */
1618: double A, fparabu;
1619: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1620: fparabu= *fa - A*(*ax-u)*(*ax-u);
1621: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1622: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
1.183 brouard 1623: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1624: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1625: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1626: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1627: #endif
1.184 brouard 1628: #ifdef MNBRAKORIGINAL
1.183 brouard 1629: #else
1.191 brouard 1630: /* if (fu > *fc) { */
1631: /* #ifdef DEBUG */
1632: /* printf("mnbrak4 fu > fc \n"); */
1633: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1634: /* #endif */
1635: /* /\* 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 *\\/ *\/ */
1636: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1637: /* dum=u; /\* Shifting c and u *\/ */
1638: /* u = *cx; */
1639: /* *cx = dum; */
1640: /* dum = fu; */
1641: /* fu = *fc; */
1642: /* *fc =dum; */
1643: /* } else { /\* end *\/ */
1644: /* #ifdef DEBUG */
1645: /* printf("mnbrak3 fu < fc \n"); */
1646: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1647: /* #endif */
1648: /* dum=u; /\* Shifting c and u *\/ */
1649: /* u = *cx; */
1650: /* *cx = dum; */
1651: /* dum = fu; */
1652: /* fu = *fc; */
1653: /* *fc =dum; */
1654: /* } */
1.183 brouard 1655: #ifdef DEBUG
1.191 brouard 1656: printf("mnbrak34 fu < or >= fc \n");
1657: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1658: #endif
1.191 brouard 1659: dum=u; /* Shifting c and u */
1660: u = *cx;
1661: *cx = dum;
1662: dum = fu;
1663: fu = *fc;
1664: *fc =dum;
1.183 brouard 1665: #endif
1.162 brouard 1666: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1667: #ifdef DEBUG
1668: printf("mnbrak2 u after c but before ulim\n");
1669: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1670: #endif
1.126 brouard 1671: fu=(*func)(u);
1672: if (fu < *fc) {
1.183 brouard 1673: #ifdef DEBUG
1674: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1675: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1676: #endif
1.126 brouard 1677: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1678: SHFT(*fb,*fc,fu,(*func)(u))
1679: }
1.162 brouard 1680: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1681: #ifdef DEBUG
1682: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1683: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1684: #endif
1.126 brouard 1685: u=ulim;
1686: fu=(*func)(u);
1.183 brouard 1687: } else { /* u could be left to b (if r > q parabola has a maximum) */
1688: #ifdef DEBUG
1689: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1690: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1691: #endif
1.126 brouard 1692: u=(*cx)+GOLD*(*cx-*bx);
1693: fu=(*func)(u);
1.183 brouard 1694: } /* end tests */
1.126 brouard 1695: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1696: SHFT(*fa,*fb,*fc,fu)
1697: #ifdef DEBUG
1698: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1699: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1700: #endif
1701: } /* 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 1702: }
1703:
1704: /*************** linmin ************************/
1.162 brouard 1705: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1706: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1707: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1708: the value of func at the returned location p . This is actually all accomplished by calling the
1709: routines mnbrak and brent .*/
1.126 brouard 1710: int ncom;
1711: double *pcom,*xicom;
1712: double (*nrfunc)(double []);
1713:
1714: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1715: {
1716: double brent(double ax, double bx, double cx,
1717: double (*f)(double), double tol, double *xmin);
1718: double f1dim(double x);
1719: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1720: double *fc, double (*func)(double));
1721: int j;
1722: double xx,xmin,bx,ax;
1723: double fx,fb,fa;
1.187 brouard 1724:
1.203 brouard 1725: #ifdef LINMINORIGINAL
1726: #else
1727: double scale=10., axs, xxs; /* Scale added for infinity */
1728: #endif
1729:
1.126 brouard 1730: ncom=n;
1731: pcom=vector(1,n);
1732: xicom=vector(1,n);
1733: nrfunc=func;
1734: for (j=1;j<=n;j++) {
1735: pcom[j]=p[j];
1.202 brouard 1736: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1737: }
1.187 brouard 1738:
1.203 brouard 1739: #ifdef LINMINORIGINAL
1740: xx=1.;
1741: #else
1742: axs=0.0;
1743: xxs=1.;
1744: do{
1745: xx= xxs;
1746: #endif
1.187 brouard 1747: ax=0.;
1748: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1749: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1750: /* 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)) */
1751: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1752: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1753: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1754: /* 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 1755: #ifdef LINMINORIGINAL
1756: #else
1757: if (fx != fx){
1758: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1759: printf("|");
1760: fprintf(ficlog,"|");
1761: #ifdef DEBUGLINMIN
1762: 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);
1763: #endif
1764: }
1765: }while(fx != fx);
1766: #endif
1767:
1.191 brouard 1768: #ifdef DEBUGLINMIN
1769: 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 1770: 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 1771: #endif
1.187 brouard 1772: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1773: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1774: /* fmin = f(p[j] + xmin * xi[j]) */
1775: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1776: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1777: #ifdef DEBUG
1778: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1779: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1780: #endif
1.191 brouard 1781: #ifdef DEBUGLINMIN
1782: printf("linmin end ");
1.202 brouard 1783: fprintf(ficlog,"linmin end ");
1.191 brouard 1784: #endif
1.126 brouard 1785: for (j=1;j<=n;j++) {
1.203 brouard 1786: #ifdef LINMINORIGINAL
1787: xi[j] *= xmin;
1788: #else
1789: #ifdef DEBUGLINMIN
1790: if(xxs <1.0)
1791: printf(" before xi[%d]=%12.8f", j,xi[j]);
1792: #endif
1793: 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) */
1794: #ifdef DEBUGLINMIN
1795: if(xxs <1.0)
1796: 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 );
1797: #endif
1798: #endif
1.187 brouard 1799: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1800: }
1.191 brouard 1801: #ifdef DEBUGLINMIN
1.203 brouard 1802: printf("\n");
1.191 brouard 1803: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1804: 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 1805: for (j=1;j<=n;j++) {
1.202 brouard 1806: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1807: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1808: if(j % ncovmodel == 0){
1.191 brouard 1809: printf("\n");
1.202 brouard 1810: fprintf(ficlog,"\n");
1811: }
1.191 brouard 1812: }
1.203 brouard 1813: #else
1.191 brouard 1814: #endif
1.126 brouard 1815: free_vector(xicom,1,n);
1816: free_vector(pcom,1,n);
1817: }
1818:
1819:
1820: /*************** powell ************************/
1.162 brouard 1821: /*
1822: Minimization of a function func of n variables. Input consists of an initial starting point
1823: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1824: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1825: such that failure to decrease by more than this amount on one iteration signals doneness. On
1826: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1827: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1828: */
1.126 brouard 1829: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1830: double (*func)(double []))
1831: {
1832: void linmin(double p[], double xi[], int n, double *fret,
1833: double (*func)(double []));
1834: int i,ibig,j;
1835: double del,t,*pt,*ptt,*xit;
1.181 brouard 1836: double directest;
1.126 brouard 1837: double fp,fptt;
1838: double *xits;
1839: int niterf, itmp;
1840:
1841: pt=vector(1,n);
1842: ptt=vector(1,n);
1843: xit=vector(1,n);
1844: xits=vector(1,n);
1845: *fret=(*func)(p);
1846: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1847: rcurr_time = time(NULL);
1.126 brouard 1848: for (*iter=1;;++(*iter)) {
1.187 brouard 1849: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1850: ibig=0;
1851: del=0.0;
1.157 brouard 1852: rlast_time=rcurr_time;
1853: /* (void) gettimeofday(&curr_time,&tzp); */
1854: rcurr_time = time(NULL);
1855: curr_time = *localtime(&rcurr_time);
1856: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1857: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1858: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1859: for (i=1;i<=n;i++) {
1.126 brouard 1860: printf(" %d %.12f",i, p[i]);
1861: fprintf(ficlog," %d %.12lf",i, p[i]);
1862: fprintf(ficrespow," %.12lf", p[i]);
1863: }
1864: printf("\n");
1865: fprintf(ficlog,"\n");
1866: fprintf(ficrespow,"\n");fflush(ficrespow);
1867: if(*iter <=3){
1.157 brouard 1868: tml = *localtime(&rcurr_time);
1869: strcpy(strcurr,asctime(&tml));
1870: rforecast_time=rcurr_time;
1.126 brouard 1871: itmp = strlen(strcurr);
1872: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1873: strcurr[itmp-1]='\0';
1.162 brouard 1874: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1875: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1876: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1877: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1878: forecast_time = *localtime(&rforecast_time);
1879: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1880: itmp = strlen(strfor);
1881: if(strfor[itmp-1]=='\n')
1882: strfor[itmp-1]='\0';
1.157 brouard 1883: 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);
1884: 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 1885: }
1886: }
1.187 brouard 1887: for (i=1;i<=n;i++) { /* For each direction i */
1888: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1889: fptt=(*fret);
1890: #ifdef DEBUG
1.203 brouard 1891: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1892: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1893: #endif
1.203 brouard 1894: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1895: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1896: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1897: /* Outputs are fret(new point p) p is updated and xit rescaled */
1898: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1899: /* because that direction will be replaced unless the gain del is small */
1900: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1901: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1902: /* with the new direction. */
1.126 brouard 1903: del=fabs(fptt-(*fret));
1904: ibig=i;
1905: }
1906: #ifdef DEBUG
1907: printf("%d %.12e",i,(*fret));
1908: fprintf(ficlog,"%d %.12e",i,(*fret));
1909: for (j=1;j<=n;j++) {
1910: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1911: printf(" x(%d)=%.12e",j,xit[j]);
1912: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1913: }
1914: for(j=1;j<=n;j++) {
1.162 brouard 1915: printf(" p(%d)=%.12e",j,p[j]);
1916: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1917: }
1918: printf("\n");
1919: fprintf(ficlog,"\n");
1920: #endif
1.187 brouard 1921: } /* end loop on each direction i */
1922: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1923: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1924: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1925: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1926: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1927: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1928: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1929: /* decreased of more than 3.84 */
1930: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1931: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1932: /* By adding 10 parameters more the gain should be 18.31 */
1933:
1934: /* Starting the program with initial values given by a former maximization will simply change */
1935: /* the scales of the directions and the directions, because the are reset to canonical directions */
1936: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1937: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1938: #ifdef DEBUG
1939: int k[2],l;
1940: k[0]=1;
1941: k[1]=-1;
1942: printf("Max: %.12e",(*func)(p));
1943: fprintf(ficlog,"Max: %.12e",(*func)(p));
1944: for (j=1;j<=n;j++) {
1945: printf(" %.12e",p[j]);
1946: fprintf(ficlog," %.12e",p[j]);
1947: }
1948: printf("\n");
1949: fprintf(ficlog,"\n");
1950: for(l=0;l<=1;l++) {
1951: for (j=1;j<=n;j++) {
1952: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1953: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1954: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1955: }
1956: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1957: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1958: }
1959: #endif
1960:
1961:
1962: free_vector(xit,1,n);
1963: free_vector(xits,1,n);
1964: free_vector(ptt,1,n);
1965: free_vector(pt,1,n);
1966: return;
1.192 brouard 1967: } /* enough precision */
1.126 brouard 1968: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1969: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1970: ptt[j]=2.0*p[j]-pt[j];
1971: xit[j]=p[j]-pt[j];
1972: pt[j]=p[j];
1973: }
1.181 brouard 1974: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1975: #ifdef POWELLF1F3
1976: #else
1.161 brouard 1977: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1978: #endif
1.162 brouard 1979: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1980: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1981: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1982: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1983: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1984: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1985: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1986: #ifdef NRCORIGINAL
1987: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1988: #else
1989: 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 1990: t= t- del*SQR(fp-fptt);
1.183 brouard 1991: #endif
1.202 brouard 1992: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1993: #ifdef DEBUG
1.181 brouard 1994: 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);
1995: 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 1996: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1997: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1998: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1999: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
2000: 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);
2001: 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);
2002: #endif
1.183 brouard 2003: #ifdef POWELLORIGINAL
2004: if (t < 0.0) { /* Then we use it for new direction */
2005: #else
1.182 brouard 2006: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 2007: 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 2008: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.202 brouard 2009: fprintf(ficlog,"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 2010: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
2011: }
1.181 brouard 2012: if (directest < 0.0) { /* Then we use it for new direction */
2013: #endif
1.191 brouard 2014: #ifdef DEBUGLINMIN
2015: printf("Before linmin in direction P%d-P0\n",n);
2016: for (j=1;j<=n;j++) {
1.202 brouard 2017: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2018: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2019: if(j % ncovmodel == 0){
1.191 brouard 2020: printf("\n");
1.202 brouard 2021: fprintf(ficlog,"\n");
2022: }
1.191 brouard 2023: }
2024: #endif
1.187 brouard 2025: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 2026: #ifdef DEBUGLINMIN
2027: for (j=1;j<=n;j++) {
2028: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 2029: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
2030: if(j % ncovmodel == 0){
1.191 brouard 2031: printf("\n");
1.202 brouard 2032: fprintf(ficlog,"\n");
2033: }
1.191 brouard 2034: }
2035: #endif
1.126 brouard 2036: for (j=1;j<=n;j++) {
1.181 brouard 2037: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
2038: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 2039: }
1.181 brouard 2040: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
2041: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 2042:
1.126 brouard 2043: #ifdef DEBUG
1.164 brouard 2044: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2045: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2046: for(j=1;j<=n;j++){
2047: printf(" %.12e",xit[j]);
2048: fprintf(ficlog," %.12e",xit[j]);
2049: }
2050: printf("\n");
2051: fprintf(ficlog,"\n");
2052: #endif
1.192 brouard 2053: } /* end of t or directest negative */
2054: #ifdef POWELLF1F3
2055: #else
1.162 brouard 2056: } /* end if (fptt < fp) */
1.192 brouard 2057: #endif
2058: } /* loop iteration */
1.126 brouard 2059: }
2060:
2061: /**** Prevalence limit (stable or period prevalence) ****************/
2062:
1.203 brouard 2063: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2064: {
1.218 brouard 2065: /* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit
1.203 brouard 2066: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2067: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2068: /* Wx is row vector: population in state 1, population in state 2, population dead */
2069: /* or prevalence in state 1, prevalence in state 2, 0 */
2070: /* newm is the matrix after multiplications, its rows are identical at a factor */
2071: /* Initial matrix pimij */
2072: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2073: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2074: /* 0, 0 , 1} */
2075: /*
2076: * and after some iteration: */
2077: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2078: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2079: /* 0, 0 , 1} */
2080: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2081: /* {0.51571254859325999, 0.4842874514067399, */
2082: /* 0.51326036147820708, 0.48673963852179264} */
2083: /* If we start from prlim again, prlim tends to a constant matrix */
2084:
1.126 brouard 2085: int i, ii,j,k;
1.209 brouard 2086: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2087: /* double **matprod2(); */ /* test */
1.218 brouard 2088: double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
1.126 brouard 2089: double **newm;
1.209 brouard 2090: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2091: int ncvloop=0;
1.169 brouard 2092:
1.209 brouard 2093: min=vector(1,nlstate);
2094: max=vector(1,nlstate);
2095: meandiff=vector(1,nlstate);
2096:
1.218 brouard 2097: /* Starting with matrix unity */
1.126 brouard 2098: for (ii=1;ii<=nlstate+ndeath;ii++)
2099: for (j=1;j<=nlstate+ndeath;j++){
2100: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2101: }
1.169 brouard 2102:
2103: cov[1]=1.;
2104:
2105: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2106: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2107: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2108: ncvloop++;
1.126 brouard 2109: newm=savm;
2110: /* Covariates have to be included here again */
1.138 brouard 2111: cov[2]=agefin;
1.187 brouard 2112: if(nagesqr==1)
2113: cov[3]= agefin*agefin;;
1.138 brouard 2114: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2115: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.218 brouard 2116: /* Here comes the value of the covariate 'ij' */
1.200 brouard 2117: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2118: /* 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 2119: }
1.186 brouard 2120: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2121: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2122: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2123: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2124: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2125: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2126:
2127: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2128: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2129: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2130: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2131: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2132: /* age and covariate values of ij are in 'cov' */
1.142 brouard 2133: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2134:
1.126 brouard 2135: savm=oldm;
2136: oldm=newm;
1.209 brouard 2137:
2138: for(j=1; j<=nlstate; j++){
2139: max[j]=0.;
2140: min[j]=1.;
2141: }
2142: for(i=1;i<=nlstate;i++){
2143: sumnew=0;
2144: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2145: for(j=1; j<=nlstate; j++){
2146: prlim[i][j]= newm[i][j]/(1-sumnew);
2147: max[j]=FMAX(max[j],prlim[i][j]);
2148: min[j]=FMIN(min[j],prlim[i][j]);
2149: }
2150: }
2151:
1.126 brouard 2152: maxmax=0.;
1.209 brouard 2153: for(j=1; j<=nlstate; j++){
2154: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2155: maxmax=FMAX(maxmax,meandiff[j]);
2156: /* 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 2157: } /* j loop */
1.203 brouard 2158: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2159: /* 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 2160: if(maxmax < ftolpl){
1.209 brouard 2161: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2162: free_vector(min,1,nlstate);
2163: free_vector(max,1,nlstate);
2164: free_vector(meandiff,1,nlstate);
1.126 brouard 2165: return prlim;
2166: }
1.169 brouard 2167: } /* age loop */
1.208 brouard 2168: /* After some age loop it doesn't converge */
1.209 brouard 2169: 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 2170: 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 2171: /* 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); */
2172: free_vector(min,1,nlstate);
2173: free_vector(max,1,nlstate);
2174: free_vector(meandiff,1,nlstate);
1.208 brouard 2175:
1.169 brouard 2176: return prlim; /* should not reach here */
1.126 brouard 2177: }
2178:
1.217 brouard 2179:
2180: /**** Back Prevalence limit (stable or period prevalence) ****************/
2181:
1.218 brouard 2182: /* 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) */
2183: /* 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) */
2184: double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)
1.217 brouard 2185: {
1.218 brouard 2186: /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
1.217 brouard 2187: matrix by transitions matrix until convergence is reached with precision ftolpl */
2188: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2189: /* Wx is row vector: population in state 1, population in state 2, population dead */
2190: /* or prevalence in state 1, prevalence in state 2, 0 */
2191: /* newm is the matrix after multiplications, its rows are identical at a factor */
2192: /* Initial matrix pimij */
2193: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2194: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2195: /* 0, 0 , 1} */
2196: /*
2197: * and after some iteration: */
2198: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2199: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2200: /* 0, 0 , 1} */
2201: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2202: /* {0.51571254859325999, 0.4842874514067399, */
2203: /* 0.51326036147820708, 0.48673963852179264} */
2204: /* If we start from prlim again, prlim tends to a constant matrix */
2205:
2206: int i, ii,j,k;
2207: double *min, *max, *meandiff, maxmax,sumnew=0.;
2208: /* double **matprod2(); */ /* test */
2209: double **out, cov[NCOVMAX+1], **bmij();
2210: double **newm;
1.218 brouard 2211: double **dnewm, **doldm, **dsavm; /* for use */
2212: double **oldm, **savm; /* for use */
2213:
1.217 brouard 2214: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
2215: int ncvloop=0;
2216:
2217: min=vector(1,nlstate);
2218: max=vector(1,nlstate);
2219: meandiff=vector(1,nlstate);
2220:
1.218 brouard 2221: dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
2222: oldm=oldms; savm=savms;
2223:
2224: /* Starting with matrix unity */
2225: for (ii=1;ii<=nlstate+ndeath;ii++)
2226: for (j=1;j<=nlstate+ndeath;j++){
1.217 brouard 2227: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2228: }
2229:
2230: cov[1]=1.;
2231:
2232: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2233: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.218 brouard 2234: /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
2235: for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */
1.217 brouard 2236: ncvloop++;
1.218 brouard 2237: newm=savm; /* oldm should be kept from previous iteration or unity at start */
2238: /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
1.217 brouard 2239: /* Covariates have to be included here again */
2240: cov[2]=agefin;
2241: if(nagesqr==1)
2242: cov[3]= agefin*agefin;;
2243: for (k=1; k<=cptcovn;k++) {
2244: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2245: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2246: /* 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])]); */
2247: }
2248: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2249: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2250: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
2251: for (k=1; k<=cptcovprod;k++) /* Useless */
2252: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2253: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
2254:
2255: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2256: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2257: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
2258: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2259: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.218 brouard 2260: /* ij should be linked to the correct index of cov */
2261: /* age and covariate values ij are in 'cov', but we need to pass
2262: * ij for the observed prevalence at age and status and covariate
2263: * number: prevacurrent[(int)agefin][ii][ij]
2264: */
2265: /* 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 *\/ */
2266: /* 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 *\/ */
2267: 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 2268: savm=oldm;
2269: oldm=newm;
2270: for(j=1; j<=nlstate; j++){
2271: max[j]=0.;
2272: min[j]=1.;
2273: }
2274: for(j=1; j<=nlstate; j++){
2275: for(i=1;i<=nlstate;i++){
1.218 brouard 2276: /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
2277: bprlim[i][j]= newm[i][j];
2278: max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
2279: min[i]=FMIN(min[i],bprlim[i][j]);
1.217 brouard 2280: }
2281: }
1.218 brouard 2282:
1.217 brouard 2283: maxmax=0.;
2284: for(i=1; i<=nlstate; i++){
2285: meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
2286: maxmax=FMAX(maxmax,meandiff[i]);
2287: /* 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); */
2288: } /* j loop */
2289: *ncvyear= -( (int)age- (int)agefin);
1.218 brouard 2290: /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/
1.217 brouard 2291: if(maxmax < ftolpl){
1.220 brouard 2292: /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.217 brouard 2293: free_vector(min,1,nlstate);
2294: free_vector(max,1,nlstate);
2295: free_vector(meandiff,1,nlstate);
2296: return bprlim;
2297: }
2298: } /* age loop */
2299: /* After some age loop it doesn't converge */
2300: 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\
2301: 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);
2302: /* 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); */
2303: free_vector(min,1,nlstate);
2304: free_vector(max,1,nlstate);
2305: free_vector(meandiff,1,nlstate);
2306:
2307: return bprlim; /* should not reach here */
2308: }
2309:
1.126 brouard 2310: /*************** transition probabilities ***************/
2311:
2312: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2313: {
1.138 brouard 2314: /* According to parameters values stored in x and the covariate's values stored in cov,
2315: computes the probability to be observed in state j being in state i by appying the
2316: model to the ncovmodel covariates (including constant and age).
2317: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2318: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2319: ncth covariate in the global vector x is given by the formula:
2320: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2321: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2322: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2323: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2324: Outputs ps[i][j] the probability to be observed in j being in j according to
2325: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2326: */
2327: double s1, lnpijopii;
1.126 brouard 2328: /*double t34;*/
1.164 brouard 2329: int i,j, nc, ii, jj;
1.126 brouard 2330:
1.218 brouard 2331: for(i=1; i<= nlstate; i++){
2332: for(j=1; j<i;j++){
2333: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2334: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2335: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2336: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2337: }
2338: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2339: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2340: }
2341: for(j=i+1; j<=nlstate+ndeath;j++){
2342: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2343: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2344: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2345: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2346: }
2347: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2348: }
2349: }
2350:
2351: for(i=1; i<= nlstate; i++){
2352: s1=0;
2353: for(j=1; j<i; j++){
2354: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2355: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2356: }
2357: for(j=i+1; j<=nlstate+ndeath; j++){
2358: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2359: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2360: }
2361: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2362: ps[i][i]=1./(s1+1.);
2363: /* Computing other pijs */
2364: for(j=1; j<i; j++)
2365: ps[i][j]= exp(ps[i][j])*ps[i][i];
2366: for(j=i+1; j<=nlstate+ndeath; j++)
2367: ps[i][j]= exp(ps[i][j])*ps[i][i];
2368: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2369: } /* end i */
2370:
2371: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2372: for(jj=1; jj<= nlstate+ndeath; jj++){
2373: ps[ii][jj]=0;
2374: ps[ii][ii]=1;
2375: }
2376: }
2377:
2378:
2379: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2380: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2381: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2382: /* } */
2383: /* printf("\n "); */
2384: /* } */
2385: /* printf("\n ");printf("%lf ",cov[2]);*/
2386: /*
2387: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2388: goto end;*/
2389: return ps;
1.126 brouard 2390: }
2391:
1.218 brouard 2392: /*************** backward transition probabilities ***************/
2393:
2394: /* 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 ) */
2395: /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
2396: double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate, double ***prevacurrent, int ij )
2397: {
2398: /* Computes the backward probability at age agefin and covariate ij
2399: * and returns in **ps as well as **bmij.
2400: */
2401: int i, ii, j,k;
2402:
2403: double **out, **pmij();
2404: double sumnew=0.;
2405: double agefin;
2406:
2407: double **dnewm, **dsavm, **doldm;
2408: double **bbmij;
2409:
2410: doldm=ddoldms; /* global pointers */
2411: dnewm=ddnewms;
2412: dsavm=ddsavms;
2413:
2414: agefin=cov[2];
2415: /* bmij *//* age is cov[2], ij is included in cov, but we need for
2416: the observed prevalence (with this covariate ij) */
2417: dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);
2418: /* We do have the matrix Px in savm and we need pij */
2419: for (j=1;j<=nlstate+ndeath;j++){
2420: sumnew=0.; /* w1 p11 + w2 p21 only on live states */
2421: for (ii=1;ii<=nlstate;ii++){
2422: sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];
2423: } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
2424: for (ii=1;ii<=nlstate+ndeath;ii++){
2425: if(sumnew >= 1.e-10){
2426: /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
2427: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2428: /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
2429: /* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
2430: /* }else */
2431: doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
2432: }else{
2433: 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);
2434: }
2435: } /*End ii */
2436: } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
2437: /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */
2438: bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
2439: /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */
2440: /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2441: /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */
2442: /* left Product of this matrix by diag matrix of prevalences (savm) */
2443: for (j=1;j<=nlstate+ndeath;j++){
2444: for (ii=1;ii<=nlstate+ndeath;ii++){
2445: dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
2446: }
2447: } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
2448: ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
2449: /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
2450: /* end bmij */
2451: return ps;
2452: }
1.217 brouard 2453: /*************** transition probabilities ***************/
2454:
1.218 brouard 2455: double **bpmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1.217 brouard 2456: {
2457: /* According to parameters values stored in x and the covariate's values stored in cov,
2458: computes the probability to be observed in state j being in state i by appying the
2459: model to the ncovmodel covariates (including constant and age).
2460: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2461: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2462: ncth covariate in the global vector x is given by the formula:
2463: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2464: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2465: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2466: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2467: Outputs ps[i][j] the probability to be observed in j being in j according to
2468: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2469: */
2470: double s1, lnpijopii;
2471: /*double t34;*/
2472: int i,j, nc, ii, jj;
2473:
1.218 brouard 2474: for(i=1; i<= nlstate; i++){
2475: for(j=1; j<i;j++){
2476: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2477: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2478: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2479: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2480: }
2481: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2482: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
2483: }
2484: for(j=i+1; j<=nlstate+ndeath;j++){
2485: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2486: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2487: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2488: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
2489: }
2490: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2491: }
2492: }
2493:
2494: for(i=1; i<= nlstate; i++){
2495: s1=0;
2496: for(j=1; j<i; j++){
2497: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2498: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2499: }
2500: for(j=i+1; j<=nlstate+ndeath; j++){
2501: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
2502: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2503: }
2504: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
2505: ps[i][i]=1./(s1+1.);
2506: /* Computing other pijs */
2507: for(j=1; j<i; j++)
2508: ps[i][j]= exp(ps[i][j])*ps[i][i];
2509: for(j=i+1; j<=nlstate+ndeath; j++)
2510: ps[i][j]= exp(ps[i][j])*ps[i][i];
2511: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2512: } /* end i */
2513:
2514: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2515: for(jj=1; jj<= nlstate+ndeath; jj++){
2516: ps[ii][jj]=0;
2517: ps[ii][ii]=1;
2518: }
2519: }
2520: /* Added for backcast */ /* Transposed matrix too */
2521: for(jj=1; jj<= nlstate+ndeath; jj++){
2522: s1=0.;
2523: for(ii=1; ii<= nlstate+ndeath; ii++){
2524: s1+=ps[ii][jj];
2525: }
2526: for(ii=1; ii<= nlstate; ii++){
2527: ps[ii][jj]=ps[ii][jj]/s1;
2528: }
2529: }
2530: /* Transposition */
2531: for(jj=1; jj<= nlstate+ndeath; jj++){
2532: for(ii=jj; ii<= nlstate+ndeath; ii++){
2533: s1=ps[ii][jj];
2534: ps[ii][jj]=ps[jj][ii];
2535: ps[jj][ii]=s1;
2536: }
2537: }
2538: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2539: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2540: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2541: /* } */
2542: /* printf("\n "); */
2543: /* } */
2544: /* printf("\n ");printf("%lf ",cov[2]);*/
2545: /*
2546: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2547: goto end;*/
2548: return ps;
1.217 brouard 2549: }
2550:
2551:
1.126 brouard 2552: /**************** Product of 2 matrices ******************/
2553:
1.145 brouard 2554: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2555: {
2556: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2557: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2558: /* in, b, out are matrice of pointers which should have been initialized
2559: before: only the contents of out is modified. The function returns
2560: a pointer to pointers identical to out */
1.145 brouard 2561: int i, j, k;
1.126 brouard 2562: for(i=nrl; i<= nrh; i++)
1.145 brouard 2563: for(k=ncolol; k<=ncoloh; k++){
2564: out[i][k]=0.;
2565: for(j=ncl; j<=nch; j++)
2566: out[i][k] +=in[i][j]*b[j][k];
2567: }
1.126 brouard 2568: return out;
2569: }
2570:
2571:
2572: /************* Higher Matrix Product ***************/
2573:
2574: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2575: {
1.218 brouard 2576: /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
1.126 brouard 2577: 'nhstepm*hstepm*stepm' months (i.e. until
2578: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2579: nhstepm*hstepm matrices.
2580: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2581: (typically every 2 years instead of every month which is too big
2582: for the memory).
2583: Model is determined by parameters x and covariates have to be
2584: included manually here.
2585:
2586: */
2587:
2588: int i, j, d, h, k;
1.131 brouard 2589: double **out, cov[NCOVMAX+1];
1.126 brouard 2590: double **newm;
1.187 brouard 2591: double agexact;
1.214 brouard 2592: double agebegin, ageend;
1.126 brouard 2593:
2594: /* Hstepm could be zero and should return the unit matrix */
2595: for (i=1;i<=nlstate+ndeath;i++)
2596: for (j=1;j<=nlstate+ndeath;j++){
2597: oldm[i][j]=(i==j ? 1.0 : 0.0);
2598: po[i][j][0]=(i==j ? 1.0 : 0.0);
2599: }
2600: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2601: for(h=1; h <=nhstepm; h++){
2602: for(d=1; d <=hstepm; d++){
2603: newm=savm;
2604: /* Covariates have to be included here again */
2605: cov[1]=1.;
1.214 brouard 2606: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2607: cov[2]=agexact;
2608: if(nagesqr==1)
1.218 brouard 2609: cov[3]= agexact*agexact;
1.131 brouard 2610: for (k=1; k<=cptcovn;k++)
1.218 brouard 2611: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2612: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2613: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2614: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2615: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2616: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2617: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2618: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2619: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.126 brouard 2620:
2621:
2622: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2623: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2624: /* right multiplication of oldm by the current matrix */
1.126 brouard 2625: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2626: pmij(pmmij,cov,ncovmodel,x,nlstate));
1.217 brouard 2627: /* if((int)age == 70){ */
2628: /* printf(" Forward hpxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2629: /* for(i=1; i<=nlstate+ndeath; i++) { */
2630: /* printf("%d pmmij ",i); */
2631: /* for(j=1;j<=nlstate+ndeath;j++) { */
2632: /* printf("%f ",pmmij[i][j]); */
2633: /* } */
2634: /* printf(" oldm "); */
2635: /* for(j=1;j<=nlstate+ndeath;j++) { */
2636: /* printf("%f ",oldm[i][j]); */
2637: /* } */
2638: /* printf("\n"); */
2639: /* } */
2640: /* } */
1.126 brouard 2641: savm=oldm;
2642: oldm=newm;
2643: }
2644: for(i=1; i<=nlstate+ndeath; i++)
2645: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2646: po[i][j][h]=newm[i][j];
2647: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2648: }
1.128 brouard 2649: /*printf("h=%d ",h);*/
1.126 brouard 2650: } /* end h */
1.218 brouard 2651: /* printf("\n H=%d \n",h); */
1.126 brouard 2652: return po;
2653: }
2654:
1.217 brouard 2655: /************* Higher Back Matrix Product ***************/
1.218 brouard 2656: /* 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 ) */
2657: double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )
1.217 brouard 2658: {
1.218 brouard 2659: /* Computes the transition matrix starting at age 'age' over
1.217 brouard 2660: 'nhstepm*hstepm*stepm' months (i.e. until
1.218 brouard 2661: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2662: nhstepm*hstepm matrices.
2663: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2664: (typically every 2 years instead of every month which is too big
1.217 brouard 2665: for the memory).
1.218 brouard 2666: Model is determined by parameters x and covariates have to be
2667: included manually here.
1.217 brouard 2668:
2669: */
2670:
2671: int i, j, d, h, k;
2672: double **out, cov[NCOVMAX+1];
2673: double **newm;
2674: double agexact;
2675: double agebegin, ageend;
1.218 brouard 2676: double **oldm, **savm;
1.217 brouard 2677:
1.218 brouard 2678: oldm=oldms;savm=savms;
1.217 brouard 2679: /* Hstepm could be zero and should return the unit matrix */
2680: for (i=1;i<=nlstate+ndeath;i++)
2681: for (j=1;j<=nlstate+ndeath;j++){
2682: oldm[i][j]=(i==j ? 1.0 : 0.0);
2683: po[i][j][0]=(i==j ? 1.0 : 0.0);
2684: }
2685: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2686: for(h=1; h <=nhstepm; h++){
2687: for(d=1; d <=hstepm; d++){
2688: newm=savm;
2689: /* Covariates have to be included here again */
2690: cov[1]=1.;
2691: agexact=age-((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
2692: /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
2693: cov[2]=agexact;
2694: if(nagesqr==1)
1.218 brouard 2695: cov[3]= agexact*agexact;
2696: for (k=1; k<=cptcovn;k++)
2697: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2698: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.217 brouard 2699: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
1.218 brouard 2700: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2701: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2702: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.217 brouard 2703: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.218 brouard 2704: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2705: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2706:
2707:
1.217 brouard 2708: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2709: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1.218 brouard 2710: /* Careful transposed matrix */
2711: /* age is in cov[2] */
2712: /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
2713: /* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
2714: out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
2715: 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1.217 brouard 2716: /* if((int)age == 70){ */
2717: /* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
2718: /* for(i=1; i<=nlstate+ndeath; i++) { */
2719: /* printf("%d pmmij ",i); */
2720: /* for(j=1;j<=nlstate+ndeath;j++) { */
2721: /* printf("%f ",pmmij[i][j]); */
2722: /* } */
2723: /* printf(" oldm "); */
2724: /* for(j=1;j<=nlstate+ndeath;j++) { */
2725: /* printf("%f ",oldm[i][j]); */
2726: /* } */
2727: /* printf("\n"); */
2728: /* } */
2729: /* } */
2730: savm=oldm;
2731: oldm=newm;
2732: }
2733: for(i=1; i<=nlstate+ndeath; i++)
2734: for(j=1;j<=nlstate+ndeath;j++) {
1.218 brouard 2735: po[i][j][h]=newm[i][j];
2736: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.217 brouard 2737: }
2738: /*printf("h=%d ",h);*/
2739: } /* end h */
1.218 brouard 2740: /* printf("\n H=%d \n",h); */
1.217 brouard 2741: return po;
2742: }
2743:
2744:
1.162 brouard 2745: #ifdef NLOPT
2746: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2747: double fret;
2748: double *xt;
2749: int j;
2750: myfunc_data *d2 = (myfunc_data *) pd;
2751: /* xt = (p1-1); */
2752: xt=vector(1,n);
2753: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2754:
2755: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2756: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2757: printf("Function = %.12lf ",fret);
2758: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2759: printf("\n");
2760: free_vector(xt,1,n);
2761: return fret;
2762: }
2763: #endif
1.126 brouard 2764:
2765: /*************** log-likelihood *************/
2766: double func( double *x)
2767: {
2768: int i, ii, j, k, mi, d, kk;
1.131 brouard 2769: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2770: double **out;
2771: double sw; /* Sum of weights */
2772: double lli; /* Individual log likelihood */
2773: int s1, s2;
2774: double bbh, survp;
2775: long ipmx;
1.187 brouard 2776: double agexact;
1.126 brouard 2777: /*extern weight */
2778: /* We are differentiating ll according to initial status */
2779: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2780: /*for(i=1;i<imx;i++)
2781: printf(" %d\n",s[4][i]);
2782: */
1.162 brouard 2783:
2784: ++countcallfunc;
2785:
1.126 brouard 2786: cov[1]=1.;
2787:
2788: for(k=1; k<=nlstate; k++) ll[k]=0.;
2789:
2790: if(mle==1){
2791: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2792: /* Computes the values of the ncovmodel covariates of the model
2793: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2794: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2795: to be observed in j being in i according to the model.
2796: */
1.145 brouard 2797: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2798: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2799: }
1.137 brouard 2800: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2801: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2802: has been calculated etc */
1.126 brouard 2803: for(mi=1; mi<= wav[i]-1; mi++){
2804: for (ii=1;ii<=nlstate+ndeath;ii++)
2805: for (j=1;j<=nlstate+ndeath;j++){
2806: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2807: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2808: }
2809: for(d=0; d<dh[mi][i]; d++){
2810: newm=savm;
1.187 brouard 2811: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2812: cov[2]=agexact;
2813: if(nagesqr==1)
2814: cov[3]= agexact*agexact;
1.126 brouard 2815: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2816: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2817: }
2818: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2819: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2820: savm=oldm;
2821: oldm=newm;
2822: } /* end mult */
2823:
2824: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2825: /* But now since version 0.9 we anticipate for bias at large stepm.
2826: * If stepm is larger than one month (smallest stepm) and if the exact delay
2827: * (in months) between two waves is not a multiple of stepm, we rounded to
2828: * the nearest (and in case of equal distance, to the lowest) interval but now
2829: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2830: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2831: * probability in order to take into account the bias as a fraction of the way
2832: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2833: * -stepm/2 to stepm/2 .
2834: * For stepm=1 the results are the same as for previous versions of Imach.
2835: * For stepm > 1 the results are less biased than in previous versions.
2836: */
2837: s1=s[mw[mi][i]][i];
2838: s2=s[mw[mi+1][i]][i];
2839: bbh=(double)bh[mi][i]/(double)stepm;
2840: /* bias bh is positive if real duration
2841: * is higher than the multiple of stepm and negative otherwise.
2842: */
2843: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2844: if( s2 > nlstate){
2845: /* i.e. if s2 is a death state and if the date of death is known
2846: then the contribution to the likelihood is the probability to
2847: die between last step unit time and current step unit time,
2848: which is also equal to probability to die before dh
2849: minus probability to die before dh-stepm .
2850: In version up to 0.92 likelihood was computed
2851: as if date of death was unknown. Death was treated as any other
2852: health state: the date of the interview describes the actual state
2853: and not the date of a change in health state. The former idea was
2854: to consider that at each interview the state was recorded
2855: (healthy, disable or death) and IMaCh was corrected; but when we
2856: introduced the exact date of death then we should have modified
2857: the contribution of an exact death to the likelihood. This new
2858: contribution is smaller and very dependent of the step unit
2859: stepm. It is no more the probability to die between last interview
2860: and month of death but the probability to survive from last
2861: interview up to one month before death multiplied by the
2862: probability to die within a month. Thanks to Chris
2863: Jackson for correcting this bug. Former versions increased
2864: mortality artificially. The bad side is that we add another loop
2865: which slows down the processing. The difference can be up to 10%
2866: lower mortality.
2867: */
1.183 brouard 2868: /* If, at the beginning of the maximization mostly, the
2869: cumulative probability or probability to be dead is
2870: constant (ie = 1) over time d, the difference is equal to
2871: 0. out[s1][3] = savm[s1][3]: probability, being at state
2872: s1 at precedent wave, to be dead a month before current
2873: wave is equal to probability, being at state s1 at
2874: precedent wave, to be dead at mont of the current
2875: wave. Then the observed probability (that this person died)
2876: is null according to current estimated parameter. In fact,
2877: it should be very low but not zero otherwise the log go to
2878: infinity.
2879: */
2880: /* #ifdef INFINITYORIGINAL */
2881: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2882: /* #else */
2883: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2884: /* lli=log(mytinydouble); */
2885: /* else */
2886: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2887: /* #endif */
1.216 brouard 2888: lli=log(out[s1][s2] - savm[s1][s2]);
2889:
2890: } else if ( s2==-1 ) { /* alive */
1.126 brouard 2891: for (j=1,survp=0. ; j<=nlstate; j++)
2892: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2893: /*survp += out[s1][j]; */
2894: lli= log(survp);
2895: }
2896: else if (s2==-4) {
2897: for (j=3,survp=0. ; j<=nlstate; j++)
2898: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2899: lli= log(survp);
2900: }
2901: else if (s2==-5) {
2902: for (j=1,survp=0. ; j<=2; j++)
2903: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2904: lli= log(survp);
2905: }
2906: else{
2907: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2908: /* 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 */
2909: }
2910: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2911: /*if(lli ==000.0)*/
2912: /*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); */
2913: ipmx +=1;
2914: sw += weight[i];
2915: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2916: /* if (lli < log(mytinydouble)){ */
2917: /* 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); */
2918: /* 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]); */
2919: /* } */
1.126 brouard 2920: } /* end of wave */
2921: } /* end of individual */
2922: } else if(mle==2){
2923: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2924: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2925: for(mi=1; mi<= wav[i]-1; mi++){
2926: for (ii=1;ii<=nlstate+ndeath;ii++)
2927: for (j=1;j<=nlstate+ndeath;j++){
2928: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2929: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2930: }
2931: for(d=0; d<=dh[mi][i]; d++){
2932: newm=savm;
1.187 brouard 2933: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2934: cov[2]=agexact;
2935: if(nagesqr==1)
2936: cov[3]= agexact*agexact;
1.126 brouard 2937: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2938: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2939: }
2940: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2941: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2942: savm=oldm;
2943: oldm=newm;
2944: } /* end mult */
2945:
2946: s1=s[mw[mi][i]][i];
2947: s2=s[mw[mi+1][i]][i];
2948: bbh=(double)bh[mi][i]/(double)stepm;
2949: 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 */
2950: ipmx +=1;
2951: sw += weight[i];
2952: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2953: } /* end of wave */
2954: } /* end of individual */
2955: } else if(mle==3){ /* exponential inter-extrapolation */
2956: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2957: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2958: for(mi=1; mi<= wav[i]-1; mi++){
2959: for (ii=1;ii<=nlstate+ndeath;ii++)
2960: for (j=1;j<=nlstate+ndeath;j++){
2961: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2962: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2963: }
2964: for(d=0; d<dh[mi][i]; d++){
2965: newm=savm;
1.187 brouard 2966: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2967: cov[2]=agexact;
2968: if(nagesqr==1)
2969: cov[3]= agexact*agexact;
1.126 brouard 2970: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2971: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2972: }
2973: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2974: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2975: savm=oldm;
2976: oldm=newm;
2977: } /* end mult */
2978:
2979: s1=s[mw[mi][i]][i];
2980: s2=s[mw[mi+1][i]][i];
2981: bbh=(double)bh[mi][i]/(double)stepm;
2982: 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 */
2983: ipmx +=1;
2984: sw += weight[i];
2985: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2986: } /* end of wave */
2987: } /* end of individual */
2988: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2989: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2990: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2991: for(mi=1; mi<= wav[i]-1; mi++){
2992: for (ii=1;ii<=nlstate+ndeath;ii++)
2993: for (j=1;j<=nlstate+ndeath;j++){
2994: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2995: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2996: }
2997: for(d=0; d<dh[mi][i]; d++){
2998: newm=savm;
1.187 brouard 2999: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3000: cov[2]=agexact;
3001: if(nagesqr==1)
3002: cov[3]= agexact*agexact;
1.126 brouard 3003: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3004: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3005: }
3006:
3007: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3008: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3009: savm=oldm;
3010: oldm=newm;
3011: } /* end mult */
3012:
3013: s1=s[mw[mi][i]][i];
3014: s2=s[mw[mi+1][i]][i];
3015: if( s2 > nlstate){
3016: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3017: } else if ( s2==-1 ) { /* alive */
3018: for (j=1,survp=0. ; j<=nlstate; j++)
3019: survp += out[s1][j];
3020: lli= log(survp);
1.126 brouard 3021: }else{
3022: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3023: }
3024: ipmx +=1;
3025: sw += weight[i];
3026: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3027: /* 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]); */
3028: } /* end of wave */
3029: } /* end of individual */
3030: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
3031: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3032: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3033: for(mi=1; mi<= wav[i]-1; mi++){
3034: for (ii=1;ii<=nlstate+ndeath;ii++)
3035: for (j=1;j<=nlstate+ndeath;j++){
3036: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3037: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3038: }
3039: for(d=0; d<dh[mi][i]; d++){
3040: newm=savm;
1.187 brouard 3041: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3042: cov[2]=agexact;
3043: if(nagesqr==1)
3044: cov[3]= agexact*agexact;
1.126 brouard 3045: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3046: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3047: }
3048:
3049: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3050: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
3051: savm=oldm;
3052: oldm=newm;
3053: } /* end mult */
3054:
3055: s1=s[mw[mi][i]][i];
3056: s2=s[mw[mi+1][i]][i];
3057: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
3058: ipmx +=1;
3059: sw += weight[i];
3060: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
3061: /*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]);*/
3062: } /* end of wave */
3063: } /* end of individual */
3064: } /* End of if */
3065: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3066: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3067: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3068: return -l;
3069: }
3070:
3071: /*************** log-likelihood *************/
3072: double funcone( double *x)
3073: {
3074: /* Same as likeli but slower because of a lot of printf and if */
3075: int i, ii, j, k, mi, d, kk;
1.131 brouard 3076: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 3077: double **out;
3078: double lli; /* Individual log likelihood */
3079: double llt;
3080: int s1, s2;
3081: double bbh, survp;
1.187 brouard 3082: double agexact;
1.214 brouard 3083: double agebegin, ageend;
1.126 brouard 3084: /*extern weight */
3085: /* We are differentiating ll according to initial status */
3086: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
3087: /*for(i=1;i<imx;i++)
3088: printf(" %d\n",s[4][i]);
3089: */
3090: cov[1]=1.;
3091:
3092: for(k=1; k<=nlstate; k++) ll[k]=0.;
3093:
3094: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 3095: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 3096: for(mi=1; mi<= wav[i]-1; mi++){
3097: for (ii=1;ii<=nlstate+ndeath;ii++)
3098: for (j=1;j<=nlstate+ndeath;j++){
3099: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
3100: savm[ii][j]=(ii==j ? 1.0 : 0.0);
3101: }
1.214 brouard 3102:
3103: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
3104: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
3105: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
3106: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3107: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 3108: newm=savm;
1.187 brouard 3109: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
3110: cov[2]=agexact;
3111: if(nagesqr==1)
3112: cov[3]= agexact*agexact;
1.126 brouard 3113: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 3114: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 3115: }
1.187 brouard 3116:
1.145 brouard 3117: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 3118: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
3119: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 3120: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
3121: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 3122: savm=oldm;
3123: oldm=newm;
3124: } /* end mult */
3125:
3126: s1=s[mw[mi][i]][i];
3127: s2=s[mw[mi+1][i]][i];
1.217 brouard 3128: /* if(s2==-1){ */
3129: /* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */
3130: /* /\* exit(1); *\/ */
3131: /* } */
1.126 brouard 3132: bbh=(double)bh[mi][i]/(double)stepm;
3133: /* bias is positive if real duration
3134: * is higher than the multiple of stepm and negative otherwise.
3135: */
3136: if( s2 > nlstate && (mle <5) ){ /* Jackson */
3137: lli=log(out[s1][s2] - savm[s1][s2]);
1.216 brouard 3138: } else if ( s2==-1 ) { /* alive */
1.126 brouard 3139: for (j=1,survp=0. ; j<=nlstate; j++)
3140: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
3141: lli= log(survp);
3142: }else if (mle==1){
3143: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3144: } else if(mle==2){
3145: 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 */
3146: } else if(mle==3){ /* exponential inter-extrapolation */
3147: 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 */
3148: } else if (mle==4){ /* mle=4 no inter-extrapolation */
3149: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 3150: } else{ /* mle=0 back to 1 */
3151: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
3152: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 3153: } /* End of if */
3154: ipmx +=1;
3155: sw += weight[i];
3156: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 3157: /*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 3158: if(globpr){
1.214 brouard 3159: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 3160: %11.6f %11.6f %11.6f ", \
1.214 brouard 3161: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 3162: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
3163: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
3164: llt +=ll[k]*gipmx/gsw;
3165: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
3166: }
3167: fprintf(ficresilk," %10.6f\n", -llt);
3168: }
3169: } /* end of wave */
3170: } /* end of individual */
3171: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
3172: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
3173: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
3174: if(globpr==0){ /* First time we count the contributions and weights */
3175: gipmx=ipmx;
3176: gsw=sw;
3177: }
3178: return -l;
3179: }
3180:
3181:
3182: /*************** function likelione ***********/
3183: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
3184: {
3185: /* This routine should help understanding what is done with
3186: the selection of individuals/waves and
3187: to check the exact contribution to the likelihood.
3188: Plotting could be done.
3189: */
3190: int k;
3191:
3192: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 3193: strcpy(fileresilk,"ILK_");
1.202 brouard 3194: strcat(fileresilk,fileresu);
1.126 brouard 3195: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
3196: printf("Problem with resultfile: %s\n", fileresilk);
3197: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
3198: }
1.214 brouard 3199: 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");
3200: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 3201: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
3202: for(k=1; k<=nlstate; k++)
3203: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
3204: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
3205: }
3206:
3207: *fretone=(*funcone)(p);
3208: if(*globpri !=0){
3209: fclose(ficresilk);
1.205 brouard 3210: if (mle ==0)
3211: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
3212: else if(mle >=1)
3213: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
3214: 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 3215:
1.208 brouard 3216:
3217: for (k=1; k<= nlstate ; k++) {
1.211 brouard 3218: 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 3219: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
3220: }
1.207 brouard 3221: 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 3222: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3223: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 3224: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 3225: fflush(fichtm);
1.205 brouard 3226: }
1.126 brouard 3227: return;
3228: }
3229:
3230:
3231: /*********** Maximum Likelihood Estimation ***************/
3232:
3233: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
3234: {
1.165 brouard 3235: int i,j, iter=0;
1.126 brouard 3236: double **xi;
3237: double fret;
3238: double fretone; /* Only one call to likelihood */
3239: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 3240:
3241: #ifdef NLOPT
3242: int creturn;
3243: nlopt_opt opt;
3244: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
3245: double *lb;
3246: double minf; /* the minimum objective value, upon return */
3247: double * p1; /* Shifted parameters from 0 instead of 1 */
3248: myfunc_data dinst, *d = &dinst;
3249: #endif
3250:
3251:
1.126 brouard 3252: xi=matrix(1,npar,1,npar);
3253: for (i=1;i<=npar;i++)
3254: for (j=1;j<=npar;j++)
3255: xi[i][j]=(i==j ? 1.0 : 0.0);
3256: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 3257: strcpy(filerespow,"POW_");
1.126 brouard 3258: strcat(filerespow,fileres);
3259: if((ficrespow=fopen(filerespow,"w"))==NULL) {
3260: printf("Problem with resultfile: %s\n", filerespow);
3261: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
3262: }
3263: fprintf(ficrespow,"# Powell\n# iter -2*LL");
3264: for (i=1;i<=nlstate;i++)
3265: for(j=1;j<=nlstate+ndeath;j++)
3266: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
3267: fprintf(ficrespow,"\n");
1.162 brouard 3268: #ifdef POWELL
1.126 brouard 3269: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 3270: #endif
1.126 brouard 3271:
1.162 brouard 3272: #ifdef NLOPT
3273: #ifdef NEWUOA
3274: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
3275: #else
3276: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
3277: #endif
3278: lb=vector(0,npar-1);
3279: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
3280: nlopt_set_lower_bounds(opt, lb);
3281: nlopt_set_initial_step1(opt, 0.1);
3282:
3283: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
3284: d->function = func;
3285: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
3286: nlopt_set_min_objective(opt, myfunc, d);
3287: nlopt_set_xtol_rel(opt, ftol);
3288: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
3289: printf("nlopt failed! %d\n",creturn);
3290: }
3291: else {
3292: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
3293: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
3294: iter=1; /* not equal */
3295: }
3296: nlopt_destroy(opt);
3297: #endif
1.126 brouard 3298: free_matrix(xi,1,npar,1,npar);
3299: fclose(ficrespow);
1.203 brouard 3300: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
3301: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 3302: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 3303:
3304: }
3305:
3306: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 3307: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 3308: {
3309: double **a,**y,*x,pd;
1.203 brouard 3310: /* double **hess; */
1.164 brouard 3311: int i, j;
1.126 brouard 3312: int *indx;
3313:
3314: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 3315: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 3316: void lubksb(double **a, int npar, int *indx, double b[]) ;
3317: void ludcmp(double **a, int npar, int *indx, double *d) ;
3318: double gompertz(double p[]);
1.203 brouard 3319: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 3320:
3321: printf("\nCalculation of the hessian matrix. Wait...\n");
3322: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
3323: for (i=1;i<=npar;i++){
1.203 brouard 3324: printf("%d-",i);fflush(stdout);
3325: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 3326:
3327: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
3328:
3329: /* printf(" %f ",p[i]);
3330: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
3331: }
3332:
3333: for (i=1;i<=npar;i++) {
3334: for (j=1;j<=npar;j++) {
3335: if (j>i) {
1.203 brouard 3336: printf(".%d-%d",i,j);fflush(stdout);
3337: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
3338: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 3339:
3340: hess[j][i]=hess[i][j];
3341: /*printf(" %lf ",hess[i][j]);*/
3342: }
3343: }
3344: }
3345: printf("\n");
3346: fprintf(ficlog,"\n");
3347:
3348: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
3349: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
3350:
3351: a=matrix(1,npar,1,npar);
3352: y=matrix(1,npar,1,npar);
3353: x=vector(1,npar);
3354: indx=ivector(1,npar);
3355: for (i=1;i<=npar;i++)
3356: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
3357: ludcmp(a,npar,indx,&pd);
3358:
3359: for (j=1;j<=npar;j++) {
3360: for (i=1;i<=npar;i++) x[i]=0;
3361: x[j]=1;
3362: lubksb(a,npar,indx,x);
3363: for (i=1;i<=npar;i++){
3364: matcov[i][j]=x[i];
3365: }
3366: }
3367:
3368: printf("\n#Hessian matrix#\n");
3369: fprintf(ficlog,"\n#Hessian matrix#\n");
3370: for (i=1;i<=npar;i++) {
3371: for (j=1;j<=npar;j++) {
1.203 brouard 3372: printf("%.6e ",hess[i][j]);
3373: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 3374: }
3375: printf("\n");
3376: fprintf(ficlog,"\n");
3377: }
3378:
1.203 brouard 3379: /* printf("\n#Covariance matrix#\n"); */
3380: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
3381: /* for (i=1;i<=npar;i++) { */
3382: /* for (j=1;j<=npar;j++) { */
3383: /* printf("%.6e ",matcov[i][j]); */
3384: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
3385: /* } */
3386: /* printf("\n"); */
3387: /* fprintf(ficlog,"\n"); */
3388: /* } */
3389:
1.126 brouard 3390: /* Recompute Inverse */
1.203 brouard 3391: /* for (i=1;i<=npar;i++) */
3392: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
3393: /* ludcmp(a,npar,indx,&pd); */
3394:
3395: /* printf("\n#Hessian matrix recomputed#\n"); */
3396:
3397: /* for (j=1;j<=npar;j++) { */
3398: /* for (i=1;i<=npar;i++) x[i]=0; */
3399: /* x[j]=1; */
3400: /* lubksb(a,npar,indx,x); */
3401: /* for (i=1;i<=npar;i++){ */
3402: /* y[i][j]=x[i]; */
3403: /* printf("%.3e ",y[i][j]); */
3404: /* fprintf(ficlog,"%.3e ",y[i][j]); */
3405: /* } */
3406: /* printf("\n"); */
3407: /* fprintf(ficlog,"\n"); */
3408: /* } */
3409:
3410: /* Verifying the inverse matrix */
3411: #ifdef DEBUGHESS
3412: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 3413:
1.203 brouard 3414: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
3415: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 3416:
3417: for (j=1;j<=npar;j++) {
3418: for (i=1;i<=npar;i++){
1.203 brouard 3419: printf("%.2f ",y[i][j]);
3420: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 3421: }
3422: printf("\n");
3423: fprintf(ficlog,"\n");
3424: }
1.203 brouard 3425: #endif
1.126 brouard 3426:
3427: free_matrix(a,1,npar,1,npar);
3428: free_matrix(y,1,npar,1,npar);
3429: free_vector(x,1,npar);
3430: free_ivector(indx,1,npar);
1.203 brouard 3431: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 3432:
3433:
3434: }
3435:
3436: /*************** hessian matrix ****************/
3437: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 3438: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 3439: int i;
3440: int l=1, lmax=20;
1.203 brouard 3441: double k1,k2, res, fx;
1.132 brouard 3442: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 3443: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
3444: int k=0,kmax=10;
3445: double l1;
3446:
3447: fx=func(x);
3448: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3449: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3450: l1=pow(10,l);
3451: delts=delt;
3452: for(k=1 ; k <kmax; k=k+1){
3453: delt = delta*(l1*k);
3454: p2[theta]=x[theta] +delt;
1.145 brouard 3455: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3456: p2[theta]=x[theta]-delt;
3457: k2=func(p2)-fx;
3458: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3459: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3460:
1.203 brouard 3461: #ifdef DEBUGHESSII
1.126 brouard 3462: 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);
3463: 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);
3464: #endif
3465: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3466: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3467: k=kmax;
3468: }
3469: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3470: k=kmax; l=lmax*10;
1.126 brouard 3471: }
3472: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3473: delts=delt;
3474: }
1.203 brouard 3475: } /* End loop k */
1.126 brouard 3476: }
3477: delti[theta]=delts;
3478: return res;
3479:
3480: }
3481:
1.203 brouard 3482: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3483: {
3484: int i;
1.164 brouard 3485: int l=1, lmax=20;
1.126 brouard 3486: double k1,k2,k3,k4,res,fx;
1.132 brouard 3487: double p2[MAXPARM+1];
1.203 brouard 3488: int k, kmax=1;
3489: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3490:
3491: int firstime=0;
1.203 brouard 3492:
1.126 brouard 3493: fx=func(x);
1.203 brouard 3494: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3495: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3496: p2[thetai]=x[thetai]+delti[thetai]*k;
3497: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3498: k1=func(p2)-fx;
3499:
1.203 brouard 3500: p2[thetai]=x[thetai]+delti[thetai]*k;
3501: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3502: k2=func(p2)-fx;
3503:
1.203 brouard 3504: p2[thetai]=x[thetai]-delti[thetai]*k;
3505: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3506: k3=func(p2)-fx;
3507:
1.203 brouard 3508: p2[thetai]=x[thetai]-delti[thetai]*k;
3509: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3510: k4=func(p2)-fx;
1.203 brouard 3511: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3512: if(k1*k2*k3*k4 <0.){
1.208 brouard 3513: firstime=1;
1.203 brouard 3514: kmax=kmax+10;
1.208 brouard 3515: }
3516: if(kmax >=10 || firstime ==1){
1.218 brouard 3517: 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);
3518: 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 3519: 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);
3520: 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);
3521: }
3522: #ifdef DEBUGHESSIJ
3523: v1=hess[thetai][thetai];
3524: v2=hess[thetaj][thetaj];
3525: cv12=res;
3526: /* Computing eigen value of Hessian matrix */
3527: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3528: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3529: if ((lc2 <0) || (lc1 <0) ){
3530: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3531: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3532: 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);
3533: 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);
3534: }
1.126 brouard 3535: #endif
3536: }
3537: return res;
3538: }
3539:
1.203 brouard 3540: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3541: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3542: /* { */
3543: /* int i; */
3544: /* int l=1, lmax=20; */
3545: /* double k1,k2,k3,k4,res,fx; */
3546: /* double p2[MAXPARM+1]; */
3547: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3548: /* int k=0,kmax=10; */
3549: /* double l1; */
3550:
3551: /* fx=func(x); */
3552: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3553: /* l1=pow(10,l); */
3554: /* delts=delt; */
3555: /* for(k=1 ; k <kmax; k=k+1){ */
3556: /* delt = delti*(l1*k); */
3557: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3558: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3559: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3560: /* k1=func(p2)-fx; */
3561:
3562: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3563: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3564: /* k2=func(p2)-fx; */
3565:
3566: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3567: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3568: /* k3=func(p2)-fx; */
3569:
3570: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3571: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3572: /* k4=func(p2)-fx; */
3573: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3574: /* #ifdef DEBUGHESSIJ */
3575: /* 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); */
3576: /* 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); */
3577: /* #endif */
3578: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3579: /* k=kmax; */
3580: /* } */
3581: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3582: /* k=kmax; l=lmax*10; */
3583: /* } */
3584: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3585: /* delts=delt; */
3586: /* } */
3587: /* } /\* End loop k *\/ */
3588: /* } */
3589: /* delti[theta]=delts; */
3590: /* return res; */
3591: /* } */
3592:
3593:
1.126 brouard 3594: /************** Inverse of matrix **************/
3595: void ludcmp(double **a, int n, int *indx, double *d)
3596: {
3597: int i,imax,j,k;
3598: double big,dum,sum,temp;
3599: double *vv;
3600:
3601: vv=vector(1,n);
3602: *d=1.0;
3603: for (i=1;i<=n;i++) {
3604: big=0.0;
3605: for (j=1;j<=n;j++)
3606: if ((temp=fabs(a[i][j])) > big) big=temp;
3607: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3608: vv[i]=1.0/big;
3609: }
3610: for (j=1;j<=n;j++) {
3611: for (i=1;i<j;i++) {
3612: sum=a[i][j];
3613: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3614: a[i][j]=sum;
3615: }
3616: big=0.0;
3617: for (i=j;i<=n;i++) {
3618: sum=a[i][j];
3619: for (k=1;k<j;k++)
3620: sum -= a[i][k]*a[k][j];
3621: a[i][j]=sum;
3622: if ( (dum=vv[i]*fabs(sum)) >= big) {
3623: big=dum;
3624: imax=i;
3625: }
3626: }
3627: if (j != imax) {
3628: for (k=1;k<=n;k++) {
3629: dum=a[imax][k];
3630: a[imax][k]=a[j][k];
3631: a[j][k]=dum;
3632: }
3633: *d = -(*d);
3634: vv[imax]=vv[j];
3635: }
3636: indx[j]=imax;
3637: if (a[j][j] == 0.0) a[j][j]=TINY;
3638: if (j != n) {
3639: dum=1.0/(a[j][j]);
3640: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3641: }
3642: }
3643: free_vector(vv,1,n); /* Doesn't work */
3644: ;
3645: }
3646:
3647: void lubksb(double **a, int n, int *indx, double b[])
3648: {
3649: int i,ii=0,ip,j;
3650: double sum;
3651:
3652: for (i=1;i<=n;i++) {
3653: ip=indx[i];
3654: sum=b[ip];
3655: b[ip]=b[i];
3656: if (ii)
3657: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3658: else if (sum) ii=i;
3659: b[i]=sum;
3660: }
3661: for (i=n;i>=1;i--) {
3662: sum=b[i];
3663: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3664: b[i]=sum/a[i][i];
3665: }
3666: }
3667:
3668: void pstamp(FILE *fichier)
3669: {
1.196 brouard 3670: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3671: }
3672:
3673: /************ Frequencies ********************/
1.220 brouard 3674: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3675: int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
3676: int firstpass, int lastpass, int stepm, int weightopt, char model[])
3677: { /* Some frequencies */
3678:
3679: int i, m, jk, j1, bool, z1,j;
3680: int iind=0, iage=0;
3681: int mi; /* Effective wave */
3682: int first;
3683: double ***freq; /* Frequencies */
3684: double *pp, **prop, *posprop, *pospropt;
3685: double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
3686: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3687: double agebegin, ageend;
3688:
3689: pp=vector(1,nlstate);
3690: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3691: posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
3692: pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
3693: /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
3694: strcpy(fileresp,"P_");
3695: strcat(fileresp,fileresu);
3696: /*strcat(fileresphtm,fileresu);*/
3697: if((ficresp=fopen(fileresp,"w"))==NULL) {
3698: printf("Problem with prevalence resultfile: %s\n", fileresp);
3699: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3700: exit(0);
3701: }
1.214 brouard 3702:
1.220 brouard 3703: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3704: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3705: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3706: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3707: fflush(ficlog);
3708: exit(70);
3709: }
3710: else{
3711: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
1.214 brouard 3712: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3713: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3714: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3715: }
3716: 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 3717:
1.220 brouard 3718: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3719: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3720: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3721: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3722: fflush(ficlog);
3723: exit(70);
3724: }
3725: else{
3726: 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 3727: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3728: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.220 brouard 3729: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3730: }
3731: 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 3732:
1.220 brouard 3733: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
3734: j1=0;
1.126 brouard 3735:
1.220 brouard 3736: j=cptcoveff;
3737: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3738:
3739: first=1;
3740:
3741: /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
3742: reference=low_education V1=0,V2=0
3743: med_educ V1=1 V2=0,
3744: high_educ V1=0 V2=1
3745: Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
3746: */
1.126 brouard 3747:
1.220 brouard 3748: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
3749: posproptt=0.;
3750: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3751: scanf("%d", i);*/
3752: for (i=-5; i<=nlstate+ndeath; i++)
3753: for (jk=-5; jk<=nlstate+ndeath; jk++)
3754: for(m=iagemin; m <= iagemax+3; m++)
3755: freq[i][jk][m]=0;
3756:
3757: for (i=1; i<=nlstate; i++) {
3758: for(m=iagemin; m <= iagemax+3; m++)
3759: prop[i][m]=0;
3760: posprop[i]=0;
3761: pospropt[i]=0;
3762: }
3763:
3764: dateintsum=0;
3765: k2cpt=0;
1.126 brouard 3766:
1.220 brouard 3767: for (iind=1; iind<=imx; iind++) { /* For each individual iind */
3768: bool=1;
3769: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3770: for (z1=1; z1<=cptcoveff; z1++) {
3771: if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
3772: /* Tests if the value of each of the covariates of i is equal to filter j1 */
3773: bool=0;
3774: /* 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",
1.198 brouard 3775: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3776: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
1.220 brouard 3777: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
3778: }
3779: } /* end z1 */
3780: } /* cptcovn > 0 */
3781:
3782: if (bool==1){
3783: /* for(m=firstpass; m<=lastpass; m++){ */
3784: for(mi=1; mi<wav[iind];mi++){
3785: m=mw[mi][iind];
3786: /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
3787: and mw[mi+1][iind]. dh depends on stepm. */
3788: agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
3789: ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
3790: if(m >=firstpass && m <=lastpass){
3791: k2=anint[m][iind]+(mint[m][iind]/12.);
3792: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3793: if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3794: if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3795: if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
3796: prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3797: if (m<lastpass) {
3798: /* if(s[m][iind]==4 && s[m+1][iind]==4) */
3799: /* 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]); */
3800: if(s[m][iind]==-1)
3801: 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.));
3802: freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
3803: /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
3804: 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 */
3805: }
3806: }
3807: if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
3808: dateintsum=dateintsum+k2;
3809: k2cpt++;
3810: /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3811: }
3812: /*}*/
3813: } /* end m */
3814: } /* end bool */
3815: } /* end iind = 1 to imx */
3816: /* prop[s][age] is feeded for any initial and valid live state as well as
3817: freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
3818:
3819:
3820: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3821: pstamp(ficresp);
3822: if (cptcovn>0) {
3823: fprintf(ficresp, "\n#********** Variable ");
3824: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3825: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
3826: for (z1=1; z1<=cptcoveff; z1++){
3827: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3828: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3829: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3830: }
3831: fprintf(ficresp, "**********\n#");
3832: fprintf(ficresphtm, "**********</h3>\n");
3833: fprintf(ficresphtmfr, "**********</h3>\n");
3834: fprintf(ficlog, "\n#********** Variable ");
3835: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3836: fprintf(ficlog, "**********\n");
3837: }
3838: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
3839: for(i=1; i<=nlstate;i++) {
3840: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3841: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3842: }
3843: fprintf(ficresp, "\n");
3844: fprintf(ficresphtm, "\n");
3845:
3846: /* Header of frequency table by age */
3847: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3848: fprintf(ficresphtmfr,"<th>Age</th> ");
3849: for(jk=-1; jk <=nlstate+ndeath; jk++){
3850: for(m=-1; m <=nlstate+ndeath; m++){
3851: if(jk!=0 && m!=0)
3852: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3853: }
3854: }
3855: fprintf(ficresphtmfr, "\n");
1.214 brouard 3856:
1.220 brouard 3857: /* For each age */
3858: for(iage=iagemin; iage <= iagemax+3; iage++){
3859: fprintf(ficresphtm,"<tr>");
3860: if(iage==iagemax+1){
3861: fprintf(ficlog,"1");
3862: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3863: }else if(iage==iagemax+2){
3864: fprintf(ficlog,"0");
3865: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3866: }else if(iage==iagemax+3){
3867: fprintf(ficlog,"Total");
3868: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
3869: }else{
3870: if(first==1){
3871: first=0;
3872: printf("See log file for details...\n");
3873: }
3874: fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
3875: fprintf(ficlog,"Age %d", iage);
3876: }
3877: for(jk=1; jk <=nlstate ; jk++){
3878: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3879: pp[jk] += freq[jk][m][iage];
3880: }
3881: for(jk=1; jk <=nlstate ; jk++){
3882: for(m=-1, pos=0; m <=0 ; m++)
3883: pos += freq[jk][m][iage];
3884: if(pp[jk]>=1.e-10){
3885: if(first==1){
3886: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3887: }
3888: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3889: }else{
3890: if(first==1)
3891: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3892: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3893: }
3894: }
3895:
3896: for(jk=1; jk <=nlstate ; jk++){
3897: /* posprop[jk]=0; */
3898: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
3899: pp[jk] += freq[jk][m][iage];
3900: } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
3901:
3902: for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
3903: pos += pp[jk]; /* pos is the total number of transitions until this age */
3904: posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
3905: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3906: pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
3907: from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
3908: }
3909: for(jk=1; jk <=nlstate ; jk++){
3910: if(pos>=1.e-5){
3911: if(first==1)
3912: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3913: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3914: }else{
3915: if(first==1)
3916: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3917: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3918: }
3919: if( iage <= iagemax){
3920: if(pos>=1.e-5){
3921: fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3922: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
3923: /*probs[iage][jk][j1]= pp[jk]/pos;*/
3924: /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/
3925: }
3926: else{
3927: fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
3928: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
3929: }
3930: }
3931: pospropt[jk] +=posprop[jk];
3932: } /* end loop jk */
3933: /* pospropt=0.; */
3934: for(jk=-1; jk <=nlstate+ndeath; jk++){
3935: for(m=-1; m <=nlstate+ndeath; m++){
3936: if(freq[jk][m][iage] !=0 ) { /* minimizing output */
3937: if(first==1){
3938: printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
3939: }
3940: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
3941: }
3942: if(jk!=0 && m!=0)
3943: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
3944: }
3945: } /* end loop jk */
3946: posproptt=0.;
3947: for(jk=1; jk <=nlstate; jk++){
3948: posproptt += pospropt[jk];
3949: }
3950: fprintf(ficresphtmfr,"</tr>\n ");
3951: if(iage <= iagemax){
3952: fprintf(ficresp,"\n");
3953: fprintf(ficresphtm,"</tr>\n");
3954: }
3955: if(first==1)
3956: printf("Others in log...\n");
3957: fprintf(ficlog,"\n");
3958: } /* end loop age iage */
3959: fprintf(ficresphtm,"<tr><th>Tot</th>");
3960: for(jk=1; jk <=nlstate ; jk++){
3961: if(posproptt < 1.e-5){
1.221 ! brouard 3962: fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
! 3963: }else{
1.220 brouard 3964: fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
3965: }
3966: }
3967: fprintf(ficresphtm,"</tr>\n");
3968: fprintf(ficresphtm,"</table>\n");
3969: fprintf(ficresphtmfr,"</table>\n");
3970: if(posproptt < 1.e-5){
3971: fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
3972: fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
3973: fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
3974: invalidvarcomb[j1]=1;
3975: }else{
3976: fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
3977: invalidvarcomb[j1]=0;
3978: }
3979: fprintf(ficresphtmfr,"</table>\n");
3980: } /* end selected combination of covariate j1 */
3981: dateintmean=dateintsum/k2cpt;
3982:
3983: fclose(ficresp);
3984: fclose(ficresphtm);
3985: fclose(ficresphtmfr);
3986: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
3987: free_vector(pospropt,1,nlstate);
3988: free_vector(posprop,1,nlstate);
3989: free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
3990: free_vector(pp,1,nlstate);
3991: /* End of Freq */
3992: }
1.126 brouard 3993:
3994: /************ Prevalence ********************/
3995: 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)
3996: {
3997: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3998: in each health status at the date of interview (if between dateprev1 and dateprev2).
3999: We still use firstpass and lastpass as another selection.
4000: */
4001:
1.164 brouard 4002: int i, m, jk, j1, bool, z1,j;
1.214 brouard 4003: int mi; /* Effective wave */
4004: int iage;
4005: double agebegin, ageend;
1.164 brouard 4006:
4007: double **prop;
4008: double posprop;
1.126 brouard 4009: double y2; /* in fractional years */
4010: int iagemin, iagemax;
1.145 brouard 4011: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 4012:
4013: iagemin= (int) agemin;
4014: iagemax= (int) agemax;
4015: /*pp=vector(1,nlstate);*/
1.218 brouard 4016: prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
1.126 brouard 4017: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
4018: j1=0;
4019:
1.145 brouard 4020: /*j=cptcoveff;*/
1.126 brouard 4021: if (cptcovn<1) {j=1;ncodemax[1]=1;}
4022:
1.145 brouard 4023: first=1;
1.219 brouard 4024: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
1.214 brouard 4025: for (i=1; i<=nlstate; i++)
1.218 brouard 4026: for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)
4027: prop[i][iage]=0.0;
1.214 brouard 4028:
4029: for (i=1; i<=imx; i++) { /* Each individual */
4030: bool=1;
4031: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.219 brouard 4032: for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/
1.218 brouard 4033: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
4034: bool=0;
1.214 brouard 4035: }
1.219 brouard 4036: if (bool==1) { /* For this combination of covariates values, this individual fits */
1.218 brouard 4037: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
4038: for(mi=1; mi<wav[i];mi++){
4039: m=mw[mi][i];
4040: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
4041: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
4042: if(m >=firstpass && m <=lastpass){
4043: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
4044: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
4045: if(agev[m][i]==0) agev[m][i]=iagemax+1;
4046: if(agev[m][i]==1) agev[m][i]=iagemax+2;
4047: if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
4048: 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);
4049: exit(1);
4050: }
4051: if (s[m][i]>0 && s[m][i]<=nlstate) {
4052: /*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]]);*/
4053: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
4054: prop[s[m][i]][iagemax+3] += weight[i];
4055: } /* end valid statuses */
4056: } /* end selection of dates */
4057: } /* end selection of waves */
4058: } /* end effective waves */
1.214 brouard 4059: } /* end bool */
4060: }
4061: for(i=iagemin; i <= iagemax+3; i++){
4062: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1.218 brouard 4063: posprop += prop[jk][i];
1.214 brouard 4064: }
4065:
4066: for(jk=1; jk <=nlstate ; jk++){
1.218 brouard 4067: if( i <= iagemax){
4068: if(posprop>=1.e-5){
4069: probs[i][jk][j1]= prop[jk][i]/posprop;
4070: } else{
4071: if(first==1){
4072: first=0;
4073: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
4074: }
4075: }
4076: }
1.214 brouard 4077: }/* end jk */
4078: }/* end i */
1.145 brouard 4079: /*} *//* end i1 */
4080: } /* end j1 */
1.126 brouard 4081:
4082: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
4083: /*free_vector(pp,1,nlstate);*/
1.218 brouard 4084: free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);
1.126 brouard 4085: } /* End of prevalence */
4086:
4087: /************* Waves Concatenation ***************/
4088:
4089: 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)
4090: {
4091: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
4092: Death is a valid wave (if date is known).
4093: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
4094: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
4095: and mw[mi+1][i]. dh depends on stepm.
4096: */
4097:
4098: int i, mi, m;
4099: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
4100: double sum=0., jmean=0.;*/
1.218 brouard 4101: int first, firstwo, firsthree, firstfour;
1.126 brouard 4102: int j, k=0,jk, ju, jl;
4103: double sum=0.;
4104: first=0;
1.214 brouard 4105: firstwo=0;
1.217 brouard 4106: firsthree=0;
1.218 brouard 4107: firstfour=0;
1.164 brouard 4108: jmin=100000;
1.126 brouard 4109: jmax=-1;
4110: jmean=0.;
1.214 brouard 4111: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 4112: mi=0;
4113: m=firstpass;
1.214 brouard 4114: while(s[m][i] <= nlstate){ /* a live state */
1.216 brouard 4115: 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 */
1.126 brouard 4116: mw[++mi][i]=m;
1.216 brouard 4117: }
4118: if(m >=lastpass){
4119: if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
1.217 brouard 4120: if(firsthree == 0){
4121: printf("Information! Unknown health 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.\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);
4122: firsthree=1;
4123: }
1.218 brouard 4124: 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.\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);
1.216 brouard 4125: mw[++mi][i]=m;
4126: }
4127: if(s[m][i]==-2){ /* Vital status is really unknown */
4128: nbwarn++;
4129: if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */
4130: 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);
4131: 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.\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);
4132: }
4133: break;
4134: }
1.126 brouard 4135: break;
1.216 brouard 4136: }
1.126 brouard 4137: else
4138: m++;
4139: }/* end while */
1.216 brouard 4140:
4141: /* After last pass */
1.214 brouard 4142: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 4143: mi++; /* Death is another wave */
4144: /* if(mi==0) never been interviewed correctly before death */
4145: /* Only death is a correct wave */
4146: mw[mi][i]=m;
1.216 brouard 4147: }else if ((int) andc[i] != 9999) { /* Status is either death or negative. A death occured after lastpass, we can't take it into account because of potential bias */
4148: /* m++; */
4149: /* mi++; */
4150: /* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state *\/ */
4151: /* mw[mi][i]=m; */
4152: nberr++;
1.218 brouard 4153: if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
4154: if(firstwo==0){
4155: printf("Error! Death for individual %ld line=%d occurred %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 );
4156: firstwo=1;
4157: }
4158: fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %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 );
4159: }else{ /* end date of interview is known */
4160: /* death is known but not confirmed by death status at any wave */
4161: if(firstfour==0){
4162: 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 );
4163: firstfour=1;
4164: }
4165: 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 4166: }
1.126 brouard 4167: }
4168: wav[i]=mi;
4169: if(mi==0){
4170: nbwarn++;
4171: if(first==0){
4172: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
4173: first=1;
4174: }
4175: if(first==1){
4176: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
4177: }
4178: } /* end mi==0 */
4179: } /* End individuals */
1.214 brouard 4180: /* wav and mw are no more changed */
1.126 brouard 4181:
1.214 brouard 4182:
1.126 brouard 4183: for(i=1; i<=imx; i++){
4184: for(mi=1; mi<wav[i];mi++){
4185: if (stepm <=0)
4186: dh[mi][i]=1;
4187: else{
4188: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
4189: if (agedc[i] < 2*AGESUP) {
4190: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
4191: if(j==0) j=1; /* Survives at least one month after exam */
4192: else if(j<0){
4193: nberr++;
4194: 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]);
4195: j=1; /* Temporary Dangerous patch */
4196: 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);
4197: 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]);
4198: 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);
4199: }
4200: k=k+1;
4201: if (j >= jmax){
4202: jmax=j;
4203: ijmax=i;
4204: }
4205: if (j <= jmin){
4206: jmin=j;
4207: ijmin=i;
4208: }
4209: sum=sum+j;
4210: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
4211: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
4212: }
4213: }
4214: else{
4215: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
4216: /* 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]); */
4217:
4218: k=k+1;
4219: if (j >= jmax) {
4220: jmax=j;
4221: ijmax=i;
4222: }
4223: else if (j <= jmin){
4224: jmin=j;
4225: ijmin=i;
4226: }
4227: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
4228: /*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]);*/
4229: if(j<0){
4230: nberr++;
4231: 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]);
4232: 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]);
4233: }
4234: sum=sum+j;
4235: }
4236: jk= j/stepm;
4237: jl= j -jk*stepm;
4238: ju= j -(jk+1)*stepm;
4239: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
4240: if(jl==0){
4241: dh[mi][i]=jk;
4242: bh[mi][i]=0;
4243: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 4244: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 4245: dh[mi][i]=jk+1;
4246: bh[mi][i]=ju;
4247: }
4248: }else{
4249: if(jl <= -ju){
4250: dh[mi][i]=jk;
4251: bh[mi][i]=jl; /* bias is positive if real duration
4252: * is higher than the multiple of stepm and negative otherwise.
4253: */
4254: }
4255: else{
4256: dh[mi][i]=jk+1;
4257: bh[mi][i]=ju;
4258: }
4259: if(dh[mi][i]==0){
4260: dh[mi][i]=1; /* At least one step */
4261: bh[mi][i]=ju; /* At least one step */
4262: /* 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);*/
4263: }
4264: } /* end if mle */
4265: }
4266: } /* end wave */
4267: }
4268: jmean=sum/k;
4269: 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 4270: 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);
1.126 brouard 4271: }
4272:
4273: /*********** Tricode ****************************/
1.220 brouard 4274: void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 4275: {
1.144 brouard 4276: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
4277: /* 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 4278: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 4279: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.220 brouard 4280: * nbcode[Tvar[5]][1]= nbcode[2][1]=0, nbcode[2][2]=1 (usually);
1.144 brouard 4281: */
1.130 brouard 4282:
1.145 brouard 4283: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 4284: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 4285: int cptcode=0; /* Modality max of covariates j */
4286: int modmincovj=0; /* Modality min of covariates j */
4287:
4288:
1.220 brouard 4289: /* cptcoveff=0; */
4290: *cptcov=0;
1.126 brouard 4291:
1.144 brouard 4292: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 4293:
1.145 brouard 4294: /* Loop on covariates without age and products */
1.186 brouard 4295: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 4296: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 4297: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.219 brouard 4298: modality of this covariate Vj*/
1.145 brouard 4299: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
1.219 brouard 4300: * If product of Vn*Vm, still boolean *:
4301: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
4302: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
1.145 brouard 4303: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 4304: modality of the nth covariate of individual i. */
1.145 brouard 4305: if (ij > modmaxcovj)
4306: modmaxcovj=ij;
4307: else if (ij < modmincovj)
1.219 brouard 4308: modmincovj=ij;
1.145 brouard 4309: if ((ij < -1) && (ij > NCOVMAX)){
1.219 brouard 4310: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
4311: exit(1);
1.145 brouard 4312: }else
1.136 brouard 4313: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 4314: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 4315: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 4316: /* getting the maximum value of the modality of the covariate
4317: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
4318: female is 1, then modmaxcovj=1.*/
1.192 brouard 4319: } /* end for loop on individuals i */
1.145 brouard 4320: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 4321: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 4322: cptcode=modmaxcovj;
1.137 brouard 4323: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 4324: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 4325: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
4326: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4327: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
4328: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
1.219 brouard 4329: if( k != -1){
4330: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
4331: covariate for which somebody answered excluding
4332: undefined. Usually 2: 0 and 1. */
4333: }
4334: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
4335: covariate for which somebody answered including
4336: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 4337: }
4338: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
1.219 brouard 4339: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 4340: } /* Ndum[-1] number of undefined modalities */
1.219 brouard 4341:
1.136 brouard 4342: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 4343: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
4344: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 4345: modmincovj=3; modmaxcovj = 7;
1.186 brouard 4346: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
4347: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
4348: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 4349: nbcode[Tvar[j]][ij]=k;
4350: nbcode[Tvar[j]][1]=0;
4351: nbcode[Tvar[j]][2]=1;
4352: nbcode[Tvar[j]][3]=2;
1.197 brouard 4353: To be continued (not working yet).
1.145 brouard 4354: */
1.197 brouard 4355: ij=0; /* ij is similar to i but can jump over null modalities */
4356: 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*/
4357: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.219 brouard 4358: break;
4359: }
1.192 brouard 4360: ij++;
1.197 brouard 4361: nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
1.192 brouard 4362: cptcode = ij; /* New max modality for covar j */
4363: } /* end of loop on modality i=-1 to 1 or more */
4364:
4365: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
4366: /* /\*recode from 0 *\/ */
4367: /* k is a modality. If we have model=V1+V1*sex */
4368: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
4369: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
4370: /* } */
4371: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
4372: /* if (ij > ncodemax[j]) { */
4373: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4374: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
4375: /* break; */
4376: /* } */
4377: /* } /\* end of loop on modality k *\/ */
1.137 brouard 4378: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
4379:
1.219 brouard 4380: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 4381:
1.187 brouard 4382: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.219 brouard 4383: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
4384: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
4385: Ndum[ij]++; /* Might be supersed V1 + V1*age */
4386: }
4387:
4388: ij=0;
4389: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
4390: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
4391: if((Ndum[i]!=0) && (i<=ncovcol)){
4392: ij++;
4393: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
4394: Tvaraff[ij]=i; /*For printing (unclear) */
4395: }else{
4396: /* Tvaraff[ij]=0; */
4397: }
4398: }
4399: /* ij--; */
1.220 brouard 4400: /* cptcoveff=ij; /\*Number of total covariates*\/ */
4401: *cptcov=ij; /*Number of total covariates*/
1.219 brouard 4402:
1.126 brouard 4403: }
4404:
1.145 brouard 4405:
1.126 brouard 4406: /*********** Health Expectancies ****************/
4407:
1.127 brouard 4408: 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 4409:
4410: {
4411: /* Health expectancies, no variances */
1.164 brouard 4412: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 4413: int nhstepma, nstepma; /* Decreasing with age */
4414: double age, agelim, hf;
4415: double ***p3mat;
4416: double eip;
4417:
4418: pstamp(ficreseij);
4419: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
4420: fprintf(ficreseij,"# Age");
4421: for(i=1; i<=nlstate;i++){
4422: for(j=1; j<=nlstate;j++){
4423: fprintf(ficreseij," e%1d%1d ",i,j);
4424: }
4425: fprintf(ficreseij," e%1d. ",i);
4426: }
4427: fprintf(ficreseij,"\n");
4428:
4429:
4430: if(estepm < stepm){
4431: printf ("Problem %d lower than %d\n",estepm, stepm);
4432: }
4433: else hstepm=estepm;
4434: /* We compute the life expectancy from trapezoids spaced every estepm months
4435: * This is mainly to measure the difference between two models: for example
4436: * if stepm=24 months pijx are given only every 2 years and by summing them
4437: * we are calculating an estimate of the Life Expectancy assuming a linear
4438: * progression in between and thus overestimating or underestimating according
4439: * to the curvature of the survival function. If, for the same date, we
4440: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4441: * to compare the new estimate of Life expectancy with the same linear
4442: * hypothesis. A more precise result, taking into account a more precise
4443: * curvature will be obtained if estepm is as small as stepm. */
4444:
4445: /* For example we decided to compute the life expectancy with the smallest unit */
4446: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4447: nhstepm is the number of hstepm from age to agelim
4448: nstepm is the number of stepm from age to agelin.
4449: Look at hpijx to understand the reason of that which relies in memory size
4450: and note for a fixed period like estepm months */
4451: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4452: survival function given by stepm (the optimization length). Unfortunately it
4453: means that if the survival funtion is printed only each two years of age and if
4454: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4455: results. So we changed our mind and took the option of the best precision.
4456: */
4457: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4458:
4459: agelim=AGESUP;
4460: /* If stepm=6 months */
4461: /* Computed by stepm unit matrices, product of hstepm matrices, stored
4462: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
4463:
4464: /* nhstepm age range expressed in number of stepm */
4465: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4466: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4467: /* if (stepm >= YEARM) hstepm=1;*/
4468: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4469: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4470:
4471: for (age=bage; age<=fage; age ++){
4472: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4473: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4474: /* if (stepm >= YEARM) hstepm=1;*/
4475: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4476:
4477: /* If stepm=6 months */
4478: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4479: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4480:
4481: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4482:
4483: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4484:
4485: printf("%d|",(int)age);fflush(stdout);
4486: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4487:
4488: /* Computing expectancies */
4489: for(i=1; i<=nlstate;i++)
4490: for(j=1; j<=nlstate;j++)
4491: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4492: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
4493:
4494: /* 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]);*/
4495:
4496: }
4497:
4498: fprintf(ficreseij,"%3.0f",age );
4499: for(i=1; i<=nlstate;i++){
4500: eip=0;
4501: for(j=1; j<=nlstate;j++){
4502: eip +=eij[i][j][(int)age];
4503: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
4504: }
4505: fprintf(ficreseij,"%9.4f", eip );
4506: }
4507: fprintf(ficreseij,"\n");
4508:
4509: }
4510: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4511: printf("\n");
4512: fprintf(ficlog,"\n");
4513:
4514: }
4515:
1.127 brouard 4516: 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 4517:
4518: {
4519: /* Covariances of health expectancies eij and of total life expectancies according
4520: to initial status i, ei. .
4521: */
4522: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
4523: int nhstepma, nstepma; /* Decreasing with age */
4524: double age, agelim, hf;
4525: double ***p3matp, ***p3matm, ***varhe;
4526: double **dnewm,**doldm;
4527: double *xp, *xm;
4528: double **gp, **gm;
4529: double ***gradg, ***trgradg;
4530: int theta;
4531:
4532: double eip, vip;
4533:
4534: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4535: xp=vector(1,npar);
4536: xm=vector(1,npar);
4537: dnewm=matrix(1,nlstate*nlstate,1,npar);
4538: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4539:
4540: pstamp(ficresstdeij);
4541: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4542: fprintf(ficresstdeij,"# Age");
4543: for(i=1; i<=nlstate;i++){
4544: for(j=1; j<=nlstate;j++)
4545: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4546: fprintf(ficresstdeij," e%1d. ",i);
4547: }
4548: fprintf(ficresstdeij,"\n");
4549:
4550: pstamp(ficrescveij);
4551: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4552: fprintf(ficrescveij,"# Age");
4553: for(i=1; i<=nlstate;i++)
4554: for(j=1; j<=nlstate;j++){
4555: cptj= (j-1)*nlstate+i;
4556: for(i2=1; i2<=nlstate;i2++)
4557: for(j2=1; j2<=nlstate;j2++){
4558: cptj2= (j2-1)*nlstate+i2;
4559: if(cptj2 <= cptj)
4560: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4561: }
4562: }
4563: fprintf(ficrescveij,"\n");
4564:
4565: if(estepm < stepm){
4566: printf ("Problem %d lower than %d\n",estepm, stepm);
4567: }
4568: else hstepm=estepm;
4569: /* We compute the life expectancy from trapezoids spaced every estepm months
4570: * This is mainly to measure the difference between two models: for example
4571: * if stepm=24 months pijx are given only every 2 years and by summing them
4572: * we are calculating an estimate of the Life Expectancy assuming a linear
4573: * progression in between and thus overestimating or underestimating according
4574: * to the curvature of the survival function. If, for the same date, we
4575: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4576: * to compare the new estimate of Life expectancy with the same linear
4577: * hypothesis. A more precise result, taking into account a more precise
4578: * curvature will be obtained if estepm is as small as stepm. */
4579:
4580: /* For example we decided to compute the life expectancy with the smallest unit */
4581: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4582: nhstepm is the number of hstepm from age to agelim
4583: nstepm is the number of stepm from age to agelin.
4584: Look at hpijx to understand the reason of that which relies in memory size
4585: and note for a fixed period like estepm months */
4586: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4587: survival function given by stepm (the optimization length). Unfortunately it
4588: means that if the survival funtion is printed only each two years of age and if
4589: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4590: results. So we changed our mind and took the option of the best precision.
4591: */
4592: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4593:
4594: /* If stepm=6 months */
4595: /* nhstepm age range expressed in number of stepm */
4596: agelim=AGESUP;
4597: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4598: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4599: /* if (stepm >= YEARM) hstepm=1;*/
4600: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4601:
4602: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4603: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4604: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4605: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4606: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4607: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4608:
4609: for (age=bage; age<=fage; age ++){
4610: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4611: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4612: /* if (stepm >= YEARM) hstepm=1;*/
4613: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
1.218 brouard 4614:
1.126 brouard 4615: /* If stepm=6 months */
4616: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4617: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4618:
4619: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1.218 brouard 4620:
1.126 brouard 4621: /* Computing Variances of health expectancies */
4622: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4623: decrease memory allocation */
4624: for(theta=1; theta <=npar; theta++){
4625: for(i=1; i<=npar; i++){
1.218 brouard 4626: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4627: xm[i] = x[i] - (i==theta ?delti[theta]:0);
1.126 brouard 4628: }
4629: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4630: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
1.218 brouard 4631:
1.126 brouard 4632: for(j=1; j<= nlstate; j++){
1.218 brouard 4633: for(i=1; i<=nlstate; i++){
4634: for(h=0; h<=nhstepm-1; h++){
4635: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4636: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4637: }
4638: }
1.126 brouard 4639: }
1.218 brouard 4640:
1.126 brouard 4641: for(ij=1; ij<= nlstate*nlstate; ij++)
1.218 brouard 4642: for(h=0; h<=nhstepm-1; h++){
4643: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4644: }
1.126 brouard 4645: }/* End theta */
4646:
4647:
4648: for(h=0; h<=nhstepm-1; h++)
4649: for(j=1; j<=nlstate*nlstate;j++)
1.218 brouard 4650: for(theta=1; theta <=npar; theta++)
4651: trgradg[h][j][theta]=gradg[h][theta][j];
1.126 brouard 4652:
1.218 brouard 4653:
4654: for(ij=1;ij<=nlstate*nlstate;ij++)
1.126 brouard 4655: for(ji=1;ji<=nlstate*nlstate;ji++)
1.218 brouard 4656: varhe[ij][ji][(int)age] =0.;
4657:
4658: printf("%d|",(int)age);fflush(stdout);
4659: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4660: for(h=0;h<=nhstepm-1;h++){
1.126 brouard 4661: for(k=0;k<=nhstepm-1;k++){
1.218 brouard 4662: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4663: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4664: for(ij=1;ij<=nlstate*nlstate;ij++)
4665: for(ji=1;ji<=nlstate*nlstate;ji++)
4666: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
1.126 brouard 4667: }
4668: }
1.218 brouard 4669:
1.126 brouard 4670: /* Computing expectancies */
4671: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4672: for(i=1; i<=nlstate;i++)
4673: for(j=1; j<=nlstate;j++)
1.218 brouard 4674: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4675: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4676:
4677: /* 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]);*/
4678:
4679: }
4680:
1.126 brouard 4681: fprintf(ficresstdeij,"%3.0f",age );
4682: for(i=1; i<=nlstate;i++){
4683: eip=0.;
4684: vip=0.;
4685: for(j=1; j<=nlstate;j++){
1.218 brouard 4686: eip += eij[i][j][(int)age];
4687: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4688: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4689: 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 4690: }
4691: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4692: }
4693: fprintf(ficresstdeij,"\n");
1.218 brouard 4694:
1.126 brouard 4695: fprintf(ficrescveij,"%3.0f",age );
4696: for(i=1; i<=nlstate;i++)
4697: for(j=1; j<=nlstate;j++){
1.218 brouard 4698: cptj= (j-1)*nlstate+i;
4699: for(i2=1; i2<=nlstate;i2++)
4700: for(j2=1; j2<=nlstate;j2++){
4701: cptj2= (j2-1)*nlstate+i2;
4702: if(cptj2 <= cptj)
4703: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4704: }
1.126 brouard 4705: }
4706: fprintf(ficrescveij,"\n");
1.218 brouard 4707:
1.126 brouard 4708: }
4709: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4710: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4711: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4712: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4713: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4714: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4715: printf("\n");
4716: fprintf(ficlog,"\n");
1.218 brouard 4717:
1.126 brouard 4718: free_vector(xm,1,npar);
4719: free_vector(xp,1,npar);
4720: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4721: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4722: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4723: }
1.218 brouard 4724:
1.126 brouard 4725: /************ Variance ******************/
1.209 brouard 4726: 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 4727: {
4728: /* Variance of health expectancies */
4729: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4730: /* double **newm;*/
4731: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4732:
4733: /* int movingaverage(); */
4734: double **dnewm,**doldm;
4735: double **dnewmp,**doldmp;
4736: int i, j, nhstepm, hstepm, h, nstepm ;
4737: int k;
4738: double *xp;
4739: double **gp, **gm; /* for var eij */
4740: double ***gradg, ***trgradg; /*for var eij */
4741: double **gradgp, **trgradgp; /* for var p point j */
4742: double *gpp, *gmp; /* for var p point j */
4743: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4744: double ***p3mat;
4745: double age,agelim, hf;
4746: /* double ***mobaverage; */
4747: int theta;
4748: char digit[4];
4749: char digitp[25];
4750:
4751: char fileresprobmorprev[FILENAMELENGTH];
4752:
4753: if(popbased==1){
4754: if(mobilav!=0)
4755: strcpy(digitp,"-POPULBASED-MOBILAV_");
4756: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
4757: }
4758: else
4759: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4760:
1.218 brouard 4761: /* if (mobilav!=0) { */
4762: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
4763: /* if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ */
4764: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
4765: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
4766: /* } */
4767: /* } */
4768:
4769: strcpy(fileresprobmorprev,"PRMORPREV-");
4770: sprintf(digit,"%-d",ij);
4771: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4772: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4773: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
4774: strcat(fileresprobmorprev,fileresu);
4775: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4776: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4777: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4778: }
4779: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4780: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4781: pstamp(ficresprobmorprev);
4782: 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);
4783: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4784: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4785: fprintf(ficresprobmorprev," p.%-d SE",j);
4786: for(i=1; i<=nlstate;i++)
4787: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4788: }
4789: fprintf(ficresprobmorprev,"\n");
4790:
4791: fprintf(ficgp,"\n# Routine varevsij");
4792: fprintf(ficgp,"\nunset title \n");
4793: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
4794: 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");
4795: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4796: /* } */
4797: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4798: pstamp(ficresvij);
4799: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4800: if(popbased==1)
4801: 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);
4802: else
4803: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4804: fprintf(ficresvij,"# Age");
4805: for(i=1; i<=nlstate;i++)
4806: for(j=1; j<=nlstate;j++)
4807: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4808: fprintf(ficresvij,"\n");
4809:
4810: xp=vector(1,npar);
4811: dnewm=matrix(1,nlstate,1,npar);
4812: doldm=matrix(1,nlstate,1,nlstate);
4813: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4814: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4815:
4816: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4817: gpp=vector(nlstate+1,nlstate+ndeath);
4818: gmp=vector(nlstate+1,nlstate+ndeath);
4819: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.126 brouard 4820:
1.218 brouard 4821: if(estepm < stepm){
4822: printf ("Problem %d lower than %d\n",estepm, stepm);
4823: }
4824: else hstepm=estepm;
4825: /* For example we decided to compute the life expectancy with the smallest unit */
4826: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4827: nhstepm is the number of hstepm from age to agelim
4828: nstepm is the number of stepm from age to agelim.
4829: Look at function hpijx to understand why because of memory size limitations,
4830: we decided (b) to get a life expectancy respecting the most precise curvature of the
4831: survival function given by stepm (the optimization length). Unfortunately it
4832: means that if the survival funtion is printed every two years of age and if
4833: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4834: results. So we changed our mind and took the option of the best precision.
4835: */
4836: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4837: agelim = AGESUP;
4838: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4839: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4840: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4841: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4842: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4843: gp=matrix(0,nhstepm,1,nlstate);
4844: gm=matrix(0,nhstepm,1,nlstate);
4845:
4846:
4847: for(theta=1; theta <=npar; theta++){
4848: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4849: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4850: }
4851:
4852: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4853:
4854: if (popbased==1) {
4855: if(mobilav ==0){
4856: for(i=1; i<=nlstate;i++)
4857: prlim[i][i]=probs[(int)age][i][ij];
4858: }else{ /* mobilav */
4859: for(i=1; i<=nlstate;i++)
4860: prlim[i][i]=mobaverage[(int)age][i][ij];
4861: }
4862: }
4863:
4864: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
4865: for(j=1; j<= nlstate; j++){
4866: for(h=0; h<=nhstepm; h++){
4867: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4868: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4869: }
4870: }
4871: /* Next for computing probability of death (h=1 means
4872: computed over hstepm matrices product = hstepm*stepm months)
4873: as a weighted average of prlim.
4874: */
4875: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4876: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4877: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4878: }
4879: /* end probability of death */
4880:
4881: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4882: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4883:
4884: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
4885:
4886: if (popbased==1) {
4887: if(mobilav ==0){
4888: for(i=1; i<=nlstate;i++)
4889: prlim[i][i]=probs[(int)age][i][ij];
4890: }else{ /* mobilav */
4891: for(i=1; i<=nlstate;i++)
4892: prlim[i][i]=mobaverage[(int)age][i][ij];
4893: }
4894: }
4895:
4896: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4897:
4898: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
4899: for(h=0; h<=nhstepm; h++){
4900: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4901: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4902: }
4903: }
4904: /* This for computing probability of death (h=1 means
4905: computed over hstepm matrices product = hstepm*stepm months)
4906: as a weighted average of prlim.
4907: */
4908: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4909: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4910: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4911: }
4912: /* end probability of death */
4913:
4914: for(j=1; j<= nlstate; j++) /* vareij */
4915: for(h=0; h<=nhstepm; h++){
4916: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4917: }
4918:
4919: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4920: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4921: }
4922:
4923: } /* End theta */
4924:
4925: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4926:
4927: for(h=0; h<=nhstepm; h++) /* veij */
4928: for(j=1; j<=nlstate;j++)
4929: for(theta=1; theta <=npar; theta++)
4930: trgradg[h][j][theta]=gradg[h][theta][j];
4931:
4932: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4933: for(theta=1; theta <=npar; theta++)
4934: trgradgp[j][theta]=gradgp[theta][j];
4935:
4936:
4937: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4938: for(i=1;i<=nlstate;i++)
4939: for(j=1;j<=nlstate;j++)
4940: vareij[i][j][(int)age] =0.;
4941:
4942: for(h=0;h<=nhstepm;h++){
4943: for(k=0;k<=nhstepm;k++){
4944: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4945: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4946: for(i=1;i<=nlstate;i++)
4947: for(j=1;j<=nlstate;j++)
4948: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4949: }
4950: }
4951:
4952: /* pptj */
4953: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4954: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4955: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4956: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4957: varppt[j][i]=doldmp[j][i];
4958: /* end ppptj */
4959: /* x centered again */
4960:
4961: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
4962:
4963: if (popbased==1) {
4964: if(mobilav ==0){
4965: for(i=1; i<=nlstate;i++)
4966: prlim[i][i]=probs[(int)age][i][ij];
4967: }else{ /* mobilav */
4968: for(i=1; i<=nlstate;i++)
4969: prlim[i][i]=mobaverage[(int)age][i][ij];
4970: }
4971: }
4972:
4973: /* This for computing probability of death (h=1 means
4974: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4975: as a weighted average of prlim.
4976: */
4977: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4978: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4979: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4980: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4981: }
4982: /* end probability of death */
4983:
4984: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4985: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4986: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4987: for(i=1; i<=nlstate;i++){
4988: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4989: }
4990: }
4991: fprintf(ficresprobmorprev,"\n");
4992:
4993: fprintf(ficresvij,"%.0f ",age );
4994: for(i=1; i<=nlstate;i++)
4995: for(j=1; j<=nlstate;j++){
4996: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4997: }
4998: fprintf(ficresvij,"\n");
4999: free_matrix(gp,0,nhstepm,1,nlstate);
5000: free_matrix(gm,0,nhstepm,1,nlstate);
5001: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
5002: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
5003: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5004: } /* End age */
5005: free_vector(gpp,nlstate+1,nlstate+ndeath);
5006: free_vector(gmp,nlstate+1,nlstate+ndeath);
5007: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
5008: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
5009: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
5010: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
5011: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
5012: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
5013: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
5014: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
5015: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
5016: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
5017: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
5018: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
5019: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
5020: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
5021: 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);
5022: /* 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 5023: */
1.218 brouard 5024: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
5025: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 5026:
1.218 brouard 5027: free_vector(xp,1,npar);
5028: free_matrix(doldm,1,nlstate,1,nlstate);
5029: free_matrix(dnewm,1,nlstate,1,npar);
5030: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5031: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
5032: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
5033: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
5034: fclose(ficresprobmorprev);
5035: fflush(ficgp);
5036: fflush(fichtm);
5037: } /* end varevsij */
1.126 brouard 5038:
5039: /************ Variance of prevlim ******************/
1.209 brouard 5040: 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 5041: {
1.205 brouard 5042: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 5043: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 5044:
1.126 brouard 5045: double **dnewm,**doldm;
5046: int i, j, nhstepm, hstepm;
5047: double *xp;
5048: double *gp, *gm;
5049: double **gradg, **trgradg;
1.208 brouard 5050: double **mgm, **mgp;
1.126 brouard 5051: double age,agelim;
5052: int theta;
5053:
5054: pstamp(ficresvpl);
5055: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
5056: fprintf(ficresvpl,"# Age");
5057: for(i=1; i<=nlstate;i++)
5058: fprintf(ficresvpl," %1d-%1d",i,i);
5059: fprintf(ficresvpl,"\n");
5060:
5061: xp=vector(1,npar);
5062: dnewm=matrix(1,nlstate,1,npar);
5063: doldm=matrix(1,nlstate,1,nlstate);
5064:
5065: hstepm=1*YEARM; /* Every year of age */
5066: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
5067: agelim = AGESUP;
5068: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
5069: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5070: if (stepm >= YEARM) hstepm=1;
5071: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5072: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 5073: mgp=matrix(1,npar,1,nlstate);
5074: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 5075: gp=vector(1,nlstate);
5076: gm=vector(1,nlstate);
5077:
5078: for(theta=1; theta <=npar; theta++){
5079: for(i=1; i<=npar; i++){ /* Computes gradient */
5080: xp[i] = x[i] + (i==theta ?delti[theta]:0);
5081: }
1.209 brouard 5082: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5083: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5084: else
5085: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5086: for(i=1;i<=nlstate;i++){
1.126 brouard 5087: gp[i] = prlim[i][i];
1.208 brouard 5088: mgp[theta][i] = prlim[i][i];
5089: }
1.126 brouard 5090: for(i=1; i<=npar; i++) /* Computes gradient */
5091: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 5092: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
5093: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
5094: else
5095: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 5096: for(i=1;i<=nlstate;i++){
1.126 brouard 5097: gm[i] = prlim[i][i];
1.208 brouard 5098: mgm[theta][i] = prlim[i][i];
5099: }
1.126 brouard 5100: for(i=1;i<=nlstate;i++)
5101: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 5102: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 5103: } /* End theta */
5104:
5105: trgradg =matrix(1,nlstate,1,npar);
5106:
5107: for(j=1; j<=nlstate;j++)
5108: for(theta=1; theta <=npar; theta++)
5109: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 5110: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5111: /* printf("\nmgm mgp %d ",(int)age); */
5112: /* for(j=1; j<=nlstate;j++){ */
5113: /* printf(" %d ",j); */
5114: /* for(theta=1; theta <=npar; theta++) */
5115: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
5116: /* printf("\n "); */
5117: /* } */
5118: /* } */
5119: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
5120: /* printf("\n gradg %d ",(int)age); */
5121: /* for(j=1; j<=nlstate;j++){ */
5122: /* printf("%d ",j); */
5123: /* for(theta=1; theta <=npar; theta++) */
5124: /* printf("%d %lf ",theta,gradg[theta][j]); */
5125: /* printf("\n "); */
5126: /* } */
5127: /* } */
1.126 brouard 5128:
5129: for(i=1;i<=nlstate;i++)
5130: varpl[i][(int)age] =0.;
1.209 brouard 5131: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 5132: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5133: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
5134: }else{
1.126 brouard 5135: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
5136: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 5137: }
1.126 brouard 5138: for(i=1;i<=nlstate;i++)
5139: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
5140:
5141: fprintf(ficresvpl,"%.0f ",age );
5142: for(i=1; i<=nlstate;i++)
5143: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
5144: fprintf(ficresvpl,"\n");
5145: free_vector(gp,1,nlstate);
5146: free_vector(gm,1,nlstate);
1.208 brouard 5147: free_matrix(mgm,1,npar,1,nlstate);
5148: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 5149: free_matrix(gradg,1,npar,1,nlstate);
5150: free_matrix(trgradg,1,nlstate,1,npar);
5151: } /* End age */
5152:
5153: free_vector(xp,1,npar);
5154: free_matrix(doldm,1,nlstate,1,npar);
5155: free_matrix(dnewm,1,nlstate,1,nlstate);
5156:
5157: }
5158:
5159: /************ Variance of one-step probabilities ******************/
5160: 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[])
5161: {
1.164 brouard 5162: int i, j=0, k1, l1, tj;
1.126 brouard 5163: int k2, l2, j1, z1;
1.164 brouard 5164: int k=0, l;
1.145 brouard 5165: int first=1, first1, first2;
1.126 brouard 5166: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
5167: double **dnewm,**doldm;
5168: double *xp;
5169: double *gp, *gm;
5170: double **gradg, **trgradg;
5171: double **mu;
1.164 brouard 5172: double age, cov[NCOVMAX+1];
1.126 brouard 5173: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
5174: int theta;
5175: char fileresprob[FILENAMELENGTH];
5176: char fileresprobcov[FILENAMELENGTH];
5177: char fileresprobcor[FILENAMELENGTH];
5178: double ***varpij;
5179:
1.201 brouard 5180: strcpy(fileresprob,"PROB_");
1.126 brouard 5181: strcat(fileresprob,fileres);
5182: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
5183: printf("Problem with resultfile: %s\n", fileresprob);
5184: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
5185: }
1.201 brouard 5186: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 5187: strcat(fileresprobcov,fileresu);
1.126 brouard 5188: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
5189: printf("Problem with resultfile: %s\n", fileresprobcov);
5190: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
5191: }
1.201 brouard 5192: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 5193: strcat(fileresprobcor,fileresu);
1.126 brouard 5194: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
5195: printf("Problem with resultfile: %s\n", fileresprobcor);
5196: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
5197: }
5198: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5199: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
5200: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5201: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
5202: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5203: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
5204: pstamp(ficresprob);
5205: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
5206: fprintf(ficresprob,"# Age");
5207: pstamp(ficresprobcov);
5208: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
5209: fprintf(ficresprobcov,"# Age");
5210: pstamp(ficresprobcor);
5211: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
5212: fprintf(ficresprobcor,"# Age");
5213:
5214:
5215: for(i=1; i<=nlstate;i++)
5216: for(j=1; j<=(nlstate+ndeath);j++){
5217: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
5218: fprintf(ficresprobcov," p%1d-%1d ",i,j);
5219: fprintf(ficresprobcor," p%1d-%1d ",i,j);
5220: }
5221: /* fprintf(ficresprob,"\n");
5222: fprintf(ficresprobcov,"\n");
5223: fprintf(ficresprobcor,"\n");
5224: */
1.131 brouard 5225: xp=vector(1,npar);
1.126 brouard 5226: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5227: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5228: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
5229: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
5230: first=1;
5231: fprintf(ficgp,"\n# Routine varprob");
5232: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
5233: fprintf(fichtm,"\n");
5234:
1.200 brouard 5235: 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);
1.197 brouard 5236: 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);
5237: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 5238: and drawn. It helps understanding how is the covariance between two incidences.\
5239: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
5240: 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. \
5241: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
5242: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
5243: standard deviations wide on each axis. <br>\
5244: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
5245: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
5246: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
5247:
5248: cov[1]=1;
1.145 brouard 5249: /* tj=cptcoveff; */
5250: tj = (int) pow(2,cptcoveff);
1.126 brouard 5251: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
5252: j1=0;
1.220 brouard 5253: for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates */
5254: if (cptcovn>0) {
5255: fprintf(ficresprob, "\n#********** Variable ");
5256: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5257: fprintf(ficresprob, "**********\n#\n");
5258: fprintf(ficresprobcov, "\n#********** Variable ");
5259: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5260: fprintf(ficresprobcov, "**********\n#\n");
5261:
5262: fprintf(ficgp, "\n#********** Variable ");
5263: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5264: fprintf(ficgp, "**********\n#\n");
5265:
5266:
5267: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
5268: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5269: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
5270:
5271: fprintf(ficresprobcor, "\n#********** Variable ");
5272: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
5273: fprintf(ficresprobcor, "**********\n#");
5274: if(invalidvarcomb[j1]){
5275: fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
5276: fprintf(fichtmcov,"\n<h3>Combination (%d) ignored because no cases </h3>\n",j1);
5277: continue;
5278: }
5279: }
5280: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
5281: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
5282: gp=vector(1,(nlstate)*(nlstate+ndeath));
5283: gm=vector(1,(nlstate)*(nlstate+ndeath));
5284: for (age=bage; age<=fage; age ++){
5285: cov[2]=age;
5286: if(nagesqr==1)
5287: cov[3]= age*age;
5288: for (k=1; k<=cptcovn;k++) {
5289: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
5290: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
5291: * 1 1 1 1 1
5292: * 2 2 1 1 1
5293: * 3 1 2 1 1
5294: */
5295: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
5296: }
5297: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5298: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
5299: for (k=1; k<=cptcovprod;k++)
5300: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
5301:
5302:
5303: for(theta=1; theta <=npar; theta++){
5304: for(i=1; i<=npar; i++)
5305: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
5306:
5307: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5308:
5309: k=0;
5310: for(i=1; i<= (nlstate); i++){
5311: for(j=1; j<=(nlstate+ndeath);j++){
5312: k=k+1;
5313: gp[k]=pmmij[i][j];
5314: }
5315: }
5316:
5317: for(i=1; i<=npar; i++)
5318: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
5319:
5320: pmij(pmmij,cov,ncovmodel,xp,nlstate);
5321: k=0;
5322: for(i=1; i<=(nlstate); i++){
5323: for(j=1; j<=(nlstate+ndeath);j++){
5324: k=k+1;
5325: gm[k]=pmmij[i][j];
5326: }
5327: }
5328:
5329: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
5330: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
5331: }
1.126 brouard 5332:
1.220 brouard 5333: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
5334: for(theta=1; theta <=npar; theta++)
5335: trgradg[j][theta]=gradg[theta][j];
5336:
5337: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
5338: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
5339:
5340: pmij(pmmij,cov,ncovmodel,x,nlstate);
5341:
5342: k=0;
5343: for(i=1; i<=(nlstate); i++){
5344: for(j=1; j<=(nlstate+ndeath);j++){
5345: k=k+1;
5346: mu[k][(int) age]=pmmij[i][j];
5347: }
5348: }
1.126 brouard 5349: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
1.220 brouard 5350: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
5351: varpij[i][j][(int)age] = doldm[i][j];
5352:
5353: /*printf("\n%d ",(int)age);
5354: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5355: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5356: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
5357: }*/
5358:
5359: fprintf(ficresprob,"\n%d ",(int)age);
5360: fprintf(ficresprobcov,"\n%d ",(int)age);
5361: fprintf(ficresprobcor,"\n%d ",(int)age);
5362:
5363: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
5364: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
5365: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
5366: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
5367: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
5368: }
5369: i=0;
5370: for (k=1; k<=(nlstate);k++){
5371: for (l=1; l<=(nlstate+ndeath);l++){
5372: i++;
5373: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
5374: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
5375: for (j=1; j<=i;j++){
5376: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
5377: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
5378: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
5379: }
5380: }
5381: }/* end of loop for state */
5382: } /* end of loop for age */
5383: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
5384: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
5385: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5386: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
5387:
5388: /* Confidence intervalle of pij */
5389: /*
5390: fprintf(ficgp,"\nunset parametric;unset label");
5391: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
5392: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
5393: 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);
5394: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
5395: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
5396: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
5397: */
5398:
5399: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
5400: first1=1;first2=2;
5401: for (k2=1; k2<=(nlstate);k2++){
5402: for (l2=1; l2<=(nlstate+ndeath);l2++){
5403: if(l2==k2) continue;
5404: j=(k2-1)*(nlstate+ndeath)+l2;
5405: for (k1=1; k1<=(nlstate);k1++){
5406: for (l1=1; l1<=(nlstate+ndeath);l1++){
5407: if(l1==k1) continue;
5408: i=(k1-1)*(nlstate+ndeath)+l1;
5409: if(i<=j) continue;
5410: for (age=bage; age<=fage; age ++){
5411: if ((int)age %5==0){
5412: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
5413: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
5414: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
5415: mu1=mu[i][(int) age]/stepm*YEARM ;
5416: mu2=mu[j][(int) age]/stepm*YEARM;
5417: c12=cv12/sqrt(v1*v2);
5418: /* Computing eigen value of matrix of covariance */
5419: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5420: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
5421: if ((lc2 <0) || (lc1 <0) ){
5422: if(first2==1){
5423: first1=0;
5424: 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);
5425: }
5426: 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);
5427: /* lc1=fabs(lc1); */ /* If we want to have them positive */
5428: /* lc2=fabs(lc2); */
5429: }
5430:
5431: /* Eigen vectors */
5432: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
5433: /*v21=sqrt(1.-v11*v11); *//* error */
5434: v21=(lc1-v1)/cv12*v11;
5435: v12=-v21;
5436: v22=v11;
5437: tnalp=v21/v11;
5438: if(first1==1){
5439: first1=0;
5440: 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);
5441: }
5442: 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);
5443: /*printf(fignu*/
5444: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
5445: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
5446: if(first==1){
5447: first=0;
5448: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
5449: fprintf(ficgp,"\nset parametric;unset label");
5450: 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);
5451: fprintf(ficgp,"\nset ter svg size 640, 480");
5452: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
5453: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
1.201 brouard 5454: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
1.220 brouard 5455: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
5456: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5457: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5458: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
5459: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 5460: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5461: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
1.220 brouard 5462: 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", \
5463: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5464: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5465: }else{
5466: first=0;
5467: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
5468: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
5469: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
5470: 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", \
5471: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \
5472: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
5473: }/* if first */
5474: } /* age mod 5 */
5475: } /* end loop age */
5476: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
5477: first=1;
5478: } /*l12 */
5479: } /* k12 */
5480: } /*l1 */
5481: }/* k1 */
5482: } /* loop on combination of covariates j1 */
1.126 brouard 5483: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
5484: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
5485: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
5486: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
5487: free_vector(xp,1,npar);
5488: fclose(ficresprob);
5489: fclose(ficresprobcov);
5490: fclose(ficresprobcor);
5491: fflush(ficgp);
5492: fflush(fichtmcov);
5493: }
5494:
5495:
5496: /******************* Printing html file ***********/
1.201 brouard 5497: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5498: int lastpass, int stepm, int weightopt, char model[],\
5499: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.217 brouard 5500: int popforecast, int prevfcast, int backcast, int estepm , \
1.213 brouard 5501: double jprev1, double mprev1,double anprev1, double dateprev1, \
5502: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 5503: int jj1, k1, i1, cpt;
5504:
5505: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
5506: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
5507: </ul>");
1.214 brouard 5508: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
5509: 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",
5510: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
5511: 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 5512: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
5513: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 5514: fprintf(fichtm,"\
5515: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 5516: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 5517: fprintf(fichtm,"\
1.217 brouard 5518: - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
5519: stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
5520: fprintf(fichtm,"\
1.126 brouard 5521: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5522: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 5523: fprintf(fichtm,"\
1.217 brouard 5524: - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
5525: subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
5526: fprintf(fichtm,"\
1.211 brouard 5527: - (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 5528: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5529: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 5530: if(prevfcast==1){
5531: fprintf(fichtm,"\
5532: - Prevalence projections by age and states: \
1.201 brouard 5533: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 5534: }
1.126 brouard 5535:
5536: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
5537:
1.145 brouard 5538: m=pow(2,cptcoveff);
1.126 brouard 5539: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5540:
5541: jj1=0;
5542: for(k1=1; k1<=m;k1++){
1.220 brouard 5543:
1.192 brouard 5544: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.220 brouard 5545: jj1++;
5546: if (cptcovn > 0) {
5547: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5548: for (cpt=1; cpt<=cptcoveff;cpt++){
5549: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5550: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
5551: }
5552: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5553: if(invalidvarcomb[k1]){
5554: fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
5555: printf("\nCombination (%d) ignored because no cases \n",k1);
5556: continue;
5557: }
5558: }
5559: /* aij, bij */
5560: 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 5561: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.220 brouard 5562: /* Pij */
5563: 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 5564: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.220 brouard 5565: /* Quasi-incidences */
5566: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
5567: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
1.211 brouard 5568: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5569: 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 5570: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.220 brouard 5571: /* Survival functions (period) in state j */
5572: for(cpt=1; cpt<=nlstate;cpt++){
5573: 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 5574: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
1.220 brouard 5575: }
5576: /* State specific survival functions (period) */
5577: for(cpt=1; cpt<=nlstate;cpt++){
5578: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
5579: Or probability to survive in various states (1 to %d) being in state %d at different ages. \
1.201 brouard 5580: <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);
1.220 brouard 5581: }
5582: /* Period (stable) prevalence in each health state */
5583: for(cpt=1; cpt<=nlstate;cpt++){
5584: 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 5585: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
1.220 brouard 5586: }
5587: if(backcast==1){
1.217 brouard 5588: /* Period (stable) back prevalence in each health state */
5589: for(cpt=1; cpt<=nlstate;cpt++){
5590: 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> \
5591: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);
5592: }
1.220 brouard 5593: }
5594: if(prevfcast==1){
5595: /* Projection of prevalence up to period (stable) prevalence in each health state */
5596: for(cpt=1; cpt<=nlstate;cpt++){
5597: 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 5598: <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);
1.220 brouard 5599: }
5600: }
5601:
5602: for(cpt=1; cpt<=nlstate;cpt++) {
5603: 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 5604: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.220 brouard 5605: }
1.192 brouard 5606: /* } /\* end i1 *\/ */
1.126 brouard 5607: }/* End k1 */
5608: fprintf(fichtm,"</ul>");
5609:
5610: fprintf(fichtm,"\
5611: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5612: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5613: - 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 5614: But because parameters are usually highly correlated (a higher incidence of disability \
5615: and a higher incidence of recovery can give very close observed transition) it might \
5616: be very useful to look not only at linear confidence intervals estimated from the \
5617: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5618: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5619: covariance matrix of the one-step probabilities. \
5620: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5621:
1.193 brouard 5622: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5623: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5624: fprintf(fichtm,"\
5625: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5626: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5627:
5628: fprintf(fichtm,"\
5629: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5630: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5631: fprintf(fichtm,"\
5632: - 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): \
5633: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5634: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5635: fprintf(fichtm,"\
5636: - (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): \
5637: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5638: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5639: fprintf(fichtm,"\
1.128 brouard 5640: - 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",
1.201 brouard 5641: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5642: fprintf(fichtm,"\
1.128 brouard 5643: - 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",
1.201 brouard 5644: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5645: fprintf(fichtm,"\
5646: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5647: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5648:
5649: /* if(popforecast==1) fprintf(fichtm,"\n */
5650: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5651: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5652: /* <br>",fileres,fileres,fileres,fileres); */
5653: /* else */
5654: /* 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); */
5655: fflush(fichtm);
5656: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5657:
1.145 brouard 5658: m=pow(2,cptcoveff);
1.126 brouard 5659: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5660:
5661: jj1=0;
5662: for(k1=1; k1<=m;k1++){
1.220 brouard 5663: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
5664: jj1++;
1.126 brouard 5665: if (cptcovn > 0) {
5666: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5667: for (cpt=1; cpt<=cptcoveff;cpt++)
1.220 brouard 5668: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5669: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
1.220 brouard 5670:
5671: if(invalidvarcomb[k1]){
5672: fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
5673: continue;
5674: }
1.126 brouard 5675: }
5676: for(cpt=1; cpt<=nlstate;cpt++) {
1.218 brouard 5677: fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
5678: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\
1.205 brouard 5679: <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 5680: }
5681: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5682: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5683: true period expectancies (those weighted with period prevalences are also\
5684: drawn in addition to the population based expectancies computed using\
1.218 brouard 5685: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\
1.205 brouard 5686: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5687: /* } /\* end i1 *\/ */
1.126 brouard 5688: }/* End k1 */
5689: fprintf(fichtm,"</ul>");
5690: fflush(fichtm);
5691: }
5692:
5693: /******************* Gnuplot file **************/
1.218 brouard 5694: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){
1.126 brouard 5695:
5696: char dirfileres[132],optfileres[132];
1.220 brouard 5697: char gplotcondition[132];
1.164 brouard 5698: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5699: int lv=0, vlv=0, kl=0;
1.130 brouard 5700: int ng=0;
1.201 brouard 5701: int vpopbased;
1.219 brouard 5702: int ioffset; /* variable offset for columns */
5703:
1.126 brouard 5704: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5705: /* printf("Problem with file %s",optionfilegnuplot); */
5706: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5707: /* } */
5708:
5709: /*#ifdef windows */
5710: fprintf(ficgp,"cd \"%s\" \n",pathc);
5711: /*#endif */
5712: m=pow(2,cptcoveff);
5713:
1.202 brouard 5714: /* Contribution to likelihood */
5715: /* Plot the probability implied in the likelihood */
5716: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5717: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5718: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5719: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5720: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5721: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5722: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5723: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5724: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5725: 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));
1.204 brouard 5726: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5727: 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));
1.204 brouard 5728: for (i=1; i<= nlstate ; i ++) {
5729: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5730: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5731: 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);
1.204 brouard 5732: for (j=2; j<= nlstate+ndeath ; j ++) {
1.219 brouard 5733: 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);
1.204 brouard 5734: }
5735: fprintf(ficgp,";\nset out; unset ylabel;\n");
5736: }
5737: /* 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 */
5738: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5739: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
1.203 brouard 5740: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5741: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5742:
1.126 brouard 5743: strcpy(dirfileres,optionfilefiname);
5744: strcpy(optfileres,"vpl");
5745: /* 1eme*/
1.211 brouard 5746: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
1.220 brouard 5747: for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */
1.211 brouard 5748: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5749: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
1.219 brouard 5750: for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
5751: lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
5752: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5753: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5754: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5755: vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
5756: /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
1.220 brouard 5757: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5758: }
5759: fprintf(ficgp,"\n#\n");
1.220 brouard 5760: if(invalidvarcomb[k1]){
5761: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5762: continue;
5763: }
1.211 brouard 5764:
1.219 brouard 5765: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5766: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
5767: fprintf(ficgp,"set xlabel \"Age\" \n\
5768: set ylabel \"Probability\" \n \
5769: set ter svg size 640, 480\n \
1.201 brouard 5770: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.219 brouard 5771:
5772: for (i=1; i<= nlstate ; i ++) {
5773: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5774: else fprintf(ficgp," %%*lf (%%*lf)");
5775: }
5776: 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);
5777: for (i=1; i<= nlstate ; i ++) {
5778: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5779: else fprintf(ficgp," %%*lf (%%*lf)");
5780: }
5781: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
5782: for (i=1; i<= nlstate ; i ++) {
5783: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5784: else fprintf(ficgp," %%*lf (%%*lf)");
5785: }
5786: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5787: if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
5788: /* 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); */
5789: fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */
5790: kl=0;
5791: for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
5792: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5793: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5794: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5795: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5796: vlv= nbcode[Tvaraff[k]][lv];
5797: kl++;
5798: /* 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 *\/ */
5799: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5800: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5801: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5802: if(k==cptcoveff){
1.220 brouard 5803: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
5804: 6+(cpt-1), cpt );
1.219 brouard 5805: }else{
1.220 brouard 5806: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
1.219 brouard 5807: kl++;
5808: }
5809: } /* end covariate */
5810: }
5811: fprintf(ficgp,"\nset out \n");
1.201 brouard 5812: } /* k1 */
5813: } /* cpt */
1.126 brouard 5814: /*2 eme*/
5815: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5816:
1.211 brouard 5817: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5818: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 brouard 5819: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5820: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5821: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5822: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5823: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 5824: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5825: }
5826: fprintf(ficgp,"\n#\n");
1.220 brouard 5827: if(invalidvarcomb[k1]){
5828: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5829: continue;
5830: }
1.219 brouard 5831:
5832: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5833: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5834: if(vpopbased==0)
5835: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5836: else
5837: fprintf(ficgp,"\nreplot ");
5838: for (i=1; i<= nlstate+1 ; i ++) {
5839: k=2*i;
5840: 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);
5841: for (j=1; j<= nlstate+1 ; j ++) {
5842: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5843: else fprintf(ficgp," %%*lf (%%*lf)");
5844: }
5845: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5846: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5847: 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);
5848: for (j=1; j<= nlstate+1 ; j ++) {
5849: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5850: else fprintf(ficgp," %%*lf (%%*lf)");
5851: }
5852: fprintf(ficgp,"\" t\"\" w l lt 0,");
5853: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5854: for (j=1; j<= nlstate+1 ; j ++) {
5855: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5856: else fprintf(ficgp," %%*lf (%%*lf)");
5857: }
5858: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5859: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5860: } /* state */
5861: } /* vpopbased */
5862: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
1.201 brouard 5863: } /* k1 */
1.219 brouard 5864:
5865:
1.126 brouard 5866: /*3eme*/
5867: for (k1=1; k1<= m ; k1 ++) {
1.220 brouard 5868:
1.126 brouard 5869: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5870: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5871: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.219 brouard 5872: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5873: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5874: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5875: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5876: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 5877: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5878: }
5879: fprintf(ficgp,"\n#\n");
1.220 brouard 5880: if(invalidvarcomb[k1]){
5881: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5882: continue;
5883: }
1.219 brouard 5884:
1.126 brouard 5885: /* k=2+nlstate*(2*cpt-2); */
5886: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5887: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5888: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5889: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5890: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
1.219 brouard 5891: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5892: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5893: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5894: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5895: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5896:
1.126 brouard 5897: */
5898: for (i=1; i< nlstate ; i ++) {
1.219 brouard 5899: 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);
5900: /* 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);*/
5901:
1.126 brouard 5902: }
1.201 brouard 5903: 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 5904: }
5905: }
5906:
1.220 brouard 5907: /* 4eme */
1.201 brouard 5908: /* Survival functions (period) from state i in state j by initial state i */
5909: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
1.220 brouard 5910:
1.201 brouard 5911: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5912: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5913: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 5914: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5915: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5916: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5917: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5918: vlv= nbcode[Tvaraff[k]][lv];
5919: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5920: }
5921: fprintf(ficgp,"\n#\n");
1.220 brouard 5922: if(invalidvarcomb[k1]){
5923: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5924: continue;
5925: }
5926:
1.201 brouard 5927: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5928: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 5929: set ter svg size 640, 480\n \
5930: unset log y\n \
1.201 brouard 5931: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5932: k=3;
1.201 brouard 5933: for (i=1; i<= nlstate ; i ++){
1.220 brouard 5934: if(i==1){
5935: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5936: }else{
5937: fprintf(ficgp,", '' ");
5938: }
5939: l=(nlstate+ndeath)*(i-1)+1;
5940: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5941: for (j=2; j<= nlstate+ndeath ; j ++)
5942: fprintf(ficgp,"+$%d",k+l+j-1);
5943: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
1.201 brouard 5944: } /* nlstate */
5945: fprintf(ficgp,"\nset out\n");
5946: } /* end cpt state*/
5947: } /* end covariate */
1.220 brouard 5948:
5949: /* 5eme */
1.201 brouard 5950: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5951: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5952: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
1.220 brouard 5953:
1.201 brouard 5954: 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);
1.211 brouard 5955: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 5956: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5957: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5958: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5959: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5960: vlv= nbcode[Tvaraff[k]][lv];
5961: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 5962: }
5963: fprintf(ficgp,"\n#\n");
1.220 brouard 5964: if(invalidvarcomb[k1]){
5965: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
5966: continue;
5967: }
5968:
1.201 brouard 5969: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5970: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
1.220 brouard 5971: set ter svg size 640, 480\n \
5972: unset log y\n \
1.201 brouard 5973: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5974: k=3;
1.201 brouard 5975: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 5976: if(j==1)
5977: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5978: else
5979: fprintf(ficgp,", '' ");
5980: l=(nlstate+ndeath)*(cpt-1) +j;
5981: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5982: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5983: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5984: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
1.201 brouard 5985: } /* nlstate */
5986: fprintf(ficgp,", '' ");
5987: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5988: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
1.220 brouard 5989: l=(nlstate+ndeath)*(cpt-1) +j;
5990: if(j < nlstate)
5991: fprintf(ficgp,"$%d +",k+l);
5992: else
5993: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
1.201 brouard 5994: }
5995: fprintf(ficgp,"\nset out\n");
5996: } /* end cpt state*/
5997: } /* end covariate */
1.220 brouard 5998:
5999: /* 6eme */
1.202 brouard 6000: /* CV preval stable (period) for each covariate */
1.211 brouard 6001: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 6002: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6003:
1.211 brouard 6004: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6005: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
1.220 brouard 6006: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6007: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6008: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6009: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6010: vlv= nbcode[Tvaraff[k]][lv];
6011: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.211 brouard 6012: }
6013: fprintf(ficgp,"\n#\n");
1.220 brouard 6014: if(invalidvarcomb[k1]){
6015: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6016: continue;
6017: }
1.211 brouard 6018:
1.201 brouard 6019: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 6020: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 6021: set ter svg size 640, 480\n\
1.126 brouard 6022: unset log y\n\
1.153 brouard 6023: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 6024: k=3; /* Offset */
1.153 brouard 6025: for (i=1; i<= nlstate ; i ++){
1.220 brouard 6026: if(i==1)
6027: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
6028: else
6029: fprintf(ficgp,", '' ");
6030: l=(nlstate+ndeath)*(i-1)+1;
6031: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
6032: for (j=2; j<= nlstate ; j ++)
6033: fprintf(ficgp,"+$%d",k+l+j-1);
6034: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
1.153 brouard 6035: } /* nlstate */
1.201 brouard 6036: fprintf(ficgp,"\nset out\n");
1.153 brouard 6037: } /* end cpt state*/
6038: } /* end covariate */
1.220 brouard 6039:
6040:
6041: /* 7eme */
1.218 brouard 6042: if(backcast == 1){
1.217 brouard 6043: /* CV back preval stable (period) for each covariate */
1.218 brouard 6044: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
6045: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.220 brouard 6046: fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
6047: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
6048: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
6049: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6050: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6051: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6052: vlv= nbcode[Tvaraff[k]][lv];
6053: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
6054: }
6055: fprintf(ficgp,"\n#\n");
6056: if(invalidvarcomb[k1]){
6057: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6058: continue;
6059: }
6060:
6061: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
6062: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
6063: set ter svg size 640, 480\n \
6064: unset log y\n \
1.218 brouard 6065: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.220 brouard 6066: k=3; /* Offset */
6067: for (i=1; i<= nlstate ; i ++){
6068: if(i==1)
6069: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
6070: else
6071: fprintf(ficgp,", '' ");
6072: /* l=(nlstate+ndeath)*(i-1)+1; */
6073: l=(nlstate+ndeath)*(cpt-1)+1;
6074: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
6075: /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
6076: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */
6077: /* for (j=2; j<= nlstate ; j ++) */
6078: /* fprintf(ficgp,"+$%d",k+l+j-1); */
6079: /* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
6080: fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
6081: } /* nlstate */
6082: fprintf(ficgp,"\nset out\n");
1.218 brouard 6083: } /* end cpt state*/
6084: } /* end covariate */
6085: } /* End if backcast */
6086:
1.220 brouard 6087: /* 8eme */
1.218 brouard 6088: if(prevfcast==1){
6089: /* Projection from cross-sectional to stable (period) for each covariate */
6090:
6091: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.211 brouard 6092: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.219 brouard 6093: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
6094: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
6095: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
6096: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6097: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6098: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
6099: vlv= nbcode[Tvaraff[k]][lv];
1.220 brouard 6100: fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
1.219 brouard 6101: }
6102: fprintf(ficgp,"\n#\n");
1.220 brouard 6103: if(invalidvarcomb[k1]){
6104: fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
6105: continue;
6106: }
1.219 brouard 6107:
6108: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
6109: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
6110: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
6111: set ter svg size 640, 480\n \
6112: unset log y\n \
6113: plot [%.f:%.f] ", ageminpar, agemaxpar);
6114: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
6115: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6116: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6117: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6118: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6119: if(i==1){
6120: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
6121: }else{
6122: fprintf(ficgp,",\\\n '' ");
6123: }
6124: if(cptcoveff ==0){ /* No covariate */
6125: ioffset=2; /* Age is in 2 */
6126: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6127: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6128: /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
6129: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
6130: fprintf(ficgp," u %d:(", ioffset);
6131: if(i==nlstate+1)
6132: fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \
6133: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6134: else
6135: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
6136: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6137: }else{ /* more than 2 covariates */
6138: if(cptcoveff ==1){
6139: ioffset=4; /* Age is in 4 */
6140: }else{
6141: ioffset=6; /* Age is in 6 */
6142: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
6143: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
6144: }
1.220 brouard 6145: fprintf(ficgp," u %d:(",ioffset);
1.219 brouard 6146: kl=0;
1.220 brouard 6147: strcpy(gplotcondition,"(");
6148: for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
1.219 brouard 6149: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
6150: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
6151: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
6152: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
1.220 brouard 6153: vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
6154: kl++;
6155: sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
1.219 brouard 6156: kl++;
1.220 brouard 6157: if(k <cptcoveff && cptcoveff>1)
6158: sprintf(gplotcondition+strlen(gplotcondition)," && ");
6159: }
6160: strcpy(gplotcondition+strlen(gplotcondition),")");
6161: /* 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 *\/ */
6162: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
6163: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
6164: /* '' 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*/
6165: if(i==nlstate+1){
6166: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \
6167: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
6168: }else{
6169: fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
6170: ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)*nlstate,i,cpt );
6171: }
1.219 brouard 6172: } /* end if covariate */
6173: } /* nlstate */
6174: fprintf(ficgp,"\nset out\n");
6175: } /* end cpt state*/
6176: } /* end covariate */
6177: } /* End if prevfcast */
6178:
1.211 brouard 6179:
1.219 brouard 6180: /* proba elementaires */
6181: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 6182: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 6183: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 6184: for(k=1; k <=(nlstate+ndeath); k++){
6185: if (k != i) {
1.187 brouard 6186: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 6187: for(j=1; j <=ncovmodel; j++){
1.187 brouard 6188: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 6189: jk++;
6190: }
1.187 brouard 6191: fprintf(ficgp,"\n");
1.126 brouard 6192: }
6193: }
6194: }
1.187 brouard 6195: fprintf(ficgp,"##############\n#\n");
6196:
1.145 brouard 6197: /*goto avoid;*/
1.200 brouard 6198: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 6199: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
6200: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
6201: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
6202: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
6203: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6204: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6205: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6206: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
6207: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
6208: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
6209: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
6210: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
6211: fprintf(ficgp,"#\n");
1.201 brouard 6212: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 6213: fprintf(ficgp,"# ng=%d\n",ng);
6214: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 6215: for(jk=1; jk <=m; jk++) {
1.187 brouard 6216: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 6217: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
6218: fprintf(ficgp,"\nset ter svg size 640, 480 ");
6219: if (ng==1){
6220: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
6221: fprintf(ficgp,"\nunset log y");
6222: }else if (ng==2){
6223: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
6224: fprintf(ficgp,"\nset log y");
6225: }else if (ng==3){
1.126 brouard 6226: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 6227: fprintf(ficgp,"\nset log y");
6228: }else
6229: fprintf(ficgp,"\nunset title ");
6230: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 6231: i=1;
6232: for(k2=1; k2<=nlstate; k2++) {
6233: k3=i;
6234: for(k=1; k<=(nlstate+ndeath); k++) {
6235: if (k != k2){
1.201 brouard 6236: switch( ng) {
6237: case 1:
1.187 brouard 6238: if(nagesqr==0)
1.201 brouard 6239: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 6240: else /* nagesqr =1 */
1.201 brouard 6241: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6242: break;
6243: case 2: /* ng=2 */
1.187 brouard 6244: if(nagesqr==0)
6245: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
6246: else /* nagesqr =1 */
1.201 brouard 6247: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
6248: break;
6249: case 3:
6250: if(nagesqr==0)
6251: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
6252: else /* nagesqr =1 */
6253: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
6254: break;
6255: }
1.141 brouard 6256: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 6257: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 6258: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
6259: if(ij <=cptcovage) { /* Bug valgrind */
6260: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 6261: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6262: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 6263: ij++;
6264: }
1.186 brouard 6265: }
6266: else
1.198 brouard 6267: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6268: }
1.217 brouard 6269: }else{
6270: i=i-ncovmodel;
6271: if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
6272: fprintf(ficgp," (1.");
6273: }
6274:
6275: if(ng != 1){
6276: fprintf(ficgp,")/(1");
1.126 brouard 6277:
1.217 brouard 6278: for(k1=1; k1 <=nlstate; k1++){
6279: if(nagesqr==0)
6280: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
6281: else /* nagesqr =1 */
6282: 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);
6283:
6284: ij=1;
6285: for(j=3; j <=ncovmodel-nagesqr; j++){
6286: if(ij <=cptcovage) { /* Bug valgrind */
6287: if((j-2)==Tage[ij]) { /* Bug valgrind */
6288: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
6289: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
6290: ij++;
1.197 brouard 6291: }
1.186 brouard 6292: }
1.217 brouard 6293: else
6294: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 6295: }
6296: fprintf(ficgp,")");
1.217 brouard 6297: }
6298: fprintf(ficgp,")");
6299: if(ng ==2)
6300: fprintf(ficgp," t \"p%d%d\" ", k2,k);
6301: else /* ng= 3 */
6302: fprintf(ficgp," t \"i%d%d\" ", k2,k);
6303: }else{ /* end ng <> 1 */
6304: if( k !=k2) /* logit p11 is hard to draw */
1.201 brouard 6305: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 6306: }
1.217 brouard 6307: if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
6308: fprintf(ficgp,",");
6309: if (ng == 1 && k!=k2 && (k+k2)!= (nlstate*2+ndeath))
6310: fprintf(ficgp,",");
6311: i=i+ncovmodel;
1.126 brouard 6312: } /* end k */
6313: } /* end k2 */
1.201 brouard 6314: fprintf(ficgp,"\n set out\n");
1.126 brouard 6315: } /* end jk */
6316: } /* end ng */
1.164 brouard 6317: /* avoid: */
1.126 brouard 6318: fflush(ficgp);
6319: } /* end gnuplot */
6320:
6321:
6322: /*************** Moving average **************/
1.219 brouard 6323: /* int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav, double bageout, double fageout){ */
1.218 brouard 6324: int movingaverage(double ***probs, double bage, double fage, double ***mobaverage, int mobilav){
6325:
1.126 brouard 6326: int i, cpt, cptcod;
6327: int modcovmax =1;
6328: int mobilavrange, mob;
1.219 brouard 6329: int iage=0;
6330:
6331: double sum=0.;
1.126 brouard 6332: double age;
1.218 brouard 6333: double *sumnewp, *sumnewm;
6334: double *agemingood, *agemaxgood; /* Currently identical for all covariates */
6335:
1.219 brouard 6336:
1.220 brouard 6337: /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
6338: /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
1.219 brouard 6339:
1.220 brouard 6340: sumnewp = vector(1,ncovcombmax);
6341: sumnewm = vector(1,ncovcombmax);
6342: agemingood = vector(1,ncovcombmax);
6343: agemaxgood = vector(1,ncovcombmax);
1.219 brouard 6344:
1.220 brouard 6345: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.219 brouard 6346: sumnewm[cptcod]=0.;
6347: sumnewp[cptcod]=0.;
6348: agemingood[cptcod]=0;
6349: agemaxgood[cptcod]=0;
6350: }
1.220 brouard 6351: if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
1.218 brouard 6352:
1.126 brouard 6353: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
6354: if(mobilav==1) mobilavrange=5; /* default */
6355: else mobilavrange=mobilav;
6356: for (age=bage; age<=fage; age++)
6357: for (i=1; i<=nlstate;i++)
1.220 brouard 6358: for (cptcod=1;cptcod<=ncovcombmax;cptcod++)
1.219 brouard 6359: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
1.126 brouard 6360: /* We keep the original values on the extreme ages bage, fage and for
6361: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
6362: we use a 5 terms etc. until the borders are no more concerned.
6363: */
6364: for (mob=3;mob <=mobilavrange;mob=mob+2){
6365: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
1.219 brouard 6366: for (i=1; i<=nlstate;i++){
1.220 brouard 6367: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.219 brouard 6368: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
6369: for (cpt=1;cpt<=(mob-1)/2;cpt++){
6370: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
6371: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
6372: }
6373: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
6374: }
6375: }
1.126 brouard 6376: }/* end age */
6377: }/* end mob */
1.218 brouard 6378: }else
6379: return -1;
1.220 brouard 6380: for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
1.218 brouard 6381: /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
1.219 brouard 6382: agemingood[cptcod]=fage-(mob-1)/2;
1.218 brouard 6383: for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
6384: sumnewm[cptcod]=0.;
6385: for (i=1; i<=nlstate;i++){
6386: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6387: }
6388: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
1.219 brouard 6389: agemingood[cptcod]=age;
1.218 brouard 6390: }else{ /* bad */
1.219 brouard 6391: for (i=1; i<=nlstate;i++){
6392: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6393: } /* i */
1.218 brouard 6394: } /* end bad */
6395: }/* age */
1.219 brouard 6396: sum=0.;
6397: for (i=1; i<=nlstate;i++){
6398: sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
1.218 brouard 6399: }
1.219 brouard 6400: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6401: 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);
6402: /* for (i=1; i<=nlstate;i++){ */
6403: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6404: /* } /\* i *\/ */
6405: } /* end bad */
6406: /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
6407: /* From youngest, finding the oldest wrong */
6408: agemaxgood[cptcod]=bage+(mob-1)/2;
6409: for (age=bage+(mob-1)/2; age<=fage; age++){
6410: sumnewm[cptcod]=0.;
6411: for (i=1; i<=nlstate;i++){
6412: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6413: }
6414: if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
6415: agemaxgood[cptcod]=age;
6416: }else{ /* bad */
6417: for (i=1; i<=nlstate;i++){
6418: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6419: } /* i */
6420: } /* end bad */
6421: }/* age */
6422: sum=0.;
6423: for (i=1; i<=nlstate;i++){
6424: sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6425: }
6426: if(fabs(sum - 1.) > 1.e-3) { /* bad */
6427: 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);
6428: /* for (i=1; i<=nlstate;i++){ */
6429: /* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
6430: /* } /\* i *\/ */
6431: } /* end bad */
6432:
6433: for (age=bage; age<=fage; age++){
6434: printf("%d %d ", cptcod, (int)age);
6435: sumnewp[cptcod]=0.;
6436: sumnewm[cptcod]=0.;
6437: for (i=1; i<=nlstate;i++){
6438: sumnewp[cptcod]+=probs[(int)age][i][cptcod];
6439: sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
6440: /* printf("%.4f %.4f ",probs[(int)age][i][cptcod], mobaverage[(int)age][i][cptcod]); */
6441: }
6442: /* printf("%.4f %.4f \n",sumnewp[cptcod], sumnewm[cptcod]); */
6443: }
6444: /* printf("\n"); */
6445: /* } */
1.218 brouard 6446: /* brutal averaging */
6447: for (i=1; i<=nlstate;i++){
6448: for (age=1; age<=bage; age++){
1.219 brouard 6449: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
6450: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
1.218 brouard 6451: }
6452: for (age=fage; age<=AGESUP; age++){
1.219 brouard 6453: mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
6454: /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */
1.218 brouard 6455: }
6456: } /* end i status */
6457: for (i=nlstate+1; i<=nlstate+ndeath;i++){
6458: for (age=1; age<=AGESUP; age++){
1.219 brouard 6459: /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/
6460: mobaverage[(int)age][i][cptcod]=0.;
1.218 brouard 6461: }
6462: }
6463: }/* end cptcod */
1.220 brouard 6464: free_vector(sumnewm,1, ncovcombmax);
6465: free_vector(sumnewp,1, ncovcombmax);
6466: free_vector(agemaxgood,1, ncovcombmax);
6467: free_vector(agemingood,1, ncovcombmax);
1.126 brouard 6468: return 0;
6469: }/* End movingaverage */
1.218 brouard 6470:
1.126 brouard 6471:
6472: /************** Forecasting ******************/
1.169 brouard 6473: 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 6474: /* proj1, year, month, day of starting projection
6475: agemin, agemax range of age
6476: dateprev1 dateprev2 range of dates during which prevalence is computed
6477: anproj2 year of en of projection (same day and month as proj1).
6478: */
1.164 brouard 6479: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 6480: double agec; /* generic age */
6481: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
6482: double *popeffectif,*popcount;
6483: double ***p3mat;
1.218 brouard 6484: /* double ***mobaverage; */
1.126 brouard 6485: char fileresf[FILENAMELENGTH];
6486:
6487: agelim=AGESUP;
1.211 brouard 6488: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
6489: in each health status at the date of interview (if between dateprev1 and dateprev2).
6490: We still use firstpass and lastpass as another selection.
6491: */
1.214 brouard 6492: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
6493: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 6494:
1.201 brouard 6495: strcpy(fileresf,"F_");
6496: strcat(fileresf,fileresu);
1.126 brouard 6497: if((ficresf=fopen(fileresf,"w"))==NULL) {
6498: printf("Problem with forecast resultfile: %s\n", fileresf);
6499: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
6500: }
1.215 brouard 6501: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
6502: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 6503:
6504: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6505:
6506:
6507: stepsize=(int) (stepm+YEARM-1)/YEARM;
6508: if (stepm<=12) stepsize=1;
6509: if(estepm < stepm){
6510: printf ("Problem %d lower than %d\n",estepm, stepm);
6511: }
6512: else hstepm=estepm;
6513:
6514: hstepm=hstepm/stepm;
6515: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
6516: fractional in yp1 */
6517: anprojmean=yp;
6518: yp2=modf((yp1*12),&yp);
6519: mprojmean=yp;
6520: yp1=modf((yp2*30.5),&yp);
6521: jprojmean=yp;
6522: if(jprojmean==0) jprojmean=1;
6523: if(mprojmean==0) jprojmean=1;
6524:
6525: i1=cptcoveff;
6526: if (cptcovn < 1){i1=1;}
6527:
6528: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
6529:
6530: fprintf(ficresf,"#****** Routine prevforecast **\n");
6531:
6532: /* if (h==(int)(YEARM*yearp)){ */
6533: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
6534: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
6535: k=k+1;
1.211 brouard 6536: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 6537: for(j=1;j<=cptcoveff;j++) {
1.219 brouard 6538: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6539: }
1.211 brouard 6540: fprintf(ficresf," yearproj age");
1.126 brouard 6541: for(j=1; j<=nlstate+ndeath;j++){
1.219 brouard 6542: for(i=1; i<=nlstate;i++)
1.126 brouard 6543: fprintf(ficresf," p%d%d",i,j);
1.219 brouard 6544: fprintf(ficresf," wp.%d",j);
1.126 brouard 6545: }
1.217 brouard 6546: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
1.219 brouard 6547: fprintf(ficresf,"\n");
6548: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
6549: for (agec=fage; agec>=(ageminpar-1); agec--){
6550: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
6551: nhstepm = nhstepm/hstepm;
6552: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6553: oldm=oldms;savm=savms;
6554: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
6555:
6556: for (h=0; h<=nhstepm; h++){
6557: if (h*hstepm/YEARM*stepm ==yearp) {
1.126 brouard 6558: fprintf(ficresf,"\n");
6559: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6560: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 6561: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
6562: }
6563: for(j=1; j<=nlstate+ndeath;j++) {
6564: ppij=0.;
6565: for(i=1; i<=nlstate;i++) {
6566: if (mobilav==1)
6567: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
6568: else {
6569: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
6570: }
6571: if (h*hstepm/YEARM*stepm== yearp) {
6572: fprintf(ficresf," %.3f", p3mat[i][j][h]);
6573: }
6574: } /* end i */
6575: if (h*hstepm/YEARM*stepm==yearp) {
6576: fprintf(ficresf," %.3f", ppij);
6577: }
6578: }/* end j */
6579: } /* end h */
6580: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6581: } /* end agec */
1.126 brouard 6582: } /* end yearp */
6583: } /* end cptcod */
6584: } /* end cptcov */
1.219 brouard 6585:
1.126 brouard 6586: fclose(ficresf);
1.215 brouard 6587: printf("End of Computing forecasting \n");
6588: fprintf(ficlog,"End of Computing forecasting\n");
6589:
1.126 brouard 6590: }
6591:
1.218 brouard 6592: /* /\************** Back Forecasting ******************\/ */
6593: /* 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){ */
6594: /* /\* back1, year, month, day of starting backection */
6595: /* agemin, agemax range of age */
6596: /* dateprev1 dateprev2 range of dates during which prevalence is computed */
6597: /* anback2 year of en of backection (same day and month as back1). */
6598: /* *\/ */
6599: /* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
6600: /* double agec; /\* generic age *\/ */
6601: /* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
6602: /* double *popeffectif,*popcount; */
6603: /* double ***p3mat; */
6604: /* /\* double ***mobaverage; *\/ */
6605: /* char fileresfb[FILENAMELENGTH]; */
6606:
6607: /* agelim=AGESUP; */
6608: /* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
6609: /* in each health status at the date of interview (if between dateprev1 and dateprev2). */
6610: /* We still use firstpass and lastpass as another selection. */
6611: /* *\/ */
6612: /* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */
6613: /* /\* firstpass, lastpass, stepm, weightopt, model); *\/ */
6614: /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
6615:
6616: /* strcpy(fileresfb,"FB_"); */
6617: /* strcat(fileresfb,fileresu); */
6618: /* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
6619: /* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
6620: /* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
6621: /* } */
6622: /* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6623: /* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
6624:
6625: /* if (cptcoveff==0) ncodemax[cptcoveff]=1; */
6626:
6627: /* /\* if (mobilav!=0) { *\/ */
6628: /* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6629: /* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */
6630: /* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6631: /* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */
6632: /* /\* } *\/ */
6633: /* /\* } *\/ */
6634:
6635: /* stepsize=(int) (stepm+YEARM-1)/YEARM; */
6636: /* if (stepm<=12) stepsize=1; */
6637: /* if(estepm < stepm){ */
6638: /* printf ("Problem %d lower than %d\n",estepm, stepm); */
6639: /* } */
6640: /* else hstepm=estepm; */
6641:
6642: /* hstepm=hstepm/stepm; */
6643: /* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
6644: /* fractional in yp1 *\/ */
6645: /* anprojmean=yp; */
6646: /* yp2=modf((yp1*12),&yp); */
6647: /* mprojmean=yp; */
6648: /* yp1=modf((yp2*30.5),&yp); */
6649: /* jprojmean=yp; */
6650: /* if(jprojmean==0) jprojmean=1; */
6651: /* if(mprojmean==0) jprojmean=1; */
6652:
6653: /* i1=cptcoveff; */
6654: /* if (cptcovn < 1){i1=1;} */
1.217 brouard 6655:
1.218 brouard 6656: /* fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); */
1.217 brouard 6657:
1.218 brouard 6658: /* fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */
6659:
6660: /* /\* if (h==(int)(YEARM*yearp)){ *\/ */
6661: /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
6662: /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
6663: /* k=k+1; */
6664: /* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
6665: /* for(j=1;j<=cptcoveff;j++) { */
6666: /* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6667: /* } */
6668: /* fprintf(ficresfb," yearbproj age"); */
6669: /* for(j=1; j<=nlstate+ndeath;j++){ */
6670: /* for(i=1; i<=nlstate;i++) */
6671: /* fprintf(ficresfb," p%d%d",i,j); */
6672: /* fprintf(ficresfb," p.%d",j); */
6673: /* } */
6674: /* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
6675: /* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { *\/ */
6676: /* fprintf(ficresfb,"\n"); */
6677: /* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
6678: /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
6679: /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
6680: /* nhstepm = nhstepm/hstepm; */
6681: /* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6682: /* oldm=oldms;savm=savms; */
6683: /* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
6684: /* for (h=0; h<=nhstepm; h++){ */
6685: /* if (h*hstepm/YEARM*stepm ==yearp) { */
6686: /* fprintf(ficresfb,"\n"); */
6687: /* for(j=1;j<=cptcoveff;j++) */
6688: /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
6689: /* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */
6690: /* } */
6691: /* for(j=1; j<=nlstate+ndeath;j++) { */
6692: /* ppij=0.; */
6693: /* for(i=1; i<=nlstate;i++) { */
6694: /* if (mobilav==1) */
6695: /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */
6696: /* else { */
6697: /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */
6698: /* } */
6699: /* if (h*hstepm/YEARM*stepm== yearp) { */
6700: /* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
6701: /* } */
6702: /* } /\* end i *\/ */
6703: /* if (h*hstepm/YEARM*stepm==yearp) { */
6704: /* fprintf(ficresfb," %.3f", ppij); */
6705: /* } */
6706: /* }/\* end j *\/ */
6707: /* } /\* end h *\/ */
6708: /* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
6709: /* } /\* end agec *\/ */
6710: /* } /\* end yearp *\/ */
6711: /* } /\* end cptcod *\/ */
6712: /* } /\* end cptcov *\/ */
6713:
6714: /* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
6715:
6716: /* fclose(ficresfb); */
6717: /* printf("End of Computing Back forecasting \n"); */
6718: /* fprintf(ficlog,"End of Computing Back forecasting\n"); */
1.217 brouard 6719:
1.218 brouard 6720: /* } */
1.217 brouard 6721:
1.126 brouard 6722: /************** Forecasting *****not tested NB*************/
1.169 brouard 6723: void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
1.126 brouard 6724:
6725: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
6726: int *popage;
6727: double calagedatem, agelim, kk1, kk2;
6728: double *popeffectif,*popcount;
6729: double ***p3mat,***tabpop,***tabpopprev;
1.218 brouard 6730: /* double ***mobaverage; */
1.126 brouard 6731: char filerespop[FILENAMELENGTH];
6732:
6733: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6734: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6735: agelim=AGESUP;
6736: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
6737:
6738: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6739:
6740:
1.201 brouard 6741: strcpy(filerespop,"POP_");
6742: strcat(filerespop,fileresu);
1.126 brouard 6743: if((ficrespop=fopen(filerespop,"w"))==NULL) {
6744: printf("Problem with forecast resultfile: %s\n", filerespop);
6745: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
6746: }
6747: printf("Computing forecasting: result on file '%s' \n", filerespop);
6748: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
6749:
6750: if (cptcoveff==0) ncodemax[cptcoveff]=1;
6751:
1.218 brouard 6752: /* if (mobilav!=0) { */
6753: /* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6754: /* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */
6755: /* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); */
6756: /* printf(" Error in movingaverage mobilav=%d\n",mobilav); */
6757: /* } */
6758: /* } */
1.126 brouard 6759:
6760: stepsize=(int) (stepm+YEARM-1)/YEARM;
6761: if (stepm<=12) stepsize=1;
6762:
6763: agelim=AGESUP;
6764:
6765: hstepm=1;
6766: hstepm=hstepm/stepm;
1.218 brouard 6767:
1.126 brouard 6768: if (popforecast==1) {
6769: if((ficpop=fopen(popfile,"r"))==NULL) {
6770: printf("Problem with population file : %s\n",popfile);exit(0);
6771: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
6772: }
6773: popage=ivector(0,AGESUP);
6774: popeffectif=vector(0,AGESUP);
6775: popcount=vector(0,AGESUP);
6776:
6777: i=1;
6778: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
1.218 brouard 6779:
1.126 brouard 6780: imx=i;
6781: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
6782: }
1.218 brouard 6783:
1.126 brouard 6784: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
1.218 brouard 6785: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
1.126 brouard 6786: k=k+1;
6787: fprintf(ficrespop,"\n#******");
6788: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6789: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 6790: }
6791: fprintf(ficrespop,"******\n");
6792: fprintf(ficrespop,"# Age");
6793: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
6794: if (popforecast==1) fprintf(ficrespop," [Population]");
6795:
6796: for (cpt=0; cpt<=0;cpt++) {
6797: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6798:
1.218 brouard 6799: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
1.126 brouard 6800: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6801: nhstepm = nhstepm/hstepm;
6802:
6803: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6804: oldm=oldms;savm=savms;
6805: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
1.218 brouard 6806:
1.126 brouard 6807: for (h=0; h<=nhstepm; h++){
6808: if (h==(int) (calagedatem+YEARM*cpt)) {
6809: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6810: }
6811: for(j=1; j<=nlstate+ndeath;j++) {
6812: kk1=0.;kk2=0;
6813: for(i=1; i<=nlstate;i++) {
6814: if (mobilav==1)
6815: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
6816: else {
6817: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
6818: }
6819: }
6820: if (h==(int)(calagedatem+12*cpt)){
6821: tabpop[(int)(agedeb)][j][cptcod]=kk1;
1.218 brouard 6822: /*fprintf(ficrespop," %.3f", kk1);
6823: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
1.126 brouard 6824: }
6825: }
6826: for(i=1; i<=nlstate;i++){
6827: kk1=0.;
1.218 brouard 6828: for(j=1; j<=nlstate;j++){
6829: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
6830: }
6831: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
1.126 brouard 6832: }
1.218 brouard 6833:
6834: if (h==(int)(calagedatem+12*cpt))
6835: for(j=1; j<=nlstate;j++)
6836: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
1.126 brouard 6837: }
6838: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6839: }
6840: }
1.218 brouard 6841:
6842: /******/
6843:
1.126 brouard 6844: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
6845: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
6846: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
6847: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
6848: nhstepm = nhstepm/hstepm;
6849:
6850: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6851: oldm=oldms;savm=savms;
6852: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6853: for (h=0; h<=nhstepm; h++){
6854: if (h==(int) (calagedatem+YEARM*cpt)) {
6855: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
6856: }
6857: for(j=1; j<=nlstate+ndeath;j++) {
6858: kk1=0.;kk2=0;
6859: for(i=1; i<=nlstate;i++) {
6860: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
6861: }
6862: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
6863: }
6864: }
6865: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6866: }
6867: }
1.218 brouard 6868: }
1.126 brouard 6869: }
1.218 brouard 6870:
6871: /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
6872:
1.126 brouard 6873: if (popforecast==1) {
6874: free_ivector(popage,0,AGESUP);
6875: free_vector(popeffectif,0,AGESUP);
6876: free_vector(popcount,0,AGESUP);
6877: }
6878: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6879: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6880: fclose(ficrespop);
6881: } /* End of popforecast */
1.218 brouard 6882:
1.126 brouard 6883: int fileappend(FILE *fichier, char *optionfich)
6884: {
6885: if((fichier=fopen(optionfich,"a"))==NULL) {
6886: printf("Problem with file: %s\n", optionfich);
6887: fprintf(ficlog,"Problem with file: %s\n", optionfich);
6888: return (0);
6889: }
6890: fflush(fichier);
6891: return (1);
6892: }
6893:
6894:
6895: /**************** function prwizard **********************/
6896: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
6897: {
6898:
6899: /* Wizard to print covariance matrix template */
6900:
1.164 brouard 6901: char ca[32], cb[32];
6902: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 6903: int numlinepar;
6904:
6905: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6906: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6907: for(i=1; i <=nlstate; i++){
6908: jj=0;
6909: for(j=1; j <=nlstate+ndeath; j++){
6910: if(j==i) continue;
6911: jj++;
6912: /*ca[0]= k+'a'-1;ca[1]='\0';*/
6913: printf("%1d%1d",i,j);
6914: fprintf(ficparo,"%1d%1d",i,j);
6915: for(k=1; k<=ncovmodel;k++){
6916: /* printf(" %lf",param[i][j][k]); */
6917: /* fprintf(ficparo," %lf",param[i][j][k]); */
6918: printf(" 0.");
6919: fprintf(ficparo," 0.");
6920: }
6921: printf("\n");
6922: fprintf(ficparo,"\n");
6923: }
6924: }
6925: printf("# Scales (for hessian or gradient estimation)\n");
6926: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6927: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6928: for(i=1; i <=nlstate; i++){
6929: jj=0;
6930: for(j=1; j <=nlstate+ndeath; j++){
6931: if(j==i) continue;
6932: jj++;
6933: fprintf(ficparo,"%1d%1d",i,j);
6934: printf("%1d%1d",i,j);
6935: fflush(stdout);
6936: for(k=1; k<=ncovmodel;k++){
6937: /* printf(" %le",delti3[i][j][k]); */
6938: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6939: printf(" 0.");
6940: fprintf(ficparo," 0.");
6941: }
6942: numlinepar++;
6943: printf("\n");
6944: fprintf(ficparo,"\n");
6945: }
6946: }
6947: printf("# Covariance matrix\n");
6948: /* # 121 Var(a12)\n\ */
6949: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6950: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6951: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6952: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6953: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6954: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6955: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6956: fflush(stdout);
6957: fprintf(ficparo,"# Covariance matrix\n");
6958: /* # 121 Var(a12)\n\ */
6959: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6960: /* # ...\n\ */
6961: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6962:
6963: for(itimes=1;itimes<=2;itimes++){
6964: jj=0;
6965: for(i=1; i <=nlstate; i++){
6966: for(j=1; j <=nlstate+ndeath; j++){
6967: if(j==i) continue;
6968: for(k=1; k<=ncovmodel;k++){
6969: jj++;
6970: ca[0]= k+'a'-1;ca[1]='\0';
6971: if(itimes==1){
6972: printf("#%1d%1d%d",i,j,k);
6973: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6974: }else{
6975: printf("%1d%1d%d",i,j,k);
6976: fprintf(ficparo,"%1d%1d%d",i,j,k);
6977: /* printf(" %.5le",matcov[i][j]); */
6978: }
6979: ll=0;
6980: for(li=1;li <=nlstate; li++){
6981: for(lj=1;lj <=nlstate+ndeath; lj++){
6982: if(lj==li) continue;
6983: for(lk=1;lk<=ncovmodel;lk++){
6984: ll++;
6985: if(ll<=jj){
6986: cb[0]= lk +'a'-1;cb[1]='\0';
6987: if(ll<jj){
6988: if(itimes==1){
6989: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6990: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6991: }else{
6992: printf(" 0.");
6993: fprintf(ficparo," 0.");
6994: }
6995: }else{
6996: if(itimes==1){
6997: printf(" Var(%s%1d%1d)",ca,i,j);
6998: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6999: }else{
7000: printf(" 0.");
7001: fprintf(ficparo," 0.");
7002: }
7003: }
7004: }
7005: } /* end lk */
7006: } /* end lj */
7007: } /* end li */
7008: printf("\n");
7009: fprintf(ficparo,"\n");
7010: numlinepar++;
7011: } /* end k*/
7012: } /*end j */
7013: } /* end i */
7014: } /* end itimes */
7015:
7016: } /* end of prwizard */
7017: /******************* Gompertz Likelihood ******************************/
7018: double gompertz(double x[])
7019: {
7020: double A,B,L=0.0,sump=0.,num=0.;
7021: int i,n=0; /* n is the size of the sample */
7022:
1.220 brouard 7023: for (i=1;i<=imx ; i++) {
1.126 brouard 7024: sump=sump+weight[i];
7025: /* sump=sump+1;*/
7026: num=num+1;
7027: }
7028:
7029:
7030: /* for (i=0; i<=imx; i++)
7031: 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]);*/
7032:
7033: for (i=1;i<=imx ; i++)
7034: {
7035: if (cens[i] == 1 && wav[i]>1)
7036: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
7037:
7038: if (cens[i] == 0 && wav[i]>1)
7039: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
7040: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
7041:
7042: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7043: if (wav[i] > 1 ) { /* ??? */
7044: L=L+A*weight[i];
7045: /* 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]);*/
7046: }
7047: }
7048:
7049: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7050:
7051: return -2*L*num/sump;
7052: }
7053:
1.136 brouard 7054: #ifdef GSL
7055: /******************* Gompertz_f Likelihood ******************************/
7056: double gompertz_f(const gsl_vector *v, void *params)
7057: {
7058: double A,B,LL=0.0,sump=0.,num=0.;
7059: double *x= (double *) v->data;
7060: int i,n=0; /* n is the size of the sample */
7061:
7062: for (i=0;i<=imx-1 ; i++) {
7063: sump=sump+weight[i];
7064: /* sump=sump+1;*/
7065: num=num+1;
7066: }
7067:
7068:
7069: /* for (i=0; i<=imx; i++)
7070: 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]);*/
7071: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
7072: for (i=1;i<=imx ; i++)
7073: {
7074: if (cens[i] == 1 && wav[i]>1)
7075: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
7076:
7077: if (cens[i] == 0 && wav[i]>1)
7078: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
7079: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
7080:
7081: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
7082: if (wav[i] > 1 ) { /* ??? */
7083: LL=LL+A*weight[i];
7084: /* 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]);*/
7085: }
7086: }
7087:
7088: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
7089: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
7090:
7091: return -2*LL*num/sump;
7092: }
7093: #endif
7094:
1.126 brouard 7095: /******************* Printing html file ***********/
1.201 brouard 7096: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 7097: int lastpass, int stepm, int weightopt, char model[],\
7098: int imx, double p[],double **matcov,double agemortsup){
7099: int i,k;
7100:
7101: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
7102: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
7103: for (i=1;i<=2;i++)
7104: 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 7105: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 7106: fprintf(fichtm,"</ul>");
7107:
7108: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
7109:
7110: 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>");
7111:
7112: for (k=agegomp;k<(agemortsup-2);k++)
7113: 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]);
7114:
7115:
7116: fflush(fichtm);
7117: }
7118:
7119: /******************* Gnuplot file **************/
1.201 brouard 7120: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 7121:
7122: char dirfileres[132],optfileres[132];
1.164 brouard 7123:
1.126 brouard 7124: int ng;
7125:
7126:
7127: /*#ifdef windows */
7128: fprintf(ficgp,"cd \"%s\" \n",pathc);
7129: /*#endif */
7130:
7131:
7132: strcpy(dirfileres,optionfilefiname);
7133: strcpy(optfileres,"vpl");
1.199 brouard 7134: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 7135: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 7136: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 7137: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 7138: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
7139:
7140: }
7141:
1.136 brouard 7142: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
7143: {
1.126 brouard 7144:
1.136 brouard 7145: /*-------- data file ----------*/
7146: FILE *fic;
7147: char dummy[]=" ";
1.164 brouard 7148: int i=0, j=0, n=0;
1.136 brouard 7149: int linei, month, year,iout;
7150: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 7151: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 7152: char *stratrunc;
7153: int lstra;
1.126 brouard 7154:
7155:
1.136 brouard 7156: if((fic=fopen(datafile,"r"))==NULL) {
1.218 brouard 7157: printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
7158: fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
1.136 brouard 7159: }
1.126 brouard 7160:
1.136 brouard 7161: i=1;
7162: linei=0;
7163: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
7164: linei=linei+1;
7165: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
7166: if(line[j] == '\t')
7167: line[j] = ' ';
7168: }
7169: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
7170: ;
7171: };
7172: line[j+1]=0; /* Trims blanks at end of line */
7173: if(line[0]=='#'){
7174: fprintf(ficlog,"Comment line\n%s\n",line);
7175: printf("Comment line\n%s\n",line);
7176: continue;
7177: }
7178: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 7179: strcpy(line, linetmp);
1.136 brouard 7180:
1.126 brouard 7181:
1.136 brouard 7182: for (j=maxwav;j>=1;j--){
1.137 brouard 7183: cutv(stra, strb, line, ' ');
1.136 brouard 7184: if(strb[0]=='.') { /* Missing status */
7185: lval=-1;
7186: }else{
7187: errno=0;
7188: lval=strtol(strb,&endptr,10);
7189: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
7190: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7191: 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);
7192: 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);
1.136 brouard 7193: return 1;
7194: }
7195: }
7196: s[j][i]=lval;
7197:
7198: strcpy(line,stra);
7199: cutv(stra, strb,line,' ');
1.169 brouard 7200: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7201: }
1.169 brouard 7202: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7203: month=99;
7204: year=9999;
7205: }else{
1.141 brouard 7206: 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);
7207: 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);
1.136 brouard 7208: return 1;
7209: }
7210: anint[j][i]= (double) year;
7211: mint[j][i]= (double)month;
7212: strcpy(line,stra);
7213: } /* ENd Waves */
7214:
7215: cutv(stra, strb,line,' ');
1.169 brouard 7216: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7217: }
1.169 brouard 7218: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 7219: month=99;
7220: year=9999;
7221: }else{
1.141 brouard 7222: 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);
7223: 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);
1.136 brouard 7224: return 1;
7225: }
7226: andc[i]=(double) year;
7227: moisdc[i]=(double) month;
7228: strcpy(line,stra);
7229:
7230: cutv(stra, strb,line,' ');
1.169 brouard 7231: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 7232: }
1.169 brouard 7233: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 7234: month=99;
7235: year=9999;
7236: }else{
1.141 brouard 7237: 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);
7238: 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);
1.136 brouard 7239: return 1;
7240: }
7241: if (year==9999) {
1.141 brouard 7242: 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);
7243: 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);
1.136 brouard 7244: return 1;
1.126 brouard 7245:
1.136 brouard 7246: }
7247: annais[i]=(double)(year);
7248: moisnais[i]=(double)(month);
7249: strcpy(line,stra);
7250:
7251: cutv(stra, strb,line,' ');
7252: errno=0;
7253: dval=strtod(strb,&endptr);
7254: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7255: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
7256: 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 7257: fflush(ficlog);
7258: return 1;
7259: }
7260: weight[i]=dval;
7261: strcpy(line,stra);
7262:
7263: for (j=ncovcol;j>=1;j--){
7264: cutv(stra, strb,line,' ');
7265: if(strb[0]=='.') { /* Missing status */
7266: lval=-1;
7267: }else{
7268: errno=0;
7269: lval=strtol(strb,&endptr,10);
7270: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 7271: 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);
7272: 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);
1.136 brouard 7273: return 1;
7274: }
7275: }
7276: if(lval <-1 || lval >1){
1.141 brouard 7277: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7278: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7279: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7280: For example, for multinomial values like 1, 2 and 3,\n \
7281: build V1=0 V2=0 for the reference value (1),\n \
7282: V1=1 V2=0 for (2) \n \
7283: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7284: output of IMaCh is often meaningless.\n \
7285: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 7286: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 7287: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
7288: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
7289: For example, for multinomial values like 1, 2 and 3,\n \
7290: build V1=0 V2=0 for the reference value (1),\n \
7291: V1=1 V2=0 for (2) \n \
7292: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
7293: output of IMaCh is often meaningless.\n \
7294: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
7295: return 1;
7296: }
7297: covar[j][i]=(double)(lval);
7298: strcpy(line,stra);
7299: }
7300: lstra=strlen(stra);
7301:
7302: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
7303: stratrunc = &(stra[lstra-9]);
7304: num[i]=atol(stratrunc);
7305: }
7306: else
7307: num[i]=atol(stra);
7308: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
7309: 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;}*/
7310:
7311: i=i+1;
7312: } /* End loop reading data */
1.126 brouard 7313:
1.136 brouard 7314: *imax=i-1; /* Number of individuals */
7315: fclose(fic);
7316:
7317: return (0);
1.164 brouard 7318: /* endread: */
1.136 brouard 7319: printf("Exiting readdata: ");
7320: fclose(fic);
7321: return (1);
1.126 brouard 7322:
7323:
7324:
1.136 brouard 7325: }
1.145 brouard 7326: void removespace(char *str) {
7327: char *p1 = str, *p2 = str;
7328: do
7329: while (*p2 == ' ')
7330: p2++;
1.169 brouard 7331: while (*p1++ == *p2++);
1.145 brouard 7332: }
7333:
7334: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 7335: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
7336: * - nagesqr = 1 if age*age in the model, otherwise 0.
7337: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
7338: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 7339: * - cptcovage number of covariates with age*products =2
7340: * - cptcovs number of simple covariates
7341: * - 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
7342: * which is a new column after the 9 (ncovcol) variables.
7343: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
7344: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
7345: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
7346: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
7347: */
1.136 brouard 7348: {
1.145 brouard 7349: int i, j, k, ks;
1.164 brouard 7350: int j1, k1, k2;
1.136 brouard 7351: char modelsav[80];
1.145 brouard 7352: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 7353: char *strpt;
1.136 brouard 7354:
1.145 brouard 7355: /*removespace(model);*/
1.136 brouard 7356: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 7357: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 7358: if (strstr(model,"AGE") !=0){
1.192 brouard 7359: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
7360: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 7361: return 1;
7362: }
1.141 brouard 7363: if (strstr(model,"v") !=0){
7364: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
7365: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
7366: return 1;
7367: }
1.187 brouard 7368: strcpy(modelsav,model);
7369: if ((strpt=strstr(model,"age*age")) !=0){
7370: printf(" strpt=%s, model=%s\n",strpt, model);
7371: if(strpt != model){
7372: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7373: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7374: corresponding column of parameters.\n",model);
7375: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 7376: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 7377: corresponding column of parameters.\n",model); fflush(ficlog);
7378: return 1;
7379: }
7380:
7381: nagesqr=1;
7382: if (strstr(model,"+age*age") !=0)
7383: substrchaine(modelsav, model, "+age*age");
7384: else if (strstr(model,"age*age+") !=0)
7385: substrchaine(modelsav, model, "age*age+");
7386: else
7387: substrchaine(modelsav, model, "age*age");
7388: }else
7389: nagesqr=0;
7390: if (strlen(modelsav) >1){
7391: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
7392: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
7393: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
7394: cptcovt= j+1; /* Number of total covariates in the model, not including
7395: * cst, age and age*age
7396: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
7397: /* including age products which are counted in cptcovage.
7398: * but the covariates which are products must be treated
7399: * separately: ncovn=4- 2=2 (V1+V3). */
7400: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
7401: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
7402:
7403:
7404: /* Design
7405: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
7406: * < ncovcol=8 >
7407: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
7408: * k= 1 2 3 4 5 6 7 8
7409: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
7410: * covar[k,i], value of kth covariate if not including age for individual i:
7411: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
7412: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
7413: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
7414: * Tage[++cptcovage]=k
7415: * if products, new covar are created after ncovcol with k1
7416: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
7417: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
7418: * 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
7419: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
7420: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
7421: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
7422: * < ncovcol=8 >
7423: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
7424: * k= 1 2 3 4 5 6 7 8 9 10 11 12
7425: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
7426: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7427: * p Tprod[1]@2={ 6, 5}
7428: *p Tvard[1][1]@4= {7, 8, 5, 6}
7429: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
7430: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
7431: *How to reorganize?
7432: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
7433: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
7434: * {2, 1, 4, 8, 5, 6, 3, 7}
7435: * Struct []
7436: */
1.145 brouard 7437:
1.187 brouard 7438: /* This loop fills the array Tvar from the string 'model'.*/
7439: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
7440: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
7441: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
7442: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
7443: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
7444: /* k=1 Tvar[1]=2 (from V2) */
7445: /* k=5 Tvar[5] */
7446: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 7447: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 7448: /* } */
1.198 brouard 7449: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 7450: /*
7451: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
7452: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 7453: Tvar[k]=0;
1.187 brouard 7454: cptcovage=0;
7455: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
7456: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
7457: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
7458: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
7459: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
7460: /*scanf("%d",i);*/
7461: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
7462: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
7463: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
7464: /* covar is not filled and then is empty */
7465: cptcovprod--;
7466: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
7467: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
7468: cptcovage++; /* Sums the number of covariates which include age as a product */
7469: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
7470: /*printf("stre=%s ", stre);*/
7471: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
7472: cptcovprod--;
7473: cutl(stre,strb,strc,'V');
7474: Tvar[k]=atoi(stre);
7475: cptcovage++;
7476: Tage[cptcovage]=k;
7477: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
7478: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
7479: cptcovn++;
7480: cptcovprodnoage++;k1++;
7481: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
7482: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
7483: because this model-covariate is a construction we invent a new column
7484: ncovcol + k1
7485: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
7486: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
7487: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
7488: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
7489: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
7490: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
7491: k2=k2+2;
7492: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
7493: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
7494: for (i=1; i<=lastobs;i++){
7495: /* Computes the new covariate which is a product of
7496: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
7497: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
7498: }
7499: } /* End age is not in the model */
7500: } /* End if model includes a product */
7501: else { /* no more sum */
7502: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
7503: /* scanf("%d",i);*/
7504: cutl(strd,strc,strb,'V');
7505: ks++; /**< Number of simple covariates */
1.145 brouard 7506: cptcovn++;
1.187 brouard 7507: Tvar[k]=atoi(strd);
7508: }
7509: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
7510: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
7511: scanf("%d",i);*/
7512: } /* end of loop + on total covariates */
7513: } /* end if strlen(modelsave == 0) age*age might exist */
7514: } /* end if strlen(model == 0) */
1.136 brouard 7515:
7516: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
7517: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
7518:
7519: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
7520: printf("cptcovprod=%d ", cptcovprod);
7521: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
7522:
7523: scanf("%d ",i);*/
7524:
7525:
1.137 brouard 7526: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 7527: /*endread:*/
1.136 brouard 7528: printf("Exiting decodemodel: ");
7529: return (1);
7530: }
7531:
1.169 brouard 7532: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 7533: {
7534: int i, m;
1.218 brouard 7535: int firstone=0;
7536:
1.136 brouard 7537: for (i=1; i<=imx; i++) {
7538: for(m=2; (m<= maxwav); m++) {
7539: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
7540: anint[m][i]=9999;
1.216 brouard 7541: if (s[m][i] != -2) /* Keeping initial status of unknown vital status */
7542: s[m][i]=-1;
1.136 brouard 7543: }
7544: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 7545: *nberr = *nberr + 1;
1.218 brouard 7546: if(firstone == 0){
7547: firstone=1;
7548: 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);
7549: }
7550: 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 7551: s[m][i]=-1;
7552: }
7553: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 7554: (*nberr)++;
1.136 brouard 7555: 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]);
7556: 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]);
7557: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
7558: }
7559: }
7560: }
7561:
7562: for (i=1; i<=imx; i++) {
7563: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
7564: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 7565: 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 7566: if (s[m][i] >= nlstate+1) {
1.169 brouard 7567: if(agedc[i]>0){
7568: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 7569: agev[m][i]=agedc[i];
1.214 brouard 7570: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 7571: }else {
1.136 brouard 7572: if ((int)andc[i]!=9999){
7573: nbwarn++;
7574: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
7575: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
7576: agev[m][i]=-1;
7577: }
7578: }
1.169 brouard 7579: } /* agedc > 0 */
1.214 brouard 7580: } /* end if */
1.136 brouard 7581: else if(s[m][i] !=9){ /* Standard case, age in fractional
7582: years but with the precision of a month */
7583: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
7584: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
7585: agev[m][i]=1;
7586: else if(agev[m][i] < *agemin){
7587: *agemin=agev[m][i];
7588: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
7589: }
7590: else if(agev[m][i] >*agemax){
7591: *agemax=agev[m][i];
1.156 brouard 7592: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 7593: }
7594: /*agev[m][i]=anint[m][i]-annais[i];*/
7595: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 7596: } /* en if 9*/
1.136 brouard 7597: else { /* =9 */
1.214 brouard 7598: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 7599: agev[m][i]=1;
7600: s[m][i]=-1;
7601: }
7602: }
1.214 brouard 7603: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 7604: agev[m][i]=1;
1.214 brouard 7605: else{
7606: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7607: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
7608: agev[m][i]=0;
7609: }
7610: } /* End for lastpass */
7611: }
1.136 brouard 7612:
7613: for (i=1; i<=imx; i++) {
7614: for(m=firstpass; (m<=lastpass); m++){
7615: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 7616: (*nberr)++;
1.136 brouard 7617: 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);
7618: 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);
7619: return 1;
7620: }
7621: }
7622: }
7623:
7624: /*for (i=1; i<=imx; i++){
7625: for (m=firstpass; (m<lastpass); m++){
7626: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
7627: }
7628:
7629: }*/
7630:
7631:
1.139 brouard 7632: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
7633: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 7634:
7635: return (0);
1.164 brouard 7636: /* endread:*/
1.136 brouard 7637: printf("Exiting calandcheckages: ");
7638: return (1);
7639: }
7640:
1.172 brouard 7641: #if defined(_MSC_VER)
7642: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7643: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
7644: //#include "stdafx.h"
7645: //#include <stdio.h>
7646: //#include <tchar.h>
7647: //#include <windows.h>
7648: //#include <iostream>
7649: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
7650:
7651: LPFN_ISWOW64PROCESS fnIsWow64Process;
7652:
7653: BOOL IsWow64()
7654: {
7655: BOOL bIsWow64 = FALSE;
7656:
7657: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
7658: // (HANDLE, PBOOL);
7659:
7660: //LPFN_ISWOW64PROCESS fnIsWow64Process;
7661:
7662: HMODULE module = GetModuleHandle(_T("kernel32"));
7663: const char funcName[] = "IsWow64Process";
7664: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
7665: GetProcAddress(module, funcName);
7666:
7667: if (NULL != fnIsWow64Process)
7668: {
7669: if (!fnIsWow64Process(GetCurrentProcess(),
7670: &bIsWow64))
7671: //throw std::exception("Unknown error");
7672: printf("Unknown error\n");
7673: }
7674: return bIsWow64 != FALSE;
7675: }
7676: #endif
1.177 brouard 7677:
1.191 brouard 7678: void syscompilerinfo(int logged)
1.167 brouard 7679: {
7680: /* #include "syscompilerinfo.h"*/
1.185 brouard 7681: /* command line Intel compiler 32bit windows, XP compatible:*/
7682: /* /GS /W3 /Gy
7683: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
7684: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
7685: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 7686: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
7687: */
7688: /* 64 bits */
1.185 brouard 7689: /*
7690: /GS /W3 /Gy
7691: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
7692: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
7693: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
7694: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
7695: /* Optimization are useless and O3 is slower than O2 */
7696: /*
7697: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
7698: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
7699: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
7700: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
7701: */
1.186 brouard 7702: /* Link is */ /* /OUT:"visual studio
1.185 brouard 7703: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
7704: /PDB:"visual studio
7705: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
7706: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
7707: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
7708: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
7709: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
7710: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
7711: uiAccess='false'"
7712: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
7713: /NOLOGO /TLBID:1
7714: */
1.177 brouard 7715: #if defined __INTEL_COMPILER
1.178 brouard 7716: #if defined(__GNUC__)
7717: struct utsname sysInfo; /* For Intel on Linux and OS/X */
7718: #endif
1.177 brouard 7719: #elif defined(__GNUC__)
1.179 brouard 7720: #ifndef __APPLE__
1.174 brouard 7721: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 7722: #endif
1.177 brouard 7723: struct utsname sysInfo;
1.178 brouard 7724: int cross = CROSS;
7725: if (cross){
7726: printf("Cross-");
1.191 brouard 7727: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 7728: }
1.174 brouard 7729: #endif
7730:
1.171 brouard 7731: #include <stdint.h>
1.178 brouard 7732:
1.191 brouard 7733: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 7734: #if defined(__clang__)
1.191 brouard 7735: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 7736: #endif
7737: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 7738: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 7739: #endif
7740: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 7741: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 7742: #endif
7743: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 7744: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 7745: #endif
7746: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 7747: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 7748: #endif
7749: #if defined(_MSC_VER)
1.191 brouard 7750: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 7751: #endif
7752: #if defined(__PGI)
1.191 brouard 7753: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 7754: #endif
7755: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 7756: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 7757: #endif
1.191 brouard 7758: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 7759:
1.167 brouard 7760: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
7761: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
7762: // Windows (x64 and x86)
1.191 brouard 7763: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 7764: #elif __unix__ // all unices, not all compilers
7765: // Unix
1.191 brouard 7766: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 7767: #elif __linux__
7768: // linux
1.191 brouard 7769: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 7770: #elif __APPLE__
1.174 brouard 7771: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 7772: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 7773: #endif
7774:
7775: /* __MINGW32__ */
7776: /* __CYGWIN__ */
7777: /* __MINGW64__ */
7778: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
7779: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
7780: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
7781: /* _WIN64 // Defined for applications for Win64. */
7782: /* _M_X64 // Defined for compilations that target x64 processors. */
7783: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 7784:
1.167 brouard 7785: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 7786: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 7787: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 7788: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 7789: #else
1.191 brouard 7790: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 7791: #endif
7792:
1.169 brouard 7793: #if defined(__GNUC__)
7794: # if defined(__GNUC_PATCHLEVEL__)
7795: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7796: + __GNUC_MINOR__ * 100 \
7797: + __GNUC_PATCHLEVEL__)
7798: # else
7799: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
7800: + __GNUC_MINOR__ * 100)
7801: # endif
1.174 brouard 7802: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 7803: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 7804:
7805: if (uname(&sysInfo) != -1) {
7806: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 7807: 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 7808: }
7809: else
7810: perror("uname() error");
1.179 brouard 7811: //#ifndef __INTEL_COMPILER
7812: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 7813: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 7814: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 7815: #endif
1.169 brouard 7816: #endif
1.172 brouard 7817:
7818: // void main()
7819: // {
1.169 brouard 7820: #if defined(_MSC_VER)
1.174 brouard 7821: if (IsWow64()){
1.191 brouard 7822: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
7823: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 7824: }
7825: else{
1.191 brouard 7826: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
7827: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 7828: }
1.172 brouard 7829: // printf("\nPress Enter to continue...");
7830: // getchar();
7831: // }
7832:
1.169 brouard 7833: #endif
7834:
1.167 brouard 7835:
1.219 brouard 7836: }
1.136 brouard 7837:
1.219 brouard 7838: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 7839: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7840: int i, j, k, i1 ;
1.202 brouard 7841: /* double ftolpl = 1.e-10; */
1.180 brouard 7842: double age, agebase, agelim;
1.203 brouard 7843: double tot;
1.180 brouard 7844:
1.202 brouard 7845: strcpy(filerespl,"PL_");
7846: strcat(filerespl,fileresu);
7847: if((ficrespl=fopen(filerespl,"w"))==NULL) {
7848: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7849: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
7850: }
7851: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7852: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
7853: pstamp(ficrespl);
1.203 brouard 7854: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 7855: fprintf(ficrespl,"#Age ");
7856: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
7857: fprintf(ficrespl,"\n");
1.180 brouard 7858:
1.219 brouard 7859: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
1.180 brouard 7860:
1.219 brouard 7861: agebase=ageminpar;
7862: agelim=agemaxpar;
1.180 brouard 7863:
1.219 brouard 7864: i1=pow(2,cptcoveff);
7865: if (cptcovn < 1){i1=1;}
1.180 brouard 7866:
1.220 brouard 7867: for(k=1; k<=i1;k++){
7868: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.180 brouard 7869: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.219 brouard 7870: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 7871: /* k=k+1; */
1.219 brouard 7872: /* to clean */
7873: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
7874: fprintf(ficrespl,"#******");
7875: printf("#******");
7876: fprintf(ficlog,"#******");
7877: for(j=1;j<=cptcoveff;j++) {
7878: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7879: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7880: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7881: }
7882: fprintf(ficrespl,"******\n");
7883: printf("******\n");
7884: fprintf(ficlog,"******\n");
1.220 brouard 7885: if(invalidvarcomb[k]){
7886: printf("\nCombination (%d) ignored because no cases \n",k);
7887: fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);
7888: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
7889: continue;
7890: }
1.219 brouard 7891:
7892: fprintf(ficrespl,"#Age ");
7893: for(j=1;j<=cptcoveff;j++) {
7894: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7895: }
7896: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
7897: fprintf(ficrespl,"Total Years_to_converge\n");
7898:
7899: for (age=agebase; age<=agelim; age++){
7900: /* for (age=agebase; age<=agebase; age++){ */
7901: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
7902: fprintf(ficrespl,"%.0f ",age );
7903: for(j=1;j<=cptcoveff;j++)
1.220 brouard 7904: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 7905: tot=0.;
7906: for(i=1; i<=nlstate;i++){
1.220 brouard 7907: tot += prlim[i][i];
7908: fprintf(ficrespl," %.5f", prlim[i][i]);
1.219 brouard 7909: }
7910: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
7911: } /* Age */
7912: /* was end of cptcod */
7913: } /* cptcov */
7914: return 0;
1.180 brouard 7915: }
7916:
1.218 brouard 7917: 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){
7918: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
7919:
7920: /* Computes the back prevalence limit for any combination of covariate values
7921: * at any age between ageminpar and agemaxpar
7922: */
1.217 brouard 7923: int i, j, k, i1 ;
7924: /* double ftolpl = 1.e-10; */
7925: double age, agebase, agelim;
7926: double tot;
1.218 brouard 7927: /* double ***mobaverage; */
7928: /* double **dnewm, **doldm, **dsavm; /\* for use *\/ */
1.217 brouard 7929:
7930: strcpy(fileresplb,"PLB_");
7931: strcat(fileresplb,fileresu);
7932: if((ficresplb=fopen(fileresplb,"w"))==NULL) {
7933: printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7934: fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;
7935: }
7936: printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7937: fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);
7938: pstamp(ficresplb);
7939: fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);
7940: fprintf(ficresplb,"#Age ");
7941: for(i=1; i<=nlstate;i++) fprintf(ficresplb,"%d-%d ",i,i);
7942: fprintf(ficresplb,"\n");
7943:
1.218 brouard 7944:
7945: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
7946:
7947: agebase=ageminpar;
7948: agelim=agemaxpar;
7949:
7950:
7951: i1=pow(2,cptcoveff);
7952: if (cptcovn < 1){i1=1;}
1.220 brouard 7953:
7954: for(k=1; k<=i1;k++){
7955: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
1.217 brouard 7956: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
1.218 brouard 7957: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
1.220 brouard 7958: /* k=k+1; */
1.218 brouard 7959: /* to clean */
7960: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
7961: fprintf(ficresplb,"#******");
7962: printf("#******");
7963: fprintf(ficlog,"#******");
7964: for(j=1;j<=cptcoveff;j++) {
7965: fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7966: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7967: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7968: }
7969: fprintf(ficresplb,"******\n");
7970: printf("******\n");
7971: fprintf(ficlog,"******\n");
1.220 brouard 7972: if(invalidvarcomb[k]){
7973: printf("\nCombination (%d) ignored because no cases \n",k);
7974: fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
7975: fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
7976: continue;
7977: }
1.218 brouard 7978:
7979: fprintf(ficresplb,"#Age ");
7980: for(j=1;j<=cptcoveff;j++) {
7981: fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
7982: }
7983: for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
7984: fprintf(ficresplb,"Total Years_to_converge\n");
7985:
7986:
7987: for (age=agebase; age<=agelim; age++){
7988: /* for (age=agebase; age<=agebase; age++){ */
7989: if(mobilavproj > 0){
7990: /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
7991: /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
1.219 brouard 7992: bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 7993: }else if (mobilavproj == 0){
1.219 brouard 7994: 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);
7995: 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);
7996: exit(1);
1.218 brouard 7997: }else{
1.219 brouard 7998: /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
7999: bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);
1.218 brouard 8000: }
8001: fprintf(ficresplb,"%.0f ",age );
8002: for(j=1;j<=cptcoveff;j++)
1.219 brouard 8003: fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.218 brouard 8004: tot=0.;
8005: for(i=1; i<=nlstate;i++){
1.219 brouard 8006: tot += bprlim[i][i];
8007: fprintf(ficresplb," %.5f", bprlim[i][i]);
1.218 brouard 8008: }
8009: fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
8010: } /* Age */
8011: /* was end of cptcod */
8012: } /* cptcov */
8013:
8014: /* hBijx(p, bage, fage); */
8015: /* fclose(ficrespijb); */
8016:
8017: return 0;
1.217 brouard 8018: }
1.218 brouard 8019:
1.180 brouard 8020: int hPijx(double *p, int bage, int fage){
8021: /*------------- h Pij x at various ages ------------*/
8022:
8023: int stepsize;
8024: int agelim;
8025: int hstepm;
8026: int nhstepm;
8027: int h, i, i1, j, k;
8028:
8029: double agedeb;
8030: double ***p3mat;
8031:
1.201 brouard 8032: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 8033: if((ficrespij=fopen(filerespij,"w"))==NULL) {
8034: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
8035: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
8036: }
8037: printf("Computing pij: result on file '%s' \n", filerespij);
8038: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
8039:
8040: stepsize=(int) (stepm+YEARM-1)/YEARM;
8041: /*if (stepm<=24) stepsize=2;*/
8042:
8043: agelim=AGESUP;
8044: hstepm=stepsize*YEARM; /* Every year of age */
8045: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
1.218 brouard 8046:
1.180 brouard 8047: /* hstepm=1; aff par mois*/
8048: pstamp(ficrespij);
8049: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
8050: i1= pow(2,cptcoveff);
1.218 brouard 8051: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8052: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8053: /* k=k+1; */
1.183 brouard 8054: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8055: fprintf(ficrespij,"\n#****** ");
8056: for(j=1;j<=cptcoveff;j++)
1.198 brouard 8057: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 8058: fprintf(ficrespij,"******\n");
8059:
8060: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
8061: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8062: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
8063:
8064: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 8065:
1.183 brouard 8066: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8067: oldm=oldms;savm=savms;
8068: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
8069: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
8070: for(i=1; i<=nlstate;i++)
8071: for(j=1; j<=nlstate+ndeath;j++)
8072: fprintf(ficrespij," %1d-%1d",i,j);
8073: fprintf(ficrespij,"\n");
8074: for (h=0; h<=nhstepm; h++){
8075: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8076: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 8077: for(i=1; i<=nlstate;i++)
8078: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 8079: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 8080: fprintf(ficrespij,"\n");
8081: }
1.183 brouard 8082: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8083: fprintf(ficrespij,"\n");
8084: }
1.180 brouard 8085: /*}*/
8086: }
1.218 brouard 8087: return 0;
1.180 brouard 8088: }
1.218 brouard 8089:
8090: int hBijx(double *p, int bage, int fage, double ***prevacurrent){
1.217 brouard 8091: /*------------- h Bij x at various ages ------------*/
8092:
8093: int stepsize;
1.218 brouard 8094: /* int agelim; */
8095: int ageminl;
1.217 brouard 8096: int hstepm;
8097: int nhstepm;
8098: int h, i, i1, j, k;
1.218 brouard 8099:
1.217 brouard 8100: double agedeb;
8101: double ***p3mat;
1.218 brouard 8102:
8103: strcpy(filerespijb,"PIJB_"); strcat(filerespijb,fileresu);
8104: if((ficrespijb=fopen(filerespijb,"w"))==NULL) {
8105: printf("Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8106: fprintf(ficlog,"Problem with Pij back resultfile: %s\n", filerespijb); return 1;
8107: }
8108: printf("Computing pij back: result on file '%s' \n", filerespijb);
8109: fprintf(ficlog,"Computing pij back: result on file '%s' \n", filerespijb);
8110:
8111: stepsize=(int) (stepm+YEARM-1)/YEARM;
8112: /*if (stepm<=24) stepsize=2;*/
1.217 brouard 8113:
1.218 brouard 8114: /* agelim=AGESUP; */
8115: ageminl=30;
8116: hstepm=stepsize*YEARM; /* Every year of age */
8117: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
8118:
8119: /* hstepm=1; aff par mois*/
8120: pstamp(ficrespijb);
8121: fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");
8122: i1= pow(2,cptcoveff);
8123: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
8124: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
8125: /* k=k+1; */
8126: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8127: fprintf(ficrespijb,"\n#****** ");
8128: for(j=1;j<=cptcoveff;j++)
8129: fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8130: fprintf(ficrespijb,"******\n");
8131:
8132: /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
8133: for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
8134: /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
8135: nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
8136: nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
8137:
8138: /* nhstepm=nhstepm*YEARM; aff par mois*/
8139:
8140: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8141: /* oldm=oldms;savm=savms; */
8142: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
8143: hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
8144: /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
8145: fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
8146: for(i=1; i<=nlstate;i++)
8147: for(j=1; j<=nlstate+ndeath;j++)
8148: fprintf(ficrespijb," %1d-%1d",i,j);
8149: fprintf(ficrespijb,"\n");
8150: for (h=0; h<=nhstepm; h++){
8151: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
8152: fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
8153: /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
1.217 brouard 8154: for(i=1; i<=nlstate;i++)
8155: for(j=1; j<=nlstate+ndeath;j++)
1.218 brouard 8156: fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
1.217 brouard 8157: fprintf(ficrespijb,"\n");
8158: }
1.218 brouard 8159: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
8160: fprintf(ficrespijb,"\n");
1.217 brouard 8161: }
1.218 brouard 8162: /*}*/
8163: }
8164: return 0;
8165: } /* hBijx */
1.217 brouard 8166:
1.180 brouard 8167:
1.136 brouard 8168: /***********************************************/
8169: /**************** Main Program *****************/
8170: /***********************************************/
8171:
8172: int main(int argc, char *argv[])
8173: {
8174: #ifdef GSL
8175: const gsl_multimin_fminimizer_type *T;
8176: size_t iteri = 0, it;
8177: int rval = GSL_CONTINUE;
8178: int status = GSL_SUCCESS;
8179: double ssval;
8180: #endif
8181: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 8182: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 8183: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 8184: int jj, ll, li, lj, lk;
1.136 brouard 8185: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 8186: int num_filled;
1.136 brouard 8187: int itimes;
8188: int NDIM=2;
8189: int vpopbased=0;
8190:
1.164 brouard 8191: char ca[32], cb[32];
1.136 brouard 8192: /* FILE *fichtm; *//* Html File */
8193: /* FILE *ficgp;*/ /*Gnuplot File */
8194: struct stat info;
1.191 brouard 8195: double agedeb=0.;
1.194 brouard 8196:
8197: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.219 brouard 8198: double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
1.136 brouard 8199:
1.165 brouard 8200: double fret;
1.191 brouard 8201: double dum=0.; /* Dummy variable */
1.136 brouard 8202: double ***p3mat;
1.218 brouard 8203: /* double ***mobaverage; */
1.164 brouard 8204:
8205: char line[MAXLINE];
1.197 brouard 8206: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
8207:
8208: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 8209: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 8210: char *tok, *val; /* pathtot */
1.136 brouard 8211: int firstobs=1, lastobs=10;
1.195 brouard 8212: int c, h , cpt, c2;
1.191 brouard 8213: int jl=0;
8214: int i1, j1, jk, stepsize=0;
1.194 brouard 8215: int count=0;
8216:
1.164 brouard 8217: int *tab;
1.136 brouard 8218: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
1.217 brouard 8219: int backcast=0;
1.136 brouard 8220: int mobilav=0,popforecast=0;
1.191 brouard 8221: int hstepm=0, nhstepm=0;
1.136 brouard 8222: int agemortsup;
8223: float sumlpop=0.;
8224: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
8225: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
8226:
1.191 brouard 8227: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 8228: double ftolpl=FTOL;
8229: double **prlim;
1.217 brouard 8230: double **bprlim;
1.136 brouard 8231: double ***param; /* Matrix of parameters */
8232: double *p;
8233: double **matcov; /* Matrix of covariance */
1.203 brouard 8234: double **hess; /* Hessian matrix */
1.136 brouard 8235: double ***delti3; /* Scale */
8236: double *delti; /* Scale */
8237: double ***eij, ***vareij;
8238: double **varpl; /* Variances of prevalence limits by age */
8239: double *epj, vepp;
1.164 brouard 8240:
1.136 brouard 8241: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
1.217 brouard 8242: double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;
8243:
1.136 brouard 8244: double **ximort;
1.145 brouard 8245: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 8246: int *dcwave;
8247:
1.164 brouard 8248: char z[1]="c";
1.136 brouard 8249:
8250: /*char *strt;*/
8251: char strtend[80];
1.126 brouard 8252:
1.164 brouard 8253:
1.126 brouard 8254: /* setlocale (LC_ALL, ""); */
8255: /* bindtextdomain (PACKAGE, LOCALEDIR); */
8256: /* textdomain (PACKAGE); */
8257: /* setlocale (LC_CTYPE, ""); */
8258: /* setlocale (LC_MESSAGES, ""); */
8259:
8260: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 8261: rstart_time = time(NULL);
8262: /* (void) gettimeofday(&start_time,&tzp);*/
8263: start_time = *localtime(&rstart_time);
1.126 brouard 8264: curr_time=start_time;
1.157 brouard 8265: /*tml = *localtime(&start_time.tm_sec);*/
8266: /* strcpy(strstart,asctime(&tml)); */
8267: strcpy(strstart,asctime(&start_time));
1.126 brouard 8268:
8269: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 8270: /* tp.tm_sec = tp.tm_sec +86400; */
8271: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 8272: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
8273: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
8274: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 8275: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 8276: /* strt=asctime(&tmg); */
8277: /* printf("Time(after) =%s",strstart); */
8278: /* (void) time (&time_value);
8279: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
8280: * tm = *localtime(&time_value);
8281: * strstart=asctime(&tm);
8282: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
8283: */
8284:
8285: nberr=0; /* Number of errors and warnings */
8286: nbwarn=0;
1.184 brouard 8287: #ifdef WIN32
8288: _getcwd(pathcd, size);
8289: #else
1.126 brouard 8290: getcwd(pathcd, size);
1.184 brouard 8291: #endif
1.191 brouard 8292: syscompilerinfo(0);
1.196 brouard 8293: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 8294: if(argc <=1){
8295: printf("\nEnter the parameter file name: ");
1.205 brouard 8296: if(!fgets(pathr,FILENAMELENGTH,stdin)){
8297: printf("ERROR Empty parameter file name\n");
8298: goto end;
8299: }
1.126 brouard 8300: i=strlen(pathr);
8301: if(pathr[i-1]=='\n')
8302: pathr[i-1]='\0';
1.156 brouard 8303: i=strlen(pathr);
1.205 brouard 8304: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 8305: pathr[i-1]='\0';
1.205 brouard 8306: }
8307: i=strlen(pathr);
8308: if( i==0 ){
8309: printf("ERROR Empty parameter file name\n");
8310: goto end;
8311: }
8312: for (tok = pathr; tok != NULL; ){
1.126 brouard 8313: printf("Pathr |%s|\n",pathr);
8314: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
8315: printf("val= |%s| pathr=%s\n",val,pathr);
8316: strcpy (pathtot, val);
8317: if(pathr[0] == '\0') break; /* Dirty */
8318: }
8319: }
8320: else{
8321: strcpy(pathtot,argv[1]);
8322: }
8323: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
8324: /*cygwin_split_path(pathtot,path,optionfile);
8325: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
8326: /* cutv(path,optionfile,pathtot,'\\');*/
8327:
8328: /* Split argv[0], imach program to get pathimach */
8329: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
8330: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8331: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
8332: /* strcpy(pathimach,argv[0]); */
8333: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
8334: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
8335: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 8336: #ifdef WIN32
8337: _chdir(path); /* Can be a relative path */
8338: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
8339: #else
1.126 brouard 8340: chdir(path); /* Can be a relative path */
1.184 brouard 8341: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
8342: #endif
8343: printf("Current directory %s!\n",pathcd);
1.126 brouard 8344: strcpy(command,"mkdir ");
8345: strcat(command,optionfilefiname);
8346: if((outcmd=system(command)) != 0){
1.169 brouard 8347: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 8348: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
8349: /* fclose(ficlog); */
8350: /* exit(1); */
8351: }
8352: /* if((imk=mkdir(optionfilefiname))<0){ */
8353: /* perror("mkdir"); */
8354: /* } */
8355:
8356: /*-------- arguments in the command line --------*/
8357:
1.186 brouard 8358: /* Main Log file */
1.126 brouard 8359: strcat(filelog, optionfilefiname);
8360: strcat(filelog,".log"); /* */
8361: if((ficlog=fopen(filelog,"w"))==NULL) {
8362: printf("Problem with logfile %s\n",filelog);
8363: goto end;
8364: }
8365: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 8366: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 8367: fprintf(ficlog,"\nEnter the parameter file name: \n");
8368: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
8369: path=%s \n\
8370: optionfile=%s\n\
8371: optionfilext=%s\n\
1.156 brouard 8372: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 8373:
1.197 brouard 8374: syscompilerinfo(1);
1.167 brouard 8375:
1.126 brouard 8376: printf("Local time (at start):%s",strstart);
8377: fprintf(ficlog,"Local time (at start): %s",strstart);
8378: fflush(ficlog);
8379: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 8380: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 8381:
8382: /* */
8383: strcpy(fileres,"r");
8384: strcat(fileres, optionfilefiname);
1.201 brouard 8385: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 8386: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 8387: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 8388:
1.186 brouard 8389: /* Main ---------arguments file --------*/
1.126 brouard 8390:
8391: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 8392: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
8393: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 8394: fflush(ficlog);
1.149 brouard 8395: /* goto end; */
8396: exit(70);
1.126 brouard 8397: }
8398:
8399:
8400:
8401: strcpy(filereso,"o");
1.201 brouard 8402: strcat(filereso,fileresu);
1.126 brouard 8403: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
8404: printf("Problem with Output resultfile: %s\n", filereso);
8405: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
8406: fflush(ficlog);
8407: goto end;
8408: }
8409:
8410: /* Reads comments: lines beginning with '#' */
8411: numlinepar=0;
1.197 brouard 8412:
8413: /* First parameter line */
8414: while(fgets(line, MAXLINE, ficpar)) {
8415: /* If line starts with a # it is a comment */
8416: if (line[0] == '#') {
8417: numlinepar++;
8418: fputs(line,stdout);
8419: fputs(line,ficparo);
8420: fputs(line,ficlog);
8421: continue;
8422: }else
8423: break;
8424: }
8425: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
8426: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
8427: if (num_filled != 5) {
8428: printf("Should be 5 parameters\n");
8429: }
1.126 brouard 8430: numlinepar++;
1.197 brouard 8431: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
8432: }
8433: /* Second parameter line */
8434: while(fgets(line, MAXLINE, ficpar)) {
8435: /* If line starts with a # it is a comment */
8436: if (line[0] == '#') {
8437: numlinepar++;
8438: fputs(line,stdout);
8439: fputs(line,ficparo);
8440: fputs(line,ficlog);
8441: continue;
8442: }else
8443: break;
8444: }
8445: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
8446: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
8447: if (num_filled != 8) {
1.209 brouard 8448: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
8449: printf("but line=%s\n",line);
1.197 brouard 8450: }
8451: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 8452: }
1.203 brouard 8453: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 8454: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 8455: /* Third parameter line */
8456: while(fgets(line, MAXLINE, ficpar)) {
8457: /* If line starts with a # it is a comment */
8458: if (line[0] == '#') {
8459: numlinepar++;
8460: fputs(line,stdout);
8461: fputs(line,ficparo);
8462: fputs(line,ficlog);
8463: continue;
8464: }else
8465: break;
8466: }
1.201 brouard 8467: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
8468: if (num_filled == 0)
8469: model[0]='\0';
8470: else if (num_filled != 1){
1.197 brouard 8471: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8472: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
8473: model[0]='\0';
8474: goto end;
8475: }
8476: else{
8477: if (model[0]=='+'){
8478: for(i=1; i<=strlen(model);i++)
8479: modeltemp[i-1]=model[i];
1.201 brouard 8480: strcpy(model,modeltemp);
1.197 brouard 8481: }
8482: }
1.199 brouard 8483: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 8484: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 8485: }
8486: /* 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); */
8487: /* numlinepar=numlinepar+3; /\* In general *\/ */
8488: /* 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); */
1.203 brouard 8489: fprintf(ficparo,"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);
8490: fprintf(ficlog,"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);
1.126 brouard 8491: fflush(ficlog);
1.190 brouard 8492: /* if(model[0]=='#'|| model[0]== '\0'){ */
8493: if(model[0]=='#'){
1.187 brouard 8494: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
8495: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
8496: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
8497: if(mle != -1){
8498: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
8499: exit(1);
8500: }
8501: }
1.126 brouard 8502: while((c=getc(ficpar))=='#' && c!= EOF){
8503: ungetc(c,ficpar);
8504: fgets(line, MAXLINE, ficpar);
8505: numlinepar++;
1.195 brouard 8506: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
8507: z[0]=line[1];
8508: }
8509: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 8510: fputs(line, stdout);
8511: //puts(line);
1.126 brouard 8512: fputs(line,ficparo);
8513: fputs(line,ficlog);
8514: }
8515: ungetc(c,ficpar);
8516:
8517:
1.145 brouard 8518: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 8519: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
8520: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
8521: v1+v2*age+v2*v3 makes cptcovn = 3
8522: */
8523: if (strlen(model)>1)
1.187 brouard 8524: 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 8525: else
1.187 brouard 8526: ncovmodel=2; /* Constant and age */
1.133 brouard 8527: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
8528: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 8529: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
8530: 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);
8531: 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);
8532: fflush(stdout);
8533: fclose (ficlog);
8534: goto end;
8535: }
1.126 brouard 8536: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8537: delti=delti3[1][1];
8538: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
8539: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
8540: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 8541: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
8542: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8543: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8544: fclose (ficparo);
8545: fclose (ficlog);
8546: goto end;
8547: exit(0);
1.220 brouard 8548: } else if(mle==-5) { /* Main Wizard */
1.126 brouard 8549: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 8550: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
8551: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 8552: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8553: matcov=matrix(1,npar,1,npar);
1.203 brouard 8554: hess=matrix(1,npar,1,npar);
1.220 brouard 8555: } else{ /* Begin of mle != -1 or -5 */
1.145 brouard 8556: /* Read guessed parameters */
1.126 brouard 8557: /* Reads comments: lines beginning with '#' */
8558: while((c=getc(ficpar))=='#' && c!= EOF){
8559: ungetc(c,ficpar);
8560: fgets(line, MAXLINE, ficpar);
8561: numlinepar++;
1.141 brouard 8562: fputs(line,stdout);
1.126 brouard 8563: fputs(line,ficparo);
8564: fputs(line,ficlog);
8565: }
8566: ungetc(c,ficpar);
8567:
8568: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
8569: for(i=1; i <=nlstate; i++){
1.220 brouard 8570: j=0;
1.126 brouard 8571: for(jj=1; jj <=nlstate+ndeath; jj++){
1.220 brouard 8572: if(jj==i) continue;
8573: j++;
8574: fscanf(ficpar,"%1d%1d",&i1,&j1);
8575: if ((i1 != i) || (j1 != jj)){
8576: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
1.126 brouard 8577: It might be a problem of design; if ncovcol and the model are correct\n \
8578: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
1.220 brouard 8579: exit(1);
8580: }
8581: fprintf(ficparo,"%1d%1d",i1,j1);
8582: if(mle==1)
8583: printf("%1d%1d",i,jj);
8584: fprintf(ficlog,"%1d%1d",i,jj);
8585: for(k=1; k<=ncovmodel;k++){
8586: fscanf(ficpar," %lf",¶m[i][j][k]);
8587: if(mle==1){
8588: printf(" %lf",param[i][j][k]);
8589: fprintf(ficlog," %lf",param[i][j][k]);
8590: }
8591: else
8592: fprintf(ficlog," %lf",param[i][j][k]);
8593: fprintf(ficparo," %lf",param[i][j][k]);
8594: }
8595: fscanf(ficpar,"\n");
8596: numlinepar++;
8597: if(mle==1)
8598: printf("\n");
8599: fprintf(ficlog,"\n");
8600: fprintf(ficparo,"\n");
1.126 brouard 8601: }
8602: }
8603: fflush(ficlog);
8604:
1.145 brouard 8605: /* Reads scales values */
1.126 brouard 8606: p=param[1][1];
8607:
8608: /* Reads comments: lines beginning with '#' */
8609: while((c=getc(ficpar))=='#' && c!= EOF){
8610: ungetc(c,ficpar);
8611: fgets(line, MAXLINE, ficpar);
8612: numlinepar++;
1.141 brouard 8613: fputs(line,stdout);
1.126 brouard 8614: fputs(line,ficparo);
8615: fputs(line,ficlog);
8616: }
8617: ungetc(c,ficpar);
8618:
8619: for(i=1; i <=nlstate; i++){
8620: for(j=1; j <=nlstate+ndeath-1; j++){
1.220 brouard 8621: fscanf(ficpar,"%1d%1d",&i1,&j1);
8622: if ( (i1-i) * (j1-j) != 0){
8623: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
8624: exit(1);
8625: }
8626: printf("%1d%1d",i,j);
8627: fprintf(ficparo,"%1d%1d",i1,j1);
8628: fprintf(ficlog,"%1d%1d",i1,j1);
8629: for(k=1; k<=ncovmodel;k++){
8630: fscanf(ficpar,"%le",&delti3[i][j][k]);
8631: printf(" %le",delti3[i][j][k]);
8632: fprintf(ficparo," %le",delti3[i][j][k]);
8633: fprintf(ficlog," %le",delti3[i][j][k]);
8634: }
8635: fscanf(ficpar,"\n");
8636: numlinepar++;
8637: printf("\n");
8638: fprintf(ficparo,"\n");
8639: fprintf(ficlog,"\n");
1.126 brouard 8640: }
8641: }
8642: fflush(ficlog);
1.220 brouard 8643:
1.145 brouard 8644: /* Reads covariance matrix */
1.126 brouard 8645: delti=delti3[1][1];
1.220 brouard 8646:
8647:
1.126 brouard 8648: /* 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 8649:
1.126 brouard 8650: /* Reads comments: lines beginning with '#' */
8651: while((c=getc(ficpar))=='#' && c!= EOF){
8652: ungetc(c,ficpar);
8653: fgets(line, MAXLINE, ficpar);
8654: numlinepar++;
1.141 brouard 8655: fputs(line,stdout);
1.126 brouard 8656: fputs(line,ficparo);
8657: fputs(line,ficlog);
8658: }
8659: ungetc(c,ficpar);
1.220 brouard 8660:
1.126 brouard 8661: matcov=matrix(1,npar,1,npar);
1.203 brouard 8662: hess=matrix(1,npar,1,npar);
1.131 brouard 8663: for(i=1; i <=npar; i++)
8664: for(j=1; j <=npar; j++) matcov[i][j]=0.;
1.220 brouard 8665:
1.194 brouard 8666: /* Scans npar lines */
1.126 brouard 8667: for(i=1; i <=npar; i++){
1.194 brouard 8668: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
8669: if(count != 3){
1.220 brouard 8670: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8671: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8672: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8673: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
1.194 brouard 8674: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
8675: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
1.220 brouard 8676: exit(1);
8677: }else{
8678: if(mle==1)
8679: printf("%1d%1d%1d",i1,j1,jk);
8680: }
1.194 brouard 8681: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
8682: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 8683: for(j=1; j <=i; j++){
1.220 brouard 8684: fscanf(ficpar," %le",&matcov[i][j]);
8685: if(mle==1){
8686: printf(" %.5le",matcov[i][j]);
8687: }
8688: fprintf(ficlog," %.5le",matcov[i][j]);
8689: fprintf(ficparo," %.5le",matcov[i][j]);
1.126 brouard 8690: }
8691: fscanf(ficpar,"\n");
8692: numlinepar++;
8693: if(mle==1)
1.220 brouard 8694: printf("\n");
1.126 brouard 8695: fprintf(ficlog,"\n");
8696: fprintf(ficparo,"\n");
8697: }
1.194 brouard 8698: /* End of read covariance matrix npar lines */
1.126 brouard 8699: for(i=1; i <=npar; i++)
8700: for(j=i+1;j<=npar;j++)
1.220 brouard 8701: matcov[i][j]=matcov[j][i];
1.126 brouard 8702:
8703: if(mle==1)
8704: printf("\n");
8705: fprintf(ficlog,"\n");
8706:
8707: fflush(ficlog);
8708:
8709: /*-------- Rewriting parameter file ----------*/
8710: strcpy(rfileres,"r"); /* "Rparameterfile */
8711: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
8712: strcat(rfileres,"."); /* */
8713: strcat(rfileres,optionfilext); /* Other files have txt extension */
8714: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 8715: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
8716: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 8717: }
8718: fprintf(ficres,"#%s\n",version);
8719: } /* End of mle != -3 */
1.218 brouard 8720:
1.186 brouard 8721: /* Main data
8722: */
1.126 brouard 8723: n= lastobs;
8724: num=lvector(1,n);
8725: moisnais=vector(1,n);
8726: annais=vector(1,n);
8727: moisdc=vector(1,n);
8728: andc=vector(1,n);
1.220 brouard 8729: weight=vector(1,n);
1.126 brouard 8730: agedc=vector(1,n);
8731: cod=ivector(1,n);
1.220 brouard 8732: for(i=1;i<=n;i++){
8733: num[i]=0;
8734: moisnais[i]=0;
8735: annais[i]=0;
8736: moisdc[i]=0;
8737: andc[i]=0;
8738: agedc[i]=0;
8739: cod[i]=0;
8740: weight[i]=1.0; /* Equal weights, 1 by default */
8741: }
1.126 brouard 8742: mint=matrix(1,maxwav,1,n);
8743: anint=matrix(1,maxwav,1,n);
1.131 brouard 8744: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 8745: tab=ivector(1,NCOVMAX);
1.144 brouard 8746: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 8747: 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 8748:
1.136 brouard 8749: /* Reads data from file datafile */
8750: if (readdata(datafile, firstobs, lastobs, &imx)==1)
8751: goto end;
8752:
8753: /* Calculation of the number of parameters from char model */
1.137 brouard 8754: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
8755: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
8756: k=3 V4 Tvar[k=3]= 4 (from V4)
8757: k=2 V1 Tvar[k=2]= 1 (from V1)
8758: k=1 Tvar[1]=2 (from V2)
8759: */
8760: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
8761: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
8762: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
8763: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
8764: */
8765: /* For model-covariate k tells which data-covariate to use but
8766: because this model-covariate is a construction we invent a new column
8767: ncovcol + k1
8768: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
8769: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 8770: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 8771: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
8772: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
8773: */
1.145 brouard 8774: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
8775: 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 8776: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
8777: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 8778: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 8779: 4 covariates (3 plus signs)
8780: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
8781: */
1.136 brouard 8782:
1.186 brouard 8783: /* Main decodemodel */
8784:
1.187 brouard 8785:
1.136 brouard 8786: if(decodemodel(model, lastobs) == 1)
8787: goto end;
8788:
1.137 brouard 8789: if((double)(lastobs-imx)/(double)imx > 1.10){
8790: nbwarn++;
8791: 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);
8792: 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);
8793: }
1.136 brouard 8794: /* if(mle==1){*/
1.137 brouard 8795: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
8796: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 8797: }
8798:
8799: /*-calculation of age at interview from date of interview and age at death -*/
8800: agev=matrix(1,maxwav,1,imx);
8801:
8802: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
8803: goto end;
8804:
1.126 brouard 8805:
1.136 brouard 8806: agegomp=(int)agemin;
8807: free_vector(moisnais,1,n);
8808: free_vector(annais,1,n);
1.126 brouard 8809: /* free_matrix(mint,1,maxwav,1,n);
8810: free_matrix(anint,1,maxwav,1,n);*/
1.215 brouard 8811: /* free_vector(moisdc,1,n); */
8812: /* free_vector(andc,1,n); */
1.145 brouard 8813: /* */
8814:
1.126 brouard 8815: wav=ivector(1,imx);
1.214 brouard 8816: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
8817: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
8818: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
8819: 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.*/
8820: bh=imatrix(1,lastpass-firstpass+2,1,imx);
8821: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 8822:
8823: /* Concatenates waves */
1.214 brouard 8824: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
8825: Death is a valid wave (if date is known).
8826: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
8827: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
8828: and mw[mi+1][i]. dh depends on stepm.
8829: */
8830:
1.126 brouard 8831: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 8832: /* */
8833:
1.215 brouard 8834: free_vector(moisdc,1,n);
8835: free_vector(andc,1,n);
8836:
1.126 brouard 8837: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
8838: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
8839: ncodemax[1]=1;
1.145 brouard 8840: Ndum =ivector(-1,NCOVMAX);
1.220 brouard 8841: cptcoveff=0;
8842: if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
8843: tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
8844: }
8845:
8846: ncovcombmax=pow(2,cptcoveff);
8847: invalidvarcomb=ivector(1, ncovcombmax);
8848: for(i=1;i<ncovcombmax;i++)
8849: invalidvarcomb[i]=0;
8850:
1.211 brouard 8851: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 8852: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 8853: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 8854:
1.200 brouard 8855: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 8856: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 8857: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 8858: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
8859: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
8860: * (currently 0 or 1) in the data.
8861: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
8862: * corresponding modality (h,j).
8863: */
8864:
1.145 brouard 8865: h=0;
8866: /*if (cptcovn > 0) */
1.126 brouard 8867: m=pow(2,cptcoveff);
8868:
1.144 brouard 8869: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 8870: * For k=4 covariates, h goes from 1 to m=2**k
8871: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
8872: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 8873: * h\k 1 2 3 4
1.143 brouard 8874: *______________________________
8875: * 1 i=1 1 i=1 1 i=1 1 i=1 1
8876: * 2 2 1 1 1
8877: * 3 i=2 1 2 1 1
8878: * 4 2 2 1 1
8879: * 5 i=3 1 i=2 1 2 1
8880: * 6 2 1 2 1
8881: * 7 i=4 1 2 2 1
8882: * 8 2 2 2 1
1.197 brouard 8883: * 9 i=5 1 i=3 1 i=2 1 2
8884: * 10 2 1 1 2
8885: * 11 i=6 1 2 1 2
8886: * 12 2 2 1 2
8887: * 13 i=7 1 i=4 1 2 2
8888: * 14 2 1 2 2
8889: * 15 i=8 1 2 2 2
8890: * 16 2 2 2 2
1.143 brouard 8891: */
1.212 brouard 8892: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 8893: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
8894: * and the value of each covariate?
8895: * V1=1, V2=1, V3=2, V4=1 ?
8896: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
8897: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
8898: * In order to get the real value in the data, we use nbcode
8899: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
8900: * We are keeping this crazy system in order to be able (in the future?)
8901: * to have more than 2 values (0 or 1) for a covariate.
8902: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
8903: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
8904: * bbbbbbbb
8905: * 76543210
8906: * h-1 00000101 (6-1=5)
1.219 brouard 8907: *(h-1)>>(k-1)= 00000010 >> (2-1) = 1 right shift
1.211 brouard 8908: * &
8909: * 1 00000001 (1)
1.219 brouard 8910: * 00000000 = 1 & ((h-1) >> (k-1))
8911: * +1= 00000001 =1
1.211 brouard 8912: *
8913: * h=14, k=3 => h'=h-1=13, k'=k-1=2
8914: * h' 1101 =2^3+2^2+0x2^1+2^0
8915: * >>k' 11
8916: * & 00000001
8917: * = 00000001
8918: * +1 = 00000010=2 = codtabm(14,3)
8919: * Reverse h=6 and m=16?
8920: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
8921: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
8922: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
8923: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
8924: * V3=decodtabm(14,3,2**4)=2
8925: * h'=13 1101 =2^3+2^2+0x2^1+2^0
8926: *(h-1) >> (j-1) 0011 =13 >> 2
8927: * &1 000000001
8928: * = 000000001
8929: * +1= 000000010 =2
8930: * 2211
8931: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
8932: * V3=2
1.220 brouard 8933: * codtabm and decodtabm are identical
1.211 brouard 8934: */
8935:
1.145 brouard 8936:
8937: free_ivector(Ndum,-1,NCOVMAX);
8938:
8939:
1.126 brouard 8940:
1.186 brouard 8941: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 8942: strcpy(optionfilegnuplot,optionfilefiname);
8943: if(mle==-3)
1.201 brouard 8944: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 8945: strcat(optionfilegnuplot,".gp");
8946:
8947: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
8948: printf("Problem with file %s",optionfilegnuplot);
8949: }
8950: else{
1.204 brouard 8951: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 8952: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 8953: //fprintf(ficgp,"set missing 'NaNq'\n");
8954: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 8955: }
8956: /* fclose(ficgp);*/
1.186 brouard 8957:
8958:
8959: /* Initialisation of --------- index.htm --------*/
1.126 brouard 8960:
8961: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
8962: if(mle==-3)
1.201 brouard 8963: strcat(optionfilehtm,"-MORT_");
1.126 brouard 8964: strcat(optionfilehtm,".htm");
8965: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 8966: printf("Problem with %s \n",optionfilehtm);
8967: exit(0);
1.126 brouard 8968: }
8969:
8970: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
8971: strcat(optionfilehtmcov,"-cov.htm");
8972: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
8973: printf("Problem with %s \n",optionfilehtmcov), exit(0);
8974: }
8975: else{
8976: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
8977: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8978: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 8979: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
8980: }
8981:
1.213 brouard 8982: 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 8983: <hr size=\"2\" color=\"#EC5E5E\"> \n\
8984: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 8985: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 8986: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 8987: \n\
8988: <hr size=\"2\" color=\"#EC5E5E\">\
8989: <ul><li><h4>Parameter files</h4>\n\
8990: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
8991: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
8992: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
8993: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
8994: - Date and time at start: %s</ul>\n",\
8995: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
8996: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
8997: fileres,fileres,\
8998: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
8999: fflush(fichtm);
9000:
9001: strcpy(pathr,path);
9002: strcat(pathr,optionfilefiname);
1.184 brouard 9003: #ifdef WIN32
9004: _chdir(optionfilefiname); /* Move to directory named optionfile */
9005: #else
1.126 brouard 9006: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 9007: #endif
9008:
1.126 brouard 9009:
1.220 brouard 9010: /* Calculates basic frequencies. Computes observed prevalence at single age
9011: and for any valid combination of covariates
1.126 brouard 9012: and prints on file fileres'p'. */
1.220 brouard 9013: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
1.214 brouard 9014: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 9015:
9016: fprintf(fichtm,"\n");
9017: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
9018: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
9019: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
9020: imx,agemin,agemax,jmin,jmax,jmean);
9021: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
1.220 brouard 9022: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9023: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9024: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
9025: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
1.218 brouard 9026:
1.126 brouard 9027: /* For Powell, parameters are in a vector p[] starting at p[1]
9028: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
9029: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
9030:
9031: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 9032: /* For mortality only */
1.126 brouard 9033: if (mle==-3){
1.136 brouard 9034: ximort=matrix(1,NDIM,1,NDIM);
1.220 brouard 9035: for(i=1;i<=NDIM;i++)
9036: for(j=1;j<=NDIM;j++)
9037: ximort[i][j]=0.;
1.186 brouard 9038: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 9039: cens=ivector(1,n);
9040: ageexmed=vector(1,n);
9041: agecens=vector(1,n);
9042: dcwave=ivector(1,n);
9043:
9044: for (i=1; i<=imx; i++){
9045: dcwave[i]=-1;
9046: for (m=firstpass; m<=lastpass; m++)
1.218 brouard 9047: if (s[m][i]>nlstate) {
9048: dcwave[i]=m;
9049: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
9050: break;
9051: }
1.126 brouard 9052: }
1.218 brouard 9053:
1.126 brouard 9054: for (i=1; i<=imx; i++) {
9055: if (wav[i]>0){
1.218 brouard 9056: ageexmed[i]=agev[mw[1][i]][i];
9057: j=wav[i];
9058: agecens[i]=1.;
9059:
9060: if (ageexmed[i]> 1 && wav[i] > 0){
9061: agecens[i]=agev[mw[j][i]][i];
9062: cens[i]= 1;
9063: }else if (ageexmed[i]< 1)
9064: cens[i]= -1;
9065: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
9066: cens[i]=0 ;
1.126 brouard 9067: }
9068: else cens[i]=-1;
9069: }
9070:
9071: for (i=1;i<=NDIM;i++) {
9072: for (j=1;j<=NDIM;j++)
1.218 brouard 9073: ximort[i][j]=(i == j ? 1.0 : 0.0);
1.126 brouard 9074: }
9075:
1.145 brouard 9076: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 9077: /*printf("%lf %lf", p[1], p[2]);*/
9078:
9079:
1.136 brouard 9080: #ifdef GSL
9081: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 9082: #else
1.126 brouard 9083: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 9084: #endif
1.201 brouard 9085: strcpy(filerespow,"POW-MORT_");
9086: strcat(filerespow,fileresu);
1.126 brouard 9087: if((ficrespow=fopen(filerespow,"w"))==NULL) {
9088: printf("Problem with resultfile: %s\n", filerespow);
9089: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
9090: }
1.136 brouard 9091: #ifdef GSL
9092: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 9093: #else
1.126 brouard 9094: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 9095: #endif
1.126 brouard 9096: /* for (i=1;i<=nlstate;i++)
9097: for(j=1;j<=nlstate+ndeath;j++)
9098: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
9099: */
9100: fprintf(ficrespow,"\n");
1.136 brouard 9101: #ifdef GSL
9102: /* gsl starts here */
9103: T = gsl_multimin_fminimizer_nmsimplex;
9104: gsl_multimin_fminimizer *sfm = NULL;
9105: gsl_vector *ss, *x;
9106: gsl_multimin_function minex_func;
9107:
9108: /* Initial vertex size vector */
9109: ss = gsl_vector_alloc (NDIM);
9110:
9111: if (ss == NULL){
9112: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
9113: }
9114: /* Set all step sizes to 1 */
9115: gsl_vector_set_all (ss, 0.001);
9116:
9117: /* Starting point */
1.126 brouard 9118:
1.136 brouard 9119: x = gsl_vector_alloc (NDIM);
9120:
9121: if (x == NULL){
9122: gsl_vector_free(ss);
9123: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
9124: }
9125:
9126: /* Initialize method and iterate */
9127: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 9128: /* gsl_vector_set(x, 0, 0.0268); */
9129: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 9130: gsl_vector_set(x, 0, p[1]);
9131: gsl_vector_set(x, 1, p[2]);
9132:
9133: minex_func.f = &gompertz_f;
9134: minex_func.n = NDIM;
9135: minex_func.params = (void *)&p; /* ??? */
9136:
9137: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
9138: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
9139:
9140: printf("Iterations beginning .....\n\n");
9141: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
9142:
9143: iteri=0;
9144: while (rval == GSL_CONTINUE){
9145: iteri++;
9146: status = gsl_multimin_fminimizer_iterate(sfm);
9147:
9148: if (status) printf("error: %s\n", gsl_strerror (status));
9149: fflush(0);
9150:
9151: if (status)
9152: break;
9153:
9154: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
9155: ssval = gsl_multimin_fminimizer_size (sfm);
9156:
9157: if (rval == GSL_SUCCESS)
9158: printf ("converged to a local maximum at\n");
9159:
9160: printf("%5d ", iteri);
9161: for (it = 0; it < NDIM; it++){
9162: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
9163: }
9164: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
9165: }
9166:
9167: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
9168:
9169: gsl_vector_free(x); /* initial values */
9170: gsl_vector_free(ss); /* inital step size */
9171: for (it=0; it<NDIM; it++){
9172: p[it+1]=gsl_vector_get(sfm->x,it);
9173: fprintf(ficrespow," %.12lf", p[it]);
9174: }
9175: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
9176: #endif
9177: #ifdef POWELL
9178: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
9179: #endif
1.126 brouard 9180: fclose(ficrespow);
9181:
1.203 brouard 9182: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 9183:
9184: for(i=1; i <=NDIM; i++)
9185: for(j=i+1;j<=NDIM;j++)
1.220 brouard 9186: matcov[i][j]=matcov[j][i];
1.126 brouard 9187:
9188: printf("\nCovariance matrix\n ");
1.203 brouard 9189: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 9190: for(i=1; i <=NDIM; i++) {
9191: for(j=1;j<=NDIM;j++){
1.220 brouard 9192: printf("%f ",matcov[i][j]);
9193: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 9194: }
1.203 brouard 9195: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 9196: }
9197:
9198: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 9199: for (i=1;i<=NDIM;i++) {
1.126 brouard 9200: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 9201: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
9202: }
1.126 brouard 9203: lsurv=vector(1,AGESUP);
9204: lpop=vector(1,AGESUP);
9205: tpop=vector(1,AGESUP);
9206: lsurv[agegomp]=100000;
9207:
9208: for (k=agegomp;k<=AGESUP;k++) {
9209: agemortsup=k;
9210: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
9211: }
9212:
9213: for (k=agegomp;k<agemortsup;k++)
9214: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
9215:
9216: for (k=agegomp;k<agemortsup;k++){
9217: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
9218: sumlpop=sumlpop+lpop[k];
9219: }
9220:
9221: tpop[agegomp]=sumlpop;
9222: for (k=agegomp;k<(agemortsup-3);k++){
9223: /* tpop[k+1]=2;*/
9224: tpop[k+1]=tpop[k]-lpop[k];
9225: }
9226:
9227:
9228: printf("\nAge lx qx dx Lx Tx e(x)\n");
9229: for (k=agegomp;k<(agemortsup-2);k++)
9230: 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]);
9231:
9232:
9233: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.220 brouard 9234: ageminpar=50;
9235: agemaxpar=100;
1.194 brouard 9236: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
9237: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9238: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9239: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
9240: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
9241: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9242: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9243: }else{
9244: printf("Warning! ageminpar %f and agemaxpar %f have been fixed because for simplification until it is fixed...\n\n",ageminpar,agemaxpar);
9245: 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 9246: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.220 brouard 9247: }
1.201 brouard 9248: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 9249: stepm, weightopt,\
9250: model,imx,p,matcov,agemortsup);
9251:
9252: free_vector(lsurv,1,AGESUP);
9253: free_vector(lpop,1,AGESUP);
9254: free_vector(tpop,1,AGESUP);
1.220 brouard 9255: free_matrix(ximort,1,NDIM,1,NDIM);
1.136 brouard 9256: free_ivector(cens,1,n);
9257: free_vector(agecens,1,n);
9258: free_ivector(dcwave,1,n);
1.220 brouard 9259: #ifdef GSL
1.136 brouard 9260: #endif
1.186 brouard 9261: } /* Endof if mle==-3 mortality only */
1.205 brouard 9262: /* Standard */
9263: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
9264: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9265: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 9266: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 9267: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9268: for (k=1; k<=npar;k++)
9269: printf(" %d %8.5f",k,p[k]);
9270: printf("\n");
1.205 brouard 9271: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
9272: /* mlikeli uses func not funcone */
9273: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
9274: }
9275: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
9276: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
9277: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
9278: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9279: }
9280: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 9281: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
9282: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
9283: for (k=1; k<=npar;k++)
9284: printf(" %d %8.5f",k,p[k]);
9285: printf("\n");
9286:
9287: /*--------- results files --------------*/
1.192 brouard 9288: fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
1.126 brouard 9289:
9290:
9291: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9292: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9293: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
9294: for(i=1,jk=1; i <=nlstate; i++){
9295: for(k=1; k <=(nlstate+ndeath); k++){
1.220 brouard 9296: if (k != i) {
9297: printf("%d%d ",i,k);
9298: fprintf(ficlog,"%d%d ",i,k);
9299: fprintf(ficres,"%1d%1d ",i,k);
9300: for(j=1; j <=ncovmodel; j++){
9301: printf("%12.7f ",p[jk]);
9302: fprintf(ficlog,"%12.7f ",p[jk]);
9303: fprintf(ficres,"%12.7f ",p[jk]);
9304: jk++;
9305: }
9306: printf("\n");
9307: fprintf(ficlog,"\n");
9308: fprintf(ficres,"\n");
9309: }
1.126 brouard 9310: }
9311: }
1.203 brouard 9312: if(mle != 0){
9313: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 9314: ftolhess=ftol; /* Usually correct */
1.203 brouard 9315: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
9316: 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");
9317: 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");
9318: for(i=1,jk=1; i <=nlstate; i++){
1.220 brouard 9319: for(k=1; k <=(nlstate+ndeath); k++){
9320: if (k != i) {
9321: printf("%d%d ",i,k);
9322: fprintf(ficlog,"%d%d ",i,k);
9323: for(j=1; j <=ncovmodel; j++){
9324: 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]));
9325: 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]));
9326: jk++;
9327: }
9328: printf("\n");
9329: fprintf(ficlog,"\n");
9330: }
9331: }
1.193 brouard 9332: }
1.203 brouard 9333: } /* end of hesscov and Wald tests */
1.220 brouard 9334:
1.203 brouard 9335: /* */
1.126 brouard 9336: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
9337: printf("# Scales (for hessian or gradient estimation)\n");
9338: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
9339: for(i=1,jk=1; i <=nlstate; i++){
9340: for(j=1; j <=nlstate+ndeath; j++){
1.220 brouard 9341: if (j!=i) {
9342: fprintf(ficres,"%1d%1d",i,j);
9343: printf("%1d%1d",i,j);
9344: fprintf(ficlog,"%1d%1d",i,j);
9345: for(k=1; k<=ncovmodel;k++){
9346: printf(" %.5e",delti[jk]);
9347: fprintf(ficlog," %.5e",delti[jk]);
9348: fprintf(ficres," %.5e",delti[jk]);
9349: jk++;
9350: }
9351: printf("\n");
9352: fprintf(ficlog,"\n");
9353: fprintf(ficres,"\n");
9354: }
1.126 brouard 9355: }
9356: }
9357:
9358: 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 9359: if(mle >= 1) /* To big for the screen */
1.126 brouard 9360: 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");
9361: 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");
9362: /* # 121 Var(a12)\n\ */
9363: /* # 122 Cov(b12,a12) Var(b12)\n\ */
9364: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
9365: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
9366: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
9367: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
9368: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
9369: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
9370:
9371:
9372: /* Just to have a covariance matrix which will be more understandable
9373: even is we still don't want to manage dictionary of variables
9374: */
9375: for(itimes=1;itimes<=2;itimes++){
9376: jj=0;
9377: for(i=1; i <=nlstate; i++){
1.220 brouard 9378: for(j=1; j <=nlstate+ndeath; j++){
9379: if(j==i) continue;
9380: for(k=1; k<=ncovmodel;k++){
9381: jj++;
9382: ca[0]= k+'a'-1;ca[1]='\0';
9383: if(itimes==1){
9384: if(mle>=1)
9385: printf("#%1d%1d%d",i,j,k);
9386: fprintf(ficlog,"#%1d%1d%d",i,j,k);
9387: fprintf(ficres,"#%1d%1d%d",i,j,k);
9388: }else{
9389: if(mle>=1)
9390: printf("%1d%1d%d",i,j,k);
9391: fprintf(ficlog,"%1d%1d%d",i,j,k);
9392: fprintf(ficres,"%1d%1d%d",i,j,k);
9393: }
9394: ll=0;
9395: for(li=1;li <=nlstate; li++){
9396: for(lj=1;lj <=nlstate+ndeath; lj++){
9397: if(lj==li) continue;
9398: for(lk=1;lk<=ncovmodel;lk++){
9399: ll++;
9400: if(ll<=jj){
9401: cb[0]= lk +'a'-1;cb[1]='\0';
9402: if(ll<jj){
9403: if(itimes==1){
9404: if(mle>=1)
9405: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9406: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9407: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
9408: }else{
9409: if(mle>=1)
9410: printf(" %.5e",matcov[jj][ll]);
9411: fprintf(ficlog," %.5e",matcov[jj][ll]);
9412: fprintf(ficres," %.5e",matcov[jj][ll]);
9413: }
9414: }else{
9415: if(itimes==1){
9416: if(mle>=1)
9417: printf(" Var(%s%1d%1d)",ca,i,j);
9418: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
9419: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
9420: }else{
9421: if(mle>=1)
9422: printf(" %.7e",matcov[jj][ll]);
9423: fprintf(ficlog," %.7e",matcov[jj][ll]);
9424: fprintf(ficres," %.7e",matcov[jj][ll]);
9425: }
9426: }
9427: }
9428: } /* end lk */
9429: } /* end lj */
9430: } /* end li */
9431: if(mle>=1)
9432: printf("\n");
9433: fprintf(ficlog,"\n");
9434: fprintf(ficres,"\n");
9435: numlinepar++;
9436: } /* end k*/
9437: } /*end j */
1.126 brouard 9438: } /* end i */
9439: } /* end itimes */
9440:
9441: fflush(ficlog);
9442: fflush(ficres);
1.220 brouard 9443: while(fgets(line, MAXLINE, ficpar)) {
9444: /* If line starts with a # it is a comment */
9445: if (line[0] == '#') {
9446: numlinepar++;
9447: fputs(line,stdout);
9448: fputs(line,ficparo);
9449: fputs(line,ficlog);
9450: continue;
9451: }else
9452: break;
9453: }
9454:
1.209 brouard 9455: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
9456: /* ungetc(c,ficpar); */
9457: /* fgets(line, MAXLINE, ficpar); */
9458: /* fputs(line,stdout); */
9459: /* fputs(line,ficparo); */
9460: /* } */
9461: /* ungetc(c,ficpar); */
1.126 brouard 9462:
9463: estepm=0;
1.209 brouard 9464: 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){
1.220 brouard 9465:
9466: if (num_filled != 6) {
9467: 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);
9468: 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);
9469: goto end;
9470: }
9471: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
9472: }
9473: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
9474: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
9475:
1.209 brouard 9476: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 9477: if (estepm==0 || estepm < stepm) estepm=stepm;
9478: if (fage <= 2) {
9479: bage = ageminpar;
9480: fage = agemaxpar;
9481: }
9482:
9483: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 9484: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
9485: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.220 brouard 9486:
1.186 brouard 9487: /* Other stuffs, more or less useful */
1.126 brouard 9488: while((c=getc(ficpar))=='#' && c!= EOF){
9489: ungetc(c,ficpar);
9490: fgets(line, MAXLINE, ficpar);
1.141 brouard 9491: fputs(line,stdout);
1.126 brouard 9492: fputs(line,ficparo);
9493: }
9494: ungetc(c,ficpar);
9495:
9496: 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);
9497: 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);
9498: 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);
9499: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
9500: 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);
9501:
9502: while((c=getc(ficpar))=='#' && c!= EOF){
9503: ungetc(c,ficpar);
9504: fgets(line, MAXLINE, ficpar);
1.141 brouard 9505: fputs(line,stdout);
1.126 brouard 9506: fputs(line,ficparo);
9507: }
9508: ungetc(c,ficpar);
9509:
9510:
9511: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
9512: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
9513:
9514: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 9515: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 9516: fprintf(ficparo,"pop_based=%d\n",popbased);
9517: fprintf(ficres,"pop_based=%d\n",popbased);
9518:
9519: while((c=getc(ficpar))=='#' && c!= EOF){
9520: ungetc(c,ficpar);
9521: fgets(line, MAXLINE, ficpar);
1.141 brouard 9522: fputs(line,stdout);
1.126 brouard 9523: fputs(line,ficparo);
9524: }
9525: ungetc(c,ficpar);
9526:
9527: 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);
9528: 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);
9529: 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);
9530: 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);
9531: 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);
9532: /* day and month of proj2 are not used but only year anproj2.*/
9533:
1.217 brouard 9534: while((c=getc(ficpar))=='#' && c!= EOF){
9535: ungetc(c,ficpar);
9536: fgets(line, MAXLINE, ficpar);
9537: fputs(line,stdout);
9538: fputs(line,ficparo);
9539: }
9540: ungetc(c,ficpar);
9541:
9542: 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);
1.219 brouard 9543: 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);
9544: 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);
9545: 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 9546: /* day and month of proj2 are not used but only year anproj2.*/
1.126 brouard 9547:
9548:
1.220 brouard 9549: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
1.145 brouard 9550: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 9551:
9552: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 9553: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
1.220 brouard 9554: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9555: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9556: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9557: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
1.194 brouard 9558: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
9559: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
1.220 brouard 9560: }else{
1.218 brouard 9561: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
1.220 brouard 9562: }
9563: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
9564: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \
9565: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
9566:
9567: /*------------ free_vector -------------*/
9568: /* chdir(path); */
9569:
1.215 brouard 9570: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
9571: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
9572: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
9573: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 9574: free_lvector(num,1,n);
9575: free_vector(agedc,1,n);
9576: /*free_matrix(covar,0,NCOVMAX,1,n);*/
9577: /*free_matrix(covar,1,NCOVMAX,1,n);*/
9578: fclose(ficparo);
9579: fclose(ficres);
1.220 brouard 9580:
9581:
1.186 brouard 9582: /* Other results (useful)*/
1.220 brouard 9583:
9584:
1.126 brouard 9585: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 9586: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
9587: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 9588: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 9589: fclose(ficrespl);
9590:
9591: /*------------- h Pij x at various ages ------------*/
1.180 brouard 9592: /*#include "hpijx.h"*/
9593: hPijx(p, bage, fage);
1.145 brouard 9594: fclose(ficrespij);
1.126 brouard 9595:
1.220 brouard 9596: /* ncovcombmax= pow(2,cptcoveff); */
1.219 brouard 9597: /*-------------- Variance of one-step probabilities---*/
1.145 brouard 9598: k=1;
1.126 brouard 9599: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
9600:
1.219 brouard 9601: /* Prevalence for each covariates in probs[age][status][cov] */
1.218 brouard 9602: probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.126 brouard 9603: for(i=1;i<=AGESUP;i++)
1.219 brouard 9604: for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
1.218 brouard 9605: for(k=1;k<=ncovcombmax;k++)
9606: probs[i][j][k]=0.;
1.219 brouard 9607: prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
9608: if (mobilav!=0 ||mobilavproj !=0 ) {
9609: mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
9610: for(i=1;i<=AGESUP;i++)
9611: for(j=1;j<=nlstate;j++)
9612: for(k=1;k<=ncovcombmax;k++)
9613: mobaverages[i][j][k]=0.;
9614: mobaverage=mobaverages;
9615: if (mobilav!=0) {
1.218 brouard 9616: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
9617: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
9618: printf(" Error in movingaverage mobilav=%d\n",mobilav);
9619: }
1.219 brouard 9620: }
9621: /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
9622: /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
9623: else if (mobilavproj !=0) {
1.218 brouard 9624: if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
9625: fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
9626: printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
9627: }
1.219 brouard 9628: }
9629: }/* end if moving average */
9630:
1.126 brouard 9631: /*---------- Forecasting ------------------*/
9632: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
9633: if(prevfcast==1){
9634: /* if(stepm ==1){*/
1.201 brouard 9635: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 9636: }
1.217 brouard 9637: if(backcast==1){
1.219 brouard 9638: ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9639: ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9640: ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
9641:
9642: /*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
9643:
9644: bprlim=matrix(1,nlstate,1,nlstate);
9645: back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
9646: fclose(ficresplb);
9647:
1.220 brouard 9648: /* hBijx(p, bage, fage, mobaverage); */
9649: /* fclose(ficrespijb); */
1.219 brouard 9650: free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
9651:
9652: /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
9653: bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
9654: free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9655: free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9656: free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
9657: }
1.217 brouard 9658:
1.186 brouard 9659:
9660: /* ------ Other prevalence ratios------------ */
1.126 brouard 9661:
1.215 brouard 9662: free_ivector(wav,1,imx);
9663: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
9664: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
9665: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
1.218 brouard 9666:
9667:
1.127 brouard 9668: /*---------- Health expectancies, no variances ------------*/
1.218 brouard 9669:
1.201 brouard 9670: strcpy(filerese,"E_");
9671: strcat(filerese,fileresu);
1.126 brouard 9672: if((ficreseij=fopen(filerese,"w"))==NULL) {
9673: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9674: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
9675: }
1.208 brouard 9676: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
9677: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.219 brouard 9678:
1.145 brouard 9679: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.219 brouard 9680: fprintf(ficreseij,"\n#****** ");
9681: for(j=1;j<=cptcoveff;j++) {
1.220 brouard 9682: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.219 brouard 9683: }
9684: fprintf(ficreseij,"******\n");
9685:
9686: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9687: oldm=oldms;savm=savms;
9688: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
1.127 brouard 9689:
1.219 brouard 9690: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.127 brouard 9691: }
9692: fclose(ficreseij);
1.208 brouard 9693: printf("done evsij\n");fflush(stdout);
9694: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.218 brouard 9695:
1.127 brouard 9696: /*---------- Health expectancies and variances ------------*/
1.218 brouard 9697:
9698:
1.201 brouard 9699: strcpy(filerest,"T_");
9700: strcat(filerest,fileresu);
1.127 brouard 9701: if((ficrest=fopen(filerest,"w"))==NULL) {
9702: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
9703: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
9704: }
1.208 brouard 9705: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
9706: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.218 brouard 9707:
1.126 brouard 9708:
1.201 brouard 9709: strcpy(fileresstde,"STDE_");
9710: strcat(fileresstde,fileresu);
1.126 brouard 9711: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
9712: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9713: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
9714: }
1.208 brouard 9715: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
9716: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 9717:
1.201 brouard 9718: strcpy(filerescve,"CVE_");
9719: strcat(filerescve,fileresu);
1.126 brouard 9720: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
9721: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9722: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
9723: }
1.208 brouard 9724: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
9725: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 9726:
1.201 brouard 9727: strcpy(fileresv,"V_");
9728: strcat(fileresv,fileresu);
1.126 brouard 9729: if((ficresvij=fopen(fileresv,"w"))==NULL) {
9730: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
9731: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
9732: }
1.208 brouard 9733: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
9734: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 9735:
1.145 brouard 9736: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9737: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9738:
9739: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 9740: fprintf(ficrest,"\n#****** ");
9741: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9742: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9743: fprintf(ficrest,"******\n");
9744:
9745: fprintf(ficresstdeij,"\n#****** ");
9746: fprintf(ficrescveij,"\n#****** ");
9747: for(j=1;j<=cptcoveff;j++) {
1.218 brouard 9748: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9749: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9750: }
9751: fprintf(ficresstdeij,"******\n");
9752: fprintf(ficrescveij,"******\n");
9753:
9754: fprintf(ficresvij,"\n#****** ");
9755: for(j=1;j<=cptcoveff;j++)
1.218 brouard 9756: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.208 brouard 9757: fprintf(ficresvij,"******\n");
9758:
9759: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9760: oldm=oldms;savm=savms;
9761: printf(" cvevsij %d, ",k);
9762: fprintf(ficlog, " cvevsij %d, ",k);
9763: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
9764: printf(" end cvevsij \n ");
9765: fprintf(ficlog, " end cvevsij \n ");
9766:
9767: /*
9768: */
9769: /* goto endfree; */
9770:
9771: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
9772: pstamp(ficrest);
9773:
9774:
9775: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.220 brouard 9776: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
9777: cptcod= 0; /* To be deleted */
9778: printf("varevsij %d \n",vpopbased);
9779: fprintf(ficlog, "varevsij %d \n",vpopbased);
9780: 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 */
9781: 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 ");
9782: if(vpopbased==1)
9783: 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);
9784: else
9785: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
9786: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
9787: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
9788: fprintf(ficrest,"\n");
9789: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
9790: epj=vector(1,nlstate+1);
9791: printf("Computing age specific period (stable) prevalences in each health state \n");
9792: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
9793: for(age=bage; age <=fage ;age++){
9794: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
9795: if (vpopbased==1) {
9796: if(mobilav ==0){
9797: for(i=1; i<=nlstate;i++)
9798: prlim[i][i]=probs[(int)age][i][k];
9799: }else{ /* mobilav */
9800: for(i=1; i<=nlstate;i++)
9801: prlim[i][i]=mobaverage[(int)age][i][k];
9802: }
9803: }
1.219 brouard 9804:
1.220 brouard 9805: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
9806: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
9807: /* printf(" age %4.0f ",age); */
9808: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
9809: for(i=1, epj[j]=0.;i <=nlstate;i++) {
9810: epj[j] += prlim[i][i]*eij[i][j][(int)age];
9811: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
9812: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
9813: }
9814: epj[nlstate+1] +=epj[j];
9815: }
9816: /* printf(" age %4.0f \n",age); */
1.219 brouard 9817:
1.220 brouard 9818: for(i=1, vepp=0.;i <=nlstate;i++)
9819: for(j=1;j <=nlstate;j++)
9820: vepp += vareij[i][j][(int)age];
9821: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
9822: for(j=1;j <=nlstate;j++){
9823: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
9824: }
9825: fprintf(ficrest,"\n");
9826: }
1.208 brouard 9827: } /* End vpopbased */
9828: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9829: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
9830: free_vector(epj,1,nlstate+1);
9831: printf("done \n");fflush(stdout);
9832: fprintf(ficlog,"done\n");fflush(ficlog);
9833:
1.145 brouard 9834: /*}*/
1.208 brouard 9835: } /* End k */
1.126 brouard 9836: free_vector(weight,1,n);
1.145 brouard 9837: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 9838: free_imatrix(s,1,maxwav+1,1,n);
9839: free_matrix(anint,1,maxwav,1,n);
9840: free_matrix(mint,1,maxwav,1,n);
9841: free_ivector(cod,1,n);
9842: free_ivector(tab,1,NCOVMAX);
9843: fclose(ficresstdeij);
9844: fclose(ficrescveij);
9845: fclose(ficresvij);
9846: fclose(ficrest);
1.208 brouard 9847: printf("done Health expectancies\n");fflush(stdout);
9848: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 9849: fclose(ficpar);
9850:
9851: /*------- Variance of period (stable) prevalence------*/
9852:
1.201 brouard 9853: strcpy(fileresvpl,"VPL_");
9854: strcat(fileresvpl,fileresu);
1.126 brouard 9855: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
9856: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
9857: exit(0);
9858: }
1.208 brouard 9859: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
9860: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 9861:
1.145 brouard 9862: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
9863: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
9864:
9865: for (k=1; k <= (int) pow(2,cptcoveff); k++){
9866: fprintf(ficresvpl,"\n#****** ");
1.218 brouard 9867: for(j=1;j<=cptcoveff;j++)
9868: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
9869: fprintf(ficresvpl,"******\n");
9870:
9871: varpl=matrix(1,nlstate,(int) bage, (int) fage);
9872: oldm=oldms;savm=savms;
9873: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
9874: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 9875: /*}*/
1.126 brouard 9876: }
1.218 brouard 9877:
1.126 brouard 9878: fclose(ficresvpl);
1.208 brouard 9879: printf("done variance-covariance of period prevalence\n");fflush(stdout);
9880: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 9881:
9882: /*---------- End : free ----------------*/
1.219 brouard 9883: if (mobilav!=0 ||mobilavproj !=0)
9884: 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 9885: free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
1.220 brouard 9886: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
9887: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
1.126 brouard 9888: } /* mle==-3 arrives here for freeing */
1.164 brouard 9889: /* endfree:*/
1.126 brouard 9890: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
9891: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
9892: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
9893: free_matrix(covar,0,NCOVMAX,1,n);
9894: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 9895: free_matrix(hess,1,npar,1,npar);
1.126 brouard 9896: /*free_vector(delti,1,npar);*/
9897: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9898: free_matrix(agev,1,maxwav,1,imx);
9899: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
9900:
1.145 brouard 9901: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 9902: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 9903: free_ivector(Tvar,1,NCOVMAX);
9904: free_ivector(Tprod,1,NCOVMAX);
9905: free_ivector(Tvaraff,1,NCOVMAX);
1.220 brouard 9906: free_ivector(invalidvarcomb,1,ncovcombmax);
1.145 brouard 9907: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 9908:
9909: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 9910: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 9911: fflush(fichtm);
9912: fflush(ficgp);
9913:
9914:
9915: if((nberr >0) || (nbwarn>0)){
1.216 brouard 9916: printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
9917: 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 9918: }else{
9919: printf("End of Imach\n");
9920: fprintf(ficlog,"End of Imach\n");
9921: }
9922: printf("See log file on %s\n",filelog);
9923: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 9924: /*(void) gettimeofday(&end_time,&tzp);*/
9925: rend_time = time(NULL);
9926: end_time = *localtime(&rend_time);
9927: /* tml = *localtime(&end_time.tm_sec); */
9928: strcpy(strtend,asctime(&end_time));
1.126 brouard 9929: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
9930: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 9931: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 9932:
1.157 brouard 9933: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
9934: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
9935: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 9936: /* printf("Total time was %d uSec.\n", total_usecs);*/
9937: /* if(fileappend(fichtm,optionfilehtm)){ */
9938: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9939: fclose(fichtm);
9940: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
9941: fclose(fichtmcov);
9942: fclose(ficgp);
9943: fclose(ficlog);
9944: /*------ End -----------*/
9945:
9946:
9947: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 9948: #ifdef WIN32
9949: if (_chdir(pathcd) != 0)
9950: printf("Can't move to directory %s!\n",path);
9951: if(_getcwd(pathcd,MAXLINE) > 0)
9952: #else
1.126 brouard 9953: if(chdir(pathcd) != 0)
1.184 brouard 9954: printf("Can't move to directory %s!\n", path);
9955: if (getcwd(pathcd, MAXLINE) > 0)
9956: #endif
1.126 brouard 9957: printf("Current directory %s!\n",pathcd);
9958: /*strcat(plotcmd,CHARSEPARATOR);*/
9959: sprintf(plotcmd,"gnuplot");
1.157 brouard 9960: #ifdef _WIN32
1.126 brouard 9961: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
9962: #endif
9963: if(!stat(plotcmd,&info)){
1.158 brouard 9964: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9965: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 9966: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 9967: }else
9968: strcpy(pplotcmd,plotcmd);
1.157 brouard 9969: #ifdef __unix
1.126 brouard 9970: strcpy(plotcmd,GNUPLOTPROGRAM);
9971: if(!stat(plotcmd,&info)){
1.158 brouard 9972: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9973: }else
9974: strcpy(pplotcmd,plotcmd);
9975: #endif
9976: }else
9977: strcpy(pplotcmd,plotcmd);
9978:
9979: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 9980: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 9981:
9982: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 9983: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 9984: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 9985: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 9986: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 9987: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 9988: }
1.158 brouard 9989: printf(" Successful, please wait...");
1.126 brouard 9990: while (z[0] != 'q') {
9991: /* chdir(path); */
1.154 brouard 9992: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 9993: scanf("%s",z);
9994: /* if (z[0] == 'c') system("./imach"); */
9995: if (z[0] == 'e') {
1.158 brouard 9996: #ifdef __APPLE__
1.152 brouard 9997: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 9998: #elif __linux
9999: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 10000: #else
1.152 brouard 10001: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 10002: #endif
10003: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
10004: system(pplotcmd);
1.126 brouard 10005: }
10006: else if (z[0] == 'g') system(plotcmd);
10007: else if (z[0] == 'q') exit(0);
10008: }
10009: end:
10010: while (z[0] != 'q') {
1.195 brouard 10011: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 10012: scanf("%s",z);
10013: }
10014: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src